Statistical Analysis Report
Species profile from shotgun metagenomic (dataset 2024)
Biomcare ApS
18/06/2025
| 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 microbial 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 microbial composition of the fields focusing on single core species and overall composition structure. We split many analysis by JB values into 2 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 split the analysis based on JB groups as we find the effect of JB overshadows the associations that may be between the microbiome and other variables of interest.
The JB groups are:
- JB 1 + JB 2
- JB 5 + JB 6 + JB 7
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.
We initiate with an evaluation of field geography and how the geography associate with some of the key variables of interest.
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.
Overview of metadata variables
We have included all variables in the collected metadata which have some level of variation across the fields (i.e. must not be all the same value across fields (like all organic) or with only very few deviations like 90%+ identical values).
Below are two overview tables; the first show the variables by category including a short description and the second show the summary statistics of each variable allowing us to inspect the variation and subgroups of fields that the variable represent.
| Category | Report_variable | Description |
|---|---|---|
| Geografi og vejrdata | GPS-koordinater | GPS-koordinater |
| Geografisk placering | Geografisk placering | |
| Geografisk placering (gruppe) | 1=Vendsyssel (V), 2=Region Nord u. Vendsyssel (NJ), 3=Region Midtjylland (MJ), 4=Region Syddanmark u. Fyn (SJ), 5=Sjaelland (S), 6=Lolland, Falster, 7=Fyn (F), 8=Bornholm (B) | |
| Nedboer | Nedboer i alt april-september paa kommuneniveau | |
| Toerkeindeks | Gn.snit toerkeindeks april-september paa kommuneniveau | |
| Middeltemperatur | Gn.snit middeltemperatur april-september paa kommuneniveau | |
| Vurdering af marken | JB | Vurderet JB-nr. |
| Regnorme | Mange regnorm: 1 Faa/ingen regnorm: 0 | |
| Kold jord | Kold jord: 1 Ikke kold jord: 0 | |
| Jordtemperatur | ||
| Kompakt jord | Er jorden kompakt : 1 Ikke kompakt: 0 | |
| Veldraenet | Er marken veldraenet: 1 Ikke veldraenet: 0 | |
| Holde paa vand | Marken kan holde paa vand i toerre perioder 1=ja, 0=nej | |
| Nedmuldning af halm | Nedmuldning af halm seneste 3 aar: 1 Ingen nedmuldning af halm: 0 | |
| Kloevergraes | Kloevergraes i 3 aar: 1 En-aarige afgroeder 3 aar: 0 | |
| Afgraesset | Er marken afgraesset hvert aar de senest 4 aar 1=ja, 0=nej | |
| Slaet | Er der taget slaet paa graesmarkerne de sidste tre aar og ikke afgraesset 1=ja, 0=nej | |
| Afgroede | Afgroede saesonen op til proeveudtagning | |
| Afgroede (gruppe) | K: Kornafgroede uden efterafgroeder KE:Kornafgroede med efterafgroede B: Hesteboenne, aert, lupin som hovedafgroede eller i blanding med korn KL: Kloevergraes G: Groensager F: Froeproduktion (graes, spinat) O: Oliefroe (raps med og uden efterafgroede) M: Majs med eller uden efterafgroede | |
| Ploejefri dyrkning | Ploejefri dyrkning: 1 Traditionel ploejning: 0 | |
| Conservation Agriculture | Conservation Agriculture: 1 Ikke Conservation Agriculture: 0 | |
| Aar_sidste_ploejning | Aar sidste ploejning (inkl. oeko bedrifter med kloevergraes) | |
| Rt | Rt | |
| Fosfor | Fosfor (mg/100g) | |
| Kalium | Kalium (mg/100g) | |
| Magnesium | Magnesium (mg/100g) | |
| Kobber | Kobber (mg/kg) | |
| Organisk stof | Organisk stof (%) | |
| Organisk stof (factor) | Organisk stof L:lav, M:middelhoej H:hoej - ift. lerindhold “Hvad gemmer sig bag tallene” | |
| Ler | Ler (%) | |
| Kvaelstof | Kvaelstof (%) | |
| Driftsform | Organic | oekologisk bedrift: 1 Ikke oekologisk bedrift: 0 |
| Organic (years) | Antal aar siden omlaegning til oekologisk produktioni | |
| Biodynamisk | Biodynamisk bedrift: 1 | |
| Biodynamisk (years) | Antal aar siden omlaegning til biodynamisk produktioni | |
| Husdyrbrug | Husdyrbrug: 1 Uden husdyr: 0 | |
| Goedningstildeling og kalkning | Husdyrgoedning | Husdyrgoedning er anvendt det seneste aar Ja: 1, Nej: 0 |
| Handelsgoedning | Handelsgoedning er anvendt det seneste aar Ja: 1, Nej: 0 | |
| Vinasse | Vinasse er anvendt det seneste aar Ja: 1, Nej: 0 | |
| Gips | Gips er anvendt det seneste aar Ja: 1, Nej: 0 | |
| Afgasset goedning | Afgasset goedning er anvendt det seneste aar Ja: 1, Nej: 0 | |
| Jordforbedringsmidler | Anvendes der jordforbedringsmidler (kompost, praeparater mv.) | |
| Kalket | Er marken kalket de seneste 3 aar: 1 Ikke kalket de seneste 3 aar: 0 |
Table 1: Overview of metadata variables. We have allowed for the overview to be in danish as the data was collected in a danish language table. In the remaining report however we have translated the variables to the report language of English.
The key variables assessed in this report are summarized with summary statistics across the 30 samples in the below table.
| Variable | NotNA | Mean | Median | PropNA |
|---|---|---|---|---|
| year | 30 | 2024 | 2024 | 0 |
| JB_groups | 30 | |||
| … JB1_JB2 | 16 | 53% | ||
| … JB5_JB6_JB7 | 14 | 47% | ||
| JB_value | 30 | 3.5 | 2 | 0 |
| Rainfall | 0 | 1 | ||
| Average_drought_index | 0 | 1 | ||
| Average_temp. | 0 | 1 | ||
| soil_tmp | 30 | 12 | 12 | 0 |
| field_keep_water | 30 | |||
| … 0 | 9 | 30% | ||
| … 1 | 21 | 70% | ||
| Clovergrass_within_3_years | 30 | |||
| … 0 | 10 | 33% | ||
| … 1 | 20 | 67% | ||
| Grazed | 30 | |||
| … 0 | 19 | 63% | ||
| … 1 | 11 | 37% | ||
| Harvested | 30 | |||
| … 0 | 22 | 73% | ||
| … 1 | 8 | 27% | ||
| Years_since_plowing | 30 | 3.5 | 2.5 | 0 |
| Rt | 30 | 5.9 | 5.8 | 0 |
| Phosphorus | 30 | 3.4 | 3.2 | 0 |
| Potassium | 30 | 8.5 | 7.2 | 0 |
| Magnesium | 30 | 7.8 | 7.5 | 0 |
| Cobber | 30 | 2.2 | 1.7 | 0 |
| Organic_material_perc | 30 | 4.1 | 3.5 | 0 |
| Organic_material_factor | 30 | |||
| … H | 7 | 23% | ||
| … M | 23 | 77% | ||
| Clay_perc | 30 | 8 | 6.2 | 0 |
| Nitrogen_perc | 30 | 0.17 | 0.16 | 0 |
| Years_since_turning_organic | 30 | 17 | 11 | 0 |
| Biodynamic_farm | 30 | |||
| … 0 | 21 | 70% | ||
| … 1 | 9 | 30% | ||
| Years_since_turning_biodynamic | 30 | 4.2 | 0 | 0 |
| Livestock_manure | 30 | |||
| … 0 | 11 | 37% | ||
| … 1 | 19 | 63% | ||
| Degassed.fertilizer | 30 | |||
| … 0 | 25 | 83% | ||
| … 1 | 5 | 17% | ||
| Crop_detail | 30 | |||
| … groenkorn vinterrug foraarssaaet med kl graes udlaeg | 1 | 3% | ||
| … Groenkorn Vinterrug m. kl. graes udlaeg | 1 | 3% | ||
| … groentsager | 1 | 3% | ||
| … Helsaed Vaarbyg/aert med undersaaet froegraes | 1 | 3% | ||
| … kl. graes | 3 | 10% | ||
| … kl. graes afgraesning | 5 | 17% | ||
| … Kl. graes afgraesning | 1 | 3% | ||
| … kl. graes afgraesning (varig?) | 1 | 3% | ||
| … Kl. graes slaet | 3 | 10% | ||
| … kl. graes slaet/afpudsning | 1 | 3% | ||
| … Kl.graes afgraesning og slaet | 1 | 3% | ||
| … kl.graes slaet | 2 | 7% | ||
| … kl.graes slaet supleret med afgraesning | 1 | 3% | ||
| … soedkirsebaer siden 2015 med kl.graes imellem | 1 | 3% | ||
| … Vaarbyg med kl. graes efterafgroede | 1 | 3% | ||
| … Vaarbyg med udlaeg af kl.graes | 1 | 3% | ||
| … vedv. kl.graes afgraesning | 1 | 3% | ||
| … vinterhvede | 1 | 3% | ||
| … Vinterraps | 1 | 3% | ||
| … Vinterrug hybrid | 1 | 3% | ||
| … Vinterspelt | 1 | 3% | ||
| Crop_category | 30 | |||
| … G | 1 | 3% | ||
| … K | 3 | 10% | ||
| … KE | 5 | 17% | ||
| … KL | 20 | 67% | ||
| … O | 1 | 3% |
Table 2: Summary statistics of the key variables selected for evaluation in relation to the fields microbiome profiles in 2024.
Evaluation of overall microbiome profiles
Microbiome communities related to factor variables
We use the overall microbiome profiles presented in the stacked barplots above, to calculate a measure of difference in the microbiome composition between samples (beta-diversity). The calculated beta-diversity measures are used for visual inspection of the relationship between the microbiome profiles in the so called ordination plots (see below), and in a statistical model named ADONIS (or PERMANOVA, see details below) to evaluate if the overall microbiome composition associates with the selected variables. For these evaluations we focus on the variables that can be viewed as binary or generating groups (e.g. JB value, Earthworm status, Crops, Mulching of straw and Years since plowing). These variables are “grouping variables” that allow us to group samples into subgroups. The remaining variables constitute continuous values (concentrations or percentages) and therefore, we use a different set of tools to evaluate how they relate to the overall microbiome composition (see below).
Note that “years since plowing” and “Years since turning organic” are analyzed as integers with increasing values (0,1,2, etc) and could be analyzed both with ADONIS and the model used for continuous variables (ENVFIT, see below). However, we find it interesting to visualize the shift in the composition according to “years” in an ordination plot, and the variable is therefore included here.
Visualization by ordination (beta-diversity)
As described in Report 2, beta-diversity is a measure of how similar or dissimilar the microbial community is between each pair of samples. The measures are useful for statistical analysis and visualization of the overall microbiome community. In ordination plots, each sample is a point and the distance between the points increases with increasing dissimilarity in the microbiome communities.
Here we evaluate the microbiome communities using the Bray-Curtis, Aitchison and Jaccard beta-diversity measures. If not all plots are shown in this report, you can find them in the project folder. We use a combination of beta-diversity measures as each measure highlights different properties of the microbiome. See more details in Report 2.
We use the different measures in combination with different microbiome profiles (taxonomic levels and normalization) as follows:
- Bray Curtis and Jaccard are computed from the relative abundance data, at the the species level
- Aitchison is computed from the total abundance data transformed with central-log-ratio (CLR), at the species level
The Aitchison distance is a simple euclidean distance calculated using CLR transformed microbiome profiles. An analysis of CLR transformed data will reveal how the organisms behave relative to the per-sample average microbiome. Values for a microbe can therefore be negative after CLR transformation - meaning that it makes up a smaller amount of the microbiome than the average abundant microbe. This is a very different way to view the microbiome than Bray-Curtis and Jaccard that uses the data as relative proportions (i.e. how big a proportion of the sample’s microbiome does the individual microbe comprise). This might appear unnecessarily mathematical and unrelated to agrobiology but the CLR transformation has proved to be able to pinpoint patterns in microbiomes that are driven by environmental factors such as nutrient content or treatment applied to the samples. We therefore evaluate structures in the dataset using all three measures.
As we move from the per-year analysis to a cross-years analysis, I have changed the ordination method from an NMDS method (metaMDS in package vegan) to MDS/dbRDA (capscale in package vegan), as the capscale approach allows me to condition (or partial out, aka. remove), the effect of year from the data allowing us to better inspect effects of other variables in the ordination plots. In the statistical analysis e.g. the ADONIS model, I do this by including a term for year in the model.
Perhaps when we have data from 2023 as well, we can try to look if any effects are specific to one year, and then discuss what was different between the years to possible cause this. But with the few samples form 2021 we cannot reliably extract such information at this point.
Permutational Multivariate Analysis of Variance
To evaluate if the compositional differences evaluated below using ordination plots explain a notable amount of the variation in the microbial composition, and if the amount of explained variation is statistically significant, we perform an analysis named Permutational Multivariate Analysis of Variance (ADONIS). ADONIS uses sums of squares of a multivariate dataset and is analogous to MANOVA (multivariate analysis of variance) using beta-diversity measures. It uses distance matrices among sources of variation and fits linear models to the distance matrices using a permutation test with pseudo-F ratios and can therefore be considered as a “permutational manova”.
For the analysis we use Bray-Curtis, Jaccard and Aitchison beta-diversity measures and perform the analysis at the phylum level down to the ASV level. The latter is used in amplicon sequencing in which a group of exact sequences is referred to as an amplicon sequence variant (ASV).
Each table shows results from evaluation of the effect of one variable and there is thus one table per variable.
In each plot, samples are colored by the variable being assessed. As biodynamic practices is a key feature of interest for this project we also indicate which sample is from a bio biodynamic farm using the shape of the dots. This help us evaluate the effect of each variable in relation to biodynamic farming.
Part-conclusion for section
The section evaluate the grouping variables (those variables that are not numeric but categorical or binary like JB groups). Key observations are:
As expected from prior years analyses we see a strong difference in the soil composition of species between the JB groups.
We do see some separation based on ‘Field keep water’ that is strongest for JB 5-7 however there is only two ‘bad (0)’ fields leaving us to state there is an indication but we are lacking power to be conclusive. In JB 1-2 there is also a trending separation at least visually which is strongest for Jaccard.
Grazing, which was strongly associate with the fungal composition, also show a tendency here where we are primarily looking at bacteria at the species level. The separation is clear in JB 1-2 with CLR transformed data.
We only have two harvested fields with JB 5-7, thus the observation here is an indication, but the ordinations does indicate a strong role of harvest practice on bacteria in fields with JB 5-7. With only two cases we cannot get a low p-value as the permutations will detect there is a too large risk the pattern can be generated randomly.
Clover grass shows some association that is strongest in JB 1-2 fields with Bray-Curtis. Thus, we see tendencies but not strong consistent pattern.
Biodynamic farming shows a very strong association with the microbial community of the soil in both JB groups. It appears to be the strongest dictator of differences in JB 1-2 as it separates the samples along the first ordination axis. It also gives strikingly consistent low p-values in the permutational analysis with high percentage of variation explained.
Livestock manure also show a notable association with the microbial composition primarily in JB 1-2 for a change in presence/absence of organisms (Jaccard).
Degassed fertilizer was only used in fields of JB 1-2. For these there was a trending association with composition that was strongest for Bray-Curtis.
Crop category has many fields in the KL group and we need more samples from the other groups to make any firm conclusions.
JB value
Figure 1: Visualization of structure of the microbial community between the samples. Ordination plots using different beta-diversity measures and data transformations as stated in the plot titles. Dots are colored by the variable of interest as seen to the right of the figure panels.
| Bray-Curtis | Jaccard | Aitchison | ||||
| Taxa level | R2 | p | R2 | p | R2 | p |
| Phylum | 0.0684 | 0.139 | 0.006 | 0.952 | 0.0429 | 0.277 |
| Class | 0.0837 | 0.043 | 0.046 | 0.203 | 0.0484 | 0.154 |
| Order | 0.0801 | 0.014 | 0.0677 | 0.017 | 0.0783 | 0.012 |
| Family | 0.0742 | 0.023 | 0.054 | 0.046 | 0.0496 | 0.108 |
| Genus | 0.0758 | 0.005 | 0.0488 | 0.062 | 0.0545 | 0.027 |
| Species | 0.077 | 0.004 | 0.0633 | 0.005 | 0.0471 | 0.034 |
Table 3: Results from ADONIS analysis. The table shows results from ADONIS analyses including samples from all fields. The analysis was performed using 999 permutations to robustly calculate significance. The table shows the obtained R-squared values that indicate the percentage of variation that the variable could explain and the corresponding p-values.
Field keep water
Figure 2: Visualization of the microbial community composition. Ordination plots using different beta-diversity measures and data transformations as stated in the plot titles. Dots are colored by the variable of interest as seen to the right of the figure panels. Samples are split by JB value with upper row showing JB value = 1-2 and bottom row showing JB value = 5-7.
| Bray-Curtis | Jaccard | Aitchison | ||||
| Taxa level | R2 | p | R2 | p | R2 | p |
| Phylum | 0.0275 | 0.73 | 0.1052 | 0.155 | 0.0234 | 0.923 |
| Class | 0.0284 | 0.797 | 0.0941 | 0.166 | 0.0287 | 0.947 |
| Order | 0.0491 | 0.656 | 0.087 | 0.182 | 0.0483 | 0.672 |
| Family | 0.0528 | 0.664 | 0.0971 | 0.07 | 0.0804 | 0.216 |
| Genus | 0.0548 | 0.643 | 0.0815 | 0.148 | 0.0688 | 0.358 |
| Species | 0.0637 | 0.485 | 0.0832 | 0.108 | 0.0721 | 0.234 |
Table 4: Results from ADONIS analysis of JB1-2. The table shows results from ADONIS analyses including samples from all fields. The analysis was performed using 999 permutations to robustly calculate significance. The table shows the obtained R-squared values that indicate the percentage of variation that the variable could explain and the corresponding p-values.
| Bray-Curtis | Jaccard | Aitchison | ||||
| Taxa level | R2 | p | R2 | p | R2 | p |
| Phylum | 0.0744 | 0.354 | 0.0652 | 0.588 | 0.1746 | 0.123 |
| Class | 0.1364 | 0.168 | 0.0825 | 0.309 | 0.1383 | 0.137 |
| Order | 0.2 | 0.1 | 0.1099 | 0.141 | 0.1318 | 0.117 |
| Family | 0.1918 | 0.033 | 0.1149 | 0.115 | 0.1042 | 0.171 |
| Genus | 0.1848 | 0.033 | 0.0944 | 0.184 | 0.0947 | 0.194 |
| Species | 0.1637 | 0.041 | 0.1084 | 0.058 | 0.1062 | 0.039 |
Table 5: Results from ADONIS analysis of JB567. The table shows results from ADONIS analyses including samples from all fields. The analysis was performed using 999 permutations to robustly calculate significance. The table shows the obtained R-squared values that indicate the percentage of variation that the variable could explain and the corresponding p-values.
Grazed
Figure 3: Visualization of the microbial community composition. Ordination plots using different beta-diversity measures and data transformations as stated in the plot titles. Dots are colored by the variable of interest as seen to the right of the figure panels. Samples are split by JB value with upper row showing JB value = 1-2 and bottom row showing JB value = 5-7.
| Bray-Curtis | Jaccard | Aitchison | ||||
| Taxa level | R2 | p | R2 | p | R2 | p |
| Phylum | 0.1224 | 0.151 | 0.0747 | 0.391 | 0.0866 | 0.22 |
| Class | 0.108 | 0.155 | 0.0792 | 0.296 | 0.0754 | 0.286 |
| Order | 0.0833 | 0.276 | 0.0723 | 0.374 | 0.0744 | 0.316 |
| Family | 0.0833 | 0.242 | 0.079 | 0.233 | 0.0823 | 0.2 |
| Genus | 0.0981 | 0.117 | 0.0884 | 0.087 | 0.0944 | 0.048 |
| Species | 0.1012 | 0.085 | 0.0945 | 0.044 | 0.0932 | 0.026 |
Table 6: Results from ADONIS analysis of JB1-2. The table shows results from ADONIS analyses including samples from all fields. The analysis was performed using 999 permutations to robustly calculate significance. The table shows the obtained R-squared values that indicate the percentage of variation that the variable could explain and the corresponding p-values.
| Bray-Curtis | Jaccard | Aitchison | ||||
| Taxa level | R2 | p | R2 | p | R2 | p |
| Phylum | 0.0454 | 0.646 | 0.0754 | 0.489 | 0.1298 | 0.077 |
| Class | 0.0551 | 0.669 | 0.1589 | 0.032 | 0.0943 | 0.228 |
| Order | 0.0924 | 0.295 | 0.1136 | 0.108 | 0.0929 | 0.204 |
| Family | 0.0893 | 0.312 | 0.0996 | 0.15 | 0.09 | 0.206 |
| Genus | 0.0984 | 0.193 | 0.0958 | 0.177 | 0.0975 | 0.124 |
| Species | 0.0879 | 0.28 | 0.0922 | 0.201 | 0.0861 | 0.185 |
Table 7: Results from ADONIS analysis of JB5-7. The table shows results from ADONIS analyses including samples from all fields. The analysis was performed using 999 permutations to robustly calculate significance. The table shows the obtained R-squared values that indicate the percentage of variation that the variable could explain and the corresponding p-values.
Harvested
Figure 4: Visualization of the microbial community composition. Ordination plots using different beta-diversity measures and data transformations as stated in the plot titles. Dots are colored by the variable of interest as seen to the right of the figure panels. Samples are split by JB value with upper row showing JB value = 1-2 and bottom row showing JB value = 5-7.
| Bray-Curtis | Jaccard | Aitchison | ||||
| Taxa level | R2 | p | R2 | p | R2 | p |
| Phylum | 0.0547 | 0.488 | 0.0214 | 0.921 | 0.0268 | 0.905 |
| Class | 0.1193 | 0.112 | 0.0587 | 0.558 | 0.0576 | 0.553 |
| Order | 0.1334 | 0.041 | 0.048 | 0.778 | 0.0398 | 0.861 |
| Family | 0.0817 | 0.233 | 0.0567 | 0.661 | 0.0576 | 0.633 |
| Genus | 0.0795 | 0.257 | 0.0712 | 0.34 | 0.0704 | 0.347 |
| Species | 0.0724 | 0.327 | 0.0682 | 0.41 | 0.0691 | 0.346 |
Table 8: Results from ADONIS analysis of JB1-2. The table shows results from ADONIS analyses including samples from all fields. The analysis was performed using 999 permutations to robustly calculate significance. The table shows the obtained R-squared values that indicate the percentage of variation that the variable could explain and the corresponding p-values.
| Bray-Curtis | Jaccard | Aitchison | ||||
| Taxa level | R2 | p | R2 | p | R2 | p |
| Phylum | 0.019 | 0.844 | 0.0993 | 0.243 | 0.0458 | 0.61 |
| Class | 0.0599 | 0.549 | 0.0942 | 0.216 | 0.0534 | 0.555 |
| Order | 0.0419 | 0.677 | 0.0862 | 0.283 | 0.0744 | 0.413 |
| Family | 0.0515 | 0.623 | 0.0728 | 0.424 | 0.0645 | 0.565 |
| Genus | 0.0726 | 0.331 | 0.0863 | 0.263 | 0.1032 | 0.109 |
| Species | 0.0831 | 0.306 | 0.0985 | 0.147 | 0.0967 | 0.085 |
Table 9: Results from ADONIS analysis of JB5-7. The table shows results from ADONIS analyses including samples from all fields. The analysis was performed using 999 permutations to robustly calculate significance. The table shows the obtained R-squared values that indicate the percentage of variation that the variable could explain and the corresponding p-values.
Clovergrass (within 3 years)
Figure 5: Visualization of the microbial community composition. Ordination plots using different beta-diversity measures and data transformations as stated in the plot titles. Dots are colored by the variable of interest as seen to the right of the figure panels. Samples are split by JB value with upper row showing JB value = 1-2 and bottom row showing JB value = 5-7.
| Bray-Curtis | Jaccard | Aitchison | ||||
| Taxa level | R2 | p | R2 | p | R2 | p |
| Phylum | 0.0108 | 0.896 | 0.1283 | 0.084 | 0.0607 | 0.476 |
| Class | 0.089 | 0.239 | 0.0931 | 0.188 | 0.0617 | 0.501 |
| Order | 0.1147 | 0.077 | 0.0719 | 0.39 | 0.0722 | 0.374 |
| Family | 0.1278 | 0.038 | 0.0792 | 0.239 | 0.0713 | 0.402 |
| Genus | 0.121 | 0.028 | 0.07 | 0.38 | 0.066 | 0.461 |
| Species | 0.1106 | 0.042 | 0.0738 | 0.275 | 0.0694 | 0.344 |
Table 10: Results from ADONIS analysis of JB1-2. The table shows results from ADONIS analyses including samples from all fields. The analysis was performed using 999 permutations to robustly calculate significance. The table shows the obtained R-squared values that indicate the percentage of variation that the variable could explain and the corresponding p-values.
| Bray-Curtis | Jaccard | Aitchison | ||||
| Taxa level | R2 | p | R2 | p | R2 | p |
| Phylum | 0.0088 | 0.951 | 0.1521 | 0.051 | 0.1729 | 0.031 |
| Class | 0.0946 | 0.287 | 0.0982 | 0.223 | 0.133 | 0.064 |
| Order | 0.1307 | 0.078 | 0.115 | 0.102 | 0.1064 | 0.119 |
| Family | 0.1027 | 0.208 | 0.1199 | 0.059 | 0.0754 | 0.463 |
| Genus | 0.0999 | 0.181 | 0.1077 | 0.084 | 0.0678 | 0.667 |
| Species | 0.0818 | 0.386 | 0.0953 | 0.141 | 0.0766 | 0.461 |
Table 11: Results from ADONIS analysis of JB5-7. The table shows results from ADONIS analyses including samples from all fields. The analysis was performed using 999 permutations to robustly calculate significance. The table shows the obtained R-squared values that indicate the percentage of variation that the variable could explain and the corresponding p-values.
Organic material (factor)
Figure 6: Visualization of the microbial community composition. Ordination plots using different beta-diversity measures and data transformations as stated in the plot titles. Dots are colored by the variable of interest as seen to the right of the figure panels. Samples are split by JB value with upper row showing JB value = 1-2 and bottom row showing JB value = 5-7.
| Bray-Curtis | Jaccard | Aitchison | ||||
| Taxa level | R2 | p | R2 | p | R2 | p |
| Phylum | 0.0361 | 0.641 | 0.0319 | 0.798 | 0.0236 | 0.927 |
| Class | 0.0676 | 0.395 | 0.058 | 0.586 | 0.0687 | 0.394 |
| Order | 0.0683 | 0.407 | 0.0556 | 0.628 | 0.0514 | 0.648 |
| Family | 0.0536 | 0.574 | 0.0627 | 0.551 | 0.0491 | 0.798 |
| Genus | 0.0503 | 0.686 | 0.0652 | 0.487 | 0.0658 | 0.463 |
| Species | 0.0494 | 0.757 | 0.0608 | 0.626 | 0.0579 | 0.792 |
Table 12: Results from ADONIS analysis of JB1-2. The table shows results from ADONIS analyses including samples from all fields. The analysis was performed using 999 permutations to robustly calculate significance. The table shows the obtained R-squared values that indicate the percentage of variation that the variable could explain and the corresponding p-values.
| Bray-Curtis | Jaccard | Aitchison | ||||
| Taxa level | R2 | p | R2 | p | R2 | p |
| Phylum | 0.0624 | 0.464 | 0.169 | 0.036 | 0.0624 | 0.498 |
| Class | 0.0631 | 0.471 | 0.1268 | 0.075 | 0.0981 | 0.245 |
| Order | 0.0666 | 0.418 | 0.109 | 0.11 | 0.0892 | 0.273 |
| Family | 0.09 | 0.295 | 0.1195 | 0.062 | 0.156 | 0.021 |
| Genus | 0.0815 | 0.35 | 0.1178 | 0.061 | 0.1138 | 0.056 |
| Species | 0.0901 | 0.286 | 0.0995 | 0.117 | 0.0886 | 0.163 |
Table 13: Results from ADONIS analysis of JB5-7. The table shows results from ADONIS analyses including samples from all fields. The analysis was performed using 999 permutations to robustly calculate significance. The table shows the obtained R-squared values that indicate the percentage of variation that the variable could explain and the corresponding p-values.
Biodynamic farm
Figure 7: Visualization of the microbial community composition. Ordination plots using different beta-diversity measures and data transformations as stated in the plot titles. Dots are colored by the variable of interest as seen to the right of the figure panels. Samples are split by JB value with upper row showing JB value = 1-2 and bottom row showing JB value = 5-7.
| Bray-Curtis | Jaccard | Aitchison | ||||
| Taxa level | R2 | p | R2 | p | R2 | p |
| Phylum | 0.0515 | 0.499 | 0.0835 | 0.269 | 0.0702 | 0.373 |
| Class | 0.0493 | 0.584 | 0.0886 | 0.193 | 0.0796 | 0.281 |
| Order | 0.0624 | 0.457 | 0.109 | 0.058 | 0.1864 | 0.002 |
| Family | 0.076 | 0.301 | 0.1233 | 0.006 | 0.1562 | 0.001 |
| Genus | 0.0807 | 0.238 | 0.1151 | 0.005 | 0.1345 | 0.002 |
| Species | 0.1203 | 0.024 | 0.1351 | 0.001 | 0.1175 | 0.001 |
Table 14: Results from ADONIS analysis of JB1-2. The table shows results from ADONIS analyses including samples from all fields. The analysis was performed using 999 permutations to robustly calculate significance. The table shows the obtained R-squared values that indicate the percentage of variation that the variable could explain and the corresponding p-values.
| Bray-Curtis | Jaccard | Aitchison | ||||
| Taxa level | R2 | p | R2 | p | R2 | p |
| Phylum | 0.1404 | 0.121 | 0.0455 | 0.716 | 0.0778 | 0.416 |
| Class | 0.1286 | 0.123 | 0.1244 | 0.079 | 0.0991 | 0.236 |
| Order | 0.0992 | 0.261 | 0.1312 | 0.047 | 0.1114 | 0.116 |
| Family | 0.1276 | 0.095 | 0.1162 | 0.071 | 0.132 | 0.019 |
| Genus | 0.123 | 0.061 | 0.1499 | 0.004 | 0.1431 | 0.005 |
| Species | 0.1619 | 0.003 | 0.1625 | 0.002 | 0.1274 | 0.003 |
Table 15: Results from ADONIS analysis of JB5-7. The table shows results from ADONIS analyses including samples from all fields. The analysis was performed using 999 permutations to robustly calculate significance. The table shows the obtained R-squared values that indicate the percentage of variation that the variable could explain and the corresponding p-values.
Livestock manure
Figure 8: Visualization of the microbial community composition. Ordination plots using different beta-diversity measures and data transformations as stated in the plot titles. Dots are colored by the variable of interest as seen to the right of the figure panels. Samples are split by JB value with upper row showing JB value = 1-2 and bottom row showing JB value = 5-7.
| Bray-Curtis | Jaccard | Aitchison | ||||
| Taxa level | R2 | p | R2 | p | R2 | p |
| Phylum | 0.0294 | 0.7 | 0.1214 | 0.095 | 0.041 | 0.708 |
| Class | 0.0277 | 0.807 | 0.0773 | 0.319 | 0.0617 | 0.498 |
| Order | 0.0514 | 0.593 | 0.0922 | 0.143 | 0.0811 | 0.25 |
| Family | 0.0654 | 0.417 | 0.1053 | 0.042 | 0.0837 | 0.196 |
| Genus | 0.0743 | 0.309 | 0.0961 | 0.031 | 0.0826 | 0.125 |
| Species | 0.0912 | 0.127 | 0.0962 | 0.033 | 0.0847 | 0.055 |
Table 16: Results from ADONIS analysis of JB1-2. The table shows results from ADONIS analyses including samples from all fields. The analysis was performed using 999 permutations to robustly calculate significance. The table shows the obtained R-squared values that indicate the percentage of variation that the variable could explain and the corresponding p-values.
| Bray-Curtis | Jaccard | Aitchison | ||||
| Taxa level | R2 | p | R2 | p | R2 | p |
| Phylum | 0.1049 | 0.23 | 0.0719 | 0.467 | 0.0567 | 0.61 |
| Class | 0.0843 | 0.339 | 0.0635 | 0.582 | 0.0708 | 0.481 |
| Order | 0.0867 | 0.332 | 0.0642 | 0.602 | 0.071 | 0.48 |
| Family | 0.0746 | 0.437 | 0.0704 | 0.517 | 0.0908 | 0.242 |
| Genus | 0.0703 | 0.489 | 0.0887 | 0.211 | 0.0954 | 0.138 |
| Species | 0.0932 | 0.238 | 0.1022 | 0.099 | 0.092 | 0.104 |
Table 17: Results from ADONIS analysis of JB5-7. The table shows results from ADONIS analyses including samples from all fields. The analysis was performed using 999 permutations to robustly calculate significance. The table shows the obtained R-squared values that indicate the percentage of variation that the variable could explain and the corresponding p-values.
Degassed fertilizer
Figure 9: Visualization of the microbial community composition. Ordination plots using different beta-diversity measures and data transformations as stated in the plot titles. Dots are colored by the variable of interest as seen to the right of the figure panels. Samples are split by JB value with upper row showing JB value = 1-2 and bottom row showing JB value = 5-7.
| Bray-Curtis | Jaccard | Aitchison | ||||
| Taxa level | R2 | p | R2 | p | R2 | p |
| Phylum | 0.1552 | 0.074 | 0.0335 | 0.817 | 0.0803 | 0.257 |
| Class | 0.1152 | 0.127 | 0.0556 | 0.641 | 0.0767 | 0.282 |
| Order | 0.1263 | 0.062 | 0.0638 | 0.519 | 0.076 | 0.318 |
| Family | 0.1485 | 0.018 | 0.0685 | 0.42 | 0.0835 | 0.206 |
| Genus | 0.1141 | 0.052 | 0.0777 | 0.217 | 0.0861 | 0.103 |
| Species | 0.1032 | 0.067 | 0.0788 | 0.174 | 0.0785 | 0.132 |
Table 18: Results from ADONIS analysis of JB1-2. The table shows results from ADONIS analyses including samples from all fields. The analysis was performed using 999 permutations to robustly calculate significance. The table shows the obtained R-squared values that indicate the percentage of variation that the variable could explain and the corresponding p-values.
The variable “Degassed.fertilizer” does not have enough variation across the fields with JB 5-7 to perform an analysis in this subgroup.
Crop category
Figure 10: Visualization of the microbial community composition. Ordination plots using different beta-diversity measures and data transformations as stated in the plot titles. Dots are colored by the variable of interest as seen to the right of the figure panels. Samples are split by JB value with upper row showing JB value = 1-2 and bottom row showing JB value = 5-7.
| Bray-Curtis | Jaccard | Aitchison | ||||
| Taxa level | R2 | p | R2 | p | R2 | p |
| Phylum | 0.1691 | 0.285 | 0.2081 | 0.128 | 0.0822 | 0.826 |
| Class | 0.2322 | 0.053 | 0.1474 | 0.328 | 0.1048 | 0.728 |
| Order | 0.2629 | 0.014 | 0.1226 | 0.589 | 0.1203 | 0.628 |
| Family | 0.2142 | 0.076 | 0.1348 | 0.462 | 0.1267 | 0.569 |
| Genus | 0.208 | 0.073 | 0.1164 | 0.751 | 0.1155 | 0.771 |
| Species | 0.1867 | 0.109 | 0.1219 | 0.681 | 0.1248 | 0.672 |
Table 19: Results from ADONIS analysis of JB1-2. The table shows results from ADONIS analyses including samples from all fields. The analysis was performed using 999 permutations to robustly calculate significance. The table shows the obtained R-squared values that indicate the percentage of variation that the variable could explain and the corresponding p-values.
| Bray-Curtis | Jaccard | Aitchison | ||||
| Taxa level | R2 | p | R2 | p | R2 | p |
| Phylum | 0.3798 | 0.285 | 0.3467 | 0.279 | 0.4075 | 0.242 |
| Class | 0.3912 | 0.241 | 0.3222 | 0.372 | 0.3236 | 0.432 |
| Order | 0.3896 | 0.25 | 0.3004 | 0.501 | 0.2709 | 0.558 |
| Family | 0.3445 | 0.275 | 0.3436 | 0.262 | 0.2876 | 0.53 |
| Genus | 0.3425 | 0.26 | 0.3332 | 0.301 | 0.2691 | 0.75 |
| Species | 0.327 | 0.316 | 0.3018 | 0.484 | 0.3083 | 0.449 |
Table 20: Results from ADONIS analysis of JB5-7. The table shows results from ADONIS analyses including samples from all fields. The analysis was performed using 999 permutations to robustly calculate significance. The table shows the obtained R-squared values that indicate the percentage of variation that the variable could explain and the corresponding p-values.
Overall microbiome communities related to continuous variables
We now turn to the continuous variables. We continue to use the beta-diversity measure from the microbiome, but use a different analysis model named ENVFIT. We again display the samples in ordination plots but add to these plots arrows representing the association of the variables with the microbiome.
ENVFIT
The function fits environmental variables onto an ordination using multiple regression and thus looks for linear relationships between the axis that drive the main variation in the microbiome and the environmental variables.
