Customer Innovation Centre for Organic Farming, Tove Mariegaard Pedersen
Customer ID DA00204-24
Project Markens motor (2024).
Sample Type Soil
Number of samples 30 samples
Type of data shotgun metagenomics

Introduction to the biostatistical analysis

The Project

This report describes the functional capacity of the microbiome profiles of 30 samples collected across 30 organic fields in Denmark in 2024. For each field, one sample was collected to represent the field. These samples were taken for each field based on 16 sub-samples taken in a w-pattern throughout the field.

In this report we analyse the functional capasity of the fields focusing on genes central to key functions of the soil microbiome in relation to agriculture and healthy soils. A total of 280 genes across 19 functional categories are included in Biomcare’s soil gene database for bacteria. We use KO IDs for genes of interest to ensure taxonomy-independent identification of genes across the many different bacteria. See the categories (sections) and genes below.

When analyzing the genes association ot metadata variables in the dataset, we consider the strong association of soil JB. We define two JB groups based on both analyses of this dataset and prior analyses of data from 2021-2022 where we saw a strong association between JB and microbiome profiles. We consider JB in the analyses as we find the effect of JB overshadows the associations that may be between the microbiome and other variables of interest. The each approach to used to consider JB values vary by analyses type. See details by each analyses.

The JB groups are:

A special focus for this project is the association of the microbiome with biodynamic farming, groupings with grazing versus mowing, and annual crops. The aim is to evaluate how the microbiome of the fields associate with other field parameters of both agricultural practices and soil indicators of nutrients, type and structure.

Practical notes

In “Report 3”, biostatistical analyses are performed and the results presented, building on the data generated and evaluated in the 2 prior reports (Report 1: Sequencing and data processing report, Report 2: Microbiome profiling report).
Through biostatistical analysis we relate the microbiome profiles to the key variables.

Target genes and processes

Biomcare has constructed a soil bacterial gene database that include 280 genes across 19 different functional categories. We have selected the genes and the categories base dn on their key relevance for soil microbes in connection with agriculture.

We first evaluate which of the genes are found in the current dataset by matching their KO IDs. The tables below show the genes found in the dataset (>0 abundance in any sample). The tables include information on each gene (it symbol, KO ID and name) and a description of its role. The tables also show the mean abundance and the q10 and q90 levels.

Functional categories

Antibiotic Production – Microbial production of antibiotics can suppress soil pathogens, contributing to plant health and natural disease control.

Antibiotic Resistance – The presence of antibiotic resistance genes reflects microbial adaptation and potential risks of resistance spread in agroecosystems.

Biocontrol – Microbes involved in biocontrol inhibit plant pests and pathogens, reducing reliance on chemical pesticides.

Calcium Cycling – Calcium availability is essential for plant cell wall structure and signaling, and is influenced by microbial solubilization and transport.

Carbon Fixation – Soil microorganisms fix atmospheric CO₂ into organic carbon, contributing to soil organic matter and global carbon sequestration.

Chloride Cycling – Chloride is an essential micronutrient and its cycling affects plant water regulation and microbial osmotic balance.

Copper Cycling – Microbial copper mobilization affects its availability for enzymatic processes in both microbes and plants, while preventing toxicity.

Hormone Production – Soil microbes produce phytohormones (e.g., auxins, gibberellins) that influence plant growth, root development, and stress responses.

Iron Cycling – Microbial iron acquisition and redox transformation regulate iron bioavailability, which is critical for plant metabolism and microbial competition.

Magnesium Cycling – Magnesium is vital for chlorophyll and enzyme function, and its cycling ensures sufficient availability for plant uptake.

Manganese Cycling – Microbial redox transformations of manganese affect soil fertility and the detoxification of reactive oxygen species in plants.

Nitrogen Fixation – Microorganisms fix atmospheric nitrogen into bioavailable forms, significantly boosting soil fertility without synthetic fertilizers.

Nitrogen Release – Decomposition and mineralization processes release nitrogen from organic matter, supporting plant nutrition and microbial activity.

Nodulation – Nodulation reflects symbiotic interactions between legumes and rhizobia, a key mechanism for biological nitrogen input in soils.

Phosphorus Solubilization – Microbial solubilization of inorganic phosphorus enhances plant access to this often limiting nutrient.

Potassium Solubilization – Microorganisms can mobilize potassium from soil minerals, making it available for plant growth and stress resistance.

Stress Adaptation – Genes linked to stress adaptation enable microbes to persist under drought, salinity, or other challenging soil conditions, supporting ecosystem resilience.

Sulfur Cycling – Sulfur transformations by microbes ensure the supply of this essential nutrient for amino acid and coenzyme synthesis.

Zinc Cycling – Microbial activity influences zinc availability, a crucial micronutrient for both plant development and microbial function.

Below are tables of genes in each functional category.

Antibiotic Production

Soil microbes are a major source of naturally occurring antibiotics, which play a key role in microbial competition, pathogen suppression, and plant protection. Bacteria such as Actinobacteria (e.g., Streptomyces), Pseudomonas, and Bacillus produce a wide range of bioactive compounds that inhibit competing microorganisms. These antibiotics function through various biosynthetic pathways, including polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), and aminoglycoside synthesis genes. The ability of soil bacteria to produce antibiotics influences microbial diversity, disease suppression, and biocontrol applications in agriculture.

Section Gene Name Essential Cagetory KO.ID Description Mean Abundance Q10 Q90
Antibiotic Production bacB Bacilysin biosynthesis protein BacB Yes Bacilysin K19547 Converts HPP to tetrahydrotyrosine (H4Tyr), a bacilysin precursor.
0.00 0.00
Antibiotic Production bacC Dihydroanticapsin dehydrogenase BacC Yes Bacilysin K19548 Oxidizes dihydroanticapsin to anticapsin, a bacilysin component.
0.00 0.00
Antibiotic Production E4.1.1.82 Phosphonopyruvate decarboxylase Yes Fosfomycin K09459 Enzyme catalyzing decarboxylation of phosphonopyruvate, a key step in fosfomycin biosynthesis.
72.33 146.87
Antibiotic Production eryA Erythromycin polyketide synthase Yes Macrolides K00862 Catalyzes the formation of the macrolide core in erythromycin biosynthesis.
19.00 55.42
Antibiotic Production penM Pentalenolactone synthase No Pentalenolactone K17476 Finalizes the biosynthesis of pentalenolactone, forming the active antibiotic compound.
0.00 7.76
Antibiotic Production pntE Pentalenolactone D synthase Yes Pentalenolactone K18091 Catalyzes the formation of pentalenolactone D, a precursor in pentalenolactone biosynthesis.
0.00 21.14
Antibiotic Production pntH 1-deoxypentalenic acid 11β-hydroxylase Yes Pentalenolactone K18056 Hydroxylates 1-deoxypentalenic acid at the 11β position, a key modification in pentalenolactone biosynthesis.
0.00 0.00
Antibiotic Production ptlF 1-deoxy-11β-hydroxypentalenate dehydrogenase Yes Pentalenolactone K17747 Oxidizes 1-deoxy-11β-hydroxypentalenate to 1-deoxy-11-oxopentalenate in pentalenolactone biosynthesis.
0.00 0.00
Antibiotic Production rifG 3-Amino-5-hydroxybenzoic acid synthase Yes Rifamycin K16020 Synthesizes AHBA, the starter unit for rifamycin biosynthesis.
0.00 12.30
Antibiotic Production strA Streptomycin 6-phosphate aminotransferase Yes Streptomycin K00547 Catalyzes the transfer of an amino group in streptomycin biosynthesis.
212.24 323.18

Table 1: Core microbial genera grouped into key functional groups. The table shows the detected core species (species level) assigned to a functional group. The table gives a short description of the species and show summary statistics for the organism across the fields with mean abundance and variation indicators (quantile 10 and 90).

Interpretation of Results

Bacilysin Production
- Bacilysin Biosynthesis (bacA, bacB, bacC, bacD, bacF, bacG):
- These genes are essential for the synthesis of bacilysin, a peptide antibiotic that inhibits cell wall synthesis in target bacteria.
- bacA and bacB are core enzymes catalyzing the formation of bacilysin’s peptide backbone.
- bacG and bacF are involved in the conversion of intermediates, ensuring efficient bacilysin synthesis.
- bacC (Dihydroanticapsin Dehydrogenase) and bacD (L-alanine-L-anticapsin Ligase) further refine the final bacilysin molecule.

Bacillaene Production
- Bacillaene Biosynthesis (pksA, pksC, pksE):
- These genes form a large polyketide synthase (PKSA-N) cluster responsible for the biosynthesis of bacillaene, a linear polyketide antibiotic that inhibits prokaryotic protein synthesis.
- pksA–pksD encode the early modules of the type I PKS system, initiating chain assembly and elongation through the condensation of acyl-CoA building blocks. - pksE functions as a stand-alone acyltransferase, supplying extender units in trans to modules that lack embedded AT domains, a hallmark of trans-AT PKS systems.
- pksF–pksN include additional PKS modules and accessory enzymes that introduce structural modifications, including dehydration and oxidation, essential for the activity and stability of bacillaene.
- The complete pathway assembles a complex polyketide backbone through iterative chain elongation, followed by selective tailoring to yield the active antibiotic compound.

Vancomycin Production and Resistance
- Vancomycin Biosynthesis (vanA, vanH, vanX):
- These genes encode enzymes that produce and modify vancomycin, a glycopeptide antibiotic.
- vanA is a D-Ala-D-Lac ligase, which alters peptidoglycan, making cells resistant to vancomycin.
- vanH (D-lactate Dehydrogenase) and vanX (D,D-Dipeptidase) modify the cell wall precursors, providing self-resistance against vancomycin.

Multidrug Resistance
- Efflux Pump (norM):
- norM (MATE Family Multidrug Efflux Pump) enables the organism to export multiple antibiotics, providing broad resistance.
- While not directly involved in antibiotic production, it is critical for self-protection in antibiotic-producing strains.

Fosfomycin Production - Fosfomycin Biosynthesis (fom1, E4.1.1.82):
- These genes enable the synthesis of fosfomycin, an antibiotic that inhibits bacterial cell wall synthesis.
- fom1 initiates the pathway by converting phosphoenolpyruvate into a phosphonate precursor.
- E4.1.1.82 (Phosphonopyruvate Decarboxylase) finalizes the formation of the active antibiotic.

Pentalenolactone Production - Pentalenolactone Biosynthesis (ptlA, ptlI, pntH, pntE, pntD, penM):
- These genes synthesize pentalenolactone, an antibiotic with a distinct structure and mode of action.
- ptlA and ptlI initiate the pathway by synthesizing the core pentalenene molecule.
- pntH (1-Deoxypentalenic Acid 11β-Hydroxylase) and pntE (Pentalenolactone D Synthase) add critical functional groups.
- pntD and penM provide additional modifications, creating various pentalenolactone derivatives.

Dapdiamides Production
- Dapdiamide Biosynthesis (ddaG, ddaH, ddaF):
- These genes produce dapdiamides, a group of amino acid-derived antibiotics.
- ddaG (Fumarate Ligase) and ddaH (Amidotransferase) catalyze the formation of the core dapdiamide structure.
- ddaF (Dapdiamide Synthase) completes the synthesis by forming the final structure.

Streptomycin Production
- Streptomycin Biosynthesis (strA, strB1, strC):
- These genes enable the production of streptomycin, an aminoglycoside antibiotic that inhibits protein synthesis in bacteria.
- strA (Streptomycin 6-Phosphate Aminotransferase) is crucial for the formation of the aminoglycoside structure.
- strB1 and strC further modify the molecule, enhancing its antibacterial activity.

Macrolide Production (Erythromycin)
- Erythromycin Biosynthesis (eryA, eryB, eryC):
- These genes are involved in the synthesis of erythromycin, a macrolide antibiotic that targets bacterial ribosomes.
- eryA (Polyketide Synthase) is the primary enzyme creating the macrolide ring.
- eryB and eryC add sugar residues, which are critical for erythromycin’s biological activity.

Daptomycin Production - Daptomycin Biosynthesis (dptA, dptBC, dptD):
- These genes enable the production of daptomycin, a lipopeptide antibiotic that disrupts bacterial cell membranes.
- dptA is the core enzyme assembling the peptide backbone.
- dptBC and dptD add specific modifications, creating the final active antibiotic.

Rifamycin Production
- Rifamycin Biosynthesis (rifA, rifB, rifC, rifD, rifE, rifF, rifG):
- These genes enable the synthesis of rifamycin, an antibiotic that inhibits bacterial RNA polymerase.
- rifA to rifE encode a modular polyketide synthase system, which assembles the core structure.
- rifG (3-Amino-5-hydroxybenzoic Acid Synthase) produces the aromatic building block of rifamycin.

Teixobactin Production
- Teixobactin Biosynthesis (txbA, txbB, txbC, txbD):
- These genes synthesize teixobactin, a non-ribosomal peptide antibiotic that targets cell wall synthesis.
- txbA and txbB are non-ribosomal peptide synthetases, creating the core peptide structure.
- txbC and txbD further modify the peptide, enhancing its antibiotic potency.

Malacidin Production
- Malacidin Biosynthesis (mlcA, mlcB, mlcC, mlcD):
- These genes produce malacidin, a non-ribosomal peptide antibiotic that disrupts bacterial cell walls.
- mlcA to mlcD are non-ribosomal peptide synthetases that assemble the malacidin structure.

Biocontrol

Soil microbes play a crucial role in biological pest control, producing antimicrobial and insecticidal compounds that suppress plant pathogens and pests. These microbes produce fungicidal, bactericidal, insecticidal, and nematicidal agents, enhancing plant health and reducing the need for synthetic pesticides. Many biocontrol agents belong to genera such as Bacillus, Pseudomonas, Streptomyces, and Serratia. The microbial production of lipopeptides, phenazines, hydrogen cyanide, and chitinases helps in pathogen suppression, insect resistance, and nematode control, supporting sustainable agriculture.

Section Gene Name Essential Cagetory KO.ID Description Mean Abundance Q10 Q90
Biocontrol chiA Chitinase A Yes Fungicidal agents K06904 Degrades chitin in fungal cell walls, aiding in pathogen suppression.
22.77 168.07
Biocontrol chiB Chitinase B No Fungicidal agents, Insecticide agents K20547 Breaks down chitin in insect exoskeletons and fungal cell walls.
0.00 0.00
Biocontrol dapB 4-hydroxy-tetrahydrodipicolinate reductase No Bactericidal agents K00215 Involved in lysine biosynthesis; indirectly contributes to daptomycin production.
2581.87 3276.92
Biocontrol phzF Phenazine biosynthesis protein PhzF Yes Fungicidal agents, Bactericidal agents K06998 Involved in the biosynthesis of phenazine, a broad-spectrum antimicrobial compound.
293.33 469.24
Biocontrol prnA Pyrrolnitrin biosynthesis halogenase Yes Fungicidal agents K14266 Catalyzes the initial chlorination step in pyrrolnitrin biosynthesis, an antifungal compound.
19.21 95.89
Biocontrol prnC Pyrrolnitrin biosynthesis halogenase Yes Fungicidal agents K14257 Catalyzes a chlorination step in pyrrolnitrin biosynthesis, an antifungal compound.
87.09 130.73
Biocontrol tcaB Toxin complex component B Yes Insecticide agents K07552 Encodes a component of the insecticidal toxin complex, involved in toxin delivery.
505.54 968.03

Table 2: Core microbial genera grouped into key functional groups. The table shows the detected core species (species level) assigned to a functional group. The table gives a short description of the species and show summary statistics for the organism across the fields with mean abundance and variation indicators (quantile 10 and 90).

Interpretation of Results

Fungicidal Agents
These genes encode enzymes and compounds that specifically target and suppress fungal pathogens, enhancing plant protection.
- Chitinase Production (chiA, chiB):
- chiA (Chitinase A) directly degrades fungal cell walls by breaking down chitin, a major component of fungal cell walls.
- chiB (Chitinase B) provides additional fungal degradation capacity, though it is also involved in insecticidal activity.
- Hydrogen Cyanide Production (hcnA):
- This gene enables the synthesis of hydrogen cyanide, a volatile compound that inhibits fungal and bacterial growth by interfering with cellular respiration.
- Phenazine Biosynthesis (phzF):
- This gene produces phenazine derivatives, which are redox-active compounds with strong antifungal and antibacterial properties.
- Pyrrolnitrin Production (prnA, prnC):
- These genes are responsible for synthesizing pyrrolnitrin, an antifungal compound that disrupts fungal membrane integrity.
- Pyoluteorin Production (pltA, pltB):
- These genes produce pyoluteorin, a polyketide antibiotic with strong antifungal properties.
- pltA (Halogenase) introduces halogen atoms, enhancing the compound’s bioactivity.
- 2,4-Diacetylphloroglucinol (DAPG) Production (phlD):
- This gene synthesizes DAPG, a broad-spectrum antimicrobial that inhibits fungal growth and promotes plant root health.

Bactericidal Agents
These genes produce compounds that inhibit or kill bacterial competitors, ensuring the dominance of the beneficial strain.
- Phenazine Production (phzF):
- As mentioned above, phenazines are highly redox-active and can generate reactive oxygen species that damage bacterial cell membranes.
- Syringomycin Production (syrB):
- syrB produces syringomycin, a lipopeptide antibiotic that disrupts bacterial membranes, leading to cell lysis.
- Hydrogen Cyanide Production (hcnA):
- Beyond its fungicidal properties, hydrogen cyanide also inhibits bacterial respiration, providing a dual biocontrol function.
- DAPG Production (phlD):
- As a broad-spectrum antimicrobial, DAPG also exhibits bactericidal effects, making it a versatile biocontrol agent.

Insecticidal Agents
These genes encode toxins and compounds that specifically target insect pests, reducing herbivory and improving plant protection.
- Insecticidal Toxin Production (mcf, mcf1, mcf2):
- These genes produce the “Makes Caterpillars Floppy” (MCF) toxin, which targets insect gut cells, leading to paralysis and death.
- Toxin Complex Production (tcaA, tcaB, tcaC, tccA, tccB, tccC):
- These genes encode a multi-component toxin complex that disrupts insect gut cells, providing broad-spectrum insecticidal activity.
- Chitinase Production (chiB):
- As a chitinase, chiB can also degrade the chitinous exoskeleton of insects, providing an additional insecticidal mechanism.

Nematicidal Agents
These genes produce proteins and toxins that specifically target plant-parasitic nematodes, protecting plant roots from nematode damage.
- Crystal Protein Production (cry5B, cry6A):
- These genes produce crystal proteins that form pores in the gut cells of nematodes, leading to cell lysis and death.
- Hemolysin Production (hlyA):
- This gene encodes hemolysin, a toxin that disrupts cell membranes, including those of nematodes, leading to death.

Associations of target genes and processes with metadata variables

Next we analyse how the gene abundances associate with the environmental and management variables presented in the metadata.

As we learned both in this project and prior years datasets, JB is an important factor shaping the soil microbiome. Therefore we consider this variable in the analysis of each gene as we have done for analysis of organisms as well. Each gene is analysed using a linear regression. We perform a step wise analysis flow where we first evaluate if there is an interaction between JB groups and the variable meaning that the relationship between the gene and the variable differ between the two JB groups. If there is no interaction we run a simple model to evaluate the relationship between the variable and the gene, (‘main_effect’ in the table) and if there is a significant interaction we evaluate the association within each JB group (resulting in 3 rows in the table; one for the interaction and one for each JB group).

We test all genes from the database that is found in the dataset. The significant associations are highlighted with green.

Biodynamic farm

Key findings from the table on biodynamic management:

  • Many genes relevant for nitrogen fixation are increased in abundance in fileds with biodynamic farming. This agrees with the finding from taxonomic analyses where we found that nitrogen-fixing symbionts such as Bradyrhizobium erythrophlei, B. lablabi, B. ottawaense, and Bradyrhizobium Ash2021 were significantly more abundant under biodynamic management.
Section Gene Essential Cagetory KO.ID Estimate SE t p-value Model
Antibiotic Production bacB Yes Bacilysin K19547 −0.403 0.622 −0.65 0.5222 main_effect
bacC Yes Bacilysin K19548 −0.775 0.828 −0.94 0.3571 main_effect
E4.1.1.82 Yes Fosfomycin K09459 −12.434 10.377 −1.20 0.2409 main_effect
eryA Yes Macrolides K00862 1.858 6.487 0.29 0.7766 main_effect
penM No Pentalenolactone K17476 −1.951 1.228 −1.59 0.1234 main_effect
pntE Yes Pentalenolactone K18091 −1.506 3.324 −0.45 0.6541 main_effect
pntH Yes Pentalenolactone K18056 0.889 0.568 1.57 0.1288 main_effect
ptlF Yes Pentalenolactone K17747 −0.490 0.757 −0.65 0.5222 main_effect
rifG Yes Rifamycin K16020 −2.327 2.602 −0.89 0.3787 main_effect
strA Yes Streptomycin K00547 14.149 18.943 0.75 0.4613 main_effect
Antibiotic Resistance vanA Yes Vancomycin K15739 −2.407 3.099 −0.78 0.4438 main_effect
vanH Yes Vancomycin K18347 −4.745 3.173 −1.50 0.1460 main_effect
vanX Yes Vancomycin K08641 −35.639 35.481 −1.00 0.3238 main_effect
Biocontrol chiA Yes Fungicidal agents K06904 −49.514 25.860 −1.91 0.0658 main_effect
chiB No Fungicidal agents, Insecticide agents K20547 3.061 1.449 2.11 0.0436 main_effect
dapB No Bactericidal agents K00215 7.888 122.666 0.06 0.9492 main_effect
phzF Yes Fungicidal agents, Bactericidal agents K06998 −3.544 26.981 −0.13 0.8964 main_effect
prnA Yes Fungicidal agents K14266 −33.232 10.382 −3.20 0.0034 main_effect
prnC Yes Fungicidal agents K14257 −13.140 7.168 −1.83 0.0774 main_effect
tcaB Yes Insecticide agents K07552 −116.092 62.666 −1.85 0.0745 main_effect
Calcium Cycling chaA Yes K07300 −122.697 65.357 −1.88 0.0709 main_effect
mgtC Yes K07507 33.428 76.213 0.44 0.6643 main_effect
phaC No K03821 33.533 77.442 0.43 0.6683 main_effect
ureC Yes K01428 −107.405 39.029 −2.75 0.0103 main_effect
Carbon Fixation ccmK No Calvin–Benson–Bassham (CBB) Cycle K08696 −0.466 2.246 −0.21 0.8372 main_effect
ccmL No Calvin–Benson–Bassham (CBB) Cycle K08697 1.863 2.749 0.68 0.5034 main_effect
codH Yes Wood–Ljungdahl (WL) pathway K00192 2.296 1.467 1.57 0.1288 main_effect
korA Yes Reductive TCA (rTCA) cycle K00174 −54.270 31.801 −1.71 0.0990 main_effect
korB Yes Reductive TCA (rTCA) cycle K00175 86.038 50.592 1.70 0.1001 main_effect
prk Yes Calvin–Benson–Bassham (CBB) Cycle K00855 15.870 11.291 1.41 0.1708 main_effect
rbcL Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01601 13.803 26.922 0.51 0.6122 main_effect
rbcS Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01602 8.736 79.691 0.11 0.9135 main_effect
frdA No Reductive TCA (rTCA) cycle K00244 −7.012 8.927 −0.79 0.4388 main_effect
mcl No 3HP bicycle K08691 −0.513 14.042 −0.04 0.9711 main_effect
Chloride Cycling clcA Yes K03281 324.152 105.340 3.08 0.0046 main_effect
clcB Yes K03281 324.152 105.340 3.08 0.0046 main_effect
clcN Yes K05011 −0.665 1.026 −0.65 0.5222 main_effect
gltT No K11102 74.025 26.481 2.80 0.0093 main_effect
kefC No K11745 −7.980 4.208 −1.90 0.0683 main_effect
Copper Cycling copA Yes K17686 −47.526 62.317 −0.76 0.4520 main_effect
copB Yes K01533 54.573 34.706 1.57 0.1271 main_effect
ctrA Yes K13584 187.756 91.760 2.05 0.0502 main_effect
cueO No K14588 18.699 6.158 3.04 0.0051 main_effect
cusA Yes K07787 124.627 28.543 4.37 0.0002 main_effect
cusB No K07798 135.692 32.027 4.24 0.0002 main_effect
Hormone Production acdS Yes Ethylene K01505 −55.881 35.714 −1.56 0.1289 main_effect
aldA Yes IAA K07248 −11.147 5.299 −2.10 0.0445 main_effect
aldH No IAA K00128 −167.428 88.781 −1.89 0.0697 main_effect
amiE Yes IAA K01426 −94.209 43.085 −2.19 0.0373 main_effect
aspC Yes IAA K00813 −4.954 4.569 −1.08 0.2874 main_effect
entC No GA K02361 −1.785 2.532 −0.70 0.4867 main_effect
etfA No Ethylene K03522 −469.752 223.452 −2.10 0.0454 interaction
etfA No Ethylene K03522 351.145 152.840 2.30 0.0375 by_group_JB1_JB2
etfA No Ethylene K03522 −118.607 162.141 −0.73 0.4785 by_group_JB5_JB6_JB7
iaaH No IAA K21801 −0.348 5.928 −0.06 0.9537 main_effect
iaaM No IAA K00466 −9.856 5.834 −1.69 0.1022 main_effect
ipdC Yes IAA K04103 0.124 1.641 0.08 0.9401 main_effect
ipt Yes CK K00375 −65.287 55.583 −1.17 0.2501 main_effect
miaA No CK K00791 −2.888 131.757 −0.02 0.9827 main_effect
nitA No IAA K01501 −33.257 13.519 −2.46 0.0209 interaction
nitA No IAA K01501 28.295 11.789 2.40 0.0309 by_group_JB1_JB2
nitA No IAA K01501 −4.962 4.600 −1.08 0.3019 by_group_JB5_JB6_JB7
tnaA No IAA K01667 27.534 16.424 1.68 0.1048 main_effect
Iron Cycling bfr No K03594 −63.524 55.321 −1.15 0.2606 main_effect
dps No K04047 −100.588 59.540 −1.69 0.1022 main_effect
entC Yes K02361 −1.785 2.532 −0.70 0.4867 main_effect
feoB Yes K04759 −19.955 14.722 −1.36 0.1861 main_effect
fur No K03711 −268.886 118.480 −2.27 0.0318 interaction
fur No K03711 69.247 72.768 0.95 0.3574 by_group_JB1_JB2
fur No K03711 −199.639 95.796 −2.08 0.0592 by_group_JB5_JB6_JB7
iscA No K13628 −529.755 179.187 −2.96 0.0065 interaction
iscA No K13628 218.232 144.213 1.51 0.1525 by_group_JB1_JB2
iscA No K13628 −311.523 93.800 −3.32 0.0061 by_group_JB5_JB6_JB7
sufB Yes K09014 −39.201 39.732 −0.99 0.3323 main_effect
sufC No K09013 13.209 49.509 0.27 0.7916 main_effect
yqjH No K07229 −0.484 0.747 −0.65 0.5222 main_effect
Magnesium Cycling corA Yes K03284 −535.098 238.035 −2.25 0.0326 main_effect
mgtA Yes K01531 458.699 76.317 6.01 0.0000 main_effect
mgtB No K01531 458.699 76.317 6.01 0.0000 main_effect
mgtE Yes K06213 −12.374 49.879 −0.25 0.8059 main_effect
phoQ No K07637 −12.497 6.940 −1.80 0.0826 main_effect
Manganese Cycling mntA Yes K06147 −35.973 216.200 −0.17 0.8690 main_effect
mntB Yes K06148 −22.608 14.590 −1.55 0.1325 main_effect
mntC Yes K06149 −2.645 4.887 −0.54 0.5925 main_effect
mntH Yes K03322 76.712 84.787 0.90 0.3733 main_effect
mntR No K03709 −53.572 44.878 −1.19 0.2426 main_effect
mntR No K11924 −4.915 7.218 −0.68 0.5015 main_effect
sitA Yes K11604 −12.920 5.565 −2.32 0.0278 main_effect
sodA No K04564 56.518 101.829 0.56 0.5833 main_effect
Nitrogen fixation amt No K03320 345.291 126.444 2.73 0.0108 main_effect
glnB No K04751 413.917 124.931 3.31 0.0026 main_effect
iscS No K04487 102.360 98.742 1.04 0.3088 main_effect
moeA No K03750 23.598 58.943 0.40 0.6919 main_effect
nifA No K02584 −11.256 10.794 −1.04 0.3060 main_effect
nifB Yes K02585 16.680 6.686 2.49 0.0188 main_effect
nifD Yes K02586 20.482 7.870 2.60 0.0146 main_effect
nifE Yes K02587 31.167 11.547 2.70 0.0117 main_effect
nifH Yes K02588 2.072 1.324 1.57 0.1288 main_effect
nifK Yes K02591 29.216 13.019 2.24 0.0329 main_effect
nifM Yes K03769 74.905 39.701 1.89 0.0696 main_effect
nifN Yes K02592 5.062 2.173 2.33 0.0273 main_effect
nifQ No K15790 0.613 0.392 1.57 0.1288 main_effect
nifU Yes K04488 −57.777 65.712 −0.88 0.3867 main_effect
nifV Yes K02594 10.403 4.615 2.25 0.0322 main_effect
nifW No K02595 1.111 1.417 0.78 0.4394 main_effect
nifX No K02596 27.244 9.612 2.83 0.0088 interaction
nifX No K02596 −0.281 0.425 −0.66 0.5191 by_group_JB1_JB2
nifX No K02596 26.964 10.443 2.58 0.0240 by_group_JB5_JB6_JB7
nifZ No K02597 0.522 2.303 0.23 0.8223 main_effect
Nitrogen Release amoA Yes K10944 −7.044 4.447 −1.58 0.1245 main_effect
amoB Yes K10945 −14.458 4.892 −2.96 0.0063 main_effect
amoC Yes K10946 −35.975 57.384 −0.63 0.5358 main_effect
gdh No K15371 −53.882 26.167 −2.06 0.0489 main_effect
napA No K02567 −5.207 9.607 −0.54 0.5922 main_effect
napA Yes K01416 0.508 3.341 0.15 0.8803 main_effect
napB No K02568 −2.129 6.730 −0.32 0.7541 main_effect
narG Yes K00370 4.882 25.322 0.19 0.8485 main_effect
narH Yes K00371 24.727 20.401 1.21 0.2356 main_effect
narI No K00374 4.319 27.005 0.16 0.8741 main_effect
nasA Yes K00372 −155.865 32.369 −4.82 0.0000 main_effect
nasB Yes K00360 −5.337 3.046 −1.75 0.0907 main_effect
nirA Yes K00366 34.380 20.900 1.64 0.1112 main_effect
nirK Yes K00368 16.819 19.903 0.85 0.4053 main_effect
nirS Yes K15864 0.896 1.127 0.80 0.4332 main_effect
norB Yes K04561 21.373 21.126 1.01 0.3203 main_effect
norC No K02305 −55.993 20.821 −2.69 0.0119 main_effect
nosZ Yes K00376 −5.373 20.214 −0.27 0.7923 main_effect
nrfA Yes K03385 26.229 28.701 0.91 0.3686 main_effect
ureC No K01428 −107.405 39.029 −2.75 0.0103 main_effect
Nodulation nodA Yes K14658 −0.302 0.467 −0.65 0.5222 main_effect
nodD Yes K14657 2.619 3.335 0.79 0.4389 main_effect
nodI No ABC transporter complex K09694 −279.794 125.834 −2.22 0.0344 main_effect
Phosphorus Solubilization gcd Yes K00117 −81.577 64.746 −1.26 0.2181 main_effect
phnX No K06163 −12.695 13.120 −0.97 0.3415 main_effect
phoA Yes K01077 −64.584 13.605 −4.75 0.0001 main_effect
phoD No K01113 −272.839 60.602 −4.50 0.0001 main_effect
phoX No K07093 −107.872 46.563 −2.32 0.0281 main_effect
ppk No K00937 −96.561 82.260 −1.17 0.2503 main_effect
ppx No K01514 −2.224 2.860 −0.78 0.4434 main_effect
pqqB Yes K06136 −17.366 46.738 −0.37 0.7130 main_effect
pqqC Yes K06137 65.310 42.784 1.53 0.1381 main_effect
pqqD Yes K06138 70.644 46.128 1.53 0.1369 main_effect
pqqE Yes K06139 22.851 23.430 0.98 0.3378 main_effect
Potassium Solubilization gcd Yes K00117 −81.577 64.746 −1.26 0.2181 main_effect
kdsA No K01627 7.506 45.305 0.17 0.8696 main_effect
kdsB No K00979 212.461 89.647 2.37 0.0249 main_effect
kup Yes K03549 0.455 92.607 0.00 0.9961 main_effect
nhaA No K03313 −405.873 77.780 −5.22 0.0000 main_effect
pqqB Yes K06136 −17.366 46.738 −0.37 0.7130 main_effect
pqqC Yes K06137 65.310 42.784 1.53 0.1381 main_effect
pqqD Yes K06138 70.644 46.128 1.53 0.1369 main_effect
pqqE Yes K06139 22.851 23.430 0.98 0.3378 main_effect
trkA Yes K03499 −21.496 109.252 −0.20 0.8454 main_effect
trkH Yes K03498 −60.307 21.019 −2.87 0.0077 main_effect
Stress Adaptation copA Yes Heavy Metal Tolerance K17686 −47.526 62.317 −0.76 0.4520 main_effect
ectB Yes Salt tolerance K00836 −4.804 8.701 −0.55 0.5853 main_effect
entC Yes Siderophore production K02361 −1.785 2.532 −0.70 0.4867 main_effect
glnA No ACC deaminase (ACC-d) K01915 −576.196 144.298 −3.99 0.0004 main_effect
kdsA Yes Exopolysaccharide production K01627 7.506 45.305 0.17 0.8696 main_effect
kdsB No Exopolysaccharide production K00979 212.461 89.647 2.37 0.0249 main_effect
pchA Yes Salicylic acid (SA) K01851 2.170 2.595 0.84 0.4100 main_effect
pchB No Salicylic acid (SA) K04782 −17.630 14.433 −1.22 0.2321 main_effect
pqqB No Siderophore production K06136 −17.366 46.738 −0.37 0.7130 main_effect
Sulfur Cycling aprA Yes K00394 2.698 3.529 0.76 0.4510 main_effect
cysA Yes K02045 −439.367 120.608 −3.64 0.0011 main_effect
cysU Yes K02046 −31.022 14.496 −2.14 0.0412 main_effect
cysW Yes K02047 −68.352 40.502 −1.69 0.1026 main_effect
fccB Yes K17229 −7.061 2.686 −2.63 0.0138 main_effect
sat Yes K00958 5.048 39.004 0.13 0.8979 main_effect
soxA No K17222 −8.672 44.211 −0.20 0.8459 main_effect
soxB No K17224 7.584 11.526 0.66 0.5159 main_effect
soxC Yes K17225 76.201 83.722 0.91 0.3705 main_effect
soxD Yes K22622 2.322 26.046 0.09 0.9296 main_effect
soxX No K17223 0.275 30.303 0.01 0.9928 main_effect
soxY Yes K17226 11.178 44.291 0.25 0.8026 main_effect
soxZ Yes K17227 −14.445 32.521 −0.44 0.6603 main_effect
Zinc Cycling mntR No K03709 −53.572 44.878 −1.19 0.2426 main_effect
troA No K11707 −35.900 13.087 −2.74 0.0105 main_effect
zitB No K16264 70.388 63.672 1.11 0.2784 main_effect
zntA No K01534 5.279 20.014 0.26 0.7939 main_effect
znuA Yes K09815 −73.213 26.431 −2.77 0.0098 main_effect
znuB Yes K09816 −37.086 61.667 −0.60 0.5524 main_effect
znuC Yes K09817 −56.100 35.447 −1.58 0.1247 main_effect
zur No K02076 21.847 14.015 1.56 0.1303 main_effect

Table 3: Summary statistics for each gene. The table shows the summary statistics for the analysis of the metadata variable and each gene (KO gene cluster) organised by section. The table gives estimate, standard error, t-value, p-value and model. “Model” informs which model the summary statistics represents: “main_effect” originate from analysis where all fields are analyzed together. This happens when we have tested for effects of JB and not found any significant difference between JB groups. “Interaction” gives results for the interaction analysis and is included only when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.

soil tmp.

Section Gene Essential Cagetory KO.ID Estimate SE t p-value Model
Antibiotic Production bacB Yes Bacilysin K19547 0.117 0.280 0.42 0.6793 main_effect
bacC Yes Bacilysin K19548 0.744 0.350 2.13 0.0423 main_effect
E4.1.1.82 Yes Fosfomycin K09459 9.888 4.387 2.25 0.0322 main_effect
eryA Yes Macrolides K00862 1.668 2.894 0.58 0.5689 main_effect
penM No Pentalenolactone K17476 −0.193 0.574 −0.34 0.7395 main_effect
pntE Yes Pentalenolactone K18091 0.232 1.495 0.16 0.8778 main_effect
pntH Yes Pentalenolactone K18056 −0.145 0.264 −0.55 0.5884 main_effect
ptlF Yes Pentalenolactone K17747 −0.514 0.328 −1.57 0.1276 main_effect
rifG Yes Rifamycin K16020 0.133 1.182 0.11 0.9114 main_effect
strA Yes Streptomycin K00547 0.289 8.574 0.03 0.9733 main_effect
Antibiotic Resistance vanA Yes Vancomycin K15739 −0.655 1.398 −0.47 0.6432 main_effect
vanH Yes Vancomycin K18347 0.072 1.478 0.05 0.9616 main_effect
vanX Yes Vancomycin K08641 11.983 16.026 0.75 0.4608 main_effect
Biocontrol chiA Yes Fungicidal agents K06904 23.290 11.512 2.02 0.0527 main_effect
chiB No Fungicidal agents, Insecticide agents K20547 −1.132 0.666 −1.70 0.1000 main_effect
dapB No Bactericidal agents K00215 −81.922 52.753 −1.55 0.1317 main_effect
phzF Yes Fungicidal agents, Bactericidal agents K06998 −5.203 12.055 −0.43 0.6694 main_effect
prnA Yes Fungicidal agents K14266 11.174 5.011 2.23 0.0339 main_effect
prnC Yes Fungicidal agents K14257 7.131 3.121 2.28 0.0301 main_effect
tcaB Yes Insecticide agents K07552 −12.231 29.666 −0.41 0.6833 main_effect
Calcium Cycling chaA Yes K07300 76.153 27.547 2.76 0.0100 main_effect
mgtC Yes K07507 −41.691 33.355 −1.25 0.2217 main_effect
phaC No K03821 9.959 34.772 0.29 0.7767 main_effect
ureC Yes K01428 26.189 19.084 1.37 0.1809 main_effect
Carbon Fixation ccmK No Calvin–Benson–Bassham (CBB) Cycle K08696 1.520 0.965 1.57 0.1268 main_effect
ccmL No Calvin–Benson–Bassham (CBB) Cycle K08697 1.893 1.189 1.59 0.1226 main_effect
codH Yes Wood–Ljungdahl (WL) pathway K00192 0.285 0.683 0.42 0.6793 main_effect
korA Yes Reductive TCA (rTCA) cycle K00174 8.849 14.881 0.59 0.5569 main_effect
korB Yes Reductive TCA (rTCA) cycle K00175 −39.952 22.587 −1.77 0.0878 main_effect
prk Yes Calvin–Benson–Bassham (CBB) Cycle K00855 −6.733 5.079 −1.33 0.1956 main_effect
rbcL Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01601 7.796 12.032 0.65 0.5223 main_effect
rbcS Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01602 −23.774 35.439 −0.67 0.5078 main_effect
frdA No Reductive TCA (rTCA) cycle K00244 −1.902 4.029 −0.47 0.6405 main_effect
mcl No 3HP bicycle K08691 0.549 6.293 0.09 0.9311 main_effect
Chloride Cycling clcA Yes K03281 −106.876 50.740 −2.11 0.0443 main_effect
clcB Yes K03281 −106.876 50.740 −2.11 0.0443 main_effect
clcN Yes K05011 −1.142 0.410 −2.79 0.0094 main_effect
gltT No K11102 −16.884 13.037 −1.30 0.2059 main_effect
kefC No K11745 −1.930 1.970 −0.98 0.3356 main_effect
Copper Cycling copA Yes K17686 16.178 28.051 0.58 0.5687 main_effect
copB Yes K01533 −6.018 16.186 −0.37 0.7129 main_effect
ctrA Yes K13584 −31.313 43.692 −0.72 0.4795 main_effect
cueO No K14588 −1.257 3.173 −0.40 0.6949 main_effect
cusA Yes K07787 3.270 16.573 0.20 0.8450 main_effect
cusB No K07798 −6.877 18.341 −0.37 0.7105 main_effect
Hormone Production acdS Yes Ethylene K01505 −1.085 16.689 −0.07 0.9486 main_effect
aldA Yes IAA K07248 −0.731 2.552 −0.29 0.7766 main_effect
aldH No IAA K00128 −27.986 41.907 −0.67 0.5097 main_effect
amiE Yes IAA K01426 −6.372 20.858 −0.31 0.7623 main_effect
aspC Yes IAA K00813 −0.498 2.088 −0.24 0.8132 main_effect
entC No GA K02361 0.532 1.141 0.47 0.6445 main_effect
etfA No Ethylene K03522 −30.405 53.906 −0.56 0.5772 main_effect
iaaH No IAA K21801 −5.458 2.448 −2.23 0.0340 main_effect
iaaM No IAA K00466 4.746 2.594 1.83 0.0780 main_effect
ipdC Yes IAA K04103 −1.260 0.696 −1.81 0.0809 main_effect
ipt Yes CK K00375 3.210 25.509 0.13 0.9008 main_effect
miaA No CK K00791 −98.870 56.015 −1.77 0.0885 main_effect
nitA No IAA K01501 −5.325 3.698 −1.44 0.1610 main_effect
tnaA No IAA K01667 3.933 7.685 0.51 0.6128 main_effect
Iron Cycling bfr No K03594 35.299 24.477 1.44 0.1604 main_effect
dps No K04047 3.610 28.002 0.13 0.8984 main_effect
entC Yes K02361 0.532 1.141 0.47 0.6445 main_effect
feoB Yes K04759 −8.304 6.628 −1.25 0.2206 main_effect
fur No K03711 0.571 30.166 0.02 0.9850 main_effect
iscA No K13628 −44.434 47.096 −0.94 0.3535 main_effect
sufB Yes K09014 13.156 17.942 0.73 0.4695 main_effect
sufC No K09013 10.269 22.132 0.46 0.6462 main_effect
yqjH No K07229 0.140 0.336 0.42 0.6793 main_effect
Magnesium Cycling corA Yes K03284 201.709 109.458 1.84 0.0760 main_effect
mgtA Yes K01531 −80.531 49.472 −1.63 0.1148 main_effect
mgtB No K01531 −80.531 49.472 −1.63 0.1148 main_effect
mgtE Yes K06213 12.020 22.263 0.54 0.5935 main_effect
phoQ No K07637 1.665 3.270 0.51 0.6146 main_effect
Manganese Cycling mntA Yes K06147 −125.135 94.012 −1.33 0.1939 main_effect
mntB Yes K06148 −9.417 6.577 −1.43 0.1633 main_effect
mntC Yes K06149 −2.992 2.128 −1.41 0.1707 main_effect
mntH Yes K03322 −35.305 37.968 −0.93 0.3604 main_effect
mntR No K03709 −7.082 20.575 −0.34 0.7332 main_effect
mntR No K11924 0.529 3.260 0.16 0.8723 main_effect
sitA Yes K11604 1.484 2.709 0.55 0.5882 main_effect
sodA No K04564 60.676 44.430 1.37 0.1829 main_effect
Nitrogen fixation amt No K03320 −164.927 55.633 −2.96 0.0061 main_effect
glnB No K04751 −29.185 65.828 −0.44 0.6609 main_effect
iscS No K04487 −27.943 44.783 −0.62 0.5377 main_effect
moeA No K03750 −19.349 26.238 −0.74 0.4670 main_effect
nifA No K02584 6.332 4.783 1.32 0.1963 main_effect
nifB Yes K02585 −0.305 3.312 −0.09 0.9273 main_effect
nifD Yes K02586 1.635 3.919 0.42 0.6798 main_effect
nifE Yes K02587 0.029 5.809 0.01 0.9960 main_effect
nifH Yes K02588 −0.337 0.615 −0.55 0.5884 main_effect
nifK Yes K02591 0.883 6.335 0.14 0.8902 main_effect
nifM Yes K03769 14.637 18.686 0.78 0.4400 main_effect
nifN Yes K02592 −0.823 1.053 −0.78 0.4408 main_effect
nifQ No K15790 0.076 0.183 0.42 0.6793 main_effect
nifU Yes K04488 147.353 64.895 2.27 0.0317 interaction
nifU Yes K04488 −48.388 37.932 −1.28 0.2228 by_group_JB1_JB2
nifU Yes K04488 98.965 47.565 2.08 0.0596 by_group_JB5_JB6_JB7
nifV Yes K02594 −0.336 2.247 −0.15 0.8823 main_effect
nifW No K02595 −0.324 0.639 −0.51 0.6162 main_effect
nifX No K02596 0.292 2.729 0.11 0.9154 main_effect
nifZ No K02597 0.902 1.019 0.89 0.3833 main_effect
Nitrogen Release amoA Yes K10944 0.008 2.081 0.00 0.9969 main_effect
amoB Yes K10945 2.543 2.465 1.03 0.3109 main_effect
amoC Yes K10946 17.506 25.685 0.68 0.5011 main_effect
gdh No K15371 −0.771 12.583 −0.06 0.9516 main_effect
napA No K02567 4.244 4.253 1.00 0.3269 main_effect
napA Yes K01416 1.657 1.465 1.13 0.2675 main_effect
napB No K02568 0.319 3.021 0.11 0.9166 main_effect
narG Yes K00370 7.382 11.270 0.65 0.5178 main_effect
narH Yes K00371 8.888 9.228 0.96 0.3437 main_effect
narI No K00374 −21.291 11.420 −1.86 0.0728 main_effect
nasA Yes K00372 16.875 19.353 0.87 0.3906 main_effect
nasB Yes K00360 1.106 1.423 0.78 0.4434 main_effect
nirA Yes K00366 −7.408 9.708 −0.76 0.4518 main_effect
nirK Yes K00368 −0.382 9.033 −0.04 0.9666 main_effect
nirS Yes K15864 0.225 0.509 0.44 0.6623 main_effect
norB Yes K04561 2.984 9.623 0.31 0.7588 main_effect
norC No K02305 18.678 9.854 1.90 0.0684 main_effect
nosZ Yes K00376 14.040 8.674 1.62 0.1168 main_effect
nrfA Yes K03385 5.604 13.010 0.43 0.6700 main_effect
ureC No K01428 26.189 19.084 1.37 0.1809 main_effect
Nodulation nodA Yes K14658 0.088 0.210 0.42 0.6793 main_effect
nodD Yes K14657 2.188 1.453 1.51 0.1434 main_effect
nodI No ABC transporter complex K09694 59.201 60.139 0.98 0.3333 main_effect
Phosphorus Solubilization gcd Yes K00117 46.863 28.483 1.65 0.1111 main_effect
phnX No K06163 −6.924 5.833 −1.19 0.2451 main_effect
phoA Yes K01077 3.669 8.162 0.45 0.6565 main_effect
phoD No K01113 32.851 35.115 0.94 0.3575 main_effect
phoX No K07093 30.905 22.019 1.40 0.1714 main_effect
ppk No K00937 30.233 37.327 0.81 0.4248 main_effect
ppx No K01514 −3.559 1.107 −3.21 0.0033 main_effect
pqqB Yes K06136 −19.774 20.663 −0.96 0.3468 main_effect
pqqC Yes K06137 14.545 19.766 0.74 0.4679 main_effect
pqqD Yes K06138 −12.401 21.393 −0.58 0.5668 main_effect
pqqE Yes K06139 −0.194 10.677 −0.02 0.9856 main_effect
Potassium Solubilization gcd Yes K00117 46.863 28.483 1.65 0.1111 main_effect
kdsA No K01627 −25.679 19.726 −1.30 0.2036 main_effect
kdsB No K00979 −47.850 43.083 −1.11 0.2762 main_effect
kup Yes K03549 18.911 41.349 0.46 0.6509 main_effect
nhaA No K03313 41.474 48.325 0.86 0.3981 main_effect
pqqB Yes K06136 −19.774 20.663 −0.96 0.3468 main_effect
pqqC Yes K06137 14.545 19.766 0.74 0.4679 main_effect
pqqD Yes K06138 −12.401 21.393 −0.58 0.5668 main_effect
pqqE Yes K06139 −0.194 10.677 −0.02 0.9856 main_effect
trkA Yes K03499 2.446 48.994 0.05 0.9605 main_effect
trkH Yes K03498 9.774 10.555 0.93 0.3623 main_effect
Stress Adaptation copA Yes Heavy Metal Tolerance K17686 16.178 28.051 0.58 0.5687 main_effect
ectB Yes Salt tolerance K00836 7.299 3.670 1.99 0.0566 main_effect
entC Yes Siderophore production K02361 0.532 1.141 0.47 0.6445 main_effect
glnA No ACC deaminase (ACC-d) K01915 50.856 80.444 0.63 0.5324 main_effect
kdsA Yes Exopolysaccharide production K01627 −25.679 19.726 −1.30 0.2036 main_effect
kdsB No Exopolysaccharide production K00979 −47.850 43.083 −1.11 0.2762 main_effect
pchA Yes Salicylic acid (SA) K01851 0.353 1.176 0.30 0.7660 main_effect
pchB No Salicylic acid (SA) K04782 5.885 6.545 0.90 0.3762 main_effect
pqqB No Siderophore production K06136 −19.774 20.663 −0.96 0.3468 main_effect
Sulfur Cycling aprA Yes K00394 −8.989 3.490 −2.58 0.0160 interaction
aprA Yes K00394 4.679 1.789 2.61 0.0204 by_group_JB1_JB2
aprA Yes K00394 −4.311 3.068 −1.41 0.1853 by_group_JB5_JB6_JB7
cysA Yes K02045 40.625 65.172 0.62 0.5381 main_effect
cysU Yes K02046 19.034 6.014 3.16 0.0037 main_effect
cysW Yes K02047 20.969 18.636 1.13 0.2701 main_effect
fccB Yes K17229 −0.097 1.344 −0.07 0.9431 main_effect
sat Yes K00958 21.232 17.019 1.25 0.2225 main_effect
soxA No K17222 3.036 19.819 0.15 0.8794 main_effect
soxB No K17224 −4.143 5.146 −0.81 0.4275 main_effect
soxC Yes K17225 12.432 37.999 0.33 0.7460 main_effect
soxD Yes K22622 17.976 11.169 1.61 0.1187 main_effect
soxX No K17223 −13.415 13.342 −1.01 0.3233 main_effect
soxY Yes K17226 −14.254 19.689 −0.72 0.4751 main_effect
soxZ Yes K17227 −20.913 14.082 −1.49 0.1487 main_effect
Zinc Cycling mntR No K03709 −7.082 20.575 −0.34 0.7332 main_effect
troA No K11707 1.241 6.602 0.19 0.8523 main_effect
zitB No K16264 −19.090 28.927 −0.66 0.5147 main_effect
zntA No K01534 0.494 8.980 0.05 0.9565 main_effect
znuA Yes K09815 18.550 12.902 1.44 0.1616 main_effect
znuB Yes K09816 46.768 26.373 1.77 0.0871 main_effect
znuC Yes K09817 27.326 15.757 1.73 0.0939 main_effect
zur No K02076 5.790 6.456 0.90 0.3775 main_effect

Table 4: Summary statistics for each gene. The table shows the summary statistics for the analysis of the metadata variable and each gene (KO gene cluster) organised by section. The table gives estimate, standard error, t-value, p-value and model. “Model” informs which model the summary statistics represents: “main_effect” originate from analysis where all fields are analyzed together. This happens when we have tested for effects of JB and not found any significant difference between JB groups. “Interaction” gives results for the interaction analysis and is included only when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.

