
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 fungal 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 fungal composition of the fields focusing on single core genera 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.

Summary Statistics
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.

Geography

This section evaluate the geographic location of the fields included in the project. We use the collected coordinates to show the location of the fields on a map, and color the data points by key variables to get an understanding of the relationship.

Part-conclusion for section

We selected 6 key variables for this section to get an understanding of the possible geographic component of any microbial association with these variables. Two of the variables show a pattern:

Despite all samples between from Jutland with a limited variation along the vest-to-east axis we see a vest-to-east pattern for JB groups.
There is a clear north-to-south pattern for biodynamic farming. This pattern is too strong to be adjusted for in the analysis without loosing any try associations with biodynamic farming but must be considered that any other soil differences along this axis may contribute to the associations we see for biodynamic farming.

JB value

Figure 1: Visualization of the geographic location of the samples. Using the coordinates of each field in the project, we show the locations on a map and color the samples by JB group.

Grazed

Figure 2: Visualization of the geographic location of the samples. Using the coordinates of each field in the project, we show the locations on a map and color the samples by the variable “Grazed”.

Harvested

Figure 3: Visualization of the geographic location of the samples. Using the coordinates of each field in the project, we show the locations on a map and color the samples by the variable “Harvested”.

Clovergrass within 3 years

Figure 4: Visualization of the geographic location of the samples. Using the coordinates of each field in the project, we show the locations on a map and color the samples by the variable “Clovergrass (within 3 years)”.

Biodynamic farm

Figure 5: Visualization of the geographic location of the samples. Using the coordinates of each field in the project, we show the locations on a map and color the samples by the variable “Biodynamic farm”.

Years since turning organic

Figure 6: Visualization of the geographic location of the samples. Using the coordinates of each field in the project, we show the locations on a map and color the samples by the variable “Years since turning organic”.

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 fungal 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 genus level
Aitchison is computed from the total abundance data transformed with central-log-ratio (CLR), at the genus 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 fungi between the JB groups.
Grazing strongly associate with the fungal composition in both JB groups.
Clovergrass shows an association that is strongest in JB 1-2 fields.
Biodynamic farming shows a very strong association with the fungal community of the soil in both JB groups. It appears to be the strongest dictator of differences 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 fungal composition in both JB groups.
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 7: Visualization of structure of the fungal 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	0.0474	0.239	0.1066	0.003	0.2004	0.001
Class	0.0868	0.009	0.0836	0.001	0.106	0.001
Order	0.0749	0.012	0.0694	0.001	0.0832	0.001
Family	0.0635	0.019	0.0638	0.001	0.0578	0.004
Genus	0.0623	0.014	0.0614	0.001	0.0579	0.003
ASV	0.0537	0.026	0.0476	0.001	0.0544	0.001

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 8: Visualization of the fungal 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	0.0263	0.723	0.0769	0.36	0.0599	0.488
Class	0.0825	0.286	0.0756	0.295	0.1032	0.031
Order	0.0862	0.217	0.0721	0.309	0.0826	0.139
Family	0.0787	0.253	0.0735	0.207	0.0656	0.446
Genus	0.0756	0.259	0.0654	0.532	0.0668	0.43
ASV	0.0733	0.239	0.0655	0.596	0.0657	0.492

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	0.0273	0.751	0.0992	0.242	0.1774	0.045
Class	0.0525	0.711	0.0738	0.516	0.0785	0.399
Order	0.0813	0.437	0.0721	0.63	0.0612	0.736
Family	0.0696	0.518	0.0682	0.7	0.0628	0.757
Genus	0.0852	0.315	0.0749	0.428	0.0791	0.34
ASV	0.0785	0.353	0.077	0.383	0.0827	0.22

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 9: Visualization of the fungal 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	0.1797	0.051	0.051	0.652	0.0601	0.466
Class	0.1402	0.025	0.0747	0.316	0.0711	0.372
Order	0.1154	0.04	0.0698	0.389	0.0698	0.357
Family	0.1134	0.027	0.0729	0.207	0.0852	0.072
Genus	0.1191	0.012	0.0812	0.027	0.0953	0.008
ASV	0.1046	0.016	0.0749	0.016	0.0888	0.007

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	0.0458	0.656	0.0831	0.386	0.2049	0.011
Class	0.0636	0.583	0.0778	0.438	0.1028	0.15
Order	0.0882	0.285	0.0875	0.228	0.1177	0.028
Family	0.1216	0.072	0.0849	0.197	0.0998	0.081
Genus	0.12	0.06	0.0958	0.06	0.1143	0.02
ASV	0.1028	0.113	0.0823	0.145	0.0973	0.038

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 10: Visualization of the fungal 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	0.071	0.341	0.0574	0.603	0.0909	0.193
Class	0.0685	0.42	0.0711	0.39	0.0699	0.432
Order	0.0747	0.33	0.0791	0.172	0.0845	0.143
Family	0.0815	0.21	0.0768	0.158	0.0791	0.142
Genus	0.0877	0.129	0.0781	0.059	0.077	0.128
ASV	0.0777	0.162	0.0701	0.141	0.0745	0.113

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	0.0433	0.574	0.0605	0.661	0.0177	0.978
Class	0.0417	0.905	0.0364	0.99	0.0354	0.943
Order	0.0553	0.717	0.0662	0.795	0.06	0.756
Family	0.0625	0.641	0.0621	0.903	0.0805	0.409
Genus	0.062	0.713	0.0662	0.764	0.0765	0.471
ASV	0.0745	0.457	0.0726	0.56	0.077	0.38

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 11: Visualization of the fungal 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	0.132	0.127	0.074	0.354	0.1089	0.1
Class	0.1299	0.031	0.0609	0.626	0.0767	0.285
Order	0.1215	0.027	0.0742	0.215	0.0685	0.404
Family	0.1065	0.039	0.0665	0.525	0.0665	0.476
Genus	0.1045	0.027	0.0768	0.075	0.0863	0.038
ASV	0.0894	0.056	0.0692	0.177	0.0715	0.197

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	0.0371	0.708	0.0541	0.689	0.1825	0.017
Class	0.0972	0.247	0.0658	0.691	0.0663	0.593
Order	0.0981	0.196	0.1047	0.027	0.0754	0.462
Family	0.0898	0.238	0.0942	0.069	0.0809	0.31
Genus	0.0851	0.273	0.0862	0.149	0.0795	0.342
ASV	0.0765	0.36	0.0786	0.279	0.0785	0.353

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 12: Visualization of the fungal 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	0.0532	0.438	0.0792	0.33	0.1004	0.128
Class	0.0457	0.726	0.0751	0.325	0.085	0.181
Order	0.046	0.76	0.0708	0.379	0.076	0.263
Family	0.0511	0.73	0.0681	0.404	0.0635	0.553
Genus	0.0565	0.664	0.064	0.622	0.0612	0.706
ASV	0.0592	0.671	0.0643	0.747	0.0638	0.633

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	0.0765	0.35	0.1286	0.116	0.0446	0.752
Class	0.0479	0.798	0.0844	0.332	0.0688	0.539
Order	0.0897	0.279	0.0719	0.559	0.0617	0.747
Family	0.0999	0.143	0.0768	0.382	0.0786	0.407
Genus	0.098	0.145	0.0984	0.057	0.0967	0.089
ASV	0.0895	0.215	0.0879	0.077	0.0891	0.118

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 13: Visualization of the fungal 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	0.0487	0.476	0.0993	0.145	0.1233	0.059
Class	0.1211	0.056	0.0972	0.059	0.0916	0.106
Order	0.1261	0.025	0.1044	0.004	0.1591	0.002
Family	0.1535	0.007	0.1052	0.002	0.1471	0.002
Genus	0.1465	0.005	0.0968	0.003	0.1183	0.002
ASV	0.1419	0.002	0.086	0.002	0.1055	0.002

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	0.0788	0.386	0.0918	0.301	0.1305	0.13
Class	0.2098	0.006	0.1198	0.048	0.1253	0.073
Order	0.2824	0.003	0.1044	0.026	0.1234	0.032
Family	0.2507	0.003	0.1043	0.029	0.137	0.005
Genus	0.2329	0.003	0.1107	0.022	0.1446	0.003
ASV	0.2357	0.003	0.1001	0.013	0.1308	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 14: Visualization of the fungal 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	0.0831	0.286	0.0378	0.833	0.0306	0.913
Class	0.1321	0.044	0.0644	0.539	0.1026	0.039
Order	0.1296	0.025	0.0828	0.096	0.1084	0.017
Family	0.1126	0.041	0.0743	0.189	0.0825	0.096
Genus	0.0972	0.073	0.0733	0.165	0.083	0.067
ASV	0.0926	0.049	0.0708	0.102	0.0759	0.082

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	0.1205	0.201	0.0123	0.98	0.0933	0.304
Class	0.1573	0.037	0.0679	0.616	0.0834	0.34
Order	0.1575	0.029	0.0872	0.214	0.0908	0.233
Family	0.147	0.023	0.0828	0.24	0.0925	0.154
Genus	0.1314	0.032	0.084	0.217	0.0934	0.12
ASV	0.1254	0.036	0.0831	0.145	0.0968	0.045