The output of the analysis gives the direction of the association in terms of coordinates in the ordination plot (the arrow head). In the plots, the arrows are scaled by their correlation (square root of R2) so that “weak” variables have shorter arrows than “strong” variables. The arrows point in the direction where they have maximal correlations with the ordination axis. The lengths of arrows for fitted vectors are automatically adjusted for the physical size of the plot, and the arrow lengths can thus not be compared across plots, only the arrows within a plot can be compared.
Note that the ENVFIT analysis uses the ordination exes and therefore is restricted to relate the environmental factors to the part of the microbiome that is represented by these axes (and thus not the full microbiome variation). This fact is also relevant when comparing R2 (the squared correlation coefficient) from ADONIS and envfit: ADONIS decomposes the entire dissimilarity matrix into “variance” explained by each covariate. In ENVFIT, you have reduced the entire dissimilarity matrix to two dimensions and then look for correlations in those three dimensions with the covariates. The “discrepancy” is therefore due to the fact that different amounts of variation are assessed by the two models. Therefore, if ADONIS gives higher R2 values, this suggests that the effect of the variable is on the parts of the dissimilarity matrix not represented well by the 3-d NMDS solution. We are using capscale, and not the standard NMDS method, for the ENVFIT analysis, as capscale allow us to condition out the effect of year before performing the correlation analyses. * R2 - variation explained by the model of multiple regression; the square-root of this value is used to scale lengths of vectors (arrows) in the ordination diagrams (variables with higher squared (R2) are represented by longer arrows). * Pr(>r) - the significance of the multiple regression, calculated by permutation test. Indicates whether the variable is related to ordination axes more than if it is a randomly generated one.
Part-conclusion for section
This section review the continuous (numeric) variables and their association with the overall microbial soil community. Again we review the 3 different beta-diversity metrics as they each capture different aspects of the community.
We see:
A strong effect of Rt on the community across diversity measures and in both JB groups. Same as we observed for fungi.
The number of years under biodynamic management appears to be an important factor influencing the soil microbial composition across all JB fields. Although “years since turning biodynamic” is treated as a continuous numeric variable in this analysis, its uneven distribution suggests that the results should be interpreted with caution.
Magnesium show a strong association across JB groups.
Years since plowing shows quite a strong association for Jaccard and euclidean analyses, while there is no association for Bray-Curtis.
Note on the use of different diversity measures.
We used three different measures to compare soil microbiome composition: Bray-Curtis, Jaccard, and Euclidean distance on CLR-transformed data (which corresponds to Aitchison distance). Each of these measures captures different aspects of how microbial communities differ between samples — so it’s normal that they don’t always give the same result.
Bray-Curtis considers the relative abundances of microbes. It emphasizes changes in how much of each microbe is present, especially for the most abundant taxa.
Jaccard looks only at which microbes are present or absent. It tells us whether different microbes are found in different samples, regardless of their abundance.
Aitchison distance (Euclidean distance applied after centered log-ratio (CLR) transformation) is tailored for compositional data, where only the relative proportions of microbes matter. It captures balanced changes across the whole microbial community, including less abundant taxa, in a mathematically appropriate way.
In our results, ‘years since plowing’ showed a strong association with both Jaccard and Aitchison distances, but not with Bray-Curtis. This suggests that plowing history affects which microbes are present and the overall balance of the community, rather than causing major shifts in the dominant taxa that Bray-Curtis would detect.
Ordination plots
Bray Curtis
Jaccard
Aitchison
Figure 11: Visualization of the ENVFIT analysis. The association of the evaluated environmental variables with the ordination axis is displayed by arrows, with longer arrows indicating a stronger association.
ENVFIT summary statistics tables
| . | Bray | Jaccard | Euclidean | |||
| Variable | R2 | p | R2 | p | R2 | p |
| soil tmp | 0.176 | 0.295 | 0.012 | 0.93 | 0.004 | 0.971 |
| Years since plowing | 0.146 | 0.258 | 0.463 | 0.01 | 0.33 | 0.046 |
| Rt | 0.733 | 0.002 | 0.87 | 0.001 | 0.844 | 0.001 |
| Phosphorus | 0.021 | 0.832 | 0.066 | 0.655 | 0.031 | 0.826 |
| Potassium | 0.311 | 0.128 | 0.357 | 0.06 | 0.372 | 0.049 |
| Magnesium | 0.518 | 0.013 | 0.478 | 0.006 | 0.499 | 0.01 |
| Cobber | 0.095 | 0.527 | 0.083 | 0.551 | 0.085 | 0.57 |
| Organic material (%) | 0.053 | 0.589 | 0.037 | 0.795 | 0.053 | 0.74 |
| Clay (%) | 0.336 | 0.101 | 0.397 | 0.037 | 0.372 | 0.051 |
| Nitrogen (%) | 0.22 | 0.19 | 0.186 | 0.241 | 0.198 | 0.251 |
| Years since turning_organic | 0.034 | 0.859 | 0.264 | 0.144 | 0.28 | 0.107 |
| Years since turning_biodynamic | 0.127 | 0.419 | 0.596 | 0.002 | 0.586 | 0.003 |
Table 21: Results from ENVFIT analysis across JB1 and JB2 fields. The table shows results from ENVFIT analyses including samples from all fields. The table shows the obtained R-squared values and the corresponding p-values from the ENVFIT analysis, for each of the assessed variables in each of the three beta-diversity ordinations.
| . | Bray | Jaccard | Euclidean | |||
| Variable | R2 | p | R2 | p | R2 | p |
| soil tmp | 0.039 | 0.784 | 0.087 | 0.591 | 0.138 | 0.455 |
| Years since plowing | 0.092 | 0.575 | 0.463 | 0.01 | 0.33 | 0.046 |
| Rt | 0.733 | 0.002 | 0.87 | 0.001 | 0.844 | 0.001 |
| Phosphorus | 0.626 | 0.005 | 0.659 | 0.005 | 0.647 | 0.005 |
| Potassium | 0.069 | 0.637 | 0.117 | 0.486 | 0.372 | 0.049 |
| Magnesium | 0.518 | 0.013 | 0.478 | 0.006 | 0.499 | 0.01 |
| Cobber | 0.086 | 0.602 | 0.115 | 0.535 | 0.081 | 0.638 |
| Organic material (%) | 0.383 | 0.086 | 0.229 | 0.23 | 0.196 | 0.279 |
| Clay (%) | 0.518 | 0.011 | 0.397 | 0.037 | 0.562 | 0.012 |
| Nitrogen (%) | 0.547 | 0.013 | 0.402 | 0.055 | 0.381 | 0.061 |
| Years since turning_organic | 0.258 | 0.155 | 0.029 | 0.87 | 0.122 | 0.5 |
| Years since turning_biodynamic | 0.528 | 0.071 | 0.596 | 0.002 | 0.586 | 0.003 |
Table 22: Results from ENVFIT analysis across JB1 and JB2 fields. The table shows results from ENVFIT analyses including samples from all fields. The table shows the obtained R-squared values and the corresponding p-values from the ENVFIT analysis, for each of the assessed variables in each of the three beta-diversity ordinations.
Non-linear relationships for continuous environmental variables
The ENVFIT model looks for linear relationships between the main variation of the microbiome (the separation of the samples along the first ordination axes) and the environmental variables. It can also be relevant to look for non-linear relationships - so called smooth surfaces - where the environmental variable for example is highest in the centrally located samples on the ordination plot and lower in samples located towards the edges. We use a mode called Ordisurf to look for such non-linear patterns. Ordisurf internally uses generalized additive models with integrated smoothness estimation, so-called GAMs, to fit the variable. Below is a table of the results from the analysis looking for smooth surfaces for the selected variables and further down are the surfaces illustrated on ordination plots.
We have excluded ‘Years_since_turning_biodynamic’ from this analysis as the pattern of the variable does not contain a pattern that can be reviewed as continuous (e.g. the variable in JB 1-2 fields has the values: 0 0 0 22 22 18 18 18 0 0 0 0 0 0 0 0). In line with this we must interpret the results from the envfit analysis with caution but consider it an indication that we decide to keep as it is supported by the remaining analysis in the report.
Part-conclusion for section:
This section explores a less conventional type of analysis that tests whether the association between continuous variables and microbial community composition is non-linear. Specifically, we ask whether the most pronounced differences occur not gradually along a linear trend, but rather between samples with extreme values versus those closer to the average.
However, we observe little additional signal beyond what was captured in the linear analysis. This suggests that, for the variables examined, their relationship with community composition is predominantly linear.
| Euclidean | ||
| F | P | |
| soil_tmp | 0 | 6.29e-01 |
| Years_since_plowing | 3.238 | 2.26e-03 |
| Rt | 13.079 | 2.12e-05 |
| Phosphorus | 0 | 7.86e-01 |
| Potassium | 2.77 | 1.13e-02 |
| Magnesium | 1.422 | 7.50e-03 |
| Cobber | 0.304 | 2.71e-01 |
| Organic_material_perc | 1.049 | 1.03e-01 |
| Clay_perc | 1.138 | 4.99e-02 |
| Nitrogen_perc | 0.658 | 1.65e-01 |
| Years_since_turning_organic | 0.268 | 1.43e-01 |
Table 23: Results from non-linear analysis of JB 1-2. The table shows results from the non-linear analyses performed using Ordisurf for samples JB1 and JB 2. The table shows the obtained F values and the corresponding p-values, for each of the assessed variables based on the Aitchison beta-diversity.
| Euclidean | ||
| F | P | |
| soil_tmp | 0.034 | 3.95e-01 |
| Years_since_plowing | 0.014 | 3.95e-01 |
| Rt | 27.82 | 6.78e-04 |
| Phosphorus | 1.808 | 4.29e-03 |
| Potassium | 0 | 7.72e-01 |
| Magnesium | 0.481 | 9.34e-02 |
| Cobber | 0 | 6.15e-01 |
| Organic_material_perc | 0.087 | 2.96e-01 |
| Clay_perc | 1.172 | 1.52e-02 |
| Nitrogen_perc | 0.527 | 7.21e-02 |
| Years_since_turning_organic | 0 | 7.86e-01 |
Table 24: Results from non-linear analysis of JB 5-7. The table shows results from the non-linear analyses performed using Ordisurf for samples JB5, JB6 and JB 7. The table shows the obtained F values and the corresponding p-values, for each of the assessed variables based on the Aitchison beta-diversity.
Core species
We now turn to analyzing individual microbial taxa: Which species are consistently present in the soil samples? And how do their abundances associate with the environmental and management variables presented in the metadata?
To address this, we take a targeted approach by focusing on core species —those species that are consistently detected across the soil samples. This helps narrow the analysis to the microbial taxa that are most likely to represent ecologically important and functionally stable components of the community.
Description of Core Microbes
Core microbes are the microbial taxa (such as bacteria or fungi) that are consistently found across many different samples within a group—such as soil from multiple fields, roots from different plants, or manure from different farms. These microbes are thought to represent the stable and common part of a microbial community, potentially playing important or essential roles in that environment.
In contrast to rare or sporadic microbes that may appear only in a few locations or under specific conditions, core microbes are the ones most likely to be functionally relevant and ecologically important. Identifying them can help us focus on the microbial players that are reliably associated with plant health, nutrient cycling, or soil structure.
In this study, we defined core microbes as species that are present in at least 80% of soil samples (prevalence ≥ 0.80) and that reach a relative abundance of at least 1% in at least one sample (detection threshold ≥ 0.01). This ensures we focus on both frequent and biologically active members of the microbial community.
After identifying the core species, we categorized them into functional groups—such as different decomposers, opportunistic pathogen or nitrogen fixer —shown in the first column of Table below. This functional annotation helps us interpret the ecological roles these microbes may play across fields and assess whether their abundance is meaningfully associated with environmental or management variables in the dataset.
Description of each functional group:
Actinomycete Decomposer
Soil-dwelling filamentous bacteria (mostly in the order Actinomycetales)
known for breaking down complex organic matter like cellulose and
chitin. Many also produce antibiotics and secondary metabolites. Common
genera: Streptomyces, Micromonospora, Nocardioides.
Thermophilic Decomposer
Bacteria adapted to high temperatures that decompose organic substrates such as plant polymers, particularly in compost, manure, or thermal habitats. They contribute significantly to biomass turnover in hot environments. Examples include Thermobifida and Thermoactinomyces.
Anaerobic Decomposer
Strict or facultative anaerobes that degrade organic matter in oxygen-deprived environments (e.g., gut, sludge, deep soil layers). They often ferment cellulose or hemicellulose. Genera include Acetivibrio and Herbinix.
Hydrocarbon Degrader
Specialist bacteria capable of degrading aromatic or aliphatic hydrocarbons, often found in polluted soils or industrial sites. These species are key in bioremediation. Common genera: Rhodococcus, Mycolicibacterium.
Opportunistic Pathogen
Environmental or commensal bacteria that can cause disease under specific conditions, such as immune suppression or dysbiosis. They are not obligate pathogens but can become invasive. Example: Mycobacterium intracellulare, Bacillus cereus.
Plant-Associated Commensal
Non-pathogenic rhizosphere bacteria that coexist with plants, sometimes enhancing nutrient availability, producing growth hormones, or protecting against pathogens. Includes Pseudomonas and Paraburkholderia.
Nitrogen Fixer - Plant Symbiont
Bacteria that form mutualistic relationships with legumes or other plants by fixing atmospheric nitrogen into ammonia via root nodules. Critical for plant nutrition and soil fertility. Genera: Bradyrhizobium, Rhizobium, Mesorhizobium.
Immunomodulatory Soil Bacterium
Environmental species that are non-pathogenic but can interact with the host immune system in beneficial ways, often studied for vaccine adjuvant or anti-inflammatory properties (e.g., Mycolicibacterium vaccae).
Methanotroph
Bacteria that oxidize methane as their sole source of carbon and energy. Found in soils, wetlands, and sediments, they are important in controlling methane emissions. Example: Methylocapsa.
Soil Decomposer
Broad group of free-living saprotrophs in soil that break down dead organic material, contributing to nutrient cycling and soil health. Includes Bacillus, Neobacillus, Priestia.
Plant-Associated Bacterium
Bacteria that associate with plants, which may include beneficial, neutral, or pathogenic interactions. The term is used when more specific function (e.g., symbiosis, pathogenesis) is unclear. Example: Agrobacterium.
Unclassified
Bacteria for which no established ecological or metabolic role can currently be inferred due to lack of data.
Uncertain
Species or genera with limited or inconsistent functional evidence, making their ecological classification ambiguous. These are often newly described or understudied taxa.
Key Observations:
Dominance of actinomycete decomposers: A substantial proportion of core bacterial species belonged to soil-dwelling actinomycetes such as Streptomyces, Arthrobacter, Nocardioides, Micromonospora, and Kribbella. These taxa are known for their saprotrophic lifestyles and ability to degrade complex organic matter, often producing antibiotics in the process. For instance, Nocardioides panacis and Arthrobacter sp. NicSoilB8 reached Q90 values above 0.7%, indicating persistent and potentially important roles in organic matter turnover and soil health.
Evidence of functional diversity within decomposers: Beyond aerobic actinomycetes, the core also includes thermophilic (e.g., Thermobifida fusca, Saccharomonospora viridis) and anaerobic cellulose degraders (e.g., Herbinix luporum, Acetivibrio saccincola), reflecting a wide range of ecological niches and environmental conditions that support decomposition processes in the soil microbiome.
Enrichment of hydrocarbon degraders: Several Rhodococcus and Mycolicibacterium species were detected, including Mycolicibacterium vanbaalenii, which is known for polycyclic aromatic hydrocarbon degradation. Their presence hints at intrinsic bioremediation potential in these soils, possibly shaped by historical land use or input of organic materials.
High abundance of nitrogen-fixing symbionts: Multiple Bradyrhizobium species were part of the core, with some reaching strikingly high Q90 values (e.g., B. diazoefficiens at 3.9%, B. barranii at 2.5%). This points to a strong potential for biological nitrogen fixation in these fields, likely supported by legume hosts in the crop rotation or persistent soil associations.
Detection of plant-beneficial taxa: Core bacteria included several plant-associated commensals and biocontrol agents such as Pseudomonas fluorescens (Q90 = 6.4%) and Paraburkholderia hospita, known for promoting plant growth and suppressing pathogens through secondary metabolite production.
Presence of potential pathogens: Although most taxa were beneficial or neutral, a few potentially harmful species were also part of the core, including Bacillus cereus and Mycobacterium intracellulare, both of which can act as opportunistic pathogens under certain conditions. Their presence warrants monitoring, particularly in the context of human or crop health.
Functionally ambiguous and novel taxa: A notable fraction of the core community remains poorly characterized, including Allobacillus halotolerans (Q90 = 13.6%), Capillimicrobium parvum, and Baekduia alba. These taxa are either unclassified or lack detailed ecological information, highlighting the limits of current reference databases and the potential for uncovering novel functions within the soil microbiome.
| Functional Group | Species | Rationale | Mean Abundance | Q10 | Q90 |
|---|---|---|---|---|---|
| Actinomycete Decomposer | Streptomyces sp. NBC_00425 | Assigned based on genus-level traits: Streptomyces are abundant soil saprotrophs producing antibiotics and decomposing organic matter. | 0.036 | 0.559 | |
| Streptomyces sp. NBC_01537 | Assigned based on genus-level traits: Streptomyces are abundant soil saprotrophs producing antibiotics and decomposing organic matter. | 0.030 | 0.211 | ||
| Streptomyces canus | Produces antibiotics; decomposer in soil with complex secondary metabolism. | 0.216 | 0.961 | ||
| Streptomyces albidoflavus | Soil saprotroph; produces secondary metabolites including antibiotics. | 0.000 | 0.262 | ||
| Streptomyces mirabilis | Assigned based on genus-level traits: Streptomyces are abundant soil saprotrophs producing antibiotics and decomposing organic matter. | 0.091 | 0.961 | ||
| Streptomyces [Kitasatospora] papulosa | Assigned based on genus-level traits: Streptomyces are abundant soil saprotrophs producing antibiotics and decomposing organic matter. | 0.000 | 0.230 | ||
| Terrabacter sp. C0L_2 | Assigned based on genus-level traits: members of this genus are soil-dwelling actinomycetes. | 0.284 | 0.832 | ||
| Pedococcus sp. KACC 23699 | Assigned based on genus-level traits: generally saprotrophic, soil-associated. | 0.049 | 0.508 | ||
| Arthrobacter sp. NicSoilB8 | Assigned based on genus-level traits: Arthrobacter are versatile soil bacteria involved in degradation of organic compounds. | 0.321 | 0.707 | ||
| Arthrobacter sp. NicSoilB4 | Assigned based on genus-level traits: Arthrobacter are versatile soil bacteria involved in degradation of organic compounds. | 0.027 | 0.588 | ||
| Arthrobacter sp. PAMC25564 | Assigned based on genus-level traits: Arthrobacter are versatile soil bacteria involved in degradation of organic compounds. | 0.033 | 0.476 | ||
| Arthrobacter sulfonylureivorans | Assigned based on genus-level traits: Arthrobacter are versatile soil bacteria involved in degradation of organic compounds. | 0.025 | 0.869 | ||
| Nocardioides sp. T5 | Assigned based on genus-level traits: common soil bacteria involved in organic matter breakdown. | 0.065 | 1.083 | ||
| Nocardioides panacis | Assigned based on genus-level traits: common soil bacteria involved in organic matter breakdown. | 0.373 | 2.093 | ||
| Nocardioides ungokensis | Assigned based on genus-level traits: common soil bacteria involved in organic matter breakdown. | 0.117 | 1.253 | ||
| Kribbella sp. NBC_00359 | Assigned based on genus-level traits: soil actinomycetes with poorly characterized metabolism. | 0.077 | 0.516 | ||
| Kribbella sp. NBC_01484 | Assigned based on genus-level traits: soil actinomycetes with poorly characterized metabolism. | 0.110 | 0.731 | ||
| Kribbella sp. NBC_01510 | Assigned based on genus-level traits: soil actinomycetes with poorly characterized metabolism. | 0.078 | 0.863 | ||
| Micromonospora sp. NBC_00330 | Assigned based on genus-level traits: antibiotic-producing, found in soils and aquatic sediments. | 0.066 | 0.503 | ||
| Micromonospora sp. NBC_01740 | Assigned based on genus-level traits: antibiotic-producing, found in soils and aquatic sediments. | 0.037 | 0.718 | ||
| Micromonospora sp. B006 | Assigned based on genus-level traits: antibiotic-producing, found in soils and aquatic sediments. | 0.013 | 0.366 | ||
| Micromonospora zamorensis | Assigned based on genus-level traits: antibiotic-producing, found in soils and aquatic sediments. | 0.094 | 0.626 | ||
| Dactylosporangium sp. NBC_01737 | Assigned based on genus-level traits: spore-forming soil actinomycetes. | 0.199 | 0.591 | ||
| Streptosporangium sp. 'caverna' | Assigned based on genus-level traits: decomposers with filamentous growth, soil-dwelling. | 0.057 | 0.457 | ||
| Streptosporangium subroseum | Assigned based on genus-level traits: decomposers with filamentous growth, soil-dwelling. | 0.079 | 0.443 | ||
| Streptosporangium roseum | Assigned based on genus-level traits: decomposers with filamentous growth, soil-dwelling. | 0.041 | 0.140 | ||
| Nonomuraea glycinis | Assigned based on genus-level traits: known for secondary metabolite production and organic matter degradation. | 0.087 | 1.195 | ||
| Amycolatopsis sp. DSM 110486 | Assigned based on genus-level traits: antibiotic-producing soil bacteria. | 0.025 | 0.388 | ||
| Actinomycetospora sp. NBC_00405 | Assigned based on genus-level traits: rare actinomycetes with saprotrophic function. | 0.094 | 0.792 | ||
| Anaerobic Decomposer | Acetivibrio saccincola | Anaerobic cellulose degrader in gut and soil environments. | 0.028 | 0.561 | |
| Herbinix luporum | Anaerobic, thermophilic, cellulose-degrading Firmicute. | 0.079 | 0.767 | ||
| Hydrocarbon Degrader | Mycolicibacterium vanbaalenii | Known for its ability to degrade polycyclic aromatic hydrocarbons in contaminated environments. | 0.194 | 0.699 | |
| Mycolicibacterium [Mycobacterium] burgundiense | Assigned based on genus-level traits: Mycolicibacterium species are often environmental bacteria capable of degrading complex hydrocarbons. | 0.006 | 0.074 | ||
| Rhodococcus sp. MTM3W5.2 | Assigned based on genus-level traits: Rhodococcus species degrade a wide range of organic pollutants and are common in soil. | 0.184 | 0.626 | ||
| Rhodococcus sp. W8901 | Assigned based on genus-level traits: Rhodococcus species degrade a wide range of organic pollutants and are common in soil. | 0.050 | 0.260 | ||
| Rhodococcoides fascians | Assigned based on genus-level traits: Rhodococcoides are similar to Rhodococcus in ecological function. | 0.020 | 0.248 | ||
| Immunomodulatory Soil Bacterium | Mycolicibacterium vaccae | Non-pathogenic soil bacterium with immunoregulatory effects; used in allergy and tuberculosis vaccine research. | 0.014 | 0.336 | |
| Methanotroph | Methylocapsa sp. D3K7 | Capable of oxidizing methane; important in methane cycling. | 0.027 | 0.237 | |
| Nitrogen Fixer - Plant Symbiont | Bradyrhizobium sp. 170 | Forms symbiotic nitrogen-fixing nodules with legumes. | 0.892 | 2.627 | |
| Bradyrhizobium sp. 200 | Forms symbiotic nitrogen-fixing nodules with legumes. | 0.484 | 1.174 | ||
| Bradyrhizobium sp. Ash2021 | Forms symbiotic nitrogen-fixing nodules with legumes. | 0.111 | 0.344 | ||
| Bradyrhizobium sp. | Forms symbiotic nitrogen-fixing nodules with legumes. | 0.263 | 0.574 | ||
| Bradyrhizobium erythrophlei | Forms symbiotic nitrogen-fixing nodules with legumes. | 0.189 | 0.750 | ||
| Bradyrhizobium barranii | Forms symbiotic nitrogen-fixing nodules with legumes. | 1.178 | 2.522 | ||
| Bradyrhizobium lablabi | Forms symbiotic nitrogen-fixing nodules with legumes. | 0.324 | 0.872 | ||
| Bradyrhizobium japonicum | Forms root nodules on legumes; major symbiont in soybean nitrogen fixation. | 0.386 | 0.975 | ||
| Bradyrhizobium diazoefficiens | Efficient symbiont of soybeans, known for high nitrogen fixation capacity. | 0.867 | 3.928 | ||
| Bradyrhizobium ottawaense | Forms symbiotic nitrogen-fixing nodules with legumes. | 0.272 | 0.653 | ||
| Mesorhizobium sp. ANAO-SY3R2 | Forms nodules on legumes, fixing nitrogen. | 0.021 | 0.211 | ||
| Rhizobium ruizarguesonis | Symbiotic nitrogen fixer in root nodules. | 0.036 | 0.236 | ||
| Microvirga ossetica | Forms nodules with legumes; recently described symbionts. | 0.025 | 0.377 | ||
| Opportunistic Pathogen | Mycobacterium intracellulare | Member of the Mycobacterium avium complex; causes pulmonary and disseminated infections, especially in immunocompromised hosts. | 0.149 | 0.400 | |
| Bacillus cereus | Can cause food poisoning; also found in soil with saprotrophic capacity. | 0.260 | 1.121 | ||
| Plant-Associated Bacterium | Agrobacterium rosae | Includes plant pathogens and rhizosphere colonizers. | 0.000 | 0.414 | |
| Plant-Associated Commensal | Paraburkholderia hospita | Non-pathogenic member of Paraburkholderia; associated with plant rhizosphere. | 0.028 | 0.525 | |
| Plant-Associated Commensal/Decomposer | Pseudomonas fluorescens | Rhizosphere-associated; promotes plant growth and suppresses pathogens through antibiotic production. | 3.193 | 6.359 | |
| Pseudomonas sp. PONIH3 | Rhizosphere bacteria that promote plant growth and suppress pathogens. | 0.742 | 2.841 | ||
| Soil Decomposer | Bacillus mycoides | Assigned based on genus-level traits: Bacillus species are common decomposers, some with pathogenic potential. | 0.800 | 3.417 | |
| Bacillus licheniformis | Common soil bacterium; produces enzymes used in biotechnology and decomposition of organic matter. | 0.058 | 1.195 | ||
| Neobacillus sp. FSL H8-0543 | Assigned based on genus-level traits: reclassified Bacillus group with saprotrophic functions. | 0.012 | 0.261 | ||
| Neobacillus sp. OS1-33 | Assigned based on genus-level traits: reclassified Bacillus group with saprotrophic functions. | 0.016 | 0.399 | ||
| Peribacillus asahii | Assigned based on genus-level traits: spore-forming soil bacteria with saprotrophic capabilities. | 0.032 | 0.463 | ||
| Priestia megaterium | Assigned based on genus-level traits: formerly Bacillus, saprotrophic in soils. | 0.078 | 0.686 | ||
| Thermophilic Decomposer | Thermobifida fusca | Known for cellulose and hemicellulose degradation under thermophilic conditions. | 0.012 | 0.580 | |
| Saccharomonospora viridis | Assigned based on genus-level traits: thermophilic actinomycetes involved in organic matter degradation. | 0.012 | 0.381 | ||
| Novibacillus thermophilus | Assigned based on genus-level traits: thermophilic decomposers. | 0.019 | 0.408 | ||
| Thermoactinomyces vulgaris | Degrades cellulose and organic matter at high temperatures. | 0.033 | 0.295 | ||
| Unclassified | Humibacillus xanthopallidus | No clear ecological or metabolic information at genus level. | 0.043 | 0.524 | |
| Nakamurella multipartita | No clear ecological or metabolic information at genus level. | 0.164 | 0.550 | ||
| Baekduia alba | No clear ecological or metabolic information at genus level. | 0.291 | 0.739 | ||
| Capillimicrobium parvum | No clear ecological or metabolic information at genus level. | 0.481 | 1.248 | ||
| Allobacillus halotolerans | No clear ecological or metabolic information at genus level. | 6.145 | 13.602 | ||
| Pradoshia sp. D12 | No clear ecological or metabolic information at genus level. | 0.014 | 0.283 | ||
| Afipia sp. GAS231 | Poorly characterized; some are environmental, others potentially opportunistic. | 0.128 | 0.450 | ||
| Afipia carboxidovorans | Poorly characterized; some are environmental, others potentially opportunistic. | 0.022 | 0.366 | ||
| Bosea sp. NBC_00550 | Poorly characterized; may be opportunistic or environmental. | 0.072 | 0.545 | ||
| Skermanella cutis | Little ecological or metabolic information available. | 0.000 | 0.704 | ||
| Massilia sp. R2A-15 | Environmental bacteria with limited characterization. | 0.016 | 0.173 | ||
| Imtechella halotolerans | Little ecological or metabolic information available. | 4.189 | 10.543 |
Table 25: 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).
We continue to evaluate a possible association of each core species with the meta-data variables. 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 core taxa as we have done for other analysis as well. Each organism is analysed using a linear regression and arcsin square root transformation of abundance of the organism to ensure model fit. 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 organism 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 organism, (‘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 core microbes and in the table for each variable keep the organism organised into functional groups. The significant associations are highlighted with green. One observation is for the association between nitrogen levels and nitrogen fixers where we as expected see many positive associations, but we also observe that some of these species appear to only be significantly contributing in soil with JB 5-7. That could possible be an interesting thing to explore and valuable to understand.
Biodynamic farm
Key findings from the table on biodynamic management:
A total of 27 core bacterial species showed significant associations (p < 0.05) with biodynamic farming, suggesting that biodynamic practices selectively shape bacterial community composition—especially among decomposers and symbiotic nitrogen fixers.
Species enriched in biodynamic fields:
Nitrogen-fixing symbionts such as Bradyrhizobium erythrophlei (β = 0.028, p < 0.0001), B. lablabi (β = 0.023, p < 0.0001), B. ottawaense (β = 0.012, p = 0.040), and Bradyrhizobium Ash2021 (β = 0.012, p = 0.012) were significantly more abundant under biodynamic management. These taxa are well-known for forming symbiotic root nodules and contributing to nitrogen fixation, indicating enhanced plant–microbe cooperation in biodynamic fields.
Several Kribbella species (e.g., Kribbella sp. NBC_01510, β = 0.031, p = 0.046) and *Streptomyces [Kitasatospora] papulosa (β = 0.022, p = 0.0008) also increased in abundance. These genera are common soil actinomycetes involved in decomposition and antibiotic production, pointing to a possibly more active microbial detritus food web in biodynamic systems.
Other enriched taxa include Afipia sp. GAS231 (β = 0.013, p = 0.009) and the methanotroph Methylocapsa sp. D3K7 (β = 0.029, p = 0.003), suggesting broader metabolic diversity favored under biodynamic conditions.
Species suppressed in biodynamic fields:
Several decomposer actinomycetes were significantly less abundant in biodynamic fields, including Streptomyces canus (β = −0.025, p = 0.0015), Nocardioides sp. T5 (β = −0.037, p = 0.0028), Micromonospora sp. NBC_00330 (β = −0.022, p = 0.0009), and Actinomycetospora sp. NBC_00405 (β = −0.034, p = 0.0001). This suggests that while some decomposers thrive, others may be outcompeted or suppressed in biodynamic soils, possibly due to shifts in organic inputs or competition.
Strong suppression was also observed for species like Amycolatopsis sp. DSM 110486 (β = −0.026, p < 0.0001) and Streptosporangium subroseum (β = −0.022, p < 0.0001), indicating selective pressures acting on certain filamentous bacteria.
Interactions with farm clusters (JB_groups):
Context-specific effects were evident for multiple taxa. For example, Arthrobacter sp. PAMC25564 showed a significant interaction with JB group (p = 0.0025), being positively associated with biodynamics in JB1_JB2 (β = 0.035, p = 0.0091) but negatively associated in JB5_JB6_JB7 (β = −0.008, p = 0.0070).
Similarly, Kribbella species showed group-dependent enrichment. For instance, Kribbella sp. NBC_01484 had a strong positive association in JB5_JB6_JB7 (β = 0.048, p = 0.0002), but a more modest effect in JB1_JB2 (β = 0.017, p = 0.050), reflecting the importance of local soil context and management legacy.