Years since plowing

Section Gene Essential Cagetory KO.ID Estimate SE t p-value Model
Antibiotic Production bacB Yes Bacilysin K19547 −0.029 0.059 −0.50 0.6205 main_effect
bacC Yes Bacilysin K19548 −0.038 0.079 −0.48 0.6369 main_effect
E4.1.1.82 Yes Fosfomycin K09459 −1.057 0.983 −1.08 0.2911 main_effect
eryA Yes Macrolides K00862 0.317 0.609 0.52 0.6069 main_effect
penM No Pentalenolactone K17476 0.049 0.120 0.41 0.6882 main_effect
pntE Yes Pentalenolactone K18091 −0.371 0.306 −1.21 0.2361 main_effect
pntH Yes Pentalenolactone K18056 0.006 0.056 0.11 0.9149 main_effect
ptlF Yes Pentalenolactone K17747 −0.007 0.072 −0.09 0.9255 main_effect
rifG Yes Rifamycin K16020 −0.159 0.247 −0.64 0.5256 main_effect
strA Yes Streptomycin K00547 −1.936 1.765 −1.10 0.2821 main_effect
Antibiotic Resistance vanA Yes Vancomycin K15739 −0.039 0.295 −0.13 0.8963 main_effect
vanH Yes Vancomycin K18347 −0.418 0.301 −1.39 0.1753 main_effect
vanX Yes Vancomycin K08641 −4.538 3.293 −1.38 0.1791 main_effect
Biocontrol chiA Yes Fungicidal agents K06904 −3.019 2.528 −1.19 0.2424 main_effect
chiB No Fungicidal agents, Insecticide agents K20547 −0.063 0.147 −0.43 0.6683 main_effect
dapB No Bactericidal agents K00215 3.887 11.537 0.34 0.7387 main_effect
phzF Yes Fungicidal agents, Bactericidal agents K06998 −0.387 2.542 −0.15 0.8801 main_effect
prnA Yes Fungicidal agents K14266 −2.181 1.066 −2.05 0.0503 main_effect
prnC Yes Fungicidal agents K14257 0.247 0.713 0.35 0.7317 main_effect
tcaB Yes Insecticide agents K07552 −3.014 6.231 −0.48 0.6323 main_effect
Calcium Cycling chaA Yes K07300 −6.309 6.425 −0.98 0.3345 main_effect
mgtC Yes K07507 5.054 7.143 0.71 0.4851 main_effect
phaC No K03821 −4.982 7.261 −0.69 0.4983 main_effect
ureC Yes K01428 −1.478 4.136 −0.36 0.7235 main_effect
Carbon Fixation ccmK No Calvin–Benson–Bassham (CBB) Cycle K08696 −0.176 0.209 −0.84 0.4060 main_effect
ccmL No Calvin–Benson–Bassham (CBB) Cycle K08697 −0.112 0.260 −0.43 0.6712 main_effect
codH Yes Wood–Ljungdahl (WL) pathway K00192 −0.072 0.143 −0.50 0.6205 main_effect
korA Yes Reductive TCA (rTCA) cycle K00174 −2.621 3.110 −0.84 0.4064 main_effect
korB Yes Reductive TCA (rTCA) cycle K00175 8.983 4.711 1.91 0.0668 main_effect
prk Yes Calvin–Benson–Bassham (CBB) Cycle K00855 2.139 1.024 2.09 0.0459 main_effect
rbcL Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01601 3.952 2.437 1.62 0.1161 main_effect
rbcS Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01602 −0.542 7.510 −0.07 0.9429 main_effect
frdA No Reductive TCA (rTCA) cycle K00244 1.215 0.819 1.48 0.1489 main_effect
mcl No 3HP bicycle K08691 −0.253 1.322 −0.19 0.8499 main_effect
Chloride Cycling clcA Yes K03281 10.568 11.308 0.93 0.3580 main_effect
clcB Yes K03281 10.568 11.308 0.93 0.3580 main_effect
clcN Yes K05011 −0.068 0.097 −0.71 0.4856 main_effect
gltT No K11102 3.196 2.757 1.16 0.2561 main_effect
kefC No K11745 −0.346 0.416 −0.83 0.4130 main_effect
Copper Cycling copA Yes K17686 −2.987 5.906 −0.51 0.6170 main_effect
copB Yes K01533 3.762 3.337 1.13 0.2692 main_effect
ctrA Yes K13584 6.660 9.185 0.73 0.4744 main_effect
cueO No K14588 1.482 0.608 2.44 0.0213 main_effect
cusA Yes K07787 6.647 3.253 2.04 0.0505 main_effect
cusB No K07798 7.803 3.574 2.18 0.0376 main_effect
Hormone Production acdS Yes Ethylene K01505 −3.649 3.441 −1.06 0.2981 main_effect
aldA Yes IAA K07248 −0.016 0.537 −0.03 0.9766 main_effect
aldH No IAA K00128 −8.448 8.737 −0.97 0.3419 main_effect
amiE Yes IAA K01426 −1.961 4.377 −0.45 0.6576 main_effect
aspC Yes IAA K00813 −0.952 0.401 −2.37 0.0247 main_effect
entC No GA K02361 0.211 0.237 0.89 0.3817 main_effect
etfA No Ethylene K03522 12.017 11.170 1.08 0.2912 main_effect
iaaH No IAA K21801 0.236 0.557 0.42 0.6750 main_effect
iaaM No IAA K00466 −2.921 1.298 −2.25 0.0331 interaction
iaaM No IAA K00466 0.534 0.598 0.89 0.3868 by_group_JB1_JB2
iaaM No IAA K00466 −2.387 1.183 −2.02 0.0666 by_group_JB5_JB6_JB7
ipdC Yes IAA K04103 −0.092 0.154 −0.60 0.5522 main_effect
ipt Yes CK K00375 −10.327 4.998 −2.07 0.0482 main_effect
miaA No CK K00791 4.227 12.390 0.34 0.7355 main_effect
nitA No IAA K01501 0.807 0.791 1.02 0.3167 main_effect
tnaA No IAA K01667 4.609 1.370 3.36 0.0022 main_effect
Iron Cycling bfr No K03594 1.261 5.329 0.24 0.8146 main_effect
dps No K04047 1.064 5.886 0.18 0.8579 main_effect
entC Yes K02361 0.211 0.237 0.89 0.3817 main_effect
feoB Yes K04759 0.938 1.421 0.66 0.5145 main_effect
fur No K03711 −31.683 13.065 −2.43 0.0226 interaction
fur No K03711 1.472 5.935 0.25 0.8077 by_group_JB1_JB2
fur No K03711 −30.211 12.080 −2.50 0.0279 by_group_JB5_JB6_JB7
iscA No K13628 −8.520 9.929 −0.86 0.3982 main_effect
sufB Yes K09014 −0.443 3.808 −0.12 0.9082 main_effect
sufC No K09013 −0.350 4.671 −0.07 0.9409 main_effect
yqjH No K07229 −0.035 0.071 −0.50 0.6205 main_effect
Magnesium Cycling corA Yes K03284 −13.262 24.242 −0.55 0.5887 main_effect
mgtA Yes K01531 20.884 10.143 2.06 0.0489 main_effect
mgtB No K01531 20.884 10.143 2.06 0.0489 main_effect
mgtE Yes K06213 0.783 4.703 0.17 0.8690 main_effect
phoQ No K07637 0.187 0.690 0.27 0.7889 main_effect
Manganese Cycling mntA Yes K06147 −2.439 20.378 −0.12 0.9056 main_effect
mntB Yes K06148 −1.788 1.392 −1.28 0.2097 main_effect
mntC Yes K06149 −2.165 1.027 −2.11 0.0447 interaction
mntC Yes K06149 0.645 0.456 1.41 0.1790 by_group_JB1_JB2
mntC Yes K06149 −1.520 0.969 −1.57 0.1427 by_group_JB5_JB6_JB7
mntH Yes K03322 −1.442 8.101 −0.18 0.8600 main_effect
mntR No K03709 −0.071 4.335 −0.02 0.9870 main_effect
mntR No K11924 −0.016 0.686 −0.02 0.9820 main_effect
sitA Yes K11604 −0.156 0.572 −0.27 0.7868 main_effect
sodA No K04564 13.111 9.325 1.41 0.1707 main_effect
Nitrogen fixation amt No K03320 13.483 13.164 1.02 0.3145 main_effect
glnB No K04751 5.613 13.849 0.41 0.6884 main_effect
iscS No K04487 1.996 9.474 0.21 0.8346 main_effect
moeA No K03750 7.754 5.374 1.44 0.1601 main_effect
nifA No K02584 −0.281 1.035 −0.27 0.7882 main_effect
nifB Yes K02585 −3.241 1.475 −2.20 0.0371 interaction
nifB Yes K02585 2.081 0.602 3.46 0.0038 by_group_JB1_JB2
nifB Yes K02585 −1.160 1.486 −0.78 0.4503 by_group_JB5_JB6_JB7
nifD Yes K02586 1.656 0.765 2.16 0.0391 main_effect
nifE Yes K02587 2.596 1.119 2.32 0.0278 main_effect
nifH Yes K02588 0.040 0.130 0.31 0.7586 main_effect
nifK Yes K02591 2.475 1.248 1.98 0.0571 main_effect
nifM Yes K03769 5.617 3.827 1.47 0.1533 main_effect
nifN Yes K02592 −0.825 0.355 −2.32 0.0282 interaction
nifN Yes K02592 1.029 0.097 10.63 0.0000 by_group_JB1_JB2
nifN Yes K02592 0.205 0.417 0.49 0.6325 by_group_JB5_JB6_JB7
nifQ No K15790 0.012 0.038 0.31 0.7586 main_effect
nifU Yes K04488 1.792 6.268 0.29 0.7770 main_effect
nifV Yes K02594 1.089 0.426 2.56 0.0162 main_effect
nifW No K02595 0.040 0.135 0.29 0.7712 main_effect
nifX No K02596 0.182 0.573 0.32 0.7535 main_effect
nifZ No K02597 0.541 0.192 2.82 0.0087 main_effect
Nitrogen Release amoA Yes K10944 −0.527 0.426 −1.24 0.2267 main_effect
amoB Yes K10945 −1.047 0.490 −2.14 0.0413 main_effect
amoC Yes K10946 −6.528 5.304 −1.23 0.2286 main_effect
gdh No K15371 −0.735 2.642 −0.28 0.7828 main_effect
napA No K02567 2.123 0.817 2.60 0.0147 main_effect
napA Yes K01416 0.215 0.312 0.69 0.4962 main_effect
napB No K02568 −0.046 0.635 −0.07 0.9431 main_effect
narG Yes K00370 2.290 2.348 0.98 0.3378 main_effect
narH Yes K00371 0.324 1.971 0.16 0.8705 main_effect
narI No K00374 0.129 2.546 0.05 0.9599 main_effect
nasA Yes K00372 −4.974 4.016 −1.24 0.2257 main_effect
nasB Yes K00360 −0.239 0.299 −0.80 0.4307 main_effect
nirA Yes K00366 −1.530 2.042 −0.75 0.4598 main_effect
nirK Yes K00368 −0.720 1.894 −0.38 0.7069 main_effect
nirS Yes K15864 0.034 0.107 0.32 0.7548 main_effect
norB Yes K04561 −2.742 1.959 −1.40 0.1727 main_effect
norC No K02305 −3.508 2.099 −1.67 0.1058 main_effect
nosZ Yes K00376 −1.257 1.892 −0.66 0.5118 main_effect
nrfA Yes K03385 5.000 2.577 1.94 0.0625 main_effect
ureC No K01428 −1.478 4.136 −0.36 0.7235 main_effect
Nodulation nodA Yes K14658 −0.022 0.044 −0.50 0.6205 main_effect
nodD Yes K14657 0.078 0.317 0.24 0.8088 main_effect
nodI No ABC transporter complex K09694 −8.178 12.769 −0.64 0.5271 main_effect
Phosphorus Solubilization gcd Yes K00117 −5.409 6.188 −0.87 0.3895 main_effect
phnX No K06163 −0.555 1.252 −0.44 0.6609 main_effect
phoA Yes K01077 −2.084 1.677 −1.24 0.2243 main_effect
phoD No K01113 −13.724 7.035 −1.95 0.0612 main_effect
phoX No K07093 −3.266 4.750 −0.69 0.4974 main_effect
ppk No K00937 9.160 7.749 1.18 0.2471 main_effect
ppx No K01514 −0.170 0.271 −0.63 0.5346 main_effect
pqqB Yes K06136 −0.669 4.413 −0.15 0.8806 main_effect
pqqC Yes K06137 0.532 4.195 0.13 0.8999 main_effect
pqqD Yes K06138 5.828 4.389 1.33 0.1950 main_effect
pqqE Yes K06139 1.571 2.225 0.71 0.4861 main_effect
Potassium Solubilization gcd Yes K00117 −5.409 6.188 −0.87 0.3895 main_effect
kdsA No K01627 −24.670 7.436 −3.32 0.0027 interaction
kdsA No K01627 10.954 2.822 3.88 0.0017 by_group_JB1_JB2
kdsA No K01627 −13.716 7.809 −1.76 0.1045 by_group_JB5_JB6_JB7
kdsB No K00979 10.307 9.049 1.14 0.2643 main_effect
kup Yes K03549 −0.673 8.726 −0.08 0.9391 main_effect
nhaA No K03313 −10.120 10.115 −1.00 0.3256 main_effect
pqqB Yes K06136 −0.669 4.413 −0.15 0.8806 main_effect
pqqC Yes K06137 0.532 4.195 0.13 0.8999 main_effect
pqqD Yes K06138 5.828 4.389 1.33 0.1950 main_effect
pqqE Yes K06139 1.571 2.225 0.71 0.4861 main_effect
trkA Yes K03499 −4.911 10.260 −0.48 0.6359 main_effect
trkH Yes K03498 −2.935 2.184 −1.34 0.1898 main_effect
Stress Adaptation copA Yes Heavy Metal Tolerance K17686 −2.987 5.906 −0.51 0.6170 main_effect
ectB Yes Salt tolerance K00836 −0.401 0.821 −0.49 0.6294 main_effect
entC Yes Siderophore production K02361 0.211 0.237 0.89 0.3817 main_effect
glnA No ACC deaminase (ACC-d) K01915 −30.208 16.050 −1.88 0.0703 main_effect
kdsA Yes Exopolysaccharide production K01627 −24.670 7.436 −3.32 0.0027 interaction
kdsA Yes Exopolysaccharide production K01627 10.954 2.822 3.88 0.0017 by_group_JB1_JB2
kdsA Yes Exopolysaccharide production K01627 −13.716 7.809 −1.76 0.1045 by_group_JB5_JB6_JB7
kdsB No Exopolysaccharide production K00979 10.307 9.049 1.14 0.2643 main_effect
pchA Yes Salicylic acid (SA) K01851 −0.181 0.245 −0.74 0.4674 main_effect
pchB No Salicylic acid (SA) K04782 0.979 1.384 0.71 0.4849 main_effect
pqqB No Siderophore production K06136 −0.669 4.413 −0.15 0.8806 main_effect
Sulfur Cycling aprA Yes K00394 0.277 0.332 0.83 0.4117 main_effect
cysA Yes K02045 −13.649 13.555 −1.01 0.3226 main_effect
cysU Yes K02046 −2.219 1.413 −1.57 0.1275 main_effect
cysW Yes K02047 −2.626 3.975 −0.66 0.5144 main_effect
fccB Yes K17229 −0.423 0.271 −1.56 0.1301 main_effect
sat Yes K00958 −2.556 3.645 −0.70 0.4889 main_effect
soxA No K17222 2.797 4.135 0.68 0.5044 main_effect
soxB No K17224 0.733 1.086 0.68 0.5050 main_effect
soxC Yes K17225 15.402 7.457 2.07 0.0483 main_effect
soxD Yes K22622 2.873 2.394 1.20 0.2401 main_effect
soxX No K17223 −0.476 2.854 −0.17 0.8687 main_effect
soxY Yes K17226 5.899 4.027 1.46 0.1541 main_effect
soxZ Yes K17227 3.826 2.989 1.28 0.2111 main_effect
Zinc Cycling mntR No K03709 −0.071 4.335 −0.02 0.9870 main_effect
troA No K11707 −0.212 1.388 −0.15 0.8798 main_effect
zitB No K16264 −2.463 6.112 −0.40 0.6901 main_effect
zntA No K01534 0.462 1.886 0.25 0.8082 main_effect
znuA Yes K09815 −3.984 2.709 −1.47 0.1525 main_effect
znuB Yes K09816 −7.145 5.690 −1.26 0.2196 main_effect
znuC Yes K09817 −4.432 3.384 −1.31 0.2010 main_effect
zur No K02076 0.558 1.373 0.41 0.6873 main_effect

Table 5: Summary statistics for each gene. The table shows the summary statistics for the analysis of the metadata variable and each gene (KO gene cluster) organised by section. The table gives estimate, standard error, t-value, p-value and model. “Model” informs which model the summary statistics represents: “main_effect” originate from analysis where all fields are analyzed together. This happens when we have tested for effects of JB and not found any significant difference between JB groups. “Interaction” gives results for the interaction analysis and is included only when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.

Rt

Section Gene Essential Cagetory KO.ID Estimate SE t p-value Model
Antibiotic Production bacB Yes Bacilysin K19547 −0.730 0.669 −1.09 0.2847 main_effect
bacC Yes Bacilysin K19548 0.300 0.915 0.33 0.7452 main_effect
E4.1.1.82 Yes Fosfomycin K09459 1.837 11.602 0.16 0.8754 main_effect
eryA Yes Macrolides K00862 −9.709 6.846 −1.42 0.1672 main_effect
penM No Pentalenolactone K17476 −0.047 1.399 −0.03 0.9734 main_effect
pntE Yes Pentalenolactone K18091 3.601 3.575 1.01 0.3225 main_effect
pntH Yes Pentalenolactone K18056 2.869 1.212 2.37 0.0257 interaction
pntH Yes Pentalenolactone K18056 −2.869 1.245 −2.30 0.0371 by_group_JB1_JB2
pntH Yes Pentalenolactone K18056 0.000 0.000 NaN NaN by_group_JB5_JB6_JB7
ptlF Yes Pentalenolactone K17747 0.863 0.816 1.06 0.2993 main_effect
rifG Yes Rifamycin K16020 1.653 2.862 0.58 0.5682 main_effect
strA Yes Streptomycin K00547 −26.729 20.250 −1.32 0.1975 main_effect
Antibiotic Resistance vanA Yes Vancomycin K15739 −5.586 3.250 −1.72 0.0967 main_effect
vanH Yes Vancomycin K18347 0.660 3.595 0.18 0.8556 main_effect
vanX Yes Vancomycin K08641 −24.357 39.128 −0.62 0.5387 main_effect
Biocontrol chiA Yes Fungicidal agents K06904 91.099 34.464 2.64 0.0137 interaction
chiA Yes Fungicidal agents K06904 66.096 28.385 2.33 0.0354 by_group_JB1_JB2
chiA Yes Fungicidal agents K06904 157.194 19.922 7.89 0.0000 by_group_JB5_JB6_JB7
chiB No Fungicidal agents, Insecticide agents K20547 9.879 2.672 3.70 0.0010 interaction
chiB No Fungicidal agents, Insecticide agents K20547 −9.879 2.745 −3.60 0.0029 by_group_JB1_JB2
chiB No Fungicidal agents, Insecticide agents K20547 0.000 0.000 NaN NaN by_group_JB5_JB6_JB7
dapB No Bactericidal agents K00215 −224.926 126.898 −1.77 0.0872 main_effect
phzF Yes Fungicidal agents, Bactericidal agents K06998 −16.319 29.281 −0.56 0.5817 main_effect
prnA Yes Fungicidal agents K14266 50.698 9.133 5.55 0.0000 main_effect
prnC Yes Fungicidal agents K14257 6.137 8.194 0.75 0.4601 main_effect
tcaB Yes Insecticide agents K07552 −1.991 72.431 −0.03 0.9783 main_effect
Calcium Cycling chaA Yes K07300 262.945 57.045 4.61 0.0001 main_effect
mgtC Yes K07507 −237.433 70.334 −3.38 0.0022 main_effect
phaC No K03821 153.660 79.636 1.93 0.0639 main_effect
ureC Yes K01428 55.130 46.846 1.18 0.2492 main_effect
Carbon Fixation ccmK No Calvin–Benson–Bassham (CBB) Cycle K08696 0.666 2.449 0.27 0.7875 main_effect
ccmL No Calvin–Benson–Bassham (CBB) Cycle K08697 4.272 2.913 1.47 0.1537 main_effect
codH Yes Wood–Ljungdahl (WL) pathway K00192 −0.221 1.668 −0.13 0.8955 main_effect
korA Yes Reductive TCA (rTCA) cycle K00174 58.242 34.751 1.68 0.1049 main_effect
korB Yes Reductive TCA (rTCA) cycle K00175 −98.870 54.879 −1.80 0.0824 main_effect
prk Yes Calvin–Benson–Bassham (CBB) Cycle K00855 −35.925 10.785 −3.33 0.0024 main_effect
rbcL Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01601 16.155 29.349 0.55 0.5864 main_effect
rbcS Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01602 −227.949 75.535 −3.02 0.0054 main_effect
frdA No Reductive TCA (rTCA) cycle K00244 21.498 8.968 2.40 0.0234 main_effect
mcl No 3HP bicycle K08691 12.935 15.123 0.86 0.3996 main_effect
Chloride Cycling clcA Yes K03281 407.456 134.243 3.04 0.0054 interaction
clcA Yes K03281 −771.949 108.085 −7.14 0.0000 by_group_JB1_JB2
clcA Yes K03281 −364.493 80.637 −4.52 0.0007 by_group_JB5_JB6_JB7
clcB Yes K03281 407.456 134.243 3.04 0.0054 interaction
clcB Yes K03281 −771.949 108.085 −7.14 0.0000 by_group_JB1_JB2
clcB Yes K03281 −364.493 80.637 −4.52 0.0007 by_group_JB5_JB6_JB7
clcN Yes K05011 −0.149 1.127 −0.13 0.8955 main_effect
gltT No K11102 107.773 51.414 2.10 0.0459 interaction
gltT No K11102 −176.976 42.549 −4.16 0.0010 by_group_JB1_JB2
gltT No K11102 −69.204 29.461 −2.35 0.0368 by_group_JB5_JB6_JB7
kefC No K11745 6.673 4.711 1.42 0.1676 main_effect
Copper Cycling copA Yes K17686 188.730 58.699 3.22 0.0033 main_effect
copB Yes K01533 46.310 38.515 1.20 0.2393 main_effect
ctrA Yes K13584 −337.827 86.273 −3.92 0.0005 main_effect
cueO No K14588 0.438 7.745 0.06 0.9553 main_effect
cusA Yes K07787 −95.738 36.089 −2.65 0.0130 main_effect
cusB No K07798 −87.161 41.617 −2.09 0.0454 main_effect
Hormone Production acdS Yes Ethylene K01505 −7.439 40.604 −0.18 0.8559 main_effect
aldA Yes IAA K07248 12.538 5.752 2.18 0.0379 main_effect
aldH No IAA K00128 −38.741 102.559 −0.38 0.7085 main_effect
amiE Yes IAA K01426 38.863 50.324 0.77 0.4464 main_effect
aspC Yes IAA K00813 −6.059 4.957 −1.22 0.2318 main_effect
entC No GA K02361 −2.235 2.755 −0.81 0.4240 main_effect
etfA No Ethylene K03522 −220.466 125.212 −1.76 0.0892 main_effect
iaaH No IAA K21801 −15.273 5.787 −2.64 0.0134 main_effect
iaaM No IAA K00466 0.879 6.679 0.13 0.8962 main_effect
ipdC Yes IAA K04103 −1.553 1.766 −0.88 0.3868 main_effect
ipt Yes CK K00375 −60.043 61.067 −0.98 0.3339 main_effect
miaA No CK K00791 −376.130 124.932 −3.01 0.0055 main_effect
nitA No IAA K01501 57.459 13.150 4.37 0.0002 interaction
nitA No IAA K01501 −49.741 12.637 −3.94 0.0015 by_group_JB1_JB2
nitA No IAA K01501 7.717 4.492 1.72 0.1115 by_group_JB5_JB6_JB7
tnaA No IAA K01667 0.410 18.794 0.02 0.9827 main_effect
Iron Cycling bfr No K03594 109.443 58.189 1.88 0.0704 main_effect
dps No K04047 140.918 62.768 2.25 0.0328 main_effect
entC Yes K02361 −2.235 2.755 −0.81 0.4240 main_effect
feoB Yes K04759 −9.675 16.478 −0.59 0.5618 main_effect
fur No K03711 −67.095 72.327 −0.93 0.3615 main_effect
iscA No K13628 614.193 188.453 3.26 0.0031 interaction
iscA No K13628 −586.715 130.052 −4.51 0.0005 by_group_JB1_JB2
iscA No K13628 27.478 135.023 0.20 0.8422 by_group_JB5_JB6_JB7
sufB Yes K09014 25.132 43.834 0.57 0.5710 main_effect
sufC No K09013 305.949 98.546 3.10 0.0046 interaction
sufC No K09013 −152.125 70.329 −2.16 0.0483 by_group_JB1_JB2
sufC No K09013 153.825 68.560 2.24 0.0445 by_group_JB5_JB6_JB7
yqjH No K07229 −0.876 0.804 −1.09 0.2847 main_effect
Magnesium Cycling corA Yes K03284 −861.038 415.452 −2.07 0.0483 interaction
corA Yes K03284 1,392.615 240.956 5.78 0.0000 by_group_JB1_JB2
corA Yes K03284 531.577 331.677 1.60 0.1350 by_group_JB5_JB6_JB7
mgtA Yes K01531 415.763 197.763 2.10 0.0454 interaction
mgtA Yes K01531 −673.929 158.742 −4.25 0.0008 by_group_JB1_JB2
mgtA Yes K01531 −258.165 119.368 −2.16 0.0515 by_group_JB5_JB6_JB7
mgtB No K01531 415.763 197.763 2.10 0.0454 interaction
mgtB No K01531 −673.929 158.742 −4.25 0.0008 by_group_JB1_JB2
mgtB No K01531 −258.165 119.368 −2.16 0.0515 by_group_JB5_JB6_JB7
mgtE Yes K06213 −101.137 51.010 −1.98 0.0573 main_effect
phoQ No K07637 10.932 7.726 1.41 0.1681 main_effect
Manganese Cycling mntA Yes K06147 −643.771 202.193 −3.18 0.0035 main_effect
mntB Yes K06148 −8.198 16.512 −0.50 0.6234 main_effect
mntC Yes K06149 4.726 5.284 0.89 0.3787 main_effect
mntH Yes K03322 243.063 116.579 2.08 0.0470 interaction
mntH Yes K03322 −440.994 98.934 −4.46 0.0005 by_group_JB1_JB2
mntH Yes K03322 −197.932 63.536 −3.12 0.0089 by_group_JB5_JB6_JB7
mntR No K03709 34.401 49.766 0.69 0.4951 main_effect
mntR No K11924 −7.194 7.822 −0.92 0.3656 main_effect
sitA Yes K11604 24.591 4.728 5.20 0.0000 main_effect
sodA No K04564 88.129 110.447 0.80 0.4316 main_effect
Nitrogen fixation amt No K03320 −648.582 95.245 −6.81 0.0000 main_effect
glnB No K04751 −242.944 154.107 −1.58 0.1262 main_effect
iscS No K04487 442.853 177.088 2.50 0.0190 interaction
iscS No K04487 −505.056 116.334 −4.34 0.0007 by_group_JB1_JB2
iscS No K04487 −62.203 131.686 −0.47 0.6451 by_group_JB5_JB6_JB7
moeA No K03750 −65.147 63.300 −1.03 0.3122 main_effect
nifA No K02584 19.302 11.435 1.69 0.1025 main_effect
nifB Yes K02585 −7.188 7.948 −0.90 0.3735 main_effect
nifD Yes K02586 4.550 9.529 0.48 0.6367 main_effect
nifE Yes K02587 −4.258 14.118 −0.30 0.7652 main_effect
nifH Yes K02588 −0.552 1.503 −0.37 0.7161 main_effect
nifK Yes K02591 4.459 15.404 0.29 0.7743 main_effect
nifM Yes K03769 −43.633 45.236 −0.96 0.3430 main_effect
nifN Yes K02592 −2.345 2.552 −0.92 0.3661 main_effect
nifQ No K15790 −0.059 0.446 −0.13 0.8955 main_effect
nifU Yes K04488 −53.721 71.957 −0.75 0.4615 main_effect
nifV Yes K02594 −6.927 5.313 −1.30 0.2030 main_effect
nifW No K02595 −0.901 1.553 −0.58 0.5667 main_effect
nifX No K02596 0.873 6.641 0.13 0.8964 main_effect
nifZ No K02597 3.138 2.444 1.28 0.2096 main_effect
Nitrogen Release amoA Yes K10944 9.398 4.743 1.98 0.0574 main_effect
amoB Yes K10945 12.317 5.652 2.18 0.0379 main_effect
amoC Yes K10946 127.598 58.245 2.19 0.0370 main_effect
gdh No K15371 90.365 25.429 3.55 0.0014 main_effect
napA No K02567 17.361 10.012 1.73 0.0939 main_effect
napA Yes K01416 5.361 3.503 1.53 0.1371 main_effect
napB No K02568 3.475 7.326 0.47 0.6389 main_effect
narG Yes K00370 2.700 27.638 0.10 0.9229 main_effect
narH Yes K00371 1.448 22.830 0.06 0.9499 main_effect
narI No K00374 29.040 28.958 1.00 0.3245 main_effect
nasA Yes K00372 138.582 39.920 3.47 0.0017 main_effect
nasB Yes K00360 7.875 3.168 2.49 0.0192 main_effect
nirA Yes K00366 −64.897 20.486 −3.17 0.0037 main_effect
nirK Yes K00368 −38.208 20.769 −1.84 0.0764 main_effect
nirS Yes K15864 2.299 1.165 1.97 0.0585 main_effect
norB Yes K04561 −8.735 23.406 −0.37 0.7118 main_effect
norC No K02305 96.139 17.864 5.38 0.0000 main_effect
nosZ Yes K00376 42.851 20.541 2.09 0.0462 main_effect
nrfA Yes K03385 66.600 29.174 2.28 0.0302 main_effect
ureC No K01428 55.130 46.846 1.18 0.2492 main_effect
Nodulation nodA Yes K14658 −0.548 0.502 −1.09 0.2847 main_effect
nodD Yes K14657 −0.943 3.674 −0.26 0.7993 main_effect
nodI No ABC transporter complex K09694 467.630 119.840 3.90 0.0005 main_effect
Phosphorus Solubilization gcd Yes K00117 117.685 69.117 1.70 0.0997 main_effect
phnX No K06163 −12.480 14.358 −0.87 0.3921 main_effect
phoA Yes K01077 69.399 15.019 4.62 0.0001 main_effect
phoD No K01113 158.550 81.468 1.95 0.0617 main_effect
phoX No K07093 261.407 25.186 10.38 0.0000 main_effect
ppk No K00937 95.179 90.144 1.06 0.3001 main_effect
ppx No K01514 −0.811 3.150 −0.26 0.7987 main_effect
pqqB Yes K06136 −81.752 48.722 −1.68 0.1045 main_effect
pqqC Yes K06137 −91.013 45.430 −2.00 0.0549 main_effect
pqqD Yes K06138 −92.532 49.382 −1.87 0.0714 main_effect
pqqE Yes K06139 −53.385 23.953 −2.23 0.0340 main_effect
Potassium Solubilization gcd Yes K00117 117.685 69.117 1.70 0.0997 main_effect
kdsA No K01627 −97.456 45.890 −2.12 0.0427 main_effect
kdsB No K00979 375.407 134.968 2.78 0.0099 interaction
kdsB No K00979 −562.794 111.092 −5.07 0.0002 by_group_JB1_JB2
kdsB No K00979 −187.387 78.106 −2.40 0.0336 by_group_JB5_JB6_JB7
kup Yes K03549 −7.729 101.016 −0.08 0.9396 main_effect
nhaA No K03313 529.113 64.830 8.16 0.0000 main_effect
pqqB Yes K06136 −81.752 48.722 −1.68 0.1045 main_effect
pqqC Yes K06137 −91.013 45.430 −2.00 0.0549 main_effect
pqqD Yes K06138 −92.532 49.382 −1.87 0.0714 main_effect
pqqE Yes K06139 −53.385 23.953 −2.23 0.0340 main_effect
trkA Yes K03499 83.894 118.209 0.71 0.4838 main_effect
trkH Yes K03498 106.684 35.336 3.02 0.0056 interaction
trkH Yes K03498 39.615 28.286 1.40 0.1831 by_group_JB1_JB2
trkH Yes K03498 146.300 21.420 6.83 0.0000 by_group_JB5_JB6_JB7
Stress Adaptation copA Yes Heavy Metal Tolerance K17686 188.730 58.699 3.22 0.0033 main_effect
ectB Yes Salt tolerance K00836 −2.338 9.534 −0.25 0.8081 main_effect
entC Yes Siderophore production K02361 −2.235 2.755 −0.81 0.4240 main_effect
glnA No ACC deaminase (ACC-d) K01915 −853.102 349.161 −2.44 0.0217 interaction
glnA No ACC deaminase (ACC-d) K01915 1,013.043 219.320 4.62 0.0004 by_group_JB1_JB2
glnA No ACC deaminase (ACC-d) K01915 159.941 267.236 0.60 0.5606 by_group_JB5_JB6_JB7
kdsA Yes Exopolysaccharide production K01627 −97.456 45.890 −2.12 0.0427 main_effect
kdsB No Exopolysaccharide production K00979 375.407 134.968 2.78 0.0099 interaction
kdsB No Exopolysaccharide production K00979 −562.794 111.092 −5.07 0.0002 by_group_JB1_JB2
kdsB No Exopolysaccharide production K00979 −187.387 78.106 −2.40 0.0336 by_group_JB5_JB6_JB7
pchA Yes Salicylic acid (SA) K01851 −5.866 2.643 −2.22 0.0347 main_effect
pchB No Salicylic acid (SA) K04782 20.176 15.703 1.28 0.2094 main_effect
pqqB No Siderophore production K06136 −81.752 48.722 −1.68 0.1045 main_effect
Sulfur Cycling aprA Yes K00394 0.449 3.889 0.12 0.9089 main_effect
cysA Yes K02045 −536.436 246.970 −2.17 0.0392 interaction
cysA Yes K02045 861.646 137.992 6.24 0.0000 by_group_JB1_JB2
cysA Yes K02045 325.209 200.459 1.62 0.1307 by_group_JB5_JB6_JB7
cysU Yes K02046 42.240 15.076 2.80 0.0091 main_effect
cysW Yes K02047 90.894 43.079 2.11 0.0439 main_effect
fccB Yes K17229 7.402 2.958 2.50 0.0184 main_effect
sat Yes K00958 78.716 39.878 1.97 0.0583 main_effect
soxA No K17222 56.515 47.067 1.20 0.2399 main_effect
soxB No K17224 −37.364 10.521 −3.55 0.0014 main_effect
soxC Yes K17225 30.429 92.496 0.33 0.7446 main_effect
soxD Yes K22622 −15.538 28.266 −0.55 0.5869 main_effect
soxX No K17223 −8.755 33.016 −0.27 0.7928 main_effect
soxY Yes K17226 −91.210 45.198 −2.02 0.0533 main_effect
soxZ Yes K17227 −7.898 35.572 −0.22 0.8259 main_effect
Zinc Cycling mntR No K03709 34.401 49.766 0.69 0.4951 main_effect
troA No K11707 66.788 28.535 2.34 0.0272 interaction
troA No K11707 6.422 20.575 0.31 0.7595 by_group_JB1_JB2
troA No K11707 73.210 19.659 3.72 0.0029 by_group_JB5_JB6_JB7
zitB No K16264 −198.578 60.225 −3.30 0.0027 main_effect
zntA No K01534 −31.528 21.033 −1.50 0.1451 main_effect
znuA Yes K09815 104.384 25.885 4.03 0.0004 main_effect
znuB Yes K09816 206.647 55.309 3.74 0.0008 main_effect
znuC Yes K09817 105.251 35.121 3.00 0.0057 main_effect
zur No K02076 −29.978 14.898 −2.01 0.0539 main_effect

Table 6: Summary statistics for each gene. The table shows the summary statistics for the analysis of the metadata variable and each gene (KO gene cluster) organised by section. The table gives estimate, standard error, t-value, p-value and model. “Model” informs which model the summary statistics represents: “main_effect” originate from analysis where all fields are analyzed together. This happens when we have tested for effects of JB and not found any significant difference between JB groups. “Interaction” gives results for the interaction analysis and is included only when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.