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 15: Visualization of the fungal 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	0.0753	0.266	0.1127	0.091	0.0862	0.233
Class	0.0513	0.656	0.0666	0.484	0.0656	0.494
Order	0.0587	0.576	0.0779	0.146	0.0726	0.277
Family	0.0856	0.165	0.0734	0.188	0.0783	0.139
Genus	0.0766	0.241	0.0646	0.587	0.067	0.435
ASV	0.073	0.25	0.0687	0.206	0.0679	0.337

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 16: Visualization of the fungal 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	0.1524	0.34	0.1768	0.156	0.214	0.042
Class	0.154	0.295	0.1377	0.348	0.176	0.124
Order	0.1478	0.289	0.1459	0.191	0.1475	0.235
Family	0.1413	0.364	0.1405	0.27	0.1547	0.112
Genus	0.1528	0.218	0.1526	0.052	0.1674	0.016
ASV	0.1513	0.177	0.142	0.096	0.1388	0.331

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	0.5978	0.061	0.2669	0.753	0.4132	0.126
Class	0.4051	0.089	0.3345	0.225	0.3582	0.228
Order	0.3525	0.219	0.3325	0.184	0.3694	0.126
Family	0.3544	0.146	0.3491	0.095	0.3329	0.266
Genus	0.3516	0.12	0.3514	0.09	0.3339	0.175
ASV	0.342	0.13	0.3401	0.073	0.3312	0.173

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 fungal 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.
Both the years since turning organic and the years as biodynamic are important for the soil fungal composition. The strongest effect is seen for biodynamic but that variable may also hold more variation as we have both non-biodynamic and biodynamic fields.

Ordination plots

Bray Curtis

Jaccard

Aitchison

Figure 17: 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

ENVFIT for JB 1 & JB2
.	Bray		Jaccard		Euclidean
Variable	R2	p	R2	p	R2	p
soil tmp	0.18	0.271	0.069	0.619	0.086	0.525
Years since plowing	0.311	0.084	0.292	0.103	0.474	0.054
Rt	0.244	0.15	0.587	0.003	0.566	0.004
Phosphorus	0.084	0.545	0.084	0.602	0.027	0.818
Potassium	0.073	0.615	0.085	0.563	0.208	0.178
Magnesium	0.018	0.89	0.123	0.409	0.277	0.115
Cobber	0.009	0.95	0.046	0.753	0.211	0.203
Organic material (%)	0.042	0.77	0.134	0.385	0.053	0.655
Clay (%)	0.181	0.271	0.214	0.21	0.207	0.205
Nitrogen (%)	0.026	0.86	0.13	0.369	0.068	0.625
Years since turning_organic	0.347	0.06	0.538	0.008	0.455	0.016
Years since turning_biodynamic	0.541	0.008	0.621	0.004	0.638	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.

ENVFIT for JB 1 & JB2
.	Bray		Jaccard		Euclidean
Variable	R2	p	R2	p	R2	p
soil tmp	0.057	0.701	0.198	0.289	0.259	0.201
Years since plowing	0.275	0.154	0.234	0.223	0.262	0.18
Rt	0.197	0.295	0.587	0.003	0.566	0.004
Phosphorus	0.223	0.25	0.298	0.131	0.199	0.278
Potassium	0.019	0.905	0.034	0.823	0.044	0.78
Magnesium	0.328	0.096	0.097	0.563	0.137	0.422
Cobber	0.113	0.502	0.094	0.614	0.046	0.777
Organic material (%)	0.03	0.84	0.342	0.104	0.166	0.348
Clay (%)	0.545	0.017	0.504	0.015	0.622	0.002
Nitrogen (%)	0.07	0.653	0.374	0.075	0.187	0.301
Years since turning_organic	0.057	0.739	0.538	0.008	0.455	0.016
Years since turning_biodynamic	0.541	0.008	0.621	0.004	0.638	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. JB 1-2 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 holds a less common type of analysis where we review if the effect or association of the continuous variables is not linear but perhaps the strongest difference may be e.g. between mean levels and the extremes. We do see some additional associations that we did not detect in the linear relationship analysis. For JB 1-2 years since plowing is important (this also had a trending association in the linear analysis). Rt also shows a non-linear relationship but only in JB 1-2 where we also see cobber, clay content and years since turning organic presenting with a significant p-value.
For JB 5-7, phosphorus levels and clay content appear to have a non-linear association with the community.


Euclidean
	F	P
soil_tmp	0	8.43e-01
Years_since_plowing	4.444	7.38e-04
Rt	1.68	4.30e-03
Phosphorus	0.877	1.16e-01
Potassium	1.149	6.44e-02
Magnesium	0.427	1.03e-01
Cobber	3.073	1.78e-02
Organic_material_perc	0	7.70e-01
Clay_perc	1.389	4.21e-02
Nitrogen_perc	0	6.19e-01
Years_since_turning_organic	0.645	4.58e-02

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	0.203	1.88e-01
Years_since_plowing	0.26	1.58e-01
Rt	0.167	2.21e-01
Phosphorus	1.956	2.97e-02
Potassium	0.916	9.20e-02
Magnesium	0	4.40e-01
Cobber	0	7.55e-01
Organic_material_perc	0.023	3.64e-01
Clay_perc	2.788	8.08e-03
Nitrogen_perc	0.083	3.37e-01
Years_since_turning_organic	0	4.76e-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 fungi

We now turn to analyzing individual fungal taxa: Which fungi are consistently present in the soil samples, and how do their abundances associate with the environmental and management variables captured in the metadata?

To address this, we take a targeted approach by focusing on core fungi—those genera 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 fungi as genera 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 fungal community.

After identifying the core genera, we categorized them into functional groups—such as saprotrophs, mycorrhizal fungi, and potential plant pathogens—shown in the first column of Table 25. This functional annotation helps us interpret the ecological roles these fungi may play across fields and assess whether their abundance is meaningfully associated with environmental or management variables in the dataset.

Key Observations:

Dominance of saprotrophs: The majority of core fungi fall into the saprotrophic category, indicating a strong role in organic matter decomposition and nutrient cycling. Genera such as Gibellulopsis, Cladosporium, Penicillium, and Mortierella showed consistently high abundances (e.g., Gibellulopsis with Q90 of 14.9%), suggesting stable contributions to soil organic matter turnover.
Presence of functional redundancy: Multiple dung-associated fungi (Cheilymenia, Podospora, Cercophora) were present, pointing to a robust decomposition guild likely shaped by manure inputs or past livestock activity—a hallmark of organic systems.
Ecological generalists and biocontrol taxa: Notably, beneficial genera like Clonostachys and Trichoderma—known for biocontrol activity—were also detected, though at moderate abundance. Their presence hints at a natural disease suppression potential in these soils.
Plant pathogenic taxa: Genera such as Fusarium, Boeremia, and Dactylonectria—which include species known to cause crop disease—were also part of the core. Their consistent presence emphasizes the need for monitoring potentially harmful fungi even in well-managed organic fields.
Yeasts and unclassified fungi: A considerable fraction of the core genera (e.g., Solicoccozyma, Apiotrichum, Saitozyma) are yeast-like or poorly characterized, with unclear ecological roles. This highlights both the limits of current functional annotation and the potential for novel insights into fungal ecology.