Mesorhizobium sp. ANAO-SY3R2 also showed interaction with JB group, being positively associated with biodynamics in JB1_JB2 (β = 0.024, p = 0.0462), but not in JB5_JB6_JB7.
| Functional Group | Species | Estimate | SE | t | p-value | Model |
|---|---|---|---|---|---|---|
| Actinomycete Decomposer | Streptomyces sp. NBC 00425 | −0.020 | 0.008 | −2.36 | 0.0254 | main_effect |
| Streptomyces sp. NBC 01537 | 0.004 | 0.006 | 0.67 | 0.5080 | main_effect | |
| Streptomyces canus | −0.025 | 0.007 | −3.53 | 0.0015 | main_effect | |
| Streptomyces albidoflavus | 0.002 | 0.007 | 0.30 | 0.7666 | main_effect | |
| Streptomyces mirabilis | 0.017 | 0.012 | 1.39 | 0.1762 | main_effect | |
| Streptomyces [Kitasatospora] papulosa | 0.022 | 0.006 | 3.77 | 0.0008 | main_effect | |
| Terrabacter sp. C0L 2 | 0.009 | 0.006 | 1.54 | 0.1344 | main_effect | |
| Pedococcus sp. KACC 23699 | −0.002 | 0.009 | −0.23 | 0.8201 | main_effect | |
| Arthrobacter sp. NicSoilB8 | 0.003 | 0.005 | 0.73 | 0.4689 | main_effect | |
| Arthrobacter sp. NicSoilB4 | −0.030 | 0.008 | −3.71 | 0.0009 | main_effect | |
| Arthrobacter sp. PAMC25564 | −0.043 | 0.013 | −3.35 | 0.0025 | interaction | |
| Arthrobacter sp. PAMC25564 | 0.035 | 0.012 | 3.02 | 0.0091 | by_group_JB1_JB2 | |
| Arthrobacter sp. PAMC25564 | −0.008 | 0.002 | −3.25 | 0.0070 | by_group_JB5_JB6_JB7 | |
| Arthrobacter sulfonylureivorans | −0.017 | 0.011 | −1.51 | 0.1434 | main_effect | |
| Nocardioides sp. T5 | −0.037 | 0.011 | −3.28 | 0.0028 | main_effect | |
| Nocardioides panacis | −0.023 | 0.012 | −1.95 | 0.0608 | main_effect | |
| Nocardioides ungokensis | 0.034 | 0.010 | 3.50 | 0.0016 | main_effect | |
| Kribbella sp. NBC 00359 | 0.031 | 0.012 | 2.54 | 0.0175 | interaction | |
| Kribbella sp. NBC 00359 | −0.010 | 0.008 | −1.20 | 0.2508 | by_group_JB1_JB2 | |
| Kribbella sp. NBC 00359 | 0.021 | 0.009 | 2.33 | 0.0381 | by_group_JB5_JB6_JB7 | |
| Kribbella sp. NBC 01484 | 0.031 | 0.012 | 2.61 | 0.0150 | interaction | |
| Kribbella sp. NBC 01484 | 0.017 | 0.008 | 2.14 | 0.0500 | by_group_JB1_JB2 | |
| Kribbella sp. NBC 01484 | 0.048 | 0.009 | 5.34 | 0.0002 | by_group_JB5_JB6_JB7 | |
| Kribbella sp. NBC 01510 | 0.031 | 0.015 | 2.10 | 0.0461 | interaction | |
| Kribbella sp. NBC 01510 | 0.013 | 0.010 | 1.28 | 0.2226 | by_group_JB1_JB2 | |
| Kribbella sp. NBC 01510 | 0.044 | 0.011 | 3.88 | 0.0022 | by_group_JB5_JB6_JB7 | |
| Micromonospora sp. NBC 00330 | −0.022 | 0.006 | −3.72 | 0.0009 | main_effect | |
| Micromonospora sp. NBC 01740 | −0.027 | 0.010 | −2.69 | 0.0119 | main_effect | |
| Micromonospora sp. B006 | 0.020 | 0.009 | 2.15 | 0.0405 | main_effect | |
| Micromonospora zamorensis | −0.009 | 0.009 | −1.05 | 0.3007 | main_effect | |
| Dactylosporangium sp. NBC 01737 | −0.014 | 0.004 | −3.59 | 0.0013 | main_effect | |
| Streptosporangium sp. 'caverna' | −0.024 | 0.004 | −5.72 | 0.0000 | main_effect | |
| Streptosporangium subroseum | −0.022 | 0.004 | −5.35 | 0.0000 | main_effect | |
| Streptosporangium roseum | 0.018 | 0.005 | 3.83 | 0.0007 | main_effect | |
| Nonomuraea glycinis | −0.041 | 0.011 | −3.75 | 0.0008 | main_effect | |
| Amycolatopsis sp. DSM 110486 | −0.026 | 0.005 | −5.68 | 0.0000 | main_effect | |
| Actinomycetospora sp. NBC 00405 | −0.034 | 0.007 | −4.59 | 0.0001 | main_effect | |
| Anaerobic Decomposer | Acetivibrio saccincola | 0.004 | 0.010 | 0.36 | 0.7248 | main_effect |
| Herbinix luporum | −0.007 | 0.010 | −0.65 | 0.5205 | main_effect | |
| Hydrocarbon Degrader | Mycolicibacterium vanbaalenii | −0.016 | 0.010 | −1.67 | 0.1054 | main_effect |
| Mycolicibacterium [Mycobacterium] burgundiense | −0.007 | 0.008 | −0.94 | 0.3570 | main_effect | |
| Rhodococcus sp. MTM3W5.2 | −0.003 | 0.008 | −0.41 | 0.6883 | main_effect | |
| Rhodococcus sp. W8901 | 0.006 | 0.006 | 1.07 | 0.2941 | main_effect | |
| Rhodococcoides fascians | −0.014 | 0.006 | −2.53 | 0.0174 | main_effect | |
| Immunomodulatory Soil Bacterium | Mycolicibacterium vaccae | 0.015 | 0.008 | 1.91 | 0.0661 | main_effect |
| Methanotroph | Methylocapsa sp. D3K7 | 0.029 | 0.009 | 3.21 | 0.0033 | main_effect |
| Nitrogen Fixer - Plant Symbiont | Bradyrhizobium sp. 170 | −0.015 | 0.012 | −1.23 | 0.2299 | main_effect |
| Bradyrhizobium sp. 200 | −0.010 | 0.007 | −1.43 | 0.1625 | main_effect | |
| Bradyrhizobium sp. Ash2021 | 0.012 | 0.004 | 2.70 | 0.0116 | main_effect | |
| Bradyrhizobium sp. | 0.000 | 0.004 | 0.09 | 0.9290 | main_effect | |
| Bradyrhizobium erythrophlei | 0.028 | 0.005 | 6.21 | 0.0000 | main_effect | |
| Bradyrhizobium barranii | −0.002 | 0.010 | −0.20 | 0.8398 | main_effect | |
| Bradyrhizobium lablabi | 0.023 | 0.005 | 4.94 | 0.0000 | main_effect | |
| Bradyrhizobium japonicum | 0.004 | 0.005 | 0.78 | 0.4394 | main_effect | |
| Bradyrhizobium diazoefficiens | 0.020 | 0.017 | 1.17 | 0.2501 | main_effect | |
| Bradyrhizobium ottawaense | 0.012 | 0.006 | 2.15 | 0.0404 | main_effect | |
| Mesorhizobium sp. ANAO-SY3R2 | −0.030 | 0.013 | −2.31 | 0.0288 | interaction | |
| Mesorhizobium sp. ANAO-SY3R2 | 0.024 | 0.011 | 2.19 | 0.0462 | by_group_JB1_JB2 | |
| Mesorhizobium sp. ANAO-SY3R2 | −0.006 | 0.005 | −1.14 | 0.2777 | by_group_JB5_JB6_JB7 | |
| Rhizobium ruizarguesonis | −0.016 | 0.009 | −1.69 | 0.1013 | main_effect | |
| Microvirga ossetica | −0.021 | 0.009 | −2.40 | 0.0232 | main_effect | |
| Opportunistic Pathogen | Mycobacterium intracellulare | 0.007 | 0.005 | 1.44 | 0.1611 | main_effect |
| Bacillus cereus | 0.017 | 0.009 | 1.82 | 0.0791 | main_effect | |
| Plant-Associated Bacterium | Agrobacterium rosae | −0.010 | 0.009 | −1.11 | 0.2777 | main_effect |
| Plant-Associated Commensal | Paraburkholderia hospita | 0.009 | 0.009 | 0.94 | 0.3564 | main_effect |
| Plant-Associated Commensal/Decomposer | Pseudomonas fluorescens | −0.003 | 0.015 | −0.22 | 0.8261 | main_effect |
| Pseudomonas sp. PONIH3 | 0.015 | 0.013 | 1.16 | 0.2547 | main_effect | |
| Soil Decomposer | Bacillus mycoides | −0.002 | 0.016 | −0.14 | 0.8934 | main_effect |
| Bacillus licheniformis | −0.006 | 0.019 | −0.34 | 0.7398 | main_effect | |
| Neobacillus sp. FSL H8-0543 | 0.019 | 0.006 | 3.23 | 0.0031 | main_effect | |
| Neobacillus sp. OS1-33 | 0.015 | 0.007 | 1.99 | 0.0566 | main_effect | |
| Peribacillus asahii | −0.016 | 0.010 | −1.56 | 0.1304 | main_effect | |
| Priestia megaterium | 0.013 | 0.010 | 1.38 | 0.1776 | main_effect | |
| Thermophilic Decomposer | Thermobifida fusca | 0.004 | 0.011 | 0.35 | 0.7256 | main_effect |
| Saccharomonospora viridis | −0.002 | 0.008 | −0.20 | 0.8459 | main_effect | |
| Novibacillus thermophilus | 0.004 | 0.010 | 0.47 | 0.6448 | main_effect | |
| Thermoactinomyces vulgaris | 0.002 | 0.007 | 0.25 | 0.8034 | main_effect | |
| Unclassified | Humibacillus xanthopallidus | −0.008 | 0.008 | −0.96 | 0.3462 | main_effect |
| Nakamurella multipartita | −0.014 | 0.006 | −2.39 | 0.0239 | main_effect | |
| Baekduia alba | −0.009 | 0.005 | −1.75 | 0.0906 | main_effect | |
| Capillimicrobium parvum | −0.004 | 0.007 | −0.58 | 0.5641 | main_effect | |
| Allobacillus halotolerans | 0.020 | 0.019 | 1.03 | 0.3101 | main_effect | |
| Pradoshia sp. D12 | 0.005 | 0.007 | 0.70 | 0.4897 | main_effect | |
| Afipia sp. GAS231 | 0.013 | 0.004 | 2.79 | 0.0094 | main_effect | |
| Afipia carboxidovorans | 0.008 | 0.008 | 0.98 | 0.3373 | main_effect | |
| Bosea sp. NBC 00550 | −0.018 | 0.008 | −2.23 | 0.0340 | main_effect | |
| Skermanella cutis | −0.033 | 0.009 | −3.57 | 0.0013 | main_effect | |
| Massilia sp. R2A-15 | −0.012 | 0.006 | −2.08 | 0.0471 | main_effect | |
| Imtechella halotolerans | 0.015 | 0.019 | 0.77 | 0.4478 | main_effect |
Table 26: Summary statistics for each core microbial species. The table shows the summary statistics for the analysis of the metadata variable and each core species (species level) organised into functional groups. The table gives estimate, standard error, t-value, p-value and model. Model tells which model the summary statistics represents: “main_effect” analysis all fields together as we see no difference between JB groups, “interaction” gives results for the interaction analysis and is included when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.
soil tmp.
| Functional Group | Species | Estimate | SE | t | p-value | Model |
|---|---|---|---|---|---|---|
| Actinomycete Decomposer | Streptomyces sp. NBC 00425 | −0.002 | 0.004 | −0.48 | 0.6339 | main_effect |
| Streptomyces sp. NBC 01537 | −0.002 | 0.003 | −0.89 | 0.3800 | main_effect | |
| Streptomyces canus | 0.007 | 0.004 | 1.87 | 0.0725 | main_effect | |
| Streptomyces albidoflavus | 0.000 | 0.003 | −0.01 | 0.9956 | main_effect | |
| Streptomyces mirabilis | −0.011 | 0.005 | −2.07 | 0.0474 | main_effect | |
| Streptomyces [Kitasatospora] papulosa | 0.000 | 0.003 | 0.08 | 0.9393 | main_effect | |
| Terrabacter sp. C0L 2 | −0.002 | 0.003 | −0.57 | 0.5741 | main_effect | |
| Pedococcus sp. KACC 23699 | −0.006 | 0.004 | −1.76 | 0.0885 | main_effect | |
| Arthrobacter sp. NicSoilB8 | −0.001 | 0.002 | −0.26 | 0.7994 | main_effect | |
| Arthrobacter sp. NicSoilB4 | 0.005 | 0.004 | 1.12 | 0.2719 | main_effect | |
| Arthrobacter sp. PAMC25564 | −0.007 | 0.004 | −1.84 | 0.0766 | main_effect | |
| Arthrobacter sulfonylureivorans | −0.006 | 0.005 | −1.16 | 0.2555 | main_effect | |
| Nocardioides sp. T5 | −0.002 | 0.006 | −0.42 | 0.6789 | main_effect | |
| Nocardioides panacis | 0.010 | 0.005 | 1.99 | 0.0569 | main_effect | |
| Nocardioides ungokensis | 0.000 | 0.005 | −0.04 | 0.9715 | main_effect | |
| Kribbella sp. NBC 00359 | 0.004 | 0.003 | 1.25 | 0.2211 | main_effect | |
| Kribbella sp. NBC 01484 | 0.001 | 0.004 | 0.27 | 0.7910 | main_effect | |
| Kribbella sp. NBC 01510 | 0.004 | 0.005 | 0.81 | 0.4259 | main_effect | |
| Micromonospora sp. NBC 00330 | −0.003 | 0.003 | −0.93 | 0.3608 | main_effect | |
| Micromonospora sp. NBC 01740 | −0.005 | 0.005 | −0.91 | 0.3719 | main_effect | |
| Micromonospora sp. B006 | 0.004 | 0.004 | 0.82 | 0.4167 | main_effect | |
| Micromonospora zamorensis | 0.021 | 0.009 | 2.38 | 0.0249 | interaction | |
| Micromonospora zamorensis | −0.002 | 0.005 | −0.29 | 0.7725 | by_group_JB1_JB2 | |
| Micromonospora zamorensis | 0.019 | 0.006 | 3.42 | 0.0051 | by_group_JB5_JB6_JB7 | |
| Dactylosporangium sp. NBC 01737 | 0.005 | 0.002 | 2.55 | 0.0166 | main_effect | |
| Streptosporangium sp. 'caverna' | 0.004 | 0.003 | 1.40 | 0.1715 | main_effect | |
| Streptosporangium subroseum | 0.003 | 0.002 | 1.32 | 0.1971 | main_effect | |
| Streptosporangium roseum | 0.002 | 0.003 | 0.76 | 0.4529 | main_effect | |
| Nonomuraea glycinis | 0.018 | 0.005 | 3.67 | 0.0010 | main_effect | |
| Amycolatopsis sp. DSM 110486 | 0.005 | 0.003 | 1.61 | 0.1184 | main_effect | |
| Actinomycetospora sp. NBC 00405 | 0.002 | 0.004 | 0.43 | 0.6733 | main_effect | |
| Anaerobic Decomposer | Acetivibrio saccincola | 0.010 | 0.004 | 2.34 | 0.0269 | main_effect |
| Herbinix luporum | 0.008 | 0.004 | 1.91 | 0.0670 | main_effect | |
| Hydrocarbon Degrader | Mycolicibacterium vanbaalenii | 0.003 | 0.004 | 0.75 | 0.4566 | main_effect |
| Mycolicibacterium [Mycobacterium] burgundiense | 0.004 | 0.003 | 1.16 | 0.2542 | main_effect | |
| Rhodococcus sp. MTM3W5.2 | −0.002 | 0.003 | −0.45 | 0.6540 | main_effect | |
| Rhodococcus sp. W8901 | −0.001 | 0.003 | −0.52 | 0.6096 | main_effect | |
| Rhodococcoides fascians | −0.001 | 0.003 | −0.51 | 0.6171 | main_effect | |
| Immunomodulatory Soil Bacterium | Mycolicibacterium vaccae | −0.003 | 0.004 | −0.70 | 0.4908 | main_effect |
| Methanotroph | Methylocapsa sp. D3K7 | −0.007 | 0.005 | −1.44 | 0.1617 | main_effect |
| Nitrogen Fixer - Plant Symbiont | Bradyrhizobium sp. 170 | 0.005 | 0.006 | 0.96 | 0.3471 | main_effect |
| Bradyrhizobium sp. 200 | 0.002 | 0.003 | 0.76 | 0.4529 | main_effect | |
| Bradyrhizobium sp. Ash2021 | −0.001 | 0.002 | −0.55 | 0.5849 | main_effect | |
| Bradyrhizobium sp. | 0.001 | 0.002 | 0.39 | 0.6987 | main_effect | |
| Bradyrhizobium erythrophlei | −0.004 | 0.003 | −1.47 | 0.1538 | main_effect | |
| Bradyrhizobium barranii | 0.000 | 0.004 | 0.09 | 0.9291 | main_effect | |
| Bradyrhizobium lablabi | −0.003 | 0.003 | −1.18 | 0.2477 | main_effect | |
| Bradyrhizobium japonicum | −0.002 | 0.002 | −0.82 | 0.4201 | main_effect | |
| Bradyrhizobium diazoefficiens | −0.015 | 0.007 | −1.96 | 0.0602 | main_effect | |
| Bradyrhizobium ottawaense | −0.001 | 0.003 | −0.38 | 0.7075 | main_effect | |
| Mesorhizobium sp. ANAO-SY3R2 | −0.002 | 0.003 | −0.59 | 0.5619 | main_effect | |
| Rhizobium ruizarguesonis | 0.005 | 0.004 | 1.15 | 0.2594 | main_effect | |
| Microvirga ossetica | 0.006 | 0.004 | 1.43 | 0.1644 | main_effect | |
| Opportunistic Pathogen | Mycobacterium intracellulare | −0.003 | 0.002 | −1.54 | 0.1344 | main_effect |
| Bacillus cereus | 0.000 | 0.004 | 0.07 | 0.9443 | main_effect | |
| Plant-Associated Bacterium | Agrobacterium rosae | −0.001 | 0.004 | −0.19 | 0.8544 | main_effect |
| Plant-Associated Commensal | Paraburkholderia hospita | −0.003 | 0.004 | −0.73 | 0.4732 | main_effect |
| Plant-Associated Commensal/Decomposer | Pseudomonas fluorescens | 0.011 | 0.006 | 1.81 | 0.0808 | main_effect |
| Pseudomonas sp. PONIH3 | 0.002 | 0.006 | 0.35 | 0.7302 | main_effect | |
| Soil Decomposer | Bacillus mycoides | 0.008 | 0.007 | 1.18 | 0.2490 | main_effect |
| Bacillus licheniformis | −0.001 | 0.009 | −0.06 | 0.9489 | main_effect | |
| Neobacillus sp. FSL H8-0543 | 0.001 | 0.003 | 0.35 | 0.7262 | main_effect | |
| Neobacillus sp. OS1-33 | −0.017 | 0.007 | −2.32 | 0.0286 | interaction | |
| Neobacillus sp. OS1-33 | 0.005 | 0.003 | 1.85 | 0.0857 | by_group_JB1_JB2 | |
| Neobacillus sp. OS1-33 | −0.011 | 0.008 | −1.52 | 0.1544 | by_group_JB5_JB6_JB7 | |
| Peribacillus asahii | −0.003 | 0.005 | −0.69 | 0.4981 | main_effect | |
| Priestia megaterium | 0.005 | 0.004 | 1.18 | 0.2465 | main_effect | |
| Thermophilic Decomposer | Thermobifida fusca | 0.023 | 0.011 | 2.06 | 0.0493 | interaction |
| Thermobifida fusca | −0.001 | 0.005 | −0.20 | 0.8453 | by_group_JB1_JB2 | |
| Thermobifida fusca | 0.022 | 0.011 | 2.05 | 0.0626 | by_group_JB5_JB6_JB7 | |
| Saccharomonospora viridis | 0.006 | 0.004 | 1.83 | 0.0780 | main_effect | |
| Novibacillus thermophilus | 0.006 | 0.004 | 1.33 | 0.1928 | main_effect | |
| Thermoactinomyces vulgaris | 0.003 | 0.003 | 0.93 | 0.3607 | main_effect | |
| Unclassified | Humibacillus xanthopallidus | 0.003 | 0.004 | 0.84 | 0.4074 | main_effect |
| Nakamurella multipartita | −0.003 | 0.003 | −1.17 | 0.2526 | main_effect | |
| Baekduia alba | 0.000 | 0.002 | −0.10 | 0.9194 | main_effect | |
| Capillimicrobium parvum | 0.006 | 0.003 | 2.00 | 0.0551 | main_effect | |
| Allobacillus halotolerans | 0.004 | 0.009 | 0.48 | 0.6341 | main_effect | |
| Pradoshia sp. D12 | 0.001 | 0.003 | 0.37 | 0.7172 | main_effect | |
| Afipia sp. GAS231 | −0.004 | 0.002 | −1.83 | 0.0776 | main_effect | |
| Afipia carboxidovorans | 0.004 | 0.004 | 1.02 | 0.3150 | main_effect | |
| Bosea sp. NBC 00550 | 0.002 | 0.004 | 0.48 | 0.6325 | main_effect | |
| Skermanella cutis | 0.008 | 0.005 | 1.68 | 0.1032 | main_effect | |
| Massilia sp. R2A-15 | 0.003 | 0.003 | 1.13 | 0.2684 | main_effect | |
| Imtechella halotolerans | 0.002 | 0.009 | 0.26 | 0.7937 | main_effect |
Table 27: Summary statistics for each core microbial species. The table shows the summary statistics for the analysis of the metadata variable and each core species (species level) organised into functional groups. The table gives estimate, standard error, t-value, p-value and model. Model tells which model the summary statistics represents: “main_effect” analysis all fields together as we see no difference between JB groups, “interaction” gives results for the interaction analysis and is included 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
| Functional Group | Species | Estimate | SE | t | p-value | Model |
|---|---|---|---|---|---|---|
| Actinomycete Decomposer | Streptomyces sp. NBC 00425 | −0.001 | 0.001 | −0.82 | 0.4164 | main_effect |
| Streptomyces sp. NBC 01537 | 0.001 | 0.001 | 0.93 | 0.3578 | main_effect | |
| Streptomyces canus | 0.000 | 0.001 | −0.42 | 0.6758 | main_effect | |
| Streptomyces albidoflavus | 0.000 | 0.001 | −0.19 | 0.8515 | main_effect | |
| Streptomyces mirabilis | 0.001 | 0.001 | 0.51 | 0.6162 | main_effect | |
| Streptomyces [Kitasatospora] papulosa | 0.000 | 0.001 | −0.11 | 0.9133 | main_effect | |
| Terrabacter sp. C0L 2 | −0.001 | 0.001 | −1.25 | 0.2234 | main_effect | |
| Pedococcus sp. KACC 23699 | −0.001 | 0.001 | −1.73 | 0.0953 | main_effect | |
| Arthrobacter sp. NicSoilB8 | 0.000 | 0.000 | 0.53 | 0.6036 | main_effect | |
| Arthrobacter sp. NicSoilB4 | −0.001 | 0.001 | −1.47 | 0.1526 | main_effect | |
| Arthrobacter sp. PAMC25564 | 0.002 | 0.001 | 1.77 | 0.0872 | main_effect | |
| Arthrobacter sulfonylureivorans | 0.002 | 0.001 | 1.80 | 0.0833 | main_effect | |
| Nocardioides sp. T5 | −0.001 | 0.001 | −0.90 | 0.3764 | main_effect | |
| Nocardioides panacis | −0.003 | 0.001 | −2.45 | 0.0208 | main_effect | |
| Nocardioides ungokensis | 0.001 | 0.001 | 0.67 | 0.5107 | main_effect | |
| Kribbella sp. NBC 00359 | 0.000 | 0.001 | 0.06 | 0.9533 | main_effect | |
| Kribbella sp. NBC 01484 | 0.002 | 0.001 | 2.48 | 0.0193 | main_effect | |
| Kribbella sp. NBC 01510 | 0.001 | 0.001 | 1.41 | 0.1704 | main_effect | |
| Micromonospora sp. NBC 00330 | 0.000 | 0.001 | −0.25 | 0.8038 | main_effect | |
| Micromonospora sp. NBC 01740 | −0.005 | 0.002 | −2.31 | 0.0290 | interaction | |
| Micromonospora sp. NBC 01740 | 0.000 | 0.001 | 0.00 | 0.9965 | by_group_JB1_JB2 | |
| Micromonospora sp. NBC 01740 | −0.005 | 0.002 | −2.26 | 0.0430 | by_group_JB5_JB6_JB7 | |
| Micromonospora sp. B006 | 0.001 | 0.001 | 0.67 | 0.5063 | main_effect | |
| Micromonospora zamorensis | 0.000 | 0.001 | 0.45 | 0.6551 | main_effect | |
| Dactylosporangium sp. NBC 01737 | −0.001 | 0.000 | −2.08 | 0.0467 | main_effect | |
| Streptosporangium sp. 'caverna' | −0.001 | 0.001 | −2.15 | 0.0405 | main_effect | |
| Streptosporangium subroseum | −0.001 | 0.000 | −2.28 | 0.0306 | main_effect | |
| Streptosporangium roseum | 0.001 | 0.001 | 1.24 | 0.2236 | main_effect | |
| Nonomuraea glycinis | −0.002 | 0.001 | −1.49 | 0.1484 | main_effect | |
| Amycolatopsis sp. DSM 110486 | −0.001 | 0.001 | −1.76 | 0.0899 | main_effect | |
| Actinomycetospora sp. NBC 00405 | 0.000 | 0.001 | 0.08 | 0.9356 | main_effect | |
| Anaerobic Decomposer | Acetivibrio saccincola | −0.001 | 0.001 | −0.98 | 0.3368 | main_effect |
| Herbinix luporum | −0.001 | 0.001 | −1.53 | 0.1369 | main_effect | |
| Hydrocarbon Degrader | Mycolicibacterium vanbaalenii | −0.001 | 0.001 | −1.64 | 0.1117 | main_effect |
| Mycolicibacterium [Mycobacterium] burgundiense | −0.001 | 0.001 | −0.72 | 0.4763 | main_effect | |
| Rhodococcus sp. MTM3W5.2 | 0.000 | 0.001 | 0.56 | 0.5825 | main_effect | |
| Rhodococcus sp. W8901 | 0.001 | 0.001 | 1.38 | 0.1797 | main_effect | |
| Rhodococcoides fascians | −0.001 | 0.001 | −2.68 | 0.0121 | main_effect | |
| Immunomodulatory Soil Bacterium | Mycolicibacterium vaccae | 0.002 | 0.001 | 2.71 | 0.0114 | main_effect |
| Methanotroph | Methylocapsa sp. D3K7 | −0.004 | 0.001 | −3.65 | 0.0012 | interaction |
| Methylocapsa sp. D3K7 | 0.005 | 0.001 | 7.68 | 0.0000 | by_group_JB1_JB2 | |
| Methylocapsa sp. D3K7 | 0.001 | 0.001 | 1.08 | 0.3009 | by_group_JB5_JB6_JB7 | |
| Nitrogen Fixer - Plant Symbiont | Bradyrhizobium sp. 170 | 0.000 | 0.001 | 0.07 | 0.9420 | main_effect |
| Bradyrhizobium sp. 200 | 0.000 | 0.001 | 0.04 | 0.9653 | main_effect | |
| Bradyrhizobium sp. Ash2021 | 0.001 | 0.000 | 1.16 | 0.2551 | main_effect | |
| Bradyrhizobium sp. | 0.000 | 0.000 | 0.64 | 0.5275 | main_effect | |
| Bradyrhizobium erythrophlei | 0.001 | 0.001 | 1.95 | 0.0611 | main_effect | |
| Bradyrhizobium barranii | 0.001 | 0.001 | 0.57 | 0.5725 | main_effect | |
| Bradyrhizobium lablabi | 0.001 | 0.001 | 2.43 | 0.0217 | main_effect | |
| Bradyrhizobium japonicum | 0.001 | 0.000 | 1.01 | 0.3203 | main_effect | |
| Bradyrhizobium diazoefficiens | 0.001 | 0.002 | 0.46 | 0.6516 | main_effect | |
| Bradyrhizobium ottawaense | 0.001 | 0.001 | 1.17 | 0.2530 | main_effect | |
| Mesorhizobium sp. ANAO-SY3R2 | −0.003 | 0.001 | −3.61 | 0.0013 | interaction | |
| Mesorhizobium sp. ANAO-SY3R2 | 0.003 | 0.001 | 6.39 | 0.0000 | by_group_JB1_JB2 | |
| Mesorhizobium sp. ANAO-SY3R2 | 0.000 | 0.001 | −0.23 | 0.8221 | by_group_JB5_JB6_JB7 | |
| Rhizobium ruizarguesonis | 0.000 | 0.001 | −0.29 | 0.7721 | main_effect | |
| Microvirga ossetica | −0.001 | 0.001 | −0.86 | 0.3956 | main_effect | |
| Opportunistic Pathogen | Mycobacterium intracellulare | 0.000 | 0.000 | −0.52 | 0.6065 | main_effect |
| Bacillus cereus | 0.001 | 0.001 | 1.42 | 0.1653 | main_effect | |
| Plant-Associated Bacterium | Agrobacterium rosae | −0.001 | 0.001 | −1.26 | 0.2184 | main_effect |
| Plant-Associated Commensal | Paraburkholderia hospita | 0.000 | 0.001 | −0.15 | 0.8847 | main_effect |
| Plant-Associated Commensal/Decomposer | Pseudomonas fluorescens | 0.001 | 0.001 | 1.07 | 0.2952 | main_effect |
| Pseudomonas sp. PONIH3 | 0.001 | 0.001 | 0.71 | 0.4844 | main_effect | |
| Soil Decomposer | Bacillus mycoides | 0.001 | 0.001 | 0.80 | 0.4285 | main_effect |
| Bacillus licheniformis | 0.000 | 0.002 | 0.04 | 0.9671 | main_effect | |
| Neobacillus sp. FSL H8-0543 | 0.002 | 0.001 | 2.96 | 0.0062 | main_effect | |
| Neobacillus sp. OS1-33 | 0.001 | 0.001 | 0.92 | 0.3644 | main_effect | |
| Peribacillus asahii | 0.000 | 0.001 | 0.12 | 0.9065 | main_effect | |
| Priestia megaterium | 0.000 | 0.001 | 0.05 | 0.9582 | main_effect | |
| Thermophilic Decomposer | Thermobifida fusca | −0.001 | 0.001 | −0.79 | 0.4357 | main_effect |
| Saccharomonospora viridis | −0.001 | 0.001 | −0.89 | 0.3802 | main_effect | |
| Novibacillus thermophilus | −0.001 | 0.001 | −0.70 | 0.4911 | main_effect | |
| Thermoactinomyces vulgaris | 0.000 | 0.001 | −0.29 | 0.7767 | main_effect | |
| Unclassified | Humibacillus xanthopallidus | −0.001 | 0.001 | −0.69 | 0.4969 | main_effect |
| Nakamurella multipartita | 0.000 | 0.001 | 0.16 | 0.8701 | main_effect | |
| Baekduia alba | 0.000 | 0.001 | −0.90 | 0.3772 | main_effect | |
| Capillimicrobium parvum | 0.000 | 0.001 | 0.12 | 0.9068 | main_effect | |
| Allobacillus halotolerans | 0.001 | 0.002 | 0.79 | 0.4358 | main_effect | |
| Pradoshia sp. D12 | 0.002 | 0.001 | 2.71 | 0.0115 | main_effect | |
| Afipia sp. GAS231 | 0.001 | 0.000 | 1.40 | 0.1731 | main_effect | |
| Afipia carboxidovorans | 0.000 | 0.001 | 0.08 | 0.9347 | main_effect | |
| Bosea sp. NBC 00550 | 0.000 | 0.001 | 0.43 | 0.6729 | main_effect | |
| Skermanella cutis | −0.005 | 0.002 | −2.15 | 0.0414 | interaction | |
| Skermanella cutis | 0.000 | 0.001 | −0.18 | 0.8633 | by_group_JB1_JB2 | |
| Skermanella cutis | −0.005 | 0.002 | −2.53 | 0.0265 | by_group_JB5_JB6_JB7 | |
| Massilia sp. R2A-15 | −0.002 | 0.001 | −3.33 | 0.0025 | main_effect | |
| Imtechella halotolerans | 0.000 | 0.002 | 0.19 | 0.8473 | main_effect |
Table 28: Summary statistics for each core microbial species. The table shows the summary statistics for the analysis of the metadata variable and each core species (species level) organised into functional groups. The table gives estimate, standard error, t-value, p-value and model. Model tells which model the summary statistics represents: “main_effect” analysis all fields together as we see no difference between JB groups, “interaction” gives results for the interaction analysis and is included when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.
Rt
| Functional Group | Species | Estimate | SE | t | p-value | Model |
|---|---|---|---|---|---|---|
| Actinomycete Decomposer | Streptomyces sp. NBC 00425 | −0.045 | 0.018 | −2.54 | 0.0174 | interaction |
| Streptomyces sp. NBC 00425 | 0.039 | 0.012 | 3.21 | 0.0063 | by_group_JB1_JB2 | |
| Streptomyces sp. NBC 00425 | −0.006 | 0.013 | −0.46 | 0.6547 | by_group_JB5_JB6_JB7 | |
| Streptomyces sp. NBC 01537 | −0.011 | 0.006 | −1.70 | 0.1010 | main_effect | |
| Streptomyces canus | 0.038 | 0.006 | 6.94 | 0.0000 | main_effect | |
| Streptomyces albidoflavus | 0.003 | 0.008 | 0.42 | 0.6743 | main_effect | |
| Streptomyces mirabilis | 0.053 | 0.014 | 3.85 | 0.0007 | interaction | |
| Streptomyces mirabilis | −0.071 | 0.012 | −5.98 | 0.0000 | by_group_JB1_JB2 | |
| Streptomyces mirabilis | −0.019 | 0.007 | −2.67 | 0.0205 | by_group_JB5_JB6_JB7 | |
| Streptomyces [Kitasatospora] papulosa | −0.018 | 0.007 | −2.62 | 0.0140 | main_effect | |
| Terrabacter sp. C0L 2 | −0.008 | 0.006 | −1.21 | 0.2381 | main_effect | |
| Pedococcus sp. KACC 23699 | −0.027 | 0.008 | −3.48 | 0.0017 | main_effect | |
| Arthrobacter sp. NicSoilB8 | −0.003 | 0.005 | −0.58 | 0.5684 | main_effect | |
| Arthrobacter sp. NicSoilB4 | 0.048 | 0.006 | 8.58 | 0.0000 | main_effect | |
| Arthrobacter sp. PAMC25564 | 0.055 | 0.013 | 4.29 | 0.0002 | interaction | |
| Arthrobacter sp. PAMC25564 | −0.055 | 0.013 | −4.39 | 0.0006 | by_group_JB1_JB2 | |
| Arthrobacter sp. PAMC25564 | 0.000 | 0.003 | −0.15 | 0.8864 | by_group_JB5_JB6_JB7 | |
| Arthrobacter sulfonylureivorans | 0.013 | 0.013 | 1.03 | 0.3141 | main_effect | |
| Nocardioides sp. T5 | 0.055 | 0.010 | 5.48 | 0.0000 | main_effect | |
| Nocardioides panacis | −0.053 | 0.025 | −2.12 | 0.0435 | interaction | |
| Nocardioides panacis | 0.051 | 0.021 | 2.47 | 0.0268 | by_group_JB1_JB2 | |
| Nocardioides panacis | −0.002 | 0.014 | −0.14 | 0.8938 | by_group_JB5_JB6_JB7 | |
| Nocardioides ungokensis | −0.013 | 0.012 | −1.03 | 0.3119 | main_effect | |
| Kribbella sp. NBC 00359 | 0.014 | 0.008 | 1.81 | 0.0815 | main_effect | |
| Kribbella sp. NBC 01484 | −0.002 | 0.010 | −0.23 | 0.8186 | main_effect | |
| Kribbella sp. NBC 01510 | 0.008 | 0.011 | 0.74 | 0.4632 | main_effect | |
| Micromonospora sp. NBC 00330 | 0.014 | 0.007 | 1.84 | 0.0761 | main_effect | |
| Micromonospora sp. NBC 01740 | 0.035 | 0.011 | 3.27 | 0.0028 | main_effect | |
| Micromonospora sp. B006 | −0.011 | 0.011 | −1.06 | 0.2971 | main_effect | |
| Micromonospora zamorensis | 0.006 | 0.010 | 0.64 | 0.5260 | main_effect | |
| Dactylosporangium sp. NBC 01737 | 0.008 | 0.005 | 1.55 | 0.1329 | main_effect | |
| Streptosporangium sp. 'caverna' | 0.012 | 0.006 | 1.85 | 0.0755 | main_effect | |
| Streptosporangium subroseum | 0.009 | 0.006 | 1.59 | 0.1235 | main_effect | |
| Streptosporangium roseum | −0.006 | 0.006 | −0.87 | 0.3920 | main_effect | |
| Nonomuraea glycinis | 0.033 | 0.013 | 2.50 | 0.0185 | main_effect | |
| Amycolatopsis sp. DSM 110486 | 0.010 | 0.007 | 1.45 | 0.1580 | main_effect | |
| Actinomycetospora sp. NBC 00405 | 0.027 | 0.009 | 2.95 | 0.0063 | main_effect | |
| Anaerobic Decomposer | Acetivibrio saccincola | 0.003 | 0.011 | 0.23 | 0.8176 | main_effect |
| Herbinix luporum | 0.003 | 0.011 | 0.31 | 0.7594 | main_effect | |
| Hydrocarbon Degrader | Mycolicibacterium vanbaalenii | −0.047 | 0.019 | −2.43 | 0.0223 | interaction |
| Mycolicibacterium vanbaalenii | 0.044 | 0.018 | 2.39 | 0.0313 | by_group_JB1_JB2 | |
| Mycolicibacterium vanbaalenii | −0.003 | 0.007 | −0.39 | 0.7035 | by_group_JB5_JB6_JB7 | |
| Mycolicibacterium [Mycobacterium] burgundiense | 0.007 | 0.008 | 0.89 | 0.3807 | main_effect | |
| Rhodococcus sp. MTM3W5.2 | 0.019 | 0.008 | 2.49 | 0.0190 | main_effect | |
| Rhodococcus sp. W8901 | −0.011 | 0.006 | −1.76 | 0.0891 | main_effect | |
| Rhodococcoides fascians | 0.002 | 0.007 | 0.24 | 0.8109 | main_effect | |
| Immunomodulatory Soil Bacterium | Mycolicibacterium vaccae | −0.005 | 0.009 | −0.51 | 0.6112 | main_effect |
| Methanotroph | Methylocapsa sp. D3K7 | −0.021 | 0.011 | −1.96 | 0.0605 | main_effect |
| Nitrogen Fixer - Plant Symbiont | Bradyrhizobium sp. 170 | −0.056 | 0.025 | −2.23 | 0.0349 | interaction |
| Bradyrhizobium sp. 170 | 0.068 | 0.016 | 4.20 | 0.0009 | by_group_JB1_JB2 | |
| Bradyrhizobium sp. 170 | 0.012 | 0.019 | 0.65 | 0.5286 | by_group_JB5_JB6_JB7 | |
| Bradyrhizobium sp. 200 | 0.009 | 0.007 | 1.23 | 0.2302 | main_effect | |
| Bradyrhizobium sp. Ash2021 | −0.006 | 0.005 | −1.05 | 0.3048 | main_effect | |
| Bradyrhizobium sp. | 0.000 | 0.004 | −0.03 | 0.9774 | main_effect | |
| Bradyrhizobium erythrophlei | −0.023 | 0.006 | −3.72 | 0.0009 | main_effect | |
| Bradyrhizobium barranii | −0.014 | 0.010 | −1.40 | 0.1711 | main_effect | |
| Bradyrhizobium lablabi | −0.014 | 0.006 | −2.29 | 0.0299 | main_effect | |
| Bradyrhizobium japonicum | −0.012 | 0.005 | −2.13 | 0.0420 | main_effect | |
| Bradyrhizobium diazoefficiens | −0.067 | 0.015 | −4.62 | 0.0001 | main_effect | |
| Bradyrhizobium ottawaense | −0.001 | 0.007 | −0.12 | 0.9057 | main_effect | |
| Mesorhizobium sp. ANAO-SY3R2 | −0.004 | 0.008 | −0.52 | 0.6103 | main_effect | |
| Rhizobium ruizarguesonis | 0.019 | 0.010 | 1.98 | 0.0580 | main_effect | |
| Microvirga ossetica | 0.026 | 0.010 | 2.55 | 0.0172 | interaction | |
| Microvirga ossetica | 0.031 | 0.005 | 5.77 | 0.0000 | by_group_JB1_JB2 | |
| Microvirga ossetica | 0.057 | 0.008 | 6.87 | 0.0000 | by_group_JB5_JB6_JB7 | |
| Opportunistic Pathogen | Mycobacterium intracellulare | 0.021 | 0.009 | 2.53 | 0.0180 | interaction |
| Mycobacterium intracellulare | −0.031 | 0.007 | −4.12 | 0.0010 | by_group_JB1_JB2 | |
| Mycobacterium intracellulare | −0.009 | 0.004 | −2.17 | 0.0504 | by_group_JB5_JB6_JB7 | |
| Bacillus cereus | −0.012 | 0.010 | −1.14 | 0.2654 | main_effect | |
| Plant-Associated Bacterium | Agrobacterium rosae | 0.002 | 0.010 | 0.20 | 0.8404 | main_effect |
| Plant-Associated Commensal | Paraburkholderia hospita | −0.037 | 0.008 | −4.97 | 0.0000 | main_effect |
| Plant-Associated Commensal/Decomposer | Pseudomonas fluorescens | 0.018 | 0.016 | 1.15 | 0.2587 | main_effect |
| Pseudomonas sp. PONIH3 | 0.081 | 0.027 | 2.94 | 0.0069 | interaction | |
| Pseudomonas sp. PONIH3 | −0.056 | 0.022 | −2.57 | 0.0222 | by_group_JB1_JB2 | |
| Pseudomonas sp. PONIH3 | 0.024 | 0.017 | 1.45 | 0.1714 | by_group_JB5_JB6_JB7 | |
| Soil Decomposer | Bacillus mycoides | 0.029 | 0.017 | 1.73 | 0.0943 | main_effect |
| Bacillus licheniformis | 0.013 | 0.021 | 0.60 | 0.5535 | main_effect | |
| Neobacillus sp. FSL H8-0543 | −0.005 | 0.007 | −0.75 | 0.4608 | main_effect | |
| Neobacillus sp. OS1-33 | 0.007 | 0.008 | 0.80 | 0.4285 | main_effect | |
| Peribacillus asahii | 0.021 | 0.011 | 1.95 | 0.0617 | main_effect | |
| Priestia megaterium | −0.015 | 0.011 | −1.40 | 0.1730 | main_effect | |
| Thermophilic Decomposer | Thermobifida fusca | 0.005 | 0.012 | 0.42 | 0.6751 | main_effect |
| Saccharomonospora viridis | 0.006 | 0.009 | 0.68 | 0.5028 | main_effect | |
| Novibacillus thermophilus | −0.007 | 0.010 | −0.72 | 0.4765 | main_effect | |
| Thermoactinomyces vulgaris | −0.011 | 0.007 | −1.49 | 0.1484 | main_effect | |
| Unclassified | Humibacillus xanthopallidus | 0.030 | 0.008 | 3.98 | 0.0004 | main_effect |
| Nakamurella multipartita | 0.018 | 0.006 | 2.95 | 0.0064 | main_effect | |
| Baekduia alba | 0.002 | 0.006 | 0.29 | 0.7749 | main_effect | |
| Capillimicrobium parvum | 0.018 | 0.007 | 2.71 | 0.0113 | main_effect | |
| Allobacillus halotolerans | 0.100 | 0.043 | 2.31 | 0.0292 | interaction | |
| Allobacillus halotolerans | −0.076 | 0.034 | −2.26 | 0.0401 | by_group_JB1_JB2 | |
| Allobacillus halotolerans | 0.024 | 0.027 | 0.87 | 0.4031 | by_group_JB5_JB6_JB7 | |
| Pradoshia sp. D12 | −0.004 | 0.008 | −0.54 | 0.5920 | main_effect | |
| Afipia sp. GAS231 | 0.017 | 0.006 | 3.00 | 0.0059 | interaction | |
| Afipia sp. GAS231 | −0.030 | 0.005 | −6.02 | 0.0000 | by_group_JB1_JB2 | |
| Afipia sp. GAS231 | −0.013 | 0.003 | −4.27 | 0.0011 | by_group_JB5_JB6_JB7 | |
| Afipia carboxidovorans | −0.001 | 0.009 | −0.13 | 0.9009 | main_effect | |
| Bosea sp. NBC 00550 | 0.025 | 0.008 | 3.01 | 0.0055 | main_effect | |
| Skermanella cutis | 0.038 | 0.010 | 3.92 | 0.0005 | main_effect | |
| Massilia sp. R2A-15 | 0.002 | 0.007 | 0.30 | 0.7633 | main_effect | |
| Imtechella halotolerans | −0.027 | 0.021 | −1.31 | 0.2015 | main_effect |
Table 29: Summary statistics for each core microbial species. The table shows the summary statistics for the analysis of the metadata variable and each core species (species level) organised into functional groups. The table gives estimate, standard error, t-value, p-value and model. Model tells which model the summary statistics represents: “main_effect” analysis all fields together as we see no difference between JB groups, “interaction” gives results for the interaction analysis and is included when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.