Phosphorus

Section Gene Essential Cagetory KO.ID Estimate SE t p-value Model
Antibiotic Production bacB Yes Bacilysin K19547 1.072 0.342 3.13 0.0043 interaction
bacB Yes Bacilysin K19547 0.000 0.000 NaN NaN by_group_JB1_JB2
bacB Yes Bacilysin K19547 1.072 0.365 2.94 0.0125 by_group_JB5_JB6_JB7
bacC Yes Bacilysin K19548 −0.038 0.276 −0.14 0.8907 main_effect
E4.1.1.82 Yes Fosfomycin K09459 1.872 3.479 0.54 0.5949 main_effect
eryA Yes Macrolides K00862 3.526 2.029 1.74 0.0932 main_effect
penM No Pentalenolactone K17476 0.240 0.419 0.57 0.5718 main_effect
pntE Yes Pentalenolactone K18091 −0.772 1.087 −0.71 0.4836 main_effect
pntH Yes Pentalenolactone K18056 0.932 0.333 2.80 0.0095 interaction
pntH Yes Pentalenolactone K18056 −0.932 0.313 −2.98 0.0099 by_group_JB1_JB2
pntH Yes Pentalenolactone K18056 0.000 0.000 NaN NaN by_group_JB5_JB6_JB7
ptlF Yes Pentalenolactone K17747 −0.047 0.250 −0.19 0.8540 main_effect
rifG Yes Rifamycin K16020 −1.279 0.833 −1.54 0.1360 main_effect
strA Yes Streptomycin K00547 25.178 12.147 2.07 0.0482 interaction
strA Yes Streptomycin K00547 0.128 9.813 0.01 0.9898 by_group_JB1_JB2
strA Yes Streptomycin K00547 25.306 6.597 3.84 0.0024 by_group_JB5_JB6_JB7
Antibiotic Resistance vanA Yes Vancomycin K15739 1.020 1.011 1.01 0.3217 main_effect
vanH Yes Vancomycin K18347 0.637 1.077 0.59 0.5593 main_effect
vanX Yes Vancomycin K08641 41.003 8.993 4.56 0.0001 main_effect
Biocontrol chiA Yes Fungicidal agents K06904 −8.512 8.895 −0.96 0.3468 main_effect
chiB No Fungicidal agents, Insecticide agents K20547 −0.098 0.512 −0.19 0.8497 main_effect
dapB No Bactericidal agents K00215 64.012 38.466 1.66 0.1072 main_effect
phzF Yes Fungicidal agents, Bactericidal agents K06998 −8.231 8.734 −0.94 0.3540 main_effect
prnA Yes Fungicidal agents K14266 0.492 3.987 0.12 0.9027 main_effect
prnC Yes Fungicidal agents K14257 4.287 2.358 1.82 0.0798 main_effect
tcaB Yes Insecticide agents K07552 42.022 20.328 2.07 0.0481 main_effect
Calcium Cycling chaA Yes K07300 −5.776 22.769 −0.25 0.8016 main_effect
mgtC Yes K07507 142.844 40.292 3.55 0.0015 interaction
mgtC Yes K07507 −62.449 29.477 −2.12 0.0525 by_group_JB1_JB2
mgtC Yes K07507 80.396 26.937 2.98 0.0114 by_group_JB5_JB6_JB7
phaC No K03821 −99.053 44.405 −2.23 0.0345 interaction
phaC No K03821 14.231 31.637 0.45 0.6597 by_group_JB1_JB2
phaC No K03821 −84.821 30.849 −2.75 0.0176 by_group_JB5_JB6_JB7
ureC Yes K01428 6.021 14.415 0.42 0.6794 main_effect
Carbon Fixation ccmK No Calvin–Benson–Bassham (CBB) Cycle K08696 0.892 0.719 1.24 0.2250 main_effect
ccmL No Calvin–Benson–Bassham (CBB) Cycle K08697 −1.364 0.874 −1.56 0.1296 main_effect
codH Yes Wood–Ljungdahl (WL) pathway K00192 0.474 0.495 0.96 0.3466 main_effect
korA Yes Reductive TCA (rTCA) cycle K00174 12.681 10.719 1.18 0.2467 main_effect
korB Yes Reductive TCA (rTCA) cycle K00175 7.609 17.408 0.44 0.6654 main_effect
prk Yes Calvin–Benson–Bassham (CBB) Cycle K00855 0.442 3.839 0.12 0.9091 main_effect
rbcL Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01601 −7.421 8.779 −0.85 0.4051 main_effect
rbcS Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01602 136.172 47.839 2.85 0.0085 interaction
rbcS Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01602 −17.271 15.882 −1.09 0.2952 by_group_JB1_JB2
rbcS Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01602 118.901 47.754 2.49 0.0284 by_group_JB5_JB6_JB7
frdA No Reductive TCA (rTCA) cycle K00244 −2.001 2.942 −0.68 0.5021 main_effect
mcl No 3HP bicycle K08691 −4.433 4.539 −0.98 0.3371 main_effect
Chloride Cycling clcA Yes K03281 49.967 38.926 1.28 0.2098 main_effect
clcB Yes K03281 49.967 38.926 1.28 0.2098 main_effect
clcN Yes K05011 0.128 0.339 0.38 0.7074 main_effect
gltT No K11102 −9.385 9.683 −0.97 0.3407 main_effect
kefC No K11745 2.622 1.383 1.90 0.0684 main_effect
Copper Cycling copA Yes K17686 21.801 20.281 1.07 0.2916 main_effect
copB Yes K01533 −2.131 11.894 −0.18 0.8591 main_effect
ctrA Yes K13584 17.459 32.169 0.54 0.5916 main_effect
cueO No K14588 −0.568 2.331 −0.24 0.8092 main_effect
cusA Yes K07787 −11.101 11.981 −0.93 0.3621 main_effect
cusB No K07798 −11.920 13.296 −0.90 0.3776 main_effect
Hormone Production acdS Yes Ethylene K01505 4.409 12.213 0.36 0.7208 main_effect
aldA Yes IAA K07248 2.725 1.802 1.51 0.1417 main_effect
aldH No IAA K00128 54.450 29.221 1.86 0.0729 main_effect
amiE Yes IAA K01426 12.525 15.140 0.83 0.4150 main_effect
aspC Yes IAA K00813 8.387 2.917 2.88 0.0080 interaction
aspC Yes IAA K00813 −2.804 2.103 −1.33 0.2037 by_group_JB1_JB2
aspC Yes IAA K00813 5.583 1.993 2.80 0.0160 by_group_JB5_JB6_JB7
entC No GA K02361 3.674 1.621 2.27 0.0319 interaction
entC No GA K02361 −0.268 1.063 −0.25 0.8043 by_group_JB1_JB2
entC No GA K02361 3.406 1.238 2.75 0.0175 by_group_JB5_JB6_JB7
etfA No Ethylene K03522 8.248 39.730 0.21 0.8371 main_effect
iaaH No IAA K21801 −1.606 1.925 −0.83 0.4112 main_effect
iaaM No IAA K00466 0.709 2.008 0.35 0.7266 main_effect
ipdC Yes IAA K04103 0.076 0.539 0.14 0.8889 main_effect
ipt Yes CK K00375 34.514 17.541 1.97 0.0591 main_effect
miaA No CK K00791 174.427 77.553 2.25 0.0332 interaction
miaA No CK K00791 −58.524 55.045 −1.06 0.3057 by_group_JB1_JB2
miaA No CK K00791 115.903 54.154 2.14 0.0536 by_group_JB5_JB6_JB7
nitA No IAA K01501 0.537 2.809 0.19 0.8497 main_effect
tnaA No IAA K01667 −10.852 5.278 −2.06 0.0492 main_effect
Iron Cycling bfr No K03594 3.362 18.596 0.18 0.8578 main_effect
dps No K04047 14.197 20.368 0.70 0.4916 main_effect
entC Yes K02361 3.674 1.621 2.27 0.0319 interaction
entC Yes K02361 −0.268 1.063 −0.25 0.8043 by_group_JB1_JB2
entC Yes K02361 3.406 1.238 2.75 0.0175 by_group_JB5_JB6_JB7
feoB Yes K04759 2.271 4.977 0.46 0.6516 main_effect
fur No K03711 63.442 18.595 3.41 0.0020 main_effect
iscA No K13628 51.259 33.723 1.52 0.1397 main_effect
sufB Yes K09014 30.628 11.958 2.56 0.0161 main_effect
sufC No K09013 −7.577 16.231 −0.47 0.6442 main_effect
yqjH No K07229 1.287 0.411 3.13 0.0043 interaction
yqjH No K07229 0.000 0.000 NaN NaN by_group_JB1_JB2
yqjH No K07229 1.287 0.438 2.94 0.0125 by_group_JB5_JB6_JB7
Magnesium Cycling corA Yes K03284 −103.851 82.713 −1.26 0.2197 main_effect
mgtA Yes K01531 −23.070 37.712 −0.61 0.5456 main_effect
mgtB No K01531 −23.070 37.712 −0.61 0.5456 main_effect
mgtE Yes K06213 65.436 29.602 2.21 0.0361 interaction
mgtE Yes K06213 4.796 22.450 0.21 0.8339 by_group_JB1_JB2
mgtE Yes K06213 70.232 18.612 3.77 0.0027 by_group_JB5_JB6_JB7
phoQ No K07637 1.369 2.396 0.57 0.5723 main_effect
Manganese Cycling mntA Yes K06147 163.490 64.036 2.55 0.0164 main_effect
mntB Yes K06148 6.010 4.866 1.24 0.2271 main_effect
mntC Yes K06149 0.580 1.611 0.36 0.7216 main_effect
mntH Yes K03322 52.689 26.463 1.99 0.0563 main_effect
mntR No K03709 19.535 14.665 1.33 0.1936 main_effect
mntR No K11924 11.167 4.103 2.72 0.0114 interaction
mntR No K11924 0.990 2.096 0.47 0.6442 by_group_JB1_JB2
mntR No K11924 12.157 3.673 3.31 0.0062 by_group_JB5_JB6_JB7
sitA Yes K11604 0.893 1.990 0.45 0.6573 main_effect
sodA No K04564 −27.264 33.258 −0.82 0.4193 main_effect
Nitrogen fixation amt No K03320 28.333 46.463 0.61 0.5469 main_effect
glnB No K04751 −18.436 48.325 −0.38 0.7057 main_effect
iscS No K04487 148.007 57.822 2.56 0.0166 interaction
iscS No K04487 −34.234 47.857 −0.72 0.4862 by_group_JB1_JB2
iscS No K04487 113.773 29.100 3.91 0.0021 by_group_JB5_JB6_JB7
moeA No K03750 2.096 19.426 0.11 0.9148 main_effect
nifA No K02584 −8.366 3.252 −2.57 0.0157 main_effect
nifB Yes K02585 −3.348 2.346 −1.43 0.1646 main_effect
nifD Yes K02586 −7.237 2.538 −2.85 0.0081 main_effect
nifE Yes K02587 −10.746 3.745 −2.87 0.0077 main_effect
nifH Yes K02588 −0.500 0.444 −1.13 0.2695 main_effect
nifK Yes K02591 −12.055 4.052 −2.98 0.0060 main_effect
nifM Yes K03769 −11.674 13.678 −0.85 0.4006 main_effect
nifN Yes K02592 −0.634 0.771 −0.82 0.4183 main_effect
nifQ No K15790 −0.233 0.127 −1.84 0.0767 main_effect
nifU Yes K04488 23.178 21.453 1.08 0.2892 main_effect
nifV Yes K02594 −1.811 1.613 −1.12 0.2709 main_effect
nifW No K02595 0.196 0.469 0.42 0.6788 main_effect
nifX No K02596 −4.078 1.847 −2.21 0.0356 main_effect
nifZ No K02597 −0.986 0.734 −1.34 0.1901 main_effect
Nitrogen Release amoA Yes K10944 −0.366 1.524 −0.24 0.8119 main_effect
amoB Yes K10945 2.274 1.791 1.27 0.2147 main_effect
amoC Yes K10946 −11.653 18.866 −0.62 0.5418 main_effect
gdh No K15371 −7.213 9.128 −0.79 0.4360 main_effect
napA No K02567 −3.611 3.100 −1.16 0.2540 main_effect
napA Yes K01416 −0.469 1.095 −0.43 0.6717 main_effect
napB No K02568 −0.915 2.209 −0.41 0.6820 main_effect
narG Yes K00370 14.042 7.895 1.78 0.0862 main_effect
narH Yes K00371 8.748 6.678 1.31 0.2008 main_effect
narI No K00374 10.441 8.659 1.21 0.2380 main_effect
nasA Yes K00372 3.569 14.370 0.25 0.8056 main_effect
nasB Yes K00360 0.949 1.039 0.91 0.3689 main_effect
nirA Yes K00366 5.476 7.119 0.77 0.4482 main_effect
nirK Yes K00368 19.124 5.553 3.44 0.0018 main_effect
nirS Yes K15864 −0.205 0.373 −0.55 0.5864 main_effect
norB Yes K04561 5.994 6.978 0.86 0.3977 main_effect
norC No K02305 −11.516 7.362 −1.56 0.1290 main_effect
nosZ Yes K00376 5.654 6.566 0.86 0.3965 main_effect
nrfA Yes K03385 −19.667 8.823 −2.23 0.0340 main_effect
ureC No K01428 6.021 14.415 0.42 0.6794 main_effect
Nodulation nodA Yes K14658 0.804 0.257 3.13 0.0043 interaction
nodA Yes K14658 0.000 0.000 NaN NaN by_group_JB1_JB2
nodA Yes K14658 0.804 0.274 2.94 0.0125 by_group_JB5_JB6_JB7
nodD Yes K14657 −4.677 2.253 −2.08 0.0480 interaction
nodD Yes K14657 1.965 1.725 1.14 0.2739 by_group_JB1_JB2
nodD Yes K14657 −2.712 1.391 −1.95 0.0749 by_group_JB5_JB6_JB7
nodI No ABC transporter complex K09694 −42.974 44.124 −0.97 0.3384 main_effect
Phosphorus Solubilization gcd Yes K00117 −5.337 21.854 −0.24 0.8088 main_effect
phnX No K06163 8.013 4.114 1.95 0.0616 main_effect
phoA Yes K01077 8.417 5.793 1.45 0.1574 main_effect
phoD No K01113 46.051 24.664 1.87 0.0724 main_effect
phoX No K07093 −13.548 16.510 −0.82 0.4188 main_effect
ppk No K00937 −17.812 27.491 −0.65 0.5223 main_effect
ppx No K01514 0.373 0.948 0.39 0.6966 main_effect
pqqB Yes K06136 11.014 15.259 0.72 0.4764 main_effect
pqqC Yes K06137 11.833 14.465 0.82 0.4202 main_effect
pqqD Yes K06138 −1.144 15.783 −0.07 0.9428 main_effect
pqqE Yes K06139 11.956 7.498 1.59 0.1221 main_effect
Potassium Solubilization gcd Yes K00117 −5.337 21.854 −0.24 0.8088 main_effect
kdsA No K01627 30.288 13.756 2.20 0.0361 main_effect
kdsB No K00979 54.269 30.615 1.77 0.0872 main_effect
kup Yes K03549 −1.882 30.438 −0.06 0.9511 main_effect
nhaA No K03313 18.371 35.738 0.51 0.6113 main_effect
pqqB Yes K06136 11.014 15.259 0.72 0.4764 main_effect
pqqC Yes K06137 11.833 14.465 0.82 0.4202 main_effect
pqqD Yes K06138 −1.144 15.783 −0.07 0.9428 main_effect
pqqE Yes K06139 11.956 7.498 1.59 0.1221 main_effect
trkA Yes K03499 −21.821 35.699 −0.61 0.5460 main_effect
trkH Yes K03498 5.164 7.799 0.66 0.5133 main_effect
Stress Adaptation copA Yes Heavy Metal Tolerance K17686 21.801 20.281 1.07 0.2916 main_effect
ectB Yes Salt tolerance K00836 13.099 5.324 2.46 0.0208 interaction
ectB Yes Salt tolerance K00836 −0.256 4.393 −0.06 0.9543 by_group_JB1_JB2
ectB Yes Salt tolerance K00836 12.842 2.707 4.74 0.0005 by_group_JB5_JB6_JB7
entC Yes Siderophore production K02361 3.674 1.621 2.27 0.0319 interaction
entC Yes Siderophore production K02361 −0.268 1.063 −0.25 0.8043 by_group_JB1_JB2
entC Yes Siderophore production K02361 3.406 1.238 2.75 0.0175 by_group_JB5_JB6_JB7
glnA No ACC deaminase (ACC-d) K01915 53.158 58.565 0.91 0.3718 main_effect
kdsA Yes Exopolysaccharide production K01627 30.288 13.756 2.20 0.0361 main_effect
kdsB No Exopolysaccharide production K00979 54.269 30.615 1.77 0.0872 main_effect
pchA Yes Salicylic acid (SA) K01851 1.625 0.807 2.01 0.0538 main_effect
pchB No Salicylic acid (SA) K04782 0.574 4.868 0.12 0.9070 main_effect
pqqB No Siderophore production K06136 11.014 15.259 0.72 0.4764 main_effect
Sulfur Cycling aprA Yes K00394 0.018 1.172 0.02 0.9875 main_effect
cysA Yes K02045 −31.836 47.753 −0.67 0.5104 main_effect
cysU Yes K02046 −1.465 5.132 −0.29 0.7774 main_effect
cysW Yes K02047 −19.488 13.480 −1.45 0.1594 main_effect
fccB Yes K17229 −0.345 0.984 −0.35 0.7287 main_effect
sat Yes K00958 −7.599 12.744 −0.60 0.5558 main_effect
soxA No K17222 −12.640 14.345 −0.88 0.3857 main_effect
soxB No K17224 6.097 3.640 1.68 0.1051 main_effect
soxC Yes K17225 −126.025 47.783 −2.64 0.0139 interaction
soxC Yes K17225 −16.459 36.122 −0.46 0.6556 by_group_JB1_JB2
soxC Yes K17225 −142.484 30.222 −4.71 0.0005 by_group_JB5_JB6_JB7
soxD Yes K22622 −7.336 8.450 −0.87 0.3926 main_effect
soxX No K17223 −6.154 9.892 −0.62 0.5389 main_effect
soxY Yes K17226 −6.257 14.527 −0.43 0.6699 main_effect
soxZ Yes K17227 17.222 10.222 1.68 0.1031 main_effect
Zinc Cycling mntR No K03709 19.535 14.665 1.33 0.1936 main_effect
troA No K11707 1.855 4.833 0.38 0.7040 main_effect
zitB No K16264 48.852 19.285 2.53 0.0172 main_effect
zntA No K01534 13.458 6.076 2.21 0.0351 main_effect
znuA Yes K09815 −12.669 9.509 −1.33 0.1935 main_effect
znuB Yes K09816 −101.652 34.256 −2.97 0.0064 interaction
znuB Yes K09816 24.927 23.183 1.08 0.3005 by_group_JB1_JB2
znuB Yes K09816 −76.725 25.331 −3.03 0.0105 by_group_JB5_JB6_JB7
znuC Yes K09817 6.159 12.106 0.51 0.6149 main_effect
zur No K02076 4.280 4.734 0.90 0.3736 main_effect

Table 7: Summary statistics for each gene. The table shows the summary statistics for the analysis of the metadata variable and each gene (KO gene cluster) organised by section. The table gives estimate, standard error, t-value, p-value and model. “Model” informs which model the summary statistics represents: “main_effect” originate from analysis where all fields are analyzed together. This happens when we have tested for effects of JB and not found any significant difference between JB groups. “Interaction” gives results for the interaction analysis and is included only when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.

Potassium

Section Gene Essential Cagetory KO.ID Estimate SE t p-value Model
Antibiotic Production bacB Yes Bacilysin K19547 0.037 0.056 0.67 0.5082 main_effect
bacC Yes Bacilysin K19548 −0.324 0.148 −2.18 0.0381 interaction
bacC Yes Bacilysin K19548 0.258 0.095 2.73 0.0164 by_group_JB1_JB2
bacC Yes Bacilysin K19548 −0.066 0.116 −0.57 0.5808 by_group_JB5_JB6_JB7
E4.1.1.82 Yes Fosfomycin K09459 0.226 0.951 0.24 0.8141 main_effect
eryA Yes Macrolides K00862 −1.374 0.520 −2.64 0.0133 main_effect
penM No Pentalenolactone K17476 0.127 0.112 1.13 0.2675 main_effect
pntE Yes Pentalenolactone K18091 0.448 0.286 1.57 0.1285 main_effect
pntH Yes Pentalenolactone K18056 −0.065 0.052 −1.27 0.2149 main_effect
ptlF Yes Pentalenolactone K17747 −0.328 0.115 −2.86 0.0083 interaction
ptlF Yes Pentalenolactone K17747 0.328 0.105 3.13 0.0074 by_group_JB1_JB2
ptlF Yes Pentalenolactone K17747 0.000 0.000 NaN NaN by_group_JB5_JB6_JB7
rifG Yes Rifamycin K16020 −0.266 0.231 −1.15 0.2588 main_effect
strA Yes Streptomycin K00547 4.327 1.504 2.88 0.0076 main_effect
Antibiotic Resistance vanA Yes Vancomycin K15739 0.179 0.278 0.64 0.5259 main_effect
vanH Yes Vancomycin K18347 0.444 0.283 1.57 0.1275 main_effect
vanX Yes Vancomycin K08641 0.615 3.229 0.19 0.8502 main_effect
Biocontrol chiA Yes Fungicidal agents K06904 3.378 2.376 1.42 0.1662 main_effect
chiB No Fungicidal agents, Insecticide agents K20547 −0.177 0.135 −1.31 0.2017 main_effect
dapB No Bactericidal agents K00215 8.668 10.852 0.80 0.4311 main_effect
phzF Yes Fungicidal agents, Bactericidal agents K06998 −4.662 2.248 −2.07 0.0474 main_effect
prnA Yes Fungicidal agents K14266 −0.028 1.085 −0.03 0.9793 main_effect
prnC Yes Fungicidal agents K14257 0.430 0.674 0.64 0.5286 main_effect
tcaB Yes Insecticide agents K07552 −5.516 5.848 −0.94 0.3536 main_effect
Calcium Cycling chaA Yes K07300 6.793 6.070 1.12 0.2726 main_effect
mgtC Yes K07507 −9.619 6.596 −1.46 0.1559 main_effect
phaC No K03821 −29.857 12.341 −2.42 0.0228 interaction
phaC No K03821 15.028 7.431 2.02 0.0627 by_group_JB1_JB2
phaC No K03821 −14.829 10.137 −1.46 0.1692 by_group_JB5_JB6_JB7
ureC Yes K01428 −2.159 3.914 −0.55 0.5856 main_effect
Carbon Fixation ccmK No Calvin–Benson–Bassham (CBB) Cycle K08696 0.449 0.182 2.46 0.0202 main_effect
ccmL No Calvin–Benson–Bassham (CBB) Cycle K08697 0.233 0.244 0.95 0.3481 main_effect
codH Yes Wood–Ljungdahl (WL) pathway K00192 0.837 0.201 4.17 0.0003 interaction
codH Yes Wood–Ljungdahl (WL) pathway K00192 0.000 0.000 NaN NaN by_group_JB1_JB2
codH Yes Wood–Ljungdahl (WL) pathway K00192 0.837 0.219 3.81 0.0025 by_group_JB5_JB6_JB7
korA Yes Reductive TCA (rTCA) cycle K00174 −13.922 5.841 −2.38 0.0247 interaction
korA Yes Reductive TCA (rTCA) cycle K00174 10.232 4.176 2.45 0.0280 by_group_JB1_JB2
korA Yes Reductive TCA (rTCA) cycle K00174 −3.690 3.968 −0.93 0.3707 by_group_JB5_JB6_JB7
korB Yes Reductive TCA (rTCA) cycle K00175 −8.265 4.490 −1.84 0.0763 main_effect
prk Yes Calvin–Benson–Bassham (CBB) Cycle K00855 −2.412 0.940 −2.56 0.0160 main_effect
rbcL Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01601 −3.478 2.329 −1.49 0.1466 main_effect
rbcS Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01602 −1.464 7.125 −0.21 0.8387 main_effect
frdA No Reductive TCA (rTCA) cycle K00244 −0.178 0.807 −0.22 0.8273 main_effect
mcl No 3HP bicycle K08691 −5.900 2.505 −2.36 0.0263 interaction
mcl No 3HP bicycle K08691 3.122 1.412 2.21 0.0442 by_group_JB1_JB2
mcl No 3HP bicycle K08691 −2.779 2.154 −1.29 0.2214 by_group_JB5_JB6_JB7
Chloride Cycling clcA Yes K03281 41.187 19.988 2.06 0.0495 interaction
clcA Yes K03281 −22.627 15.761 −1.44 0.1731 by_group_JB1_JB2
clcA Yes K03281 18.561 10.992 1.69 0.1171 by_group_JB5_JB6_JB7
clcB Yes K03281 41.187 19.988 2.06 0.0495 interaction
clcB Yes K03281 −22.627 15.761 −1.44 0.1731 by_group_JB1_JB2
clcB Yes K03281 18.561 10.992 1.69 0.1171 by_group_JB5_JB6_JB7
clcN Yes K05011 −0.011 0.092 −0.12 0.9041 main_effect
gltT No K11102 −1.271 2.669 −0.48 0.6376 main_effect
kefC No K11745 0.514 0.388 1.32 0.1960 main_effect
Copper Cycling copA Yes K17686 9.616 5.331 1.80 0.0821 main_effect
copB Yes K01533 1.809 3.221 0.56 0.5789 main_effect
ctrA Yes K13584 −19.784 7.968 −2.48 0.0193 main_effect
cueO No K14588 −0.075 0.635 −0.12 0.9062 main_effect
cusA Yes K07787 −1.758 3.294 −0.53 0.5978 main_effect
cusB No K07798 −0.417 3.670 −0.11 0.9103 main_effect
Hormone Production acdS Yes Ethylene K01505 −1.642 3.317 −0.49 0.6245 main_effect
aldA Yes IAA K07248 0.601 0.497 1.21 0.2373 main_effect
aldH No IAA K00128 −11.513 8.146 −1.41 0.1686 main_effect
amiE Yes IAA K01426 4.037 4.100 0.98 0.3333 main_effect
aspC Yes IAA K00813 2.297 0.800 2.87 0.0081 interaction
aspC Yes IAA K00813 −1.228 0.492 −2.49 0.0258 by_group_JB1_JB2
aspC Yes IAA K00813 1.069 0.646 1.65 0.1242 by_group_JB5_JB6_JB7
entC No GA K02361 0.239 0.224 1.07 0.2945 main_effect
etfA No Ethylene K03522 8.696 10.696 0.81 0.4231 main_effect
iaaH No IAA K21801 −0.387 0.525 −0.74 0.4673 main_effect
iaaM No IAA K00466 0.487 0.540 0.90 0.3744 main_effect
ipdC Yes IAA K04103 −0.205 0.142 −1.45 0.1585 main_effect
ipt Yes CK K00375 7.216 4.908 1.47 0.1526 main_effect
miaA No CK K00791 4.483 11.757 0.38 0.7058 main_effect
nitA No IAA K01501 −1.922 0.673 −2.85 0.0080 main_effect
tnaA No IAA K01667 0.469 1.539 0.30 0.7628 main_effect
Iron Cycling bfr No K03594 −4.585 4.990 −0.92 0.3660 main_effect
dps No K04047 −27.632 11.058 −2.50 0.0191 interaction
dps No K04047 16.752 5.975 2.80 0.0141 by_group_JB1_JB2
dps No K04047 −10.880 9.742 −1.12 0.2859 by_group_JB5_JB6_JB7
entC Yes K02361 0.239 0.224 1.07 0.2945 main_effect
feoB Yes K04759 −2.478 1.276 −1.94 0.0623 main_effect
fur No K03711 0.123 6.022 0.02 0.9838 main_effect
iscA No K13628 −21.672 8.627 −2.51 0.0180 main_effect
sufB Yes K09014 6.197 3.421 1.81 0.0808 main_effect
sufC No K09013 −0.098 4.435 −0.02 0.9826 main_effect
yqjH No K07229 0.045 0.067 0.67 0.5082 main_effect
Magnesium Cycling corA Yes K03284 −118.645 39.477 −3.01 0.0058 interaction
corA Yes K03284 77.426 24.588 3.15 0.0071 by_group_JB1_JB2
corA Yes K03284 −41.219 31.542 −1.31 0.2158 by_group_JB5_JB6_JB7
mgtA Yes K01531 −13.882 9.994 −1.39 0.1758 main_effect
mgtB No K01531 −13.882 9.994 −1.39 0.1758 main_effect
mgtE Yes K06213 25.981 8.057 3.22 0.0034 interaction
mgtE Yes K06213 −14.502 4.528 −3.20 0.0064 by_group_JB1_JB2
mgtE Yes K06213 11.479 6.939 1.65 0.1240 by_group_JB5_JB6_JB7
phoQ No K07637 0.253 0.654 0.39 0.7023 main_effect
Manganese Cycling mntA Yes K06147 1.819 19.348 0.09 0.9258 main_effect
mntB Yes K06148 1.035 1.346 0.77 0.4482 main_effect
mntC Yes K06149 0.377 0.434 0.87 0.3921 main_effect
mntH Yes K03322 29.999 11.755 2.55 0.0169 interaction
mntH Yes K03322 −27.013 8.501 −3.18 0.0067 by_group_JB1_JB2
mntH Yes K03322 2.985 7.835 0.38 0.7099 by_group_JB5_JB6_JB7
mntR No K03709 −3.771 4.054 −0.93 0.3602 main_effect
mntR No K11924 −0.026 0.651 −0.04 0.9688 main_effect
sitA Yes K11604 0.086 0.543 0.16 0.8757 main_effect
sodA No K04564 −11.332 8.906 −1.27 0.2137 main_effect
Nitrogen fixation amt No K03320 −20.340 12.135 −1.68 0.1048 main_effect
glnB No K04751 −9.023 13.076 −0.69 0.4958 main_effect
iscS No K04487 41.030 16.152 2.54 0.0174 interaction
iscS No K04487 −20.180 11.736 −1.72 0.1075 by_group_JB1_JB2
iscS No K04487 20.850 10.681 1.95 0.0746 by_group_JB5_JB6_JB7
moeA No K03750 5.283 5.193 1.02 0.3177 main_effect
nifA No K02584 0.638 0.977 0.65 0.5191 main_effect
nifB Yes K02585 −0.050 0.661 −0.08 0.9405 main_effect
nifD Yes K02586 −0.085 0.784 −0.11 0.9141 main_effect
nifE Yes K02587 0.097 1.159 0.08 0.9341 main_effect
nifH Yes K02588 0.035 0.123 0.28 0.7802 main_effect
nifK Yes K02591 0.381 1.263 0.30 0.7651 main_effect
nifM Yes K03769 −1.541 3.759 −0.41 0.6850 main_effect
nifN Yes K02592 −0.073 0.212 −0.34 0.7347 main_effect
nifQ No K15790 −0.009 0.037 −0.24 0.8145 main_effect
nifU Yes K04488 0.798 5.957 0.13 0.8945 main_effect
nifV Yes K02594 0.110 0.448 0.25 0.8077 main_effect
nifW No K02595 0.031 0.128 0.24 0.8090 main_effect
nifX No K02596 0.002 0.545 0.00 0.9966 main_effect
nifZ No K02597 −0.147 0.204 −0.72 0.4764 main_effect
Nitrogen Release amoA Yes K10944 −0.409 0.408 −1.00 0.3250 main_effect
amoB Yes K10945 0.261 0.499 0.52 0.6043 main_effect
amoC Yes K10946 4.672 5.094 0.92 0.3669 main_effect
gdh No K15371 −18.541 3.901 −4.75 0.0001 interaction
gdh No K15371 11.542 1.932 5.97 0.0000 by_group_JB1_JB2
gdh No K15371 −6.999 3.583 −1.95 0.0745 by_group_JB5_JB6_JB7
napA No K02567 −1.299 0.828 −1.57 0.1282 main_effect
napA Yes K01416 −0.260 0.295 −0.88 0.3852 main_effect
napB No K02568 0.703 0.588 1.19 0.2425 main_effect
narG Yes K00370 0.456 2.265 0.20 0.8418 main_effect
narH Yes K00371 2.935 1.788 1.64 0.1120 main_effect
narI No K00374 4.449 2.266 1.96 0.0596 main_effect
nasA Yes K00372 1.607 3.904 0.41 0.6838 main_effect
nasB Yes K00360 −0.177 0.285 −0.62 0.5396 main_effect
nirA Yes K00366 2.610 1.895 1.38 0.1793 main_effect
nirK Yes K00368 0.189 1.803 0.10 0.9172 main_effect
nirS Yes K15864 −0.014 0.102 −0.13 0.8952 main_effect
norB Yes K04561 1.146 1.912 0.60 0.5539 main_effect
norC No K02305 0.666 2.086 0.32 0.7520 main_effect
nosZ Yes K00376 0.872 1.803 0.48 0.6323 main_effect
nrfA Yes K03385 −1.708 2.586 −0.66 0.5143 main_effect
ureC No K01428 −2.159 3.914 −0.55 0.5856 main_effect
Nodulation nodA Yes K14658 0.028 0.042 0.67 0.5082 main_effect
nodD Yes K14657 −0.299 0.296 −1.01 0.3223 main_effect
nodI No ABC transporter complex K09694 −71.297 20.959 −3.40 0.0022 interaction
nodI No ABC transporter complex K09694 48.367 11.389 4.25 0.0008 by_group_JB1_JB2
nodI No ABC transporter complex K09694 −22.931 18.409 −1.25 0.2367 by_group_JB5_JB6_JB7
Phosphorus Solubilization gcd Yes K00117 2.099 5.941 0.35 0.7264 main_effect
phnX No K06163 −1.546 1.157 −1.34 0.1922 main_effect
phoA Yes K01077 1.746 1.601 1.09 0.2850 main_effect
phoD No K01113 2.334 7.105 0.33 0.7449 main_effect
phoX No K07093 8.316 4.267 1.95 0.0614 main_effect
ppk No K00937 −46.533 13.534 −3.44 0.0020 interaction
ppk No K00937 18.684 9.539 1.96 0.0704 by_group_JB1_JB2
ppk No K00937 −27.849 9.397 −2.96 0.0118 by_group_JB5_JB6_JB7
ppx No K01514 −0.047 0.258 −0.18 0.8570 main_effect
pqqB Yes K06136 −6.715 3.995 −1.68 0.1039 main_effect
pqqC Yes K06137 −5.675 3.837 −1.48 0.1503 main_effect
pqqD Yes K06138 −1.612 4.285 −0.38 0.7096 main_effect
pqqE Yes K06139 −1.175 2.120 −0.55 0.5837 main_effect
Potassium Solubilization gcd Yes K00117 2.099 5.941 0.35 0.7264 main_effect
kdsA No K01627 −2.640 4.024 −0.66 0.5171 main_effect
kdsB No K00979 37.630 14.750 2.55 0.0170 interaction
kdsB No K00979 −25.973 11.641 −2.23 0.0425 by_group_JB1_JB2
kdsB No K00979 11.657 8.092 1.44 0.1753 by_group_JB5_JB6_JB7
kup Yes K03549 2.413 8.272 0.29 0.7726 main_effect
nhaA No K03313 9.694 9.599 1.01 0.3212 main_effect
pqqB Yes K06136 −6.715 3.995 −1.68 0.1039 main_effect
pqqC Yes K06137 −5.675 3.837 −1.48 0.1503 main_effect
pqqD Yes K06138 −1.612 4.285 −0.38 0.7096 main_effect
pqqE Yes K06139 −1.175 2.120 −0.55 0.5837 main_effect
trkA Yes K03499 −45.739 18.974 −2.41 0.0233 interaction
trkA Yes K03499 35.155 13.837 2.54 0.0235 by_group_JB1_JB2
trkA Yes K03499 −10.584 12.466 −0.85 0.4125 by_group_JB5_JB6_JB7
trkH Yes K03498 0.182 2.139 0.09 0.9327 main_effect
Stress Adaptation copA Yes Heavy Metal Tolerance K17686 9.616 5.331 1.80 0.0821 main_effect
ectB Yes Salt tolerance K00836 1.048 0.757 1.38 0.1775 main_effect
entC Yes Siderophore production K02361 0.239 0.224 1.07 0.2945 main_effect
glnA No ACC deaminase (ACC-d) K01915 −92.755 28.031 −3.31 0.0027 interaction
glnA No ACC deaminase (ACC-d) K01915 74.932 15.386 4.87 0.0002 by_group_JB1_JB2
glnA No ACC deaminase (ACC-d) K01915 −17.823 24.482 −0.73 0.4806 by_group_JB5_JB6_JB7
kdsA Yes Exopolysaccharide production K01627 −2.640 4.024 −0.66 0.5171 main_effect
kdsB No Exopolysaccharide production K00979 37.630 14.750 2.55 0.0170 interaction
kdsB No Exopolysaccharide production K00979 −25.973 11.641 −2.23 0.0425 by_group_JB1_JB2
kdsB No Exopolysaccharide production K00979 11.657 8.092 1.44 0.1753 by_group_JB5_JB6_JB7
pchA Yes Salicylic acid (SA) K01851 −0.261 0.230 −1.14 0.2651 main_effect
pchB No Salicylic acid (SA) K04782 −1.592 1.291 −1.23 0.2276 main_effect
pqqB No Siderophore production K06136 −6.715 3.995 −1.68 0.1039 main_effect
Sulfur Cycling aprA Yes K00394 0.792 0.282 2.81 0.0090 main_effect
cysA Yes K02045 −73.967 23.510 −3.15 0.0041 interaction
cysA Yes K02045 49.285 14.322 3.44 0.0040 by_group_JB1_JB2
cysA Yes K02045 −24.682 19.135 −1.29 0.2214 by_group_JB5_JB6_JB7
cysU Yes K02046 0.964 1.387 0.69 0.4929 main_effect
cysW Yes K02047 −26.128 6.435 −4.06 0.0004 interaction
cysW Yes K02047 10.777 3.797 2.84 0.0132 by_group_JB1_JB2
cysW Yes K02047 −15.351 5.366 −2.86 0.0143 by_group_JB5_JB6_JB7
fccB Yes K17229 −1.693 0.488 −3.47 0.0018 interaction
fccB Yes K17229 0.922 0.305 3.02 0.0092 by_group_JB1_JB2
fccB Yes K17229 −0.771 0.389 −1.98 0.0707 by_group_JB5_JB6_JB7
sat Yes K00958 −15.795 7.012 −2.25 0.0330 interaction
sat Yes K00958 8.994 4.253 2.11 0.0529 by_group_JB1_JB2
sat Yes K00958 −6.801 5.727 −1.19 0.2580 by_group_JB5_JB6_JB7
soxA No K17222 −4.242 3.876 −1.09 0.2830 main_effect
soxB No K17224 −2.534 0.922 −2.75 0.0104 main_effect
soxC Yes K17225 0.867 7.598 0.11 0.9100 main_effect
soxD Yes K22622 −3.633 2.227 −1.63 0.1141 main_effect
soxX No K17223 −0.447 2.710 −0.16 0.8703 main_effect
soxY Yes K17226 −8.863 3.596 −2.46 0.0201 main_effect
soxZ Yes K17227 −5.113 2.755 −1.86 0.0740 main_effect
Zinc Cycling mntR No K03709 −3.771 4.054 −0.93 0.3602 main_effect
troA No K11707 −1.974 1.265 −1.56 0.1298 main_effect
zitB No K16264 2.333 5.802 0.40 0.6907 main_effect
zntA No K01534 1.414 1.773 0.80 0.4316 main_effect
znuA Yes K09815 0.957 2.663 0.36 0.7219 main_effect
znuB Yes K09816 6.210 5.427 1.14 0.2622 main_effect
znuC Yes K09817 −1.953 3.289 −0.59 0.5574 main_effect
zur No K02076 1.178 1.288 0.91 0.3683 main_effect

Table 8: Summary statistics for each gene. The table shows the summary statistics for the analysis of the metadata variable and each gene (KO gene cluster) organised by section. The table gives estimate, standard error, t-value, p-value and model. “Model” informs which model the summary statistics represents: “main_effect” originate from analysis where all fields are analyzed together. This happens when we have tested for effects of JB and not found any significant difference between JB groups. “Interaction” gives results for the interaction analysis and is included only when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.

Magnesium

Section Gene Essential Cagetory KO.ID Estimate SE t p-value Model
Antibiotic Production bacB Yes Bacilysin K19547 −0.122 0.093 −1.32 0.1988 main_effect
bacC Yes Bacilysin K19548 −0.048 0.128 −0.37 0.7110 main_effect
E4.1.1.82 Yes Fosfomycin K09459 −0.495 1.617 −0.31 0.7617 main_effect
eryA Yes Macrolides K00862 −0.461 0.985 −0.47 0.6434 main_effect
penM No Pentalenolactone K17476 0.130 0.194 0.67 0.5064 main_effect
pntE Yes Pentalenolactone K18091 0.432 0.501 0.86 0.3960 main_effect
pntH Yes Pentalenolactone K18056 −0.109 0.088 −1.25 0.2234 main_effect
ptlF Yes Pentalenolactone K17747 0.121 0.114 1.06 0.2978 main_effect
rifG Yes Rifamycin K16020 0.005 0.402 0.01 0.9901 main_effect
strA Yes Streptomycin K00547 −2.557 2.872 −0.89 0.3808 main_effect
Antibiotic Resistance vanA Yes Vancomycin K15739 −0.984 0.439 −2.24 0.0332 main_effect
vanH Yes Vancomycin K18347 0.063 0.502 0.13 0.9011 main_effect
vanX Yes Vancomycin K08641 −8.625 5.250 −1.64 0.1116 main_effect
Biocontrol chiA Yes Fungicidal agents K06904 8.718 3.849 2.27 0.0314 main_effect
chiB No Fungicidal agents, Insecticide agents K20547 −0.376 0.227 −1.66 0.1079 main_effect
dapB No Bactericidal agents K00215 −5.494 18.645 −0.29 0.7704 main_effect
phzF Yes Fungicidal agents, Bactericidal agents K06998 −4.546 4.018 −1.13 0.2675 main_effect
prnA Yes Fungicidal agents K14266 4.684 1.621 2.89 0.0074 main_effect
prnC Yes Fungicidal agents K14257 −1.027 1.138 −0.90 0.3746 main_effect
tcaB Yes Insecticide agents K07552 0.995 10.105 0.10 0.9223 main_effect
Calcium Cycling chaA Yes K07300 31.351 8.737 3.59 0.0013 main_effect
mgtC Yes K07507 −31.593 9.994 −3.16 0.0038 main_effect
phaC No K03821 26.048 10.755 2.42 0.0222 main_effect
ureC Yes K01428 7.068 6.562 1.08 0.2907 main_effect
Carbon Fixation ccmK No Calvin–Benson–Bassham (CBB) Cycle K08696 0.327 0.337 0.97 0.3399 main_effect
ccmL No Calvin–Benson–Bassham (CBB) Cycle K08697 0.258 0.419 0.62 0.5428 main_effect
codH Yes Wood–Ljungdahl (WL) pathway K00192 −0.016 0.233 −0.07 0.9450 main_effect
korA Yes Reductive TCA (rTCA) cycle K00174 11.099 4.634 2.40 0.0235 main_effect
korB Yes Reductive TCA (rTCA) cycle K00175 3.167 8.067 0.39 0.6976 main_effect
prk Yes Calvin–Benson–Bassham (CBB) Cycle K00855 −3.506 1.650 −2.12 0.0426 main_effect
rbcL Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01601 3.442 4.066 0.85 0.4043 main_effect
rbcS Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01602 −23.451 11.295 −2.08 0.0472 main_effect
frdA No Reductive TCA (rTCA) cycle K00244 1.073 1.359 0.79 0.4365 main_effect
mcl No 3HP bicycle K08691 2.814 2.070 1.36 0.1849 main_effect
Chloride Cycling clcA Yes K03281 −42.808 16.693 −2.56 0.0160 main_effect
clcB Yes K03281 −42.808 16.693 −2.56 0.0160 main_effect
clcN Yes K05011 −0.144 0.155 −0.93 0.3591 main_effect
gltT No K11102 −9.852 4.161 −2.37 0.0251 main_effect
kefC No K11745 −2.878 1.284 −2.24 0.0337 interaction
kefC No K11745 2.263 0.644 3.51 0.0034 by_group_JB1_JB2
kefC No K11745 −0.616 1.186 −0.52 0.6130 by_group_JB5_JB6_JB7
Copper Cycling copA Yes K17686 10.656 9.370 1.14 0.2651 main_effect
copB Yes K01533 7.124 5.344 1.33 0.1933 main_effect
ctrA Yes K13584 −41.662 12.739 −3.27 0.0028 main_effect
cueO No K14588 0.824 1.069 0.77 0.4473 main_effect
cusA Yes K07787 −7.205 5.466 −1.32 0.1981 main_effect
cusB No K07798 −0.763 6.244 −0.12 0.9036 main_effect
Hormone Production acdS Yes Ethylene K01505 0.663 5.668 0.12 0.9078 main_effect
aldA Yes IAA K07248 1.293 0.833 1.55 0.1318 main_effect
aldH No IAA K00128 −6.958 14.287 −0.49 0.6300 main_effect
amiE Yes IAA K01426 12.600 6.685 1.88 0.0699 main_effect
aspC Yes IAA K00813 −1.351 0.662 −2.04 0.0509 main_effect
entC No GA K02361 −0.617 0.371 −1.66 0.1075 main_effect
etfA No Ethylene K03522 −11.026 18.296 −0.60 0.5516 main_effect
iaaH No IAA K21801 −0.694 0.893 −0.78 0.4432 main_effect
iaaM No IAA K00466 −1.119 0.908 −1.23 0.2278 main_effect
ipdC Yes IAA K04103 0.013 0.250 0.05 0.9603 main_effect
ipt Yes CK K00375 −9.101 8.495 −1.07 0.2932 main_effect
miaA No CK K00791 −34.334 18.978 −1.81 0.0812 main_effect
nitA No IAA K01501 −2.522 1.212 −2.08 0.0467 main_effect
tnaA No IAA K01667 0.864 2.617 0.33 0.7437 main_effect
Iron Cycling bfr No K03594 −3.086 8.598 −0.36 0.7224 main_effect
dps No K04047 9.120 9.357 0.97 0.3381 main_effect
entC Yes K02361 −0.617 0.371 −1.66 0.1075 main_effect
feoB Yes K04759 0.704 2.310 0.30 0.7628 main_effect
fur No K03711 −5.976 10.184 −0.59 0.5620 main_effect
iscA No K13628 −38.439 14.535 −2.64 0.0133 main_effect
sufB Yes K09014 −3.966 6.107 −0.65 0.5214 main_effect
sufC No K09013 3.804 7.512 0.51 0.6165 main_effect
yqjH No K07229 −0.146 0.111 −1.32 0.1988 main_effect
Magnesium Cycling corA Yes K03284 115.165 32.806 3.51 0.0015 main_effect
mgtA Yes K01531 −26.250 16.867 −1.56 0.1309 main_effect
mgtB No K01531 −26.250 16.867 −1.56 0.1309 main_effect
mgtE Yes K06213 −17.566 6.838 −2.57 0.0158 main_effect
phoQ No K07637 0.497 1.112 0.45 0.6582 main_effect
Manganese Cycling mntA Yes K06147 −74.737 29.744 −2.51 0.0180 main_effect
mntB Yes K06148 −2.800 2.253 −1.24 0.2241 main_effect
mntC Yes K06149 −0.253 0.746 −0.34 0.7366 main_effect
mntH Yes K03322 −35.379 11.258 −3.14 0.0039 main_effect
mntR No K03709 −0.234 7.003 −0.03 0.9736 main_effect
mntR No K11924 −4.409 2.109 −2.09 0.0464 interaction
mntR No K11924 0.266 0.885 0.30 0.7684 by_group_JB1_JB2
mntR No K11924 −4.144 2.084 −1.99 0.0701 by_group_JB5_JB6_JB7
sitA Yes K11604 1.778 0.862 2.06 0.0485 main_effect
sodA No K04564 15.513 15.308 1.01 0.3195 main_effect
Nitrogen fixation amt No K03320 −40.275 20.279 −1.99 0.0569 main_effect
glnB No K04751 −0.128 22.438 −0.01 0.9955 main_effect
iscS No K04487 −45.957 12.616 −3.64 0.0011 main_effect
moeA No K03750 3.473 8.974 0.39 0.7017 main_effect
nifA No K02584 0.795 1.668 0.48 0.6373 main_effect
nifB Yes K02585 −0.144 1.125 −0.13 0.8990 main_effect
nifD Yes K02586 0.640 1.330 0.48 0.6339 main_effect
nifE Yes K02587 1.083 1.963 0.55 0.5855 main_effect
nifH Yes K02588 0.095 0.209 0.45 0.6531 main_effect
nifK Yes K02591 2.138 2.114 1.01 0.3207 main_effect
nifM Yes K03769 1.148 6.412 0.18 0.8592 main_effect
nifN Yes K02592 −0.097 0.361 −0.27 0.7893 main_effect
nifQ No K15790 0.010 0.062 0.16 0.8749 main_effect
nifU Yes K04488 −0.573 10.140 −0.06 0.9553 main_effect
nifV Yes K02594 −0.153 0.763 −0.20 0.8428 main_effect
nifW No K02595 0.125 0.217 0.58 0.5683 main_effect
nifX No K02596 0.672 0.918 0.73 0.4702 main_effect
nifZ No K02597 0.085 0.351 0.24 0.8105 main_effect
Nitrogen Release amoA Yes K10944 0.602 0.697 0.86 0.3957 main_effect
amoB Yes K10945 −0.450 0.849 −0.53 0.5999 main_effect
amoC Yes K10946 11.606 8.519 1.36 0.1839 main_effect
gdh No K15371 10.242 3.811 2.69 0.0120 main_effect
napA No K02567 4.546 1.193 3.81 0.0007 main_effect
napA Yes K01416 0.562 0.498 1.13 0.2686 main_effect
napB No K02568 −0.076 1.026 −0.07 0.9414 main_effect
narG Yes K00370 −0.701 3.855 −0.18 0.8570 main_effect
narH Yes K00371 2.493 3.151 0.79 0.4355 main_effect
narI No K00374 2.081 4.094 0.51 0.6152 main_effect
nasA Yes K00372 11.694 6.285 1.86 0.0733 main_effect
nasB Yes K00360 0.117 0.488 0.24 0.8122 main_effect
nirA Yes K00366 −3.405 3.269 −1.04 0.3065 main_effect
nirK Yes K00368 −4.570 2.944 −1.55 0.1319 main_effect
nirS Yes K15864 0.109 0.172 0.63 0.5333 main_effect
norB Yes K04561 −1.593 3.260 −0.49 0.6290 main_effect
norC No K02305 6.227 3.355 1.86 0.0740 main_effect
nosZ Yes K00376 5.062 2.929 1.73 0.0949 main_effect
nrfA Yes K03385 9.260 4.074 2.27 0.0309 main_effect
ureC No K01428 7.068 6.562 1.08 0.2907 main_effect
Nodulation nodA Yes K14658 −0.091 0.069 −1.32 0.1988 main_effect
nodD Yes K14657 0.268 0.511 0.52 0.6039 main_effect
nodI No ABC transporter complex K09694 53.172 18.186 2.92 0.0068 main_effect
Phosphorus Solubilization gcd Yes K00117 5.317 10.081 0.53 0.6021 main_effect
phnX No K06163 1.583 2.008 0.79 0.4373 main_effect
phoA Yes K01077 5.005 2.617 1.91 0.0661 main_effect
phoD No K01113 0.343 12.112 0.03 0.9776 main_effect
phoX No K07093 21.151 6.625 3.19 0.0035 main_effect
ppk No K00937 15.938 12.468 1.28 0.2116 main_effect
ppx No K01514 −0.453 0.432 −1.05 0.3030 main_effect
pqqB Yes K06136 −6.741 7.018 −0.96 0.3450 main_effect
pqqC Yes K06137 −9.667 6.528 −1.48 0.1498 main_effect
pqqD Yes K06138 −2.209 7.298 −0.30 0.7644 main_effect
pqqE Yes K06139 −5.970 3.447 −1.73 0.0943 main_effect
Potassium Solubilization gcd Yes K00117 5.317 10.081 0.53 0.6021 main_effect
kdsA No K01627 −9.989 6.637 −1.51 0.1435 main_effect
kdsB No K00979 −35.546 13.359 −2.66 0.0128 main_effect
kup Yes K03549 16.100 13.765 1.17 0.2520 main_effect
nhaA No K03313 41.670 14.646 2.85 0.0082 main_effect
pqqB Yes K06136 −6.741 7.018 −0.96 0.3450 main_effect
pqqC Yes K06137 −9.667 6.528 −1.48 0.1498 main_effect
pqqD Yes K06138 −2.209 7.298 −0.30 0.7644 main_effect
pqqE Yes K06139 −5.970 3.447 −1.73 0.0943 main_effect
trkA Yes K03499 20.559 16.182 1.27 0.2144 main_effect
trkH Yes K03498 6.735 3.410 1.97 0.0582 main_effect
Stress Adaptation copA Yes Heavy Metal Tolerance K17686 10.656 9.370 1.14 0.2651 main_effect
ectB Yes Salt tolerance K00836 −1.010 1.318 −0.77 0.4501 main_effect
entC Yes Siderophore production K02361 −0.617 0.371 −1.66 0.1075 main_effect
glnA No ACC deaminase (ACC-d) K01915 45.951 26.112 1.76 0.0894 main_effect
kdsA Yes Exopolysaccharide production K01627 −9.989 6.637 −1.51 0.1435 main_effect
kdsB No Exopolysaccharide production K00979 −35.546 13.359 −2.66 0.0128 main_effect
pchA Yes Salicylic acid (SA) K01851 −0.510 0.388 −1.31 0.1996 main_effect
pchB No Salicylic acid (SA) K04782 −1.579 2.235 −0.71 0.4857 main_effect
pqqB No Siderophore production K06136 −6.741 7.018 −0.96 0.3450 main_effect
Sulfur Cycling aprA Yes K00394 −0.094 0.543 −0.17 0.8630 main_effect
cysA Yes K02045 60.984 19.079 3.20 0.0034 main_effect
cysU Yes K02046 −0.667 2.377 −0.28 0.7810 main_effect
cysW Yes K02047 15.077 5.810 2.59 0.0149 main_effect
fccB Yes K17229 0.381 0.451 0.84 0.4058 main_effect
sat Yes K00958 10.104 5.624 1.80 0.0832 main_effect
soxA No K17222 −30.278 12.333 −2.46 0.0211 interaction
soxA No K17222 21.963 8.263 2.66 0.0187 by_group_JB1_JB2
soxA No K17222 −8.316 8.979 −0.93 0.3726 by_group_JB5_JB6_JB7
soxB No K17224 −2.793 1.688 −1.65 0.1091 main_effect
soxC Yes K17225 25.746 11.981 2.15 0.0404 main_effect
soxD Yes K22622 0.079 3.965 0.02 0.9842 main_effect
soxX No K17223 3.023 4.577 0.66 0.5144 main_effect
soxY Yes K17226 −2.657 6.731 −0.39 0.6960 main_effect
soxZ Yes K17227 0.024 4.968 0.00 0.9962 main_effect
Zinc Cycling mntR No K03709 −0.234 7.003 −0.03 0.9736 main_effect
troA No K11707 2.411 2.197 1.10 0.2818 main_effect
zitB No K16264 −22.425 8.949 −2.51 0.0183 main_effect
zntA No K01534 −6.747 2.771 −2.43 0.0215 main_effect
znuA Yes K09815 10.813 4.056 2.67 0.0126 main_effect
znuB Yes K09816 23.072 8.381 2.75 0.0103 main_effect
znuC Yes K09817 7.777 5.437 1.43 0.1636 main_effect
zur No K02076 −5.853 1.930 −3.03 0.0052 main_effect

Table 9: Summary statistics for each gene. The table shows the summary statistics for the analysis of the metadata variable and each gene (KO gene cluster) organised by section. The table gives estimate, standard error, t-value, p-value and model. “Model” informs which model the summary statistics represents: “main_effect” originate from analysis where all fields are analyzed together. This happens when we have tested for effects of JB and not found any significant difference between JB groups. “Interaction” gives results for the interaction analysis and is included only when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.