Functional Group	Genus	Rationale	Q10	Q90
Ectomycorrhizal Symbionts	Cortinarius	A well-known ectomycorrhizal genus forming symbiotic relationships with trees, enhancing nutrient uptake.	0.032	0.626
Fungal Saprotrophs	Gibellulopsis	Identified as a soil-borne saprophytic fungus, decomposing organic matter.	3.475	14.918
	Cladosporium	Commonly found on decaying organic material, contributing to decomposition.	0.780	4.973
	Cheilymenia	Dung-loving ascomycete, decomposing animal feces.	0.047	6.876
	Thelebolus	Grows on dung or soil, aiding in decomposition processes.	0.048	2.540
	Penicillium	Ubiquitous soil fungus involved in decomposing organic materials.	1.332	5.022
	Preussia	Found on herbivore dung, participating in organic matter breakdown.	0.177	3.252
	Mortierella	Soil saprotroph decomposing organic matter; some species promote plant growth.	0.378	2.298
	Pseudeurotium	Isolated from crop field soil; likely involved in organic matter decomposition.	0.048	5.539
	Podospora	Coprophilous fungus, decomposing dung.	0.026	3.135
	Cercophora	Dung-inhabiting fungus, contributing to decomposition.	0.045	0.850
	Papulaspora	Soil saprotroph involved in decomposing organic materials.	0.000	0.428
	Aspergillus	Common saprotroph, decomposing various organic substrates.	0.014	0.580
	Gliomastix	A genus often found in soil and decaying organic matter, suggesting a saprotrophic lifestyle.	0.000	0.330
	Podila	NA	0.543	3.893
Plant Pathogens	Fusarium	Includes species causing diseases in various crops, such as Fusarium wilt.	0.821	4.860
	Boeremia	Contains species like B. exigua, known to cause plant diseases.	0.188	2.864
	Dactylonectria	Known to cause root rot diseases in plants.	0.186	1.291
	Plectosphaerella	Includes plant pathogenic species affecting various hosts.	0.000	1.163
	Pyrenochaetopsis	Contains species associated with plant diseases.	0.092	1.213
	Ophiosphaerella	Known for causing dollar spot disease in turf grasses.	0.013	0.620
	Acremonium	Some species are plant pathogens, while others are endophytes.	0.211	1.059
	Exophiala	Includes opportunistic plant pathogens.	0.277	2.345
	Pseudoechria	Contains species with potential pathogenicity to plants.	0.000	0.326
Biocontrol Agents / Beneficial Fungi	Clonostachys	Species like C. rosea are known biocontrol agents against plant pathogens.	0.516	2.416
	Trichoderma	Widely used in agriculture for biocontrol and plant growth promotion.	0.326	1.029
	Mortierella	Some species promote plant growth and suppress soil-borne pathogens.	0.378	2.298
	Penicillium	Certain species produce antibiotics and promote plant health.	1.332	5.022
	Aspergillus	Some species are used in biocontrol and industrial applications.	0.014	0.580
Unclassified	Solicoccozyma	Yeast-like fungus; ecological role in agriculture not well-defined.	2.671	8.701
	Nadsonia	Yeast genus with limited information on agricultural relevance.	0.080	11.006
	Apiotrichum	Yeast-like fungi; ecological functions in soil are not well-characterized.	0.374	4.280
	Saitozyma	Basidiomycetous yeast; role in agriculture remains unclear.	0.052	4.814
	Triangularia	Limited information available on ecological role.	0.000	1.430
	Enterocarpus	Ecological functions not well-documented.	0.096	2.128
	Hymenoscyphus	Includes species like H. fraxineus, which causes ash dieback; however, not all species are pathogenic.	0.007	0.748
	Linnemannia	Formerly classified under Mortierella; ecological role varies.	0.136	1.989
	Aaosphaeria	Limited data on ecological functions.	0.008	0.662
	Dendryphion	Ecological role not well-established.	0.008	0.599
	Pleotrichocladium	Insufficient information on ecological functions.	0.000	0.433
	Arthrographis	Some species are opportunistic pathogens; ecological role in soil is unclear.	0.065	0.630
	Atractospora	Limited information on ecological role.	0.031	0.773
	Arachniotus	Ecological functions not well-documented.	0.098	0.597
	Myrmecridium	Insufficient data on ecological role.	0.000	0.605
	Chaetasbolisia	Ecological functions not well-characterized.	0.000	0.543
	Trichosporiella	Limited information available on ecological role.	0.000	0.469
	Tetracladium	Aquatic hyphomycetes; some species may play roles in nutrient cycling.	0.072	0.658
Uncertain	Gliomastix	A genus often found in soil and decaying organic matter, suggesting a saprotrophic lifestyle.	0.000	0.330
	Podila	Podila species (related to Mortierella) are typically saprotrophic and occur in decomposing plant debris and soil.	0.543	3.893
	Keithomyces	Likely related to Cordyceps, with possible roles as insect pathogens or saprotrophs on decaying insect tissue, though its classification is still being resolved.	0.611	2.069
	Fusicolla	Closely related to Fusarium, with several species associated with plant material and possibly mild pathogenic traits.	0.405	1.477
	Paraphaeosphaeria	Known from both endophytic and necrotrophic contexts in plant tissues; some species are weak pathogens or decomposers.	0.065	2.087

Table 25: Core fungal genera grouped into key functional groups. The table shows the detected core fungi (genus level) assigned to a functional group. The table gives a short description of the fungi 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 fungi 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.

Biodynamic farm

Key Findings from the table below:

Significant differences (p < 0.05) were observed for 15 core fungal genera, suggesting that biodynamic management consistently alters the abundance of a subset of the soil mycobiome.

Fungi enriched in biodynamic fields:

Cortinarius (Ectomycorrhizal): Strong positive effect (β = 0.028, p = 0.0005), suggesting greater tree/fungal symbiosis potential.
Pseudeurotium, Saitozyma, Pleotrichocladium, and Paraphaeosphaeria all showed significantly higher abundance in biodynamic systems—spanning diverse ecological roles from saprotrophs to yeasts and endophytes.

Fungi suppressed in biodynamic fields:

Cheilymenia and Thelebolus (coprophilous/dung fungi) showed strongly negative effects (p < 0.01), possibly reflecting differences in manure handling or composting.
Dactylonectria (plant pathogen) and Nadsonia (yeast) were also significantly less abundant, which could imply reduced pathogen risk or shifts in niche availability.

Interactions with farming group clusters (JB_groups):

For Gibellulopsis, Ophiosphaerella, Saitozyma, Pleotrichocladium, and Atractospora, interaction models were significant. This means that the response to biodynamics differed by JB grouping—highlighting the importance of considering context and legacy effects.
E.g., Gibellulopsis was significantly enriched only in JB5_JB6_JB7 farms (β = 0.122, p = 0.0014), but not in JB1_JB2.
Atractospora showed a strong negative association in JB1_JB2 but not in JB5_JB6_JB7, suggesting local soil/farm history shapes the effect of biodynamic practices.

Functional Group	Genus	Estimate	SE	t	p-value	Model
Ectomycorrhizal Symbionts	Cortinarius	0.028	0.007	3.90	0.0005	main_effect
Fungal Saprotrophs	Gibellulopsis	0.131	0.057	2.29	0.0306	interaction
	Gibellulopsis	−0.009	0.046	−0.19	0.8521	by_group_JB1_JB2
	Gibellulopsis	0.122	0.030	4.11	0.0014	by_group_JB5_JB6_JB7
	Cladosporium	−0.021	0.026	−0.81	0.4241	main_effect
	Cheilymenia	−0.113	0.032	−3.49	0.0016	main_effect
	Thelebolus	−0.100	0.017	−5.76	0.0000	main_effect
	Penicillium	−0.011	0.025	−0.42	0.6743	main_effect
	Preussia	0.039	0.020	1.93	0.0638	main_effect
	Mortierella	0.004	0.017	0.24	0.8130	main_effect
	Pseudeurotium	0.114	0.025	4.55	0.0001	main_effect
	Podospora	−0.015	0.024	−0.61	0.5443	main_effect
	Cercophora	−0.018	0.011	−1.69	0.1018	main_effect
	Papulaspora	0.005	0.010	0.53	0.6020	main_effect
	Aspergillus	0.016	0.012	1.37	0.1827	main_effect
	Gliomastix	0.004	0.009	0.48	0.6329	main_effect
	Podila	−0.011	0.020	−0.53	0.5987	main_effect
Plant Pathogens	Fusarium	0.036	0.019	1.84	0.0768	main_effect
	Boeremia	−0.023	0.021	−1.12	0.2733	main_effect
	Dactylonectria	−0.030	0.011	−2.83	0.0086	main_effect
	Plectosphaerella	−0.014	0.017	−0.83	0.4112	main_effect
	Pyrenochaetopsis	−0.007	0.013	−0.52	0.6095	main_effect
	Ophiosphaerella	0.034	0.017	2.06	0.0493	interaction
	Ophiosphaerella	−0.029	0.012	−2.33	0.0352	by_group_JB1_JB2
	Ophiosphaerella	0.005	0.010	0.49	0.6297	by_group_JB5_JB6_JB7
	Acremonium	−0.001	0.009	−0.09	0.9267	main_effect
	Exophiala	−0.037	0.014	−2.57	0.0157	main_effect
	Pseudoechria	0.002	0.011	0.18	0.8599	main_effect
Biocontrol Agents / Beneficial Fungi	Clonostachys	−0.003	0.013	−0.22	0.8310	main_effect
	Trichoderma	0.005	0.008	0.66	0.5177	main_effect
	Mortierella	0.004	0.017	0.24	0.8130	main_effect
	Penicillium	−0.011	0.025	−0.42	0.6743	main_effect
	Aspergillus	0.016	0.012	1.37	0.1827	main_effect
Unclassified	Solicoccozyma	−0.052	0.023	−2.32	0.0281	main_effect
	Nadsonia	−0.134	0.043	−3.14	0.0039	main_effect
	Apiotrichum	−0.009	0.024	−0.39	0.7006	main_effect
	Saitozyma	0.115	0.031	3.70	0.0010	interaction
	Saitozyma	0.063	0.023	2.69	0.0176	by_group_JB1_JB2
	Saitozyma	0.178	0.020	9.06	0.0000	by_group_JB5_JB6_JB7
	Triangularia	−0.058	0.014	−4.19	0.0002	main_effect
	Enterocarpus	−0.024	0.020	−1.19	0.2431	main_effect
	Hymenoscyphus	0.005	0.030	0.16	0.8765	main_effect
	Linnemannia	−0.060	0.013	−4.62	0.0001	main_effect
	Aaosphaeria	−0.007	0.012	−0.55	0.5848	main_effect
	Dendryphion	−0.017	0.010	−1.58	0.1262	main_effect
	Pleotrichocladium	0.039	0.018	2.16	0.0402	interaction
	Pleotrichocladium	−0.008	0.012	−0.69	0.5041	by_group_JB1_JB2
	Pleotrichocladium	0.031	0.014	2.25	0.0444	by_group_JB5_JB6_JB7
	Arthrographis	−0.018	0.011	−1.69	0.1018	main_effect
	Atractospora	0.068	0.032	2.14	0.0420	interaction
	Atractospora	−0.041	0.012	−3.30	0.0052	by_group_JB1_JB2
	Atractospora	0.027	0.031	0.86	0.4071	by_group_JB5_JB6_JB7
	Arachniotus	−0.005	0.008	−0.59	0.5619	main_effect
	Myrmecridium	−0.008	0.011	−0.80	0.4288	main_effect
	Chaetasbolisia	−0.027	0.011	−2.37	0.0251	main_effect
	Trichosporiella	0.012	0.009	1.34	0.1914	main_effect
	Tetracladium	−0.008	0.010	−0.77	0.4484	main_effect
Uncertain	Gliomastix	0.004	0.009	0.48	0.6329	main_effect
	Podila	−0.011	0.020	−0.53	0.5987	main_effect
	Keithomyces	−0.012	0.012	−0.95	0.3486	main_effect
	Fusicolla	0.002	0.009	0.20	0.8463	main_effect
	Paraphaeosphaeria	0.059	0.017	3.37	0.0022	main_effect