Phosphorus
| Functional Group | Species | Estimate | SE | t | p-value | Model |
|---|---|---|---|---|---|---|
| Actinomycete Decomposer | Streptomyces sp. NBC 00425 | 0.008 | 0.003 | 3.03 | 0.0053 | main_effect |
| Streptomyces sp. NBC 01537 | 0.000 | 0.002 | 0.25 | 0.8039 | main_effect | |
| Streptomyces canus | −0.001 | 0.003 | −0.55 | 0.5881 | main_effect | |
| Streptomyces albidoflavus | 0.000 | 0.002 | −0.03 | 0.9737 | main_effect | |
| Streptomyces mirabilis | 0.001 | 0.004 | 0.19 | 0.8521 | main_effect | |
| Streptomyces [Kitasatospora] papulosa | −0.001 | 0.002 | −0.52 | 0.6041 | main_effect | |
| Terrabacter sp. C0L 2 | −0.002 | 0.002 | −0.93 | 0.3584 | main_effect | |
| Pedococcus sp. KACC 23699 | 0.005 | 0.003 | 2.10 | 0.0446 | main_effect | |
| Arthrobacter sp. NicSoilB8 | −0.004 | 0.001 | −3.30 | 0.0026 | main_effect | |
| Arthrobacter sp. NicSoilB4 | −0.002 | 0.003 | −0.72 | 0.4780 | main_effect | |
| Arthrobacter sp. PAMC25564 | 0.003 | 0.003 | 1.08 | 0.2891 | main_effect | |
| Arthrobacter sulfonylureivorans | 0.001 | 0.004 | 0.28 | 0.7836 | main_effect | |
| Nocardioides sp. T5 | 0.000 | 0.004 | 0.03 | 0.9786 | main_effect | |
| Nocardioides panacis | −0.018 | 0.008 | −2.31 | 0.0290 | interaction | |
| Nocardioides panacis | 0.008 | 0.006 | 1.30 | 0.2155 | by_group_JB1_JB2 | |
| Nocardioides panacis | −0.009 | 0.004 | −2.47 | 0.0295 | by_group_JB5_JB6_JB7 | |
| Nocardioides ungokensis | −0.019 | 0.007 | −2.56 | 0.0167 | interaction | |
| Nocardioides ungokensis | 0.005 | 0.005 | 1.01 | 0.3297 | by_group_JB1_JB2 | |
| Nocardioides ungokensis | −0.013 | 0.005 | −2.70 | 0.0193 | by_group_JB5_JB6_JB7 | |
| Kribbella sp. NBC 00359 | −0.008 | 0.004 | −2.08 | 0.0473 | interaction | |
| Kribbella sp. NBC 00359 | −0.001 | 0.003 | −0.33 | 0.7482 | by_group_JB1_JB2 | |
| Kribbella sp. NBC 00359 | −0.009 | 0.003 | −3.65 | 0.0033 | by_group_JB5_JB6_JB7 | |
| Kribbella sp. NBC 01484 | −0.008 | 0.003 | −2.83 | 0.0085 | main_effect | |
| Kribbella sp. NBC 01510 | −0.014 | 0.006 | −2.33 | 0.0279 | interaction | |
| Kribbella sp. NBC 01510 | 0.001 | 0.004 | 0.22 | 0.8279 | by_group_JB1_JB2 | |
| Kribbella sp. NBC 01510 | −0.013 | 0.005 | −2.80 | 0.0160 | by_group_JB5_JB6_JB7 | |
| Micromonospora sp. NBC 00330 | 0.001 | 0.002 | 0.47 | 0.6400 | main_effect | |
| Micromonospora sp. NBC 01740 | 0.000 | 0.004 | −0.08 | 0.9356 | main_effect | |
| Micromonospora sp. B006 | 0.007 | 0.003 | 2.31 | 0.0286 | main_effect | |
| Micromonospora zamorensis | 0.003 | 0.003 | 1.16 | 0.2542 | main_effect | |
| Dactylosporangium sp. NBC 01737 | 0.003 | 0.001 | 2.07 | 0.0483 | main_effect | |
| Streptosporangium sp. 'caverna' | 0.001 | 0.002 | 0.72 | 0.4791 | main_effect | |
| Streptosporangium subroseum | 0.001 | 0.002 | 0.59 | 0.5592 | main_effect | |
| Streptosporangium roseum | −0.001 | 0.002 | −0.67 | 0.5111 | main_effect | |
| Nonomuraea glycinis | 0.006 | 0.004 | 1.36 | 0.1833 | main_effect | |
| Amycolatopsis sp. DSM 110486 | 0.002 | 0.002 | 1.05 | 0.3007 | main_effect | |
| Actinomycetospora sp. NBC 00405 | 0.002 | 0.003 | 0.76 | 0.4512 | main_effect | |
| Anaerobic Decomposer | Acetivibrio saccincola | 0.000 | 0.003 | 0.09 | 0.9285 | main_effect |
| Herbinix luporum | 0.000 | 0.003 | −0.14 | 0.8882 | main_effect | |
| Hydrocarbon Degrader | Mycolicibacterium vanbaalenii | −0.002 | 0.003 | −0.56 | 0.5797 | main_effect |
| Mycolicibacterium [Mycobacterium] burgundiense | 0.000 | 0.003 | 0.03 | 0.9759 | main_effect | |
| Rhodococcus sp. MTM3W5.2 | −0.005 | 0.002 | −2.10 | 0.0451 | main_effect | |
| Rhodococcus sp. W8901 | −0.003 | 0.002 | −1.77 | 0.0869 | main_effect | |
| Rhodococcoides fascians | 0.004 | 0.002 | 1.85 | 0.0747 | main_effect | |
| Immunomodulatory Soil Bacterium | Mycolicibacterium vaccae | 0.000 | 0.003 | 0.15 | 0.8781 | main_effect |
| Methanotroph | Methylocapsa sp. D3K7 | −0.002 | 0.003 | −0.45 | 0.6582 | main_effect |
| Nitrogen Fixer - Plant Symbiont | Bradyrhizobium sp. 170 | −0.006 | 0.004 | −1.43 | 0.1626 | main_effect |
| Bradyrhizobium sp. 200 | 0.001 | 0.002 | 0.22 | 0.8263 | main_effect | |
| Bradyrhizobium sp. Ash2021 | −0.004 | 0.001 | −2.45 | 0.0210 | main_effect | |
| Bradyrhizobium sp. | 0.000 | 0.001 | −0.32 | 0.7533 | main_effect | |
| Bradyrhizobium erythrophlei | −0.004 | 0.002 | −1.84 | 0.0771 | main_effect | |
| Bradyrhizobium barranii | 0.001 | 0.003 | 0.17 | 0.8683 | main_effect | |
| Bradyrhizobium lablabi | −0.004 | 0.002 | −2.29 | 0.0299 | main_effect | |
| Bradyrhizobium japonicum | −0.001 | 0.002 | −0.64 | 0.5297 | main_effect | |
| Bradyrhizobium diazoefficiens | 0.009 | 0.006 | 1.66 | 0.1073 | main_effect | |
| Bradyrhizobium ottawaense | −0.009 | 0.003 | −2.79 | 0.0098 | interaction | |
| Bradyrhizobium ottawaense | −0.001 | 0.002 | −0.65 | 0.5287 | by_group_JB1_JB2 | |
| Bradyrhizobium ottawaense | −0.011 | 0.003 | −3.75 | 0.0028 | by_group_JB5_JB6_JB7 | |
| Mesorhizobium sp. ANAO-SY3R2 | −0.003 | 0.002 | −1.04 | 0.3059 | main_effect | |
| Rhizobium ruizarguesonis | −0.003 | 0.003 | −0.96 | 0.3439 | main_effect | |
| Microvirga ossetica | −0.003 | 0.003 | −0.91 | 0.3713 | main_effect | |
| Opportunistic Pathogen | Mycobacterium intracellulare | 0.001 | 0.002 | 0.65 | 0.5182 | main_effect |
| Bacillus cereus | −0.009 | 0.003 | −3.16 | 0.0038 | main_effect | |
| Plant-Associated Bacterium | Agrobacterium rosae | 0.002 | 0.003 | 0.65 | 0.5192 | main_effect |
| Plant-Associated Commensal | Paraburkholderia hospita | 0.002 | 0.003 | 0.64 | 0.5275 | main_effect |
| Plant-Associated Commensal/Decomposer | Pseudomonas fluorescens | −0.006 | 0.005 | −1.17 | 0.2521 | main_effect |
| Pseudomonas sp. PONIH3 | −0.002 | 0.004 | −0.51 | 0.6143 | main_effect | |
| Soil Decomposer | Bacillus mycoides | −0.012 | 0.005 | −2.46 | 0.0203 | main_effect |
| Bacillus licheniformis | 0.002 | 0.006 | 0.25 | 0.8012 | main_effect | |
| Neobacillus sp. FSL H8-0543 | −0.003 | 0.002 | −1.58 | 0.1243 | main_effect | |
| Neobacillus sp. OS1-33 | −0.005 | 0.002 | −2.14 | 0.0409 | main_effect | |
| Peribacillus asahii | −0.004 | 0.003 | −1.14 | 0.2638 | main_effect | |
| Priestia megaterium | 0.008 | 0.003 | 2.85 | 0.0080 | main_effect | |
| Thermophilic Decomposer | Thermobifida fusca | 0.001 | 0.004 | 0.24 | 0.8100 | main_effect |
| Saccharomonospora viridis | 0.011 | 0.005 | 2.19 | 0.0376 | interaction | |
| Saccharomonospora viridis | −0.001 | 0.003 | −0.20 | 0.8470 | by_group_JB1_JB2 | |
| Saccharomonospora viridis | 0.011 | 0.004 | 2.66 | 0.0208 | by_group_JB5_JB6_JB7 | |
| Novibacillus thermophilus | 0.005 | 0.003 | 1.71 | 0.0977 | main_effect | |
| Thermoactinomyces vulgaris | 0.003 | 0.002 | 1.20 | 0.2402 | main_effect | |
| Unclassified | Humibacillus xanthopallidus | −0.006 | 0.003 | −2.33 | 0.0270 | main_effect |
| Nakamurella multipartita | −0.002 | 0.002 | −0.94 | 0.3568 | main_effect | |
| Baekduia alba | 0.000 | 0.002 | −0.09 | 0.9309 | main_effect | |
| Capillimicrobium parvum | −0.003 | 0.002 | −1.25 | 0.2200 | main_effect | |
| Allobacillus halotolerans | −0.002 | 0.006 | −0.30 | 0.7656 | main_effect | |
| Pradoshia sp. D12 | −0.001 | 0.002 | −0.38 | 0.7046 | main_effect | |
| Afipia sp. GAS231 | 0.001 | 0.002 | 0.72 | 0.4792 | main_effect | |
| Afipia carboxidovorans | 0.005 | 0.003 | 1.83 | 0.0776 | main_effect | |
| Bosea sp. NBC 00550 | −0.001 | 0.003 | −0.27 | 0.7884 | main_effect | |
| Skermanella cutis | 0.001 | 0.004 | 0.15 | 0.8785 | main_effect | |
| Massilia sp. R2A-15 | 0.001 | 0.002 | 0.37 | 0.7135 | main_effect | |
| Imtechella halotolerans | 0.005 | 0.006 | 0.86 | 0.3957 | main_effect |
Table 30: Summary statistics for each core microbial species. The table shows the summary statistics for the analysis of the metadata variable and each core species (species level) organised into functional groups. The table gives estimate, standard error, t-value, p-value and model. Model tells which model the summary statistics represents: “main_effect” analysis all fields together as we see no difference between JB groups, “interaction” gives results for the interaction analysis and is included when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.
Potassium
| Functional Group | Species | Estimate | SE | t | p-value | Model |
|---|---|---|---|---|---|---|
| Actinomycete Decomposer | Streptomyces sp. NBC 00425 | 0.000 | 0.001 | −0.46 | 0.6464 | main_effect |
| Streptomyces sp. NBC 01537 | −0.001 | 0.001 | −1.70 | 0.1007 | main_effect | |
| Streptomyces canus | −0.004 | 0.001 | −2.50 | 0.0189 | interaction | |
| Streptomyces canus | 0.001 | 0.001 | 1.39 | 0.1871 | by_group_JB1_JB2 | |
| Streptomyces canus | −0.002 | 0.001 | −2.24 | 0.0446 | by_group_JB5_JB6_JB7 | |
| Streptomyces albidoflavus | 0.001 | 0.001 | 1.47 | 0.1522 | main_effect | |
| Streptomyces mirabilis | −0.003 | 0.001 | −3.01 | 0.0054 | main_effect | |
| Streptomyces [Kitasatospora] papulosa | 0.003 | 0.001 | 2.66 | 0.0131 | interaction | |
| Streptomyces [Kitasatospora] papulosa | −0.001 | 0.001 | −0.90 | 0.3849 | by_group_JB1_JB2 | |
| Streptomyces [Kitasatospora] papulosa | 0.003 | 0.001 | 2.47 | 0.0293 | by_group_JB5_JB6_JB7 | |
| Terrabacter sp. C0L 2 | 0.000 | 0.001 | 0.79 | 0.4352 | main_effect | |
| Pedococcus sp. KACC 23699 | −0.001 | 0.001 | −0.78 | 0.4428 | main_effect | |
| Arthrobacter sp. NicSoilB8 | −0.001 | 0.000 | −1.35 | 0.1891 | main_effect | |
| Arthrobacter sp. NicSoilB4 | 0.000 | 0.001 | 0.08 | 0.9399 | main_effect | |
| Arthrobacter sp. PAMC25564 | −0.002 | 0.001 | −2.81 | 0.0089 | main_effect | |
| Arthrobacter sulfonylureivorans | −0.005 | 0.002 | −2.58 | 0.0158 | interaction | |
| Arthrobacter sulfonylureivorans | 0.003 | 0.001 | 1.86 | 0.0846 | by_group_JB1_JB2 | |
| Arthrobacter sulfonylureivorans | −0.003 | 0.001 | −1.83 | 0.0924 | by_group_JB5_JB6_JB7 | |
| Nocardioides sp. T5 | 0.003 | 0.001 | 2.58 | 0.0156 | main_effect | |
| Nocardioides panacis | 0.000 | 0.001 | 0.43 | 0.6717 | main_effect | |
| Nocardioides ungokensis | 0.000 | 0.001 | −0.13 | 0.8954 | main_effect | |
| Kribbella sp. NBC 00359 | 0.001 | 0.001 | 2.28 | 0.0303 | main_effect | |
| Kribbella sp. NBC 01484 | 0.002 | 0.001 | 1.95 | 0.0616 | main_effect | |
| Kribbella sp. NBC 01510 | 0.002 | 0.001 | 2.21 | 0.0356 | main_effect | |
| Micromonospora sp. NBC 00330 | −0.003 | 0.001 | −2.83 | 0.0088 | interaction | |
| Micromonospora sp. NBC 00330 | 0.002 | 0.001 | 2.65 | 0.0191 | by_group_JB1_JB2 | |
| Micromonospora sp. NBC 00330 | −0.001 | 0.001 | −1.41 | 0.1850 | by_group_JB5_JB6_JB7 | |
| Micromonospora sp. NBC 01740 | 0.002 | 0.001 | 2.14 | 0.0408 | main_effect | |
| Micromonospora sp. B006 | 0.001 | 0.001 | 0.86 | 0.3950 | main_effect | |
| Micromonospora zamorensis | −0.004 | 0.001 | −2.69 | 0.0122 | interaction | |
| Micromonospora zamorensis | 0.003 | 0.001 | 3.46 | 0.0038 | by_group_JB1_JB2 | |
| Micromonospora zamorensis | −0.001 | 0.001 | −0.73 | 0.4818 | by_group_JB5_JB6_JB7 | |
| Dactylosporangium sp. NBC 01737 | 0.000 | 0.000 | 0.01 | 0.9913 | main_effect | |
| Streptosporangium sp. 'caverna' | 0.000 | 0.001 | 0.64 | 0.5278 | main_effect | |
| Streptosporangium subroseum | 0.000 | 0.001 | 0.59 | 0.5613 | main_effect | |
| Streptosporangium roseum | 0.003 | 0.001 | 2.98 | 0.0062 | interaction | |
| Streptosporangium roseum | 0.000 | 0.000 | −0.02 | 0.9853 | by_group_JB1_JB2 | |
| Streptosporangium roseum | 0.003 | 0.001 | 3.15 | 0.0084 | by_group_JB5_JB6_JB7 | |
| Nonomuraea glycinis | −0.005 | 0.002 | −2.27 | 0.0319 | interaction | |
| Nonomuraea glycinis | 0.002 | 0.002 | 1.35 | 0.1981 | by_group_JB1_JB2 | |
| Nonomuraea glycinis | −0.003 | 0.002 | −1.85 | 0.0888 | by_group_JB5_JB6_JB7 | |
| Amycolatopsis sp. DSM 110486 | −0.003 | 0.001 | −2.40 | 0.0239 | interaction | |
| Amycolatopsis sp. DSM 110486 | 0.001 | 0.001 | 2.10 | 0.0539 | by_group_JB1_JB2 | |
| Amycolatopsis sp. DSM 110486 | −0.002 | 0.001 | −1.46 | 0.1710 | by_group_JB5_JB6_JB7 | |
| Actinomycetospora sp. NBC 00405 | −0.004 | 0.002 | −2.33 | 0.0280 | interaction | |
| Actinomycetospora sp. NBC 00405 | 0.003 | 0.001 | 2.89 | 0.0119 | by_group_JB1_JB2 | |
| Actinomycetospora sp. NBC 00405 | −0.001 | 0.002 | −0.85 | 0.4097 | by_group_JB5_JB6_JB7 | |
| Anaerobic Decomposer | Acetivibrio saccincola | 0.001 | 0.001 | 0.75 | 0.4578 | main_effect |
| Herbinix luporum | 0.000 | 0.001 | −0.26 | 0.7930 | main_effect | |
| Hydrocarbon Degrader | Mycolicibacterium vanbaalenii | 0.002 | 0.001 | 2.06 | 0.0488 | main_effect |
| Mycolicibacterium [Mycobacterium] burgundiense | 0.000 | 0.001 | 0.16 | 0.8775 | main_effect | |
| Rhodococcus sp. MTM3W5.2 | 0.001 | 0.001 | 1.06 | 0.2973 | main_effect | |
| Rhodococcus sp. W8901 | 0.000 | 0.001 | −0.27 | 0.7895 | main_effect | |
| Rhodococcoides fascians | 0.000 | 0.001 | 0.31 | 0.7577 | main_effect | |
| Immunomodulatory Soil Bacterium | Mycolicibacterium vaccae | 0.001 | 0.001 | 1.29 | 0.2082 | main_effect |
| Methanotroph | Methylocapsa sp. D3K7 | −0.001 | 0.001 | −1.11 | 0.2756 | main_effect |
| Nitrogen Fixer - Plant Symbiont | Bradyrhizobium sp. 170 | −0.005 | 0.002 | −2.23 | 0.0343 | interaction |
| Bradyrhizobium sp. 170 | 0.001 | 0.002 | 0.53 | 0.6040 | by_group_JB1_JB2 | |
| Bradyrhizobium sp. 170 | −0.004 | 0.001 | −3.14 | 0.0085 | by_group_JB5_JB6_JB7 | |
| Bradyrhizobium sp. 200 | −0.003 | 0.001 | −2.80 | 0.0094 | interaction | |
| Bradyrhizobium sp. 200 | 0.001 | 0.001 | 0.79 | 0.4413 | by_group_JB1_JB2 | |
| Bradyrhizobium sp. 200 | −0.002 | 0.000 | −4.95 | 0.0003 | by_group_JB5_JB6_JB7 | |
| Bradyrhizobium sp. Ash2021 | 0.000 | 0.000 | −0.48 | 0.6370 | main_effect | |
| Bradyrhizobium sp. | 0.000 | 0.000 | 0.20 | 0.8429 | main_effect | |
| Bradyrhizobium erythrophlei | −0.001 | 0.001 | −1.25 | 0.2202 | main_effect | |
| Bradyrhizobium barranii | −0.001 | 0.001 | −1.58 | 0.1247 | main_effect | |
| Bradyrhizobium lablabi | −0.001 | 0.001 | −1.42 | 0.1671 | main_effect | |
| Bradyrhizobium japonicum | −0.001 | 0.000 | −2.99 | 0.0057 | main_effect | |
| Bradyrhizobium diazoefficiens | −0.004 | 0.001 | −2.98 | 0.0059 | main_effect | |
| Bradyrhizobium ottawaense | 0.000 | 0.001 | −0.83 | 0.4145 | main_effect | |
| Mesorhizobium sp. ANAO-SY3R2 | −0.001 | 0.001 | −1.01 | 0.3199 | main_effect | |
| Rhizobium ruizarguesonis | 0.000 | 0.001 | 0.02 | 0.9834 | main_effect | |
| Microvirga ossetica | 0.000 | 0.001 | 0.35 | 0.7309 | main_effect | |
| Opportunistic Pathogen | Mycobacterium intracellulare | −0.001 | 0.000 | −1.32 | 0.1979 | main_effect |
| Bacillus cereus | −0.001 | 0.001 | −1.12 | 0.2721 | main_effect | |
| Plant-Associated Bacterium | Agrobacterium rosae | 0.000 | 0.001 | −0.49 | 0.6301 | main_effect |
| Plant-Associated Commensal | Paraburkholderia hospita | −0.002 | 0.001 | −2.30 | 0.0293 | main_effect |
| Plant-Associated Commensal/Decomposer | Pseudomonas fluorescens | 0.000 | 0.001 | 0.20 | 0.8454 | main_effect |
| Pseudomonas sp. PONIH3 | 0.005 | 0.002 | 2.21 | 0.0361 | interaction | |
| Pseudomonas sp. PONIH3 | −0.004 | 0.002 | −2.21 | 0.0439 | by_group_JB1_JB2 | |
| Pseudomonas sp. PONIH3 | 0.002 | 0.002 | 0.93 | 0.3689 | by_group_JB5_JB6_JB7 | |
| Soil Decomposer | Bacillus mycoides | 0.002 | 0.001 | 1.20 | 0.2390 | main_effect |
| Bacillus licheniformis | 0.001 | 0.002 | 0.46 | 0.6477 | main_effect | |
| Neobacillus sp. FSL H8-0543 | 0.001 | 0.001 | 1.24 | 0.2263 | main_effect | |
| Neobacillus sp. OS1-33 | 0.001 | 0.001 | 2.17 | 0.0390 | main_effect | |
| Peribacillus asahii | 0.000 | 0.001 | −0.03 | 0.9737 | main_effect | |
| Priestia megaterium | −0.001 | 0.001 | −1.28 | 0.2100 | main_effect | |
| Thermophilic Decomposer | Thermobifida fusca | 0.002 | 0.001 | 1.83 | 0.0782 | main_effect |
| Saccharomonospora viridis | 0.001 | 0.001 | 2.03 | 0.0521 | main_effect | |
| Novibacillus thermophilus | 0.001 | 0.001 | 1.02 | 0.3146 | main_effect | |
| Thermoactinomyces vulgaris | 0.000 | 0.001 | −0.78 | 0.4403 | main_effect | |
| Unclassified | Humibacillus xanthopallidus | 0.001 | 0.001 | 2.03 | 0.0518 | main_effect |
| Nakamurella multipartita | 0.001 | 0.001 | 1.12 | 0.2719 | main_effect | |
| Baekduia alba | −0.003 | 0.001 | −3.10 | 0.0046 | interaction | |
| Baekduia alba | 0.002 | 0.001 | 3.10 | 0.0079 | by_group_JB1_JB2 | |
| Baekduia alba | −0.001 | 0.001 | −1.40 | 0.1873 | by_group_JB5_JB6_JB7 | |
| Capillimicrobium parvum | −0.003 | 0.001 | −3.30 | 0.0028 | interaction | |
| Capillimicrobium parvum | 0.002 | 0.001 | 3.05 | 0.0086 | by_group_JB1_JB2 | |
| Capillimicrobium parvum | −0.001 | 0.001 | −1.67 | 0.1212 | by_group_JB5_JB6_JB7 | |
| Allobacillus halotolerans | −0.001 | 0.002 | −0.42 | 0.6763 | main_effect | |
| Pradoshia sp. D12 | 0.000 | 0.001 | −0.42 | 0.6748 | main_effect | |
| Afipia sp. GAS231 | −0.001 | 0.000 | −2.67 | 0.0125 | main_effect | |
| Afipia carboxidovorans | 0.001 | 0.001 | 1.37 | 0.1815 | main_effect | |
| Bosea sp. NBC 00550 | 0.001 | 0.001 | 1.21 | 0.2364 | main_effect | |
| Skermanella cutis | −0.001 | 0.001 | −0.88 | 0.3880 | main_effect | |
| Massilia sp. R2A-15 | 0.000 | 0.001 | 0.24 | 0.8117 | main_effect | |
| Imtechella halotolerans | 0.011 | 0.003 | 3.37 | 0.0024 | interaction | |
| Imtechella halotolerans | −0.006 | 0.002 | −2.50 | 0.0253 | by_group_JB1_JB2 | |
| Imtechella halotolerans | 0.005 | 0.002 | 2.39 | 0.0339 | by_group_JB5_JB6_JB7 |
Table 31: Summary statistics for each core microbial species. The table shows the summary statistics for the analysis of the metadata variable and each core species (species level) organised into functional groups. The table gives estimate, standard error, t-value, p-value and model. Model tells which model the summary statistics represents: “main_effect” analysis all fields together as we see no difference between JB groups, “interaction” gives results for the interaction analysis and is included when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.
Magnesium
| Functional Group | Species | Estimate | SE | t | p-value | Model |
|---|---|---|---|---|---|---|
| Actinomycete Decomposer | Streptomyces sp. NBC 00425 | 0.001 | 0.001 | 0.95 | 0.3519 | main_effect |
| Streptomyces sp. NBC 01537 | −0.001 | 0.001 | −1.02 | 0.3183 | main_effect | |
| Streptomyces canus | 0.004 | 0.001 | 4.51 | 0.0001 | main_effect | |
| Streptomyces albidoflavus | 0.001 | 0.001 | 0.94 | 0.3573 | main_effect | |
| Streptomyces mirabilis | −0.005 | 0.002 | −3.18 | 0.0036 | main_effect | |
| Streptomyces [Kitasatospora] papulosa | −0.002 | 0.001 | −1.47 | 0.1523 | main_effect | |
| Terrabacter sp. C0L 2 | −0.001 | 0.001 | −1.24 | 0.2242 | main_effect | |
| Pedococcus sp. KACC 23699 | −0.004 | 0.001 | −4.24 | 0.0002 | main_effect | |
| Arthrobacter sp. NicSoilB8 | 0.001 | 0.001 | 1.03 | 0.3106 | main_effect | |
| Arthrobacter sp. NicSoilB4 | 0.003 | 0.001 | 2.37 | 0.0251 | main_effect | |
| Arthrobacter sp. PAMC25564 | −0.002 | 0.001 | −1.51 | 0.1414 | main_effect | |
| Arthrobacter sulfonylureivorans | 0.003 | 0.002 | 2.04 | 0.0511 | main_effect | |
| Nocardioides sp. T5 | 0.005 | 0.002 | 3.02 | 0.0054 | main_effect | |
| Nocardioides panacis | 0.001 | 0.002 | 0.72 | 0.4805 | main_effect | |
| Nocardioides ungokensis | 0.001 | 0.002 | 0.68 | 0.5038 | main_effect | |
| Kribbella sp. NBC 00359 | 0.002 | 0.001 | 1.82 | 0.0790 | main_effect | |
| Kribbella sp. NBC 01484 | 0.002 | 0.001 | 1.33 | 0.1942 | main_effect | |
| Kribbella sp. NBC 01510 | 0.003 | 0.001 | 2.37 | 0.0249 | main_effect | |
| Micromonospora sp. NBC 00330 | 0.000 | 0.001 | 0.00 | 0.9988 | main_effect | |
| Micromonospora sp. NBC 01740 | 0.002 | 0.002 | 1.14 | 0.2636 | main_effect | |
| Micromonospora sp. B006 | 0.000 | 0.002 | 0.04 | 0.9680 | main_effect | |
| Micromonospora zamorensis | 0.000 | 0.001 | −0.08 | 0.9343 | main_effect | |
| Dactylosporangium sp. NBC 01737 | 0.000 | 0.001 | −0.26 | 0.8002 | main_effect | |
| Streptosporangium sp. 'caverna' | −0.001 | 0.001 | −0.56 | 0.5832 | main_effect | |
| Streptosporangium subroseum | −0.001 | 0.001 | −0.69 | 0.4984 | main_effect | |
| Streptosporangium roseum | −0.001 | 0.001 | −0.57 | 0.5706 | main_effect | |
| Nonomuraea glycinis | 0.002 | 0.002 | 1.19 | 0.2424 | main_effect | |
| Amycolatopsis sp. DSM 110486 | 0.000 | 0.001 | 0.12 | 0.9093 | main_effect | |
| Actinomycetospora sp. NBC 00405 | 0.003 | 0.001 | 2.25 | 0.0324 | main_effect | |
| Anaerobic Decomposer | Acetivibrio saccincola | −0.001 | 0.002 | −0.41 | 0.6814 | main_effect |
| Herbinix luporum | 0.000 | 0.002 | −0.03 | 0.9751 | main_effect | |
| Hydrocarbon Degrader | Mycolicibacterium vanbaalenii | 0.004 | 0.001 | 2.92 | 0.0069 | main_effect |
| Mycolicibacterium [Mycobacterium] burgundiense | −0.001 | 0.001 | −0.57 | 0.5722 | main_effect | |
| Rhodococcus sp. MTM3W5.2 | 0.003 | 0.001 | 2.71 | 0.0113 | main_effect | |
| Rhodococcus sp. W8901 | 0.000 | 0.001 | 0.04 | 0.9679 | main_effect | |
| Rhodococcoides fascians | −0.001 | 0.001 | −1.05 | 0.3031 | main_effect | |
| Immunomodulatory Soil Bacterium | Mycolicibacterium vaccae | 0.002 | 0.001 | 1.91 | 0.0658 | main_effect |
| Methanotroph | Methylocapsa sp. D3K7 | −0.001 | 0.002 | −0.57 | 0.5714 | main_effect |
| Nitrogen Fixer - Plant Symbiont | Bradyrhizobium sp. 170 | 0.005 | 0.002 | 3.02 | 0.0054 | main_effect |
| Bradyrhizobium sp. 200 | 0.002 | 0.001 | 1.94 | 0.0627 | main_effect | |
| Bradyrhizobium sp. Ash2021 | 0.001 | 0.001 | 1.25 | 0.2209 | main_effect | |
| Bradyrhizobium sp. | 0.001 | 0.001 | 2.44 | 0.0213 | main_effect | |
| Bradyrhizobium erythrophlei | 0.000 | 0.001 | −0.44 | 0.6611 | main_effect | |
| Bradyrhizobium barranii | −0.002 | 0.001 | −1.20 | 0.2408 | main_effect | |
| Bradyrhizobium lablabi | 0.001 | 0.001 | 0.59 | 0.5574 | main_effect | |
| Bradyrhizobium japonicum | 0.000 | 0.001 | −0.32 | 0.7538 | main_effect | |
| Bradyrhizobium diazoefficiens | −0.005 | 0.003 | −1.96 | 0.0594 | main_effect | |
| Bradyrhizobium ottawaense | 0.002 | 0.001 | 2.42 | 0.0222 | main_effect | |
| Mesorhizobium sp. ANAO-SY3R2 | 0.001 | 0.001 | 0.46 | 0.6456 | main_effect | |
| Rhizobium ruizarguesonis | 0.002 | 0.001 | 1.13 | 0.2687 | main_effect | |
| Microvirga ossetica | 0.004 | 0.001 | 2.96 | 0.0062 | main_effect | |
| Opportunistic Pathogen | Mycobacterium intracellulare | −0.001 | 0.001 | −2.06 | 0.0491 | main_effect |
| Bacillus cereus | 0.000 | 0.001 | −0.06 | 0.9513 | main_effect | |
| Plant-Associated Bacterium | Agrobacterium rosae | −0.002 | 0.001 | −1.23 | 0.2299 | main_effect |
| Plant-Associated Commensal | Paraburkholderia hospita | −0.005 | 0.001 | −4.52 | 0.0001 | main_effect |
| Plant-Associated Commensal/Decomposer | Pseudomonas fluorescens | 0.003 | 0.002 | 1.45 | 0.1591 | main_effect |
| Pseudomonas sp. PONIH3 | 0.000 | 0.002 | −0.16 | 0.8731 | main_effect | |
| Soil Decomposer | Bacillus mycoides | 0.006 | 0.002 | 2.51 | 0.0179 | main_effect |
| Bacillus licheniformis | 0.000 | 0.003 | 0.07 | 0.9425 | main_effect | |
| Neobacillus sp. FSL H8-0543 | 0.002 | 0.001 | 1.70 | 0.1011 | main_effect | |
| Neobacillus sp. OS1-33 | 0.003 | 0.001 | 2.48 | 0.0192 | main_effect | |
| Peribacillus asahii | 0.004 | 0.001 | 2.95 | 0.0063 | main_effect | |
| Priestia megaterium | −0.001 | 0.002 | −0.98 | 0.3377 | main_effect | |
| Thermophilic Decomposer | Thermobifida fusca | −0.002 | 0.002 | −1.51 | 0.1432 | main_effect |
| Saccharomonospora viridis | −0.002 | 0.001 | −1.57 | 0.1288 | main_effect | |
| Novibacillus thermophilus | −0.002 | 0.001 | −1.72 | 0.0969 | main_effect | |
| Thermoactinomyces vulgaris | −0.002 | 0.001 | −2.12 | 0.0432 | main_effect | |
| Unclassified | Humibacillus xanthopallidus | 0.003 | 0.001 | 3.07 | 0.0047 | main_effect |
| Nakamurella multipartita | 0.002 | 0.001 | 2.33 | 0.0275 | main_effect | |
| Baekduia alba | 0.000 | 0.001 | 0.23 | 0.8165 | main_effect | |
| Capillimicrobium parvum | 0.002 | 0.001 | 2.68 | 0.0122 | main_effect | |
| Allobacillus halotolerans | −0.004 | 0.003 | −1.31 | 0.2010 | main_effect | |
| Pradoshia sp. D12 | 0.003 | 0.001 | 2.86 | 0.0079 | main_effect | |
| Afipia sp. GAS231 | −0.001 | 0.001 | −1.79 | 0.0845 | main_effect | |
| Afipia carboxidovorans | 0.001 | 0.001 | 0.64 | 0.5265 | main_effect | |
| Bosea sp. NBC 00550 | 0.004 | 0.001 | 3.28 | 0.0028 | main_effect | |
| Skermanella cutis | 0.003 | 0.002 | 1.63 | 0.1141 | main_effect | |
| Massilia sp. R2A-15 | −0.001 | 0.001 | −0.94 | 0.3561 | main_effect | |
| Imtechella halotolerans | −0.005 | 0.003 | −1.95 | 0.0614 | main_effect |
Table 32: Summary statistics for each core microbial species. The table shows the summary statistics for the analysis of the metadata variable and each core species (species level) organised into functional groups. The table gives estimate, standard error, t-value, p-value and model. Model tells which model the summary statistics represents: “main_effect” analysis all fields together as we see no difference between JB groups, “interaction” gives results for the interaction analysis and is included when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.