Cobber

Section Gene Essential Cagetory KO.ID Estimate SE t p-value Model
Antibiotic Production bacB Yes Bacilysin K19547 −0.154 0.250 −0.62 0.5416 main_effect
bacC Yes Bacilysin K19548 −0.433 0.327 −1.32 0.1961 main_effect
E4.1.1.82 Yes Fosfomycin K09459 −7.149 4.051 −1.76 0.0885 main_effect
eryA Yes Macrolides K00862 0.340 2.607 0.13 0.8970 main_effect
penM No Pentalenolactone K17476 −0.295 0.512 −0.58 0.5694 main_effect
pntE Yes Pentalenolactone K18091 −0.404 1.337 −0.30 0.7649 main_effect
pntH Yes Pentalenolactone K18056 −0.269 0.232 −1.16 0.2571 main_effect
ptlF Yes Pentalenolactone K17747 0.023 0.306 0.07 0.9411 main_effect
rifG Yes Rifamycin K16020 −0.202 1.058 −0.19 0.8501 main_effect
strA Yes Streptomycin K00547 1.340 7.674 0.17 0.8626 main_effect
Antibiotic Resistance vanA Yes Vancomycin K15739 −0.728 1.250 −0.58 0.5651 main_effect
vanH Yes Vancomycin K18347 −0.286 1.322 −0.22 0.8302 main_effect
vanX Yes Vancomycin K08641 −4.960 14.463 −0.34 0.7342 main_effect
Biocontrol chiA Yes Fungicidal agents K06904 −9.760 10.882 −0.90 0.3774 main_effect
chiB No Fungicidal agents, Insecticide agents K20547 1.364 0.570 2.39 0.0237 main_effect
dapB No Bactericidal agents K00215 0.537 49.233 0.01 0.9914 main_effect
phzF Yes Fungicidal agents, Bactericidal agents K06998 12.127 10.586 1.15 0.2617 main_effect
prnA Yes Fungicidal agents K14266 −1.864 4.857 −0.38 0.7040 main_effect
prnC Yes Fungicidal agents K14257 −1.696 3.028 −0.56 0.5797 main_effect
tcaB Yes Insecticide agents K07552 −3.160 26.640 −0.12 0.9064 main_effect
Calcium Cycling chaA Yes K07300 −38.978 26.839 −1.45 0.1575 main_effect
mgtC Yes K07507 34.375 29.996 1.15 0.2615 main_effect
phaC No K03821 −23.045 30.878 −0.75 0.4617 main_effect
ureC Yes K01428 −13.388 17.473 −0.77 0.4499 main_effect
Carbon Fixation ccmK No Calvin–Benson–Bassham (CBB) Cycle K08696 −0.732 0.891 −0.82 0.4187 main_effect
ccmL No Calvin–Benson–Bassham (CBB) Cycle K08697 −1.045 1.094 −0.95 0.3479 main_effect
codH Yes Wood–Ljungdahl (WL) pathway K00192 −0.271 0.612 −0.44 0.6610 main_effect
korA Yes Reductive TCA (rTCA) cycle K00174 8.256 13.319 0.62 0.5403 main_effect
korB Yes Reductive TCA (rTCA) cycle K00175 50.346 19.087 2.64 0.0135 main_effect
prk Yes Calvin–Benson–Bassham (CBB) Cycle K00855 6.465 4.526 1.43 0.1642 main_effect
rbcL Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01601 12.026 10.615 1.13 0.2668 main_effect
rbcS Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01602 10.658 31.926 0.33 0.7410 main_effect
frdA No Reductive TCA (rTCA) cycle K00244 2.855 3.582 0.80 0.4321 main_effect
mcl No 3HP bicycle K08691 27.686 12.756 2.17 0.0393 interaction
mcl No 3HP bicycle K08691 −5.790 6.083 −0.95 0.3574 by_group_JB1_JB2
mcl No 3HP bicycle K08691 21.896 11.757 1.86 0.0872 by_group_JB5_JB6_JB7
Chloride Cycling clcA Yes K03281 74.955 46.809 1.60 0.1205 main_effect
clcB Yes K03281 74.955 46.809 1.60 0.1205 main_effect
clcN Yes K05011 0.102 0.414 0.25 0.8067 main_effect
gltT No K11102 −76.121 24.641 −3.09 0.0047 interaction
gltT No K11102 34.051 15.124 2.25 0.0409 by_group_JB1_JB2
gltT No K11102 −42.070 14.702 −2.86 0.0143 by_group_JB5_JB6_JB7
kefC No K11745 0.049 1.794 0.03 0.9785 main_effect
Copper Cycling copA Yes K17686 32.722 24.500 1.34 0.1924 main_effect
copB Yes K01533 31.460 13.258 2.37 0.0248 main_effect
ctrA Yes K13584 24.782 39.205 0.63 0.5324 main_effect
cueO No K14588 1.931 2.826 0.68 0.5000 main_effect
cusA Yes K07787 33.369 13.446 2.48 0.0193 main_effect
cusB No K07798 32.629 15.267 2.14 0.0415 main_effect
Hormone Production acdS Yes Ethylene K01505 −3.849 14.929 −0.26 0.7984 main_effect
aldA Yes IAA K07248 −0.703 2.285 −0.31 0.7605 main_effect
aldH No IAA K00128 −3.160 37.821 −0.08 0.9340 main_effect
amiE Yes IAA K01426 −7.907 18.650 −0.42 0.6748 main_effect
aspC Yes IAA K00813 −0.204 1.871 −0.11 0.9141 main_effect
entC No GA K02361 −0.392 1.023 −0.38 0.7044 main_effect
etfA No Ethylene K03522 50.110 47.614 1.05 0.3016 main_effect
iaaH No IAA K21801 1.375 2.365 0.58 0.5655 main_effect
iaaM No IAA K00466 0.481 2.456 0.20 0.8461 main_effect
ipdC Yes IAA K04103 1.881 0.555 3.39 0.0021 main_effect
ipt Yes CK K00375 −28.836 22.191 −1.30 0.2044 main_effect
miaA No CK K00791 25.712 52.655 0.49 0.6291 main_effect
nitA No IAA K01501 9.184 2.961 3.10 0.0044 main_effect
tnaA No IAA K01667 10.878 6.602 1.65 0.1106 main_effect
Iron Cycling bfr No K03594 −115.339 51.355 −2.25 0.0334 interaction
bfr No K03594 19.430 28.096 0.69 0.5005 by_group_JB1_JB2
bfr No K03594 −95.909 40.172 −2.39 0.0343 by_group_JB5_JB6_JB7
dps No K04047 −15.134 24.920 −0.61 0.5486 main_effect
entC Yes K02361 −0.392 1.023 −0.38 0.7044 main_effect
feoB Yes K04759 6.158 5.987 1.03 0.3125 main_effect
fur No K03711 −11.840 26.921 −0.44 0.6635 main_effect
iscA No K13628 49.732 41.796 1.19 0.2441 main_effect
sufB Yes K09014 −4.142 16.201 −0.26 0.8001 main_effect
sufC No K09013 21.031 19.494 1.08 0.2899 main_effect
yqjH No K07229 −0.185 0.300 −0.62 0.5416 main_effect
Magnesium Cycling corA Yes K03284 −204.035 96.365 −2.12 0.0432 main_effect
mgtA Yes K01531 105.635 41.832 2.53 0.0175 main_effect
mgtB No K01531 105.635 41.832 2.53 0.0175 main_effect
mgtE Yes K06213 2.815 20.033 0.14 0.8893 main_effect
phoQ No K07637 −0.807 2.938 −0.27 0.7855 main_effect
Manganese Cycling mntA Yes K06147 26.673 86.664 0.31 0.7605 main_effect
mntB Yes K06148 −2.558 6.082 −0.42 0.6772 main_effect
mntC Yes K06149 2.142 1.929 1.11 0.2763 main_effect
mntH Yes K03322 49.866 33.210 1.50 0.1444 main_effect
mntR No K03709 3.381 18.453 0.18 0.8559 main_effect
mntR No K11924 −3.266 2.855 −1.14 0.2623 main_effect
sitA Yes K11604 0.813 2.434 0.33 0.7408 main_effect
sodA No K04564 8.854 41.057 0.22 0.8308 main_effect
Nitrogen fixation amt No K03320 128.938 51.645 2.50 0.0187 main_effect
glnB No K04751 9.702 59.127 0.16 0.8708 main_effect
iscS No K04487 48.516 39.327 1.23 0.2276 main_effect
moeA No K03750 48.849 21.853 2.24 0.0336 main_effect
nifA No K02584 −3.195 4.374 −0.73 0.4712 main_effect
nifB Yes K02585 6.014 2.740 2.19 0.0366 main_effect
nifD Yes K02586 2.030 3.499 0.58 0.5665 main_effect
nifE Yes K02587 6.828 5.039 1.35 0.1863 main_effect
nifH Yes K02588 2.784 1.194 2.33 0.0278 interaction
nifH Yes K02588 0.000 0.000 NaN NaN by_group_JB1_JB2
nifH Yes K02588 2.784 1.511 1.84 0.0903 by_group_JB5_JB6_JB7
nifK Yes K02591 5.851 5.566 1.05 0.3022 main_effect
nifM Yes K03769 18.421 16.554 1.11 0.2752 main_effect
nifN Yes K02592 2.093 0.867 2.41 0.0225 main_effect
nifQ No K15790 −0.044 0.164 −0.27 0.7892 main_effect
nifU Yes K04488 1.350 26.732 0.05 0.9601 main_effect
nifV Yes K02594 4.139 1.855 2.23 0.0338 main_effect
nifW No K02595 0.102 0.575 0.18 0.8600 main_effect
nifX No K02596 11.839 5.085 2.33 0.0279 interaction
nifX No K02596 −0.136 0.152 −0.90 0.3857 by_group_JB1_JB2
nifX No K02596 11.703 6.429 1.82 0.0937 by_group_JB5_JB6_JB7
nifZ No K02597 0.738 0.915 0.81 0.4267 main_effect
Nitrogen Release amoA Yes K10944 −1.041 1.853 −0.56 0.5787 main_effect
amoB Yes K10945 −3.322 2.159 −1.54 0.1352 main_effect
amoC Yes K10946 2.660 23.186 0.11 0.9095 main_effect
gdh No K15371 −4.391 11.238 −0.39 0.6989 main_effect
napA No K02567 1.283 3.868 0.33 0.7427 main_effect
napA Yes K01416 −0.178 1.341 −0.13 0.8956 main_effect
napB No K02568 −0.133 2.706 −0.05 0.9610 main_effect
narG Yes K00370 16.183 9.699 1.67 0.1063 main_effect
narH Yes K00371 4.863 8.349 0.58 0.5649 main_effect
narI No K00374 18.746 10.248 1.83 0.0780 main_effect
nasA Yes K00372 −18.881 17.198 −1.10 0.2816 main_effect
nasB Yes K00360 1.611 1.251 1.29 0.2084 main_effect
nirA Yes K00366 −4.350 8.745 −0.50 0.6228 main_effect
nirK Yes K00368 3.070 8.068 0.38 0.7064 main_effect
nirS Yes K15864 3.073 0.838 3.67 0.0011 interaction
nirS Yes K15864 0.000 0.000 NaN NaN by_group_JB1_JB2
nirS Yes K15864 3.073 1.060 2.90 0.0134 by_group_JB5_JB6_JB7
norB Yes K04561 12.278 8.314 1.48 0.1509 main_effect
norC No K02305 −0.601 9.373 −0.06 0.9493 main_effect
nosZ Yes K00376 4.571 8.077 0.57 0.5759 main_effect
nrfA Yes K03385 23.488 10.813 2.17 0.0385 main_effect
ureC No K01428 −13.388 17.473 −0.77 0.4499 main_effect
Nodulation nodA Yes K14658 −0.116 0.187 −0.62 0.5416 main_effect
nodD Yes K14657 −1.058 1.338 −0.79 0.4359 main_effect
nodI No ABC transporter complex K09694 −71.105 53.104 −1.34 0.1913 main_effect
Phosphorus Solubilization gcd Yes K00117 −18.863 26.472 −0.71 0.4820 main_effect
phnX No K06163 3.680 5.308 0.69 0.4938 main_effect
phoA Yes K01077 −5.373 7.265 −0.74 0.4657 main_effect
phoD No K01113 −39.238 31.061 −1.26 0.2169 main_effect
phoX No K07093 −10.519 20.302 −0.52 0.6084 main_effect
ppk No K00937 8.906 33.774 0.26 0.7940 main_effect
ppx No K01514 0.153 1.160 0.13 0.8962 main_effect
pqqB Yes K06136 5.704 18.773 0.30 0.7635 main_effect
pqqC Yes K06137 −2.674 17.864 −0.15 0.8821 main_effect
pqqD Yes K06138 11.958 19.139 0.62 0.5372 main_effect
pqqE Yes K06139 −1.787 9.556 −0.19 0.8530 main_effect
Potassium Solubilization gcd Yes K00117 −18.863 26.472 −0.71 0.4820 main_effect
kdsA No K01627 −81.181 36.052 −2.25 0.0330 interaction
kdsA No K01627 17.484 18.054 0.97 0.3493 by_group_JB1_JB2
kdsA No K01627 −63.697 31.684 −2.01 0.0674 by_group_JB5_JB6_JB7
kdsB No K00979 84.778 36.019 2.35 0.0258 main_effect
kup Yes K03549 −13.661 37.076 −0.37 0.7153 main_effect
nhaA No K03313 −31.389 43.437 −0.72 0.4759 main_effect
pqqB Yes K06136 5.704 18.773 0.30 0.7635 main_effect
pqqC Yes K06137 −2.674 17.864 −0.15 0.8821 main_effect
pqqD Yes K06138 11.958 19.139 0.62 0.5372 main_effect
pqqE Yes K06139 −1.787 9.556 −0.19 0.8530 main_effect
trkA Yes K03499 −81.570 41.079 −1.99 0.0569 main_effect
trkH Yes K03498 3.385 9.575 0.35 0.7264 main_effect
Stress Adaptation copA Yes Heavy Metal Tolerance K17686 32.722 24.500 1.34 0.1924 main_effect
ectB Yes Salt tolerance K00836 −1.711 3.496 −0.49 0.6283 main_effect
entC Yes Siderophore production K02361 −0.392 1.023 −0.38 0.7044 main_effect
glnA No ACC deaminase (ACC-d) K01915 −95.519 70.268 −1.36 0.1849 main_effect
kdsA Yes Exopolysaccharide production K01627 −81.181 36.052 −2.25 0.0330 interaction
kdsA Yes Exopolysaccharide production K01627 17.484 18.054 0.97 0.3493 by_group_JB1_JB2
kdsA Yes Exopolysaccharide production K01627 −63.697 31.684 −2.01 0.0674 by_group_JB5_JB6_JB7
kdsB No Exopolysaccharide production K00979 84.778 36.019 2.35 0.0258 main_effect
pchA Yes Salicylic acid (SA) K01851 −0.378 1.052 −0.36 0.7220 main_effect
pchB No Salicylic acid (SA) K04782 6.298 5.825 1.08 0.2888 main_effect
pqqB No Siderophore production K06136 5.704 18.773 0.30 0.7635 main_effect
Sulfur Cycling aprA Yes K00394 −0.862 1.422 −0.61 0.5494 main_effect
cysA Yes K02045 −84.696 56.543 −1.50 0.1453 main_effect
cysU Yes K02046 −4.806 6.209 −0.77 0.4454 main_effect
cysW Yes K02047 −27.319 16.262 −1.68 0.1041 main_effect
fccB Yes K17229 0.120 1.203 0.10 0.9213 main_effect
sat Yes K00958 −8.931 15.567 −0.57 0.5707 main_effect
soxA No K17222 1.320 17.753 0.07 0.9413 main_effect
soxB No K17224 4.300 4.590 0.94 0.3569 main_effect
soxC Yes K17225 10.729 34.033 0.32 0.7549 main_effect
soxD Yes K22622 17.588 9.912 1.77 0.0869 main_effect
soxX No K17223 −1.904 12.156 −0.16 0.8767 main_effect
soxY Yes K17226 23.583 17.228 1.37 0.1819 main_effect
soxZ Yes K17227 11.169 12.926 0.86 0.3949 main_effect
Zinc Cycling mntR No K03709 3.381 18.453 0.18 0.8559 main_effect
troA No K11707 9.007 5.666 1.59 0.1231 main_effect
zitB No K16264 24.201 25.701 0.94 0.3544 main_effect
zntA No K01534 2.725 8.026 0.34 0.7367 main_effect
znuA Yes K09815 −14.046 11.675 −1.20 0.2390 main_effect
znuB Yes K09816 −14.259 24.762 −0.58 0.5693 main_effect
znuC Yes K09817 9.340 14.743 0.63 0.5315 main_effect
zur No K02076 1.282 5.859 0.22 0.8284 main_effect

Table 10: Summary statistics for each gene. The table shows the summary statistics for the analysis of the metadata variable and each gene (KO gene cluster) organised by section. The table gives estimate, standard error, t-value, p-value and model. “Model” informs which model the summary statistics represents: “main_effect” originate from analysis where all fields are analyzed together. This happens when we have tested for effects of JB and not found any significant difference between JB groups. “Interaction” gives results for the interaction analysis and is included only when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.

Organic material (perc)

Section Gene Essential Cagetory KO.ID Estimate SE t p-value Model
Antibiotic Production bacB Yes Bacilysin K19547 −0.072 0.102 −0.70 0.4876 main_effect
bacC Yes Bacilysin K19548 −0.095 0.137 −0.69 0.4965 main_effect
E4.1.1.82 Yes Fosfomycin K09459 0.839 1.746 0.48 0.6346 main_effect
eryA Yes Macrolides K00862 1.279 1.043 1.23 0.2301 main_effect
penM No Pentalenolactone K17476 −0.129 0.210 −0.61 0.5436 main_effect
pntE Yes Pentalenolactone K18091 −0.503 0.541 −0.93 0.3608 main_effect
pntH Yes Pentalenolactone K18056 0.087 0.096 0.90 0.3748 main_effect
ptlF Yes Pentalenolactone K17747 −0.005 0.126 −0.04 0.9683 main_effect
rifG Yes Rifamycin K16020 −0.088 0.434 −0.20 0.8402 main_effect
strA Yes Streptomycin K00547 −6.066 2.936 −2.07 0.0482 main_effect
Antibiotic Resistance vanA Yes Vancomycin K15739 −0.849 0.491 −1.73 0.0947 main_effect
vanH Yes Vancomycin K18347 −0.482 0.536 −0.90 0.3762 main_effect
vanX Yes Vancomycin K08641 −78.566 31.807 −2.47 0.0204 interaction
vanX Yes Vancomycin K08641 4.337 6.282 0.69 0.5013 by_group_JB1_JB2
vanX Yes Vancomycin K08641 −74.229 28.317 −2.62 0.0223 by_group_JB5_JB6_JB7
Biocontrol chiA Yes Fungicidal agents K06904 −0.573 4.530 −0.13 0.9002 main_effect
chiB No Fungicidal agents, Insecticide agents K20547 0.081 0.257 0.32 0.7548 main_effect
dapB No Bactericidal agents K00215 −12.896 20.065 −0.64 0.5257 main_effect
phzF Yes Fungicidal agents, Bactericidal agents K06998 −3.206 4.405 −0.73 0.4728 main_effect
prnA Yes Fungicidal agents K14266 1.328 1.983 0.67 0.5087 main_effect
prnC Yes Fungicidal agents K14257 −0.488 1.247 −0.39 0.6987 main_effect
tcaB Yes Insecticide agents K07552 10.430 10.761 0.97 0.3407 main_effect
Calcium Cycling chaA Yes K07300 −0.559 11.426 −0.05 0.9614 main_effect
mgtC Yes K07507 −3.580 12.582 −0.28 0.7781 main_effect
phaC No K03821 199.891 57.838 3.46 0.0019 interaction
phaC No K03821 −3.962 11.815 −0.34 0.7423 by_group_JB1_JB2
phaC No K03821 195.928 48.446 4.04 0.0016 by_group_JB5_JB6_JB7
ureC Yes K01428 14.193 6.734 2.11 0.0441 main_effect
Carbon Fixation ccmK No Calvin–Benson–Bassham (CBB) Cycle K08696 0.506 0.358 1.41 0.1685 main_effect
ccmL No Calvin–Benson–Bassham (CBB) Cycle K08697 0.076 0.456 0.17 0.8696 main_effect
codH Yes Wood–Ljungdahl (WL) pathway K00192 −0.171 0.250 −0.69 0.4988 main_effect
korA Yes Reductive TCA (rTCA) cycle K00174 −0.116 5.505 −0.02 0.9833 main_effect
korB Yes Reductive TCA (rTCA) cycle K00175 21.503 7.756 2.77 0.0098 main_effect
prk Yes Calvin–Benson–Bassham (CBB) Cycle K00855 2.442 1.869 1.31 0.2020 main_effect
rbcL Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01601 4.501 4.375 1.03 0.3123 main_effect
rbcS Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01602 −2.937 13.121 −0.22 0.8245 main_effect
frdA No Reductive TCA (rTCA) cycle K00244 1.284 1.467 0.87 0.3890 main_effect
mcl No 3HP bicycle K08691 2.044 2.281 0.90 0.3780 main_effect
Chloride Cycling clcA Yes K03281 13.520 19.915 0.68 0.5028 main_effect
clcB Yes K03281 13.520 19.915 0.68 0.5028 main_effect
clcN Yes K05011 −0.007 0.170 −0.04 0.9683 main_effect
gltT No K11102 −0.102 4.935 −0.02 0.9837 main_effect
kefC No K11745 −12.121 3.394 −3.57 0.0014 interaction
kefC No K11745 2.148 0.532 4.04 0.0012 by_group_JB1_JB2
kefC No K11745 −9.973 3.832 −2.60 0.0231 by_group_JB5_JB6_JB7
Copper Cycling copA Yes K17686 −14.364 10.012 −1.43 0.1625 main_effect
copB Yes K01533 2.771 5.942 0.47 0.6446 main_effect
ctrA Yes K13584 14.295 15.983 0.89 0.3788 main_effect
cueO No K14588 1.394 1.140 1.22 0.2316 main_effect
cusA Yes K07787 −1.009 6.094 −0.17 0.8697 main_effect
cusB No K07798 0.128 6.760 0.02 0.9850 main_effect
Hormone Production acdS Yes Ethylene K01505 2.018 6.124 0.33 0.7442 main_effect
aldA Yes IAA K07248 −12.385 5.148 −2.41 0.0236 interaction
aldA Yes IAA K07248 1.132 0.668 1.70 0.1121 by_group_JB1_JB2
aldA Yes IAA K07248 −11.253 6.374 −1.77 0.1029 by_group_JB5_JB6_JB7
aldH No IAA K00128 14.495 15.286 0.95 0.3511 main_effect
amiE Yes IAA K01426 −0.512 7.681 −0.07 0.9473 main_effect
aspC Yes IAA K00813 0.390 0.765 0.51 0.6142 main_effect
entC No GA K02361 −0.480 0.411 −1.17 0.2528 main_effect
etfA No Ethylene K03522 −22.611 19.467 −1.16 0.2553 main_effect
iaaH No IAA K21801 1.183 0.951 1.24 0.2239 main_effect
iaaM No IAA K00466 −0.429 1.006 −0.43 0.6730 main_effect
ipdC Yes IAA K04103 0.370 0.261 1.42 0.1678 main_effect
ipt Yes CK K00375 −8.613 9.239 −0.93 0.3592 main_effect
miaA No CK K00791 −4.136 21.695 −0.19 0.8502 main_effect
nitA No IAA K01501 0.442 1.407 0.31 0.7555 main_effect
tnaA No IAA K01667 0.023 2.839 0.01 0.9936 main_effect
Iron Cycling bfr No K03594 3.986 9.297 0.43 0.6714 main_effect
dps No K04047 −11.105 10.082 −1.10 0.2800 main_effect
entC Yes K02361 −0.480 0.411 −1.17 0.2528 main_effect
feoB Yes K04759 5.829 2.249 2.59 0.0150 main_effect
fur No K03711 −1.319 11.088 −0.12 0.9062 main_effect
iscA No K13628 14.618 17.370 0.84 0.4071 main_effect
sufB Yes K09014 −100.996 34.606 −2.92 0.0072 interaction
sufB Yes K09014 −5.969 7.188 −0.83 0.4202 by_group_JB1_JB2
sufB Yes K09014 −106.966 27.994 −3.82 0.0024 by_group_JB5_JB6_JB7
sufC No K09013 −3.065 8.147 −0.38 0.7096 main_effect
yqjH No K07229 −0.086 0.123 −0.70 0.4876 main_effect
Magnesium Cycling corA Yes K03284 −22.435 42.401 −0.53 0.6009 main_effect
mgtA Yes K01531 13.431 18.859 0.71 0.4823 main_effect
mgtB No K01531 13.431 18.859 0.71 0.4823 main_effect
mgtE Yes K06213 −1.702 8.221 −0.21 0.8375 main_effect
phoQ No K07637 0.542 1.204 0.45 0.6558 main_effect
Manganese Cycling mntA Yes K06147 −13.790 35.545 −0.39 0.7010 main_effect
mntB Yes K06148 −2.614 2.456 −1.06 0.2962 main_effect
mntC Yes K06149 −0.990 0.787 −1.26 0.2190 main_effect
mntH Yes K03322 14.978 13.887 1.08 0.2900 main_effect
mntR No K03709 1.685 7.574 0.22 0.8255 main_effect
mntR No K11924 −0.459 1.196 −0.38 0.7042 main_effect
sitA Yes K11604 0.493 0.997 0.49 0.6249 main_effect
sodA No K04564 29.746 15.906 1.87 0.0720 main_effect
Nitrogen fixation amt No K03320 16.166 23.244 0.70 0.4925 main_effect
glnB No K04751 22.685 23.905 0.95 0.3508 main_effect
iscS No K04487 −194.568 83.007 −2.34 0.0270 interaction
iscS No K04487 −5.926 18.069 −0.33 0.7478 by_group_JB1_JB2
iscS No K04487 −200.494 59.449 −3.37 0.0055 by_group_JB5_JB6_JB7
moeA No K03750 −0.401 9.739 −0.04 0.9675 main_effect
nifA No K02584 −2.776 1.735 −1.60 0.1209 main_effect
nifB Yes K02585 −0.245 1.217 −0.20 0.8421 main_effect
nifD Yes K02586 −1.250 1.426 −0.88 0.3882 main_effect
nifE Yes K02587 −1.918 2.105 −0.91 0.3699 main_effect
nifH Yes K02588 −0.047 0.227 −0.21 0.8380 main_effect
nifK Yes K02591 −1.621 2.310 −0.70 0.4885 main_effect
nifM Yes K03769 6.122 6.848 0.89 0.3789 main_effect
nifN Yes K02592 −0.145 0.390 −0.37 0.7125 main_effect
nifQ No K15790 −0.015 0.067 −0.22 0.8271 main_effect
nifU Yes K04488 11.668 10.752 1.09 0.2871 main_effect
nifV Yes K02594 −0.538 0.820 −0.66 0.5173 main_effect
nifW No K02595 0.468 0.219 2.14 0.0414 main_effect
nifX No K02596 −0.427 1.000 −0.43 0.6725 main_effect
nifZ No K02597 −0.339 0.374 −0.90 0.3736 main_effect
Nitrogen Release amoA Yes K10944 0.265 0.763 0.35 0.7314 main_effect
amoB Yes K10945 −15.329 4.798 −3.19 0.0036 interaction
amoB Yes K10945 1.092 1.002 1.09 0.2944 by_group_JB1_JB2
amoB Yes K10945 −14.237 3.834 −3.71 0.0030 by_group_JB5_JB6_JB7
amoC Yes K10946 −1.520 9.517 −0.16 0.8743 main_effect
gdh No K15371 −4.228 4.557 −0.93 0.3614 main_effect
napA No K02567 16.585 7.767 2.14 0.0423 interaction
napA No K02567 4.126 1.524 2.71 0.0170 by_group_JB1_JB2
napA No K02567 20.711 6.990 2.96 0.0119 by_group_JB5_JB6_JB7
napA Yes K01416 −0.204 0.549 −0.37 0.7125 main_effect
napB No K02568 −1.393 1.079 −1.29 0.2073 main_effect
narG Yes K00370 2.265 4.153 0.55 0.5898 main_effect
narH Yes K00371 −2.524 3.415 −0.74 0.4660 main_effect
narI No K00374 −3.226 4.410 −0.73 0.4705 main_effect
nasA Yes K00372 2.374 7.197 0.33 0.7440 main_effect
nasB Yes K00360 0.236 0.527 0.45 0.6576 main_effect
nirA Yes K00366 −5.441 3.456 −1.57 0.1267 main_effect
nirK Yes K00368 −1.181 3.313 −0.36 0.7241 main_effect
nirS Yes K15864 −0.108 0.187 −0.58 0.5693 main_effect
norB Yes K04561 −1.595 3.531 −0.45 0.6549 main_effect
norC No K02305 −1.109 3.843 −0.29 0.7750 main_effect
nosZ Yes K00376 2.565 3.299 0.78 0.4435 main_effect
nrfA Yes K03385 2.408 4.777 0.50 0.6181 main_effect
ureC No K01428 14.193 6.734 2.11 0.0441 main_effect
Nodulation nodA Yes K14658 −0.054 0.077 −0.70 0.4876 main_effect
nodD Yes K14657 0.683 0.540 1.26 0.2164 main_effect
nodI No ABC transporter complex K09694 −22.841 22.071 −1.03 0.3096 main_effect
Phosphorus Solubilization gcd Yes K00117 4.397 10.935 0.40 0.6906 main_effect
phnX No K06163 5.021 1.982 2.53 0.0172 main_effect
phoA Yes K01077 −1.321 3.001 −0.44 0.6632 main_effect
phoD No K01113 3.635 13.092 0.28 0.7833 main_effect
phoX No K07093 −7.586 8.251 −0.92 0.3658 main_effect
ppk No K00937 233.461 69.800 3.34 0.0025 interaction
ppk No K00937 −3.720 15.088 −0.25 0.8088 by_group_JB1_JB2
ppk No K00937 229.741 51.053 4.50 0.0007 by_group_JB5_JB6_JB7
ppx No K01514 −0.005 0.476 −0.01 0.9909 main_effect
pqqB Yes K06136 99.297 35.674 2.78 0.0099 interaction
pqqB Yes K06136 −1.613 6.780 −0.24 0.8154 by_group_JB1_JB2
pqqB Yes K06136 97.684 33.632 2.90 0.0132 by_group_JB5_JB6_JB7
pqqC Yes K06137 −0.780 7.335 −0.11 0.9161 main_effect
pqqD Yes K06138 −0.590 7.911 −0.07 0.9411 main_effect
pqqE Yes K06139 −4.085 3.849 −1.06 0.2976 main_effect
Potassium Solubilization gcd Yes K00117 4.397 10.935 0.40 0.6906 main_effect
kdsA No K01627 9.004 7.272 1.24 0.2259 main_effect
kdsB No K00979 18.375 15.808 1.16 0.2549 main_effect
kup Yes K03549 205.488 84.054 2.44 0.0216 interaction
kup Yes K03549 2.248 17.080 0.13 0.8972 by_group_JB1_JB2
kup Yes K03549 207.736 71.137 2.92 0.0128 by_group_JB5_JB6_JB7
nhaA No K03313 5.378 17.970 0.30 0.7669 main_effect
pqqB Yes K06136 99.297 35.674 2.78 0.0099 interaction
pqqB Yes K06136 −1.613 6.780 −0.24 0.8154 by_group_JB1_JB2
pqqB Yes K06136 97.684 33.632 2.90 0.0132 by_group_JB5_JB6_JB7
pqqC Yes K06137 −0.780 7.335 −0.11 0.9161 main_effect
pqqD Yes K06138 −0.590 7.911 −0.07 0.9411 main_effect
pqqE Yes K06139 −4.085 3.849 −1.06 0.2976 main_effect
trkA Yes K03499 −13.092 17.843 −0.73 0.4692 main_effect
trkH Yes K03498 0.471 3.939 0.12 0.9058 main_effect
Stress Adaptation copA Yes Heavy Metal Tolerance K17686 −14.364 10.012 −1.43 0.1625 main_effect
ectB Yes Salt tolerance K00836 −16.813 8.058 −2.09 0.0469 interaction
ectB Yes Salt tolerance K00836 −0.973 1.615 −0.60 0.5563 by_group_JB1_JB2
ectB Yes Salt tolerance K00836 −17.786 6.998 −2.54 0.0259 by_group_JB5_JB6_JB7
entC Yes Siderophore production K02361 −0.480 0.411 −1.17 0.2528 main_effect
glnA No ACC deaminase (ACC-d) K01915 −22.563 29.478 −0.77 0.4504 main_effect
kdsA Yes Exopolysaccharide production K01627 9.004 7.272 1.24 0.2259 main_effect
kdsB No Exopolysaccharide production K00979 18.375 15.808 1.16 0.2549 main_effect
pchA Yes Salicylic acid (SA) K01851 0.441 0.425 1.04 0.3085 main_effect
pchB No Salicylic acid (SA) K04782 −2.552 2.393 −1.07 0.2953 main_effect
pqqB No Siderophore production K06136 99.297 35.674 2.78 0.0099 interaction
pqqB No Siderophore production K06136 −1.613 6.780 −0.24 0.8154 by_group_JB1_JB2
pqqB No Siderophore production K06136 97.684 33.632 2.90 0.0132 by_group_JB5_JB6_JB7
Sulfur Cycling aprA Yes K00394 −0.726 0.571 −1.27 0.2141 main_effect
cysA Yes K02045 −9.776 24.055 −0.41 0.6875 main_effect
cysU Yes K02046 −2.758 2.523 −1.09 0.2837 main_effect
cysW Yes K02047 −0.421 7.004 −0.06 0.9525 main_effect
fccB Yes K17229 −0.365 0.489 −0.75 0.4617 main_effect
sat Yes K00958 −2.563 6.410 −0.40 0.6923 main_effect
soxA No K17222 17.914 6.456 2.77 0.0097 main_effect
soxB No K17224 1.891 1.880 1.01 0.3231 main_effect
soxC Yes K17225 229.647 70.319 3.27 0.0031 interaction
soxC Yes K17225 10.664 13.244 0.81 0.4342 by_group_JB1_JB2
soxC Yes K17225 240.311 67.095 3.58 0.0038 by_group_JB5_JB6_JB7
soxD Yes K22622 60.633 23.624 2.57 0.0164 interaction
soxD Yes K22622 −2.413 4.738 −0.51 0.6185 by_group_JB1_JB2
soxD Yes K22622 58.221 20.486 2.84 0.0148 by_group_JB5_JB6_JB7
soxX No K17223 5.040 4.901 1.03 0.3126 main_effect
soxY Yes K17226 107.425 35.577 3.02 0.0056 interaction
soxY Yes K17226 0.001 7.883 0.00 0.9999 by_group_JB1_JB2
soxY Yes K17226 107.426 24.026 4.47 0.0008 by_group_JB5_JB6_JB7
soxZ Yes K17227 6.921 5.216 1.33 0.1953 main_effect
Zinc Cycling mntR No K03709 1.685 7.574 0.22 0.8255 main_effect
troA No K11707 0.248 2.428 0.10 0.9193 main_effect
zitB No K16264 −8.527 10.596 −0.80 0.4277 main_effect
zntA No K01534 −37.613 18.120 −2.08 0.0479 interaction
zntA No K01534 −4.077 3.612 −1.13 0.2779 by_group_JB1_JB2
zntA No K01534 −41.690 15.884 −2.62 0.0222 by_group_JB5_JB6_JB7
znuA Yes K09815 4.454 4.843 0.92 0.3655 main_effect
znuB Yes K09816 −3.339 10.206 −0.33 0.7460 main_effect
znuC Yes K09817 −0.991 6.093 −0.16 0.8720 main_effect
zur No K02076 −4.092 2.280 −1.79 0.0835 main_effect

Table 11: Summary statistics for each gene. The table shows the summary statistics for the analysis of the metadata variable and each gene (KO gene cluster) organised by section. The table gives estimate, standard error, t-value, p-value and model. “Model” informs which model the summary statistics represents: “main_effect” originate from analysis where all fields are analyzed together. This happens when we have tested for effects of JB and not found any significant difference between JB groups. “Interaction” gives results for the interaction analysis and is included only when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.

Clay (perc)