Table 26: Summary statistics for each core fungal genus. The table shows the summary statistics for the analysis of the metadata variable and each core fungi (genus 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	Genus	Estimate	SE	t	p-value	Model
Ectomycorrhizal Symbionts	Cortinarius	−0.011	0.003	−3.31	0.0026	main_effect
Fungal Saprotrophs	Gibellulopsis	0.020	0.015	1.34	0.1920	main_effect
	Cladosporium	0.021	0.011	1.81	0.0807	main_effect
	Cheilymenia	0.026	0.017	1.53	0.1374	main_effect
	Thelebolus	−0.002	0.012	−0.15	0.8848	main_effect
	Penicillium	−0.012	0.011	−1.07	0.2959	main_effect
	Preussia	0.003	0.010	0.30	0.7668	main_effect
	Mortierella	−0.004	0.008	−0.47	0.6397	main_effect
	Pseudeurotium	−0.008	0.015	−0.57	0.5755	main_effect
	Podospora	−0.026	0.010	−2.69	0.0119	main_effect
	Cercophora	−0.003	0.005	−0.69	0.4968	main_effect
	Papulaspora	−0.008	0.004	−1.85	0.0747	main_effect
	Aspergillus	−0.008	0.005	−1.53	0.1361	main_effect
	Gliomastix	0.004	0.004	1.08	0.2872	main_effect
	Podila	0.000	0.009	−0.01	0.9942	main_effect
Plant Pathogens	Fusarium	0.008	0.009	0.90	0.3734	main_effect
	Boeremia	0.003	0.009	0.33	0.7444	main_effect
	Dactylonectria	0.004	0.005	0.73	0.4743	main_effect
	Plectosphaerella	0.001	0.008	0.11	0.9100	main_effect
	Pyrenochaetopsis	0.009	0.006	1.54	0.1356	main_effect
	Ophiosphaerella	0.007	0.004	1.67	0.1052	main_effect
	Acremonium	0.003	0.004	0.82	0.4165	main_effect
	Exophiala	0.008	0.007	1.09	0.2841	main_effect
	Pseudoechria	−0.004	0.005	−0.84	0.4065	main_effect
Biocontrol Agents / Beneficial Fungi	Clonostachys	0.007	0.006	1.26	0.2194	main_effect
	Trichoderma	−0.004	0.004	−1.00	0.3264	main_effect
	Mortierella	−0.004	0.008	−0.47	0.6397	main_effect
	Penicillium	−0.012	0.011	−1.07	0.2959	main_effect
	Aspergillus	−0.008	0.005	−1.53	0.1361	main_effect
Unclassified	Solicoccozyma	0.008	0.011	0.73	0.4707	main_effect
	Nadsonia	−0.026	0.022	−1.20	0.2417	main_effect
	Apiotrichum	−0.013	0.010	−1.22	0.2332	main_effect
	Saitozyma	−0.011	0.013	−0.85	0.4031	main_effect
	Triangularia	0.040	0.018	2.20	0.0367	interaction
	Triangularia	−0.001	0.011	−0.05	0.9594	by_group_JB1_JB2
	Triangularia	0.039	0.013	3.01	0.0108	by_group_JB5_JB6_JB7
	Enterocarpus	0.026	0.008	3.34	0.0024	main_effect
	Hymenoscyphus	−0.001	0.013	−0.05	0.9571	main_effect
	Linnemannia	0.045	0.018	2.54	0.0173	interaction
	Linnemannia	−0.011	0.011	−1.03	0.3182	by_group_JB1_JB2
	Linnemannia	0.033	0.011	2.99	0.0114	by_group_JB5_JB6_JB7
	Aaosphaeria	−0.004	0.005	−0.78	0.4420	main_effect
	Dendryphion	−0.005	0.005	−1.00	0.3282	main_effect
	Pleotrichocladium	−0.001	0.005	−0.22	0.8288	main_effect
	Arthrographis	−0.006	0.005	−1.19	0.2441	main_effect
	Atractospora	0.004	0.007	0.52	0.6051	main_effect
	Arachniotus	0.001	0.004	0.40	0.6934	main_effect
	Myrmecridium	−0.004	0.005	−0.76	0.4528	main_effect
	Chaetasbolisia	0.001	0.006	0.17	0.8683	main_effect
	Trichosporiella	0.001	0.004	0.19	0.8480	main_effect
	Tetracladium	0.005	0.004	1.04	0.3090	main_effect
Uncertain	Gliomastix	0.004	0.004	1.08	0.2872	main_effect
	Podila	0.000	0.009	−0.01	0.9942	main_effect
	Keithomyces	0.006	0.005	1.16	0.2570	main_effect
	Fusicolla	−0.001	0.004	−0.13	0.8960	main_effect
	Paraphaeosphaeria	0.009	0.009	1.01	0.3233	main_effect

Table 27: Summary statistics for each core fungal genus. The table shows the summary statistics for the analysis of the metadata variable and each core fungi (genus 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	Genus	Estimate	SE	t	p-value	Model
Ectomycorrhizal Symbionts	Cortinarius	0.002	0.001	2.35	0.0262	main_effect
Fungal Saprotrophs	Gibellulopsis	−0.001	0.003	−0.20	0.8401	main_effect
	Cladosporium	−0.001	0.003	−0.56	0.5778	main_effect
	Cheilymenia	−0.007	0.003	−2.16	0.0392	main_effect
	Thelebolus	−0.005	0.002	−2.51	0.0183	main_effect
	Penicillium	0.003	0.002	1.17	0.2522	main_effect
	Preussia	0.004	0.002	1.94	0.0628	main_effect
	Mortierella	0.000	0.002	0.08	0.9346	main_effect
	Pseudeurotium	0.004	0.003	1.27	0.2161	main_effect
	Podospora	−0.012	0.005	−2.37	0.0253	interaction
	Podospora	0.002	0.003	0.57	0.5804	by_group_JB1_JB2
	Podospora	−0.010	0.004	−2.97	0.0117	by_group_JB5_JB6_JB7
	Cercophora	−0.001	0.001	−0.90	0.3762	main_effect
	Papulaspora	0.000	0.001	0.10	0.9204	main_effect
	Aspergillus	0.001	0.001	1.22	0.2310	main_effect
	Gliomastix	0.001	0.001	1.26	0.2169	main_effect
	Podila	0.000	0.002	−0.03	0.9782	main_effect
Plant Pathogens	Fusarium	0.003	0.002	1.51	0.1420	main_effect
	Boeremia	−0.004	0.002	−2.34	0.0268	main_effect
	Dactylonectria	0.000	0.001	0.05	0.9635	main_effect
	Plectosphaerella	−0.004	0.001	−3.03	0.0052	main_effect
	Pyrenochaetopsis	0.000	0.001	0.11	0.9149	main_effect
	Ophiosphaerella	0.000	0.001	−0.50	0.6228	main_effect
	Acremonium	0.001	0.001	0.59	0.5626	main_effect
	Exophiala	−0.001	0.001	−0.69	0.4972	main_effect
	Pseudoechria	0.001	0.001	0.82	0.4196	main_effect
Biocontrol Agents / Beneficial Fungi	Clonostachys	0.007	0.002	2.91	0.0074	interaction
	Clonostachys	0.000	0.001	−0.13	0.9007	by_group_JB1_JB2
	Clonostachys	0.007	0.002	3.34	0.0058	by_group_JB5_JB6_JB7
	Trichoderma	0.002	0.001	2.27	0.0314	main_effect
	Mortierella	0.000	0.002	0.08	0.9346	main_effect
	Penicillium	0.003	0.002	1.17	0.2522	main_effect
	Aspergillus	0.001	0.001	1.22	0.2310	main_effect
Unclassified	Solicoccozyma	−0.001	0.002	−0.50	0.6186	main_effect
	Nadsonia	−0.007	0.004	−1.65	0.1104	main_effect
	Apiotrichum	0.002	0.002	1.04	0.3061	main_effect
	Saitozyma	0.004	0.003	1.36	0.1837	main_effect
	Triangularia	−0.003	0.002	−1.67	0.1061	main_effect
	Enterocarpus	−0.003	0.002	−1.55	0.1313	main_effect
	Hymenoscyphus	0.000	0.003	0.17	0.8630	main_effect
	Linnemannia	−0.002	0.002	−1.16	0.2577	main_effect
	Aaosphaeria	−0.001	0.001	−0.46	0.6473	main_effect
	Dendryphion	−0.003	0.001	−2.91	0.0071	main_effect
	Pleotrichocladium	0.000	0.001	0.50	0.6209	main_effect
	Arthrographis	−0.002	0.001	−1.50	0.1452	main_effect
	Atractospora	−0.002	0.002	−1.21	0.2347	main_effect
	Arachniotus	0.000	0.001	−0.57	0.5741	main_effect
	Myrmecridium	−0.002	0.001	−1.73	0.0955	main_effect
	Chaetasbolisia	−0.001	0.001	−1.03	0.3136	main_effect
	Trichosporiella	0.000	0.001	0.29	0.7760	main_effect
	Tetracladium	−0.001	0.001	−1.34	0.1921	main_effect
Uncertain	Gliomastix	0.001	0.001	1.26	0.2169	main_effect
	Podila	0.000	0.002	−0.03	0.9782	main_effect
	Keithomyces	0.000	0.001	−0.30	0.7632	main_effect
	Fusicolla	0.000	0.001	0.07	0.9475	main_effect
	Paraphaeosphaeria	−0.001	0.002	−0.47	0.6427	main_effect