Cobber
| Functional Group | Species | Estimate | SE | t | p-value | Model |
|---|---|---|---|---|---|---|
| Actinomycete Decomposer | Streptomyces sp. NBC 00425 | −0.002 | 0.004 | −0.63 | 0.5370 | main_effect |
| Streptomyces sp. NBC 01537 | 0.000 | 0.002 | 0.14 | 0.8865 | main_effect | |
| Streptomyces canus | −0.003 | 0.003 | −0.90 | 0.3751 | main_effect | |
| Streptomyces albidoflavus | 0.001 | 0.003 | 0.46 | 0.6492 | main_effect | |
| Streptomyces mirabilis | 0.004 | 0.005 | 0.86 | 0.3974 | main_effect | |
| Streptomyces [Kitasatospora] papulosa | −0.002 | 0.003 | −0.73 | 0.4703 | main_effect | |
| Terrabacter sp. C0L 2 | −0.001 | 0.002 | −0.25 | 0.8021 | main_effect | |
| Pedococcus sp. KACC 23699 | 0.003 | 0.003 | 0.91 | 0.3713 | main_effect | |
| Arthrobacter sp. NicSoilB8 | 0.003 | 0.002 | 1.65 | 0.1108 | main_effect | |
| Arthrobacter sp. NicSoilB4 | −0.001 | 0.004 | −0.22 | 0.8237 | main_effect | |
| Arthrobacter sp. PAMC25564 | 0.008 | 0.004 | 2.10 | 0.0451 | main_effect | |
| Arthrobacter sulfonylureivorans | 0.000 | 0.005 | −0.06 | 0.9494 | main_effect | |
| Nocardioides sp. T5 | −0.007 | 0.005 | −1.26 | 0.2176 | main_effect | |
| Nocardioides panacis | −0.009 | 0.005 | −1.85 | 0.0750 | main_effect | |
| Nocardioides ungokensis | 0.003 | 0.005 | 0.67 | 0.5078 | main_effect | |
| Kribbella sp. NBC 00359 | −0.003 | 0.003 | −1.15 | 0.2612 | main_effect | |
| Kribbella sp. NBC 01484 | −0.001 | 0.004 | −0.35 | 0.7268 | main_effect | |
| Kribbella sp. NBC 01510 | −0.004 | 0.004 | −0.96 | 0.3453 | main_effect | |
| Micromonospora sp. NBC 00330 | −0.002 | 0.003 | −0.79 | 0.4372 | main_effect | |
| Micromonospora sp. NBC 01740 | −0.007 | 0.004 | −1.50 | 0.1442 | main_effect | |
| Micromonospora sp. B006 | −0.004 | 0.004 | −1.08 | 0.2887 | main_effect | |
| Micromonospora zamorensis | −0.003 | 0.004 | −0.84 | 0.4078 | main_effect | |
| Dactylosporangium sp. NBC 01737 | −0.002 | 0.002 | −1.25 | 0.2206 | main_effect | |
| Streptosporangium sp. 'caverna' | −0.005 | 0.002 | −1.94 | 0.0621 | main_effect | |
| Streptosporangium subroseum | −0.004 | 0.002 | −2.07 | 0.0473 | main_effect | |
| Streptosporangium roseum | −0.002 | 0.002 | −0.81 | 0.4275 | main_effect | |
| Nonomuraea glycinis | −0.004 | 0.005 | −0.71 | 0.4845 | main_effect | |
| Amycolatopsis sp. DSM 110486 | −0.004 | 0.003 | −1.39 | 0.1741 | main_effect | |
| Actinomycetospora sp. NBC 00405 | −0.004 | 0.004 | −0.93 | 0.3601 | main_effect | |
| Anaerobic Decomposer | Acetivibrio saccincola | −0.001 | 0.004 | −0.14 | 0.8908 | main_effect |
| Herbinix luporum | 0.003 | 0.004 | 0.79 | 0.4362 | main_effect | |
| Hydrocarbon Degrader | Mycolicibacterium vanbaalenii | −0.009 | 0.004 | −2.32 | 0.0279 | main_effect |
| Mycolicibacterium [Mycobacterium] burgundiense | 0.001 | 0.003 | 0.43 | 0.6676 | main_effect | |
| Rhodococcus sp. MTM3W5.2 | −0.002 | 0.003 | −0.80 | 0.4329 | main_effect | |
| Rhodococcus sp. W8901 | −0.002 | 0.002 | −0.95 | 0.3499 | main_effect | |
| Rhodococcoides fascians | −0.001 | 0.003 | −0.46 | 0.6501 | main_effect | |
| Immunomodulatory Soil Bacterium | Mycolicibacterium vaccae | 0.016 | 0.007 | 2.14 | 0.0416 | interaction |
| Mycolicibacterium vaccae | −0.004 | 0.005 | −0.74 | 0.4723 | by_group_JB1_JB2 | |
| Mycolicibacterium vaccae | 0.012 | 0.003 | 3.91 | 0.0021 | by_group_JB5_JB6_JB7 | |
| Methanotroph | Methylocapsa sp. D3K7 | 0.011 | 0.004 | 2.95 | 0.0063 | main_effect |
| Nitrogen Fixer - Plant Symbiont | Bradyrhizobium sp. 170 | −0.001 | 0.005 | −0.29 | 0.7709 | main_effect |
| Bradyrhizobium sp. 200 | −0.002 | 0.003 | −0.59 | 0.5616 | main_effect | |
| Bradyrhizobium sp. Ash2021 | 0.001 | 0.002 | 0.59 | 0.5614 | main_effect | |
| Bradyrhizobium sp. | 0.000 | 0.002 | 0.21 | 0.8314 | main_effect | |
| Bradyrhizobium erythrophlei | 0.005 | 0.003 | 1.87 | 0.0719 | main_effect | |
| Bradyrhizobium barranii | −0.001 | 0.004 | −0.16 | 0.8745 | main_effect | |
| Bradyrhizobium lablabi | 0.004 | 0.002 | 1.60 | 0.1203 | main_effect | |
| Bradyrhizobium japonicum | 0.001 | 0.002 | 0.57 | 0.5762 | main_effect | |
| Bradyrhizobium diazoefficiens | 0.009 | 0.007 | 1.25 | 0.2227 | main_effect | |
| Bradyrhizobium ottawaense | 0.002 | 0.002 | 0.78 | 0.4405 | main_effect | |
| Mesorhizobium sp. ANAO-SY3R2 | 0.004 | 0.003 | 1.36 | 0.1857 | main_effect | |
| Rhizobium ruizarguesonis | −0.003 | 0.004 | −0.87 | 0.3935 | main_effect | |
| Microvirga ossetica | −0.001 | 0.004 | −0.28 | 0.7792 | main_effect | |
| Opportunistic Pathogen | Mycobacterium intracellulare | 0.002 | 0.002 | 1.22 | 0.2322 | main_effect |
| Bacillus cereus | 0.000 | 0.004 | −0.06 | 0.9540 | main_effect | |
| Plant-Associated Bacterium | Agrobacterium rosae | −0.019 | 0.009 | −2.28 | 0.0311 | interaction |
| Agrobacterium rosae | 0.007 | 0.004 | 1.48 | 0.1600 | by_group_JB1_JB2 | |
| Agrobacterium rosae | −0.013 | 0.007 | −1.79 | 0.0987 | by_group_JB5_JB6_JB7 | |
| Plant-Associated Commensal | Paraburkholderia hospita | −0.001 | 0.004 | −0.18 | 0.8613 | main_effect |
| Plant-Associated Commensal/Decomposer | Pseudomonas fluorescens | 0.000 | 0.006 | −0.05 | 0.9592 | main_effect |
| Pseudomonas sp. PONIH3 | 0.008 | 0.005 | 1.56 | 0.1296 | main_effect | |
| Soil Decomposer | Bacillus mycoides | 0.000 | 0.006 | −0.06 | 0.9545 | main_effect |
| Bacillus licheniformis | −0.001 | 0.008 | −0.16 | 0.8744 | main_effect | |
| Neobacillus sp. FSL H8-0543 | 0.001 | 0.003 | 0.25 | 0.8054 | main_effect | |
| Neobacillus sp. OS1-33 | −0.001 | 0.003 | −0.41 | 0.6851 | main_effect | |
| Peribacillus asahii | 0.001 | 0.004 | 0.25 | 0.8062 | main_effect | |
| Priestia megaterium | 0.000 | 0.004 | −0.03 | 0.9796 | main_effect | |
| Thermophilic Decomposer | Thermobifida fusca | 0.000 | 0.005 | −0.09 | 0.9277 | main_effect |
| Saccharomonospora viridis | −0.001 | 0.003 | −0.19 | 0.8469 | main_effect | |
| Novibacillus thermophilus | 0.003 | 0.004 | 0.82 | 0.4217 | main_effect | |
| Thermoactinomyces vulgaris | 0.003 | 0.003 | 1.02 | 0.3153 | main_effect | |
| Unclassified | Humibacillus xanthopallidus | −0.004 | 0.003 | −1.05 | 0.3042 | main_effect |
| Nakamurella multipartita | −0.001 | 0.003 | −0.21 | 0.8380 | main_effect | |
| Baekduia alba | −0.004 | 0.002 | −1.72 | 0.0971 | main_effect | |
| Capillimicrobium parvum | −0.006 | 0.003 | −2.36 | 0.0255 | main_effect | |
| Allobacillus halotolerans | 0.003 | 0.008 | 0.35 | 0.7317 | main_effect | |
| Pradoshia sp. D12 | 0.002 | 0.003 | 0.55 | 0.5890 | main_effect | |
| Afipia sp. GAS231 | 0.003 | 0.002 | 1.32 | 0.1976 | main_effect | |
| Afipia carboxidovorans | −0.002 | 0.003 | −0.74 | 0.4652 | main_effect | |
| Bosea sp. NBC 00550 | −0.003 | 0.003 | −1.02 | 0.3146 | main_effect | |
| Skermanella cutis | −0.004 | 0.004 | −0.89 | 0.3826 | main_effect | |
| Massilia sp. R2A-15 | −0.002 | 0.003 | −0.69 | 0.4933 | main_effect | |
| Imtechella halotolerans | 0.006 | 0.008 | 0.73 | 0.4695 | main_effect |
Table 33: Summary statistics for each core microbial species. The table shows the summary statistics for the analysis of the metadata variable and each core species (species level) organised into functional groups. The table gives estimate, standard error, t-value, p-value and model. Model tells which model the summary statistics represents: “main_effect” analysis all fields together as we see no difference between JB groups, “interaction” gives results for the interaction analysis and is included 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)
| Functional Group | Species | Estimate | SE | t | p-value | Model |
|---|---|---|---|---|---|---|
| Actinomycete Decomposer | Streptomyces sp. NBC 00425 | 0.002 | 0.001 | 1.40 | 0.1722 | main_effect |
| Streptomyces sp. NBC 01537 | 0.001 | 0.001 | 1.09 | 0.2842 | main_effect | |
| Streptomyces canus | 0.001 | 0.001 | 0.85 | 0.4019 | main_effect | |
| Streptomyces albidoflavus | −0.001 | 0.001 | −0.46 | 0.6507 | main_effect | |
| Streptomyces mirabilis | 0.002 | 0.002 | 1.05 | 0.3009 | main_effect | |
| Streptomyces [Kitasatospora] papulosa | 0.000 | 0.001 | 0.39 | 0.6990 | main_effect | |
| Terrabacter sp. C0L 2 | −0.001 | 0.001 | −0.96 | 0.3469 | main_effect | |
| Pedococcus sp. KACC 23699 | 0.000 | 0.001 | −0.01 | 0.9889 | main_effect | |
| Arthrobacter sp. NicSoilB8 | 0.012 | 0.004 | 3.11 | 0.0045 | interaction | |
| Arthrobacter sp. NicSoilB8 | 0.001 | 0.001 | 1.70 | 0.1118 | by_group_JB1_JB2 | |
| Arthrobacter sp. NicSoilB8 | 0.013 | 0.003 | 3.75 | 0.0028 | by_group_JB5_JB6_JB7 | |
| Arthrobacter sp. NicSoilB4 | 0.001 | 0.002 | 0.32 | 0.7512 | main_effect | |
| Arthrobacter sp. PAMC25564 | 0.003 | 0.001 | 1.96 | 0.0600 | main_effect | |
| Arthrobacter sulfonylureivorans | 0.003 | 0.002 | 1.75 | 0.0907 | main_effect | |
| Nocardioides sp. T5 | −0.001 | 0.002 | −0.32 | 0.7545 | main_effect | |
| Nocardioides panacis | −0.002 | 0.002 | −0.85 | 0.4048 | main_effect | |
| Nocardioides ungokensis | 0.001 | 0.002 | 0.53 | 0.6017 | main_effect | |
| Kribbella sp. NBC 00359 | −0.002 | 0.001 | −1.27 | 0.2161 | main_effect | |
| Kribbella sp. NBC 01484 | −0.002 | 0.002 | −0.99 | 0.3330 | main_effect | |
| Kribbella sp. NBC 01510 | −0.002 | 0.002 | −0.94 | 0.3537 | main_effect | |
| Micromonospora sp. NBC 00330 | −0.001 | 0.001 | −0.94 | 0.3550 | main_effect | |
| Micromonospora sp. NBC 01740 | −0.002 | 0.002 | −1.13 | 0.2687 | main_effect | |
| Micromonospora sp. B006 | 0.000 | 0.002 | −0.24 | 0.8131 | main_effect | |
| Micromonospora zamorensis | 0.000 | 0.001 | −0.22 | 0.8242 | main_effect | |
| Dactylosporangium sp. NBC 01737 | 0.000 | 0.001 | 0.35 | 0.7281 | main_effect | |
| Streptosporangium sp. 'caverna' | −0.001 | 0.001 | −1.09 | 0.2851 | main_effect | |
| Streptosporangium subroseum | −0.001 | 0.001 | −1.03 | 0.3108 | main_effect | |
| Streptosporangium roseum | −0.001 | 0.001 | −1.04 | 0.3055 | main_effect | |
| Nonomuraea glycinis | 0.000 | 0.002 | 0.06 | 0.9521 | main_effect | |
| Amycolatopsis sp. DSM 110486 | 0.000 | 0.001 | 0.05 | 0.9623 | main_effect | |
| Actinomycetospora sp. NBC 00405 | 0.000 | 0.002 | −0.30 | 0.7674 | main_effect | |
| Anaerobic Decomposer | Acetivibrio saccincola | −0.003 | 0.002 | −1.76 | 0.0890 | main_effect |
| Herbinix luporum | −0.002 | 0.002 | −1.15 | 0.2595 | main_effect | |
| Hydrocarbon Degrader | Mycolicibacterium vanbaalenii | 0.000 | 0.002 | 0.08 | 0.9355 | main_effect |
| Mycolicibacterium [Mycobacterium] burgundiense | 0.000 | 0.001 | −0.18 | 0.8612 | main_effect | |
| Rhodococcus sp. MTM3W5.2 | 0.001 | 0.001 | 0.87 | 0.3929 | main_effect | |
| Rhodococcus sp. W8901 | 0.000 | 0.001 | 0.06 | 0.9505 | main_effect | |
| Rhodococcoides fascians | −0.001 | 0.001 | −0.93 | 0.3583 | main_effect | |
| Immunomodulatory Soil Bacterium | Mycolicibacterium vaccae | 0.000 | 0.001 | −0.11 | 0.9161 | main_effect |
| Methanotroph | Methylocapsa sp. D3K7 | 0.001 | 0.002 | 0.44 | 0.6634 | main_effect |
| Nitrogen Fixer - Plant Symbiont | Bradyrhizobium sp. 170 | 0.026 | 0.011 | 2.36 | 0.0262 | interaction |
| Bradyrhizobium sp. 170 | 0.003 | 0.002 | 1.37 | 0.1914 | by_group_JB1_JB2 | |
| Bradyrhizobium sp. 170 | 0.029 | 0.009 | 3.41 | 0.0051 | by_group_JB5_JB6_JB7 | |
| Bradyrhizobium sp. 200 | 0.002 | 0.001 | 2.13 | 0.0422 | main_effect | |
| Bradyrhizobium sp. Ash2021 | 0.013 | 0.004 | 3.08 | 0.0048 | interaction | |
| Bradyrhizobium sp. Ash2021 | 0.000 | 0.001 | 0.57 | 0.5767 | by_group_JB1_JB2 | |
| Bradyrhizobium sp. Ash2021 | 0.014 | 0.005 | 2.59 | 0.0236 | by_group_JB5_JB6_JB7 | |
| Bradyrhizobium sp. | 0.002 | 0.001 | 2.62 | 0.0141 | main_effect | |
| Bradyrhizobium erythrophlei | 0.014 | 0.007 | 2.06 | 0.0497 | interaction | |
| Bradyrhizobium erythrophlei | 0.000 | 0.001 | −0.09 | 0.9319 | by_group_JB1_JB2 | |
| Bradyrhizobium erythrophlei | 0.014 | 0.007 | 2.05 | 0.0626 | by_group_JB5_JB6_JB7 | |
| Bradyrhizobium barranii | 0.000 | 0.002 | 0.02 | 0.9862 | main_effect | |
| Bradyrhizobium lablabi | 0.015 | 0.006 | 2.64 | 0.0139 | interaction | |
| Bradyrhizobium lablabi | 0.001 | 0.001 | 0.54 | 0.5992 | by_group_JB1_JB2 | |
| Bradyrhizobium lablabi | 0.015 | 0.006 | 2.56 | 0.0250 | by_group_JB5_JB6_JB7 | |
| Bradyrhizobium japonicum | 0.011 | 0.004 | 2.36 | 0.0259 | interaction | |
| Bradyrhizobium japonicum | 0.000 | 0.001 | 0.11 | 0.9102 | by_group_JB1_JB2 | |
| Bradyrhizobium japonicum | 0.011 | 0.003 | 3.59 | 0.0037 | by_group_JB5_JB6_JB7 | |
| Bradyrhizobium diazoefficiens | 0.005 | 0.003 | 1.66 | 0.1085 | main_effect | |
| Bradyrhizobium ottawaense | 0.016 | 0.005 | 3.29 | 0.0029 | interaction | |
| Bradyrhizobium ottawaense | 0.001 | 0.001 | 2.11 | 0.0536 | by_group_JB1_JB2 | |
| Bradyrhizobium ottawaense | 0.017 | 0.006 | 2.88 | 0.0138 | by_group_JB5_JB6_JB7 | |
| Mesorhizobium sp. ANAO-SY3R2 | 0.001 | 0.001 | 0.93 | 0.3583 | main_effect | |
| Rhizobium ruizarguesonis | 0.000 | 0.002 | 0.23 | 0.8160 | main_effect | |
| Microvirga ossetica | 0.000 | 0.002 | −0.18 | 0.8602 | main_effect | |
| Opportunistic Pathogen | Mycobacterium intracellulare | 0.000 | 0.001 | 0.17 | 0.8675 | main_effect |
| Bacillus cereus | 0.001 | 0.002 | 0.58 | 0.5685 | main_effect | |
| Plant-Associated Bacterium | Agrobacterium rosae | 0.000 | 0.002 | −0.09 | 0.9281 | main_effect |
| Plant-Associated Commensal | Paraburkholderia hospita | 0.000 | 0.002 | −0.01 | 0.9955 | main_effect |
| Plant-Associated Commensal/Decomposer | Pseudomonas fluorescens | 0.002 | 0.002 | 0.95 | 0.3480 | main_effect |
| Pseudomonas sp. PONIH3 | 0.001 | 0.002 | 0.65 | 0.5205 | main_effect | |
| Soil Decomposer | Bacillus mycoides | 0.000 | 0.003 | 0.06 | 0.9496 | main_effect |
| Bacillus licheniformis | −0.002 | 0.003 | −0.52 | 0.6067 | main_effect | |
| Neobacillus sp. FSL H8-0543 | 0.000 | 0.001 | −0.07 | 0.9473 | main_effect | |
| Neobacillus sp. OS1-33 | −0.001 | 0.001 | −0.64 | 0.5251 | main_effect | |
| Peribacillus asahii | 0.002 | 0.002 | 1.07 | 0.2957 | main_effect | |
| Priestia megaterium | 0.000 | 0.002 | 0.00 | 0.9963 | main_effect | |
| Thermophilic Decomposer | Thermobifida fusca | −0.003 | 0.002 | −1.67 | 0.1066 | main_effect |
| Saccharomonospora viridis | −0.018 | 0.007 | −2.50 | 0.0190 | interaction | |
| Saccharomonospora viridis | −0.002 | 0.001 | −1.40 | 0.1847 | by_group_JB1_JB2 | |
| Saccharomonospora viridis | −0.019 | 0.008 | −2.49 | 0.0283 | by_group_JB5_JB6_JB7 | |
| Novibacillus thermophilus | −0.003 | 0.001 | −1.89 | 0.0688 | main_effect | |
| Thermoactinomyces vulgaris | −0.001 | 0.001 | −0.77 | 0.4488 | main_effect | |
| Unclassified | Humibacillus xanthopallidus | −0.001 | 0.001 | −1.02 | 0.3176 | main_effect |
| Nakamurella multipartita | 0.000 | 0.001 | −0.33 | 0.7463 | main_effect | |
| Baekduia alba | 0.000 | 0.001 | −0.38 | 0.7091 | main_effect | |
| Capillimicrobium parvum | −0.001 | 0.001 | −0.95 | 0.3509 | main_effect | |
| Allobacillus halotolerans | −0.002 | 0.003 | −0.66 | 0.5169 | main_effect | |
| Pradoshia sp. D12 | 0.003 | 0.001 | 2.47 | 0.0200 | main_effect | |
| Afipia sp. GAS231 | 0.001 | 0.001 | 1.64 | 0.1131 | main_effect | |
| Afipia carboxidovorans | 0.000 | 0.001 | −0.28 | 0.7820 | main_effect | |
| Bosea sp. NBC 00550 | 0.001 | 0.001 | 0.67 | 0.5061 | main_effect | |
| Skermanella cutis | 0.001 | 0.002 | 0.77 | 0.4483 | main_effect | |
| Massilia sp. R2A-15 | 0.000 | 0.001 | 0.24 | 0.8107 | main_effect | |
| Imtechella halotolerans | −0.001 | 0.003 | −0.28 | 0.7847 | main_effect |
Table 34: Summary statistics for each core microbial species. The table shows the summary statistics for the analysis of the metadata variable and each core species (species level) organised into functional groups. The table gives estimate, standard error, t-value, p-value and model. Model tells which model the summary statistics represents: “main_effect” analysis all fields together as we see no difference between JB groups, “interaction” gives results for the interaction analysis and is included when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.
Clay (perc)
| Functional Group | Species | Estimate | SE | t | p-value | Model |
|---|---|---|---|---|---|---|
| Actinomycete Decomposer | Streptomyces sp. NBC 00425 | −0.003 | 0.001 | −3.17 | 0.0037 | main_effect |
| Streptomyces sp. NBC 01537 | 0.005 | 0.002 | 2.09 | 0.0466 | interaction | |
| Streptomyces sp. NBC 01537 | −0.004 | 0.002 | −1.85 | 0.0860 | by_group_JB1_JB2 | |
| Streptomyces sp. NBC 01537 | 0.001 | 0.001 | 0.94 | 0.3658 | by_group_JB5_JB6_JB7 | |
| Streptomyces canus | 0.001 | 0.001 | 0.97 | 0.3388 | main_effect | |
| Streptomyces albidoflavus | 0.001 | 0.001 | 0.71 | 0.4826 | main_effect | |
| Streptomyces mirabilis | 0.012 | 0.004 | 3.01 | 0.0058 | interaction | |
| Streptomyces mirabilis | −0.013 | 0.004 | −3.00 | 0.0096 | by_group_JB1_JB2 | |
| Streptomyces mirabilis | −0.001 | 0.001 | −1.52 | 0.1546 | by_group_JB5_JB6_JB7 | |
| Streptomyces [Kitasatospora] papulosa | 0.001 | 0.001 | 1.06 | 0.2963 | main_effect | |
| Terrabacter sp. C0L 2 | 0.002 | 0.001 | 3.47 | 0.0017 | main_effect | |
| Pedococcus sp. KACC 23699 | −0.002 | 0.001 | −1.89 | 0.0691 | main_effect | |
| Arthrobacter sp. NicSoilB8 | 0.001 | 0.000 | 2.11 | 0.0438 | main_effect | |
| Arthrobacter sp. NicSoilB4 | 0.001 | 0.001 | 1.27 | 0.2132 | main_effect | |
| Arthrobacter sp. PAMC25564 | −0.003 | 0.001 | −3.90 | 0.0005 | main_effect | |
| Arthrobacter sulfonylureivorans | −0.011 | 0.005 | −2.13 | 0.0424 | interaction | |
| Arthrobacter sulfonylureivorans | 0.007 | 0.005 | 1.44 | 0.1710 | by_group_JB1_JB2 | |
| Arthrobacter sulfonylureivorans | −0.004 | 0.002 | −2.02 | 0.0658 | by_group_JB5_JB6_JB7 | |
| Nocardioides sp. T5 | 0.001 | 0.001 | 0.75 | 0.4624 | main_effect | |
| Nocardioides panacis | 0.002 | 0.001 | 1.96 | 0.0606 | main_effect | |
| Nocardioides ungokensis | 0.003 | 0.001 | 3.04 | 0.0050 | main_effect | |
| Kribbella sp. NBC 00359 | 0.003 | 0.001 | 5.33 | 0.0000 | main_effect | |
| Kribbella sp. NBC 01484 | 0.004 | 0.001 | 4.79 | 0.0000 | main_effect | |
| Kribbella sp. NBC 01510 | 0.004 | 0.001 | 5.62 | 0.0000 | main_effect | |
| Micromonospora sp. NBC 00330 | −0.002 | 0.001 | −2.22 | 0.0349 | main_effect | |
| Micromonospora sp. NBC 01740 | 0.002 | 0.001 | 1.43 | 0.1637 | main_effect | |
| Micromonospora sp. B006 | −0.001 | 0.001 | −1.29 | 0.2080 | main_effect | |
| Micromonospora zamorensis | −0.002 | 0.001 | −2.95 | 0.0063 | main_effect | |
| Dactylosporangium sp. NBC 01737 | −0.005 | 0.002 | −2.61 | 0.0149 | interaction | |
| Dactylosporangium sp. NBC 01737 | 0.002 | 0.002 | 0.90 | 0.3820 | by_group_JB1_JB2 | |
| Dactylosporangium sp. NBC 01737 | −0.003 | 0.000 | −7.56 | 0.0000 | by_group_JB5_JB6_JB7 | |
| Streptosporangium sp. 'caverna' | −0.008 | 0.002 | −3.17 | 0.0039 | interaction | |
| Streptosporangium sp. 'caverna' | 0.004 | 0.002 | 1.59 | 0.1346 | by_group_JB1_JB2 | |
| Streptosporangium sp. 'caverna' | −0.004 | 0.001 | −4.83 | 0.0004 | by_group_JB5_JB6_JB7 | |
| Streptosporangium subroseum | −0.006 | 0.002 | −2.90 | 0.0074 | interaction | |
| Streptosporangium subroseum | 0.003 | 0.002 | 1.37 | 0.1913 | by_group_JB1_JB2 | |
| Streptosporangium subroseum | −0.003 | 0.001 | −4.68 | 0.0005 | by_group_JB5_JB6_JB7 | |
| Streptosporangium roseum | 0.001 | 0.001 | 2.10 | 0.0444 | main_effect | |
| Nonomuraea glycinis | −0.018 | 0.005 | −3.48 | 0.0018 | interaction | |
| Nonomuraea glycinis | 0.012 | 0.005 | 2.26 | 0.0406 | by_group_JB1_JB2 | |
| Nonomuraea glycinis | −0.006 | 0.002 | −3.56 | 0.0039 | by_group_JB5_JB6_JB7 | |
| Amycolatopsis sp. DSM 110486 | −0.009 | 0.002 | −4.11 | 0.0004 | interaction | |
| Amycolatopsis sp. DSM 110486 | 0.005 | 0.002 | 2.43 | 0.0291 | by_group_JB1_JB2 | |
| Amycolatopsis sp. DSM 110486 | −0.004 | 0.001 | −4.87 | 0.0004 | by_group_JB5_JB6_JB7 | |
| Actinomycetospora sp. NBC 00405 | −0.010 | 0.004 | −2.35 | 0.0265 | interaction | |
| Actinomycetospora sp. NBC 00405 | 0.004 | 0.004 | 1.11 | 0.2863 | by_group_JB1_JB2 | |
| Actinomycetospora sp. NBC 00405 | −0.005 | 0.001 | −3.60 | 0.0037 | by_group_JB5_JB6_JB7 | |
| Anaerobic Decomposer | Acetivibrio saccincola | 0.002 | 0.001 | 1.68 | 0.1049 | main_effect |
| Herbinix luporum | 0.001 | 0.001 | 0.94 | 0.3558 | main_effect | |
| Hydrocarbon Degrader | Mycolicibacterium vanbaalenii | −0.012 | 0.004 | −3.10 | 0.0046 | interaction |
| Mycolicibacterium vanbaalenii | 0.012 | 0.005 | 2.67 | 0.0183 | by_group_JB1_JB2 | |
| Mycolicibacterium vanbaalenii | 0.000 | 0.001 | 0.09 | 0.9288 | by_group_JB5_JB6_JB7 | |
| Mycolicibacterium [Mycobacterium] burgundiense | 0.000 | 0.001 | −0.56 | 0.5793 | main_effect | |
| Rhodococcus sp. MTM3W5.2 | 0.002 | 0.001 | 2.64 | 0.0133 | main_effect | |
| Rhodococcus sp. W8901 | 0.000 | 0.001 | 0.28 | 0.7786 | main_effect | |
| Rhodococcoides fascians | −0.001 | 0.001 | −0.87 | 0.3900 | main_effect | |
| Immunomodulatory Soil Bacterium | Mycolicibacterium vaccae | −0.001 | 0.001 | −0.58 | 0.5662 | main_effect |
| Methanotroph | Methylocapsa sp. D3K7 | −0.001 | 0.001 | −0.79 | 0.4369 | main_effect |
| Nitrogen Fixer - Plant Symbiont | Bradyrhizobium sp. 170 | 0.001 | 0.001 | 0.59 | 0.5598 | main_effect |
| Bradyrhizobium sp. 200 | −0.001 | 0.001 | −1.70 | 0.0999 | main_effect | |
| Bradyrhizobium sp. Ash2021 | 0.001 | 0.000 | 2.26 | 0.0316 | main_effect | |
| Bradyrhizobium sp. | 0.000 | 0.000 | 0.32 | 0.7518 | main_effect | |
| Bradyrhizobium erythrophlei | 0.001 | 0.001 | 0.91 | 0.3697 | main_effect | |
| Bradyrhizobium barranii | −0.003 | 0.001 | −2.75 | 0.0103 | main_effect | |
| Bradyrhizobium lablabi | 0.001 | 0.001 | 0.93 | 0.3591 | main_effect | |
| Bradyrhizobium japonicum | −0.001 | 0.001 | −2.07 | 0.0477 | main_effect | |
| Bradyrhizobium diazoefficiens | 0.015 | 0.006 | 2.58 | 0.0158 | interaction | |
| Bradyrhizobium diazoefficiens | −0.017 | 0.006 | −2.75 | 0.0157 | by_group_JB1_JB2 | |
| Bradyrhizobium diazoefficiens | −0.002 | 0.002 | −0.87 | 0.4015 | by_group_JB5_JB6_JB7 | |
| Bradyrhizobium ottawaense | 0.002 | 0.001 | 3.00 | 0.0056 | main_effect | |
| Mesorhizobium sp. ANAO-SY3R2 | −0.001 | 0.001 | −1.43 | 0.1637 | main_effect | |
| Rhizobium ruizarguesonis | 0.001 | 0.001 | 1.16 | 0.2562 | main_effect | |
| Microvirga ossetica | 0.002 | 0.001 | 1.64 | 0.1129 | main_effect | |
| Opportunistic Pathogen | Mycobacterium intracellulare | −0.001 | 0.001 | −1.84 | 0.0768 | main_effect |
| Bacillus cereus | 0.000 | 0.001 | −0.07 | 0.9437 | main_effect | |
| Plant-Associated Bacterium | Agrobacterium rosae | 0.000 | 0.001 | −0.18 | 0.8569 | main_effect |
| Plant-Associated Commensal | Paraburkholderia hospita | 0.010 | 0.003 | 3.18 | 0.0037 | interaction |
| Paraburkholderia hospita | −0.011 | 0.003 | −3.53 | 0.0033 | by_group_JB1_JB2 | |
| Paraburkholderia hospita | −0.002 | 0.001 | −1.67 | 0.1212 | by_group_JB5_JB6_JB7 | |
| Plant-Associated Commensal/Decomposer | Pseudomonas fluorescens | 0.001 | 0.002 | 0.55 | 0.5872 | main_effect |
| Pseudomonas sp. PONIH3 | 0.000 | 0.001 | 0.12 | 0.9065 | main_effect | |
| Soil Decomposer | Bacillus mycoides | 0.004 | 0.002 | 2.25 | 0.0328 | main_effect |
| Bacillus licheniformis | 0.002 | 0.002 | 1.03 | 0.3119 | main_effect | |
| Neobacillus sp. FSL H8-0543 | 0.001 | 0.001 | 1.75 | 0.0916 | main_effect | |
| Neobacillus sp. OS1-33 | 0.004 | 0.001 | 6.85 | 0.0000 | main_effect | |
| Peribacillus asahii | 0.001 | 0.001 | 1.14 | 0.2624 | main_effect | |
| Priestia megaterium | −0.002 | 0.001 | −2.51 | 0.0183 | main_effect | |
| Thermophilic Decomposer | Thermobifida fusca | 0.001 | 0.001 | 0.74 | 0.4656 | main_effect |
| Saccharomonospora viridis | 0.000 | 0.001 | 0.40 | 0.6928 | main_effect | |
| Novibacillus thermophilus | 0.000 | 0.001 | −0.36 | 0.7246 | main_effect | |
| Thermoactinomyces vulgaris | −0.002 | 0.001 | −2.38 | 0.0242 | main_effect | |
| Unclassified | Humibacillus xanthopallidus | 0.004 | 0.001 | 6.11 | 0.0000 | main_effect |
| Nakamurella multipartita | −0.007 | 0.003 | −2.37 | 0.0257 | interaction | |
| Nakamurella multipartita | 0.006 | 0.002 | 2.70 | 0.0173 | by_group_JB1_JB2 | |
| Nakamurella multipartita | −0.001 | 0.001 | −0.44 | 0.6648 | by_group_JB5_JB6_JB7 | |
| Baekduia alba | −0.001 | 0.001 | −1.88 | 0.0705 | main_effect | |
| Capillimicrobium parvum | 0.001 | 0.001 | 1.87 | 0.0717 | main_effect | |
| Allobacillus halotolerans | 0.000 | 0.002 | 0.09 | 0.9310 | main_effect | |
| Pradoshia sp. D12 | 0.000 | 0.001 | −0.61 | 0.5468 | main_effect | |
| Afipia sp. GAS231 | 0.004 | 0.002 | 2.24 | 0.0337 | interaction | |
| Afipia sp. GAS231 | −0.004 | 0.002 | −2.12 | 0.0525 | by_group_JB1_JB2 | |
| Afipia sp. GAS231 | 0.000 | 0.001 | −0.10 | 0.9182 | by_group_JB5_JB6_JB7 | |
| Afipia carboxidovorans | 0.000 | 0.001 | 0.48 | 0.6328 | main_effect | |
| Bosea sp. NBC 00550 | −0.010 | 0.004 | −2.74 | 0.0109 | interaction | |
| Bosea sp. NBC 00550 | 0.009 | 0.003 | 2.80 | 0.0141 | by_group_JB1_JB2 | |
| Bosea sp. NBC 00550 | −0.001 | 0.002 | −0.89 | 0.3917 | by_group_JB5_JB6_JB7 | |
| Skermanella cutis | 0.001 | 0.001 | 0.60 | 0.5509 | main_effect | |
| Massilia sp. R2A-15 | 0.000 | 0.001 | −0.29 | 0.7713 | main_effect | |
| Imtechella halotolerans | 0.000 | 0.002 | 0.18 | 0.8548 | main_effect |
Table 35: Summary statistics for each core microbial species. The table shows the summary statistics for the analysis of the metadata variable and each core species (species level) organised into functional groups. The table gives estimate, standard error, t-value, p-value and model. Model tells which model the summary statistics represents: “main_effect” analysis all fields together as we see no difference between JB groups, “interaction” gives results for the interaction analysis and is included when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.