Section Gene Essential Cagetory KO.ID Estimate SE t p-value Model
Antibiotic Production bacB Yes Bacilysin K19547 −0.036 0.067 −0.54 0.5920 main_effect
bacC Yes Bacilysin K19548 −1.038 0.371 −2.79 0.0096 interaction
bacC Yes Bacilysin K19548 0.817 0.348 2.35 0.0341 by_group_JB1_JB2
bacC Yes Bacilysin K19548 −0.221 0.140 −1.58 0.1400 by_group_JB5_JB6_JB7
E4.1.1.82 Yes Fosfomycin K09459 0.163 1.148 0.14 0.8882 main_effect
eryA Yes Macrolides K00862 −1.450 0.646 −2.25 0.0327 main_effect
penM No Pentalenolactone K17476 −0.131 0.136 −0.96 0.3439 main_effect
pntE Yes Pentalenolactone K18091 0.147 0.359 0.41 0.6848 main_effect
pntH Yes Pentalenolactone K18056 −0.063 0.063 −1.00 0.3277 main_effect
ptlF Yes Pentalenolactone K17747 −0.037 0.082 −0.45 0.6574 main_effect
rifG Yes Rifamycin K16020 0.098 0.284 0.34 0.7340 main_effect
strA Yes Streptomycin K00547 −1.067 2.055 −0.52 0.6076 main_effect
Antibiotic Resistance vanA Yes Vancomycin K15739 −0.581 0.320 −1.82 0.0799 main_effect
vanH Yes Vancomycin K18347 0.214 0.354 0.61 0.5494 main_effect
vanX Yes Vancomycin K08641 −7.034 3.665 −1.92 0.0652 main_effect
Biocontrol chiA Yes Fungicidal agents K06904 7.051 2.653 2.66 0.0128 main_effect
chiB No Fungicidal agents, Insecticide agents K20547 −0.208 0.164 −1.27 0.2140 main_effect
dapB No Bactericidal agents K00215 −35.021 11.469 −3.05 0.0049 main_effect
phzF Yes Fungicidal agents, Bactericidal agents K06998 28.332 12.090 2.34 0.0270 interaction
phzF Yes Fungicidal agents, Bactericidal agents K06998 −28.474 9.540 −2.98 0.0098 by_group_JB1_JB2
phzF Yes Fungicidal agents, Bactericidal agents K06998 −0.141 5.315 −0.03 0.9792 by_group_JB5_JB6_JB7
prnA Yes Fungicidal agents K14266 0.645 1.304 0.49 0.6246 main_effect
prnC Yes Fungicidal agents K14257 −0.440 0.815 −0.54 0.5936 main_effect
tcaB Yes Insecticide agents K07552 −26.099 5.200 −5.02 0.0000 main_effect
Calcium Cycling chaA Yes K07300 −70.585 27.725 −2.55 0.0172 interaction
chaA Yes K07300 77.455 25.621 3.02 0.0091 by_group_JB1_JB2
chaA Yes K07300 6.870 10.621 0.65 0.5299 by_group_JB5_JB6_JB7
mgtC Yes K07507 −29.748 6.045 −4.92 0.0000 main_effect
phaC No K03821 28.266 6.466 4.37 0.0002 main_effect
ureC Yes K01428 −6.969 4.562 −1.53 0.1378 main_effect
Carbon Fixation ccmK No Calvin–Benson–Bassham (CBB) Cycle K08696 −2.619 0.923 −2.84 0.0087 interaction
ccmK No Calvin–Benson–Bassham (CBB) Cycle K08696 2.936 1.032 2.85 0.0130 by_group_JB1_JB2
ccmK No Calvin–Benson–Bassham (CBB) Cycle K08696 0.318 0.239 1.33 0.2093 by_group_JB5_JB6_JB7
ccmL No Calvin–Benson–Bassham (CBB) Cycle K08697 0.686 0.270 2.54 0.0168 main_effect
codH Yes Wood–Ljungdahl (WL) pathway K00192 0.312 0.154 2.02 0.0525 main_effect
korA Yes Reductive TCA (rTCA) cycle K00174 1.372 3.598 0.38 0.7057 main_effect
korB Yes Reductive TCA (rTCA) cycle K00175 −14.525 5.037 −2.88 0.0075 main_effect
prk Yes Calvin–Benson–Bassham (CBB) Cycle K00855 9.893 4.623 2.14 0.0419 interaction
prk Yes Calvin–Benson–Bassham (CBB) Cycle K00855 −9.920 4.482 −2.21 0.0440 by_group_JB1_JB2
prk Yes Calvin–Benson–Bassham (CBB) Cycle K00855 −0.027 1.663 −0.02 0.9874 by_group_JB5_JB6_JB7
rbcL Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01601 3.601 2.839 1.27 0.2152 main_effect
rbcS Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01602 −16.554 8.015 −2.07 0.0483 main_effect
frdA No Reductive TCA (rTCA) cycle K00244 0.052 0.974 0.05 0.9575 main_effect
mcl No 3HP bicycle K08691 −0.277 1.515 −0.18 0.8564 main_effect
Chloride Cycling clcA Yes K03281 −31.775 11.703 −2.72 0.0112 main_effect
clcB Yes K03281 −31.775 11.703 −2.72 0.0112 main_effect
clcN Yes K05011 −0.086 0.110 −0.78 0.4425 main_effect
gltT No K11102 −1.020 3.227 −0.32 0.7543 main_effect
kefC No K11745 −0.079 0.482 −0.16 0.8717 main_effect
Copper Cycling copA Yes K17686 7.257 6.656 1.09 0.2849 main_effect
copB Yes K01533 3.008 3.867 0.78 0.4431 main_effect
ctrA Yes K13584 −20.432 9.893 −2.07 0.0483 main_effect
cueO No K14588 0.638 0.757 0.84 0.4067 main_effect
cusA Yes K07787 5.719 3.846 1.49 0.1482 main_effect
cusB No K07798 34.965 16.799 2.08 0.0474 interaction
cusB No K07798 −11.634 16.650 −0.70 0.4962 by_group_JB1_JB2
cusB No K07798 23.331 5.842 3.99 0.0018 by_group_JB5_JB6_JB7
Hormone Production acdS Yes Ethylene K01505 −7.202 3.783 −1.90 0.0672 main_effect
aldA Yes IAA K07248 −0.222 0.614 −0.36 0.7204 main_effect
aldH No IAA K00128 −38.828 7.047 −5.51 0.0000 main_effect
amiE Yes IAA K01426 −5.225 4.934 −1.06 0.2987 main_effect
aspC Yes IAA K00813 −0.715 0.485 −1.48 0.1514 main_effect
entC No GA K02361 −0.312 0.269 −1.16 0.2572 main_effect
etfA No Ethylene K03522 −18.490 12.581 −1.47 0.1528 main_effect
iaaH No IAA K21801 −0.203 0.639 −0.32 0.7525 main_effect
iaaM No IAA K00466 −0.210 0.660 −0.32 0.7527 main_effect
ipdC Yes IAA K04103 −0.212 0.173 −1.23 0.2290 main_effect
ipt Yes CK K00375 −13.294 5.609 −2.37 0.0249 main_effect
miaA No CK K00791 −46.418 11.195 −4.15 0.0003 main_effect
nitA No IAA K01501 −2.255 0.819 −2.75 0.0102 main_effect
tnaA No IAA K01667 2.923 1.776 1.65 0.1109 main_effect
Iron Cycling bfr No K03594 −2.746 6.089 −0.45 0.6555 main_effect
dps No K04047 −6.499 6.634 −0.98 0.3357 main_effect
entC Yes K02361 −0.312 0.269 −1.16 0.2572 main_effect
feoB Yes K04759 −2.821 1.551 −1.82 0.0797 main_effect
fur No K03711 −18.534 6.366 −2.91 0.0070 main_effect
iscA No K13628 −32.643 9.732 −3.35 0.0023 main_effect
sufB Yes K09014 −3.742 4.305 −0.87 0.3921 main_effect
sufC No K09013 8.043 5.131 1.57 0.1282 main_effect
yqjH No K07229 −0.044 0.081 −0.54 0.5920 main_effect
Magnesium Cycling corA Yes K03284 −259.740 107.229 −2.42 0.0227 interaction
corA Yes K03284 233.483 93.736 2.49 0.0259 by_group_JB1_JB2
corA Yes K03284 −26.257 43.532 −0.60 0.5576 by_group_JB5_JB6_JB7
mgtA Yes K01531 111.347 49.987 2.23 0.0348 interaction
mgtA Yes K01531 −64.748 58.468 −1.11 0.2868 by_group_JB1_JB2
mgtA Yes K01531 46.599 10.419 4.47 0.0008 by_group_JB5_JB6_JB7
mgtB No K01531 111.347 49.987 2.23 0.0348 interaction
mgtB No K01531 −64.748 58.468 −1.11 0.2868 by_group_JB1_JB2
mgtB No K01531 46.599 10.419 4.47 0.0008 by_group_JB5_JB6_JB7
mgtE Yes K06213 −11.123 4.963 −2.24 0.0331 main_effect
phoQ No K07637 −1.249 0.755 −1.65 0.1094 main_effect
Manganese Cycling mntA Yes K06147 −84.424 17.048 −4.95 0.0000 main_effect
mntB Yes K06148 −3.152 1.529 −2.06 0.0487 main_effect
mntC Yes K06149 0.426 0.524 0.81 0.4229 main_effect
mntH Yes K03322 −29.398 7.440 −3.95 0.0005 main_effect
mntR No K03709 −8.329 4.710 −1.77 0.0879 main_effect
mntR No K11924 −1.027 0.761 −1.35 0.1883 main_effect
sitA Yes K11604 −0.515 0.649 −0.79 0.4340 main_effect
sodA No K04564 9.784 10.896 0.90 0.3769 main_effect
Nitrogen fixation amt No K03320 −26.508 14.519 −1.83 0.0786 main_effect
glnB No K04751 −6.388 15.865 −0.40 0.6903 main_effect
iscS No K04487 −26.710 9.617 −2.78 0.0097 main_effect
moeA No K03750 −8.336 6.183 −1.35 0.1884 main_effect
nifA No K02584 2.361 1.101 2.15 0.0407 main_effect
nifB Yes K02585 1.272 0.761 1.67 0.1058 main_effect
nifD Yes K02586 3.086 0.746 4.14 0.0003 main_effect
nifE Yes K02587 4.233 1.148 3.69 0.0010 main_effect
nifH Yes K02588 0.282 0.139 2.02 0.0525 main_effect
nifK Yes K02591 4.914 1.212 4.06 0.0004 main_effect
nifM Yes K03769 6.099 4.401 1.39 0.1768 main_effect
nifN Yes K02592 0.113 0.255 0.44 0.6618 main_effect
nifQ No K15790 0.084 0.041 2.05 0.0495 main_effect
nifU Yes K04488 −21.181 5.973 −3.55 0.0014 main_effect
nifV Yes K02594 0.866 0.516 1.68 0.1046 main_effect
nifW No K02595 0.149 0.152 0.98 0.3365 main_effect
nifX No K02596 1.968 0.542 3.63 0.0011 main_effect
nifZ No K02597 0.240 0.245 0.98 0.3355 main_effect
Nitrogen Release amoA Yes K10944 0.079 0.501 0.16 0.8751 main_effect
amoB Yes K10945 −0.129 0.604 −0.21 0.8324 main_effect
amoC Yes K10946 21.119 4.794 4.41 0.0001 main_effect
gdh No K15371 2.894 2.981 0.97 0.3400 main_effect
napA No K02567 0.460 1.039 0.44 0.6611 main_effect
napA Yes K01416 0.204 0.359 0.57 0.5740 main_effect
napB No K02568 1.422 0.676 2.10 0.0446 main_effect
narG Yes K00370 −0.833 2.731 −0.31 0.7626 main_effect
narH Yes K00371 1.364 2.244 0.61 0.5482 main_effect
narI No K00374 −0.650 2.914 −0.22 0.8252 main_effect
nasA Yes K00372 −0.633 4.723 −0.13 0.8943 main_effect
nasB Yes K00360 −0.208 0.344 −0.60 0.5511 main_effect
nirA Yes K00366 −0.702 2.359 −0.30 0.7683 main_effect
nirK Yes K00368 −5.371 1.924 −2.79 0.0094 main_effect
nirS Yes K15864 0.210 0.116 1.80 0.0824 main_effect
norB Yes K04561 1.840 2.296 0.80 0.4295 main_effect
norC No K02305 4.202 2.393 1.76 0.0900 main_effect
nosZ Yes K00376 3.241 2.097 1.55 0.1335 main_effect
nrfA Yes K03385 7.856 2.771 2.83 0.0084 main_effect
ureC No K01428 −6.969 4.562 −1.53 0.1378 main_effect
Nodulation nodA Yes K14658 −0.027 0.050 −0.54 0.5920 main_effect
nodD Yes K14657 −0.232 0.361 −0.64 0.5255 main_effect
nodI No ABC transporter complex K09694 13.553 14.509 0.93 0.3582 main_effect
Phosphorus Solubilization gcd Yes K00117 9.315 6.965 1.34 0.1919 main_effect
phnX No K06163 −3.388 1.290 −2.63 0.0138 main_effect
phoA Yes K01077 −1.266 1.958 −0.65 0.5232 main_effect
phoD No K01113 −12.002 8.284 −1.45 0.1585 main_effect
phoX No K07093 11.152 5.066 2.20 0.0361 main_effect
ppk No K00937 −10.699 8.868 −1.21 0.2377 main_effect
ppx No K01514 −0.292 0.307 −0.95 0.3496 main_effect
pqqB Yes K06136 −14.440 4.258 −3.39 0.0021 main_effect
pqqC Yes K06137 −6.653 4.639 −1.43 0.1627 main_effect
pqqD Yes K06138 −7.154 5.004 −1.43 0.1639 main_effect
pqqE Yes K06139 −5.155 2.380 −2.17 0.0390 main_effect
Potassium Solubilization gcd Yes K00117 9.315 6.965 1.34 0.1919 main_effect
kdsA No K01627 −12.882 4.244 −3.04 0.0051 main_effect
kdsB No K00979 80.914 38.393 2.11 0.0449 interaction
kdsB No K00979 −88.154 41.234 −2.14 0.0506 by_group_JB1_JB2
kdsB No K00979 −7.240 11.296 −0.64 0.5336 by_group_JB5_JB6_JB7
kup Yes K03549 10.390 9.802 1.06 0.2982 main_effect
nhaA No K03313 −1.354 11.789 −0.11 0.9094 main_effect
pqqB Yes K06136 −14.440 4.258 −3.39 0.0021 main_effect
pqqC Yes K06137 −6.653 4.639 −1.43 0.1627 main_effect
pqqD Yes K06138 −7.154 5.004 −1.43 0.1639 main_effect
pqqE Yes K06139 −5.155 2.380 −2.17 0.0390 main_effect
trkA Yes K03499 −10.188 11.643 −0.88 0.3890 main_effect
trkH Yes K03498 1.156 2.572 0.45 0.6564 main_effect
Stress Adaptation copA Yes Heavy Metal Tolerance K17686 7.257 6.656 1.09 0.2849 main_effect
ectB Yes Salt tolerance K00836 −0.552 0.939 −0.59 0.5610 main_effect
entC Yes Siderophore production K02361 −0.312 0.269 −1.16 0.2572 main_effect
glnA No ACC deaminase (ACC-d) K01915 −237.086 75.080 −3.16 0.0040 interaction
glnA No ACC deaminase (ACC-d) K01915 161.034 77.322 2.08 0.0561 by_group_JB1_JB2
glnA No ACC deaminase (ACC-d) K01915 −76.052 24.356 −3.12 0.0088 by_group_JB5_JB6_JB7
kdsA Yes Exopolysaccharide production K01627 −12.882 4.244 −3.04 0.0051 main_effect
kdsB No Exopolysaccharide production K00979 80.914 38.393 2.11 0.0449 interaction
kdsB No Exopolysaccharide production K00979 −88.154 41.234 −2.14 0.0506 by_group_JB1_JB2
kdsB No Exopolysaccharide production K00979 −7.240 11.296 −0.64 0.5336 by_group_JB5_JB6_JB7
pchA Yes Salicylic acid (SA) K01851 −0.521 0.266 −1.96 0.0602 main_effect
pchB No Salicylic acid (SA) K04782 −1.604 1.570 −1.02 0.3156 main_effect
pqqB No Siderophore production K06136 −14.440 4.258 −3.39 0.0021 main_effect
Sulfur Cycling aprA Yes K00394 0.668 0.364 1.84 0.0769 main_effect
cysA Yes K02045 6.695 15.755 0.42 0.6741 main_effect
cysU Yes K02046 1.801 1.653 1.09 0.2852 main_effect
cysW Yes K02047 0.359 4.588 0.08 0.9382 main_effect
fccB Yes K17229 −0.330 0.318 −1.04 0.3079 main_effect
sat Yes K00958 5.437 4.084 1.33 0.1938 main_effect
soxA No K17222 −0.707 4.774 −0.15 0.8833 main_effect
soxB No K17224 11.287 3.770 2.99 0.0060 interaction
soxB No K17224 −14.248 3.765 −3.78 0.0020 by_group_JB1_JB2
soxB No K17224 −2.961 1.295 −2.29 0.0411 by_group_JB5_JB6_JB7
soxC Yes K17225 21.164 8.252 2.56 0.0160 main_effect
soxD Yes K22622 0.946 2.806 0.34 0.7385 main_effect
soxX No K17223 −4.759 3.145 −1.51 0.1414 main_effect
soxY Yes K17226 −9.522 4.435 −2.15 0.0406 main_effect
soxZ Yes K17227 −11.420 2.784 −4.10 0.0003 main_effect
Zinc Cycling mntR No K03709 −8.329 4.710 −1.77 0.0879 main_effect
troA No K11707 −1.815 1.554 −1.17 0.2527 main_effect
zitB No K16264 −11.406 6.682 −1.71 0.0989 main_effect
zntA No K01534 −1.059 2.154 −0.49 0.6268 main_effect
znuA Yes K09815 2.560 3.184 0.80 0.4281 main_effect
znuB Yes K09816 21.830 5.279 4.14 0.0003 main_effect
znuC Yes K09817 0.861 3.990 0.22 0.8308 main_effect
zur No K02076 −1.100 1.563 −0.70 0.4876 main_effect

Table 12: Summary statistics for each gene. The table shows the summary statistics for the analysis of the metadata variable and each gene (KO gene cluster) organised by section. The table gives estimate, standard error, t-value, p-value and model. “Model” informs which model the summary statistics represents: “main_effect” originate from analysis where all fields are analyzed together. This happens when we have tested for effects of JB and not found any significant difference between JB groups. “Interaction” gives results for the interaction analysis and is included only when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.

Nitrogen (perc)

Section Gene Essential Cagetory KO.ID Estimate SE t p-value Model
Antibiotic Production bacB Yes Bacilysin K19547 −30.073 10.956 −2.74 0.0108 interaction
bacB Yes Bacilysin K19547 0.000 0.000 NaN NaN by_group_JB1_JB2
bacB Yes Bacilysin K19547 −30.073 14.249 −2.11 0.0565 by_group_JB5_JB6_JB7
bacC Yes Bacilysin K19548 −3.855 6.813 −0.57 0.5760 main_effect
E4.1.1.82 Yes Fosfomycin K09459 −33.620 86.471 −0.39 0.7004 main_effect
eryA Yes Macrolides K00862 11.433 52.899 0.22 0.8305 main_effect
penM No Pentalenolactone K17476 −7.109 10.364 −0.69 0.4984 main_effect
pntE Yes Pentalenolactone K18091 −9.651 27.126 −0.36 0.7247 main_effect
pntH Yes Pentalenolactone K18056 1.405 4.819 0.29 0.7727 main_effect
ptlF Yes Pentalenolactone K17747 2.895 6.189 0.47 0.6436 main_effect
rifG Yes Rifamycin K16020 −11.901 21.388 −0.56 0.5823 main_effect
strA Yes Streptomycin K00547 −326.410 143.177 −2.28 0.0304 main_effect
Antibiotic Resistance vanA Yes Vancomycin K15739 −52.381 23.529 −2.23 0.0342 main_effect
vanH Yes Vancomycin K18347 −28.589 26.322 −1.09 0.2867 main_effect
vanX Yes Vancomycin K08641 −1,491.645 629.807 −2.37 0.0256 interaction
vanX Yes Vancomycin K08641 −120.691 332.350 −0.36 0.7219 by_group_JB1_JB2
vanX Yes Vancomycin K08641 −1,612.335 460.759 −3.50 0.0044 by_group_JB5_JB6_JB7
Biocontrol chiA Yes Fungicidal agents K06904 125.793 222.845 0.56 0.5769 main_effect
chiB No Fungicidal agents, Insecticide agents K20547 −5.648 12.667 −0.45 0.6591 main_effect
dapB No Bactericidal agents K00215 −667.143 991.715 −0.67 0.5066 main_effect
phzF Yes Fungicidal agents, Bactericidal agents K06998 1,079.259 511.476 2.11 0.0446 interaction
phzF Yes Fungicidal agents, Bactericidal agents K06998 −393.277 233.061 −1.69 0.1137 by_group_JB1_JB2
phzF Yes Fungicidal agents, Bactericidal agents K06998 685.982 465.791 1.47 0.1666 by_group_JB5_JB6_JB7
prnA Yes Fungicidal agents K14266 108.540 96.727 1.12 0.2713 main_effect
prnC Yes Fungicidal agents K14257 −70.239 60.380 −1.16 0.2545 main_effect
tcaB Yes Insecticide agents K07552 424.428 535.091 0.79 0.4343 main_effect
Calcium Cycling chaA Yes K07300 619.895 552.857 1.12 0.2717 main_effect
mgtC Yes K07507 −836.109 602.843 −1.39 0.1764 main_effect
phaC No K03821 3,684.426 1,167.777 3.16 0.0040 interaction
phaC No K03821 70.522 619.817 0.11 0.9110 by_group_JB1_JB2
phaC No K03821 3,754.948 843.514 4.45 0.0008 by_group_JB5_JB6_JB7
ureC Yes K01428 555.676 342.767 1.62 0.1162 main_effect
Carbon Fixation ccmK No Calvin–Benson–Bassham (CBB) Cycle K08696 16.591 18.045 0.92 0.3657 main_effect
ccmL No Calvin–Benson–Bassham (CBB) Cycle K08697 12.432 22.458 0.55 0.5843 main_effect
codH Yes Wood–Ljungdahl (WL) pathway K00192 −9.437 12.335 −0.77 0.4506 main_effect
korA Yes Reductive TCA (rTCA) cycle K00174 170.643 270.382 0.63 0.5331 main_effect
korB Yes Reductive TCA (rTCA) cycle K00175 1,102.444 379.645 2.90 0.0071 main_effect
prk Yes Calvin–Benson–Bassham (CBB) Cycle K00855 82.030 93.929 0.87 0.3899 main_effect
rbcL Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01601 333.321 211.227 1.58 0.1258 main_effect
rbcS Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01602 −773.446 632.898 −1.22 0.2319 main_effect
frdA No Reductive TCA (rTCA) cycle K00244 27.960 73.355 0.38 0.7060 main_effect
mcl No 3HP bicycle K08691 207.203 107.528 1.93 0.0642 main_effect
Chloride Cycling clcA Yes K03281 −504.381 988.453 −0.51 0.6139 main_effect
clcB Yes K03281 −504.381 988.453 −0.51 0.6139 main_effect
clcN Yes K05011 −4.905 8.370 −0.59 0.5626 main_effect
gltT No K11102 −155.574 242.285 −0.64 0.5260 main_effect
kefC No K11745 −333.861 61.129 −5.46 0.0000 interaction
kefC No K11745 129.235 21.923 5.89 0.0000 by_group_JB1_JB2
kefC No K11745 −204.627 65.764 −3.11 0.0090 by_group_JB5_JB6_JB7
Copper Cycling copA Yes K17686 −519.984 503.582 −1.03 0.3106 main_effect
copB Yes K01533 252.629 291.156 0.87 0.3929 main_effect
ctrA Yes K13584 97.090 801.519 0.12 0.9045 main_effect
cueO No K14588 97.128 54.868 1.77 0.0876 main_effect
cusA Yes K07787 −33.327 301.499 −0.11 0.9128 main_effect
cusB No K07798 83.918 333.968 0.25 0.8034 main_effect
Hormone Production acdS Yes Ethylene K01505 158.723 302.007 0.53 0.6033 main_effect
aldA Yes IAA K07248 −238.207 108.058 −2.20 0.0365 interaction
aldA Yes IAA K07248 64.847 34.168 1.90 0.0785 by_group_JB1_JB2
aldA Yes IAA K07248 −173.360 122.076 −1.42 0.1810 by_group_JB5_JB6_JB7
aldH No IAA K00128 534.463 761.394 0.70 0.4885 main_effect
amiE Yes IAA K01426 355.084 373.929 0.95 0.3504 main_effect
aspC Yes IAA K00813 −189.967 88.234 −2.15 0.0408 interaction
aspC Yes IAA K00813 13.002 43.310 0.30 0.7684 by_group_JB1_JB2
aspC Yes IAA K00813 −176.964 73.349 −2.41 0.0328 by_group_JB5_JB6_JB7
entC No GA K02361 −34.990 19.741 −1.77 0.0872 main_effect
etfA No Ethylene K03522 −870.274 971.944 −0.90 0.3782 main_effect
iaaH No IAA K21801 24.747 48.082 0.51 0.6108 main_effect
iaaM No IAA K00466 −45.517 49.157 −0.93 0.3624 main_effect
ipdC Yes IAA K04103 22.774 12.662 1.80 0.0829 main_effect
ipt Yes CK K00375 −628.796 448.506 −1.40 0.1719 main_effect
miaA No CK K00791 −531.854 1,069.008 −0.50 0.6227 main_effect
nitA No IAA K01501 −9.916 69.671 −0.14 0.8878 main_effect
tnaA No IAA K01667 64.957 139.858 0.46 0.6459 main_effect
Iron Cycling bfr No K03594 57.472 461.187 0.12 0.9017 main_effect
dps No K04047 −123.344 508.799 −0.24 0.8102 main_effect
entC Yes K02361 −34.990 19.741 −1.77 0.0872 main_effect
feoB Yes K04759 236.806 115.480 2.05 0.0498 main_effect
fur No K03711 −134.642 547.931 −0.25 0.8077 main_effect
iscA No K13628 −790.273 856.968 −0.92 0.3643 main_effect
sufB Yes K09014 −2,175.399 683.944 −3.18 0.0038 interaction
sufB Yes K09014 −53.325 384.633 −0.14 0.8917 by_group_JB1_JB2
sufB Yes K09014 −2,228.724 420.666 −5.30 0.0002 by_group_JB5_JB6_JB7
sufC No K09013 −158.801 402.856 −0.39 0.6964 main_effect
yqjH No K07229 −36.116 13.158 −2.74 0.0108 interaction
yqjH No K07229 0.000 0.000 NaN NaN by_group_JB1_JB2
yqjH No K07229 −36.116 17.112 −2.11 0.0565 by_group_JB5_JB6_JB7
Magnesium Cycling corA Yes K03284 1,503.916 2,088.323 0.72 0.4774 main_effect
mgtA Yes K01531 237.429 940.108 0.25 0.8025 main_effect
mgtB No K01531 237.429 940.108 0.25 0.8025 main_effect
mgtE Yes K06213 −656.238 387.556 −1.69 0.1015 main_effect
phoQ No K07637 −367.768 134.530 −2.73 0.0111 interaction
phoQ No K07637 89.627 69.576 1.29 0.2186 by_group_JB1_JB2
phoQ No K07637 −278.141 102.531 −2.71 0.0189 by_group_JB5_JB6_JB7
Manganese Cycling mntA Yes K06147 −1,996.736 1,721.862 −1.16 0.2560 main_effect
mntB Yes K06148 −144.090 120.858 −1.19 0.2432 main_effect
mntC Yes K06149 −60.302 38.373 −1.57 0.1273 main_effect
mntH Yes K03322 −314.679 698.442 −0.45 0.6558 main_effect
mntR No K03709 −127.976 374.131 −0.34 0.7349 main_effect
mntR No K11924 −366.867 129.940 −2.82 0.0090 interaction
mntR No K11924 26.807 40.493 0.66 0.5187 by_group_JB1_JB2
mntR No K11924 −340.060 147.480 −2.31 0.0398 by_group_JB5_JB6_JB7
sitA Yes K11604 41.221 48.909 0.84 0.4065 main_effect
sodA No K04564 1,467.673 786.921 1.87 0.0727 main_effect
Nitrogen fixation amt No K03320 62.318 1,159.480 0.05 0.9575 main_effect
glnB No K04751 944.794 1,187.837 0.80 0.4331 main_effect
iscS No K04487 −1,243.726 785.549 −1.58 0.1246 main_effect
moeA No K03750 334.207 477.553 0.70 0.4898 main_effect
nifA No K02584 −70.319 88.667 −0.79 0.4344 main_effect
nifB Yes K02585 −5.642 60.226 −0.09 0.9260 main_effect
nifD Yes K02586 −6.039 71.465 −0.08 0.9333 main_effect
nifE Yes K02587 −4.344 105.627 −0.04 0.9675 main_effect
nifH Yes K02588 5.242 11.207 0.47 0.6436 main_effect
nifK Yes K02591 19.000 115.183 0.16 0.8702 main_effect
nifM Yes K03769 386.622 335.619 1.15 0.2591 main_effect
nifN Yes K02592 −1.092 19.348 −0.06 0.9554 main_effect
nifQ No K15790 0.970 3.325 0.29 0.7727 main_effect
nifU Yes K04488 435.289 536.571 0.81 0.4241 main_effect
nifV Yes K02594 6.660 40.857 0.16 0.8717 main_effect
nifW No K02595 10.409 11.507 0.90 0.3734 main_effect
nifX No K02596 26.197 49.378 0.53 0.5999 main_effect
nifZ No K02597 −11.466 18.659 −0.61 0.5438 main_effect
Nitrogen Release amoA Yes K10944 45.830 36.827 1.24 0.2236 main_effect
amoB Yes K10945 −320.681 97.859 −3.28 0.0030 interaction
amoB Yes K10945 46.478 53.127 0.87 0.3964 by_group_JB1_JB2
amoB Yes K10945 −274.203 66.924 −4.10 0.0015 by_group_JB5_JB6_JB7
amoC Yes K10946 −1.561 470.903 0.00 0.9974 main_effect
gdh No K15371 116.428 227.757 0.51 0.6132 main_effect
napA No K02567 244.816 63.666 3.85 0.0006 main_effect
napA Yes K01416 18.897 27.002 0.70 0.4898 main_effect
napB No K02568 −61.012 53.718 −1.14 0.2657 main_effect
narG Yes K00370 24.467 206.442 0.12 0.9065 main_effect
narH Yes K00371 −95.228 169.601 −0.56 0.5789 main_effect
narI No K00374 −79.931 219.649 −0.36 0.7187 main_effect
nasA Yes K00372 280.662 352.683 0.80 0.4328 main_effect
nasB Yes K00360 −133.173 61.338 −2.17 0.0392 interaction
nasB Yes K00360 34.797 19.297 1.80 0.0929 by_group_JB1_JB2
nasB Yes K00360 −98.376 69.408 −1.42 0.1818 by_group_JB5_JB6_JB7
nirA Yes K00366 −290.840 169.678 −1.71 0.0976 main_effect
nirK Yes K00368 −151.903 161.724 −0.94 0.3556 main_effect
nirS Yes K15864 −1.015 9.287 −0.11 0.9138 main_effect
norB Yes K04561 −172.297 172.225 −1.00 0.3257 main_effect
norC No K02305 120.118 188.974 0.64 0.5302 main_effect
nosZ Yes K00376 156.131 162.278 0.96 0.3442 main_effect
nrfA Yes K03385 377.974 226.346 1.67 0.1061 main_effect
ureC No K01428 555.676 342.767 1.62 0.1162 main_effect
Nodulation nodA Yes K14658 −22.573 8.224 −2.74 0.0108 interaction
nodA Yes K14658 0.000 0.000 NaN NaN by_group_JB1_JB2
nodA Yes K14658 −22.573 10.695 −2.11 0.0565 by_group_JB5_JB6_JB7
nodD Yes K14657 49.159 25.856 1.90 0.0676 main_effect
nodI No ABC transporter complex K09694 158.317 1,111.892 0.14 0.8878 main_effect
Phosphorus Solubilization gcd Yes K00117 −202.858 541.018 −0.37 0.7105 main_effect
phnX No K06163 181.053 103.167 1.75 0.0902 main_effect
phoA Yes K01077 −50.930 148.634 −0.34 0.7344 main_effect
phoD No K01113 −167.798 647.647 −0.26 0.7975 main_effect
phoX No K07093 185.921 412.727 0.45 0.6558 main_effect
ppk No K00937 4,080.799 1,440.403 2.83 0.0088 interaction
ppk No K00937 110.451 789.882 0.14 0.8908 by_group_JB1_JB2
ppk No K00937 4,191.250 958.551 4.37 0.0009 by_group_JB5_JB6_JB7
ppx No K01514 −15.540 23.376 −0.66 0.5116 main_effect
pqqB Yes K06136 1,648.747 763.896 2.16 0.0403 interaction
pqqB Yes K06136 −162.844 352.453 −0.46 0.6512 by_group_JB1_JB2
pqqB Yes K06136 1,485.903 686.463 2.16 0.0513 by_group_JB5_JB6_JB7
pqqC Yes K06137 −6.237 362.872 −0.02 0.9864 main_effect
pqqD Yes K06138 1,835.199 838.484 2.19 0.0378 interaction
pqqD Yes K06138 −486.468 418.645 −1.16 0.2647 by_group_JB1_JB2
pqqD Yes K06138 1,348.731 679.315 1.99 0.0704 by_group_JB5_JB6_JB7
pqqE Yes K06139 −176.989 191.249 −0.93 0.3626 main_effect
Potassium Solubilization gcd Yes K00117 −202.858 541.018 −0.37 0.7105 main_effect
kdsA No K01627 141.775 368.403 0.38 0.7033 main_effect
kdsB No K00979 −221.599 799.377 −0.28 0.7837 main_effect
kup Yes K03549 936.557 733.622 1.28 0.2122 main_effect
nhaA No K03313 664.264 881.305 0.75 0.4573 main_effect
pqqB Yes K06136 1,648.747 763.896 2.16 0.0403 interaction
pqqB Yes K06136 −162.844 352.453 −0.46 0.6512 by_group_JB1_JB2
pqqB Yes K06136 1,485.903 686.463 2.16 0.0513 by_group_JB5_JB6_JB7
pqqC Yes K06137 −6.237 362.872 −0.02 0.9864 main_effect
pqqD Yes K06138 1,835.199 838.484 2.19 0.0378 interaction
pqqD Yes K06138 −486.468 418.645 −1.16 0.2647 by_group_JB1_JB2
pqqD Yes K06138 1,348.731 679.315 1.99 0.0704 by_group_JB5_JB6_JB7
pqqE Yes K06139 −176.989 191.249 −0.93 0.3626 main_effect
trkA Yes K03499 62.657 890.848 0.07 0.9444 main_effect
trkH Yes K03498 35.448 194.734 0.18 0.8569 main_effect
Stress Adaptation copA Yes Heavy Metal Tolerance K17686 −519.984 503.582 −1.03 0.3106 main_effect
ectB Yes Salt tolerance K00836 −344.776 158.638 −2.17 0.0391 interaction
ectB Yes Salt tolerance K00836 −46.608 84.588 −0.55 0.5903 by_group_JB1_JB2
ectB Yes Salt tolerance K00836 −391.383 113.396 −3.45 0.0048 by_group_JB5_JB6_JB7
entC Yes Siderophore production K02361 −34.990 19.741 −1.77 0.0872 main_effect
glnA No ACC deaminase (ACC-d) K01915 −232.760 1,472.496 −0.16 0.8755 main_effect
kdsA Yes Exopolysaccharide production K01627 141.775 368.403 0.38 0.7033 main_effect
kdsB No Exopolysaccharide production K00979 −221.599 799.377 −0.28 0.7837 main_effect
pchA Yes Salicylic acid (SA) K01851 0.781 21.409 0.04 0.9712 main_effect
pchB No Salicylic acid (SA) K04782 −145.497 117.540 −1.24 0.2261 main_effect
pqqB No Siderophore production K06136 1,648.747 763.896 2.16 0.0403 interaction
pqqB No Siderophore production K06136 −162.844 352.453 −0.46 0.6512 by_group_JB1_JB2
pqqB No Siderophore production K06136 1,485.903 686.463 2.16 0.0513 by_group_JB5_JB6_JB7
Sulfur Cycling aprA Yes K00394 −31.571 28.442 −1.11 0.2764 main_effect
cysA Yes K02045 1,117.972 1,174.398 0.95 0.3493 main_effect
cysU Yes K02046 −137.819 124.738 −1.10 0.2786 main_effect
cysW Yes K02047 373.312 339.181 1.10 0.2804 main_effect
fccB Yes K17229 −2.433 24.435 −0.10 0.9214 main_effect
sat Yes K00958 223.577 315.123 0.71 0.4839 main_effect
soxA No K17222 1,038.097 302.479 3.43 0.0019 main_effect
soxB No K17224 18.799 94.587 0.20 0.8439 main_effect
soxC Yes K17225 4,139.331 1,296.591 3.19 0.0037 interaction
soxC Yes K17225 936.275 662.458 1.41 0.1794 by_group_JB1_JB2
soxC Yes K17225 5,075.606 1,010.655 5.02 0.0003 by_group_JB5_JB6_JB7
soxD Yes K22622 1,276.210 476.205 2.68 0.0126 interaction
soxD Yes K22622 −128.547 247.576 −0.52 0.6117 by_group_JB1_JB2
soxD Yes K22622 1,147.663 359.269 3.19 0.0077 by_group_JB5_JB6_JB7
soxX No K17223 375.910 236.503 1.59 0.1232 main_effect
soxY Yes K17226 1,684.135 770.993 2.18 0.0381 interaction
soxY Yes K17226 −51.138 411.827 −0.12 0.9029 by_group_JB1_JB2
soxY Yes K17226 1,632.997 548.860 2.98 0.0116 by_group_JB5_JB6_JB7
soxZ Yes K17227 235.647 262.199 0.90 0.3765 main_effect
Zinc Cycling mntR No K03709 −127.976 374.131 −0.34 0.7349 main_effect
troA No K11707 9.638 120.112 0.08 0.9366 main_effect
zitB No K16264 −1,045.957 491.843 −2.13 0.0424 main_effect
zntA No K01534 −404.877 144.264 −2.81 0.0090 main_effect
znuA Yes K09815 288.889 236.905 1.22 0.2329 main_effect
znuB Yes K09816 372.710 500.839 0.74 0.4630 main_effect
znuC Yes K09817 238.894 298.108 0.80 0.4297 main_effect
zur No K02076 −292.904 105.414 −2.78 0.0096 main_effect

Table 13: Summary statistics for each gene. The table shows the summary statistics for the analysis of the metadata variable and each gene (KO gene cluster) organised by section. The table gives estimate, standard error, t-value, p-value and model. “Model” informs which model the summary statistics represents: “main_effect” originate from analysis where all fields are analyzed together. This happens when we have tested for effects of JB and not found any significant difference between JB groups. “Interaction” gives results for the interaction analysis and is included only when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.

Years since turning organic

Section Gene Essential Cagetory KO.ID Estimate SE t p-value Model
Antibiotic Production bacB Yes Bacilysin K19547 0.038 0.026 1.47 0.1534 main_effect
bacC Yes Bacilysin K19548 −0.042 0.036 −1.20 0.2418 main_effect
E4.1.1.82 Yes Fosfomycin K09459 −1.593 0.349 −4.57 0.0001 main_effect
eryA Yes Macrolides K00862 0.514 0.264 1.95 0.0617 main_effect
penM No Pentalenolactone K17476 0.082 0.053 1.53 0.1374 main_effect
pntE Yes Pentalenolactone K18091 0.146 0.142 1.03 0.3117 main_effect
pntH Yes Pentalenolactone K18056 0.022 0.025 0.87 0.3925 main_effect
ptlF Yes Pentalenolactone K17747 0.028 0.033 0.87 0.3925 main_effect
rifG Yes Rifamycin K16020 −0.076 0.113 −0.67 0.5060 main_effect
strA Yes Streptomycin K00547 0.557 0.821 0.68 0.5030 main_effect
Antibiotic Resistance vanA Yes Vancomycin K15739 −0.015 0.136 −0.11 0.9142 main_effect
vanH Yes Vancomycin K18347 −0.081 0.142 −0.57 0.5707 main_effect
vanX Yes Vancomycin K08641 −0.631 1.559 −0.40 0.6888 main_effect
Biocontrol chiA Yes Fungicidal agents K06904 −1.581 1.152 −1.37 0.1809 main_effect
chiB No Fungicidal agents, Insecticide agents K20547 0.076 0.066 1.15 0.2612 main_effect
dapB No Bactericidal agents K00215 10.460 4.929 2.12 0.0428 main_effect
phzF Yes Fungicidal agents, Bactericidal agents K06998 1.108 1.150 0.96 0.3435 main_effect
prnA Yes Fungicidal agents K14266 −0.408 0.520 −0.79 0.4390 main_effect
prnC Yes Fungicidal agents K14257 −0.105 0.328 −0.32 0.7521 main_effect
tcaB Yes Insecticide agents K07552 3.103 2.814 1.10 0.2796 main_effect
Calcium Cycling chaA Yes K07300 −3.630 2.923 −1.24 0.2246 main_effect
mgtC Yes K07507 6.680 3.061 2.18 0.0376 main_effect
phaC No K03821 4.578 3.251 1.41 0.1701 main_effect
ureC Yes K01428 −2.066 1.864 −1.11 0.2771 main_effect
Carbon Fixation ccmK No Calvin–Benson–Bassham (CBB) Cycle K08696 −0.122 0.095 −1.29 0.2070 main_effect
ccmL No Calvin–Benson–Bassham (CBB) Cycle K08697 0.492 0.215 2.28 0.0307 interaction
ccmL No Calvin–Benson–Bassham (CBB) Cycle K08697 −0.101 0.078 −1.30 0.2138 by_group_JB1_JB2
ccmL No Calvin–Benson–Bassham (CBB) Cycle K08697 0.391 0.222 1.77 0.1029 by_group_JB5_JB6_JB7
codH Yes Wood–Ljungdahl (WL) pathway K00192 −0.035 0.066 −0.54 0.5948 main_effect
korA Yes Reductive TCA (rTCA) cycle K00174 0.209 1.446 0.14 0.8862 main_effect
korB Yes Reductive TCA (rTCA) cycle K00175 2.389 2.256 1.06 0.2985 main_effect
prk Yes Calvin–Benson–Bassham (CBB) Cycle K00855 0.303 0.502 0.60 0.5513 main_effect
rbcL Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01601 0.230 1.170 0.20 0.8458 main_effect
rbcS Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01602 6.683 3.211 2.08 0.0467 main_effect
frdA No Reductive TCA (rTCA) cycle K00244 0.201 0.389 0.52 0.6094 main_effect
mcl No 3HP bicycle K08691 0.318 0.605 0.53 0.6027 main_effect
Chloride Cycling clcA Yes K03281 8.123 5.047 1.61 0.1187 main_effect
clcB Yes K03281 8.123 5.047 1.61 0.1187 main_effect
clcN Yes K05011 0.038 0.044 0.87 0.3925 main_effect
gltT No K11102 −5.926 2.431 −2.44 0.0219 interaction
gltT No K11102 2.367 1.926 1.23 0.2393 by_group_JB1_JB2
gltT No K11102 −3.559 1.165 −3.06 0.0100 by_group_JB5_JB6_JB7
kefC No K11745 −0.189 0.190 −0.99 0.3285 main_effect
Copper Cycling copA Yes K17686 0.168 2.726 0.06 0.9514 main_effect
copB Yes K01533 −0.494 1.565 −0.32 0.7546 main_effect
ctrA Yes K13584 4.270 4.182 1.02 0.3160 main_effect
cueO No K14588 0.047 0.307 0.15 0.8784 main_effect
cusA Yes K07787 −0.451 1.600 −0.28 0.7801 main_effect
cusB No K07798 0.017 1.776 0.01 0.9926 main_effect
Hormone Production acdS Yes Ethylene K01505 1.269 1.594 0.80 0.4328 main_effect
aldA Yes IAA K07248 −0.025 0.247 −0.10 0.9207 main_effect
aldH No IAA K00128 3.328 4.032 0.83 0.4161 main_effect
amiE Yes IAA K01426 1.367 2.002 0.68 0.5003 main_effect
aspC Yes IAA K00813 −0.242 0.197 −1.23 0.2297 main_effect
entC No GA K02361 0.067 0.110 0.61 0.5475 main_effect
etfA No Ethylene K03522 11.297 4.782 2.36 0.0253 main_effect
iaaH No IAA K21801 −0.170 0.255 −0.67 0.5086 main_effect
iaaM No IAA K00466 1.071 0.514 2.08 0.0470 interaction
iaaM No IAA K00466 −0.411 0.305 −1.35 0.1994 by_group_JB1_JB2
iaaM No IAA K00466 0.660 0.426 1.55 0.1470 by_group_JB5_JB6_JB7
ipdC Yes IAA K04103 −0.052 0.070 −0.75 0.4619 main_effect
ipt Yes CK K00375 2.788 2.408 1.16 0.2568 main_effect
miaA No CK K00791 10.733 5.331 2.01 0.0538 main_effect
nitA No IAA K01501 0.520 0.357 1.46 0.1565 main_effect
tnaA No IAA K01667 −0.176 0.745 −0.24 0.8146 main_effect
Iron Cycling bfr No K03594 −4.753 2.280 −2.08 0.0464 main_effect
dps No K04047 3.590 2.619 1.37 0.1814 main_effect
entC Yes K02361 0.067 0.110 0.61 0.5475 main_effect
feoB Yes K04759 −0.750 0.643 −1.17 0.2530 main_effect
fur No K03711 −0.468 2.913 −0.16 0.8734 main_effect
iscA No K13628 3.533 4.573 0.77 0.4463 main_effect
sufB Yes K09014 −2.431 1.688 −1.44 0.1610 main_effect
sufC No K09013 −0.584 2.143 −0.27 0.7872 main_effect
yqjH No K07229 0.046 0.031 1.47 0.1534 main_effect
Magnesium Cycling corA Yes K03284 −6.316 11.133 −0.57 0.5750 main_effect
mgtA Yes K01531 2.557 4.977 0.51 0.6115 main_effect
mgtB No K01531 2.557 4.977 0.51 0.6115 main_effect
mgtE Yes K06213 −2.238 2.120 −1.06 0.3002 main_effect
phoQ No K07637 0.089 0.317 0.28 0.7814 main_effect
Manganese Cycling mntA Yes K06147 8.012 9.241 0.87 0.3933 main_effect
mntB Yes K06148 0.324 0.655 0.49 0.6249 main_effect
mntC Yes K06149 −0.011 0.213 −0.05 0.9575 main_effect
mntH Yes K03322 0.634 3.722 0.17 0.8660 main_effect
mntR No K03709 −0.201 1.991 −0.10 0.9201 main_effect
mntR No K11924 0.467 0.302 1.55 0.1334 main_effect
sitA Yes K11604 0.288 0.257 1.12 0.2726 main_effect
sodA No K04564 −10.560 3.958 −2.67 0.0125 main_effect
Nitrogen fixation amt No K03320 8.054 5.969 1.35 0.1880 main_effect
glnB No K04751 13.968 5.810 2.40 0.0231 main_effect
iscS No K04487 −1.312 4.349 −0.30 0.7651 main_effect
moeA No K03750 3.344 2.480 1.35 0.1883 main_effect
nifA No K02584 −1.170 0.422 −2.77 0.0097 main_effect
nifB Yes K02585 −0.031 0.320 −0.10 0.9227 main_effect
nifD Yes K02586 0.186 0.378 0.49 0.6259 main_effect
nifE Yes K02587 −0.042 0.561 −0.07 0.9411 main_effect
nifH Yes K02588 −0.032 0.059 −0.54 0.5948 main_effect
nifK Yes K02591 −0.122 0.612 −0.20 0.8433 main_effect
nifM Yes K03769 −1.705 1.796 −0.95 0.3506 main_effect
nifN Yes K02592 0.040 0.103 0.39 0.7028 main_effect
nifQ No K15790 0.017 0.017 0.97 0.3425 main_effect
nifU Yes K04488 1.258 2.874 0.44 0.6650 main_effect
nifV Yes K02594 0.083 0.217 0.38 0.7040 main_effect
nifW No K02595 −0.054 0.061 −0.89 0.3823 main_effect
nifX No K02596 0.042 0.264 0.16 0.8737 main_effect
nifZ No K02597 −0.013 0.100 −0.13 0.8988 main_effect
Nitrogen Release amoA Yes K10944 −0.301 0.193 −1.56 0.1290 main_effect
amoB Yes K10945 −0.566 0.218 −2.60 0.0148 main_effect
amoC Yes K10946 −2.260 2.465 −0.92 0.3671 main_effect
gdh No K15371 1.629 1.176 1.38 0.1770 main_effect
napA No K02567 0.223 0.416 0.54 0.5957 main_effect
napA Yes K01416 0.226 0.138 1.64 0.1130 main_effect
napB No K02568 −0.123 0.291 −0.42 0.6753 main_effect
narG Yes K00370 −2.121 1.021 −2.08 0.0470 main_effect
narH Yes K00371 1.250 0.875 1.43 0.1642 main_effect
narI No K00374 0.600 1.164 0.52 0.6101 main_effect
nasA Yes K00372 −1.386 1.877 −0.74 0.4664 main_effect
nasB Yes K00360 0.607 0.262 2.32 0.0287 interaction
nasB Yes K00360 −0.139 0.123 −1.13 0.2759 by_group_JB1_JB2
nasB Yes K00360 0.468 0.250 1.87 0.0858 by_group_JB5_JB6_JB7
nirA Yes K00366 −3.890 1.739 −2.24 0.0341 interaction
nirA Yes K00366 3.165 1.166 2.72 0.0167 by_group_JB1_JB2
nirA Yes K00366 −0.724 1.261 −0.57 0.5764 by_group_JB5_JB6_JB7
nirK Yes K00368 0.187 0.872 0.21 0.8317 main_effect
nirS Yes K15864 0.023 0.049 0.47 0.6403 main_effect
norB Yes K04561 0.239 0.930 0.26 0.7991 main_effect
norC No K02305 −2.115 0.929 −2.28 0.0306 main_effect
nosZ Yes K00376 −1.406 0.835 −1.68 0.1033 main_effect
nrfA Yes K03385 −0.670 1.255 −0.53 0.5976 main_effect
ureC No K01428 −2.066 1.864 −1.11 0.2771 main_effect
Nodulation nodA Yes K14658 0.029 0.020 1.47 0.1534 main_effect
nodD Yes K14657 −0.024 0.146 −0.16 0.8711 main_effect
nodI No ABC transporter complex K09694 3.087 5.880 0.52 0.6038 main_effect
Phosphorus Solubilization gcd Yes K00117 −5.929 2.655 −2.23 0.0337 main_effect
phnX No K06163 0.446 0.571 0.78 0.4416 main_effect
phoA Yes K01077 −0.383 0.788 −0.49 0.6305 main_effect
phoD No K01113 −9.158 2.978 −3.07 0.0047 main_effect
phoX No K07093 −1.240 2.188 −0.57 0.5753 main_effect
ppk No K00937 1.386 3.638 0.38 0.7061 main_effect
ppx No K01514 0.128 0.123 1.04 0.3051 main_effect
pqqB Yes K06136 4.006 1.882 2.13 0.0422 main_effect
pqqC Yes K06137 3.191 1.831 1.74 0.0923 main_effect
pqqD Yes K06138 2.922 2.004 1.46 0.1559 main_effect
pqqE Yes K06139 2.035 0.957 2.13 0.0424 main_effect
Potassium Solubilization gcd Yes K00117 −5.929 2.655 −2.23 0.0337 main_effect
kdsA No K01627 1.419 1.944 0.73 0.4714 main_effect
kdsB No K00979 3.923 4.187 0.94 0.3568 main_effect
kup Yes K03549 3.612 3.951 0.91 0.3684 main_effect
nhaA No K03313 −5.349 4.620 −1.16 0.2567 main_effect
pqqB Yes K06136 4.006 1.882 2.13 0.0422 main_effect
pqqC Yes K06137 3.191 1.831 1.74 0.0923 main_effect
pqqD Yes K06138 2.922 2.004 1.46 0.1559 main_effect
pqqE Yes K06139 2.035 0.957 2.13 0.0424 main_effect
trkA Yes K03499 11.008 4.251 2.59 0.0151 main_effect
trkH Yes K03498 −0.593 1.029 −0.58 0.5694 main_effect
Stress Adaptation copA Yes Heavy Metal Tolerance K17686 0.168 2.726 0.06 0.9514 main_effect
ectB Yes Salt tolerance K00836 0.166 0.377 0.44 0.6626 main_effect
entC Yes Siderophore production K02361 0.067 0.110 0.61 0.5475 main_effect
glnA No ACC deaminase (ACC-d) K01915 3.298 7.801 0.42 0.6757 main_effect
kdsA Yes Exopolysaccharide production K01627 1.419 1.944 0.73 0.4714 main_effect
kdsB No Exopolysaccharide production K00979 3.923 4.187 0.94 0.3568 main_effect
pchA Yes Salicylic acid (SA) K01851 −0.128 0.111 −1.15 0.2601 main_effect
pchB No Salicylic acid (SA) K04782 0.123 0.641 0.19 0.8493 main_effect
pqqB No Siderophore production K06136 4.006 1.882 2.13 0.0422 main_effect
Sulfur Cycling aprA Yes K00394 −0.315 0.142 −2.21 0.0355 main_effect
cysA Yes K02045 2.922 6.315 0.46 0.6472 main_effect
cysU Yes K02046 −0.499 0.670 −0.74 0.4633 main_effect
cysW Yes K02047 1.761 1.810 0.97 0.3390 main_effect
fccB Yes K17229 −0.070 0.129 −0.54 0.5945 main_effect
sat Yes K00958 0.897 1.681 0.53 0.5978 main_effect
soxA No K17222 −0.038 1.915 −0.02 0.9841 main_effect
soxB No K17224 0.876 0.475 1.84 0.0757 main_effect
soxC Yes K17225 −4.961 3.556 −1.40 0.1740 main_effect
soxD Yes K22622 −0.007 1.128 −0.01 0.9948 main_effect
soxX No K17223 2.596 1.217 2.13 0.0417 main_effect
soxY Yes K17226 3.163 1.824 1.73 0.0939 main_effect
soxZ Yes K17227 2.970 1.297 2.29 0.0297 main_effect
Zinc Cycling mntR No K03709 −0.201 1.991 −0.10 0.9201 main_effect
troA No K11707 0.256 0.636 0.40 0.6905 main_effect
zitB No K16264 1.310 2.805 0.47 0.6441 main_effect
zntA No K01534 −1.340 0.830 −1.61 0.1176 main_effect
znuA Yes K09815 −0.721 1.284 −0.56 0.5792 main_effect
znuB Yes K09816 −2.311 2.651 −0.87 0.3908 main_effect
znuC Yes K09817 −0.969 1.591 −0.61 0.5477 main_effect
zur No K02076 −0.386 0.628 −0.61 0.5444 main_effect

Table 14: Summary statistics for each gene. The table shows the summary statistics for the analysis of the metadata variable and each gene (KO gene cluster) organised by section. The table gives estimate, standard error, t-value, p-value and model. “Model” informs which model the summary statistics represents: “main_effect” originate from analysis where all fields are analyzed together. This happens when we have tested for effects of JB and not found any significant difference between JB groups. “Interaction” gives results for the interaction analysis and is included only when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.