Table 28: Summary statistics for each core fungal genus. The table shows the summary statistics for the analysis of the metadata variable and each core fungi (genus 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	Genus	Estimate	SE	t	p-value	Model
Ectomycorrhizal Symbionts	Cortinarius	−0.021	0.009	−2.40	0.0231	main_effect
Fungal Saprotrophs	Gibellulopsis	0.021	0.037	0.56	0.5776	main_effect
	Cladosporium	0.017	0.029	0.59	0.5569	main_effect
	Cheilymenia	0.111	0.037	3.02	0.0053	main_effect
	Thelebolus	0.044	0.027	1.66	0.1082	main_effect
	Penicillium	0.116	0.053	2.21	0.0360	interaction
	Penicillium	−0.101	0.046	−2.18	0.0472	by_group_JB1_JB2
	Penicillium	0.015	0.026	0.59	0.5646	by_group_JB5_JB6_JB7
	Preussia	0.013	0.023	0.55	0.5849	main_effect
	Mortierella	−0.009	0.018	−0.49	0.6265	main_effect
	Pseudeurotium	0.181	0.068	2.68	0.0126	interaction
	Pseudeurotium	−0.166	0.051	−3.24	0.0059	by_group_JB1_JB2
	Pseudeurotium	0.015	0.044	0.34	0.7406	by_group_JB5_JB6_JB7
	Podospora	−0.007	0.027	−0.26	0.7949	main_effect
	Cercophora	0.023	0.011	2.08	0.0466	main_effect
	Papulaspora	−0.029	0.010	−2.96	0.0062	main_effect
	Aspergillus	−0.022	0.012	−1.75	0.0918	main_effect
	Gliomastix	0.003	0.010	0.26	0.7990	main_effect
	Podila	0.063	0.018	3.47	0.0017	main_effect
Plant Pathogens	Fusarium	−0.028	0.022	−1.26	0.2175	main_effect
	Boeremia	0.016	0.023	0.70	0.4892	main_effect
	Dactylonectria	0.029	0.012	2.44	0.0213	main_effect
	Plectosphaerella	0.006	0.019	0.31	0.7566	main_effect
	Pyrenochaetopsis	0.009	0.015	0.59	0.5626	main_effect
	Ophiosphaerella	0.010	0.011	0.94	0.3531	main_effect
	Acremonium	0.002	0.010	0.23	0.8172	main_effect
	Exophiala	−0.009	0.017	−0.51	0.6124	main_effect
	Pseudoechria	0.006	0.012	0.53	0.6033	main_effect
Biocontrol Agents / Beneficial Fungi	Clonostachys	0.011	0.014	0.74	0.4629	main_effect
	Trichoderma	−0.006	0.009	−0.71	0.4825	main_effect
	Mortierella	−0.009	0.018	−0.49	0.6265	main_effect
	Penicillium	0.116	0.053	2.21	0.0360	interaction
	Penicillium	−0.101	0.046	−2.18	0.0472	by_group_JB1_JB2
	Penicillium	0.015	0.026	0.59	0.5646	by_group_JB5_JB6_JB7
	Aspergillus	−0.022	0.012	−1.75	0.0918	main_effect
Unclassified	Solicoccozyma	0.039	0.026	1.51	0.1422	main_effect
	Nadsonia	−0.022	0.054	−0.40	0.6887	main_effect
	Apiotrichum	0.022	0.025	0.84	0.4056	main_effect
	Saitozyma	−0.080	0.027	−2.93	0.0066	main_effect
	Triangularia	0.051	0.016	3.10	0.0044	main_effect
	Enterocarpus	0.050	0.020	2.47	0.0198	main_effect
	Hymenoscyphus	−0.018	0.032	−0.56	0.5814	main_effect
	Linnemannia	0.035	0.017	1.99	0.0564	main_effect
	Aaosphaeria	0.015	0.013	1.19	0.2450	main_effect
	Dendryphion	−0.004	0.012	−0.34	0.7380	main_effect
	Pleotrichocladium	−0.058	0.020	−2.84	0.0086	interaction
	Pleotrichocladium	0.030	0.013	2.28	0.0390	by_group_JB1_JB2
	Pleotrichocladium	−0.027	0.015	−1.81	0.0953	by_group_JB5_JB6_JB7
	Arthrographis	0.010	0.012	0.84	0.4093	main_effect
	Atractospora	−0.004	0.018	−0.21	0.8360	main_effect
	Arachniotus	0.005	0.009	0.55	0.5857	main_effect
	Myrmecridium	0.001	0.012	0.10	0.9229	main_effect
	Chaetasbolisia	0.041	0.011	3.70	0.0009	main_effect
	Trichosporiella	0.042	0.020	2.07	0.0485	interaction
	Trichosporiella	−0.026	0.016	−1.60	0.1321	by_group_JB1_JB2
	Trichosporiella	0.016	0.013	1.31	0.2161	by_group_JB5_JB6_JB7
	Tetracladium	0.025	0.010	2.55	0.0165	main_effect
Uncertain	Gliomastix	0.003	0.010	0.26	0.7990	main_effect
	Podila	0.063	0.018	3.47	0.0017	main_effect
	Keithomyces	−0.004	0.013	−0.29	0.7735	main_effect
	Fusicolla	−0.005	0.010	−0.53	0.6019	main_effect
	Paraphaeosphaeria	−0.034	0.022	−1.56	0.1291	main_effect

Table 29: Summary statistics for each core fungal genus. The table shows the summary statistics for the analysis of the metadata variable and each core fungi (genus 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	Genus	Estimate	SE	t	p-value	Model
Ectomycorrhizal Symbionts	Cortinarius	0.002	0.003	0.81	0.4240	main_effect
Fungal Saprotrophs	Gibellulopsis	−0.024	0.010	−2.33	0.0272	main_effect
	Cladosporium	0.006	0.009	0.74	0.4675	main_effect
	Cheilymenia	−0.003	0.013	−0.21	0.8347	main_effect
	Thelebolus	0.006	0.008	0.77	0.4487	main_effect
	Penicillium	0.000	0.008	−0.03	0.9771	main_effect
	Preussia	−0.019	0.006	−3.24	0.0031	main_effect
	Mortierella	0.007	0.005	1.24	0.2263	main_effect
	Pseudeurotium	−0.009	0.011	−0.79	0.4366	main_effect
	Podospora	0.012	0.008	1.52	0.1409	main_effect
	Cercophora	0.005	0.004	1.30	0.2031	main_effect
	Papulaspora	0.002	0.003	0.70	0.4875	main_effect
	Aspergillus	0.003	0.004	0.71	0.4826	main_effect
	Gliomastix	0.002	0.003	0.70	0.4893	main_effect
	Podila	−0.003	0.006	−0.50	0.6241	main_effect
Plant Pathogens	Fusarium	0.007	0.007	1.13	0.2700	main_effect
	Boeremia	0.003	0.007	0.46	0.6463	main_effect
	Dactylonectria	−0.007	0.004	−1.83	0.0786	main_effect
	Plectosphaerella	0.009	0.006	1.54	0.1338	main_effect
	Pyrenochaetopsis	−0.002	0.004	−0.53	0.6033	main_effect
	Ophiosphaerella	−0.002	0.003	−0.69	0.4952	main_effect
	Acremonium	−0.004	0.003	−1.20	0.2402	main_effect
	Exophiala	0.005	0.005	0.93	0.3628	main_effect
	Pseudoechria	−0.002	0.003	−0.72	0.4772	main_effect
Biocontrol Agents / Beneficial Fungi	Clonostachys	−0.007	0.004	−1.57	0.1278	main_effect
	Trichoderma	0.001	0.003	0.42	0.6767	main_effect
	Mortierella	0.007	0.005	1.24	0.2263	main_effect
	Penicillium	0.000	0.008	−0.03	0.9771	main_effect
	Aspergillus	0.003	0.004	0.71	0.4826	main_effect
Unclassified	Solicoccozyma	0.003	0.008	0.37	0.7135	main_effect
	Nadsonia	0.037	0.015	2.52	0.0178	main_effect
	Apiotrichum	−0.010	0.008	−1.29	0.2059	main_effect
	Saitozyma	−0.012	0.009	−1.31	0.1997	main_effect
	Triangularia	0.002	0.006	0.36	0.7179	main_effect
	Enterocarpus	0.003	0.007	0.41	0.6831	main_effect
	Hymenoscyphus	−0.006	0.010	−0.58	0.5662	main_effect
	Linnemannia	0.009	0.005	1.62	0.1170	main_effect
	Aaosphaeria	0.001	0.004	0.24	0.8103	main_effect
	Dendryphion	0.006	0.003	1.61	0.1189	main_effect
	Pleotrichocladium	−0.009	0.003	−3.34	0.0024	main_effect
	Arthrographis	0.009	0.003	2.60	0.0146	main_effect
	Atractospora	−0.005	0.005	−0.91	0.3686	main_effect
	Arachniotus	0.005	0.002	2.17	0.0386	main_effect
	Myrmecridium	0.006	0.003	1.73	0.0939	main_effect
	Chaetasbolisia	0.006	0.004	1.65	0.1110	main_effect
	Trichosporiella	−0.005	0.003	−1.65	0.1105	main_effect
	Tetracladium	0.001	0.003	0.15	0.8786	main_effect
Uncertain	Gliomastix	0.002	0.003	0.70	0.4893	main_effect
	Podila	−0.003	0.006	−0.50	0.6241	main_effect
	Keithomyces	−0.007	0.004	−1.94	0.0619	main_effect
	Fusicolla	0.015	0.006	2.67	0.0128	interaction
	Fusicolla	−0.008	0.005	−1.64	0.1239	by_group_JB1_JB2
	Fusicolla	0.007	0.003	2.69	0.0197	by_group_JB5_JB6_JB7
	Paraphaeosphaeria	−0.001	0.007	−0.18	0.8620	main_effect