Nitrogen (perc)
| Functional Group | Species | Estimate | SE | t | p-value | Model |
|---|---|---|---|---|---|---|
| Actinomycete Decomposer | Streptomyces sp. NBC 00425 | 0.082 | 0.074 | 1.12 | 0.2739 | main_effect |
| Streptomyces sp. NBC 01537 | 0.054 | 0.048 | 1.14 | 0.2627 | main_effect | |
| Streptomyces canus | 0.135 | 0.063 | 2.13 | 0.0423 | main_effect | |
| Streptomyces albidoflavus | −0.002 | 0.060 | −0.03 | 0.9789 | main_effect | |
| Streptomyces mirabilis | −0.003 | 0.101 | −0.03 | 0.9749 | main_effect | |
| Streptomyces [Kitasatospora] papulosa | −0.006 | 0.058 | −0.10 | 0.9238 | main_effect | |
| Terrabacter sp. C0L 2 | −0.026 | 0.049 | −0.54 | 0.5966 | main_effect | |
| Pedococcus sp. KACC 23699 | −0.094 | 0.067 | −1.41 | 0.1708 | main_effect | |
| Arthrobacter sp. NicSoilB8 | 0.207 | 0.073 | 2.82 | 0.0091 | interaction | |
| Arthrobacter sp. NicSoilB8 | 0.054 | 0.039 | 1.39 | 0.1874 | by_group_JB1_JB2 | |
| Arthrobacter sp. NicSoilB8 | 0.261 | 0.054 | 4.84 | 0.0004 | by_group_JB5_JB6_JB7 | |
| Arthrobacter sp. NicSoilB4 | 0.086 | 0.078 | 1.10 | 0.2796 | main_effect | |
| Arthrobacter sp. PAMC25564 | 0.052 | 0.078 | 0.67 | 0.5113 | main_effect | |
| Arthrobacter sulfonylureivorans | 0.177 | 0.091 | 1.95 | 0.0611 | main_effect | |
| Nocardioides sp. T5 | 0.043 | 0.107 | 0.40 | 0.6924 | main_effect | |
| Nocardioides panacis | −0.014 | 0.100 | −0.14 | 0.8883 | main_effect | |
| Nocardioides ungokensis | 0.117 | 0.092 | 1.28 | 0.2120 | main_effect | |
| Kribbella sp. NBC 00359 | 0.000 | 0.061 | 0.01 | 0.9938 | main_effect | |
| Kribbella sp. NBC 01484 | 0.038 | 0.077 | 0.49 | 0.6265 | main_effect | |
| Kribbella sp. NBC 01510 | 0.062 | 0.085 | 0.72 | 0.4765 | main_effect | |
| Micromonospora sp. NBC 00330 | −0.058 | 0.058 | −0.99 | 0.3299 | main_effect | |
| Micromonospora sp. NBC 01740 | −0.090 | 0.091 | −0.99 | 0.3317 | main_effect | |
| Micromonospora sp. B006 | −0.014 | 0.082 | −0.17 | 0.8698 | main_effect | |
| Micromonospora zamorensis | −0.028 | 0.073 | −0.38 | 0.7036 | main_effect | |
| Dactylosporangium sp. NBC 01737 | −0.021 | 0.039 | −0.54 | 0.5953 | main_effect | |
| Streptosporangium sp. 'caverna' | −0.064 | 0.049 | −1.30 | 0.2027 | main_effect | |
| Streptosporangium subroseum | −0.058 | 0.045 | −1.29 | 0.2080 | main_effect | |
| Streptosporangium roseum | −0.049 | 0.048 | −1.03 | 0.3107 | main_effect | |
| Nonomuraea glycinis | −0.007 | 0.109 | −0.07 | 0.9468 | main_effect | |
| Amycolatopsis sp. DSM 110486 | 0.003 | 0.054 | 0.05 | 0.9631 | main_effect | |
| Actinomycetospora sp. NBC 00405 | 0.009 | 0.080 | 0.11 | 0.9148 | main_effect | |
| Anaerobic Decomposer | Acetivibrio saccincola | −0.118 | 0.079 | −1.49 | 0.1462 | main_effect |
| Herbinix luporum | −0.085 | 0.083 | −1.03 | 0.3137 | main_effect | |
| Hydrocarbon Degrader | Mycolicibacterium vanbaalenii | 0.084 | 0.080 | 1.05 | 0.3034 | main_effect |
| Mycolicibacterium [Mycobacterium] burgundiense | −0.024 | 0.063 | −0.38 | 0.7056 | main_effect | |
| Rhodococcus sp. MTM3W5.2 | 0.120 | 0.059 | 2.06 | 0.0489 | main_effect | |
| Rhodococcus sp. W8901 | 0.025 | 0.049 | 0.51 | 0.6128 | main_effect | |
| Rhodococcoides fascians | −0.065 | 0.050 | −1.32 | 0.1986 | main_effect | |
| Immunomodulatory Soil Bacterium | Mycolicibacterium vaccae | 0.061 | 0.066 | 0.92 | 0.3658 | main_effect |
| Methanotroph | Methylocapsa sp. D3K7 | 0.057 | 0.086 | 0.66 | 0.5139 | main_effect |
| Nitrogen Fixer - Plant Symbiont | Bradyrhizobium sp. 170 | 0.301 | 0.086 | 3.50 | 0.0016 | main_effect |
| Bradyrhizobium sp. 200 | 0.150 | 0.049 | 3.08 | 0.0046 | main_effect | |
| Bradyrhizobium sp. Ash2021 | 0.265 | 0.081 | 3.28 | 0.0029 | interaction | |
| Bradyrhizobium sp. Ash2021 | 0.028 | 0.030 | 0.94 | 0.3636 | by_group_JB1_JB2 | |
| Bradyrhizobium sp. Ash2021 | 0.293 | 0.086 | 3.42 | 0.0051 | by_group_JB5_JB6_JB7 | |
| Bradyrhizobium sp. | 0.090 | 0.029 | 3.15 | 0.0038 | main_effect | |
| Bradyrhizobium erythrophlei | 0.316 | 0.131 | 2.41 | 0.0233 | interaction | |
| Bradyrhizobium erythrophlei | −0.020 | 0.063 | −0.31 | 0.7589 | by_group_JB1_JB2 | |
| Bradyrhizobium erythrophlei | 0.296 | 0.113 | 2.63 | 0.0220 | by_group_JB5_JB6_JB7 | |
| Bradyrhizobium barranii | −0.010 | 0.080 | −0.13 | 0.8975 | main_effect | |
| Bradyrhizobium lablabi | 0.290 | 0.107 | 2.71 | 0.0118 | interaction | |
| Bradyrhizobium lablabi | 0.038 | 0.049 | 0.78 | 0.4494 | by_group_JB1_JB2 | |
| Bradyrhizobium lablabi | 0.328 | 0.098 | 3.36 | 0.0057 | by_group_JB5_JB6_JB7 | |
| Bradyrhizobium japonicum | 0.068 | 0.042 | 1.63 | 0.1143 | main_effect | |
| Bradyrhizobium diazoefficiens | 0.089 | 0.143 | 0.62 | 0.5389 | main_effect | |
| Bradyrhizobium ottawaense | 0.286 | 0.089 | 3.22 | 0.0034 | interaction | |
| Bradyrhizobium ottawaense | 0.087 | 0.030 | 2.89 | 0.0119 | by_group_JB1_JB2 | |
| Bradyrhizobium ottawaense | 0.374 | 0.098 | 3.82 | 0.0025 | by_group_JB5_JB6_JB7 | |
| Mesorhizobium sp. ANAO-SY3R2 | 0.082 | 0.059 | 1.39 | 0.1760 | main_effect | |
| Rhizobium ruizarguesonis | 0.011 | 0.078 | 0.14 | 0.8906 | main_effect | |
| Microvirga ossetica | 0.052 | 0.078 | 0.67 | 0.5074 | main_effect | |
| Opportunistic Pathogen | Mycobacterium intracellulare | −0.030 | 0.041 | −0.73 | 0.4708 | main_effect |
| Bacillus cereus | 0.125 | 0.076 | 1.64 | 0.1114 | main_effect | |
| Plant-Associated Bacterium | Agrobacterium rosae | −0.072 | 0.075 | −0.96 | 0.3439 | main_effect |
| Plant-Associated Commensal | Paraburkholderia hospita | −0.092 | 0.075 | −1.22 | 0.2316 | main_effect |
| Plant-Associated Commensal/Decomposer | Pseudomonas fluorescens | 0.204 | 0.115 | 1.77 | 0.0870 | main_effect |
| Pseudomonas sp. PONIH3 | 0.050 | 0.107 | 0.47 | 0.6402 | main_effect | |
| Soil Decomposer | Bacillus mycoides | 0.225 | 0.124 | 1.82 | 0.0789 | main_effect |
| Bacillus licheniformis | −0.056 | 0.158 | −0.36 | 0.7231 | main_effect | |
| Neobacillus sp. FSL H8-0543 | 0.055 | 0.054 | 1.03 | 0.3137 | main_effect | |
| Neobacillus sp. OS1-33 | 0.027 | 0.063 | 0.43 | 0.6727 | main_effect | |
| Peribacillus asahii | 0.197 | 0.078 | 2.51 | 0.0183 | main_effect | |
| Priestia megaterium | −0.044 | 0.081 | −0.54 | 0.5903 | main_effect | |
| Thermophilic Decomposer | Thermobifida fusca | −0.189 | 0.084 | −2.25 | 0.0327 | main_effect |
| Saccharomonospora viridis | −0.169 | 0.060 | −2.79 | 0.0093 | main_effect | |
| Novibacillus thermophilus | −0.191 | 0.069 | −2.76 | 0.0100 | main_effect | |
| Thermoactinomyces vulgaris | −0.086 | 0.055 | −1.57 | 0.1267 | main_effect | |
| Unclassified | Humibacillus xanthopallidus | 0.033 | 0.070 | 0.47 | 0.6398 | main_effect |
| Nakamurella multipartita | 0.030 | 0.052 | 0.58 | 0.5667 | main_effect | |
| Baekduia alba | 0.000 | 0.044 | 0.00 | 0.9969 | main_effect | |
| Capillimicrobium parvum | 0.020 | 0.056 | 0.37 | 0.7170 | main_effect | |
| Allobacillus halotolerans | −0.170 | 0.157 | −1.08 | 0.2883 | main_effect | |
| Pradoshia sp. D12 | 0.145 | 0.054 | 2.71 | 0.0113 | main_effect | |
| Afipia sp. GAS231 | 0.025 | 0.041 | 0.60 | 0.5505 | main_effect | |
| Afipia carboxidovorans | −0.005 | 0.067 | −0.07 | 0.9463 | main_effect | |
| Bosea sp. NBC 00550 | 0.101 | 0.068 | 1.48 | 0.1503 | main_effect | |
| Skermanella cutis | 0.092 | 0.090 | 1.03 | 0.3113 | main_effect | |
| Massilia sp. R2A-15 | −0.002 | 0.051 | −0.04 | 0.9645 | main_effect | |
| Imtechella halotolerans | −0.199 | 0.153 | −1.30 | 0.2041 | main_effect |
Table 36: Summary statistics for each core microbial species. The table shows the summary statistics for the analysis of the metadata variable and each core species (species level) organised into functional groups. The table gives estimate, standard error, t-value, p-value and model. Model tells which model the summary statistics represents: “main_effect” analysis all fields together as we see no difference between JB groups, “interaction” gives results for the interaction analysis and is included 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
| Functional Group | Species | Estimate | SE | t | p-value | Model |
|---|---|---|---|---|---|---|
| Actinomycete Decomposer | Streptomyces sp. NBC 00425 | 0.000 | 0.000 | −0.12 | 0.9089 | main_effect |
| Streptomyces sp. NBC 01537 | 0.000 | 0.000 | −0.70 | 0.4887 | main_effect | |
| Streptomyces canus | 0.002 | 0.001 | 2.28 | 0.0308 | interaction | |
| Streptomyces canus | −0.001 | 0.000 | −2.38 | 0.0318 | by_group_JB1_JB2 | |
| Streptomyces canus | 0.001 | 0.001 | 1.01 | 0.3333 | by_group_JB5_JB6_JB7 | |
| Streptomyces albidoflavus | 0.000 | 0.000 | −0.39 | 0.6977 | main_effect | |
| Streptomyces mirabilis | 0.000 | 0.001 | 0.94 | 0.3550 | main_effect | |
| Streptomyces [Kitasatospora] papulosa | 0.000 | 0.000 | 0.18 | 0.8622 | main_effect | |
| Terrabacter sp. C0L 2 | 0.000 | 0.000 | −0.70 | 0.4898 | main_effect | |
| Pedococcus sp. KACC 23699 | 0.000 | 0.000 | 0.13 | 0.8989 | main_effect | |
| Arthrobacter sp. NicSoilB8 | 0.000 | 0.000 | −1.56 | 0.1289 | main_effect | |
| Arthrobacter sp. NicSoilB4 | 0.000 | 0.000 | −0.56 | 0.5798 | main_effect | |
| Arthrobacter sp. PAMC25564 | 0.000 | 0.000 | 1.06 | 0.2996 | main_effect | |
| Arthrobacter sulfonylureivorans | 0.000 | 0.001 | 0.47 | 0.6453 | main_effect | |
| Nocardioides sp. T5 | 0.000 | 0.001 | 0.10 | 0.9237 | main_effect | |
| Nocardioides panacis | −0.001 | 0.001 | −0.96 | 0.3458 | main_effect | |
| Nocardioides ungokensis | 0.000 | 0.001 | −0.30 | 0.7684 | main_effect | |
| Kribbella sp. NBC 00359 | 0.000 | 0.000 | −1.33 | 0.1936 | main_effect | |
| Kribbella sp. NBC 01484 | 0.000 | 0.000 | 0.18 | 0.8598 | main_effect | |
| Kribbella sp. NBC 01510 | 0.000 | 0.000 | 0.14 | 0.8916 | main_effect | |
| Micromonospora sp. NBC 00330 | 0.000 | 0.000 | −0.22 | 0.8260 | main_effect | |
| Micromonospora sp. NBC 01740 | 0.000 | 0.000 | −0.62 | 0.5427 | main_effect | |
| Micromonospora sp. B006 | 0.001 | 0.000 | 1.78 | 0.0856 | main_effect | |
| Micromonospora zamorensis | 0.001 | 0.000 | 1.98 | 0.0581 | main_effect | |
| Dactylosporangium sp. NBC 01737 | 0.000 | 0.000 | 0.16 | 0.8747 | main_effect | |
| Streptosporangium sp. 'caverna' | 0.000 | 0.000 | −1.02 | 0.3162 | main_effect | |
| Streptosporangium subroseum | 0.000 | 0.000 | −1.01 | 0.3216 | main_effect | |
| Streptosporangium roseum | −0.001 | 0.000 | −2.11 | 0.0446 | interaction | |
| Streptosporangium roseum | 0.000 | 0.000 | 2.34 | 0.0348 | by_group_JB1_JB2 | |
| Streptosporangium roseum | −0.001 | 0.001 | −1.30 | 0.2188 | by_group_JB5_JB6_JB7 | |
| Nonomuraea glycinis | 0.003 | 0.001 | 3.41 | 0.0021 | interaction | |
| Nonomuraea glycinis | −0.002 | 0.001 | −2.85 | 0.0127 | by_group_JB1_JB2 | |
| Nonomuraea glycinis | 0.002 | 0.001 | 2.07 | 0.0609 | by_group_JB5_JB6_JB7 | |
| Amycolatopsis sp. DSM 110486 | 0.000 | 0.000 | −0.15 | 0.8784 | main_effect | |
| Actinomycetospora sp. NBC 00405 | 0.000 | 0.000 | 0.08 | 0.9391 | main_effect | |
| Anaerobic Decomposer | Acetivibrio saccincola | 0.000 | 0.000 | 0.69 | 0.4985 | main_effect |
| Herbinix luporum | 0.000 | 0.000 | 0.34 | 0.7358 | main_effect | |
| Hydrocarbon Degrader | Mycolicibacterium vanbaalenii | 0.000 | 0.000 | 0.14 | 0.8924 | main_effect |
| Mycolicibacterium [Mycobacterium] burgundiense | 0.000 | 0.000 | −0.97 | 0.3419 | main_effect | |
| Rhodococcus sp. MTM3W5.2 | 0.000 | 0.000 | −0.41 | 0.6861 | main_effect | |
| Rhodococcus sp. W8901 | 0.000 | 0.000 | 1.21 | 0.2382 | main_effect | |
| Rhodococcoides fascians | 0.000 | 0.000 | −0.30 | 0.7638 | main_effect | |
| Immunomodulatory Soil Bacterium | Mycolicibacterium vaccae | 0.001 | 0.000 | 2.36 | 0.0257 | main_effect |
| Methanotroph | Methylocapsa sp. D3K7 | 0.000 | 0.000 | 0.90 | 0.3758 | main_effect |
| Nitrogen Fixer - Plant Symbiont | Bradyrhizobium sp. 170 | 0.000 | 0.001 | −0.40 | 0.6936 | main_effect |
| Bradyrhizobium sp. 200 | 0.000 | 0.000 | 0.46 | 0.6468 | main_effect | |
| Bradyrhizobium sp. Ash2021 | 0.000 | 0.000 | 0.35 | 0.7273 | main_effect | |
| Bradyrhizobium sp. | 0.000 | 0.000 | −0.15 | 0.8787 | main_effect | |
| Bradyrhizobium erythrophlei | 0.000 | 0.000 | 1.50 | 0.1448 | main_effect | |
| Bradyrhizobium barranii | 0.001 | 0.000 | 1.33 | 0.1941 | main_effect | |
| Bradyrhizobium lablabi | 0.000 | 0.000 | 1.18 | 0.2472 | main_effect | |
| Bradyrhizobium japonicum | 0.000 | 0.000 | 1.48 | 0.1514 | main_effect | |
| Bradyrhizobium diazoefficiens | 0.001 | 0.001 | 1.70 | 0.1005 | main_effect | |
| Bradyrhizobium ottawaense | 0.000 | 0.000 | 0.19 | 0.8517 | main_effect | |
| Mesorhizobium sp. ANAO-SY3R2 | 0.000 | 0.000 | 0.93 | 0.3597 | main_effect | |
| Rhizobium ruizarguesonis | −0.001 | 0.000 | −1.95 | 0.0613 | main_effect | |
| Microvirga ossetica | 0.000 | 0.000 | 0.45 | 0.6575 | main_effect | |
| Opportunistic Pathogen | Mycobacterium intracellulare | 0.000 | 0.000 | 2.52 | 0.0178 | main_effect |
| Bacillus cereus | 0.000 | 0.000 | 0.14 | 0.8876 | main_effect | |
| Plant-Associated Bacterium | Agrobacterium rosae | 0.000 | 0.000 | −0.84 | 0.4053 | main_effect |
| Plant-Associated Commensal | Paraburkholderia hospita | 0.000 | 0.000 | 0.52 | 0.6073 | main_effect |
| Plant-Associated Commensal/Decomposer | Pseudomonas fluorescens | −0.001 | 0.001 | −1.08 | 0.2888 | main_effect |
| Pseudomonas sp. PONIH3 | −0.001 | 0.001 | −2.73 | 0.0107 | main_effect | |
| Soil Decomposer | Bacillus mycoides | −0.001 | 0.001 | −1.30 | 0.2026 | main_effect |
| Bacillus licheniformis | 0.000 | 0.001 | −0.17 | 0.8647 | main_effect | |
| Neobacillus sp. FSL H8-0543 | 0.000 | 0.000 | 0.19 | 0.8486 | main_effect | |
| Neobacillus sp. OS1-33 | 0.000 | 0.000 | −1.20 | 0.2387 | main_effect | |
| Peribacillus asahii | −0.001 | 0.000 | −1.66 | 0.1075 | main_effect | |
| Priestia megaterium | 0.000 | 0.000 | −0.26 | 0.7989 | main_effect | |
| Thermophilic Decomposer | Thermobifida fusca | 0.000 | 0.000 | 0.01 | 0.9883 | main_effect |
| Saccharomonospora viridis | 0.000 | 0.000 | −0.13 | 0.8959 | main_effect | |
| Novibacillus thermophilus | 0.000 | 0.000 | 0.27 | 0.7860 | main_effect | |
| Thermoactinomyces vulgaris | 0.000 | 0.000 | −0.23 | 0.8233 | main_effect | |
| Unclassified | Humibacillus xanthopallidus | 0.000 | 0.000 | −0.90 | 0.3732 | main_effect |
| Nakamurella multipartita | 0.000 | 0.000 | −1.01 | 0.3211 | main_effect | |
| Baekduia alba | 0.000 | 0.000 | 0.69 | 0.4943 | main_effect | |
| Capillimicrobium parvum | 0.000 | 0.000 | 0.42 | 0.6795 | main_effect | |
| Allobacillus halotolerans | −0.002 | 0.001 | −2.94 | 0.0066 | main_effect | |
| Pradoshia sp. D12 | 0.000 | 0.000 | −0.05 | 0.9617 | main_effect | |
| Afipia sp. GAS231 | 0.000 | 0.000 | 2.07 | 0.0475 | main_effect | |
| Afipia carboxidovorans | 0.000 | 0.000 | −0.26 | 0.7992 | main_effect | |
| Bosea sp. NBC 00550 | 0.000 | 0.000 | −0.55 | 0.5865 | main_effect | |
| Skermanella cutis | −0.001 | 0.000 | −1.61 | 0.1193 | main_effect | |
| Massilia sp. R2A-15 | 0.000 | 0.000 | −0.41 | 0.6849 | main_effect | |
| Imtechella halotolerans | −0.002 | 0.001 | −2.99 | 0.0058 | main_effect |
Table 37: Summary statistics for each core microbial species. The table shows the summary statistics for the analysis of the metadata variable and each core species (species level) organised into functional groups. The table gives estimate, standard error, t-value, p-value and model. Model tells which model the summary statistics represents: “main_effect” analysis all fields together as we see no difference between JB groups, “interaction” gives results for the interaction analysis and is included 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
| Functional Group | Species | Estimate | SE | t | p-value | Model |
|---|---|---|---|---|---|---|
| Actinomycete Decomposer | Streptomyces sp. NBC 00425 | 0.000 | 0.001 | −0.79 | 0.4370 | main_effect |
| Streptomyces sp. NBC 01537 | 0.000 | 0.000 | 0.75 | 0.4619 | main_effect | |
| Streptomyces canus | −0.001 | 0.000 | −3.21 | 0.0033 | main_effect | |
| Streptomyces albidoflavus | 0.000 | 0.000 | −0.19 | 0.8487 | main_effect | |
| Streptomyces mirabilis | 0.002 | 0.001 | 2.50 | 0.0186 | main_effect | |
| Streptomyces [Kitasatospora] papulosa | 0.001 | 0.000 | 2.15 | 0.0400 | main_effect | |
| Terrabacter sp. C0L 2 | 0.000 | 0.000 | 0.38 | 0.7048 | main_effect | |
| Pedococcus sp. KACC 23699 | 0.000 | 0.001 | −0.15 | 0.8828 | main_effect | |
| Arthrobacter sp. NicSoilB8 | 0.000 | 0.000 | 0.29 | 0.7743 | main_effect | |
| Arthrobacter sp. NicSoilB4 | −0.002 | 0.001 | −3.06 | 0.0049 | main_effect | |
| Arthrobacter sp. PAMC25564 | 0.002 | 0.001 | 3.36 | 0.0023 | main_effect | |
| Arthrobacter sulfonylureivorans | 0.000 | 0.001 | −0.06 | 0.9546 | main_effect | |
| Nocardioides sp. T5 | −0.002 | 0.001 | −2.80 | 0.0091 | main_effect | |
| Nocardioides panacis | −0.002 | 0.001 | −2.16 | 0.0394 | main_effect | |
| Nocardioides ungokensis | 0.002 | 0.001 | 2.28 | 0.0306 | main_effect | |
| Kribbella sp. NBC 00359 | 0.004 | 0.001 | 3.18 | 0.0038 | interaction | |
| Kribbella sp. NBC 00359 | 0.000 | 0.000 | −1.06 | 0.3052 | by_group_JB1_JB2 | |
| Kribbella sp. NBC 00359 | 0.003 | 0.001 | 3.18 | 0.0080 | by_group_JB5_JB6_JB7 | |
| Kribbella sp. NBC 01484 | 0.005 | 0.001 | 3.54 | 0.0015 | interaction | |
| Kribbella sp. NBC 01484 | 0.001 | 0.000 | 2.19 | 0.0461 | by_group_JB1_JB2 | |
| Kribbella sp. NBC 01484 | 0.006 | 0.001 | 3.97 | 0.0019 | by_group_JB5_JB6_JB7 | |
| Kribbella sp. NBC 01510 | 0.005 | 0.002 | 3.16 | 0.0039 | interaction | |
| Kribbella sp. NBC 01510 | 0.001 | 0.000 | 1.54 | 0.1456 | by_group_JB1_JB2 | |
| Kribbella sp. NBC 01510 | 0.006 | 0.002 | 3.68 | 0.0031 | by_group_JB5_JB6_JB7 | |
| Micromonospora sp. NBC 00330 | −0.001 | 0.000 | −2.15 | 0.0400 | main_effect | |
| Micromonospora sp. NBC 01740 | −0.001 | 0.001 | −2.30 | 0.0293 | main_effect | |
| Micromonospora sp. B006 | 0.002 | 0.001 | 3.41 | 0.0020 | main_effect | |
| Micromonospora zamorensis | 0.000 | 0.001 | 0.38 | 0.7081 | main_effect | |
| Dactylosporangium sp. NBC 01737 | −0.001 | 0.000 | −2.43 | 0.0220 | main_effect | |
| Streptosporangium sp. 'caverna' | −0.003 | 0.001 | −2.94 | 0.0067 | interaction | |
| Streptosporangium sp. 'caverna' | −0.001 | 0.000 | −3.03 | 0.0091 | by_group_JB1_JB2 | |
| Streptosporangium sp. 'caverna' | −0.004 | 0.001 | −4.58 | 0.0006 | by_group_JB5_JB6_JB7 | |
| Streptosporangium subroseum | −0.003 | 0.001 | −2.98 | 0.0061 | interaction | |
| Streptosporangium subroseum | −0.001 | 0.000 | −2.96 | 0.0103 | by_group_JB1_JB2 | |
| Streptosporangium subroseum | −0.003 | 0.001 | −4.63 | 0.0006 | by_group_JB5_JB6_JB7 | |
| Streptosporangium roseum | 0.001 | 0.000 | 1.73 | 0.0945 | main_effect | |
| Nonomuraea glycinis | −0.002 | 0.001 | −2.66 | 0.0127 | main_effect | |
| Amycolatopsis sp. DSM 110486 | −0.003 | 0.001 | −2.76 | 0.0105 | interaction | |
| Amycolatopsis sp. DSM 110486 | −0.001 | 0.000 | −2.85 | 0.0129 | by_group_JB1_JB2 | |
| Amycolatopsis sp. DSM 110486 | −0.004 | 0.001 | −3.28 | 0.0066 | by_group_JB5_JB6_JB7 | |
| Actinomycetospora sp. NBC 00405 | −0.002 | 0.001 | −2.95 | 0.0063 | main_effect | |
| Anaerobic Decomposer | Acetivibrio saccincola | 0.000 | 0.001 | 0.00 | 0.9980 | main_effect |
| Herbinix luporum | 0.000 | 0.001 | −0.51 | 0.6137 | main_effect | |
| Hydrocarbon Degrader | Mycolicibacterium vanbaalenii | −0.001 | 0.001 | −2.31 | 0.0283 | main_effect |
| Mycolicibacterium [Mycobacterium] burgundiense | 0.000 | 0.000 | −1.01 | 0.3204 | main_effect | |
| Rhodococcus sp. MTM3W5.2 | −0.001 | 0.000 | −1.24 | 0.2264 | main_effect | |
| Rhodococcus sp. W8901 | 0.000 | 0.000 | 1.11 | 0.2767 | main_effect | |
| Rhodococcoides fascians | −0.001 | 0.000 | −1.79 | 0.0841 | main_effect | |
| Immunomodulatory Soil Bacterium | Mycolicibacterium vaccae | 0.001 | 0.000 | 2.44 | 0.0214 | main_effect |
| Methanotroph | Methylocapsa sp. D3K7 | 0.002 | 0.001 | 3.50 | 0.0016 | main_effect |
| Nitrogen Fixer - Plant Symbiont | Bradyrhizobium sp. 170 | −0.001 | 0.001 | −0.94 | 0.3549 | main_effect |
| Bradyrhizobium sp. 200 | 0.000 | 0.000 | −0.32 | 0.7502 | main_effect | |
| Bradyrhizobium sp. Ash2021 | 0.002 | 0.001 | 2.19 | 0.0379 | interaction | |
| Bradyrhizobium sp. Ash2021 | 0.000 | 0.000 | 1.48 | 0.1600 | by_group_JB1_JB2 | |
| Bradyrhizobium sp. Ash2021 | 0.002 | 0.001 | 2.08 | 0.0596 | by_group_JB5_JB6_JB7 | |
| Bradyrhizobium sp. | 0.000 | 0.000 | −0.12 | 0.9016 | main_effect | |
| Bradyrhizobium erythrophlei | 0.002 | 0.000 | 4.55 | 0.0001 | main_effect | |
| Bradyrhizobium barranii | 0.000 | 0.001 | 0.74 | 0.4633 | main_effect | |
| Bradyrhizobium lablabi | 0.001 | 0.000 | 3.92 | 0.0005 | main_effect | |
| Bradyrhizobium japonicum | 0.001 | 0.000 | 1.67 | 0.1065 | main_effect | |
| Bradyrhizobium diazoefficiens | 0.002 | 0.001 | 2.20 | 0.0366 | main_effect | |
| Bradyrhizobium ottawaense | 0.003 | 0.001 | 2.78 | 0.0100 | interaction | |
| Bradyrhizobium ottawaense | 0.000 | 0.000 | 1.16 | 0.2668 | by_group_JB1_JB2 | |
| Bradyrhizobium ottawaense | 0.003 | 0.001 | 2.62 | 0.0225 | by_group_JB5_JB6_JB7 | |
| Mesorhizobium sp. ANAO-SY3R2 | 0.001 | 0.000 | 2.64 | 0.0135 | main_effect | |
| Rhizobium ruizarguesonis | −0.001 | 0.001 | −1.88 | 0.0701 | main_effect | |
| Microvirga ossetica | −0.001 | 0.001 | −1.99 | 0.0567 | main_effect | |
| Opportunistic Pathogen | Mycobacterium intracellulare | 0.001 | 0.000 | 1.78 | 0.0855 | main_effect |
| Bacillus cereus | 0.001 | 0.001 | 2.08 | 0.0472 | main_effect | |
| Plant-Associated Bacterium | Agrobacterium rosae | −0.001 | 0.001 | −1.36 | 0.1838 | main_effect |
| Plant-Associated Commensal | Paraburkholderia hospita | 0.001 | 0.001 | 1.67 | 0.1070 | main_effect |
| Plant-Associated Commensal/Decomposer | Pseudomonas fluorescens | 0.000 | 0.001 | −0.38 | 0.7101 | main_effect |
| Pseudomonas sp. PONIH3 | 0.000 | 0.001 | 0.61 | 0.5493 | main_effect | |
| Soil Decomposer | Bacillus mycoides | −0.001 | 0.001 | −0.85 | 0.4043 | main_effect |
| Bacillus licheniformis | 0.000 | 0.001 | 0.07 | 0.9469 | main_effect | |
| Neobacillus sp. FSL H8-0543 | 0.001 | 0.000 | 2.38 | 0.0242 | main_effect | |
| Neobacillus sp. OS1-33 | 0.000 | 0.000 | 0.43 | 0.6733 | main_effect | |
| Peribacillus asahii | −0.001 | 0.001 | −1.42 | 0.1659 | main_effect | |
| Priestia megaterium | 0.001 | 0.001 | 2.60 | 0.0148 | main_effect | |
| Thermophilic Decomposer | Thermobifida fusca | 0.000 | 0.001 | −0.32 | 0.7507 | main_effect |
| Saccharomonospora viridis | 0.000 | 0.001 | −0.81 | 0.4241 | main_effect | |
| Novibacillus thermophilus | 0.000 | 0.001 | 0.34 | 0.7392 | main_effect | |
| Thermoactinomyces vulgaris | 0.000 | 0.000 | 0.95 | 0.3504 | main_effect | |
| Unclassified | Humibacillus xanthopallidus | −0.001 | 0.000 | −2.00 | 0.0554 | main_effect |
| Nakamurella multipartita | −0.001 | 0.000 | −2.13 | 0.0419 | main_effect | |
| Baekduia alba | 0.000 | 0.000 | −0.80 | 0.4306 | main_effect | |
| Capillimicrobium parvum | 0.000 | 0.000 | −0.16 | 0.8772 | main_effect | |
| Allobacillus halotolerans | 0.000 | 0.001 | 0.24 | 0.8096 | main_effect | |
| Pradoshia sp. D12 | 0.001 | 0.000 | 1.52 | 0.1386 | main_effect | |
| Afipia sp. GAS231 | 0.001 | 0.000 | 3.84 | 0.0007 | main_effect | |
| Afipia carboxidovorans | 0.001 | 0.000 | 1.28 | 0.2128 | main_effect | |
| Bosea sp. NBC 00550 | −0.001 | 0.000 | −2.19 | 0.0373 | main_effect | |
| Skermanella cutis | −0.001 | 0.001 | −2.17 | 0.0389 | main_effect | |
| Massilia sp. R2A-15 | −0.001 | 0.000 | −1.68 | 0.1050 | main_effect | |
| Imtechella halotolerans | 0.000 | 0.001 | 0.00 | 0.9984 | main_effect |
Table 38: Summary statistics for each core microbial species. The table shows the summary statistics for the analysis of the metadata variable and each core species (species level) organised into functional groups. The table gives estimate, standard error, t-value, p-value and model. Model tells which model the summary statistics represents: “main_effect” analysis all fields together as we see no difference between JB groups, “interaction” gives results for the interaction analysis and is included 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
| Functional Group | Species | Estimate | SE | t | p-value | Model |
|---|---|---|---|---|---|---|
| Actinomycete Decomposer | Streptomyces sp. NBC 00425 | −0.024 | 0.008 | −2.98 | 0.0058 | main_effect |
| Streptomyces sp. NBC 01537 | −0.008 | 0.006 | −1.42 | 0.1672 | main_effect | |
| Streptomyces canus | 0.039 | 0.017 | 2.29 | 0.0303 | interaction | |
| Streptomyces canus | −0.021 | 0.009 | −2.27 | 0.0394 | by_group_JB1_JB2 | |
| Streptomyces canus | 0.018 | 0.015 | 1.25 | 0.2359 | by_group_JB5_JB6_JB7 | |
| Streptomyces albidoflavus | −0.003 | 0.007 | −0.47 | 0.6416 | main_effect | |
| Streptomyces mirabilis | −0.043 | 0.021 | −2.06 | 0.0493 | interaction | |
| Streptomyces mirabilis | 0.025 | 0.015 | 1.68 | 0.1145 | by_group_JB1_JB2 | |
| Streptomyces mirabilis | −0.019 | 0.010 | −1.95 | 0.0746 | by_group_JB5_JB6_JB7 | |
| Streptomyces [Kitasatospora] papulosa | 0.001 | 0.007 | 0.13 | 0.8949 | main_effect | |
| Terrabacter sp. C0L 2 | 0.007 | 0.006 | 1.20 | 0.2401 | main_effect | |
| Pedococcus sp. KACC 23699 | −0.051 | 0.017 | −3.03 | 0.0054 | interaction | |
| Pedococcus sp. KACC 23699 | 0.014 | 0.009 | 1.55 | 0.1430 | by_group_JB1_JB2 | |
| Pedococcus sp. KACC 23699 | −0.037 | 0.014 | −2.56 | 0.0250 | by_group_JB5_JB6_JB7 | |
| Arthrobacter sp. NicSoilB8 | 0.010 | 0.004 | 2.49 | 0.0191 | main_effect | |
| Arthrobacter sp. NicSoilB4 | 0.002 | 0.010 | 0.25 | 0.8016 | main_effect | |
| Arthrobacter sp. PAMC25564 | 0.002 | 0.010 | 0.18 | 0.8579 | main_effect | |
| Arthrobacter sulfonylureivorans | −0.001 | 0.012 | −0.06 | 0.9558 | main_effect | |
| Nocardioides sp. T5 | 0.005 | 0.013 | 0.42 | 0.6797 | main_effect | |
| Nocardioides panacis | −0.009 | 0.012 | −0.69 | 0.4928 | main_effect | |
| Nocardioides ungokensis | 0.015 | 0.011 | 1.37 | 0.1803 | main_effect | |
| Kribbella sp. NBC 00359 | 0.007 | 0.007 | 0.93 | 0.3610 | main_effect | |
| Kribbella sp. NBC 01484 | 0.013 | 0.009 | 1.45 | 0.1573 | main_effect | |
| Kribbella sp. NBC 01510 | 0.048 | 0.020 | 2.37 | 0.0253 | interaction | |
| Kribbella sp. NBC 01510 | −0.010 | 0.009 | −1.06 | 0.3067 | by_group_JB1_JB2 | |
| Kribbella sp. NBC 01510 | 0.038 | 0.019 | 1.96 | 0.0740 | by_group_JB5_JB6_JB7 | |
| Micromonospora sp. NBC 00330 | −0.010 | 0.007 | −1.38 | 0.1784 | main_effect | |
| Micromonospora sp. NBC 01740 | 0.009 | 0.011 | 0.80 | 0.4311 | main_effect | |
| Micromonospora sp. B006 | −0.018 | 0.009 | −1.96 | 0.0594 | main_effect | |
| Micromonospora zamorensis | −0.012 | 0.009 | −1.34 | 0.1923 | main_effect | |
| Dactylosporangium sp. NBC 01737 | −0.010 | 0.005 | −2.17 | 0.0385 | main_effect | |
| Streptosporangium sp. 'caverna' | −0.005 | 0.006 | −0.79 | 0.4373 | main_effect | |
| Streptosporangium subroseum | −0.004 | 0.006 | −0.70 | 0.4904 | main_effect | |
| Streptosporangium roseum | 0.006 | 0.006 | 0.94 | 0.3533 | main_effect | |
| Nonomuraea glycinis | −0.018 | 0.013 | −1.40 | 0.1714 | main_effect | |
| Amycolatopsis sp. DSM 110486 | −0.010 | 0.006 | −1.52 | 0.1394 | main_effect | |
| Actinomycetospora sp. NBC 00405 | −0.009 | 0.010 | −0.92 | 0.3669 | main_effect | |
| Anaerobic Decomposer | Acetivibrio saccincola | 0.005 | 0.010 | 0.50 | 0.6178 | main_effect |
| Herbinix luporum | 0.007 | 0.010 | 0.72 | 0.4763 | main_effect | |
| Hydrocarbon Degrader | Mycolicibacterium vanbaalenii | 0.008 | 0.010 | 0.83 | 0.4158 | main_effect |
| Mycolicibacterium [Mycobacterium] burgundiense | −0.014 | 0.007 | −1.94 | 0.0627 | main_effect | |
| Rhodococcus sp. MTM3W5.2 | 0.014 | 0.007 | 1.91 | 0.0665 | main_effect | |
| Rhodococcus sp. W8901 | 0.009 | 0.006 | 1.64 | 0.1121 | main_effect | |
| Rhodococcoides fascians | −0.004 | 0.006 | −0.69 | 0.4985 | main_effect | |
| Immunomodulatory Soil Bacterium | Mycolicibacterium vaccae | −0.001 | 0.008 | −0.13 | 0.8949 | main_effect |
| Methanotroph | Methylocapsa sp. D3K7 | 0.006 | 0.011 | 0.60 | 0.5525 | main_effect |
| Nitrogen Fixer - Plant Symbiont | Bradyrhizobium sp. 170 | −0.002 | 0.013 | −0.14 | 0.8875 | main_effect |
| Bradyrhizobium sp. 200 | −0.010 | 0.007 | −1.43 | 0.1635 | main_effect | |
| Bradyrhizobium sp. Ash2021 | 0.008 | 0.005 | 1.65 | 0.1110 | main_effect | |
| Bradyrhizobium sp. | 0.003 | 0.004 | 0.69 | 0.4950 | main_effect | |
| Bradyrhizobium erythrophlei | 0.013 | 0.007 | 1.91 | 0.0661 | main_effect | |
| Bradyrhizobium barranii | −0.009 | 0.010 | −0.99 | 0.3317 | main_effect | |
| Bradyrhizobium lablabi | 0.009 | 0.006 | 1.58 | 0.1261 | main_effect | |
| Bradyrhizobium japonicum | −0.001 | 0.005 | −0.25 | 0.8056 | main_effect | |
| Bradyrhizobium diazoefficiens | −0.065 | 0.029 | −2.27 | 0.0318 | interaction | |
| Bradyrhizobium diazoefficiens | 0.042 | 0.018 | 2.28 | 0.0385 | by_group_JB1_JB2 | |
| Bradyrhizobium diazoefficiens | −0.024 | 0.019 | −1.25 | 0.2342 | by_group_JB5_JB6_JB7 | |
| Bradyrhizobium ottawaense | 0.012 | 0.006 | 1.99 | 0.0564 | main_effect | |
| Mesorhizobium sp. ANAO-SY3R2 | 0.002 | 0.007 | 0.28 | 0.7799 | main_effect | |
| Rhizobium ruizarguesonis | 0.007 | 0.010 | 0.72 | 0.4748 | main_effect | |
| Microvirga ossetica | 0.005 | 0.010 | 0.52 | 0.6078 | main_effect | |
| Opportunistic Pathogen | Mycobacterium intracellulare | −0.023 | 0.010 | −2.19 | 0.0378 | interaction |
| Mycobacterium intracellulare | 0.014 | 0.007 | 1.97 | 0.0690 | by_group_JB1_JB2 | |
| Mycobacterium intracellulare | −0.009 | 0.006 | −1.58 | 0.1392 | by_group_JB5_JB6_JB7 | |
| Bacillus cereus | 0.005 | 0.010 | 0.48 | 0.6331 | main_effect | |
| Plant-Associated Bacterium | Agrobacterium rosae | 0.000 | 0.009 | 0.00 | 0.9979 | main_effect |
| Plant-Associated Commensal | Paraburkholderia hospita | −0.010 | 0.009 | −1.04 | 0.3055 | main_effect |
| Plant-Associated Commensal/Decomposer | Pseudomonas fluorescens | 0.017 | 0.015 | 1.14 | 0.2636 | main_effect |
| Pseudomonas sp. PONIH3 | 0.009 | 0.013 | 0.70 | 0.4895 | main_effect | |
| Soil Decomposer | Bacillus mycoides | 0.021 | 0.016 | 1.36 | 0.1847 | main_effect |
| Bacillus licheniformis | 0.012 | 0.019 | 0.60 | 0.5545 | main_effect | |
| Neobacillus sp. FSL H8-0543 | 0.006 | 0.007 | 0.86 | 0.3997 | main_effect | |
| Neobacillus sp. OS1-33 | 0.032 | 0.014 | 2.24 | 0.0342 | interaction | |
| Neobacillus sp. OS1-33 | −0.002 | 0.007 | −0.38 | 0.7111 | by_group_JB1_JB2 | |
| Neobacillus sp. OS1-33 | 0.030 | 0.014 | 2.11 | 0.0566 | by_group_JB5_JB6_JB7 | |
| Peribacillus asahii | 0.005 | 0.011 | 0.46 | 0.6458 | main_effect | |
| Priestia megaterium | −0.027 | 0.009 | −3.10 | 0.0044 | main_effect | |
| Thermophilic Decomposer | Thermobifida fusca | −0.001 | 0.011 | −0.10 | 0.9214 | main_effect |
| Saccharomonospora viridis | −0.006 | 0.008 | −0.70 | 0.4920 | main_effect | |
| Novibacillus thermophilus | −0.009 | 0.009 | −0.91 | 0.3723 | main_effect | |
| Thermoactinomyces vulgaris | −0.017 | 0.006 | −2.77 | 0.0097 | main_effect | |
| Unclassified | Humibacillus xanthopallidus | 0.040 | 0.013 | 3.18 | 0.0037 | interaction |
| Humibacillus xanthopallidus | −0.009 | 0.007 | −1.27 | 0.2249 | by_group_JB1_JB2 | |
| Humibacillus xanthopallidus | 0.031 | 0.010 | 3.08 | 0.0095 | by_group_JB5_JB6_JB7 | |
| Nakamurella multipartita | 0.006 | 0.006 | 0.92 | 0.3637 | main_effect | |
| Baekduia alba | −0.007 | 0.005 | −1.24 | 0.2237 | main_effect | |
| Capillimicrobium parvum | −0.002 | 0.007 | −0.27 | 0.7912 | main_effect | |
| Allobacillus halotolerans | 0.007 | 0.020 | 0.34 | 0.7381 | main_effect | |
| Pradoshia sp. D12 | 0.003 | 0.007 | 0.43 | 0.6725 | main_effect | |
| Afipia sp. GAS231 | 0.002 | 0.005 | 0.36 | 0.7197 | main_effect | |
| Afipia carboxidovorans | −0.002 | 0.008 | −0.27 | 0.7875 | main_effect | |
| Bosea sp. NBC 00550 | 0.007 | 0.009 | 0.83 | 0.4149 | main_effect | |
| Skermanella cutis | −0.006 | 0.011 | −0.56 | 0.5767 | main_effect | |
| Massilia sp. R2A-15 | −0.002 | 0.006 | −0.29 | 0.7766 | main_effect | |
| Imtechella halotolerans | 0.000 | 0.019 | 0.02 | 0.9853 | main_effect |
Table 39: Summary statistics for each core microbial species. The table shows the summary statistics for the analysis of the metadata variable and each core species (species level) organised into functional groups. The table gives estimate, standard error, t-value, p-value and model. Model tells which model the summary statistics represents: “main_effect” analysis all fields together as we see no difference between JB groups, “interaction” gives results for the interaction analysis and is included when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.