Years since turning biodynamic

Section Gene Essential Cagetory KO.ID Estimate SE t p-value Model
Antibiotic Production bacB Yes Bacilysin K19547 −0.022 0.039 −0.56 0.5819 main_effect
bacC Yes Bacilysin K19548 −0.041 0.052 −0.80 0.4286 main_effect
E4.1.1.82 Yes Fosfomycin K09459 −0.879 0.639 −1.38 0.1796 main_effect
eryA Yes Macrolides K00862 0.464 0.393 1.18 0.2484 main_effect
penM No Pentalenolactone K17476 −0.104 0.077 −1.35 0.1870 main_effect
pntE Yes Pentalenolactone K18091 −0.105 0.206 −0.51 0.6146 main_effect
pntH Yes Pentalenolactone K18056 0.068 0.034 1.96 0.0598 main_effect
ptlF Yes Pentalenolactone K17747 −0.026 0.047 −0.56 0.5819 main_effect
rifG Yes Rifamycin K16020 −0.095 0.163 −0.58 0.5651 main_effect
strA Yes Streptomycin K00547 0.876 1.175 0.75 0.4621 main_effect
Antibiotic Resistance vanA Yes Vancomycin K15739 −0.147 0.192 −0.76 0.4508 main_effect
vanH Yes Vancomycin K18347 −0.348 0.194 −1.80 0.0827 main_effect
vanX Yes Vancomycin K08641 −0.956 2.232 −0.43 0.6718 main_effect
Biocontrol chiA Yes Fungicidal agents K06904 −3.596 1.564 −2.30 0.0292 main_effect
chiB No Fungicidal agents, Insecticide agents K20547 0.233 0.086 2.70 0.0116 main_effect
dapB No Bactericidal agents K00215 7.908 7.459 1.06 0.2982 main_effect
phzF Yes Fungicidal agents, Bactericidal agents K06998 0.915 1.665 0.55 0.5870 main_effect
prnA Yes Fungicidal agents K14266 −1.602 0.689 −2.33 0.0275 main_effect
prnC Yes Fungicidal agents K14257 −0.745 0.449 −1.66 0.1083 main_effect
tcaB Yes Insecticide agents K07552 −1.573 4.107 −0.38 0.7046 main_effect
Calcium Cycling chaA Yes K07300 −6.827 4.103 −1.66 0.1073 main_effect
mgtC Yes K07507 6.382 4.587 1.39 0.1751 main_effect
phaC No K03821 1.175 4.813 0.24 0.8090 main_effect
ureC Yes K01428 −4.954 2.562 −1.93 0.0634 main_effect
Carbon Fixation ccmK No Calvin–Benson–Bassham (CBB) Cycle K08696 −0.092 0.138 −0.67 0.5111 main_effect
ccmL No Calvin–Benson–Bassham (CBB) Cycle K08697 1.672 0.450 3.72 0.0010 interaction
ccmL No Calvin–Benson–Bassham (CBB) Cycle K08697 −0.072 0.098 −0.74 0.4741 by_group_JB1_JB2
ccmL No Calvin–Benson–Bassham (CBB) Cycle K08697 1.600 0.548 2.92 0.0128 by_group_JB5_JB6_JB7
codH Yes Wood–Ljungdahl (WL) pathway K00192 0.011 0.095 0.11 0.9125 main_effect
korA Yes Reductive TCA (rTCA) cycle K00174 −2.927 1.997 −1.47 0.1539 main_effect
korB Yes Reductive TCA (rTCA) cycle K00175 8.387 2.889 2.90 0.0071 main_effect
prk Yes Calvin–Benson–Bassham (CBB) Cycle K00855 1.390 0.675 2.06 0.0489 main_effect
rbcL Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01601 13.327 5.135 2.60 0.0153 interaction
rbcL Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01601 −1.256 1.788 −0.70 0.4941 by_group_JB1_JB2
rbcL Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01601 12.072 4.567 2.64 0.0214 by_group_JB5_JB6_JB7
rbcS Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01602 2.446 4.921 0.50 0.6230 main_effect
frdA No Reductive TCA (rTCA) cycle K00244 −0.404 0.554 −0.73 0.4724 main_effect
mcl No 3HP bicycle K08691 0.046 0.871 0.05 0.9579 main_effect
Chloride Cycling clcA Yes K03281 22.645 6.228 3.64 0.0011 main_effect
clcB Yes K03281 22.645 6.228 3.64 0.0011 main_effect
clcN Yes K05011 −0.036 0.064 −0.56 0.5819 main_effect
gltT No K11102 4.502 1.651 2.73 0.0109 main_effect
kefC No K11745 −0.555 0.257 −2.16 0.0393 main_effect
Copper Cycling copA Yes K17686 −2.396 3.878 −0.62 0.5416 main_effect
copB Yes K01533 3.286 2.158 1.52 0.1390 main_effect
ctrA Yes K13584 11.860 5.674 2.09 0.0458 main_effect
cueO No K14588 0.832 0.411 2.02 0.0527 main_effect
cusA Yes K07787 18.762 6.108 3.07 0.0049 interaction
cusA Yes K07787 3.407 2.237 1.52 0.1500 by_group_JB1_JB2
cusA Yes K07787 22.169 5.001 4.43 0.0008 by_group_JB5_JB6_JB7
cusB No K07798 23.094 6.428 3.59 0.0013 interaction
cusB No K07798 3.661 2.387 1.53 0.1474 by_group_JB1_JB2
cusB No K07798 26.755 5.124 5.22 0.0002 by_group_JB5_JB6_JB7
Hormone Production acdS Yes Ethylene K01505 −2.069 2.276 −0.91 0.3711 main_effect
aldA Yes IAA K07248 −0.692 0.329 −2.11 0.0443 main_effect
aldH No IAA K00128 −41.042 14.279 −2.87 0.0080 interaction
aldH No IAA K00128 −1.614 5.780 −0.28 0.7841 by_group_JB1_JB2
aldH No IAA K00128 −42.656 8.944 −4.77 0.0005 by_group_JB5_JB6_JB7
amiE Yes IAA K01426 −3.648 2.808 −1.30 0.2045 main_effect
aspC Yes IAA K00813 −0.254 0.285 −0.89 0.3810 main_effect
entC No GA K02361 −0.057 0.158 −0.36 0.7198 main_effect
etfA No Ethylene K03522 14.443 6.987 2.07 0.0481 main_effect
iaaH No IAA K21801 −0.211 0.365 −0.58 0.5676 main_effect
iaaM No IAA K00466 −0.560 0.365 −1.53 0.1362 main_effect
ipdC Yes IAA K04103 0.038 0.102 0.38 0.7094 main_effect
ipt Yes CK K00375 −1.775 3.515 −0.50 0.6176 main_effect
miaA No CK K00791 6.977 8.064 0.87 0.3943 main_effect
nitA No IAA K01501 1.356 0.464 2.92 0.0068 main_effect
tnaA No IAA K01667 0.964 1.053 0.92 0.3675 main_effect
Iron Cycling bfr No K03594 −2.451 3.480 −0.70 0.4871 main_effect
dps No K04047 −28.483 11.971 −2.38 0.0250 interaction
dps No K04047 0.116 3.984 0.03 0.9771 by_group_JB1_JB2
dps No K04047 −28.367 11.290 −2.51 0.0273 by_group_JB5_JB6_JB7
entC Yes K02361 −0.057 0.158 −0.36 0.7198 main_effect
feoB Yes K04759 −0.645 0.935 −0.69 0.4959 main_effect
fur No K03711 −29.096 12.189 −2.39 0.0245 interaction
fur No K03711 3.946 3.654 1.08 0.2985 by_group_JB1_JB2
fur No K03711 −25.150 12.697 −1.98 0.0710 by_group_JB5_JB6_JB7
iscA No K13628 −46.349 19.036 −2.43 0.0221 interaction
iscA No K13628 9.299 7.478 1.24 0.2341 by_group_JB1_JB2
iscA No K13628 −37.050 13.214 −2.80 0.0159 by_group_JB5_JB6_JB7
sufB Yes K09014 −1.721 2.485 −0.69 0.4944 main_effect
sufC No K09013 1.343 3.064 0.44 0.6645 main_effect
yqjH No K07229 −0.026 0.046 −0.56 0.5819 main_effect
Magnesium Cycling corA Yes K03284 −26.610 15.230 −1.75 0.0915 main_effect
mgtA Yes K01531 25.986 5.214 4.98 0.0000 main_effect
mgtB No K01531 25.986 5.214 4.98 0.0000 main_effect
mgtE Yes K06213 0.330 3.096 0.11 0.9158 main_effect
phoQ No K07637 −0.474 0.446 −1.06 0.2963 main_effect
Manganese Cycling mntA Yes K06147 10.880 13.256 0.82 0.4187 main_effect
mntB Yes K06148 −1.158 0.917 −1.26 0.2171 main_effect
mntC Yes K06149 −0.212 0.302 −0.70 0.4889 main_effect
mntH Yes K03322 9.297 5.037 1.85 0.0755 main_effect
mntR No K03709 −1.401 2.841 −0.49 0.6257 main_effect
mntR No K11924 −0.049 0.451 −0.11 0.9142 main_effect
sitA Yes K11604 −0.648 0.356 −1.82 0.0798 main_effect
sodA No K04564 −0.726 6.348 −0.11 0.9098 main_effect
Nitrogen fixation amt No K03320 25.584 7.381 3.47 0.0017 main_effect
glnB No K04751 28.617 7.369 3.88 0.0006 main_effect
iscS No K04487 8.654 6.022 1.44 0.1618 main_effect
moeA No K03750 2.718 3.630 0.75 0.4603 main_effect
nifA No K02584 −1.009 0.655 −1.54 0.1347 main_effect
nifB Yes K02585 0.847 0.430 1.97 0.0586 main_effect
nifD Yes K02586 5.015 1.222 4.10 0.0004 interaction
nifD Yes K02586 0.553 0.307 1.80 0.0929 by_group_JB1_JB2
nifD Yes K02586 5.569 1.412 3.94 0.0020 by_group_JB5_JB6_JB7
nifE Yes K02587 6.396 2.075 3.08 0.0048 interaction
nifE Yes K02587 0.857 0.587 1.46 0.1666 by_group_JB1_JB2
nifE Yes K02587 7.253 2.251 3.22 0.0073 by_group_JB5_JB6_JB7
nifH Yes K02588 0.009 0.086 0.11 0.9125 main_effect
nifK Yes K02591 7.411 2.182 3.40 0.0022 interaction
nifK Yes K02591 0.701 0.611 1.15 0.2707 by_group_JB1_JB2
nifK Yes K02591 8.112 2.382 3.40 0.0052 by_group_JB5_JB6_JB7
nifM Yes K03769 2.695 2.564 1.05 0.3022 main_effect
nifN Yes K02592 0.232 0.141 1.65 0.1093 main_effect
nifQ No K15790 0.333 0.050 6.62 0.0000 interaction
nifQ No K15790 0.000 0.000 NaN NaN by_group_JB1_JB2
nifQ No K15790 0.333 0.070 4.77 0.0005 by_group_JB5_JB6_JB7
nifU Yes K04488 1.726 4.118 0.42 0.6782 main_effect
nifV Yes K02594 2.233 0.917 2.43 0.0221 interaction
nifV Yes K02594 0.269 0.342 0.79 0.4447 by_group_JB1_JB2
nifV Yes K02594 2.502 0.725 3.45 0.0048 by_group_JB5_JB6_JB7
nifW No K02595 0.022 0.089 0.25 0.8019 main_effect
nifX No K02596 4.054 0.896 4.52 0.0001 interaction
nifX No K02596 −0.014 0.022 −0.66 0.5221 by_group_JB1_JB2
nifX No K02596 4.039 1.242 3.25 0.0069 by_group_JB5_JB6_JB7
nifZ No K02597 0.026 0.143 0.18 0.8558 main_effect
Nitrogen Release amoA Yes K10944 −0.285 0.283 −1.01 0.3222 main_effect
amoB Yes K10945 −1.004 0.291 −3.45 0.0018 main_effect
amoC Yes K10946 −4.982 3.458 −1.44 0.1607 main_effect
gdh No K15371 −2.379 1.682 −1.41 0.1683 main_effect
napA No K02567 −0.101 0.599 −0.17 0.8670 main_effect
napA Yes K01416 0.197 0.204 0.97 0.3428 main_effect
napB No K02568 −0.523 0.406 −1.29 0.2082 main_effect
narG Yes K00370 0.498 1.569 0.32 0.7533 main_effect
narH Yes K00371 2.150 1.233 1.74 0.0921 main_effect
narI No K00374 0.217 1.675 0.13 0.8977 main_effect
nasA Yes K00372 −8.294 2.216 −3.74 0.0008 main_effect
nasB Yes K00360 −0.217 0.195 −1.11 0.2745 main_effect
nirA Yes K00366 2.242 1.289 1.74 0.0931 main_effect
nirK Yes K00368 2.206 1.178 1.87 0.0717 main_effect
nirS Yes K15864 −0.019 0.071 −0.26 0.7942 main_effect
norB Yes K04561 1.270 1.312 0.97 0.3414 main_effect
norC No K02305 −3.595 1.279 −2.81 0.0089 main_effect
nosZ Yes K00376 −0.515 1.251 −0.41 0.6838 main_effect
nrfA Yes K03385 0.882 1.798 0.49 0.6276 main_effect
ureC No K01428 −4.954 2.562 −1.93 0.0634 main_effect
Nodulation nodA Yes K14658 −0.016 0.029 −0.56 0.5819 main_effect
nodD Yes K14657 0.212 0.205 1.03 0.3106 main_effect
nodI No ABC transporter complex K09694 −12.277 8.140 −1.51 0.1427 main_effect
Phosphorus Solubilization gcd Yes K00117 −4.830 4.025 −1.20 0.2402 main_effect
phnX No K06163 −0.013 0.827 −0.02 0.9876 main_effect
phoA Yes K01077 −6.761 3.055 −2.21 0.0359 interaction
phoA Yes K01077 −2.499 1.012 −2.47 0.0270 by_group_JB1_JB2
phoA Yes K01077 −9.259 2.897 −3.20 0.0077 by_group_JB5_JB6_JB7
phoD No K01113 −13.426 4.232 −3.17 0.0036 main_effect
phoX No K07093 −6.766 2.881 −2.35 0.0261 main_effect
ppk No K00937 −1.048 5.222 −0.20 0.8423 main_effect
ppx No K01514 −0.119 0.178 −0.67 0.5097 main_effect
pqqB Yes K06136 2.325 2.872 0.81 0.4250 main_effect
pqqC Yes K06137 7.165 2.407 2.98 0.0059 main_effect
pqqD Yes K06138 4.989 2.825 1.77 0.0883 main_effect
pqqE Yes K06139 2.175 1.419 1.53 0.1365 main_effect
Potassium Solubilization gcd Yes K00117 −4.830 4.025 −1.20 0.2402 main_effect
kdsA No K01627 3.306 2.741 1.21 0.2378 main_effect
kdsB No K00979 15.792 5.310 2.97 0.0060 main_effect
kup Yes K03549 −2.095 5.729 −0.37 0.7173 main_effect
nhaA No K03313 −20.860 5.509 −3.79 0.0007 main_effect
pqqB Yes K06136 2.325 2.872 0.81 0.4250 main_effect
pqqC Yes K06137 7.165 2.407 2.98 0.0059 main_effect
pqqD Yes K06138 4.989 2.825 1.77 0.0883 main_effect
pqqE Yes K06139 2.175 1.419 1.53 0.1365 main_effect
trkA Yes K03499 4.685 6.722 0.70 0.4916 main_effect
trkH Yes K03498 −2.888 1.379 −2.09 0.0453 main_effect
Stress Adaptation copA Yes Heavy Metal Tolerance K17686 −2.396 3.878 −0.62 0.5416 main_effect
ectB Yes Salt tolerance K00836 −0.472 0.535 −0.88 0.3854 main_effect
entC Yes Siderophore production K02361 −0.057 0.158 −0.36 0.7198 main_effect
glnA No ACC deaminase (ACC-d) K01915 −23.761 10.272 −2.31 0.0283 main_effect
kdsA Yes Exopolysaccharide production K01627 3.306 2.741 1.21 0.2378 main_effect
kdsB No Exopolysaccharide production K00979 15.792 5.310 2.97 0.0060 main_effect
pchA Yes Salicylic acid (SA) K01851 0.167 0.160 1.05 0.3049 main_effect
pchB No Salicylic acid (SA) K04782 −0.442 0.915 −0.48 0.6326 main_effect
pqqB No Siderophore production K06136 2.325 2.872 0.81 0.4250 main_effect
Sulfur Cycling aprA Yes K00394 −0.050 0.221 −0.22 0.8238 main_effect
cysA Yes K02045 −21.576 8.114 −2.66 0.0128 main_effect
cysU Yes K02046 −2.028 0.891 −2.28 0.0306 main_effect
cysW Yes K02047 −2.289 2.601 −0.88 0.3863 main_effect
fccB Yes K17229 −0.283 0.178 −1.59 0.1227 main_effect
sat Yes K00958 0.990 2.412 0.41 0.6845 main_effect
soxA No K17222 0.023 2.744 0.01 0.9933 main_effect
soxB No K17224 1.263 0.680 1.86 0.0737 main_effect
soxC Yes K17225 36.484 16.500 2.21 0.0360 interaction
soxC Yes K17225 −2.217 5.113 −0.43 0.6712 by_group_JB1_JB2
soxC Yes K17225 34.267 16.725 2.05 0.0630 by_group_JB5_JB6_JB7
soxD Yes K22622 0.447 1.613 0.28 0.7838 main_effect
soxX No K17223 1.352 1.862 0.73 0.4736 main_effect
soxY Yes K17226 2.932 2.693 1.09 0.2857 main_effect
soxZ Yes K17227 1.953 1.990 0.98 0.3347 main_effect
Zinc Cycling mntR No K03709 −1.401 2.841 −0.49 0.6257 main_effect
troA No K11707 −1.479 0.870 −1.70 0.1004 main_effect
zitB No K16264 5.006 3.921 1.28 0.2123 main_effect
zntA No K01534 0.098 1.243 0.08 0.9375 main_effect
znuA Yes K09815 −3.498 1.728 −2.02 0.0526 main_effect
znuB Yes K09816 −3.560 3.790 −0.94 0.3556 main_effect
znuC Yes K09817 −1.603 2.274 −0.70 0.4869 main_effect
zur No K02076 1.184 0.878 1.35 0.1884 main_effect

Table 15: Summary statistics for each gene. The table shows the summary statistics for the analysis of the metadata variable and each gene (KO gene cluster) organised by section. The table gives estimate, standard error, t-value, p-value and model. “Model” informs which model the summary statistics represents: “main_effect” originate from analysis where all fields are analyzed together. This happens when we have tested for effects of JB and not found any significant difference between JB groups. “Interaction” gives results for the interaction analysis and is included only when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.

Field keep water

Section Gene Essential Cagetory KO.ID Estimate SE t p-value Model
Antibiotic Production bacB Yes Bacilysin K19547 −4.230 1.074 −3.94 0.0005 interaction
bacB Yes Bacilysin K19547 0.000 0.000 NaN NaN by_group_JB1_JB2
bacB Yes Bacilysin K19547 −4.230 1.319 −3.21 0.0075 by_group_JB5_JB6_JB7
bacC Yes Bacilysin K19548 −1.809 0.768 −2.35 0.0258 main_effect
E4.1.1.82 Yes Fosfomycin K09459 −12.917 10.356 −1.25 0.2226 main_effect
eryA Yes Macrolides K00862 2.386 6.481 0.37 0.7155 main_effect
penM No Pentalenolactone K17476 −9.370 2.388 −3.92 0.0006 interaction
penM No Pentalenolactone K17476 1.896 1.433 1.32 0.2071 by_group_JB1_JB2
penM No Pentalenolactone K17476 −7.474 1.763 −4.24 0.0011 by_group_JB5_JB6_JB7
pntE Yes Pentalenolactone K18091 0.149 3.336 0.04 0.9648 main_effect
pntH Yes Pentalenolactone K18056 0.381 0.588 0.65 0.5222 main_effect
ptlF Yes Pentalenolactone K17747 0.490 0.757 0.65 0.5222 main_effect
rifG Yes Rifamycin K16020 4.200 2.517 1.67 0.1063 main_effect
strA Yes Streptomycin K00547 −15.093 18.917 −0.80 0.4317 main_effect
Antibiotic Resistance vanA Yes Vancomycin K15739 −6.218 2.904 −2.14 0.0411 main_effect
vanH Yes Vancomycin K18347 −2.876 3.252 −0.88 0.3841 main_effect
vanX Yes Vancomycin K08641 −29.585 35.679 −0.83 0.4140 main_effect
Biocontrol chiA Yes Fungicidal agents K06904 22.241 27.178 0.82 0.4201 main_effect
chiB No Fungicidal agents, Insecticide agents K20547 1.312 1.540 0.85 0.4015 main_effect
dapB No Bactericidal agents K00215 −50.555 122.302 −0.41 0.6825 main_effect
phzF Yes Fungicidal agents, Bactericidal agents K06998 −4.242 26.977 −0.16 0.8762 main_effect
prnA Yes Fungicidal agents K14266 −9.353 12.004 −0.78 0.4424 main_effect
prnC Yes Fungicidal agents K14257 −3.591 7.556 −0.48 0.6382 main_effect
tcaB Yes Insecticide agents K07552 −120.600 62.361 −1.93 0.0633 main_effect
Calcium Cycling chaA Yes K07300 298.375 137.846 2.16 0.0398 interaction
chaA Yes K07300 −161.340 81.873 −1.97 0.0689 by_group_JB1_JB2
chaA Yes K07300 137.035 103.537 1.32 0.2103 by_group_JB5_JB6_JB7
mgtC Yes K07507 −452.949 133.034 −3.40 0.0022 interaction
mgtC Yes K07507 113.961 82.976 1.37 0.1912 by_group_JB1_JB2
mgtC Yes K07507 −338.988 90.913 −3.73 0.0029 by_group_JB5_JB6_JB7
phaC No K03821 313.339 144.157 2.17 0.0390 interaction
phaC No K03821 15.353 83.047 0.18 0.8560 by_group_JB1_JB2
phaC No K03821 328.692 113.525 2.90 0.0134 by_group_JB5_JB6_JB7
ureC Yes K01428 −33.177 43.542 −0.76 0.4525 main_effect
Carbon Fixation ccmK No Calvin–Benson–Bassham (CBB) Cycle K08696 −1.623 2.227 −0.73 0.4721 main_effect
ccmL No Calvin–Benson–Bassham (CBB) Cycle K08697 1.673 2.753 0.61 0.5481 main_effect
codH Yes Wood–Ljungdahl (WL) pathway K00192 0.984 1.518 0.65 0.5222 main_effect
korA Yes Reductive TCA (rTCA) cycle K00174 −5.346 33.399 −0.16 0.8740 main_effect
korB Yes Reductive TCA (rTCA) cycle K00175 −48.157 52.356 −0.92 0.3655 main_effect
prk Yes Calvin–Benson–Bassham (CBB) Cycle K00855 −9.511 11.543 −0.82 0.4169 main_effect
rbcL Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01601 46.987 25.549 1.84 0.0765 main_effect
rbcS Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01602 −629.282 136.257 −4.62 0.0001 interaction
rbcS Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01602 90.219 35.793 2.52 0.0245 by_group_JB1_JB2
rbcS Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01602 −539.063 156.817 −3.44 0.0049 by_group_JB5_JB6_JB7
frdA No Reductive TCA (rTCA) cycle K00244 9.409 8.848 1.06 0.2967 main_effect
mcl No 3HP bicycle K08691 −9.056 13.938 −0.65 0.5211 main_effect
Chloride Cycling clcA Yes K03281 −588.485 226.800 −2.59 0.0154 interaction
clcA Yes K03281 287.778 147.305 1.95 0.0710 by_group_JB1_JB2
clcA Yes K03281 −300.707 139.637 −2.15 0.0523 by_group_JB5_JB6_JB7
clcB Yes K03281 −588.485 226.800 −2.59 0.0154 interaction
clcB Yes K03281 287.778 147.305 1.95 0.0710 by_group_JB1_JB2
clcB Yes K03281 −300.707 139.637 −2.15 0.0523 by_group_JB5_JB6_JB7
clcN Yes K05011 0.665 1.026 0.65 0.5222 main_effect
gltT No K11102 48.445 28.516 1.70 0.1004 main_effect
kefC No K11745 −0.141 4.470 −0.03 0.9751 main_effect
Copper Cycling copA Yes K17686 0.267 62.961 0.00 0.9966 main_effect
copB Yes K01533 15.743 36.083 0.44 0.6660 main_effect
ctrA Yes K13584 2.412 98.381 0.02 0.9806 main_effect
cueO No K14588 −1.006 7.097 −0.14 0.8883 main_effect
cusA Yes K07787 49.097 35.824 1.37 0.1814 main_effect
cusB No K07798 33.376 40.540 0.82 0.4173 main_effect
Hormone Production acdS Yes Ethylene K01505 −7.070 37.218 −0.19 0.8507 main_effect
aldA Yes IAA K07248 −0.360 5.702 −0.06 0.9502 main_effect
aldH No IAA K00128 −203.327 86.062 −2.36 0.0253 main_effect
amiE Yes IAA K01426 −16.477 46.514 −0.35 0.7258 main_effect
aspC Yes IAA K00813 −7.392 4.449 −1.66 0.1078 main_effect
entC No GA K02361 −15.350 4.751 −3.23 0.0033 interaction
entC No GA K02361 −0.811 2.771 −0.29 0.7740 by_group_JB1_JB2
entC No GA K02361 −16.161 3.674 −4.40 0.0009 by_group_JB5_JB6_JB7
etfA No Ethylene K03522 −10.856 120.947 −0.09 0.9291 main_effect
iaaH No IAA K21801 −29.856 10.742 −2.78 0.0100 interaction
iaaH No IAA K21801 25.508 6.846 3.73 0.0023 by_group_JB1_JB2
iaaH No IAA K21801 −4.348 6.970 −0.62 0.5444 by_group_JB5_JB6_JB7
iaaM No IAA K00466 −0.651 6.123 −0.11 0.9161 main_effect
ipdC Yes IAA K04103 −0.620 1.637 −0.38 0.7079 main_effect
ipt Yes CK K00375 −90.364 54.315 −1.66 0.1073 main_effect
miaA No CK K00791 −733.069 238.136 −3.08 0.0049 interaction
miaA No CK K00791 200.552 139.367 1.44 0.1721 by_group_JB1_JB2
miaA No CK K00791 −532.517 183.173 −2.91 0.0131 by_group_JB5_JB6_JB7
nitA No IAA K01501 7.843 8.423 0.93 0.3597 main_effect
tnaA No IAA K01667 15.704 16.971 0.93 0.3627 main_effect
Iron Cycling bfr No K03594 −94.162 53.739 −1.75 0.0907 main_effect
dps No K04047 −74.750 60.884 −1.23 0.2298 main_effect
entC Yes K02361 −15.350 4.751 −3.23 0.0033 interaction
entC Yes K02361 −0.811 2.771 −0.29 0.7740 by_group_JB1_JB2
entC Yes K02361 −16.161 3.674 −4.40 0.0009 by_group_JB5_JB6_JB7
feoB Yes K04759 −10.732 15.062 −0.71 0.4820 main_effect
fur No K03711 −193.480 56.513 −3.42 0.0019 main_effect
iscA No K13628 −7.646 106.735 −0.07 0.9434 main_effect
sufB Yes K09014 −108.190 34.863 −3.10 0.0043 main_effect
sufC No K09013 61.136 48.207 1.27 0.2152 main_effect
yqjH No K07229 −5.080 1.289 −3.94 0.0005 interaction
yqjH No K07229 0.000 0.000 NaN NaN by_group_JB1_JB2
yqjH No K07229 −5.080 1.584 −3.21 0.0075 by_group_JB5_JB6_JB7
Magnesium Cycling corA Yes K03284 −104.316 257.872 −0.40 0.6889 main_effect
mgtA Yes K01531 127.802 112.940 1.13 0.2674 main_effect
mgtB No K01531 127.802 112.940 1.13 0.2674 main_effect
mgtE Yes K06213 −104.370 45.873 −2.28 0.0307 main_effect
phoQ No K07637 −20.873 6.179 −3.38 0.0022 main_effect
Manganese Cycling mntA Yes K06147 −1,216.413 369.662 −3.29 0.0029 interaction
mntA Yes K06147 171.289 218.799 0.78 0.4467 by_group_JB1_JB2
mntA Yes K06147 −1,045.123 279.258 −3.74 0.0028 by_group_JB5_JB6_JB7
mntB Yes K06148 −1.555 15.200 −0.10 0.9192 main_effect
mntC Yes K06149 1.593 4.903 0.32 0.7477 main_effect
mntH Yes K03322 −382.088 151.572 −2.52 0.0182 interaction
mntH Yes K03322 152.988 101.892 1.50 0.1554 by_group_JB1_JB2
mntH Yes K03322 −229.100 82.815 −2.77 0.0171 by_group_JB5_JB6_JB7
mntR No K03709 −23.793 45.786 −0.52 0.6074 main_effect
mntR No K11924 −49.055 12.756 −3.85 0.0007 interaction
mntR No K11924 0.056 5.514 0.01 0.9920 by_group_JB1_JB2
mntR No K11924 −48.999 12.812 −3.82 0.0024 by_group_JB5_JB6_JB7
sitA Yes K11604 0.637 6.076 0.10 0.9172 main_effect
sodA No K04564 39.736 102.112 0.39 0.7001 main_effect
Nitrogen fixation amt No K03320 −589.418 253.780 −2.32 0.0283 interaction
amt No K03320 452.763 150.325 3.01 0.0093 by_group_JB1_JB2
amt No K03320 −136.656 191.474 −0.71 0.4891 by_group_JB5_JB6_JB7
glnB No K04751 83.954 146.543 0.57 0.5713 main_effect
iscS No K04487 −415.234 199.175 −2.08 0.0471 interaction
iscS No K04487 79.408 125.354 0.63 0.5366 by_group_JB1_JB2
iscS No K04487 −335.826 133.320 −2.52 0.0270 by_group_JB5_JB6_JB7
moeA No K03750 −16.721 59.027 −0.28 0.7790 main_effect
nifA No K02584 −1.056 11.000 −0.10 0.9242 main_effect
nifB Yes K02585 9.357 7.177 1.30 0.2030 main_effect
nifD Yes K02586 15.831 8.245 1.92 0.0651 main_effect
nifE Yes K02587 18.749 12.468 1.50 0.1438 main_effect
nifH Yes K02588 0.888 1.370 0.65 0.5222 main_effect
nifK Yes K02591 23.354 13.435 1.74 0.0931 main_effect
nifM Yes K03769 −1.126 42.149 −0.03 0.9789 main_effect
nifN Yes K02592 2.170 2.339 0.93 0.3615 main_effect
nifQ No K15790 0.263 0.406 0.65 0.5222 main_effect
nifU Yes K04488 −118.936 62.706 −1.90 0.0682 main_effect
nifV Yes K02594 4.516 4.943 0.91 0.3687 main_effect
nifW No K02595 1.936 1.385 1.40 0.1731 main_effect
nifX No K02596 6.315 5.972 1.06 0.2993 main_effect
nifZ No K02597 3.246 2.222 1.46 0.1552 main_effect
Nitrogen Release amoA Yes K10944 −8.208 4.376 −1.88 0.0711 main_effect
amoB Yes K10945 −6.662 5.460 −1.22 0.2326 main_effect
amoC Yes K10946 112.783 53.711 2.10 0.0449 main_effect
gdh No K15371 0.641 28.078 0.02 0.9819 main_effect
napA No K02567 9.251 9.498 0.97 0.3384 main_effect
napA Yes K01416 16.471 7.177 2.29 0.0301 interaction
napA Yes K01416 −7.887 3.710 −2.13 0.0518 by_group_JB1_JB2
napA Yes K01416 8.584 6.393 1.34 0.2042 by_group_JB5_JB6_JB7
napB No K02568 −0.281 6.742 −0.04 0.9671 main_effect
narG Yes K00370 −37.544 24.326 −1.54 0.1340 main_effect
narH Yes K00371 −13.219 20.779 −0.64 0.5298 main_effect
narI No K00374 −12.665 26.911 −0.47 0.6416 main_effect
nasA Yes K00372 −10.136 43.723 −0.23 0.8184 main_effect
nasB Yes K00360 −0.455 3.208 −0.14 0.8882 main_effect
nirA Yes K00366 4.650 21.869 0.21 0.8332 main_effect
nirK Yes K00368 −59.692 16.703 −3.57 0.0013 main_effect
nirS Yes K15864 1.048 1.122 0.93 0.3584 main_effect
norB Yes K04561 −7.155 21.466 −0.33 0.7414 main_effect
norC No K02305 163.764 43.122 3.80 0.0008 interaction
norC No K02305 −71.227 25.036 −2.84 0.0130 by_group_JB1_JB2
norC No K02305 92.537 33.574 2.76 0.0174 by_group_JB5_JB6_JB7
nosZ Yes K00376 −20.257 19.875 −1.02 0.3168 main_effect
nrfA Yes K03385 40.858 28.083 1.45 0.1568 main_effect
ureC No K01428 −33.177 43.542 −0.76 0.4525 main_effect
Nodulation nodA Yes K14658 −3.175 0.806 −3.94 0.0005 interaction
nodA Yes K14658 0.000 0.000 NaN NaN by_group_JB1_JB2
nodA Yes K14658 −3.175 0.990 −3.21 0.0075 by_group_JB5_JB6_JB7
nodD Yes K14657 14.612 7.106 2.06 0.0499 interaction
nodD Yes K14657 −9.351 3.987 −2.35 0.0343 by_group_JB1_JB2
nodD Yes K14657 5.261 5.799 0.91 0.3822 by_group_JB5_JB6_JB7
nodI No ABC transporter complex K09694 10.932 136.476 0.08 0.9367 main_effect
Phosphorus Solubilization gcd Yes K00117 16.964 66.478 0.26 0.8004 main_effect
phnX No K06163 −11.103 13.172 −0.84 0.4064 main_effect
phoA Yes K01077 −16.246 18.018 −0.90 0.3749 main_effect
phoD No K01113 −203.962 69.610 −2.93 0.0067 main_effect
phoX No K07093 258.889 97.219 2.66 0.0131 interaction
phoX No K07093 −101.510 44.041 −2.30 0.0370 by_group_JB1_JB2
phoX No K07093 157.379 95.234 1.65 0.1243 by_group_JB5_JB6_JB7
ppk No K00937 4.777 84.255 0.06 0.9552 main_effect
ppx No K01514 2.224 2.860 0.78 0.4434 main_effect
pqqB Yes K06136 −6.720 46.836 −0.14 0.8869 main_effect
pqqC Yes K06137 −37.399 43.964 −0.85 0.4022 main_effect
pqqD Yes K06138 −2.241 48.019 −0.05 0.9631 main_effect
pqqE Yes K06139 −16.253 23.626 −0.69 0.4972 main_effect
Potassium Solubilization gcd Yes K00117 16.964 66.478 0.26 0.8004 main_effect
kdsA No K01627 −22.860 45.120 −0.51 0.6164 main_effect
kdsB No K00979 −47.662 97.814 −0.49 0.6299 main_effect
kup Yes K03549 100.969 90.620 1.11 0.2747 main_effect
nhaA No K03313 −98.470 107.641 −0.91 0.3681 main_effect
pqqB Yes K06136 −6.720 46.836 −0.14 0.8869 main_effect
pqqC Yes K06137 −37.399 43.964 −0.85 0.4022 main_effect
pqqD Yes K06138 −2.241 48.019 −0.05 0.9631 main_effect
pqqE Yes K06139 −16.253 23.626 −0.69 0.4972 main_effect
trkA Yes K03499 −62.539 108.687 −0.58 0.5696 main_effect
trkH Yes K03498 3.079 23.903 0.13 0.8984 main_effect
Stress Adaptation copA Yes Heavy Metal Tolerance K17686 0.267 62.961 0.00 0.9966 main_effect
ectB Yes Salt tolerance K00836 −16.474 8.176 −2.01 0.0536 main_effect
entC Yes Siderophore production K02361 −15.350 4.751 −3.23 0.0033 interaction
entC Yes Siderophore production K02361 −0.811 2.771 −0.29 0.7740 by_group_JB1_JB2
entC Yes Siderophore production K02361 −16.161 3.674 −4.40 0.0009 by_group_JB5_JB6_JB7
glnA No ACC deaminase (ACC-d) K01915 −221.364 175.866 −1.26 0.2185 main_effect
kdsA Yes Exopolysaccharide production K01627 −22.860 45.120 −0.51 0.6164 main_effect
kdsB No Exopolysaccharide production K00979 −47.662 97.814 −0.49 0.6299 main_effect
pchA Yes Salicylic acid (SA) K01851 −3.107 2.561 −1.21 0.2352 main_effect
pchB No Salicylic acid (SA) K04782 −11.140 14.663 −0.76 0.4538 main_effect
pqqB No Siderophore production K06136 −6.720 46.836 −0.14 0.8869 main_effect
Sulfur Cycling aprA Yes K00394 −2.816 3.526 −0.80 0.4313 main_effect
cysA Yes K02045 −16.476 146.393 −0.11 0.9112 main_effect
cysU Yes K02046 −1.028 15.636 −0.07 0.9481 main_effect
cysW Yes K02047 1.982 42.511 0.05 0.9631 main_effect
fccB Yes K17229 −3.496 2.925 −1.20 0.2420 main_effect
sat Yes K00958 −41.316 38.226 −1.08 0.2890 main_effect
soxA No K17222 4.578 44.233 0.10 0.9183 main_effect
soxB No K17224 −4.554 11.583 −0.39 0.6972 main_effect
soxC Yes K17225 376.383 180.762 2.08 0.0473 interaction
soxC Yes K17225 −3.271 94.949 −0.03 0.9730 by_group_JB1_JB2
soxC Yes K17225 373.112 158.631 2.35 0.0366 by_group_JB5_JB6_JB7
soxD Yes K22622 24.745 25.626 0.97 0.3425 main_effect
soxX No K17223 9.646 30.248 0.32 0.7522 main_effect
soxY Yes K17226 30.176 43.973 0.69 0.4982 main_effect
soxZ Yes K17227 −27.874 32.208 −0.87 0.3942 main_effect
Zinc Cycling mntR No K03709 −23.793 45.786 −0.52 0.6074 main_effect
troA No K11707 −5.062 14.710 −0.34 0.7333 main_effect
zitB No K16264 −63.119 63.944 −0.99 0.3320 main_effect
zntA No K01534 −21.126 19.637 −1.08 0.2912 main_effect
znuA Yes K09815 2.257 29.830 0.08 0.9402 main_effect
znuB Yes K09816 333.319 115.471 2.89 0.0077 interaction
znuB Yes K09816 −108.940 55.803 −1.95 0.0712 by_group_JB1_JB2
znuB Yes K09816 224.379 108.546 2.07 0.0610 by_group_JB5_JB6_JB7
znuC Yes K09817 −26.188 36.666 −0.71 0.4810 main_effect
zur No K02076 −24.552 13.854 −1.77 0.0873 main_effect

Table 16: Summary statistics for each gene. The table shows the summary statistics for the analysis of the metadata variable and each gene (KO gene cluster) organised by section. The table gives estimate, standard error, t-value, p-value and model. “Model” informs which model the summary statistics represents: “main_effect” originate from analysis where all fields are analyzed together. This happens when we have tested for effects of JB and not found any significant difference between JB groups. “Interaction” gives results for the interaction analysis and is included only when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.