Table 30: Summary statistics for each core fungal genus. The table shows the summary statistics for the analysis of the metadata variable and each core fungi (genus 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	Genus	Estimate	SE	t	p-value	Model
Ectomycorrhizal Symbionts	Cortinarius	−0.001	0.001	−1.71	0.0992	main_effect
Fungal Saprotrophs	Gibellulopsis	0.005	0.003	1.79	0.0846	main_effect
	Cladosporium	0.005	0.002	2.18	0.0382	main_effect
	Cheilymenia	−0.002	0.003	−0.66	0.5142	main_effect
	Thelebolus	0.001	0.002	0.38	0.7085	main_effect
	Penicillium	−0.004	0.002	−1.88	0.0703	main_effect
	Preussia	0.001	0.002	0.63	0.5328	main_effect
	Mortierella	0.001	0.002	0.51	0.6123	main_effect
	Pseudeurotium	−0.001	0.003	−0.28	0.7800	main_effect
	Podospora	−0.001	0.002	−0.41	0.6822	main_effect
	Cercophora	0.001	0.001	1.29	0.2075	main_effect
	Papulaspora	0.000	0.001	0.02	0.9867	main_effect
	Aspergillus	−0.001	0.001	−0.79	0.4355	main_effect
	Gliomastix	0.000	0.001	−0.18	0.8566	main_effect
	Podila	0.002	0.002	1.43	0.1640	main_effect
Plant Pathogens	Fusarium	0.002	0.002	1.32	0.1983	main_effect
	Boeremia	0.008	0.004	2.18	0.0389	interaction
	Boeremia	−0.003	0.002	−1.59	0.1335	by_group_JB1_JB2
	Boeremia	0.005	0.003	1.50	0.1599	by_group_JB5_JB6_JB7
	Dactylonectria	−0.001	0.001	−0.75	0.4602	main_effect
	Plectosphaerella	0.000	0.002	−0.13	0.8968	main_effect
	Pyrenochaetopsis	0.001	0.001	0.73	0.4691	main_effect
	Ophiosphaerella	0.001	0.001	1.18	0.2476	main_effect
	Acremonium	−0.001	0.001	−1.20	0.2383	main_effect
	Exophiala	−0.002	0.001	−1.19	0.2441	main_effect
	Pseudoechria	0.001	0.001	1.14	0.2629	main_effect
Biocontrol Agents / Beneficial Fungi	Clonostachys	−0.001	0.001	−0.52	0.6084	main_effect
	Trichoderma	−0.001	0.001	−2.14	0.0413	main_effect
	Mortierella	0.001	0.002	0.51	0.6123	main_effect
	Penicillium	−0.004	0.002	−1.88	0.0703	main_effect
	Aspergillus	−0.001	0.001	−0.79	0.4355	main_effect
Unclassified	Solicoccozyma	0.002	0.002	1.00	0.3279	main_effect
	Nadsonia	−0.007	0.004	−1.72	0.0971	main_effect
	Apiotrichum	0.003	0.002	1.43	0.1650	main_effect
	Saitozyma	0.014	0.005	2.77	0.0103	interaction
	Saitozyma	−0.004	0.003	−1.37	0.1909	by_group_JB1_JB2
	Saitozyma	0.010	0.004	2.28	0.0415	by_group_JB5_JB6_JB7
	Triangularia	−0.010	0.003	−3.60	0.0013	interaction
	Triangularia	0.005	0.002	2.60	0.0209	by_group_JB1_JB2
	Triangularia	−0.005	0.002	−2.50	0.0281	by_group_JB5_JB6_JB7
	Enterocarpus	0.002	0.002	1.29	0.2092	main_effect
	Hymenoscyphus	0.000	0.003	−0.04	0.9676	main_effect
	Linnemannia	−0.001	0.002	−0.51	0.6169	main_effect
	Aaosphaeria	−0.005	0.002	−2.81	0.0094	interaction
	Aaosphaeria	0.005	0.001	3.51	0.0035	by_group_JB1_JB2
	Aaosphaeria	−0.001	0.001	−0.43	0.6716	by_group_JB5_JB6_JB7
	Dendryphion	0.005	0.002	2.39	0.0244	interaction
	Dendryphion	−0.002	0.001	−1.73	0.1055	by_group_JB1_JB2
	Dendryphion	0.002	0.001	1.74	0.1066	by_group_JB5_JB6_JB7
	Pleotrichocladium	0.001	0.001	1.50	0.1441	main_effect
	Arthrographis	0.001	0.001	0.59	0.5619	main_effect
	Atractospora	−0.001	0.001	−0.96	0.3449	main_effect
	Arachniotus	−0.001	0.001	−0.83	0.4142	main_effect
	Myrmecridium	0.000	0.001	−0.17	0.8676	main_effect
	Chaetasbolisia	0.001	0.001	1.35	0.1876	main_effect
	Trichosporiella	0.000	0.001	0.38	0.7084	main_effect
	Tetracladium	0.001	0.001	1.24	0.2254	main_effect
Uncertain	Gliomastix	0.000	0.001	−0.18	0.8566	main_effect
	Podila	0.002	0.002	1.43	0.1640	main_effect
	Keithomyces	−0.002	0.001	−1.79	0.0837	main_effect
	Fusicolla	0.001	0.001	0.95	0.3503	main_effect
	Paraphaeosphaeria	0.000	0.002	0.24	0.8131	main_effect

Table 31: Summary statistics for each core fungal genus. The table shows the summary statistics for the analysis of the metadata variable and each core fungi (genus 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	Genus	Estimate	SE	t	p-value	Model
Ectomycorrhizal Symbionts	Cortinarius	−0.001	0.001	−0.58	0.5687	main_effect
Fungal Saprotrophs	Gibellulopsis	0.000	0.005	0.02	0.9876	main_effect
	Cladosporium	0.002	0.004	0.58	0.5642	main_effect
	Cheilymenia	0.010	0.006	1.74	0.0935	main_effect
	Thelebolus	0.001	0.004	0.20	0.8401	main_effect
	Penicillium	−0.001	0.004	−0.31	0.7555	main_effect
	Preussia	0.007	0.003	2.39	0.0239	main_effect
	Mortierella	−0.001	0.003	−0.43	0.6683	main_effect
	Pseudeurotium	−0.001	0.005	−0.24	0.8114	main_effect
	Podospora	0.000	0.004	0.05	0.9643	main_effect
	Cercophora	−0.001	0.002	−0.35	0.7288	main_effect
	Papulaspora	−0.003	0.001	−2.23	0.0337	main_effect
	Aspergillus	0.001	0.002	0.35	0.7264	main_effect
	Gliomastix	−0.001	0.001	−0.82	0.4191	main_effect
	Podila	0.004	0.003	1.28	0.2100	main_effect
Plant Pathogens	Fusarium	0.001	0.003	0.29	0.7753	main_effect
	Boeremia	−0.005	0.003	−1.62	0.1168	main_effect
	Dactylonectria	0.003	0.002	1.52	0.1391	main_effect
	Plectosphaerella	−0.001	0.003	−0.50	0.6244	main_effect
	Pyrenochaetopsis	0.000	0.002	0.20	0.8437	main_effect
	Ophiosphaerella	0.000	0.002	−0.20	0.8414	main_effect
	Acremonium	0.001	0.001	0.70	0.4911	main_effect
	Exophiala	−0.004	0.002	−1.80	0.0823	main_effect
	Pseudoechria	0.002	0.002	1.24	0.2256	main_effect
Biocontrol Agents / Beneficial Fungi	Clonostachys	0.003	0.002	1.41	0.1710	main_effect
	Trichoderma	0.000	0.001	−0.08	0.9348	main_effect
	Mortierella	−0.001	0.003	−0.43	0.6683	main_effect
	Penicillium	−0.001	0.004	−0.31	0.7555	main_effect
	Aspergillus	0.001	0.002	0.35	0.7264	main_effect
Unclassified	Solicoccozyma	0.004	0.004	1.17	0.2520	main_effect
	Nadsonia	−0.006	0.007	−0.79	0.4378	main_effect
	Apiotrichum	0.005	0.003	1.43	0.1643	main_effect
	Saitozyma	−0.006	0.004	−1.47	0.1529	main_effect
	Triangularia	0.004	0.003	1.51	0.1425	main_effect
	Enterocarpus	0.002	0.003	0.79	0.4350	main_effect
	Hymenoscyphus	−0.004	0.004	−0.92	0.3664	main_effect
	Linnemannia	0.001	0.003	0.34	0.7364	main_effect
	Aaosphaeria	0.000	0.002	−0.07	0.9415	main_effect
	Dendryphion	−0.004	0.002	−2.46	0.0204	main_effect
	Pleotrichocladium	0.001	0.002	0.92	0.3676	main_effect
	Arthrographis	0.000	0.002	−0.15	0.8815	main_effect
	Atractospora	−0.001	0.003	−0.30	0.7671	main_effect
	Arachniotus	0.001	0.001	0.52	0.6067	main_effect
	Myrmecridium	−0.001	0.002	−0.65	0.5221	main_effect
	Chaetasbolisia	0.003	0.002	1.78	0.0856	main_effect
	Trichosporiella	−0.001	0.001	−0.60	0.5519	main_effect
	Tetracladium	−0.001	0.002	−0.80	0.4323	main_effect
Uncertain	Gliomastix	−0.001	0.001	−0.82	0.4191	main_effect
	Podila	0.004	0.003	1.28	0.2100	main_effect
	Keithomyces	0.000	0.002	−0.16	0.8723	main_effect
	Fusicolla	−0.002	0.001	−1.15	0.2584	main_effect
	Paraphaeosphaeria	−0.004	0.003	−1.33	0.1935	main_effect