Grazed
| Functional Group | Species | Estimate | SE | t | p-value | Model |
|---|---|---|---|---|---|---|
| Actinomycete Decomposer | Streptomyces sp. NBC 00425 | −0.005 | 0.009 | −0.58 | 0.5659 | main_effect |
| Streptomyces sp. NBC 01537 | −0.003 | 0.006 | −0.55 | 0.5837 | main_effect | |
| Streptomyces canus | 0.010 | 0.008 | 1.25 | 0.2205 | main_effect | |
| Streptomyces albidoflavus | 0.012 | 0.007 | 1.84 | 0.0759 | main_effect | |
| Streptomyces mirabilis | −0.019 | 0.011 | −1.66 | 0.1081 | main_effect | |
| Streptomyces [Kitasatospora] papulosa | −0.009 | 0.007 | −1.34 | 0.1914 | main_effect | |
| Terrabacter sp. C0L 2 | −0.005 | 0.006 | −0.82 | 0.4201 | main_effect | |
| Pedococcus sp. KACC 23699 | −0.022 | 0.007 | −3.25 | 0.0030 | main_effect | |
| Arthrobacter sp. NicSoilB8 | 0.000 | 0.004 | 0.02 | 0.9804 | main_effect | |
| Arthrobacter sp. NicSoilB4 | −0.006 | 0.009 | −0.70 | 0.4893 | main_effect | |
| Arthrobacter sp. PAMC25564 | −0.004 | 0.009 | −0.46 | 0.6517 | main_effect | |
| Arthrobacter sulfonylureivorans | 0.024 | 0.010 | 2.27 | 0.0308 | main_effect | |
| Nocardioides sp. T5 | 0.003 | 0.013 | 0.21 | 0.8339 | main_effect | |
| Nocardioides panacis | 0.005 | 0.012 | 0.44 | 0.6620 | main_effect | |
| Nocardioides ungokensis | 0.010 | 0.011 | 0.88 | 0.3858 | main_effect | |
| Kribbella sp. NBC 00359 | 0.021 | 0.006 | 3.59 | 0.0013 | main_effect | |
| Kribbella sp. NBC 01484 | 0.024 | 0.008 | 3.10 | 0.0044 | main_effect | |
| Kribbella sp. NBC 01510 | 0.028 | 0.009 | 3.27 | 0.0029 | main_effect | |
| Micromonospora sp. NBC 00330 | 0.010 | 0.007 | 1.56 | 0.1299 | main_effect | |
| Micromonospora sp. NBC 01740 | 0.003 | 0.011 | 0.24 | 0.8148 | main_effect | |
| Micromonospora sp. B006 | 0.019 | 0.009 | 2.18 | 0.0382 | main_effect | |
| Micromonospora zamorensis | −0.031 | 0.015 | −2.14 | 0.0417 | interaction | |
| Micromonospora zamorensis | 0.030 | 0.009 | 3.14 | 0.0073 | by_group_JB1_JB2 | |
| Micromonospora zamorensis | −0.002 | 0.011 | −0.14 | 0.8917 | by_group_JB5_JB6_JB7 | |
| Dactylosporangium sp. NBC 01737 | −0.005 | 0.005 | −1.02 | 0.3175 | main_effect | |
| Streptosporangium sp. 'caverna' | −0.004 | 0.006 | −0.71 | 0.4860 | main_effect | |
| Streptosporangium subroseum | −0.005 | 0.005 | −0.93 | 0.3605 | main_effect | |
| Streptosporangium roseum | −0.003 | 0.006 | −0.61 | 0.5439 | main_effect | |
| Nonomuraea glycinis | 0.013 | 0.012 | 1.06 | 0.2964 | main_effect | |
| Amycolatopsis sp. DSM 110486 | −0.001 | 0.006 | −0.13 | 0.8947 | main_effect | |
| Actinomycetospora sp. NBC 00405 | 0.014 | 0.009 | 1.55 | 0.1319 | main_effect | |
| Anaerobic Decomposer | Acetivibrio saccincola | −0.005 | 0.009 | −0.56 | 0.5770 | main_effect |
| Herbinix luporum | −0.007 | 0.010 | −0.71 | 0.4852 | main_effect | |
| Hydrocarbon Degrader | Mycolicibacterium vanbaalenii | 0.006 | 0.009 | 0.65 | 0.5196 | main_effect |
| Mycolicibacterium [Mycobacterium] burgundiense | −0.008 | 0.007 | −1.08 | 0.2888 | main_effect | |
| Rhodococcus sp. MTM3W5.2 | −0.001 | 0.007 | −0.09 | 0.9263 | main_effect | |
| Rhodococcus sp. W8901 | 0.003 | 0.006 | 0.60 | 0.5523 | main_effect | |
| Rhodococcoides fascians | −0.014 | 0.005 | −2.53 | 0.0174 | main_effect | |
| Immunomodulatory Soil Bacterium | Mycolicibacterium vaccae | −0.025 | 0.010 | −2.41 | 0.0235 | interaction |
| Mycolicibacterium vaccae | 0.041 | 0.008 | 5.02 | 0.0002 | by_group_JB1_JB2 | |
| Mycolicibacterium vaccae | 0.016 | 0.006 | 2.56 | 0.0251 | by_group_JB5_JB6_JB7 | |
| Methanotroph | Methylocapsa sp. D3K7 | 0.011 | 0.010 | 1.14 | 0.2630 | main_effect |
| Nitrogen Fixer - Plant Symbiont | Bradyrhizobium sp. 170 | 0.012 | 0.012 | 1.03 | 0.3123 | main_effect |
| Bradyrhizobium sp. 200 | 0.006 | 0.006 | 0.94 | 0.3569 | main_effect | |
| Bradyrhizobium sp. Ash2021 | 0.006 | 0.005 | 1.38 | 0.1787 | main_effect | |
| Bradyrhizobium sp. | 0.002 | 0.004 | 0.60 | 0.5513 | main_effect | |
| Bradyrhizobium erythrophlei | 0.006 | 0.007 | 0.93 | 0.3601 | main_effect | |
| Bradyrhizobium barranii | −0.003 | 0.009 | −0.30 | 0.7698 | main_effect | |
| Bradyrhizobium lablabi | 0.007 | 0.006 | 1.23 | 0.2271 | main_effect | |
| Bradyrhizobium japonicum | −0.001 | 0.005 | −0.13 | 0.8962 | main_effect | |
| Bradyrhizobium diazoefficiens | −0.023 | 0.016 | −1.44 | 0.1605 | main_effect | |
| Bradyrhizobium ottawaense | 0.007 | 0.006 | 1.26 | 0.2196 | main_effect | |
| Mesorhizobium sp. ANAO-SY3R2 | 0.013 | 0.007 | 2.00 | 0.0558 | main_effect | |
| Rhizobium ruizarguesonis | 0.010 | 0.009 | 1.07 | 0.2950 | main_effect | |
| Microvirga ossetica | −0.001 | 0.009 | −0.15 | 0.8782 | main_effect | |
| Opportunistic Pathogen | Mycobacterium intracellulare | −0.008 | 0.005 | −1.76 | 0.0901 | main_effect |
| Bacillus cereus | 0.002 | 0.009 | 0.18 | 0.8612 | main_effect | |
| Plant-Associated Bacterium | Agrobacterium rosae | −0.030 | 0.007 | −4.25 | 0.0002 | main_effect |
| Plant-Associated Commensal | Paraburkholderia hospita | −0.013 | 0.009 | −1.55 | 0.1334 | main_effect |
| Plant-Associated Commensal/Decomposer | Pseudomonas fluorescens | 0.007 | 0.014 | 0.50 | 0.6176 | main_effect |
| Pseudomonas sp. PONIH3 | −0.005 | 0.012 | −0.38 | 0.7038 | main_effect | |
| Soil Decomposer | Bacillus mycoides | 0.016 | 0.015 | 1.08 | 0.2897 | main_effect |
| Bacillus licheniformis | 0.017 | 0.018 | 0.93 | 0.3599 | main_effect | |
| Neobacillus sp. FSL H8-0543 | 0.024 | 0.004 | 5.37 | 0.0000 | main_effect | |
| Neobacillus sp. OS1-33 | 0.020 | 0.006 | 3.19 | 0.0035 | main_effect | |
| Peribacillus asahii | 0.005 | 0.010 | 0.47 | 0.6406 | main_effect | |
| Priestia megaterium | 0.001 | 0.010 | 0.14 | 0.8865 | main_effect | |
| Thermophilic Decomposer | Thermobifida fusca | −0.009 | 0.011 | −0.85 | 0.4050 | main_effect |
| Saccharomonospora viridis | −0.006 | 0.008 | −0.70 | 0.4911 | main_effect | |
| Novibacillus thermophilus | −0.003 | 0.009 | −0.35 | 0.7301 | main_effect | |
| Thermoactinomyces vulgaris | −0.001 | 0.007 | −0.13 | 0.9009 | main_effect | |
| Unclassified | Humibacillus xanthopallidus | 0.010 | 0.008 | 1.25 | 0.2211 | main_effect |
| Nakamurella multipartita | 0.004 | 0.006 | 0.66 | 0.5160 | main_effect | |
| Baekduia alba | 0.010 | 0.005 | 2.05 | 0.0495 | main_effect | |
| Capillimicrobium parvum | 0.020 | 0.005 | 3.67 | 0.0010 | main_effect | |
| Allobacillus halotolerans | −0.008 | 0.019 | −0.41 | 0.6836 | main_effect | |
| Pradoshia sp. D12 | 0.022 | 0.006 | 3.79 | 0.0007 | main_effect | |
| Afipia sp. GAS231 | −0.004 | 0.005 | −0.82 | 0.4210 | main_effect | |
| Afipia carboxidovorans | −0.002 | 0.008 | −0.23 | 0.8165 | main_effect | |
| Bosea sp. NBC 00550 | 0.000 | 0.008 | 0.04 | 0.9686 | main_effect | |
| Skermanella cutis | −0.003 | 0.011 | −0.32 | 0.7534 | main_effect | |
| Massilia sp. R2A-15 | −0.015 | 0.005 | −2.84 | 0.0082 | main_effect | |
| Imtechella halotolerans | −0.028 | 0.018 | −1.59 | 0.1223 | main_effect |
Table 40: Summary statistics for each core microbial species. The table shows the summary statistics for the analysis of the metadata variable and each core species (species level) organised into functional groups. The table gives estimate, standard error, t-value, p-value and model. Model tells which model the summary statistics represents: “main_effect” analysis all fields together as we see no difference between JB groups, “interaction” gives results for the interaction analysis and is included when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.
Harvested
| Functional Group | Species | Estimate | SE | t | p-value | Model |
|---|---|---|---|---|---|---|
| Actinomycete Decomposer | Streptomyces sp. NBC 00425 | 0.005 | 0.010 | 0.51 | 0.6149 | main_effect |
| Streptomyces sp. NBC 01537 | −0.002 | 0.006 | −0.37 | 0.7150 | main_effect | |
| Streptomyces canus | 0.006 | 0.009 | 0.71 | 0.4840 | main_effect | |
| Streptomyces albidoflavus | −0.007 | 0.008 | −0.89 | 0.3821 | main_effect | |
| Streptomyces mirabilis | 0.021 | 0.012 | 1.68 | 0.1034 | main_effect | |
| Streptomyces [Kitasatospora] papulosa | −0.036 | 0.016 | −2.32 | 0.0282 | interaction | |
| Streptomyces [Kitasatospora] papulosa | 0.006 | 0.007 | 0.96 | 0.3542 | by_group_JB1_JB2 | |
| Streptomyces [Kitasatospora] papulosa | −0.030 | 0.016 | −1.90 | 0.0821 | by_group_JB5_JB6_JB7 | |
| Terrabacter sp. C0L 2 | −0.011 | 0.006 | −1.80 | 0.0819 | main_effect | |
| Pedococcus sp. KACC 23699 | −0.001 | 0.009 | −0.10 | 0.9203 | main_effect | |
| Arthrobacter sp. NicSoilB8 | −0.023 | 0.010 | −2.29 | 0.0304 | interaction | |
| Arthrobacter sp. NicSoilB8 | 0.009 | 0.005 | 1.86 | 0.0845 | by_group_JB1_JB2 | |
| Arthrobacter sp. NicSoilB8 | −0.014 | 0.009 | −1.48 | 0.1651 | by_group_JB5_JB6_JB7 | |
| Arthrobacter sp. NicSoilB4 | 0.016 | 0.010 | 1.65 | 0.1109 | main_effect | |
| Arthrobacter sp. PAMC25564 | 0.007 | 0.010 | 0.69 | 0.4976 | main_effect | |
| Arthrobacter sulfonylureivorans | 0.007 | 0.012 | 0.59 | 0.5581 | main_effect | |
| Nocardioides sp. T5 | 0.012 | 0.014 | 0.88 | 0.3872 | main_effect | |
| Nocardioides panacis | −0.025 | 0.012 | −2.07 | 0.0480 | main_effect | |
| Nocardioides ungokensis | −0.021 | 0.011 | −1.85 | 0.0743 | main_effect | |
| Kribbella sp. NBC 00359 | −0.010 | 0.008 | −1.37 | 0.1826 | main_effect | |
| Kribbella sp. NBC 01484 | −0.020 | 0.009 | −2.17 | 0.0386 | main_effect | |
| Kribbella sp. NBC 01510 | −0.021 | 0.010 | −2.01 | 0.0544 | main_effect | |
| Micromonospora sp. NBC 00330 | −0.002 | 0.008 | −0.30 | 0.7691 | main_effect | |
| Micromonospora sp. NBC 01740 | −0.004 | 0.012 | −0.37 | 0.7119 | main_effect | |
| Micromonospora sp. B006 | −0.013 | 0.010 | −1.30 | 0.2029 | main_effect | |
| Micromonospora zamorensis | −0.005 | 0.009 | −0.55 | 0.5835 | main_effect | |
| Dactylosporangium sp. NBC 01737 | −0.002 | 0.005 | −0.41 | 0.6814 | main_effect | |
| Streptosporangium sp. 'caverna' | −0.005 | 0.006 | −0.71 | 0.4815 | main_effect | |
| Streptosporangium subroseum | −0.004 | 0.006 | −0.65 | 0.5227 | main_effect | |
| Streptosporangium roseum | −0.007 | 0.006 | −1.23 | 0.2275 | main_effect | |
| Nonomuraea glycinis | −0.008 | 0.014 | −0.56 | 0.5821 | main_effect | |
| Amycolatopsis sp. DSM 110486 | −0.001 | 0.007 | −0.15 | 0.8827 | main_effect | |
| Actinomycetospora sp. NBC 00405 | 0.007 | 0.010 | 0.66 | 0.5127 | main_effect | |
| Anaerobic Decomposer | Acetivibrio saccincola | −0.018 | 0.010 | −1.84 | 0.0769 | main_effect |
| Herbinix luporum | −0.002 | 0.011 | −0.19 | 0.8507 | main_effect | |
| Hydrocarbon Degrader | Mycolicibacterium vanbaalenii | −0.002 | 0.010 | −0.22 | 0.8299 | main_effect |
| Mycolicibacterium [Mycobacterium] burgundiense | 0.012 | 0.008 | 1.61 | 0.1190 | main_effect | |
| Rhodococcus sp. MTM3W5.2 | 0.013 | 0.008 | 1.72 | 0.0966 | main_effect | |
| Rhodococcus sp. W8901 | 0.004 | 0.006 | 0.68 | 0.4991 | main_effect | |
| Rhodococcoides fascians | −0.001 | 0.007 | −0.20 | 0.8431 | main_effect | |
| Immunomodulatory Soil Bacterium | Mycolicibacterium vaccae | −0.009 | 0.008 | −1.14 | 0.2648 | main_effect |
| Methanotroph | Methylocapsa sp. D3K7 | −0.006 | 0.011 | −0.51 | 0.6168 | main_effect |
| Nitrogen Fixer - Plant Symbiont | Bradyrhizobium sp. 170 | 0.016 | 0.013 | 1.27 | 0.2157 | main_effect |
| Bradyrhizobium sp. 200 | 0.010 | 0.007 | 1.39 | 0.1749 | main_effect | |
| Bradyrhizobium sp. Ash2021 | −0.002 | 0.005 | −0.35 | 0.7256 | main_effect | |
| Bradyrhizobium sp. | 0.009 | 0.004 | 2.27 | 0.0313 | main_effect | |
| Bradyrhizobium erythrophlei | −0.004 | 0.007 | −0.62 | 0.5417 | main_effect | |
| Bradyrhizobium barranii | 0.016 | 0.010 | 1.69 | 0.1024 | main_effect | |
| Bradyrhizobium lablabi | 0.000 | 0.007 | −0.08 | 0.9394 | main_effect | |
| Bradyrhizobium japonicum | 0.010 | 0.005 | 1.89 | 0.0698 | main_effect | |
| Bradyrhizobium diazoefficiens | 0.019 | 0.018 | 1.07 | 0.2922 | main_effect | |
| Bradyrhizobium ottawaense | 0.002 | 0.006 | 0.29 | 0.7763 | main_effect | |
| Mesorhizobium sp. ANAO-SY3R2 | 0.005 | 0.008 | 0.61 | 0.5468 | main_effect | |
| Rhizobium ruizarguesonis | −0.001 | 0.010 | −0.07 | 0.9473 | main_effect | |
| Microvirga ossetica | 0.042 | 0.017 | 2.42 | 0.0228 | interaction | |
| Microvirga ossetica | 0.007 | 0.007 | 1.07 | 0.3032 | by_group_JB1_JB2 | |
| Microvirga ossetica | 0.049 | 0.018 | 2.76 | 0.0172 | by_group_JB5_JB6_JB7 | |
| Opportunistic Pathogen | Mycobacterium intracellulare | 0.000 | 0.005 | 0.04 | 0.9664 | main_effect |
| Bacillus cereus | 0.013 | 0.010 | 1.30 | 0.2053 | main_effect | |
| Plant-Associated Bacterium | Agrobacterium rosae | 0.014 | 0.009 | 1.55 | 0.1328 | main_effect |
| Plant-Associated Commensal | Paraburkholderia hospita | 0.008 | 0.010 | 0.84 | 0.4065 | main_effect |
| Plant-Associated Commensal/Decomposer | Pseudomonas fluorescens | −0.001 | 0.015 | −0.06 | 0.9511 | main_effect |
| Pseudomonas sp. PONIH3 | 0.022 | 0.013 | 1.72 | 0.0973 | main_effect | |
| Soil Decomposer | Bacillus mycoides | 0.014 | 0.016 | 0.84 | 0.4056 | main_effect |
| Bacillus licheniformis | −0.032 | 0.019 | −1.68 | 0.1031 | main_effect | |
| Neobacillus sp. FSL H8-0543 | −0.012 | 0.007 | −1.75 | 0.0912 | main_effect | |
| Neobacillus sp. OS1-33 | −0.014 | 0.008 | −1.78 | 0.0862 | main_effect | |
| Peribacillus asahii | 0.016 | 0.011 | 1.55 | 0.1327 | main_effect | |
| Priestia megaterium | −0.012 | 0.010 | −1.15 | 0.2607 | main_effect | |
| Thermophilic Decomposer | Thermobifida fusca | −0.012 | 0.011 | −1.01 | 0.3210 | main_effect |
| Saccharomonospora viridis | −0.009 | 0.009 | −1.04 | 0.3073 | main_effect | |
| Novibacillus thermophilus | −0.019 | 0.009 | −2.05 | 0.0494 | main_effect | |
| Thermoactinomyces vulgaris | −0.002 | 0.007 | −0.30 | 0.7654 | main_effect | |
| Unclassified | Humibacillus xanthopallidus | −0.003 | 0.009 | −0.29 | 0.7758 | main_effect |
| Nakamurella multipartita | 0.005 | 0.007 | 0.71 | 0.4837 | main_effect | |
| Baekduia alba | −0.008 | 0.005 | −1.46 | 0.1557 | main_effect | |
| Capillimicrobium parvum | −0.015 | 0.006 | −2.36 | 0.0255 | main_effect | |
| Allobacillus halotolerans | 0.016 | 0.020 | 0.80 | 0.4325 | main_effect | |
| Pradoshia sp. D12 | −0.001 | 0.008 | −0.17 | 0.8630 | main_effect | |
| Afipia sp. GAS231 | 0.006 | 0.005 | 1.12 | 0.2729 | main_effect | |
| Afipia carboxidovorans | −0.010 | 0.008 | −1.22 | 0.2323 | main_effect | |
| Bosea sp. NBC 00550 | 0.009 | 0.009 | 0.97 | 0.3385 | main_effect | |
| Skermanella cutis | 0.013 | 0.011 | 1.14 | 0.2638 | main_effect | |
| Massilia sp. R2A-15 | −0.003 | 0.007 | −0.44 | 0.6610 | main_effect | |
| Imtechella halotolerans | 0.016 | 0.020 | 0.78 | 0.4408 | main_effect |
Table 41: Summary statistics for each core microbial species. The table shows the summary statistics for the analysis of the metadata variable and each core species (species level) organised into functional groups. The table gives estimate, standard error, t-value, p-value and model. Model tells which model the summary statistics represents: “main_effect” analysis all fields together as we see no difference between JB groups, “interaction” gives results for the interaction analysis and is included 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)
| Functional Group | Species | Estimate | SE | t | p-value | Model |
|---|---|---|---|---|---|---|
| Actinomycete Decomposer | Streptomyces sp. NBC 00425 | −0.010 | 0.009 | −1.13 | 0.2683 | main_effect |
| Streptomyces sp. NBC 01537 | 0.022 | 0.009 | 2.36 | 0.0259 | interaction | |
| Streptomyces sp. NBC 01537 | −0.012 | 0.007 | −1.76 | 0.1007 | by_group_JB1_JB2 | |
| Streptomyces sp. NBC 01537 | 0.010 | 0.006 | 1.60 | 0.1355 | by_group_JB5_JB6_JB7 | |
| Streptomyces canus | 0.006 | 0.008 | 0.77 | 0.4466 | main_effect | |
| Streptomyces albidoflavus | 0.004 | 0.007 | 0.61 | 0.5495 | main_effect | |
| Streptomyces mirabilis | 0.015 | 0.012 | 1.25 | 0.2211 | main_effect | |
| Streptomyces [Kitasatospora] papulosa | −0.008 | 0.007 | −1.19 | 0.2432 | main_effect | |
| Terrabacter sp. C0L 2 | −0.013 | 0.005 | −2.52 | 0.0178 | main_effect | |
| Pedococcus sp. KACC 23699 | −0.016 | 0.008 | −2.11 | 0.0438 | main_effect | |
| Arthrobacter sp. NicSoilB8 | 0.001 | 0.004 | 0.29 | 0.7759 | main_effect | |
| Arthrobacter sp. NicSoilB4 | −0.004 | 0.009 | −0.37 | 0.7109 | main_effect | |
| Arthrobacter sp. PAMC25564 | 0.011 | 0.009 | 1.20 | 0.2420 | main_effect | |
| Arthrobacter sulfonylureivorans | 0.019 | 0.011 | 1.70 | 0.0998 | main_effect | |
| Nocardioides sp. T5 | 0.002 | 0.013 | 0.18 | 0.8618 | main_effect | |
| Nocardioides panacis | 0.048 | 0.017 | 2.91 | 0.0074 | interaction | |
| Nocardioides panacis | −0.058 | 0.011 | −5.31 | 0.0001 | by_group_JB1_JB2 | |
| Nocardioides panacis | −0.009 | 0.013 | −0.75 | 0.4690 | by_group_JB5_JB6_JB7 | |
| Nocardioides ungokensis | −0.010 | 0.011 | −0.90 | 0.3752 | main_effect | |
| Kribbella sp. NBC 00359 | 0.004 | 0.007 | 0.51 | 0.6120 | main_effect | |
| Kribbella sp. NBC 01484 | 0.007 | 0.009 | 0.82 | 0.4208 | main_effect | |
| Kribbella sp. NBC 01510 | 0.005 | 0.010 | 0.51 | 0.6127 | main_effect | |
| Micromonospora sp. NBC 00330 | 0.000 | 0.007 | 0.06 | 0.9518 | main_effect | |
| Micromonospora sp. NBC 01740 | −0.015 | 0.011 | −1.37 | 0.1807 | main_effect | |
| Micromonospora sp. B006 | −0.001 | 0.010 | −0.11 | 0.9108 | main_effect | |
| Micromonospora zamorensis | 0.000 | 0.009 | 0.05 | 0.9628 | main_effect | |
| Dactylosporangium sp. NBC 01737 | −0.009 | 0.004 | −2.02 | 0.0535 | main_effect | |
| Streptosporangium sp. 'caverna' | −0.011 | 0.006 | −1.98 | 0.0572 | main_effect | |
| Streptosporangium subroseum | −0.010 | 0.005 | −1.93 | 0.0637 | main_effect | |
| Streptosporangium roseum | −0.002 | 0.006 | −0.39 | 0.6999 | main_effect | |
| Nonomuraea glycinis | −0.017 | 0.013 | −1.37 | 0.1801 | main_effect | |
| Amycolatopsis sp. DSM 110486 | −0.007 | 0.006 | −1.13 | 0.2671 | main_effect | |
| Actinomycetospora sp. NBC 00405 | 0.010 | 0.009 | 1.10 | 0.2793 | main_effect | |
| Anaerobic Decomposer | Acetivibrio saccincola | −0.019 | 0.009 | −2.04 | 0.0513 | main_effect |
| Herbinix luporum | −0.009 | 0.010 | −0.95 | 0.3521 | main_effect | |
| Hydrocarbon Degrader | Mycolicibacterium vanbaalenii | −0.003 | 0.010 | −0.34 | 0.7345 | main_effect |
| Mycolicibacterium [Mycobacterium] burgundiense | −0.002 | 0.008 | −0.26 | 0.7986 | main_effect | |
| Rhodococcus sp. MTM3W5.2 | 0.006 | 0.007 | 0.87 | 0.3919 | main_effect | |
| Rhodococcus sp. W8901 | 0.007 | 0.006 | 1.28 | 0.2100 | main_effect | |
| Rhodococcoides fascians | −0.016 | 0.005 | −3.12 | 0.0042 | main_effect | |
| Immunomodulatory Soil Bacterium | Mycolicibacterium vaccae | 0.014 | 0.008 | 1.82 | 0.0788 | main_effect |
| Methanotroph | Methylocapsa sp. D3K7 | 0.013 | 0.010 | 1.34 | 0.1925 | main_effect |
| Nitrogen Fixer - Plant Symbiont | Bradyrhizobium sp. 170 | 0.016 | 0.012 | 1.32 | 0.1985 | main_effect |
| Bradyrhizobium sp. 200 | 0.007 | 0.007 | 1.14 | 0.2622 | main_effect | |
| Bradyrhizobium sp. Ash2021 | 0.007 | 0.005 | 1.47 | 0.1525 | main_effect | |
| Bradyrhizobium sp. | 0.008 | 0.004 | 2.12 | 0.0426 | main_effect | |
| Bradyrhizobium erythrophlei | 0.012 | 0.006 | 1.90 | 0.0679 | main_effect | |
| Bradyrhizobium barranii | 0.012 | 0.009 | 1.30 | 0.2030 | main_effect | |
| Bradyrhizobium lablabi | 0.013 | 0.006 | 2.41 | 0.0230 | main_effect | |
| Bradyrhizobium japonicum | 0.009 | 0.005 | 1.92 | 0.0645 | main_effect | |
| Bradyrhizobium diazoefficiens | 0.012 | 0.017 | 0.70 | 0.4885 | main_effect | |
| Bradyrhizobium ottawaense | 0.012 | 0.006 | 2.18 | 0.0379 | main_effect | |
| Mesorhizobium sp. ANAO-SY3R2 | 0.014 | 0.007 | 2.03 | 0.0521 | main_effect | |
| Rhizobium ruizarguesonis | 0.005 | 0.009 | 0.56 | 0.5799 | main_effect | |
| Microvirga ossetica | 0.000 | 0.009 | −0.03 | 0.9770 | main_effect | |
| Opportunistic Pathogen | Mycobacterium intracellulare | 0.001 | 0.005 | 0.12 | 0.9042 | main_effect |
| Bacillus cereus | 0.015 | 0.009 | 1.65 | 0.1106 | main_effect | |
| Plant-Associated Bacterium | Agrobacterium rosae | 0.001 | 0.009 | 0.16 | 0.8775 | main_effect |
| Plant-Associated Commensal | Paraburkholderia hospita | 0.002 | 0.009 | 0.26 | 0.7930 | main_effect |
| Plant-Associated Commensal/Decomposer | Pseudomonas fluorescens | 0.021 | 0.014 | 1.54 | 0.1354 | main_effect |
| Pseudomonas sp. PONIH3 | 0.019 | 0.012 | 1.55 | 0.1320 | main_effect | |
| Soil Decomposer | Bacillus mycoides | 0.027 | 0.015 | 1.79 | 0.0835 | main_effect |
| Bacillus licheniformis | −0.017 | 0.019 | −0.89 | 0.3813 | main_effect | |
| Neobacillus sp. FSL H8-0543 | 0.012 | 0.006 | 2.02 | 0.0528 | main_effect | |
| Neobacillus sp. OS1-33 | 0.002 | 0.008 | 0.26 | 0.7987 | main_effect | |
| Peribacillus asahii | 0.008 | 0.010 | 0.82 | 0.4218 | main_effect | |
| Priestia megaterium | −0.012 | 0.009 | −1.27 | 0.2156 | main_effect | |
| Thermophilic Decomposer | Thermobifida fusca | −0.013 | 0.011 | −1.23 | 0.2281 | main_effect |
| Saccharomonospora viridis | −0.013 | 0.008 | −1.73 | 0.0940 | main_effect | |
| Novibacillus thermophilus | −0.012 | 0.009 | −1.31 | 0.2017 | main_effect | |
| Thermoactinomyces vulgaris | −0.001 | 0.007 | −0.12 | 0.9032 | main_effect | |
| Unclassified | Humibacillus xanthopallidus | 0.001 | 0.008 | 0.15 | 0.8843 | main_effect |
| Nakamurella multipartita | 0.005 | 0.006 | 0.85 | 0.4014 | main_effect | |
| Baekduia alba | 0.000 | 0.005 | −0.05 | 0.9576 | main_effect | |
| Capillimicrobium parvum | −0.006 | 0.007 | −0.84 | 0.4092 | main_effect | |
| Allobacillus halotolerans | 0.028 | 0.018 | 1.55 | 0.1328 | main_effect | |
| Pradoshia sp. D12 | 0.015 | 0.007 | 2.31 | 0.0283 | main_effect | |
| Afipia sp. GAS231 | 0.007 | 0.005 | 1.55 | 0.1324 | main_effect | |
| Afipia carboxidovorans | −0.016 | 0.007 | −2.19 | 0.0372 | main_effect | |
| Bosea sp. NBC 00550 | 0.006 | 0.008 | 0.68 | 0.5045 | main_effect | |
| Skermanella cutis | −0.016 | 0.010 | −1.57 | 0.1282 | main_effect | |
| Massilia sp. R2A-15 | −0.019 | 0.005 | −3.83 | 0.0007 | main_effect | |
| Imtechella halotolerans | −0.001 | 0.019 | −0.03 | 0.9767 | main_effect |
Table 42: Summary statistics for each core microbial species. The table shows the summary statistics for the analysis of the metadata variable and each core species (species level) organised into functional groups. The table gives estimate, standard error, t-value, p-value and model. Model tells which model the summary statistics represents: “main_effect” analysis all fields together as we see no difference between JB groups, “interaction” gives results for the interaction analysis and is included 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)
| Functional Group | Species | Estimate | SE | t | p-value | Model |
|---|---|---|---|---|---|---|
| Actinomycete Decomposer | Streptomyces sp. NBC 00425 | 0.008 | 0.010 | 0.77 | 0.4495 | main_effect |
| Streptomyces sp. NBC 01537 | −0.005 | 0.006 | −0.84 | 0.4107 | main_effect | |
| Streptomyces canus | 0.000 | 0.009 | −0.03 | 0.9784 | main_effect | |
| Streptomyces albidoflavus | 0.004 | 0.008 | 0.56 | 0.5822 | main_effect | |
| Streptomyces mirabilis | −0.014 | 0.013 | −1.07 | 0.2930 | main_effect | |
| Streptomyces [Kitasatospora] papulosa | −0.009 | 0.008 | −1.20 | 0.2405 | main_effect | |
| Terrabacter sp. C0L 2 | −0.027 | 0.012 | −2.25 | 0.0328 | interaction | |
| Terrabacter sp. C0L 2 | 0.006 | 0.007 | 0.85 | 0.4088 | by_group_JB1_JB2 | |
| Terrabacter sp. C0L 2 | −0.021 | 0.010 | −2.08 | 0.0596 | by_group_JB5_JB6_JB7 | |
| Pedococcus sp. KACC 23699 | 0.000 | 0.009 | −0.04 | 0.9647 | main_effect | |
| Arthrobacter sp. NicSoilB8 | −0.015 | 0.004 | −3.78 | 0.0008 | main_effect | |