Grazed

Section Gene Essential Cagetory KO.ID Estimate SE t p-value Model
Antibiotic Production bacB Yes Bacilysin K19547 −0.445 0.590 −0.76 0.4564 main_effect
bacC Yes Bacilysin K19548 1.480 0.749 1.98 0.0581 main_effect
E4.1.1.82 Yes Fosfomycin K09459 0.278 10.118 0.03 0.9783 main_effect
eryA Yes Macrolides K00862 −4.099 6.129 −0.67 0.5091 main_effect
penM No Pentalenolactone K17476 1.669 1.178 1.42 0.1677 main_effect
pntE Yes Pentalenolactone K18091 0.009 3.173 0.00 0.9976 main_effect
pntH Yes Pentalenolactone K18056 −0.421 0.558 −0.76 0.4564 main_effect
ptlF Yes Pentalenolactone K17747 0.936 0.703 1.33 0.1937 main_effect
rifG Yes Rifamycin K16020 1.388 2.496 0.56 0.5827 main_effect
strA Yes Streptomycin K00547 11.634 18.059 0.64 0.5247 main_effect
Antibiotic Resistance vanA Yes Vancomycin K15739 −1.299 2.969 −0.44 0.6651 main_effect
vanH Yes Vancomycin K18347 −1.442 3.124 −0.46 0.6479 main_effect
vanX Yes Vancomycin K08641 −73.968 31.369 −2.36 0.0256 main_effect
Biocontrol chiA Yes Fungicidal agents K06904 0.877 26.151 0.03 0.9735 main_effect
chiB No Fungicidal agents, Insecticide agents K20547 −1.450 1.458 −0.99 0.3284 main_effect
dapB No Bactericidal agents K00215 120.310 114.420 1.05 0.3020 main_effect
phzF Yes Fungicidal agents, Bactericidal agents K06998 5.193 25.646 0.20 0.8410 main_effect
prnA Yes Fungicidal agents K14266 0.260 11.538 0.02 0.9822 main_effect
prnC Yes Fungicidal agents K14257 −29.004 13.904 −2.09 0.0469 interaction
prnC Yes Fungicidal agents K14257 13.019 9.535 1.37 0.1937 by_group_JB1_JB2
prnC Yes Fungicidal agents K14257 −15.985 10.166 −1.57 0.1418 by_group_JB5_JB6_JB7
tcaB Yes Insecticide agents K07552 −51.634 62.380 −0.83 0.4148 main_effect
Calcium Cycling chaA Yes K07300 87.092 63.860 1.36 0.1835 main_effect
mgtC Yes K07507 −71.896 71.443 −1.01 0.3229 main_effect
phaC No K03821 102.248 71.319 1.43 0.1627 main_effect
ureC Yes K01428 −29.980 41.448 −0.72 0.4755 main_effect
Carbon Fixation ccmK No Calvin–Benson–Bassham (CBB) Cycle K08696 0.979 2.129 0.46 0.6492 main_effect
ccmL No Calvin–Benson–Bassham (CBB) Cycle K08697 0.214 2.635 0.08 0.9358 main_effect
codH Yes Wood–Ljungdahl (WL) pathway K00192 −1.087 1.440 −0.76 0.4564 main_effect
korA Yes Reductive TCA (rTCA) cycle K00174 51.760 30.232 1.71 0.0979 main_effect
korB Yes Reductive TCA (rTCA) cycle K00175 21.220 50.375 0.42 0.6768 main_effect
prk Yes Calvin–Benson–Bassham (CBB) Cycle K00855 −10.334 10.936 −0.94 0.3528 main_effect
rbcL Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01601 −16.639 25.529 −0.65 0.5199 main_effect
rbcS Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01602 −46.543 75.287 −0.62 0.5414 main_effect
frdA No Reductive TCA (rTCA) cycle K00244 −11.636 8.296 −1.40 0.1717 main_effect
mcl No 3HP bicycle K08691 24.756 12.508 1.98 0.0577 main_effect
Chloride Cycling clcA Yes K03281 −98.190 114.385 −0.86 0.3980 main_effect
clcB Yes K03281 −98.190 114.385 −0.86 0.3980 main_effect
clcN Yes K05011 −0.735 0.973 −0.76 0.4564 main_effect
gltT No K11102 −1.521 28.479 −0.05 0.9578 main_effect
kefC No K11745 −8.783 3.914 −2.24 0.0329 main_effect
Copper Cycling copA Yes K17686 10.658 59.839 0.18 0.8599 main_effect
copB Yes K01533 50.418 33.085 1.52 0.1388 main_effect
ctrA Yes K13584 −177.509 87.335 −2.03 0.0517 main_effect
cueO No K14588 5.071 6.683 0.76 0.4543 main_effect
cusA Yes K07787 24.993 34.872 0.72 0.4795 main_effect
cusB No K07798 57.578 37.467 1.54 0.1356 main_effect
Hormone Production acdS Yes Ethylene K01505 −3.373 35.410 −0.10 0.9248 main_effect
aldA Yes IAA K07248 −9.020 5.148 −1.75 0.0907 main_effect
aldH No IAA K00128 −129.793 86.206 −1.51 0.1434 main_effect
amiE Yes IAA K01426 17.423 44.210 0.39 0.6965 main_effect
aspC Yes IAA K00813 −13.010 3.691 −3.52 0.0015 main_effect
entC No GA K02361 1.039 2.422 0.43 0.6713 main_effect
etfA No Ethylene K03522 280.859 102.054 2.75 0.0103 main_effect
iaaH No IAA K21801 −4.189 5.581 −0.75 0.4593 main_effect
iaaM No IAA K00466 −26.381 10.521 −2.51 0.0187 interaction
iaaM No IAA K00466 5.677 7.615 0.75 0.4683 by_group_JB1_JB2
iaaM No IAA K00466 −20.704 7.228 −2.86 0.0142 by_group_JB5_JB6_JB7
ipdC Yes IAA K04103 −2.069 1.511 −1.37 0.1816 main_effect
ipt Yes CK K00375 15.408 54.065 0.28 0.7777 main_effect
miaA No CK K00791 11.984 125.275 0.10 0.9245 main_effect
nitA No IAA K01501 −6.841 8.030 −0.85 0.4014 main_effect
tnaA No IAA K01667 30.139 15.361 1.96 0.0598 main_effect
Iron Cycling bfr No K03594 −79.526 51.692 −1.54 0.1352 main_effect
dps No K04047 22.327 59.286 0.38 0.7093 main_effect
entC Yes K02361 1.039 2.422 0.43 0.6713 main_effect
feoB Yes K04759 −13.502 14.225 −0.95 0.3506 main_effect
fur No K03711 12.068 63.968 0.19 0.8517 main_effect
iscA No K13628 −239.609 90.850 −2.64 0.0135 main_effect
sufB Yes K09014 9.827 38.389 0.26 0.7998 main_effect
sufC No K09013 −14.609 47.060 −0.31 0.7585 main_effect
yqjH No K07229 −0.535 0.708 −0.76 0.4564 main_effect
Magnesium Cycling corA Yes K03284 556.174 222.348 2.50 0.0185 main_effect
mgtA Yes K01531 −15.250 109.791 −0.14 0.8905 main_effect
mgtB No K01531 −15.250 109.791 −0.14 0.8905 main_effect
mgtE Yes K06213 −104.365 43.194 −2.42 0.0225 main_effect
phoQ No K07637 0.540 6.971 0.08 0.9388 main_effect
Manganese Cycling mntA Yes K06147 −115.266 204.541 −0.56 0.5776 main_effect
mntB Yes K06148 −9.700 14.340 −0.68 0.5043 main_effect
mntC Yes K06149 0.254 4.671 0.05 0.9570 main_effect
mntH Yes K03322 −166.219 75.526 −2.20 0.0362 main_effect
mntR No K03709 −51.878 42.637 −1.22 0.2339 main_effect
mntR No K11924 −4.567 6.867 −0.67 0.5114 main_effect
sitA Yes K11604 −2.538 5.759 −0.44 0.6629 main_effect
sodA No K04564 −54.468 96.820 −0.56 0.5782 main_effect
Nitrogen fixation amt No K03320 −72.490 134.615 −0.54 0.5945 main_effect
glnB No K04751 121.605 138.273 0.88 0.3866 main_effect
iscS No K04487 −177.463 89.613 −1.98 0.0576 main_effect
moeA No K03750 48.760 55.452 0.88 0.3867 main_effect
nifA No K02584 15.230 10.059 1.51 0.1412 main_effect
nifB Yes K02585 9.616 6.790 1.42 0.1678 main_effect
nifD Yes K02586 19.209 7.509 2.56 0.0162 main_effect
nifE Yes K02587 33.662 10.558 3.19 0.0035 main_effect
nifH Yes K02588 1.695 1.273 1.33 0.1937 main_effect
nifK Yes K02591 39.221 11.220 3.50 0.0016 main_effect
nifM Yes K03769 61.091 38.383 1.59 0.1227 main_effect
nifN Yes K02592 4.142 2.118 1.96 0.0605 main_effect
nifQ No K15790 0.502 0.377 1.33 0.1937 main_effect
nifU Yes K04488 36.509 62.969 0.58 0.5667 main_effect
nifV Yes K02594 9.363 4.430 2.11 0.0436 main_effect
nifW No K02595 −2.140 1.301 −1.65 0.1111 main_effect
nifX No K02596 11.579 5.362 2.16 0.0395 main_effect
nifZ No K02597 4.594 2.013 2.28 0.0302 main_effect
Nitrogen Release amoA Yes K10944 −3.562 4.363 −0.82 0.4212 main_effect
amoB Yes K10945 −12.939 4.734 −2.73 0.0108 main_effect
amoC Yes K10946 −36.874 54.507 −0.68 0.5043 main_effect
gdh No K15371 58.431 24.311 2.40 0.0231 main_effect
napA No K02567 12.897 8.855 1.46 0.1564 main_effect
napA Yes K01416 2.865 3.132 0.91 0.3682 main_effect
napB No K02568 6.644 6.287 1.06 0.2997 main_effect
narG Yes K00370 0.201 24.096 0.01 0.9934 main_effect
narH Yes K00371 50.012 17.515 2.86 0.0080 main_effect
narI No K00374 39.820 24.565 1.62 0.1162 main_effect
nasA Yes K00372 −16.814 41.497 −0.41 0.6884 main_effect
nasB Yes K00360 −6.557 2.788 −2.35 0.0260 main_effect
nirA Yes K00366 10.501 20.718 0.51 0.6162 main_effect
nirK Yes K00368 2.475 19.161 0.13 0.8981 main_effect
nirS Yes K15864 0.600 1.078 0.56 0.5822 main_effect
norB Yes K04561 −9.770 20.370 −0.48 0.6352 main_effect
norC No K02305 6.910 22.172 0.31 0.7576 main_effect
nosZ Yes K00376 −16.774 18.984 −0.88 0.3844 main_effect
nrfA Yes K03385 53.364 25.796 2.07 0.0479 main_effect
ureC No K01428 −29.980 41.448 −0.72 0.4755 main_effect
Nodulation nodA Yes K14658 −0.334 0.443 −0.76 0.4564 main_effect
nodD Yes K14657 −1.326 3.196 −0.41 0.6815 main_effect
nodI No ABC transporter complex K09694 278.761 118.625 2.35 0.0261 main_effect
Phosphorus Solubilization gcd Yes K00117 −49.682 62.591 −0.79 0.4340 main_effect
phnX No K06163 −14.232 12.395 −1.15 0.2606 main_effect
phoA Yes K01077 3.347 17.369 0.19 0.8486 main_effect
phoD No K01113 −81.811 74.070 −1.10 0.2788 main_effect
phoX No K07093 33.255 47.926 0.69 0.4935 main_effect
ppk No K00937 108.378 77.465 1.40 0.1728 main_effect
ppx No K01514 −2.458 2.710 −0.91 0.3721 main_effect
pqqB Yes K06136 −59.894 43.093 −1.39 0.1755 main_effect
pqqC Yes K06137 −5.929 42.330 −0.14 0.8896 main_effect
pqqD Yes K06138 77.788 43.235 1.80 0.0828 main_effect
pqqE Yes K06139 7.048 22.617 0.31 0.7576 main_effect
Potassium Solubilization gcd Yes K00117 −49.682 62.591 −0.79 0.4340 main_effect
kdsA No K01627 −177.764 68.570 −2.59 0.0154 interaction
kdsA No K01627 49.331 49.606 0.99 0.3369 by_group_JB1_JB2
kdsA No K01627 −128.433 47.138 −2.72 0.0184 by_group_JB5_JB6_JB7
kdsB No K00979 −118.580 90.682 −1.31 0.2016 main_effect
kup Yes K03549 12.188 88.035 0.14 0.8909 main_effect
nhaA No K03313 9.297 103.865 0.09 0.9293 main_effect
pqqB Yes K06136 −59.894 43.093 −1.39 0.1755 main_effect
pqqC Yes K06137 −5.929 42.330 −0.14 0.8896 main_effect
pqqD Yes K06138 77.788 43.235 1.80 0.0828 main_effect
pqqE Yes K06139 7.048 22.617 0.31 0.7576 main_effect
trkA Yes K03499 201.504 96.740 2.08 0.0465 main_effect
trkH Yes K03498 −18.715 22.461 −0.83 0.4118 main_effect
Stress Adaptation copA Yes Heavy Metal Tolerance K17686 10.658 59.839 0.18 0.8599 main_effect
ectB Yes Salt tolerance K00836 −1.799 8.313 −0.22 0.8302 main_effect
entC Yes Siderophore production K02361 1.039 2.422 0.43 0.6713 main_effect
glnA No ACC deaminase (ACC-d) K01915 213.978 167.083 1.28 0.2108 main_effect
kdsA Yes Exopolysaccharide production K01627 −177.764 68.570 −2.59 0.0154 interaction
kdsA Yes Exopolysaccharide production K01627 49.331 49.606 0.99 0.3369 by_group_JB1_JB2
kdsA Yes Exopolysaccharide production K01627 −128.433 47.138 −2.72 0.0184 by_group_JB5_JB6_JB7
kdsB No Exopolysaccharide production K00979 −118.580 90.682 −1.31 0.2016 main_effect
pchA Yes Salicylic acid (SA) K01851 −1.249 2.487 −0.50 0.6194 main_effect
pchB No Salicylic acid (SA) K04782 −13.193 13.864 −0.95 0.3495 main_effect
pqqB No Siderophore production K06136 −59.894 43.093 −1.39 0.1755 main_effect
Sulfur Cycling aprA Yes K00394 −14.943 6.193 −2.41 0.0232 interaction
aprA Yes K00394 7.737 4.509 1.72 0.1082 by_group_JB1_JB2
aprA Yes K00394 −7.207 4.221 −1.71 0.1135 by_group_JB5_JB6_JB7
cysA Yes K02045 168.947 135.534 1.25 0.2229 main_effect
cysU Yes K02046 −22.024 14.276 −1.54 0.1341 main_effect
cysW Yes K02047 87.136 36.921 2.36 0.0255 main_effect
fccB Yes K17229 2.270 2.819 0.81 0.4275 main_effect
sat Yes K00958 84.997 33.444 2.54 0.0169 main_effect
soxA No K17222 −27.857 41.740 −0.67 0.5100 main_effect
soxB No K17224 −10.781 10.856 −0.99 0.3291 main_effect
soxC Yes K17225 165.614 74.475 2.22 0.0344 main_effect
soxD Yes K22622 18.938 24.512 0.77 0.4462 main_effect
soxX No K17223 8.673 28.770 0.30 0.7653 main_effect
soxY Yes K17226 −3.103 42.162 −0.07 0.9418 main_effect
soxZ Yes K17227 −5.756 31.016 −0.19 0.8541 main_effect
Zinc Cycling mntR No K03709 −51.878 42.637 −1.22 0.2339 main_effect
troA No K11707 0.332 14.018 0.02 0.9813 main_effect
zitB No K16264 −21.962 61.717 −0.36 0.7246 main_effect
zntA No K01534 −3.191 19.046 −0.17 0.8681 main_effect
znuA Yes K09815 2.857 28.365 0.10 0.9205 main_effect
znuB Yes K09816 88.911 56.577 1.57 0.1273 main_effect
znuC Yes K09817 3.313 35.178 0.09 0.9256 main_effect
zur No K02076 10.069 13.763 0.73 0.4705 main_effect

Table 17: Summary statistics for each gene. The table shows the summary statistics for the analysis of the metadata variable and each gene (KO gene cluster) organised by section. The table gives estimate, standard error, t-value, p-value and model. “Model” informs which model the summary statistics represents: “main_effect” originate from analysis where all fields are analyzed together. This happens when we have tested for effects of JB and not found any significant difference between JB groups. “Interaction” gives results for the interaction analysis and is included only when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.

Harvested

Section Gene Essential Cagetory KO.ID Estimate SE t p-value Model
Antibiotic Production bacB Yes Bacilysin K19547 −0.385 0.645 −0.60 0.5558 main_effect
bacC Yes Bacilysin K19548 −0.740 0.860 −0.86 0.3968 main_effect
E4.1.1.82 Yes Fosfomycin K09459 −2.400 11.016 −0.22 0.8291 main_effect
eryA Yes Macrolides K00862 12.139 6.330 1.92 0.0654 main_effect
penM No Pentalenolactone K17476 −0.428 1.327 −0.32 0.7496 main_effect
pntE Yes Pentalenolactone K18091 3.591 3.390 1.06 0.2985 main_effect
pntH Yes Pentalenolactone K18056 1.000 0.584 1.71 0.0978 main_effect
ptlF Yes Pentalenolactone K17747 −0.468 0.785 −0.60 0.5558 main_effect
rifG Yes Rifamycin K16020 2.166 2.704 0.80 0.4298 main_effect
strA Yes Streptomycin K00547 −29.589 19.020 −1.56 0.1310 main_effect
Antibiotic Resistance vanA Yes Vancomycin K15739 −3.679 3.171 −1.16 0.2557 main_effect
vanH Yes Vancomycin K18347 −0.887 3.413 −0.26 0.7968 main_effect
vanX Yes Vancomycin K08641 −8.696 37.388 −0.23 0.8178 main_effect
Biocontrol chiA Yes Fungicidal agents K06904 112.482 49.746 2.26 0.0323 interaction
chiA Yes Fungicidal agents K06904 22.910 23.663 0.97 0.3494 by_group_JB1_JB2
chiA Yes Fungicidal agents K06904 135.392 47.441 2.85 0.0145 by_group_JB5_JB6_JB7
chiB No Fungicidal agents, Insecticide agents K20547 0.052 1.616 0.03 0.9747 main_effect
dapB No Bactericidal agents K00215 −83.772 126.135 −0.66 0.5120 main_effect
phzF Yes Fungicidal agents, Bactericidal agents K06998 23.586 27.610 0.85 0.4002 main_effect
prnA Yes Fungicidal agents K14266 9.191 12.453 0.74 0.4666 main_effect
prnC Yes Fungicidal agents K14257 −10.332 7.615 −1.36 0.1857 main_effect
tcaB Yes Insecticide agents K07552 150.802 62.624 2.41 0.0229 main_effect
Calcium Cycling chaA Yes K07300 −21.605 71.748 −0.30 0.7655 main_effect
mgtC Yes K07507 46.507 78.760 0.59 0.5596 main_effect
phaC No K03821 −132.273 76.541 −1.73 0.0950 main_effect
ureC Yes K01428 119.545 39.595 3.02 0.0054 main_effect
Carbon Fixation ccmK No Calvin–Benson–Bassham (CBB) Cycle K08696 −0.082 2.329 −0.04 0.9720 main_effect
ccmL No Calvin–Benson–Bassham (CBB) Cycle K08697 0.473 2.870 0.16 0.8703 main_effect
codH Yes Wood–Ljungdahl (WL) pathway K00192 −0.939 1.575 −0.60 0.5558 main_effect
korA Yes Reductive TCA (rTCA) cycle K00174 −16.051 34.493 −0.47 0.6453 main_effect
korB Yes Reductive TCA (rTCA) cycle K00175 62.901 53.770 1.17 0.2519 main_effect
prk Yes Calvin–Benson–Bassham (CBB) Cycle K00855 2.205 12.099 0.18 0.8567 main_effect
rbcL Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01601 46.502 26.616 1.75 0.0916 main_effect
rbcS Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01602 −25.078 82.464 −0.30 0.7633 main_effect
frdA No Reductive TCA (rTCA) cycle K00244 16.638 8.808 1.89 0.0693 main_effect
mcl No 3HP bicycle K08691 −11.068 14.401 −0.77 0.4486 main_effect
Chloride Cycling clcA Yes K03281 −2.055 126.277 −0.02 0.9871 main_effect
clcB Yes K03281 −2.055 126.277 −0.02 0.9871 main_effect
clcN Yes K05011 −0.635 1.064 −0.60 0.5558 main_effect
gltT No K11102 −26.366 30.633 −0.86 0.3967 main_effect
kefC No K11745 11.625 4.079 2.85 0.0081 main_effect
Copper Cycling copA Yes K17686 379.697 128.973 2.94 0.0067 interaction
copA Yes K17686 −87.800 61.277 −1.43 0.1739 by_group_JB1_JB2
copA Yes K17686 291.897 123.089 2.37 0.0353 by_group_JB5_JB6_JB7
copB Yes K01533 −7.403 37.493 −0.20 0.8449 main_effect
ctrA Yes K13584 36.159 101.721 0.36 0.7249 main_effect
cueO No K14588 −0.826 7.356 −0.11 0.9114 main_effect
cusA Yes K07787 −46.689 37.319 −1.25 0.2213 main_effect
cusB No K07798 −53.524 41.295 −1.30 0.2055 main_effect
Hormone Production acdS Yes Ethylene K01505 51.730 37.334 1.39 0.1768 main_effect
aldA Yes IAA K07248 11.470 5.497 2.09 0.0462 main_effect
aldH No IAA K00128 203.658 89.766 2.27 0.0312 main_effect
amiE Yes IAA K01426 28.447 48.010 0.59 0.5583 main_effect
aspC Yes IAA K00813 9.949 4.452 2.23 0.0336 main_effect
entC No GA K02361 −4.002 2.537 −1.58 0.1259 main_effect
etfA No Ethylene K03522 −345.723 106.979 −3.23 0.0031 main_effect
iaaH No IAA K21801 0.453 6.142 0.07 0.9417 main_effect
iaaM No IAA K00466 −0.896 6.344 −0.14 0.8886 main_effect
ipdC Yes IAA K04103 2.771 1.618 1.71 0.0979 main_effect
ipt Yes CK K00375 −46.105 58.354 −0.79 0.4361 main_effect
miaA No CK K00791 −46.450 136.255 −0.34 0.7357 main_effect
nitA No IAA K01501 4.025 8.830 0.46 0.6521 main_effect
tnaA No IAA K01667 −19.644 17.463 −1.12 0.2702 main_effect
Iron Cycling bfr No K03594 89.724 56.158 1.60 0.1213 main_effect
dps No K04047 26.205 64.579 0.41 0.6880 main_effect
entC Yes K02361 −4.002 2.537 −1.58 0.1259 main_effect
feoB Yes K04759 37.248 14.088 2.64 0.0133 main_effect
fur No K03711 −22.009 69.628 −0.32 0.7543 main_effect
iscA No K13628 143.483 107.242 1.34 0.1917 main_effect
sufB Yes K09014 −59.375 40.351 −1.47 0.1523 main_effect
sufC No K09013 30.950 51.036 0.61 0.5491 main_effect
yqjH No K07229 −0.462 0.774 −0.60 0.5558 main_effect
Magnesium Cycling corA Yes K03284 −314.170 261.346 −1.20 0.2394 main_effect
mgtA Yes K01531 −81.182 118.696 −0.68 0.4996 main_effect
mgtB No K01531 −81.182 118.696 −0.68 0.4996 main_effect
mgtE Yes K06213 41.822 51.137 0.82 0.4204 main_effect
phoQ No K07637 4.522 7.549 0.60 0.5540 main_effect
Manganese Cycling mntA Yes K06147 −45.691 223.987 −0.20 0.8398 main_effect
mntB Yes K06148 2.025 15.749 0.13 0.8986 main_effect
mntC Yes K06149 −2.349 5.071 −0.46 0.6468 main_effect
mntH Yes K03322 64.657 88.296 0.73 0.4701 main_effect
mntR No K03709 86.974 44.752 1.94 0.0621 main_effect
mntR No K11924 3.254 7.517 0.43 0.6684 main_effect
sitA Yes K11604 28.322 11.697 2.42 0.0227 interaction
sitA Yes K11604 7.037 6.119 1.15 0.2694 by_group_JB1_JB2
sitA Yes K11604 35.358 10.386 3.40 0.0052 by_group_JB5_JB6_JB7
sodA No K04564 272.089 92.809 2.93 0.0066 main_effect
Nitrogen fixation amt No K03320 −15.847 147.420 −0.11 0.9152 main_effect
glnB No K04751 −73.183 152.119 −0.48 0.6342 main_effect
iscS No K04487 95.003 102.711 0.92 0.3629 main_effect
moeA No K03750 −26.770 61.047 −0.44 0.6644 main_effect
nifA No K02584 −6.612 11.332 −0.58 0.5643 main_effect
nifB Yes K02585 −3.978 7.623 −0.52 0.6059 main_effect
nifD Yes K02586 −10.622 8.864 −1.20 0.2409 main_effect
nifE Yes K02587 −20.630 12.854 −1.60 0.1197 main_effect
nifH Yes K02588 −0.848 1.422 −0.60 0.5558 main_effect
nifK Yes K02591 −21.458 14.082 −1.52 0.1388 main_effect
nifM Yes K03769 −72.018 41.503 −1.74 0.0937 main_effect
nifN Yes K02592 −2.071 2.429 −0.85 0.4012 main_effect
nifQ No K15790 −0.251 0.421 −0.60 0.5558 main_effect
nifU Yes K04488 −11.278 68.996 −0.16 0.8713 main_effect
nifV Yes K02594 −8.388 4.950 −1.69 0.1013 main_effect
nifW No K02595 −0.035 1.484 −0.02 0.9816 main_effect
nifX No K02596 −4.817 6.245 −0.77 0.4469 main_effect
nifZ No K02597 −1.722 2.366 −0.73 0.4728 main_effect
Nitrogen Release amoA Yes K10944 7.810 4.579 1.71 0.0992 main_effect
amoB Yes K10945 9.727 5.508 1.77 0.0883 main_effect
amoC Yes K10946 12.134 59.838 0.20 0.8408 main_effect
gdh No K15371 −25.506 28.695 −0.89 0.3816 main_effect
napA No K02567 16.791 9.492 1.77 0.0878 main_effect
napA Yes K01416 0.633 3.462 0.18 0.8563 main_effect
napB No K02568 −7.964 6.823 −1.17 0.2529 main_effect
narG Yes K00370 1.136 26.258 0.04 0.9658 main_effect
narH Yes K00371 −56.938 18.830 −3.02 0.0053 main_effect
narI No K00374 −53.124 26.135 −2.03 0.0517 main_effect
nasA Yes K00372 94.452 41.692 2.27 0.0314 main_effect
nasB Yes K00360 6.446 3.094 2.08 0.0465 main_effect
nirA Yes K00366 −60.478 19.590 −3.09 0.0045 main_effect
nirK Yes K00368 −22.196 20.461 −1.08 0.2873 main_effect
nirS Yes K15864 0.663 1.174 0.56 0.5768 main_effect
norB Yes K04561 −11.703 22.179 −0.53 0.6019 main_effect
norC No K02305 25.740 23.709 1.09 0.2869 main_effect
nosZ Yes K00376 19.054 20.663 0.92 0.3643 main_effect
nrfA Yes K03385 11.111 30.109 0.37 0.7149 main_effect
ureC No K01428 119.545 39.595 3.02 0.0054 main_effect
Nodulation nodA Yes K14658 −0.289 0.484 −0.60 0.5558 main_effect
nodD Yes K14657 2.032 3.473 0.59 0.5631 main_effect
nodI No ABC transporter complex K09694 −200.048 136.297 −1.47 0.1533 main_effect
Phosphorus Solubilization gcd Yes K00117 62.521 67.950 0.92 0.3654 main_effect
phnX No K06163 20.804 13.251 1.57 0.1276 main_effect
phoA Yes K01077 12.961 18.781 0.69 0.4958 main_effect
phoD No K01113 78.000 81.127 0.96 0.3446 main_effect
phoX No K07093 285.460 89.650 3.18 0.0037 interaction
phoX No K07093 −9.732 52.940 −0.18 0.8568 by_group_JB1_JB2
phoX No K07093 275.728 69.268 3.98 0.0018 by_group_JB5_JB6_JB7
ppk No K00937 −12.923 87.282 −0.15 0.8834 main_effect
ppx No K01514 −0.718 2.993 −0.24 0.8121 main_effect
pqqB Yes K06136 24.589 48.330 0.51 0.6149 main_effect
pqqC Yes K06137 −40.638 45.501 −0.89 0.3794 main_effect
pqqD Yes K06138 −53.056 48.742 −1.09 0.2857 main_effect
pqqE Yes K06139 −10.274 24.613 −0.42 0.6795 main_effect
Potassium Solubilization gcd Yes K00117 62.521 67.950 0.92 0.3654 main_effect
kdsA No K01627 28.231 46.667 0.60 0.5501 main_effect
kdsB No K00979 51.022 101.333 0.50 0.6185 main_effect
kup Yes K03549 11.685 95.941 0.12 0.9039 main_effect
nhaA No K03313 176.391 108.181 1.63 0.1142 main_effect
pqqB Yes K06136 24.589 48.330 0.51 0.6149 main_effect
pqqC Yes K06137 −40.638 45.501 −0.89 0.3794 main_effect
pqqD Yes K06138 −53.056 48.742 −1.09 0.2857 main_effect
pqqE Yes K06139 −10.274 24.613 −0.42 0.6795 main_effect
trkA Yes K03499 −140.622 110.132 −1.28 0.2121 main_effect
trkH Yes K03498 109.576 47.059 2.33 0.0279 interaction
trkH Yes K03498 17.484 21.581 0.81 0.4314 by_group_JB1_JB2
trkH Yes K03498 127.060 45.873 2.77 0.0170 by_group_JB5_JB6_JB7
Stress Adaptation copA Yes Heavy Metal Tolerance K17686 379.697 128.973 2.94 0.0067 interaction
copA Yes Heavy Metal Tolerance K17686 −87.800 61.277 −1.43 0.1739 by_group_JB1_JB2
copA Yes Heavy Metal Tolerance K17686 291.897 123.089 2.37 0.0353 by_group_JB5_JB6_JB7
ectB Yes Salt tolerance K00836 0.706 9.065 0.08 0.9385 main_effect
entC Yes Siderophore production K02361 −4.002 2.537 −1.58 0.1259 main_effect
glnA No ACC deaminase (ACC-d) K01915 −235.995 181.944 −1.30 0.2052 main_effect
kdsA Yes Exopolysaccharide production K01627 28.231 46.667 0.60 0.5501 main_effect
kdsB No Exopolysaccharide production K00979 51.022 101.333 0.50 0.6185 main_effect
pchA Yes Salicylic acid (SA) K01851 −0.826 2.718 −0.30 0.7635 main_effect
pchB No Salicylic acid (SA) K04782 −3.413 15.337 −0.22 0.8255 main_effect
pqqB No Siderophore production K06136 24.589 48.330 0.51 0.6149 main_effect
Sulfur Cycling aprA Yes K00394 −3.209 3.645 −0.88 0.3861 main_effect
cysA Yes K02045 −3.772 151.736 −0.02 0.9803 main_effect
cysU Yes K02046 7.631 16.140 0.47 0.6400 main_effect
cysW Yes K02047 −24.891 43.803 −0.57 0.5744 main_effect
fccB Yes K17229 17.038 6.321 2.70 0.0122 interaction
fccB Yes K17229 −4.408 3.778 −1.17 0.2628 by_group_JB1_JB2
fccB Yes K17229 12.631 4.794 2.63 0.0218 by_group_JB5_JB6_JB7
sat Yes K00958 −81.739 37.363 −2.19 0.0372 main_effect
soxA No K17222 67.810 44.018 1.54 0.1347 main_effect
soxB No K17224 16.601 11.620 1.43 0.1642 main_effect
soxC Yes K17225 −35.749 87.773 −0.41 0.6869 main_effect
soxD Yes K22622 −17.324 26.795 −0.65 0.5232 main_effect
soxX No K17223 45.373 30.209 1.50 0.1443 main_effect
soxY Yes K17226 48.861 45.013 1.09 0.2870 main_effect
soxZ Yes K17227 56.835 32.069 1.77 0.0872 main_effect
Zinc Cycling mntR No K03709 86.974 44.752 1.94 0.0621 main_effect
troA No K11707 66.108 29.069 2.27 0.0314 interaction
troA No K11707 15.907 14.483 1.10 0.2906 by_group_JB1_JB2
troA No K11707 82.015 26.853 3.05 0.0100 by_group_JB5_JB6_JB7
zitB No K16264 −97.490 64.840 −1.50 0.1439 main_effect
zntA No K01534 −20.442 20.403 −1.00 0.3250 main_effect
znuA Yes K09815 46.716 29.628 1.58 0.1261 main_effect
znuB Yes K09816 −52.514 63.545 −0.83 0.4156 main_effect
znuC Yes K09817 19.783 38.158 0.52 0.6082 main_effect
zur No K02076 −26.049 14.318 −1.82 0.0796 main_effect

Table 18: Summary statistics for each gene. The table shows the summary statistics for the analysis of the metadata variable and each gene (KO gene cluster) organised by section. The table gives estimate, standard error, t-value, p-value and model. “Model” informs which model the summary statistics represents: “main_effect” originate from analysis where all fields are analyzed together. This happens when we have tested for effects of JB and not found any significant difference between JB groups. “Interaction” gives results for the interaction analysis and is included only when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.

Clovergrass (within 3 years)

Section Gene Essential Cagetory KO.ID Estimate SE t p-value Model
Antibiotic Production bacB Yes Bacilysin K19547 −0.846 0.587 −1.44 0.1609 main_effect
bacC Yes Bacilysin K19548 −0.514 0.812 −0.63 0.5320 main_effect
E4.1.1.82 Yes Fosfomycin K09459 −17.832 9.779 −1.82 0.0789 main_effect
eryA Yes Macrolides K00862 6.762 6.185 1.09 0.2836 main_effect
penM No Pentalenolactone K17476 1.163 1.227 0.95 0.3516 main_effect
pntE Yes Pentalenolactone K18091 −2.288 3.214 −0.71 0.4825 main_effect
pntH Yes Pentalenolactone K18056 0.400 0.571 0.70 0.4892 main_effect
ptlF Yes Pentalenolactone K17747 0.515 0.735 0.70 0.4892 main_effect
rifG Yes Rifamycin K16020 0.312 2.565 0.12 0.9039 main_effect
strA Yes Streptomycin K00547 −12.889 18.437 −0.70 0.4903 main_effect
Antibiotic Resistance vanA Yes Vancomycin K15739 −0.929 3.040 −0.31 0.7622 main_effect
vanH Yes Vancomycin K18347 −7.577 2.868 −2.64 0.0133 main_effect
vanX Yes Vancomycin K08641 −93.292 30.359 −3.07 0.0047 main_effect
Biocontrol chiA Yes Fungicidal agents K06904 −15.028 26.583 −0.57 0.5764 main_effect
chiB No Fungicidal agents, Insecticide agents K20547 1.377 1.494 0.92 0.3644 main_effect
dapB No Bactericidal agents K00215 79.360 118.307 0.67 0.5078 main_effect
phzF Yes Fungicidal agents, Bactericidal agents K06998 18.941 25.991 0.73 0.4722 main_effect
prnA Yes Fungicidal agents K14266 −8.011 11.698 −0.68 0.4991 main_effect
prnC Yes Fungicidal agents K14257 −14.588 6.840 −2.13 0.0418 main_effect
tcaB Yes Insecticide agents K07552 74.759 62.979 1.19 0.2452 main_effect
Calcium Cycling chaA Yes K07300 −97.444 64.850 −1.50 0.1441 main_effect
mgtC Yes K07507 10.680 74.315 0.14 0.8868 main_effect
phaC No K03821 −29.796 75.324 −0.40 0.6954 main_effect
ureC Yes K01428 73.201 40.465 1.81 0.0812 main_effect
Carbon Fixation ccmK No Calvin–Benson–Bassham (CBB) Cycle K08696 −3.136 2.103 −1.49 0.1471 main_effect
ccmL No Calvin–Benson–Bassham (CBB) Cycle K08697 −1.201 2.684 −0.45 0.6579 main_effect
codH Yes Wood–Ljungdahl (WL) pathway K00192 −2.066 1.435 −1.44 0.1609 main_effect
korA Yes Reductive TCA (rTCA) cycle K00174 0.552 32.482 0.02 0.9866 main_effect
korB Yes Reductive TCA (rTCA) cycle K00175 96.151 48.358 1.99 0.0566 main_effect
prk Yes Calvin–Benson–Bassham (CBB) Cycle K00855 6.900 11.281 0.61 0.5457 main_effect
rbcL Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01601 45.411 24.854 1.83 0.0784 main_effect
rbcS Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01602 −31.128 77.262 −0.40 0.6901 main_effect
frdA No Reductive TCA (rTCA) cycle K00244 −2.362 8.762 −0.27 0.7894 main_effect
mcl No 3HP bicycle K08691 −0.199 13.651 −0.01 0.9884 main_effect
Chloride Cycling clcA Yes K03281 74.657 117.616 0.63 0.5307 main_effect
clcB Yes K03281 74.657 117.616 0.63 0.5307 main_effect
clcN Yes K05011 −1.396 0.969 −1.44 0.1609 main_effect
gltT No K11102 13.782 28.997 0.48 0.6383 main_effect
kefC No K11745 0.292 4.345 0.07 0.9469 main_effect
Copper Cycling copA Yes K17686 −56.811 60.256 −0.94 0.3538 main_effect
copB Yes K01533 30.316 34.726 0.87 0.3901 main_effect
ctrA Yes K13584 28.895 95.482 0.30 0.7644 main_effect
cueO No K14588 8.522 6.711 1.27 0.2146 main_effect
cusA Yes K07787 24.217 35.681 0.68 0.5029 main_effect
cusB No K07798 12.028 39.819 0.30 0.7648 main_effect
Hormone Production acdS Yes Ethylene K01505 29.648 35.767 0.83 0.4142 main_effect
aldA Yes IAA K07248 −1.678 5.534 −0.30 0.7640 main_effect
aldH No IAA K00128 −315.913 145.273 −2.17 0.0389 interaction
aldH No IAA K00128 203.068 100.742 2.02 0.0634 by_group_JB1_JB2
aldH No IAA K00128 −112.845 104.725 −1.08 0.3024 by_group_JB5_JB6_JB7
amiE Yes IAA K01426 18.655 45.181 0.41 0.6828 main_effect
aspC Yes IAA K00813 −17.488 8.469 −2.06 0.0490 interaction
aspC Yes IAA K00813 3.355 6.170 0.54 0.5952 by_group_JB1_JB2
aspC Yes IAA K00813 −14.134 5.727 −2.47 0.0296 by_group_JB5_JB6_JB7
entC No GA K02361 −4.432 2.338 −1.90 0.0683 main_effect
etfA No Ethylene K03522 −47.794 117.244 −0.41 0.6866 main_effect
iaaH No IAA K21801 2.018 5.750 0.35 0.7283 main_effect
iaaM No IAA K00466 −7.780 5.769 −1.35 0.1882 main_effect
ipdC Yes IAA K04103 1.966 1.551 1.27 0.2155 main_effect
ipt Yes CK K00375 −88.849 52.740 −1.68 0.1032 main_effect
miaA No CK K00791 41.920 127.839 0.33 0.7454 main_effect
nitA No IAA K01501 4.249 8.275 0.51 0.6117 main_effect
tnaA No IAA K01667 7.631 16.685 0.46 0.6510 main_effect
Iron Cycling bfr No K03594 7.312 55.013 0.13 0.8952 main_effect
dps No K04047 66.722 59.435 1.12 0.2711 main_effect
entC Yes K02361 −4.432 2.338 −1.90 0.0683 main_effect
feoB Yes K04759 14.083 14.532 0.97 0.3408 main_effect
fur No K03711 −66.862 64.201 −1.04 0.3066 main_effect
iscA No K13628 −19.522 103.702 −0.19 0.8520 main_effect
sufB Yes K09014 −60.206 37.606 −1.60 0.1206 main_effect
sufC No K09013 −2.995 48.186 −0.06 0.9509 main_effect
yqjH No K07229 −1.016 0.705 −1.44 0.1609 main_effect
Magnesium Cycling corA Yes K03284 −123.020 250.334 −0.49 0.6270 main_effect
mgtA Yes K01531 84.733 111.125 0.76 0.4521 main_effect
mgtB No K01531 84.733 111.125 0.76 0.4521 main_effect
mgtE Yes K06213 −48.709 47.660 −1.02 0.3155 main_effect
phoQ No K07637 −1.483 7.121 −0.21 0.8365 main_effect
Manganese Cycling mntA Yes K06147 −25.749 210.218 −0.12 0.9034 main_effect
mntB Yes K06148 −20.902 14.241 −1.47 0.1533 main_effect
mntC Yes K06149 −4.219 4.708 −0.90 0.3778 main_effect
mntH Yes K03322 −0.943 83.618 −0.01 0.9911 main_effect
mntR No K03709 57.915 43.363 1.34 0.1924 main_effect
mntR No K11924 −0.606 7.074 −0.09 0.9323 main_effect
sitA Yes K11604 7.279 5.746 1.27 0.2156 main_effect
sodA No K04564 194.012 92.533 2.10 0.0452 main_effect
Nitrogen fixation amt No K03320 107.252 136.828 0.78 0.4397 main_effect
glnB No K04751 569.488 264.344 2.15 0.0407 interaction
glnB No K04751 −177.698 202.403 −0.88 0.3948 by_group_JB1_JB2
glnB No K04751 391.790 164.704 2.38 0.0348 by_group_JB5_JB6_JB7
iscS No K04487 −54.961 97.259 −0.57 0.5765 main_effect
moeA No K03750 7.529 57.446 0.13 0.8967 main_effect
nifA No K02584 −12.603 10.427 −1.21 0.2369 main_effect
nifB Yes K02585 0.534 7.185 0.07 0.9412 main_effect
nifD Yes K02586 7.163 8.418 0.85 0.4020 main_effect
nifE Yes K02587 10.483 12.444 0.84 0.4067 main_effect
nifH Yes K02588 0.933 1.330 0.70 0.4892 main_effect
nifK Yes K02591 13.729 13.500 1.02 0.3179 main_effect
nifM Yes K03769 −2.081 40.972 −0.05 0.9599 main_effect
nifN Yes K02592 2.278 2.268 1.00 0.3237 main_effect
nifQ No K15790 0.276 0.394 0.70 0.4892 main_effect
nifU Yes K04488 −298.235 106.385 −2.80 0.0094 interaction
nifU Yes K04488 196.919 74.320 2.65 0.0190 by_group_JB1_JB2
nifU Yes K04488 −101.316 76.031 −1.33 0.2074 by_group_JB5_JB6_JB7
nifV Yes K02594 3.345 4.835 0.69 0.4947 main_effect
nifW No K02595 0.410 1.390 0.29 0.7703 main_effect
nifX No K02596 4.734 5.852 0.81 0.4253 main_effect
nifZ No K02597 2.610 2.186 1.19 0.2426 main_effect
Nitrogen Release amoA Yes K10944 −2.257 4.493 −0.50 0.6193 main_effect
amoB Yes K10945 −10.144 5.099 −1.99 0.0565 main_effect
amoC Yes K10946 −78.908 54.158 −1.46 0.1562 main_effect
gdh No K15371 −4.134 27.284 −0.15 0.8807 main_effect
napA No K02567 21.946 8.422 2.61 0.0145 main_effect
napA Yes K01416 −1.611 3.235 −0.50 0.6223 main_effect
napB No K02568 −5.827 6.461 −0.90 0.3748 main_effect
narG Yes K00370 −18.622 24.380 −0.76 0.4514 main_effect
narH Yes K00371 −23.092 19.872 −1.16 0.2550 main_effect
narI No K00374 −7.314 26.227 −0.28 0.7824 main_effect
nasA Yes K00372 39.249 41.893 0.94 0.3568 main_effect
nasB Yes K00360 −1.546 3.106 −0.50 0.6225 main_effect
nirA Yes K00366 −23.902 20.791 −1.15 0.2600 main_effect
nirK Yes K00368 −14.361 19.405 −0.74 0.4654 main_effect
nirS Yes K15864 1.101 1.088 1.01 0.3206 main_effect
norB Yes K04561 −18.547 20.613 −0.90 0.3759 main_effect
norC No K02305 −11.343 22.603 −0.50 0.6197 main_effect
nosZ Yes K00376 −6.855 19.633 −0.35 0.7296 main_effect
nrfA Yes K03385 35.881 27.489 1.31 0.2024 main_effect
ureC No K01428 73.201 40.465 1.81 0.0812 main_effect
Nodulation nodA Yes K14658 −0.635 0.441 −1.44 0.1609 main_effect
nodD Yes K14657 4.510 3.165 1.42 0.1652 main_effect
nodI No ABC transporter complex K09694 −64.752 132.120 −0.49 0.6279 main_effect
Phosphorus Solubilization gcd Yes K00117 −56.808 63.803 −0.89 0.3809 main_effect
phnX No K06163 4.506 12.938 0.35 0.7302 main_effect
phoA Yes K01077 −9.850 17.670 −0.56 0.5817 main_effect
phoD No K01113 −150.451 71.935 −2.09 0.0457 main_effect
phoX No K07093 −1.254 49.411 −0.03 0.9799 main_effect
ppk No K00937 81.600 80.445 1.01 0.3191 main_effect
ppx No K01514 −3.434 2.734 −1.26 0.2196 main_effect
pqqB Yes K06136 −24.011 45.320 −0.53 0.6004 main_effect
pqqC Yes K06137 −41.449 42.572 −0.97 0.3386 main_effect
pqqD Yes K06138 39.643 46.077 0.86 0.3969 main_effect
pqqE Yes K06139 21.528 22.800 0.94 0.3532 main_effect
Potassium Solubilization gcd Yes K00117 −56.808 63.803 −0.89 0.3809 main_effect
kdsA No K01627 −14.217 43.981 −0.32 0.7489 main_effect
kdsB No K00979 58.119 94.854 0.61 0.5450 main_effect
kup Yes K03549 53.360 89.458 0.60 0.5556 main_effect
nhaA No K03313 −45.412 105.844 −0.43 0.6712 main_effect
pqqB Yes K06136 −24.011 45.320 −0.53 0.6004 main_effect
pqqC Yes K06137 −41.449 42.572 −0.97 0.3386 main_effect
pqqD Yes K06138 39.643 46.077 0.86 0.3969 main_effect
pqqE Yes K06139 21.528 22.800 0.94 0.3532 main_effect
trkA Yes K03499 70.756 105.434 0.67 0.5077 main_effect
trkH Yes K03498 −9.042 23.181 −0.39 0.6994 main_effect
Stress Adaptation copA Yes Heavy Metal Tolerance K17686 −56.811 60.256 −0.94 0.3538 main_effect
ectB Yes Salt tolerance K00836 0.635 8.504 0.07 0.9411 main_effect
entC Yes Siderophore production K02361 −4.432 2.338 −1.90 0.0683 main_effect
glnA No ACC deaminase (ACC-d) K01915 −210.134 171.186 −1.23 0.2298 main_effect
kdsA Yes Exopolysaccharide production K01627 −14.217 43.981 −0.32 0.7489 main_effect
kdsB No Exopolysaccharide production K00979 58.119 94.854 0.61 0.5450 main_effect
pchA Yes Salicylic acid (SA) K01851 −0.504 2.552 −0.20 0.8449 main_effect
pchB No Salicylic acid (SA) K04782 −17.593 14.011 −1.26 0.2196 main_effect
pqqB No Siderophore production K06136 −24.011 45.320 −0.53 0.6004 main_effect
Sulfur Cycling aprA Yes K00394 −1.922 3.448 −0.56 0.5815 main_effect
cysA Yes K02045 33.910 142.198 0.24 0.8133 main_effect
cysU Yes K02046 −28.162 14.239 −1.98 0.0579 main_effect
cysW Yes K02047 54.042 40.045 1.35 0.1880 main_effect
fccB Yes K17229 1.712 2.897 0.59 0.5593 main_effect
sat Yes K00958 −40.830 37.134 −1.10 0.2809 main_effect
soxA No K17222 51.265 41.902 1.22 0.2314 main_effect
soxB No K17224 16.302 10.863 1.50 0.1446 main_effect
soxC Yes K17225 94.415 80.631 1.17 0.2515 main_effect
soxD Yes K22622 13.965 25.185 0.55 0.5836 main_effect
soxX No K17223 26.244 29.037 0.90 0.3738 main_effect
soxY Yes K17226 60.139 41.580 1.45 0.1592 main_effect
soxZ Yes K17227 75.855 28.302 2.68 0.0122 main_effect
Zinc Cycling mntR No K03709 57.915 43.363 1.34 0.1924 main_effect
troA No K11707 19.552 13.845 1.41 0.1689 main_effect
zitB No K16264 −70.389 61.818 −1.14 0.2645 main_effect
zntA No K01534 −14.894 19.275 −0.77 0.4462 main_effect
znuA Yes K09815 −32.302 28.351 −1.14 0.2642 main_effect
znuB Yes K09816 −45.740 59.710 −0.77 0.4501 main_effect
znuC Yes K09817 −28.945 35.548 −0.81 0.4224 main_effect
zur No K02076 −7.382 14.134 −0.52 0.6056 main_effect

Table 19: Summary statistics for each gene. The table shows the summary statistics for the analysis of the metadata variable and each gene (KO gene cluster) organised by section. The table gives estimate, standard error, t-value, p-value and model. “Model” informs which model the summary statistics represents: “main_effect” originate from analysis where all fields are analyzed together. This happens when we have tested for effects of JB and not found any significant difference between JB groups. “Interaction” gives results for the interaction analysis and is included only when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.