Table 32: Summary statistics for each core fungal genus. The table shows the summary statistics for the analysis of the metadata variable and each core fungi (genus 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	Genus	Estimate	SE	t	p-value	Model
Ectomycorrhizal Symbionts	Cortinarius	0.007	0.003	2.05	0.0498	main_effect
Fungal Saprotrophs	Gibellulopsis	−0.005	0.014	−0.39	0.6990	main_effect
	Cladosporium	−0.010	0.011	−0.93	0.3628	main_effect
	Cheilymenia	−0.022	0.015	−1.46	0.1565	main_effect
	Thelebolus	−0.010	0.010	−0.96	0.3455	main_effect
	Penicillium	0.006	0.010	0.64	0.5299	main_effect
	Preussia	−0.006	0.009	−0.65	0.5190	main_effect
	Mortierella	0.007	0.007	1.07	0.2948	main_effect
	Pseudeurotium	0.017	0.013	1.35	0.1867	main_effect
	Podospora	0.005	0.010	0.51	0.6116	main_effect
	Cercophora	−0.002	0.004	−0.35	0.7259	main_effect
	Papulaspora	0.003	0.004	0.79	0.4342	main_effect
	Aspergillus	0.000	0.005	0.08	0.9354	main_effect
	Gliomastix	0.000	0.004	−0.10	0.9189	main_effect
	Podila	0.001	0.008	0.18	0.8552	main_effect
Plant Pathogens	Fusarium	−0.009	0.008	−1.13	0.2680	main_effect
	Boeremia	−0.011	0.008	−1.39	0.1749	main_effect
	Dactylonectria	0.003	0.005	0.61	0.5461	main_effect
	Plectosphaerella	0.001	0.007	0.18	0.8586	main_effect
	Pyrenochaetopsis	−0.011	0.005	−2.09	0.0457	main_effect
	Ophiosphaerella	−0.005	0.004	−1.25	0.2206	main_effect
	Acremonium	0.003	0.004	0.91	0.3731	main_effect
	Exophiala	−0.007	0.006	−1.19	0.2444	main_effect
	Pseudoechria	−0.001	0.004	−0.34	0.7349	main_effect
Biocontrol Agents / Beneficial Fungi	Clonostachys	−0.002	0.005	−0.35	0.7281	main_effect
	Trichoderma	0.001	0.003	0.20	0.8393	main_effect
	Mortierella	0.007	0.007	1.07	0.2948	main_effect
	Penicillium	0.006	0.010	0.64	0.5299	main_effect
	Aspergillus	0.000	0.005	0.08	0.9354	main_effect
Unclassified	Solicoccozyma	0.001	0.010	0.06	0.9503	main_effect
	Nadsonia	0.006	0.020	0.30	0.7685	main_effect
	Apiotrichum	−0.005	0.009	−0.49	0.6310	main_effect
	Saitozyma	0.004	0.011	0.35	0.7309	main_effect
	Triangularia	−0.008	0.007	−1.09	0.2838	main_effect
	Enterocarpus	−0.004	0.008	−0.48	0.6318	main_effect
	Hymenoscyphus	−0.007	0.012	−0.56	0.5821	main_effect
	Linnemannia	−0.002	0.007	−0.27	0.7913	main_effect
	Aaosphaeria	−0.008	0.005	−1.67	0.1052	main_effect
	Dendryphion	0.001	0.004	0.27	0.7929	main_effect
	Pleotrichocladium	−0.006	0.004	−1.40	0.1714	main_effect
	Arthrographis	−0.002	0.005	−0.44	0.6641	main_effect
	Atractospora	−0.006	0.007	−0.87	0.3893	main_effect
	Arachniotus	0.017	0.007	2.49	0.0195	interaction
	Arachniotus	−0.008	0.003	−2.89	0.0119	by_group_JB1_JB2
	Arachniotus	0.009	0.007	1.27	0.2280	by_group_JB5_JB6_JB7
	Myrmecridium	−0.007	0.004	−1.75	0.0909	main_effect
	Chaetasbolisia	−0.001	0.005	−0.21	0.8388	main_effect
	Trichosporiella	0.006	0.004	1.55	0.1321	main_effect
	Tetracladium	−0.002	0.004	−0.57	0.5744	main_effect
Uncertain	Gliomastix	0.000	0.004	−0.10	0.9189	main_effect
	Podila	0.001	0.008	0.18	0.8552	main_effect
	Keithomyces	−0.002	0.005	−0.32	0.7550	main_effect
	Fusicolla	0.001	0.004	0.25	0.8032	main_effect
	Paraphaeosphaeria	0.000	0.008	−0.04	0.9699	main_effect

Table 33: Summary statistics for each core fungal genus. The table shows the summary statistics for the analysis of the metadata variable and each core fungi (genus 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	Genus	Estimate	SE	t	p-value	Model
Ectomycorrhizal Symbionts	Cortinarius	0.002	0.001	1.33	0.1932	main_effect
Fungal Saprotrophs	Gibellulopsis	−0.006	0.006	−1.08	0.2887	main_effect
	Cladosporium	−0.003	0.004	−0.63	0.5346	main_effect
	Cheilymenia	0.002	0.006	0.31	0.7571	main_effect
	Thelebolus	0.000	0.004	−0.10	0.9180	main_effect
	Penicillium	0.007	0.004	1.75	0.0903	main_effect
	Preussia	0.002	0.004	0.65	0.5186	main_effect
	Mortierella	−0.001	0.003	−0.38	0.7087	main_effect
	Pseudeurotium	0.000	0.005	−0.06	0.9519	main_effect
	Podospora	0.005	0.004	1.35	0.1864	main_effect
	Cercophora	−0.002	0.002	−0.93	0.3598	main_effect
	Papulaspora	−0.002	0.002	−1.51	0.1432	main_effect
	Aspergillus	0.004	0.002	2.13	0.0422	main_effect
	Gliomastix	−0.002	0.001	−1.19	0.2433	main_effect
	Podila	−0.001	0.003	−0.29	0.7751	main_effect
Plant Pathogens	Fusarium	−0.003	0.003	−0.84	0.4053	main_effect
	Boeremia	−0.004	0.003	−1.03	0.3118	main_effect
	Dactylonectria	0.002	0.002	1.29	0.2059	main_effect
	Plectosphaerella	0.001	0.003	0.25	0.8020	main_effect
	Pyrenochaetopsis	−0.002	0.002	−0.83	0.4117	main_effect
	Ophiosphaerella	0.000	0.002	−0.15	0.8845	main_effect
	Acremonium	0.018	0.009	2.07	0.0484	interaction
	Acremonium	−0.001	0.002	−0.44	0.6652	by_group_JB1_JB2
	Acremonium	0.017	0.009	2.00	0.0691	by_group_JB5_JB6_JB7
	Exophiala	0.000	0.003	0.16	0.8730	main_effect
	Pseudoechria	0.000	0.002	0.11	0.9168	main_effect
Biocontrol Agents / Beneficial Fungi	Clonostachys	0.000	0.002	0.22	0.8266	main_effect
	Trichoderma	0.000	0.001	−0.07	0.9485	main_effect
	Mortierella	−0.001	0.003	−0.38	0.7087	main_effect
	Penicillium	0.007	0.004	1.75	0.0903	main_effect
	Aspergillus	0.004	0.002	2.13	0.0422	main_effect
Unclassified	Solicoccozyma	−0.004	0.004	−0.99	0.3308	main_effect
	Nadsonia	0.010	0.008	1.20	0.2415	main_effect
	Apiotrichum	−0.002	0.004	−0.39	0.6964	main_effect
	Saitozyma	−0.001	0.005	−0.23	0.8196	main_effect
	Triangularia	−0.001	0.003	−0.19	0.8504	main_effect
	Enterocarpus	−0.004	0.003	−1.25	0.2223	main_effect
	Hymenoscyphus	−0.002	0.005	−0.37	0.7165	main_effect
	Linnemannia	0.001	0.003	0.37	0.7136	main_effect
	Aaosphaeria	−0.001	0.002	−0.59	0.5579	main_effect
	Dendryphion	0.000	0.002	0.22	0.8300	main_effect
	Pleotrichocladium	0.000	0.002	−0.25	0.8016	main_effect
	Arthrographis	−0.024	0.010	−2.43	0.0226	interaction
	Arthrographis	0.001	0.002	0.69	0.4997	by_group_JB1_JB2
	Arthrographis	−0.023	0.008	−2.72	0.0187	by_group_JB5_JB6_JB7
	Atractospora	0.002	0.003	0.72	0.4773	main_effect
	Arachniotus	0.001	0.001	0.43	0.6712	main_effect
	Myrmecridium	0.001	0.002	0.59	0.5575	main_effect
	Chaetasbolisia	−0.035	0.010	−3.52	0.0016	interaction
	Chaetasbolisia	0.004	0.002	1.87	0.0832	by_group_JB1_JB2
	Chaetasbolisia	−0.032	0.009	−3.53	0.0042	by_group_JB5_JB6_JB7
	Trichosporiella	−0.001	0.002	−0.46	0.6519	main_effect
	Tetracladium	−0.026	0.009	−2.99	0.0061	interaction
	Tetracladium	0.001	0.001	0.71	0.4904	by_group_JB1_JB2
	Tetracladium	−0.025	0.010	−2.55	0.0253	by_group_JB5_JB6_JB7
Uncertain	Gliomastix	−0.002	0.001	−1.19	0.2433	main_effect
	Podila	−0.001	0.003	−0.29	0.7751	main_effect
	Keithomyces	0.026	0.011	2.24	0.0339	interaction
	Keithomyces	−0.002	0.003	−0.82	0.4245	by_group_JB1_JB2
	Keithomyces	0.023	0.008	3.11	0.0090	by_group_JB5_JB6_JB7
	Fusicolla	−0.018	0.008	−2.17	0.0395	interaction
	Fusicolla	0.000	0.002	−0.12	0.9082	by_group_JB1_JB2
	Fusicolla	−0.018	0.004	−4.42	0.0008	by_group_JB5_JB6_JB7
	Paraphaeosphaeria	−0.003	0.003	−0.76	0.4557	main_effect