| Arthrobacter sp. NicSoilB4 | −0.002 | 0.011 | −0.17 | 0.8671 | main_effect | |
| Arthrobacter sp. PAMC25564 | −0.005 | 0.010 | −0.49 | 0.6255 | main_effect | |
| Arthrobacter sulfonylureivorans | −0.002 | 0.013 | −0.16 | 0.8751 | main_effect | |
| Nocardioides sp. T5 | 0.020 | 0.014 | 1.45 | 0.1590 | main_effect | |
| Nocardioides panacis | 0.004 | 0.013 | 0.33 | 0.7418 | main_effect | |
| Nocardioides ungokensis | −0.019 | 0.012 | −1.56 | 0.1290 | main_effect | |
| Kribbella sp. NBC 00359 | −0.002 | 0.008 | −0.22 | 0.8298 | main_effect | |
| Kribbella sp. NBC 01484 | −0.010 | 0.010 | −0.95 | 0.3484 | main_effect | |
| Kribbella sp. NBC 01510 | −0.007 | 0.011 | −0.60 | 0.5520 | main_effect | |
| Micromonospora sp. NBC 00330 | 0.012 | 0.008 | 1.60 | 0.1218 | main_effect | |
| Micromonospora sp. NBC 01740 | 0.019 | 0.012 | 1.58 | 0.1243 | main_effect | |
| Micromonospora sp. B006 | 0.013 | 0.011 | 1.26 | 0.2187 | main_effect | |
| Micromonospora zamorensis | 0.014 | 0.009 | 1.45 | 0.1570 | main_effect | |
| Dactylosporangium sp. NBC 01737 | 0.007 | 0.005 | 1.29 | 0.2085 | main_effect | |
| Streptosporangium sp. 'caverna' | 0.007 | 0.007 | 1.05 | 0.3028 | main_effect | |
| Streptosporangium subroseum | 0.005 | 0.006 | 0.78 | 0.4392 | main_effect | |
| Streptosporangium roseum | 0.004 | 0.006 | 0.61 | 0.5460 | main_effect | |
| Nonomuraea glycinis | 0.013 | 0.014 | 0.90 | 0.3750 | main_effect | |
| Amycolatopsis sp. DSM 110486 | 0.002 | 0.007 | 0.31 | 0.7588 | main_effect | |
| Actinomycetospora sp. NBC 00405 | 0.018 | 0.010 | 1.82 | 0.0794 | main_effect | |
| Anaerobic Decomposer | Acetivibrio saccincola | 0.011 | 0.011 | 0.99 | 0.3303 | main_effect |
| Herbinix luporum | 0.007 | 0.011 | 0.60 | 0.5505 | main_effect | |
| Hydrocarbon Degrader | Mycolicibacterium vanbaalenii | −0.006 | 0.011 | −0.57 | 0.5763 | main_effect |
| Mycolicibacterium [Mycobacterium] burgundiense | 0.009 | 0.008 | 1.11 | 0.2774 | main_effect | |
| Rhodococcus sp. MTM3W5.2 | −0.013 | 0.008 | −1.58 | 0.1258 | main_effect | |
| Rhodococcus sp. W8901 | −0.012 | 0.006 | −1.90 | 0.0672 | main_effect | |
| Rhodococcoides fascians | 0.008 | 0.007 | 1.28 | 0.2117 | main_effect | |
| Immunomodulatory Soil Bacterium | Mycolicibacterium vaccae | 0.004 | 0.009 | 0.42 | 0.6774 | main_effect |
| Methanotroph | Methylocapsa sp. D3K7 | −0.005 | 0.011 | −0.46 | 0.6459 | main_effect |
| Nitrogen Fixer - Plant Symbiont | Bradyrhizobium sp. 170 | −0.023 | 0.013 | −1.73 | 0.0952 | main_effect |
| Bradyrhizobium sp. 200 | −0.009 | 0.007 | −1.23 | 0.2301 | main_effect | |
| Bradyrhizobium sp. Ash2021 | −0.014 | 0.005 | −3.09 | 0.0045 | main_effect | |
| Bradyrhizobium sp. | −0.007 | 0.004 | −1.70 | 0.1005 | main_effect | |
| Bradyrhizobium erythrophlei | −0.015 | 0.007 | −2.07 | 0.0478 | main_effect | |
| Bradyrhizobium barranii | −0.001 | 0.011 | −0.11 | 0.9111 | main_effect | |
| Bradyrhizobium lablabi | −0.017 | 0.006 | −2.87 | 0.0078 | main_effect | |
| Bradyrhizobium japonicum | −0.011 | 0.005 | −1.99 | 0.0564 | main_effect | |
| Bradyrhizobium diazoefficiens | −0.025 | 0.019 | −1.32 | 0.1977 | main_effect | |
| Bradyrhizobium ottawaense | −0.015 | 0.006 | −2.56 | 0.0163 | main_effect | |
| Mesorhizobium sp. ANAO-SY3R2 | −0.007 | 0.008 | −0.86 | 0.3948 | main_effect | |
| Rhizobium ruizarguesonis | 0.001 | 0.010 | 0.06 | 0.9560 | main_effect | |
| Microvirga ossetica | 0.007 | 0.010 | 0.66 | 0.5149 | main_effect | |
| Opportunistic Pathogen | Mycobacterium intracellulare | −0.003 | 0.005 | −0.54 | 0.5910 | main_effect |
| Bacillus cereus | −0.026 | 0.009 | −2.73 | 0.0108 | main_effect | |
| Plant-Associated Bacterium | Agrobacterium rosae | 0.009 | 0.010 | 0.92 | 0.3642 | main_effect |
| Plant-Associated Commensal | Paraburkholderia hospita | −0.001 | 0.010 | −0.10 | 0.9207 | main_effect |
| Plant-Associated Commensal/Decomposer | Pseudomonas fluorescens | −0.021 | 0.016 | −1.33 | 0.1951 | main_effect |
| Pseudomonas sp. PONIH3 | −0.014 | 0.014 | −1.04 | 0.3091 | main_effect | |
| Soil Decomposer | Bacillus mycoides | −0.029 | 0.016 | −1.77 | 0.0877 | main_effect |
| Bacillus licheniformis | 0.042 | 0.019 | 2.16 | 0.0393 | main_effect | |
| Neobacillus sp. FSL H8-0543 | −0.009 | 0.007 | −1.22 | 0.2341 | main_effect | |
| Neobacillus sp. OS1-33 | −0.008 | 0.008 | −0.91 | 0.3702 | main_effect | |
| Peribacillus asahii | −0.014 | 0.011 | −1.25 | 0.2205 | main_effect | |
| Priestia megaterium | 0.014 | 0.011 | 1.29 | 0.2067 | main_effect | |
| Thermophilic Decomposer | Thermobifida fusca | 0.019 | 0.012 | 1.60 | 0.1215 | main_effect |
| Saccharomonospora viridis | 0.016 | 0.009 | 1.91 | 0.0665 | main_effect | |
| Novibacillus thermophilus | 0.019 | 0.010 | 2.00 | 0.0553 | main_effect | |
| Thermoactinomyces vulgaris | 0.014 | 0.007 | 1.91 | 0.0669 | main_effect | |
| Unclassified | Humibacillus xanthopallidus | 0.000 | 0.009 | 0.01 | 0.9938 | main_effect |
| Nakamurella multipartita | 0.003 | 0.007 | 0.38 | 0.7050 | main_effect | |
| Baekduia alba | 0.005 | 0.006 | 0.87 | 0.3901 | main_effect | |
| Capillimicrobium parvum | 0.004 | 0.007 | 0.61 | 0.5486 | main_effect | |
| Allobacillus halotolerans | −0.002 | 0.021 | −0.08 | 0.9378 | main_effect | |
| Pradoshia sp. D12 | −0.011 | 0.008 | −1.48 | 0.1509 | main_effect | |
| Afipia sp. GAS231 | −0.008 | 0.005 | −1.55 | 0.1327 | main_effect | |
| Afipia carboxidovorans | 0.011 | 0.009 | 1.29 | 0.2062 | main_effect | |
| Bosea sp. NBC 00550 | 0.002 | 0.009 | 0.23 | 0.8228 | main_effect | |
| Skermanella cutis | −0.003 | 0.012 | −0.28 | 0.7852 | main_effect | |
| Massilia sp. R2A-15 | 0.002 | 0.007 | 0.34 | 0.7353 | main_effect | |
| Imtechella halotolerans | 0.005 | 0.021 | 0.22 | 0.8253 | main_effect |
Table 43: Summary statistics for each core microbial species. The table shows the summary statistics for the analysis of the metadata variable and each core species (species level) organised into functional groups. The table gives estimate, standard error, t-value, p-value and model. Model tells which model the summary statistics represents: “main_effect” analysis all fields together as we see no difference between JB groups, “interaction” gives results for the interaction analysis and is included when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.
Livestock manure
| Functional Group | Species | Estimate | SE | t | p-value | Model |
|---|---|---|---|---|---|---|
| Actinomycete Decomposer | Streptomyces sp. NBC 00425 | 0.012 | 0.009 | 1.39 | 0.1746 | main_effect |
| Streptomyces sp. NBC 01537 | −0.004 | 0.006 | −0.67 | 0.5078 | main_effect | |
| Streptomyces canus | 0.022 | 0.007 | 3.26 | 0.0029 | main_effect | |
| Streptomyces albidoflavus | 0.000 | 0.007 | 0.04 | 0.9668 | main_effect | |
| Streptomyces mirabilis | 0.035 | 0.016 | 2.12 | 0.0434 | interaction | |
| Streptomyces mirabilis | −0.036 | 0.013 | −2.81 | 0.0140 | by_group_JB1_JB2 | |
| Streptomyces mirabilis | −0.001 | 0.009 | −0.15 | 0.8857 | by_group_JB5_JB6_JB7 | |
| Streptomyces [Kitasatospora] papulosa | −0.010 | 0.007 | −1.55 | 0.1327 | main_effect | |
| Terrabacter sp. C0L 2 | 0.001 | 0.006 | 0.09 | 0.9275 | main_effect | |
| Pedococcus sp. KACC 23699 | −0.008 | 0.008 | −1.03 | 0.3116 | main_effect | |
| Arthrobacter sp. NicSoilB8 | −0.001 | 0.004 | −0.24 | 0.8088 | main_effect | |
| Arthrobacter sp. NicSoilB4 | 0.026 | 0.008 | 3.22 | 0.0033 | main_effect | |
| Arthrobacter sp. PAMC25564 | −0.013 | 0.009 | −1.52 | 0.1395 | main_effect | |
| Arthrobacter sulfonylureivorans | 0.001 | 0.011 | 0.13 | 0.8961 | main_effect | |
| Nocardioides sp. T5 | 0.013 | 0.012 | 1.06 | 0.2967 | main_effect | |
| Nocardioides panacis | 0.033 | 0.010 | 3.31 | 0.0026 | main_effect | |
| Nocardioides ungokensis | −0.002 | 0.011 | −0.14 | 0.8892 | main_effect | |
| Kribbella sp. NBC 00359 | 0.005 | 0.007 | 0.66 | 0.5142 | main_effect | |
| Kribbella sp. NBC 01484 | −0.013 | 0.009 | −1.50 | 0.1457 | main_effect | |
| Kribbella sp. NBC 01510 | −0.005 | 0.010 | −0.49 | 0.6261 | main_effect | |
| Micromonospora sp. NBC 00330 | 0.004 | 0.007 | 0.62 | 0.5386 | main_effect | |
| Micromonospora sp. NBC 01740 | 0.013 | 0.011 | 1.19 | 0.2456 | main_effect | |
| Micromonospora sp. B006 | 0.000 | 0.010 | −0.02 | 0.9814 | main_effect | |
| Micromonospora zamorensis | 0.033 | 0.016 | 2.12 | 0.0433 | interaction | |
| Micromonospora zamorensis | −0.014 | 0.011 | −1.28 | 0.2226 | by_group_JB1_JB2 | |
| Micromonospora zamorensis | 0.019 | 0.011 | 1.78 | 0.0998 | by_group_JB5_JB6_JB7 | |
| Dactylosporangium sp. NBC 01737 | 0.011 | 0.004 | 2.63 | 0.0136 | main_effect | |
| Streptosporangium sp. 'caverna' | 0.012 | 0.005 | 2.16 | 0.0394 | main_effect | |
| Streptosporangium subroseum | 0.010 | 0.005 | 1.86 | 0.0739 | main_effect | |
| Streptosporangium roseum | −0.028 | 0.010 | −2.93 | 0.0069 | interaction | |
| Streptosporangium roseum | 0.001 | 0.004 | 0.25 | 0.8069 | by_group_JB1_JB2 | |
| Streptosporangium roseum | −0.027 | 0.009 | −2.90 | 0.0134 | by_group_JB5_JB6_JB7 | |
| Nonomuraea glycinis | 0.038 | 0.011 | 3.59 | 0.0013 | main_effect | |
| Amycolatopsis sp. DSM 110486 | 0.014 | 0.006 | 2.43 | 0.0217 | main_effect | |
| Actinomycetospora sp. NBC 00405 | 0.011 | 0.009 | 1.23 | 0.2283 | main_effect | |
| Anaerobic Decomposer | Acetivibrio saccincola | 0.003 | 0.010 | 0.32 | 0.7518 | main_effect |
| Herbinix luporum | 0.000 | 0.010 | 0.03 | 0.9789 | main_effect | |
| Hydrocarbon Degrader | Mycolicibacterium vanbaalenii | 0.006 | 0.009 | 0.65 | 0.5181 | main_effect |
| Mycolicibacterium [Mycobacterium] burgundiense | 0.008 | 0.007 | 1.08 | 0.2875 | main_effect | |
| Rhodococcus sp. MTM3W5.2 | −0.003 | 0.007 | −0.43 | 0.6692 | main_effect | |
| Rhodococcus sp. W8901 | −0.013 | 0.005 | −2.43 | 0.0219 | main_effect | |
| Rhodococcoides fascians | 0.009 | 0.006 | 1.58 | 0.1264 | main_effect | |
| Immunomodulatory Soil Bacterium | Mycolicibacterium vaccae | −0.014 | 0.007 | −1.91 | 0.0665 | main_effect |
| Methanotroph | Methylocapsa sp. D3K7 | −0.018 | 0.009 | −1.85 | 0.0743 | main_effect |
| Nitrogen Fixer - Plant Symbiont | Bradyrhizobium sp. 170 | 0.018 | 0.012 | 1.53 | 0.1375 | main_effect |
| Bradyrhizobium sp. 200 | 0.008 | 0.006 | 1.30 | 0.2032 | main_effect | |
| Bradyrhizobium sp. Ash2021 | −0.009 | 0.004 | −1.99 | 0.0559 | main_effect | |
| Bradyrhizobium sp. | −0.004 | 0.004 | −1.03 | 0.3115 | main_effect | |
| Bradyrhizobium erythrophlei | −0.019 | 0.006 | −3.36 | 0.0023 | main_effect | |
| Bradyrhizobium barranii | −0.007 | 0.009 | −0.79 | 0.4381 | main_effect | |
| Bradyrhizobium lablabi | −0.014 | 0.005 | −2.61 | 0.0142 | main_effect | |
| Bradyrhizobium japonicum | −0.006 | 0.005 | −1.27 | 0.2131 | main_effect | |
| Bradyrhizobium diazoefficiens | −0.039 | 0.015 | −2.61 | 0.0145 | main_effect | |
| Bradyrhizobium ottawaense | −0.005 | 0.006 | −0.80 | 0.4332 | main_effect | |
| Mesorhizobium sp. ANAO-SY3R2 | −0.008 | 0.007 | −1.08 | 0.2894 | main_effect | |
| Rhizobium ruizarguesonis | 0.015 | 0.009 | 1.78 | 0.0856 | main_effect | |
| Microvirga ossetica | 0.022 | 0.008 | 2.63 | 0.0136 | main_effect | |
| Opportunistic Pathogen | Mycobacterium intracellulare | −0.013 | 0.004 | −3.02 | 0.0054 | main_effect |
| Bacillus cereus | −0.008 | 0.009 | −0.85 | 0.4043 | main_effect | |
| Plant-Associated Bacterium | Agrobacterium rosae | 0.007 | 0.009 | 0.79 | 0.4390 | main_effect |
| Plant-Associated Commensal | Paraburkholderia hospita | −0.013 | 0.009 | −1.52 | 0.1387 | main_effect |
| Plant-Associated Commensal/Decomposer | Pseudomonas fluorescens | 0.001 | 0.014 | 0.08 | 0.9352 | main_effect |
| Pseudomonas sp. PONIH3 | −0.008 | 0.012 | −0.67 | 0.5063 | main_effect | |
| Soil Decomposer | Bacillus mycoides | −0.004 | 0.015 | −0.25 | 0.8013 | main_effect |
| Bacillus licheniformis | 0.032 | 0.017 | 1.84 | 0.0771 | main_effect | |
| Neobacillus sp. FSL H8-0543 | −0.009 | 0.006 | −1.41 | 0.1688 | main_effect | |
| Neobacillus sp. OS1-33 | −0.026 | 0.013 | −2.08 | 0.0476 | interaction | |
| Neobacillus sp. OS1-33 | 0.006 | 0.006 | 1.00 | 0.3353 | by_group_JB1_JB2 | |
| Neobacillus sp. OS1-33 | −0.020 | 0.011 | −1.71 | 0.1121 | by_group_JB5_JB6_JB7 | |
| Peribacillus asahii | 0.013 | 0.010 | 1.32 | 0.1990 | main_effect | |
| Priestia megaterium | 0.011 | 0.009 | 1.22 | 0.2318 | main_effect | |
| Thermophilic Decomposer | Thermobifida fusca | −0.003 | 0.011 | −0.24 | 0.8098 | main_effect |
| Saccharomonospora viridis | 0.000 | 0.008 | 0.03 | 0.9781 | main_effect | |
| Novibacillus thermophilus | −0.002 | 0.009 | −0.20 | 0.8432 | main_effect | |
| Thermoactinomyces vulgaris | 0.005 | 0.007 | 0.70 | 0.4877 | main_effect | |
| Unclassified | Humibacillus xanthopallidus | 0.012 | 0.008 | 1.53 | 0.1384 | main_effect |
| Nakamurella multipartita | 0.005 | 0.006 | 0.84 | 0.4078 | main_effect | |
| Baekduia alba | 0.003 | 0.005 | 0.49 | 0.6250 | main_effect | |
| Capillimicrobium parvum | 0.013 | 0.006 | 2.22 | 0.0345 | main_effect | |
| Allobacillus halotolerans | −0.005 | 0.019 | −0.25 | 0.8019 | main_effect | |
| Pradoshia sp. D12 | −0.002 | 0.007 | −0.35 | 0.7290 | main_effect | |
| Afipia sp. GAS231 | −0.014 | 0.004 | −3.50 | 0.0016 | main_effect | |
| Afipia carboxidovorans | 0.010 | 0.008 | 1.27 | 0.2129 | main_effect | |
| Bosea sp. NBC 00550 | 0.008 | 0.008 | 0.93 | 0.3597 | main_effect | |
| Skermanella cutis | 0.039 | 0.008 | 5.04 | 0.0000 | main_effect | |
| Massilia sp. R2A-15 | 0.010 | 0.006 | 1.72 | 0.0968 | main_effect | |
| Imtechella halotolerans | 0.001 | 0.018 | 0.07 | 0.9469 | main_effect |
Table 44: Summary statistics for each core microbial species. The table shows the summary statistics for the analysis of the metadata variable and each core species (species level) organised into functional groups. The table gives estimate, standard error, t-value, p-value and model. Model tells which model the summary statistics represents: “main_effect” analysis all fields together as we see no difference between JB groups, “interaction” gives results for the interaction analysis and is included when we decide to split the dataset by JB groups and present per-group results as given in the the following rows.
Degassed fertilizer
| Functional Group | Species | Estimate | SE | t | p-value | Model |
|---|---|---|---|---|---|---|
| Actinomycete Decomposer | Streptomyces sp. NBC 00425 | 0.010 | 0.011 | 0.90 | 0.3770 | main_effect |
| Streptomyces sp. NBC 01537 | 0.006 | 0.007 | 0.77 | 0.4481 | main_effect | |
| Streptomyces canus | −0.005 | 0.010 | −0.51 | 0.6144 | main_effect | |
| Streptomyces albidoflavus | −0.002 | 0.009 | −0.23 | 0.8212 | main_effect | |
| Streptomyces mirabilis | 0.028 | 0.014 | 1.92 | 0.0647 | main_effect | |
| Streptomyces [Kitasatospora] papulosa | −0.005 | 0.009 | −0.54 | 0.5966 | main_effect | |
| Terrabacter sp. C0L 2 | −0.008 | 0.007 | −1.09 | 0.2843 | main_effect | |
| Pedococcus sp. KACC 23699 | 0.015 | 0.010 | 1.52 | 0.1406 | main_effect | |
| Arthrobacter sp. NicSoilB8 | −0.004 | 0.006 | −0.79 | 0.4339 | main_effect | |
| Arthrobacter sp. NicSoilB4 | −0.006 | 0.012 | −0.47 | 0.6421 | main_effect | |
| Arthrobacter sp. PAMC25564 | −0.004 | 0.012 | −0.30 | 0.7669 | main_effect | |
| Arthrobacter sulfonylureivorans | 0.003 | 0.015 | 0.22 | 0.8258 | main_effect | |
| Nocardioides sp. T5 | 0.005 | 0.016 | 0.32 | 0.7488 | main_effect | |
| Nocardioides panacis | −0.013 | 0.015 | −0.86 | 0.3945 | main_effect | |
| Nocardioides ungokensis | −0.036 | 0.013 | −2.88 | 0.0076 | main_effect | |
| Kribbella sp. NBC 00359 | −0.009 | 0.009 | −0.94 | 0.3550 | main_effect | |
| Kribbella sp. NBC 01484 | −0.017 | 0.011 | −1.53 | 0.1381 | main_effect | |
| Kribbella sp. NBC 01510 | −0.019 | 0.013 | −1.50 | 0.1458 | main_effect | |
| Micromonospora sp. NBC 00330 | 0.024 | 0.008 | 3.04 | 0.0051 | main_effect | |
| Micromonospora sp. NBC 01740 | 0.002 | 0.014 | 0.14 | 0.8879 | main_effect | |
| Micromonospora sp. B006 | −0.006 | 0.012 | −0.50 | 0.6183 | main_effect | |
| Micromonospora zamorensis | 0.022 | 0.010 | 2.10 | 0.0448 | main_effect | |
| Dactylosporangium sp. NBC 01737 | 0.003 | 0.006 | 0.42 | 0.6747 | main_effect | |
| Streptosporangium sp. 'caverna' | 0.005 | 0.008 | 0.64 | 0.5280 | main_effect | |
| Streptosporangium subroseum | 0.005 | 0.007 | 0.70 | 0.4903 | main_effect | |
| Streptosporangium roseum | −0.009 | 0.007 | −1.22 | 0.2321 | main_effect | |
| Nonomuraea glycinis | −0.023 | 0.016 | −1.43 | 0.1626 | main_effect | |
| Amycolatopsis sp. DSM 110486 | 0.011 | 0.008 | 1.34 | 0.1915 | main_effect | |
| Actinomycetospora sp. NBC 00405 | 0.012 | 0.012 | 0.99 | 0.3283 | main_effect | |
| Anaerobic Decomposer | Acetivibrio saccincola | −0.025 | 0.011 | −2.19 | 0.0369 | main_effect |
| Herbinix luporum | 0.009 | 0.013 | 0.75 | 0.4605 | main_effect | |
| Hydrocarbon Degrader | Mycolicibacterium vanbaalenii | 0.006 | 0.012 | 0.49 | 0.6278 | main_effect |
| Mycolicibacterium [Mycobacterium] burgundiense | 0.017 | 0.009 | 1.91 | 0.0660 | main_effect | |
| Rhodococcus sp. MTM3W5.2 | 0.006 | 0.009 | 0.61 | 0.5495 | main_effect | |
| Rhodococcus sp. W8901 | 0.006 | 0.007 | 0.80 | 0.4292 | main_effect | |
| Rhodococcoides fascians | −0.001 | 0.008 | −0.09 | 0.9276 | main_effect | |
| Immunomodulatory Soil Bacterium | Mycolicibacterium vaccae | 0.004 | 0.010 | 0.41 | 0.6842 | main_effect |
| Methanotroph | Methylocapsa sp. D3K7 | −0.012 | 0.013 | −0.94 | 0.3539 | main_effect |
| Nitrogen Fixer - Plant Symbiont | Bradyrhizobium sp. 170 | 0.020 | 0.015 | 1.30 | 0.2040 | main_effect |
| Bradyrhizobium sp. 200 | 0.016 | 0.008 | 1.99 | 0.0566 | main_effect | |
| Bradyrhizobium sp. Ash2021 | 0.001 | 0.006 | 0.13 | 0.8967 | main_effect | |
| Bradyrhizobium sp. | 0.011 | 0.005 | 2.33 | 0.0273 | main_effect | |
| Bradyrhizobium erythrophlei | −0.005 | 0.009 | −0.53 | 0.6030 | main_effect | |
| Bradyrhizobium barranii | 0.040 | 0.009 | 4.29 | 0.0002 | main_effect | |
| Bradyrhizobium lablabi | −0.004 | 0.008 | −0.58 | 0.5682 | main_effect | |
| Bradyrhizobium japonicum | 0.018 | 0.006 | 3.07 | 0.0048 | main_effect | |
| Bradyrhizobium diazoefficiens | 0.045 | 0.020 | 2.23 | 0.0341 | main_effect | |
| Bradyrhizobium ottawaense | −0.004 | 0.008 | −0.50 | 0.6232 | main_effect | |
| Mesorhizobium sp. ANAO-SY3R2 | −0.004 | 0.009 | −0.40 | 0.6893 | main_effect | |
| Rhizobium ruizarguesonis | −0.005 | 0.012 | −0.45 | 0.6571 | main_effect | |
| Microvirga ossetica | −0.009 | 0.012 | −0.74 | 0.4653 | main_effect | |
| Opportunistic Pathogen | Mycobacterium intracellulare | 0.001 | 0.006 | 0.22 | 0.8253 | main_effect |
| Bacillus cereus | −0.007 | 0.012 | −0.60 | 0.5547 | main_effect | |
| Plant-Associated Bacterium | Agrobacterium rosae | 0.002 | 0.012 | 0.14 | 0.8878 | main_effect |
| Plant-Associated Commensal | Paraburkholderia hospita | 0.023 | 0.011 | 2.15 | 0.0408 | main_effect |
| Plant-Associated Commensal/Decomposer | Pseudomonas fluorescens | −0.003 | 0.018 | −0.16 | 0.8747 | main_effect |
| Pseudomonas sp. PONIH3 | −0.026 | 0.015 | −1.66 | 0.1074 | main_effect | |
| Soil Decomposer | Bacillus mycoides | −0.007 | 0.020 | −0.35 | 0.7325 | main_effect |
| Bacillus licheniformis | −0.026 | 0.023 | −1.13 | 0.2663 | main_effect | |
| Neobacillus sp. FSL H8-0543 | −0.013 | 0.008 | −1.58 | 0.1261 | main_effect | |
| Neobacillus sp. OS1-33 | −0.018 | 0.009 | −2.03 | 0.0523 | main_effect | |
| Peribacillus asahii | −0.019 | 0.013 | −1.54 | 0.1338 | main_effect | |
| Priestia megaterium | −0.019 | 0.012 | −1.63 | 0.1147 | main_effect | |
| Thermophilic Decomposer | Thermobifida fusca | −0.015 | 0.014 | −1.14 | 0.2654 | main_effect |
| Saccharomonospora viridis | −0.011 | 0.010 | −1.07 | 0.2917 | main_effect | |
| Novibacillus thermophilus | −0.021 | 0.011 | −1.85 | 0.0744 | main_effect | |
| Thermoactinomyces vulgaris | 0.001 | 0.009 | 0.15 | 0.8840 | main_effect | |
| Unclassified | Humibacillus xanthopallidus | −0.018 | 0.010 | −1.82 | 0.0794 | main_effect |
| Nakamurella multipartita | 0.000 | 0.008 | 0.00 | 0.9968 | main_effect | |
| Baekduia alba | 0.013 | 0.006 | 2.00 | 0.0557 | main_effect | |
| Capillimicrobium parvum | −0.013 | 0.008 | −1.55 | 0.1330 | main_effect | |
| Allobacillus halotolerans | −0.046 | 0.023 | −2.02 | 0.0527 | main_effect | |
| Pradoshia sp. D12 | −0.009 | 0.009 | −0.96 | 0.3437 | main_effect | |
| Afipia sp. GAS231 | 0.007 | 0.006 | 1.14 | 0.2659 | main_effect | |
| Afipia carboxidovorans | −0.023 | 0.009 | −2.50 | 0.0186 | main_effect | |
| Bosea sp. NBC 00550 | −0.007 | 0.011 | −0.62 | 0.5425 | main_effect | |
| Skermanella cutis | −0.017 | 0.013 | −1.26 | 0.2196 | main_effect | |
| Massilia sp. R2A-15 | 0.004 | 0.008 | 0.51 | 0.6120 | main_effect | |
| Imtechella halotolerans | −0.042 | 0.022 | −1.87 | 0.0722 | main_effect |
Table 45: Summary statistics for each core microbial species. The table shows the summary statistics for the analysis of the metadata variable and each core species (species level) organised into functional groups. The table gives estimate, standard error, t-value, p-value and model. Model tells which model the summary statistics represents: “main_effect” analysis all fields together as we see no difference between JB groups, “interaction” gives results for the interaction analysis and is included 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 46: List of used software including the used R-programming environment packages.
| Package | Version | Package | Version |
|---|---|---|---|
| OS | Ubuntu 20.04.4 LTS | class | 7.3-22 |
| R | 4.3.3 | robustbase | 0.99-3 |
| splines | 4.3.3 | httr | 1.4.7 |
| bitops | 1.0-7 | htmlwidgets | 1.6.4 |
| lifecycle | 1.0.4 | S4Arrays | 1.2.1 |
| rstatix | 0.7.2 | pkgconfig | 2.0.3 |
| sf | 1.0-16 | gtable | 0.3.5 |
| MASS | 7.3-60.0.1 | hwriter | 1.3.2.1 |
| insight | 0.20.2 | pcaPP | 2.0-4 |
| backports | 1.5.0 | htmltools | 0.5.8.1 |
| magrittr | 2.0.3 | carData | 3.0-5 |
| plotly | 4.10.4 | biomformat | 1.30.0 |
| sass | 0.4.9 | png | 0.1-8 |
| rmarkdown | 2.27 | rstudioapi | 0.16.0 |
| jquerylib | 0.1.4 | tzdb | 0.4.0 |
| yaml | 2.3.9 | reshape2 | 1.4.4 |
| zip | 2.3.1 | coda | 0.19-4.1 |
| cowplot | 1.1.3 | nlme | 3.1-165 |
| DBI | 1.2.3 | curl | 5.2.1 |
| minqa | 1.2.7 | nloptr | 2.1.1 |
| ade4 | 1.7-22 | proxy | 0.4-27 |
| multcomp | 1.4-26 | cachem | 1.1.0 |
| abind | 1.4-5 | zoo | 1.8-12 |
| zlibbioc | 1.48.2 | rhdf5 | 2.46.1 |
| Rtsne | 0.17 | sjlabelled | 1.2.0 |
| RCurl | 1.98-1.16 | KernSmooth | 2.23-24 |
| 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 |
| ggrepel | 0.9.5 | ggpubr | 0.6.0 |
| units | 0.8-5 | car | 3.1-2 |
| 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 |
| farver | 2.1.2 | cli | 3.6.3 |
| multtest | 2.58.0 | compiler | 4.3.3 |
| e1071 | 1.7-14 | rlang | 1.1.4 |
| survival | 3.7-0 | crayon | 1.5.3 |
| iterators | 1.0.14 | ggsignif | 0.6.4 |
| systemfonts | 1.1.0 | rrcov | 1.7-5 |
| foreach | 1.5.2 | labeling | 0.4.3 |
| tools | 4.3.3 | classInt | 0.4-10 |
| glue | 1.8.0 | interp | 1.1-6 |
| SparseArray | 1.2.4 | rematch2 | 2.1.2 |
| xfun | 0.46 | plyr | 1.8.9 |
| mgcv | 1.9-1 | stringi | 1.8.4 |
| withr | 3.0.0 | viridisLite | 0.4.2 |
| fastmap | 1.2.0 | deldir | 2.0-4 |
| latticeExtra | 0.6-30 | munsell | 0.5.1 |
| boot | 1.3-30 | lazyeval | 0.2.2 |
| rhdf5filters | 1.14.1 | V8 | 4.4.2 |
| fansi | 1.0.6 | hms | 1.1.3 |
| digest | 0.6.36 | Rhdf5lib | 1.24.2 |
| timechange | 0.3.0 | highr | 0.11 |
| R6 | 2.5.1 | fontawesome | 0.5.2 |
| estimability | 1.5.1 | igraph | 2.0.3 |
| colorspace | 2.1-0 | RcppParallel | 5.1.8 |
| jpeg | 0.1-10 | bslib | 0.7.0 |
| utf8 | 1.2.4 | DEoptimR | 1.1-3 |
| generics | 0.1.3 | ape | 5.8 |