Organic material (factor)

Section Gene Essential Cagetory KO.ID Estimate SE t p-value Model
Antibiotic Production bacB Yes Bacilysin K19547 0.368 0.675 0.54 0.5901 main_effect
bacC Yes Bacilysin K19548 0.708 0.901 0.79 0.4387 main_effect
E4.1.1.82 Yes Fosfomycin K09459 −4.628 11.495 −0.40 0.6903 main_effect
eryA Yes Macrolides K00862 −6.685 6.925 −0.97 0.3427 main_effect
penM No Pentalenolactone K17476 1.782 1.348 1.32 0.1970 main_effect
pntE Yes Pentalenolactone K18091 2.377 3.587 0.66 0.5129 main_effect
pntH Yes Pentalenolactone K18056 −1.143 0.604 −1.89 0.0689 main_effect
ptlF Yes Pentalenolactone K17747 0.448 0.822 0.54 0.5901 main_effect
rifG Yes Rifamycin K16020 −4.723 2.716 −1.74 0.0931 main_effect
strA Yes Streptomycin K00547 34.959 19.647 1.78 0.0860 main_effect
Antibiotic Resistance vanA Yes Vancomycin K15739 7.695 3.067 2.51 0.0182 main_effect
vanH Yes Vancomycin K18347 4.750 3.458 1.37 0.1805 main_effect
vanX Yes Vancomycin K08641 58.084 37.557 1.55 0.1332 main_effect
Biocontrol chiA Yes Fungicidal agents K06904 −18.855 29.583 −0.64 0.5291 main_effect
chiB No Fungicidal agents, Insecticide agents K20547 −0.228 1.690 −0.13 0.8938 main_effect
dapB No Bactericidal agents K00215 178.195 128.578 1.39 0.1767 main_effect
phzF Yes Fungicidal agents, Bactericidal agents K06998 −20.027 28.996 −0.69 0.4955 main_effect
prnA Yes Fungicidal agents K14266 8.771 13.041 0.67 0.5068 main_effect
prnC Yes Fungicidal agents K14257 8.848 8.048 1.10 0.2809 main_effect
tcaB Yes Insecticide agents K07552 18.701 71.851 0.26 0.7966 main_effect
Calcium Cycling chaA Yes K07300 −7.501 75.124 −0.10 0.9212 main_effect
mgtC Yes K07507 20.672 82.766 0.25 0.8046 main_effect
phaC No K03821 −30.297 83.992 −0.36 0.7210 main_effect
ureC Yes K01428 216.753 87.198 2.49 0.0197 interaction
ureC Yes K01428 −145.598 59.176 −2.46 0.0275 by_group_JB1_JB2
ureC Yes K01428 71.155 63.450 1.12 0.2840 by_group_JB5_JB6_JB7
Carbon Fixation ccmK No Calvin–Benson–Bassham (CBB) Cycle K08696 −0.227 2.435 −0.09 0.9264 main_effect
ccmL No Calvin–Benson–Bassham (CBB) Cycle K08697 1.746 2.984 0.59 0.5632 main_effect
codH Yes Wood–Ljungdahl (WL) pathway K00192 0.898 1.648 0.54 0.5901 main_effect
korA Yes Reductive TCA (rTCA) cycle K00174 33.935 35.631 0.95 0.3490 main_effect
korB Yes Reductive TCA (rTCA) cycle K00175 −74.335 55.837 −1.33 0.1938 main_effect
prk Yes Calvin–Benson–Bassham (CBB) Cycle K00855 −17.106 12.237 −1.40 0.1731 main_effect
rbcL Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01601 −34.236 28.583 −1.20 0.2410 main_effect
rbcS Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01602 20.305 86.277 0.24 0.8157 main_effect
frdA No Reductive TCA (rTCA) cycle K00244 3.465 9.756 0.36 0.7251 main_effect
mcl No 3HP bicycle K08691 −13.039 15.014 −0.87 0.3925 main_effect
Chloride Cycling clcA Yes K03281 −48.876 131.706 −0.37 0.7134 main_effect
clcB Yes K03281 −48.876 131.706 −0.37 0.7134 main_effect
clcN Yes K05011 0.607 1.114 0.54 0.5901 main_effect
gltT No K11102 −30.857 31.921 −0.97 0.3420 main_effect
kefC No K11745 27.921 8.511 3.28 0.0029 interaction
kefC No K11745 −13.597 5.127 −2.65 0.0190 by_group_JB1_JB2
kefC No K11745 14.323 6.989 2.05 0.0629 by_group_JB5_JB6_JB7
Copper Cycling copA Yes K17686 152.731 61.809 2.47 0.0198 main_effect
copB Yes K01533 9.491 39.187 0.24 0.8104 main_effect
ctrA Yes K13584 −154.806 102.501 −1.51 0.1422 main_effect
cueO No K14588 −8.992 7.502 −1.20 0.2408 main_effect
cusA Yes K07787 −39.941 39.378 −1.01 0.3191 main_effect
cusB No K07798 −35.653 43.939 −0.81 0.4240 main_effect
Hormone Production acdS Yes Ethylene K01505 −2.288 40.349 −0.06 0.9552 main_effect
aldA Yes IAA K07248 24.888 11.545 2.16 0.0405 interaction
aldA Yes IAA K07248 −4.568 5.757 −0.79 0.4407 by_group_JB1_JB2
aldA Yes IAA K07248 20.320 10.606 1.92 0.0795 by_group_JB5_JB6_JB7
aldH No IAA K00128 9.198 102.103 0.09 0.9289 main_effect
amiE Yes IAA K01426 −7.431 50.490 −0.15 0.8841 main_effect
aspC Yes IAA K00813 21.059 9.642 2.18 0.0382 interaction
aspC Yes IAA K00813 −9.907 6.127 −1.62 0.1282 by_group_JB1_JB2
aspC Yes IAA K00813 11.152 7.554 1.48 0.1656 by_group_JB5_JB6_JB7
entC No GA K02361 3.828 2.672 1.43 0.1630 main_effect
etfA No Ethylene K03522 94.291 129.845 0.73 0.4738 main_effect
iaaH No IAA K21801 −12.471 5.975 −2.09 0.0461 main_effect
iaaM No IAA K00466 5.975 6.538 0.91 0.3686 main_effect
ipdC Yes IAA K04103 −3.273 1.667 −1.96 0.0596 main_effect
ipt Yes CK K00375 61.870 60.570 1.02 0.3158 main_effect
miaA No CK K00791 111.962 141.180 0.79 0.4344 main_effect
nitA No IAA K01501 −6.068 9.195 −0.66 0.5147 main_effect
tnaA No IAA K01667 −10.466 18.561 −0.56 0.5773 main_effect
Iron Cycling bfr No K03594 23.758 61.170 0.39 0.7007 main_effect
dps No K04047 82.048 65.919 1.24 0.2236 main_effect
entC Yes K02361 3.828 2.672 1.43 0.1630 main_effect
feoB Yes K04759 −37.314 14.880 −2.51 0.0182 main_effect
fur No K03711 67.383 71.808 0.94 0.3561 main_effect
iscA No K13628 0.109 115.655 0.00 0.9993 main_effect
sufB Yes K09014 108.483 38.694 2.80 0.0091 main_effect
sufC No K09013 44.038 53.061 0.83 0.4136 main_effect
yqjH No K07229 0.442 0.811 0.54 0.5901 main_effect
Magnesium Cycling corA Yes K03284 265.743 275.675 0.96 0.3433 main_effect
mgtA Yes K01531 −129.292 122.726 −1.05 0.3011 main_effect
mgtB No K01531 −129.292 122.726 −1.05 0.3011 main_effect
mgtE Yes K06213 48.573 53.317 0.91 0.3701 main_effect
phoQ No K07637 8.508 7.779 1.09 0.2834 main_effect
Manganese Cycling mntA Yes K06147 314.132 226.720 1.39 0.1768 main_effect
mntB Yes K06148 16.384 16.178 1.01 0.3199 main_effect
mntC Yes K06149 6.406 5.183 1.24 0.2267 main_effect
mntH Yes K03322 −91.483 91.580 −1.00 0.3264 main_effect
mntR No K03709 48.489 48.997 0.99 0.3308 main_effect
mntR No K11924 5.494 7.817 0.70 0.4880 main_effect
sitA Yes K11604 5.303 6.508 0.81 0.4220 main_effect
sodA No K04564 −232.710 101.844 −2.28 0.0301 main_effect
Nitrogen fixation amt No K03320 −137.365 151.965 −0.90 0.3737 main_effect
glnB No K04751 −73.581 159.096 −0.46 0.6473 main_effect
iscS No K04487 32.600 108.843 0.30 0.7668 main_effect
moeA No K03750 23.805 63.888 0.37 0.7123 main_effect
nifA No K02584 −2.586 11.910 −0.22 0.8297 main_effect
nifB Yes K02585 −2.012 8.000 −0.25 0.8032 main_effect
nifD Yes K02586 −4.876 9.458 −0.52 0.6102 main_effect
nifE Yes K02587 −8.709 13.947 −0.62 0.5374 main_effect
nifH Yes K02588 −6.217 2.599 −2.39 0.0243 interaction
nifH Yes K02588 0.000 0.000 NaN NaN by_group_JB1_JB2
nifH Yes K02588 −6.217 2.863 −2.17 0.0507 by_group_JB5_JB6_JB7
nifK Yes K02591 −7.791 15.251 −0.51 0.6135 main_effect
nifM Yes K03769 −79.180 43.146 −1.84 0.0771 main_effect
nifN Yes K02592 −1.595 2.555 −0.62 0.5375 main_effect
nifQ No K15790 0.240 0.440 0.54 0.5901 main_effect
nifU Yes K04488 68.095 71.017 0.96 0.3458 main_effect
nifV Yes K02594 0.764 5.433 0.14 0.8892 main_effect
nifW No K02595 −0.215 1.552 −0.14 0.8909 main_effect
nifX No K02596 −8.449 6.402 −1.32 0.1976 main_effect
nifZ No K02597 −1.156 2.488 −0.46 0.6458 main_effect
Nitrogen Release amoA Yes K10944 −4.878 4.945 −0.99 0.3323 main_effect
amoB Yes K10945 2.638 6.051 0.44 0.6662 main_effect
amoC Yes K10946 6.371 62.597 0.10 0.9197 main_effect
gdh No K15371 45.506 29.182 1.56 0.1301 main_effect
napA No K02567 −19.785 9.773 −2.02 0.0526 main_effect
napA Yes K01416 1.765 3.606 0.49 0.6283 main_effect
napB No K02568 −6.276 7.208 −0.87 0.3913 main_effect
narG Yes K00370 15.946 27.289 0.58 0.5637 main_effect
narH Yes K00371 20.794 22.333 0.93 0.3598 main_effect
narI No K00374 56.557 27.251 2.08 0.0473 main_effect
nasA Yes K00372 44.172 46.678 0.95 0.3521 main_effect
nasB Yes K00360 −0.171 3.476 −0.05 0.9611 main_effect
nirA Yes K00366 29.754 23.037 1.29 0.2071 main_effect
nirK Yes K00368 32.604 20.951 1.56 0.1309 main_effect
nirS Yes K15864 −1.326 1.209 −1.10 0.2823 main_effect
norB Yes K04561 17.334 23.072 0.75 0.4587 main_effect
norC No K02305 2.241 25.302 0.09 0.9300 main_effect
nosZ Yes K00376 7.276 21.886 0.33 0.7420 main_effect
nrfA Yes K03385 −38.438 30.709 −1.25 0.2211 main_effect
ureC No K01428 216.753 87.198 2.49 0.0197 interaction
ureC No K01428 −145.598 59.176 −2.46 0.0275 by_group_JB1_JB2
ureC No K01428 71.155 63.450 1.12 0.2840 by_group_JB5_JB6_JB7
Nodulation nodA Yes K14658 0.276 0.507 0.54 0.5901 main_effect
nodD Yes K14657 −2.175 3.630 −0.60 0.5538 main_effect
nodI No ABC transporter complex K09694 147.946 145.218 1.02 0.3170 main_effect
Phosphorus Solubilization gcd Yes K00117 6.421 72.101 0.09 0.9297 main_effect
phnX No K06163 −13.232 14.233 −0.93 0.3605 main_effect
phoA Yes K01077 42.738 18.081 2.36 0.0253 main_effect
phoD No K01113 48.259 85.727 0.56 0.5780 main_effect
phoX No K07093 49.507 54.272 0.91 0.3695 main_effect
ppk No K00937 −107.856 88.989 −1.21 0.2356 main_effect
ppx No K01514 2.030 3.109 0.65 0.5190 main_effect
pqqB Yes K06136 −57.366 49.593 −1.16 0.2572 main_effect
pqqC Yes K06137 7.347 48.226 0.15 0.8800 main_effect
pqqD Yes K06138 −21.879 51.865 −0.42 0.6764 main_effect
pqqE Yes K06139 30.513 25.161 1.21 0.2354 main_effect
Potassium Solubilization gcd Yes K00117 6.421 72.101 0.09 0.9297 main_effect
kdsA No K01627 11.124 49.065 0.23 0.8223 main_effect
kdsB No K00979 −19.789 106.361 −0.19 0.8537 main_effect
kup Yes K03549 −100.667 98.517 −1.02 0.3156 main_effect
nhaA No K03313 114.593 116.359 0.98 0.3331 main_effect
pqqB Yes K06136 −57.366 49.593 −1.16 0.2572 main_effect
pqqC Yes K06137 7.347 48.226 0.15 0.8800 main_effect
pqqD Yes K06138 −21.879 51.865 −0.42 0.6764 main_effect
pqqE Yes K06139 30.513 25.161 1.21 0.2354 main_effect
trkA Yes K03499 112.862 116.517 0.97 0.3410 main_effect
trkH Yes K03498 35.262 25.034 1.41 0.1700 main_effect
Stress Adaptation copA Yes Heavy Metal Tolerance K17686 152.731 61.809 2.47 0.0198 main_effect
ectB Yes Salt tolerance K00836 17.177 8.906 1.93 0.0640 main_effect
entC Yes Siderophore production K02361 3.828 2.672 1.43 0.1630 main_effect
glnA No ACC deaminase (ACC-d) K01915 329.123 185.725 1.77 0.0873 main_effect
kdsA Yes Exopolysaccharide production K01627 11.124 49.065 0.23 0.8223 main_effect
kdsB No Exopolysaccharide production K00979 −19.789 106.361 −0.19 0.8537 main_effect
pchA Yes Salicylic acid (SA) K01851 0.175 2.846 0.06 0.9513 main_effect
pchB No Salicylic acid (SA) K04782 21.619 15.521 1.39 0.1746 main_effect
pqqB No Siderophore production K06136 −57.366 49.593 −1.16 0.2572 main_effect
Sulfur Cycling aprA Yes K00394 4.101 3.785 1.08 0.2879 main_effect
cysA Yes K02045 172.253 155.273 1.11 0.2767 main_effect
cysU Yes K02046 14.980 16.704 0.90 0.3775 main_effect
cysW Yes K02047 −11.543 46.009 −0.25 0.8037 main_effect
fccB Yes K17229 1.178 3.242 0.36 0.7190 main_effect
sat Yes K00958 2.506 42.269 0.06 0.9531 main_effect
soxA No K17222 −86.910 45.032 −1.93 0.0638 main_effect
soxB No K17224 −7.720 12.500 −0.62 0.5418 main_effect
soxC Yes K17225 −187.992 84.909 −2.21 0.0351 main_effect
soxD Yes K22622 −19.763 27.976 −0.71 0.4857 main_effect
soxX No K17223 −29.051 32.370 −0.90 0.3771 main_effect
soxY Yes K17226 −85.542 45.241 −1.89 0.0690 main_effect
soxZ Yes K17227 −0.458 35.360 −0.01 0.9898 main_effect
Zinc Cycling mntR No K03709 48.489 48.997 0.99 0.3308 main_effect
troA No K11707 14.669 15.729 0.93 0.3590 main_effect
zitB No K16264 84.894 68.626 1.24 0.2263 main_effect
zntA No K01534 44.165 20.043 2.20 0.0360 main_effect
znuA Yes K09815 141.430 60.235 2.35 0.0268 interaction
znuA Yes K09815 −63.745 28.149 −2.26 0.0399 by_group_JB1_JB2
znuA Yes K09815 77.685 56.796 1.37 0.1964 by_group_JB5_JB6_JB7
znuB Yes K09816 21.170 67.125 0.32 0.7548 main_effect
znuC Yes K09817 42.135 39.288 1.07 0.2927 main_effect
zur No K02076 25.954 15.051 1.72 0.0957 main_effect

Table 20: Summary statistics for each gene. The table shows the summary statistics for the analysis of the metadata variable and each gene (KO gene cluster) organised by section. The table gives estimate, standard error, t-value, p-value and model. “Model” informs which model the summary statistics represents: “main_effect” originate from analysis where all fields are analyzed together. This happens when we have tested for effects of JB and not found any significant difference between JB groups. “Interaction” gives results for the interaction analysis and is included only when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.

Livestock manure

Section Gene Essential Cagetory KO.ID Estimate SE t p-value Model
Antibiotic Production bacB Yes Bacilysin K19547 0.445 0.590 0.76 0.4564 main_effect
bacC Yes Bacilysin K19548 0.857 0.783 1.09 0.2831 main_effect
E4.1.1.82 Yes Fosfomycin K09459 16.858 9.603 1.76 0.0901 main_effect
eryA Yes Macrolides K00862 −4.400 6.122 −0.72 0.4783 main_effect
penM No Pentalenolactone K17476 −1.396 1.191 −1.17 0.2510 main_effect
pntE Yes Pentalenolactone K18091 −1.436 3.161 −0.45 0.6531 main_effect
pntH Yes Pentalenolactone K18056 −0.727 0.546 −1.33 0.1937 main_effect
ptlF Yes Pentalenolactone K17747 −0.936 0.703 −1.33 0.1937 main_effect
rifG Yes Rifamycin K16020 10.473 4.889 2.14 0.0417 interaction
rifG Yes Rifamycin K16020 −5.507 2.363 −2.33 0.0353 by_group_JB1_JB2
rifG Yes Rifamycin K16020 4.966 4.586 1.08 0.3001 by_group_JB5_JB6_JB7
strA Yes Streptomycin K00547 −27.649 17.426 −1.59 0.1238 main_effect
Antibiotic Resistance vanA Yes Vancomycin K15739 −0.984 2.973 −0.33 0.7432 main_effect
vanH Yes Vancomycin K18347 −0.348 3.135 −0.11 0.9125 main_effect
vanX Yes Vancomycin K08641 26.551 33.974 0.78 0.4411 main_effect
Biocontrol chiA Yes Fungicidal agents K06904 48.807 24.471 1.99 0.0559 main_effect
chiB No Fungicidal agents, Insecticide agents K20547 −2.505 1.406 −1.78 0.0857 main_effect
dapB No Bactericidal agents K00215 −211.385 109.604 −1.93 0.0640 main_effect
phzF Yes Fungicidal agents, Bactericidal agents K06998 125.527 48.105 2.61 0.0148 interaction
phzF Yes Fungicidal agents, Bactericidal agents K06998 −58.617 30.493 −1.92 0.0752 by_group_JB1_JB2
phzF Yes Fungicidal agents, Bactericidal agents K06998 66.910 37.557 1.78 0.1001 by_group_JB5_JB6_JB7
prnA Yes Fungicidal agents K14266 34.757 9.486 3.66 0.0010 main_effect
prnC Yes Fungicidal agents K14257 7.208 7.084 1.02 0.3177 main_effect
tcaB Yes Insecticide agents K07552 −5.228 63.131 −0.08 0.9346 main_effect
Calcium Cycling chaA Yes K07300 207.447 53.029 3.91 0.0005 main_effect
mgtC Yes K07507 259.132 118.174 2.19 0.0375 interaction
mgtC Yes K07507 −221.033 65.750 −3.36 0.0047 by_group_JB1_JB2
mgtC Yes K07507 38.099 102.877 0.37 0.7176 by_group_JB5_JB6_JB7
phaC No K03821 40.875 73.485 0.56 0.5825 main_effect
ureC Yes K01428 44.009 40.998 1.07 0.2922 main_effect
Carbon Fixation ccmK No Calvin–Benson–Bassham (CBB) Cycle K08696 0.910 2.130 0.43 0.6726 main_effect
ccmL No Calvin–Benson–Bassham (CBB) Cycle K08697 4.017 2.523 1.59 0.1226 main_effect
codH Yes Wood–Ljungdahl (WL) pathway K00192 −1.878 1.410 −1.33 0.1937 main_effect
korA Yes Reductive TCA (rTCA) cycle K00174 26.602 31.375 0.85 0.4037 main_effect
korB Yes Reductive TCA (rTCA) cycle K00175 −62.884 49.117 −1.28 0.2109 main_effect
prk Yes Calvin–Benson–Bassham (CBB) Cycle K00855 −14.372 10.772 −1.33 0.1929 main_effect
rbcL Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01601 −12.434 25.614 −0.49 0.6311 main_effect
rbcS Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01602 −44.544 75.330 −0.59 0.5591 main_effect
frdA No Reductive TCA (rTCA) cycle K00244 1.044 8.580 0.12 0.9040 main_effect
mcl No 3HP bicycle K08691 9.680 13.228 0.73 0.4704 main_effect
Chloride Cycling clcA Yes K03281 −334.225 97.153 −3.44 0.0018 main_effect
clcB Yes K03281 −334.225 97.153 −3.44 0.0018 main_effect
clcN Yes K05011 −1.269 0.953 −1.33 0.1937 main_effect
gltT No K11102 −65.949 25.609 −2.58 0.0156 main_effect
kefC No K11745 1.635 4.240 0.39 0.7027 main_effect
Copper Cycling copA Yes K17686 77.057 58.075 1.33 0.1953 main_effect
copB Yes K01533 −4.676 34.418 −0.14 0.8929 main_effect
ctrA Yes K13584 −159.361 88.576 −1.80 0.0828 main_effect
cueO No K14588 −1.685 6.744 −0.25 0.8045 main_effect
cusA Yes K07787 −66.487 32.871 −2.02 0.0528 main_effect
cusB No K07798 −64.678 37.051 −1.75 0.0918 main_effect
Hormone Production acdS Yes Ethylene K01505 −19.473 35.224 −0.55 0.5848 main_effect
aldA Yes IAA K07248 −0.096 5.423 −0.02 0.9860 main_effect
aldH No IAA K00128 35.293 89.379 0.39 0.6959 main_effect
amiE Yes IAA K01426 −11.518 44.278 −0.26 0.7967 main_effect
aspC Yes IAA K00813 3.451 4.387 0.79 0.4380 main_effect
entC No GA K02361 1.400 2.415 0.58 0.5667 main_effect
etfA No Ethylene K03522 −172.034 110.341 −1.56 0.1302 main_effect
iaaH No IAA K21801 −14.015 4.976 −2.82 0.0088 main_effect
iaaM No IAA K00466 5.775 5.720 1.01 0.3213 main_effect
ipdC Yes IAA K04103 −1.321 1.541 −0.86 0.3985 main_effect
ipt Yes CK K00375 −20.721 54.002 −0.38 0.7041 main_effect
miaA No CK K00791 −235.475 117.127 −2.01 0.0541 main_effect
nitA No IAA K01501 32.487 12.459 2.61 0.0149 interaction
nitA No IAA K01501 −29.968 10.349 −2.90 0.0117 by_group_JB1_JB2
nitA No IAA K01501 2.519 4.762 0.53 0.6065 by_group_JB5_JB6_JB7
tnaA No IAA K01667 −10.220 16.269 −0.63 0.5350 main_effect
Iron Cycling bfr No K03594 127.657 48.124 2.65 0.0130 main_effect
dps No K04047 26.431 59.225 0.45 0.6588 main_effect
entC Yes K02361 1.400 2.415 0.58 0.5667 main_effect
feoB Yes K04759 −1.610 14.449 −0.11 0.9121 main_effect
fur No K03711 92.002 61.602 1.49 0.1465 main_effect
iscA No K13628 421.568 183.482 2.30 0.0299 interaction
iscA No K13628 −178.582 137.290 −1.30 0.2143 by_group_JB1_JB2
iscA No K13628 242.986 109.386 2.22 0.0463 by_group_JB5_JB6_JB7
sufB Yes K09014 77.270 35.552 2.17 0.0384 main_effect
sufC No K09013 39.392 46.549 0.85 0.4046 main_effect
yqjH No K07229 0.535 0.708 0.76 0.4564 main_effect
Magnesium Cycling corA Yes K03284 708.569 206.288 3.43 0.0019 main_effect
mgtA Yes K01531 −224.376 101.313 −2.21 0.0351 main_effect
mgtB No K01531 −224.376 101.313 −2.21 0.0351 main_effect
mgtE Yes K06213 17.131 47.374 0.36 0.7203 main_effect
phoQ No K07637 13.873 6.460 2.15 0.0405 main_effect
Manganese Cycling mntA Yes K06147 −245.905 200.379 −1.23 0.2300 main_effect
mntB Yes K06148 −20.609 13.922 −1.48 0.1500 main_effect
mntC Yes K06149 −0.118 4.671 −0.03 0.9801 main_effect
mntH Yes K03322 −109.354 79.144 −1.38 0.1780 main_effect
mntR No K03709 15.788 43.648 0.36 0.7203 main_effect
mntR No K11924 6.641 6.806 0.98 0.3375 main_effect
sitA Yes K11604 3.682 5.737 0.64 0.5263 main_effect
sodA No K04564 14.543 97.326 0.15 0.8823 main_effect
Nitrogen fixation amt No K03320 −384.967 114.087 −3.37 0.0022 main_effect
glnB No K04751 −169.310 136.468 −1.24 0.2250 main_effect
iscS No K04487 −105.826 93.570 −1.13 0.2677 main_effect
moeA No K03750 −96.983 53.140 −1.83 0.0787 main_effect
nifA No K02584 10.523 10.272 1.02 0.3144 main_effect
nifB Yes K02585 −6.029 6.936 −0.87 0.3921 main_effect
nifD Yes K02586 −1.449 8.336 −0.17 0.8633 main_effect
nifE Yes K02587 −8.388 12.224 −0.69 0.4983 main_effect
nifH Yes K02588 −1.695 1.273 −1.33 0.1937 main_effect
nifK Yes K02591 −3.892 13.427 −0.29 0.7740 main_effect
nifM Yes K03769 6.852 40.061 0.17 0.8654 main_effect
nifN Yes K02592 −4.142 2.118 −1.96 0.0605 main_effect
nifQ No K15790 0.291 0.385 0.76 0.4564 main_effect
nifU Yes K04488 38.367 62.929 0.61 0.5470 main_effect
nifV Yes K02594 −4.938 4.678 −1.06 0.3002 main_effect
nifW No K02595 −0.616 1.357 −0.45 0.6534 main_effect
nifX No K02596 −1.909 5.780 −0.33 0.7437 main_effect
nifZ No K02597 0.282 2.191 0.13 0.8986 main_effect
Nitrogen Release amoA Yes K10944 10.432 3.950 2.64 0.0134 main_effect
amoB Yes K10945 10.909 4.914 2.22 0.0347 main_effect
amoC Yes K10946 68.947 53.384 1.29 0.2071 main_effect
gdh No K15371 37.859 25.725 1.47 0.1523 main_effect
napA No K02567 3.921 9.154 0.43 0.6717 main_effect
napA Yes K01416 4.838 3.044 1.59 0.1233 main_effect
napB No K02568 −0.017 6.411 0.00 0.9979 main_effect
narG Yes K00370 31.443 23.352 1.35 0.1890 main_effect
narH Yes K00371 10.372 19.806 0.52 0.6046 main_effect
narI No K00374 −2.871 25.686 −0.11 0.9118 main_effect
nasA Yes K00372 86.789 38.250 2.27 0.0312 main_effect
nasB Yes K00360 3.959 2.958 1.34 0.1915 main_effect
nirA Yes K00366 −41.721 19.262 −2.17 0.0390 main_effect
nirK Yes K00368 23.567 18.642 1.26 0.2166 main_effect
nirS Yes K15864 −0.600 1.078 −0.56 0.5822 main_effect
norB Yes K04561 12.978 20.306 0.64 0.5279 main_effect
norC No K02305 64.486 18.569 3.47 0.0017 main_effect
nosZ Yes K00376 42.381 17.502 2.42 0.0222 main_effect
nrfA Yes K03385 21.174 27.406 0.77 0.4462 main_effect
ureC No K01428 44.009 40.998 1.07 0.2922 main_effect
Nodulation nodA Yes K14658 0.334 0.443 0.76 0.4564 main_effect
nodD Yes K14657 4.515 3.090 1.46 0.1551 main_effect
nodI No ABC transporter complex K09694 215.978 123.212 1.75 0.0906 main_effect
Phosphorus Solubilization gcd Yes K00117 110.659 59.736 1.85 0.0745 main_effect
phnX No K06163 −5.892 12.635 −0.47 0.6446 main_effect
phoA Yes K01077 40.789 15.578 2.62 0.0141 main_effect
phoD No K01113 204.527 65.049 3.14 0.0039 main_effect
phoX No K07093 99.836 44.502 2.24 0.0330 main_effect
ppk No K00937 24.126 79.997 0.30 0.7652 main_effect
ppx No K01514 −4.245 2.630 −1.61 0.1176 main_effect
pqqB Yes K06136 −57.318 43.218 −1.33 0.1955 main_effect
pqqC Yes K06137 24.524 42.090 0.58 0.5648 main_effect
pqqD Yes K06138 −90.595 42.335 −2.14 0.0412 main_effect
pqqE Yes K06139 −25.805 22.125 −1.17 0.2533 main_effect
Potassium Solubilization gcd Yes K00117 110.659 59.736 1.85 0.0745 main_effect
kdsA No K01627 −36.485 42.549 −0.86 0.3985 main_effect
kdsB No K00979 −175.914 87.293 −2.02 0.0536 main_effect
kup Yes K03549 −80.649 86.736 −0.93 0.3604 main_effect
nhaA No K03313 261.941 91.327 2.87 0.0078 main_effect
pqqB Yes K06136 −57.318 43.218 −1.33 0.1955 main_effect
pqqC Yes K06137 24.524 42.090 0.58 0.5648 main_effect
pqqD Yes K06138 −90.595 42.335 −2.14 0.0412 main_effect
pqqE Yes K06139 −25.805 22.125 −1.17 0.2533 main_effect
trkA Yes K03499 −8.707 103.952 −0.08 0.9338 main_effect
trkH Yes K03498 57.706 19.952 2.89 0.0073 main_effect
Stress Adaptation copA Yes Heavy Metal Tolerance K17686 77.057 58.075 1.33 0.1953 main_effect
ectB Yes Salt tolerance K00836 0.957 8.318 0.12 0.9092 main_effect
entC Yes Siderophore production K02361 1.400 2.415 0.58 0.5667 main_effect
glnA No ACC deaminase (ACC-d) K01915 346.854 158.919 2.18 0.0376 main_effect
kdsA Yes Exopolysaccharide production K01627 −36.485 42.549 −0.86 0.3985 main_effect
kdsB No Exopolysaccharide production K00979 −175.914 87.293 −2.02 0.0536 main_effect
pchA Yes Salicylic acid (SA) K01851 0.516 2.496 0.21 0.8378 main_effect
pchB No Salicylic acid (SA) K04782 13.735 13.845 0.99 0.3297 main_effect
pqqB No Siderophore production K06136 −57.318 43.218 −1.33 0.1955 main_effect
Sulfur Cycling aprA Yes K00394 1.142 3.384 0.34 0.7383 main_effect
cysA Yes K02045 226.354 132.510 1.71 0.0987 main_effect
cysU Yes K02046 28.880 13.832 2.09 0.0460 main_effect
cysW Yes K02047 55.739 39.031 1.43 0.1643 main_effect
fccB Yes K17229 2.303 2.819 0.82 0.4208 main_effect
sat Yes K00958 67.074 34.869 1.92 0.0646 main_effect
soxA No K17222 19.918 41.902 0.48 0.6382 main_effect
soxB No K17224 −18.558 10.474 −1.77 0.0873 main_effect
soxC Yes K17225 −21.720 80.680 −0.27 0.7897 main_effect
soxD Yes K22622 5.592 24.749 0.23 0.8229 main_effect
soxX No K17223 −49.031 27.286 −1.80 0.0831 main_effect
soxY Yes K17226 −78.524 39.469 −1.99 0.0565 main_effect
soxZ Yes K17227 −20.197 30.799 −0.66 0.5173 main_effect
Zinc Cycling mntR No K03709 15.788 43.648 0.36 0.7203 main_effect
troA No K11707 15.125 13.723 1.10 0.2798 main_effect
zitB No K16264 −59.829 60.814 −0.98 0.3336 main_effect
zntA No K01534 11.606 18.929 0.61 0.5448 main_effect
znuA Yes K09815 65.744 25.504 2.58 0.0155 main_effect
znuB Yes K09816 150.024 51.764 2.90 0.0072 main_effect
znuC Yes K09817 109.002 28.523 3.82 0.0007 main_effect
zur No K02076 4.734 13.865 0.34 0.7353 main_effect

Table 21: Summary statistics for each gene. The table shows the summary statistics for the analysis of the metadata variable and each gene (KO gene cluster) organised by section. The table gives estimate, standard error, t-value, p-value and model. “Model” informs which model the summary statistics represents: “main_effect” originate from analysis where all fields are analyzed together. This happens when we have tested for effects of JB and not found any significant difference between JB groups. “Interaction” gives results for the interaction analysis and is included only when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.

Degassed fertilizer

Section Gene Essential Cagetory KO.ID Estimate SE t p-value Model
Antibiotic Production bacB Yes Bacilysin K19547 −0.338 0.767 −0.44 0.6626 main_effect
bacC Yes Bacilysin K19548 −0.651 1.026 −0.63 0.5310 main_effect
E4.1.1.82 Yes Fosfomycin K09459 −16.640 12.699 −1.31 0.2007 main_effect
eryA Yes Macrolides K00862 11.498 7.687 1.50 0.1459 main_effect
penM No Pentalenolactone K17476 2.455 1.507 1.63 0.1145 main_effect
pntE Yes Pentalenolactone K18091 7.006 3.883 1.80 0.0820 main_effect
pntH Yes Pentalenolactone K18056 −0.320 0.726 −0.44 0.6626 main_effect
ptlF Yes Pentalenolactone K17747 2.060 0.853 2.42 0.0225 main_effect
rifG Yes Rifamycin K16020 2.892 3.199 0.90 0.3737 main_effect
strA Yes Streptomycin K00547 8.844 23.464 0.38 0.7091 main_effect
Antibiotic Resistance vanA Yes Vancomycin K15739 3.530 3.794 0.93 0.3601 main_effect
vanH Yes Vancomycin K18347 5.946 3.896 1.53 0.1382 main_effect
vanX Yes Vancomycin K08641 16.494 44.298 0.37 0.7124 main_effect
Biocontrol chiA Yes Fungicidal agents K06904 −46.329 32.663 −1.42 0.1671 main_effect
chiB No Fungicidal agents, Insecticide agents K20547 −1.102 1.907 −0.58 0.5679 main_effect
dapB No Bactericidal agents K00215 235.051 144.156 1.63 0.1142 main_effect
phzF Yes Fungicidal agents, Bactericidal agents K06998 54.804 31.529 1.74 0.0932 main_effect
prnA Yes Fungicidal agents K14266 5.932 14.878 0.40 0.6931 main_effect
prnC Yes Fungicidal agents K14257 −4.521 9.289 −0.49 0.6303 main_effect
tcaB Yes Insecticide agents K07552 222.226 70.012 3.17 0.0036 main_effect
Calcium Cycling chaA Yes K07300 −135.450 81.340 −1.67 0.1070 main_effect
mgtC Yes K07507 165.800 88.662 1.87 0.0720 main_effect
phaC No K03821 −55.477 94.967 −0.58 0.5638 main_effect
ureC Yes K01428 85.185 51.642 1.65 0.1102 main_effect
Carbon Fixation ccmK No Calvin–Benson–Bassham (CBB) Cycle K08696 −2.042 2.737 −0.75 0.4618 main_effect
ccmL No Calvin–Benson–Bassham (CBB) Cycle K08697 −4.604 3.294 −1.40 0.1732 main_effect
codH Yes Wood–Ljungdahl (WL) pathway K00192 −0.826 1.874 −0.44 0.6626 main_effect
korA Yes Reductive TCA (rTCA) cycle K00174 −19.151 40.928 −0.47 0.6435 main_effect
korB Yes Reductive TCA (rTCA) cycle K00175 47.360 64.728 0.73 0.4704 main_effect
prk Yes Calvin–Benson–Bassham (CBB) Cycle K00855 4.890 14.335 0.34 0.7355 main_effect
rbcL Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01601 37.764 32.485 1.16 0.2548 main_effect
rbcS Yes Calvin–Benson–Bassham (CBB) Cycle (RuBisCO) K01602 40.501 97.713 0.41 0.6817 main_effect
frdA No Reductive TCA (rTCA) cycle K00244 −1.030 11.096 −0.09 0.9267 main_effect
mcl No 3HP bicycle K08691 −2.780 17.259 −0.16 0.8732 main_effect
Chloride Cycling clcA Yes K03281 19.034 149.797 0.13 0.8998 main_effect
clcB Yes K03281 19.034 149.797 0.13 0.8998 main_effect
clcN Yes K05011 2.792 1.156 2.42 0.0225 main_effect
gltT No K11102 −24.947 36.524 −0.68 0.5002 main_effect
kefC No K11745 0.873 5.495 0.16 0.8749 main_effect
Copper Cycling copA Yes K17686 −69.999 76.281 −0.92 0.3666 main_effect
copB Yes K01533 −48.591 43.562 −1.12 0.2741 main_effect
ctrA Yes K13584 107.991 119.240 0.91 0.3728 main_effect
cueO No K14588 −12.477 8.406 −1.48 0.1489 main_effect
cusA Yes K07787 −23.562 45.285 −0.52 0.6069 main_effect
cusB No K07798 −61.211 49.105 −1.25 0.2229 main_effect
Hormone Production acdS Yes Ethylene K01505 165.617 33.429 4.95 0.0000 main_effect
aldA Yes IAA K07248 −1.704 7.005 −0.24 0.8095 main_effect
aldH No IAA K00128 298.867 101.199 2.95 0.0063 main_effect
amiE Yes IAA K01426 109.815 53.435 2.06 0.0493 main_effect
aspC Yes IAA K00813 3.243 5.702 0.57 0.5740 main_effect
entC No GA K02361 −1.756 3.124 −0.56 0.5786 main_effect
etfA No Ethylene K03522 10.357 148.729 0.07 0.9450 main_effect
iaaH No IAA K21801 4.442 7.241 0.61 0.5445 main_effect
iaaM No IAA K00466 −0.884 7.528 −0.12 0.9074 main_effect
ipdC Yes IAA K04103 1.077 2.008 0.54 0.5960 main_effect
ipt Yes CK K00375 121.073 66.166 1.83 0.0779 main_effect
miaA No CK K00791 303.728 151.506 2.00 0.0547 main_effect
nitA No IAA K01501 11.024 10.308 1.07 0.2940 main_effect
tnaA No IAA K01667 −36.390 20.037 −1.82 0.0801 main_effect
Iron Cycling bfr No K03594 −12.152 69.570 −0.17 0.8626 main_effect
dps No K04047 29.233 76.655 0.38 0.7058 main_effect
entC Yes K02361 −1.756 3.124 −0.56 0.5786 main_effect
feoB Yes K04759 15.430 18.459 0.84 0.4103 main_effect
fur No K03711 −45.735 82.314 −0.56 0.5829 main_effect
iscA No K13628 6.500 131.252 0.05 0.9609 main_effect
sufB Yes K09014 −108.248 45.292 −2.39 0.0238 main_effect
sufC No K09013 −109.876 57.310 −1.92 0.0655 main_effect
yqjH No K07229 −0.406 0.922 −0.44 0.6626 main_effect
Magnesium Cycling corA Yes K03284 −408.525 308.500 −1.32 0.1961 main_effect
mgtA Yes K01531 −223.242 135.604 −1.65 0.1109 main_effect
mgtB No K01531 −223.242 135.604 −1.65 0.1109 main_effect
mgtE Yes K06213 6.358 61.388 0.10 0.9182 main_effect
phoQ No K07637 4.220 8.979 0.47 0.6420 main_effect
Manganese Cycling mntA Yes K06147 338.274 258.182 1.31 0.2008 main_effect
mntB Yes K06148 58.190 15.117 3.85 0.0006 main_effect
mntC Yes K06149 1.669 6.032 0.28 0.7841 main_effect
mntH Yes K03322 82.810 104.606 0.79 0.4352 main_effect
mntR No K03709 21.335 56.427 0.38 0.7082 main_effect
mntR No K11924 −2.750 8.934 −0.31 0.7605 main_effect
sitA Yes K11604 7.160 7.349 0.97 0.3383 main_effect
sodA No K04564 41.792 125.651 0.33 0.7419 main_effect
Nitrogen fixation amt No K03320 136.440 173.053 0.79 0.4371 main_effect
glnB No K04751 −111.153 180.026 −0.62 0.5419 main_effect
iscS No K04487 −14.807 123.692 −0.12 0.9056 main_effect
moeA No K03750 98.072 70.283 1.40 0.1739 main_effect
nifA No K02584 −12.977 13.304 −0.98 0.3377 main_effect
nifB Yes K02585 −6.009 9.018 −0.67 0.5107 main_effect
nifD Yes K02586 −14.174 10.447 −1.36 0.1857 main_effect
nifE Yes K02587 −22.977 15.336 −1.50 0.1453 main_effect
nifH Yes K02588 −0.746 1.692 −0.44 0.6626 main_effect
nifK Yes K02591 −26.481 16.653 −1.59 0.1230 main_effect
nifM Yes K03769 −117.799 46.803 −2.52 0.0178 main_effect
nifN Yes K02592 −1.822 2.899 −0.63 0.5347 main_effect
nifQ No K15790 −0.221 0.501 −0.44 0.6626 main_effect
nifU Yes K04488 41.423 81.535 0.51 0.6154 main_effect
nifV Yes K02594 −8.422 5.959 −1.41 0.1686 main_effect
nifW No K02595 −1.626 1.734 −0.94 0.3564 main_effect
nifX No K02596 −5.717 7.410 −0.77 0.4469 main_effect
nifZ No K02597 −3.152 2.771 −1.14 0.2650 main_effect
Nitrogen Release amoA Yes K10944 −4.696 5.639 −0.83 0.4121 main_effect
amoB Yes K10945 −0.962 6.888 −0.14 0.8900 main_effect
amoC Yes K10946 −92.620 68.865 −1.34 0.1894 main_effect
gdh No K15371 17.537 34.367 0.51 0.6139 main_effect
napA No K02567 −0.709 11.875 −0.06 0.9528 main_effect
napA Yes K01416 −1.734 4.097 −0.42 0.6754 main_effect
napB No K02568 −2.698 8.275 −0.33 0.7468 main_effect
narG Yes K00370 −73.091 27.929 −2.62 0.0141 main_effect
narH Yes K00371 −48.646 24.037 −2.02 0.0526 main_effect
narI No K00374 −14.626 33.106 −0.44 0.6620 main_effect
nasA Yes K00372 102.646 50.197 2.04 0.0504 main_effect
nasB Yes K00360 0.384 3.945 0.10 0.9232 main_effect
nirA Yes K00366 −0.514 26.912 −0.02 0.9849 main_effect
nirK Yes K00368 −43.751 23.364 −1.87 0.0716 main_effect
nirS Yes K15864 −0.880 1.392 −0.63 0.5321 main_effect
norB Yes K04561 −25.616 26.001 −0.99 0.3330 main_effect
norC No K02305 −3.411 28.712 −0.12 0.9063 main_effect
nosZ Yes K00376 −53.728 22.722 −2.36 0.0252 main_effect
nrfA Yes K03385 −52.920 34.389 −1.54 0.1351 main_effect
ureC No K01428 85.185 51.642 1.65 0.1102 main_effect
Nodulation nodA Yes K14658 −0.254 0.576 −0.44 0.6626 main_effect
nodD Yes K14657 1.250 4.139 0.30 0.7649 main_effect
nodI No ABC transporter complex K09694 −81.455 167.127 −0.49 0.6298 main_effect
Phosphorus Solubilization gcd Yes K00117 −122.525 78.495 −1.56 0.1298 main_effect
phnX No K06163 36.677 14.864 2.47 0.0200 main_effect
phoA Yes K01077 9.567 22.402 0.43 0.6726 main_effect
phoD No K01113 6.834 97.832 0.07 0.9448 main_effect
phoX No K07093 −57.089 61.564 −0.93 0.3617 main_effect
ppk No K00937 82.324 102.434 0.80 0.4284 main_effect
ppx No K01514 9.340 3.086 3.03 0.0053 main_effect
pqqB Yes K06136 144.076 50.772 2.84 0.0084 main_effect
pqqC Yes K06137 17.578 54.653 0.32 0.7501 main_effect
pqqD Yes K06138 117.400 54.722 2.15 0.0407 main_effect
pqqE Yes K06139 38.949 28.356 1.37 0.1805 main_effect
Potassium Solubilization gcd Yes K00117 −122.525 78.495 −1.56 0.1298 main_effect
kdsA No K01627 56.131 54.717 1.03 0.3137 main_effect
kdsB No K00979 5.334 120.780 0.04 0.9651 main_effect
kup Yes K03549 211.821 106.605 1.99 0.0568 main_effect
nhaA No K03313 52.844 133.951 0.39 0.6962 main_effect
pqqB Yes K06136 144.076 50.772 2.84 0.0084 main_effect
pqqC Yes K06137 17.578 54.653 0.32 0.7501 main_effect
pqqD Yes K06138 117.400 54.722 2.15 0.0407 main_effect
pqqE Yes K06139 38.949 28.356 1.37 0.1805 main_effect
trkA Yes K03499 29.698 134.315 0.22 0.8266 main_effect
trkH Yes K03498 −30.012 28.849 −1.04 0.3071 main_effect
Stress Adaptation copA Yes Heavy Metal Tolerance K17686 −69.999 76.281 −0.92 0.3666 main_effect
ectB Yes Salt tolerance K00836 12.319 10.503 1.17 0.2507 main_effect
entC Yes Siderophore production K02361 −1.756 3.124 −0.56 0.5786 main_effect
glnA No ACC deaminase (ACC-d) K01915 165.782 220.066 0.75 0.4575 main_effect
kdsA Yes Exopolysaccharide production K01627 56.131 54.717 1.03 0.3137 main_effect
kdsB No Exopolysaccharide production K00979 5.334 120.780 0.04 0.9651 main_effect
pchA Yes Salicylic acid (SA) K01851 −4.684 3.107 −1.51 0.1429 main_effect
pchB No Salicylic acid (SA) K04782 −5.236 18.188 −0.29 0.7756 main_effect
pqqB No Siderophore production K06136 144.076 50.772 2.84 0.0084 main_effect
Sulfur Cycling aprA Yes K00394 −6.848 4.190 −1.63 0.1134 main_effect
cysA Yes K02045 186.212 176.578 1.05 0.3006 main_effect
cysU Yes K02046 14.504 19.031 0.76 0.4524 main_effect
cysW Yes K02047 −1.992 52.273 −0.04 0.9699 main_effect
fccB Yes K17229 5.258 3.551 1.48 0.1499 main_effect
sat Yes K00958 −48.791 47.080 −1.04 0.3089 main_effect
soxA No K17222 79.632 52.277 1.52 0.1389 main_effect
soxB No K17224 26.848 13.351 2.01 0.0541 main_effect
soxC Yes K17225 −17.570 104.406 −0.17 0.8676 main_effect
soxD Yes K22622 2.064 32.029 0.06 0.9491 main_effect
soxX No K17223 125.229 28.781 4.35 0.0002 main_effect
soxY Yes K17226 141.170 47.551 2.97 0.0061 main_effect
soxZ Yes K17227 73.852 37.625 1.96 0.0597 main_effect
Zinc Cycling mntR No K03709 21.335 56.427 0.38 0.7082 main_effect
troA No K11707 13.951 17.933 0.78 0.4431 main_effect
zitB No K16264 −57.900 79.232 −0.73 0.4710 main_effect
zntA No K01534 −34.688 23.752 −1.46 0.1553 main_effect
znuA Yes K09815 −6.630 36.662 −0.18 0.8578 main_effect
znuB Yes K09816 −92.252 74.298 −1.24 0.2247 main_effect
znuC Yes K09817 −20.928 45.322 −0.46 0.6478 main_effect
zur No K02076 −39.418 16.348 −2.41 0.0227 main_effect

Table 22: Summary statistics for each gene. The table shows the summary statistics for the analysis of the metadata variable and each gene (KO gene cluster) organised by section. The table gives estimate, standard error, t-value, p-value and model. “Model” informs which model the summary statistics represents: “main_effect” originate from analysis where all fields are analyzed together. This happens when we have tested for effects of JB and not found any significant difference between JB groups. “Interaction” gives results for the interaction analysis and is included only when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.

Version information

Table 23: List of used software including the used R-programming environment packages.

Package Version Package Version
OS Ubuntu 20.04.4 LTS utf8 1.2.4
R 4.3.3 generics 0.1.3
splines 4.3.3 robustbase 0.99-3
bitops 1.0-7 S4Arrays 1.2.1
cellranger 1.1.0 pkgconfig 2.0.3
lifecycle 1.0.4 gtable 0.3.5
MASS 7.3-60.0.1 hwriter 1.3.2.1
backports 1.5.0 pcaPP 2.0-4
magrittr 2.0.3 htmltools 0.5.8.1
sass 0.4.9 biomformat 1.30.0
rmarkdown 2.27 png 0.1-8
jquerylib 0.1.4 rstudioapi 0.16.0
yaml 2.3.9 tzdb 0.4.0
zip 2.3.1 reshape2 1.4.4
minqa 1.2.7 coda 0.19-4.1
ade4 1.7-22 nlme 3.1-165
multcomp 1.4-26 curl 5.2.1
abind 1.4-5 nloptr 2.1.1
zlibbioc 1.48.2 cachem 1.1.0
Rtsne 0.17 zoo 1.8-12
RCurl 1.98-1.16 rhdf5 2.46.1
TH.data 1.1-2 parallel 4.3.3
sandwich 3.1-0 pillar 1.9.0
GenomeInfoDbData 1.2.11 vctrs 0.6.5
svglite 2.1.3 xtable 1.8-4
codetools 0.2-20 cluster 2.1.6
DelayedArray 0.28.0 paletteer 1.6.0
xml2 1.3.6 evaluate 0.24.0
tidyselect 1.2.1 mvtnorm 1.2-5
multtest 2.58.0 cli 3.6.3
survival 3.7-0 compiler 4.3.3
iterators 1.0.14 rlang 1.1.4
systemfonts 1.1.0 crayon 1.5.3
foreach 1.5.2 rrcov 1.7-5
tools 4.3.3 interp 1.1-6
glue 1.8.0 rematch2 2.1.2
SparseArray 1.2.4 plyr 1.8.9
xfun 0.46 stringi 1.8.4
mgcv 1.9-1 viridisLite 0.4.2
withr 3.0.0 deldir 2.0-4
fastmap 1.2.0 munsell 0.5.1
latticeExtra 0.6-30 V8 4.4.2
boot 1.3-30 hms 1.1.3
rhdf5filters 1.14.1 Rhdf5lib 1.24.2
fansi 1.0.6 highr 0.11
digest 0.6.36 fontawesome 0.5.2
timechange 0.3.0 igraph 2.0.3
R6 2.5.1 RcppParallel 5.1.8
estimability 1.5.1 bslib 0.7.0
colorspace 2.1-0 DEoptimR 1.1-3
jpeg 0.1-10 ape 5.8