Table 34: Summary statistics for each core fungal genus. The table shows the summary statistics for the analysis of the metadata variable and each core fungi (genus 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	Genus	Estimate	SE	t	p-value	Model
Ectomycorrhizal Symbionts	Cortinarius	−0.002	0.001	−2.27	0.0308	main_effect
Fungal Saprotrophs	Gibellulopsis	0.012	0.003	4.43	0.0001	main_effect
	Cladosporium	−0.027	0.012	−2.20	0.0370	interaction
	Cladosporium	0.021	0.011	1.90	0.0785	by_group_JB1_JB2
	Cladosporium	−0.006	0.005	−1.21	0.2483	by_group_JB5_JB6_JB7
	Cheilymenia	0.004	0.004	0.85	0.4039	main_effect
	Thelebolus	−0.002	0.003	−0.87	0.3920	main_effect
	Penicillium	−0.006	0.002	−2.29	0.0297	main_effect
	Preussia	0.004	0.002	1.91	0.0669	main_effect
	Mortierella	−0.002	0.002	−1.30	0.2035	main_effect
	Pseudeurotium	0.002	0.004	0.69	0.4930	main_effect
	Podospora	−0.004	0.003	−1.76	0.0898	main_effect
	Cercophora	−0.001	0.001	−0.96	0.3459	main_effect
	Papulaspora	0.000	0.001	−0.29	0.7724	main_effect
	Aspergillus	−0.003	0.001	−2.87	0.0077	main_effect
	Gliomastix	0.000	0.001	−0.31	0.7605	main_effect
	Podila	0.003	0.002	1.52	0.1408	main_effect
Plant Pathogens	Fusarium	−0.001	0.002	−0.59	0.5591	main_effect
	Boeremia	0.001	0.002	0.61	0.5490	main_effect
	Dactylonectria	0.002	0.001	1.20	0.2405	main_effect
	Plectosphaerella	0.001	0.002	0.37	0.7119	main_effect
	Pyrenochaetopsis	0.002	0.001	1.58	0.1256	main_effect
	Ophiosphaerella	0.002	0.001	2.36	0.0254	main_effect
	Acremonium	0.001	0.001	1.15	0.2609	main_effect
	Exophiala	−0.003	0.002	−1.57	0.1283	main_effect
	Pseudoechria	0.003	0.001	2.47	0.0198	main_effect
Biocontrol Agents / Beneficial Fungi	Clonostachys	0.003	0.001	2.08	0.0473	main_effect
	Trichoderma	−0.001	0.001	−1.56	0.1292	main_effect
	Mortierella	−0.002	0.002	−1.30	0.2035	main_effect
	Penicillium	−0.006	0.002	−2.29	0.0297	main_effect
	Aspergillus	−0.003	0.001	−2.87	0.0077	main_effect
Unclassified	Solicoccozyma	0.004	0.003	1.43	0.1629	main_effect
	Nadsonia	−0.011	0.005	−2.34	0.0267	main_effect
	Apiotrichum	0.005	0.002	1.97	0.0582	main_effect
	Saitozyma	0.005	0.003	1.69	0.1022	main_effect
	Triangularia	−0.019	0.008	−2.49	0.0194	interaction
	Triangularia	0.013	0.007	1.89	0.0802	by_group_JB1_JB2
	Triangularia	−0.006	0.003	−1.94	0.0756	by_group_JB5_JB6_JB7
	Enterocarpus	0.002	0.002	0.91	0.3694	main_effect
	Hymenoscyphus	0.000	0.003	0.06	0.9560	main_effect
	Linnemannia	−0.004	0.002	−2.42	0.0222	main_effect
	Aaosphaeria	−0.001	0.001	−1.07	0.2953	main_effect
	Dendryphion	−0.001	0.001	−0.86	0.3956	main_effect
	Pleotrichocladium	0.003	0.001	3.87	0.0006	main_effect
	Arthrographis	−0.002	0.001	−1.49	0.1477	main_effect
	Atractospora	0.000	0.002	0.22	0.8277	main_effect
	Arachniotus	−0.001	0.001	−1.04	0.3078	main_effect
	Myrmecridium	0.000	0.001	−0.17	0.8694	main_effect
	Chaetasbolisia	−0.013	0.006	−2.20	0.0372	interaction
	Chaetasbolisia	0.011	0.005	2.31	0.0369	by_group_JB1_JB2
	Chaetasbolisia	−0.002	0.002	−0.70	0.5002	by_group_JB5_JB6_JB7
	Trichosporiella	0.002	0.001	1.63	0.1152	main_effect
	Tetracladium	0.001	0.001	1.22	0.2342	main_effect
Uncertain	Gliomastix	0.000	0.001	−0.31	0.7605	main_effect
	Podila	0.003	0.002	1.52	0.1408	main_effect
	Keithomyces	0.000	0.001	−0.15	0.8856	main_effect
	Fusicolla	−0.001	0.001	−1.19	0.2427	main_effect
	Paraphaeosphaeria	0.002	0.002	1.05	0.3008	main_effect

Table 35: Summary statistics for each core fungal genus. The table shows the summary statistics for the analysis of the metadata variable and each core fungi (genus 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	Genus	Estimate	SE	t	p-value	Model
Ectomycorrhizal Symbionts	Cortinarius	0.081	0.071	1.14	0.2660	main_effect
Fungal Saprotrophs	Gibellulopsis	−0.150	0.277	−0.54	0.5917	main_effect
	Cladosporium	−0.253	0.213	−1.19	0.2449	main_effect
	Cheilymenia	0.151	0.316	0.48	0.6355	main_effect
	Thelebolus	−0.071	0.209	−0.34	0.7361	main_effect
	Penicillium	0.167	0.201	0.83	0.4143	main_effect
	Preussia	0.318	0.164	1.94	0.0630	main_effect
	Mortierella	−0.070	0.138	−0.51	0.6145	main_effect
	Pseudeurotium	0.082	0.270	0.31	0.7626	main_effect
	Podospora	0.218	0.196	1.11	0.2748	main_effect
	Cercophora	−0.081	0.089	−0.92	0.3679	main_effect
	Papulaspora	−0.180	0.078	−2.30	0.0288	main_effect
	Aspergillus	0.203	0.089	2.28	0.0307	main_effect
	Gliomastix	−0.040	0.074	−0.54	0.5947	main_effect
	Podila	0.045	0.161	0.28	0.7813	main_effect
Plant Pathogens	Fusarium	−0.154	0.165	−0.93	0.3600	main_effect
	Boeremia	−0.206	0.168	−1.23	0.2295	main_effect
	Dactylonectria	0.151	0.094	1.61	0.1192	main_effect
	Plectosphaerella	−0.024	0.143	−0.17	0.8689	main_effect
	Pyrenochaetopsis	−0.013	0.110	−0.12	0.9039	main_effect
	Ophiosphaerella	−0.041	0.080	−0.51	0.6114	main_effect
	Acremonium	0.380	0.172	2.20	0.0366	interaction
	Acremonium	−0.037	0.081	−0.46	0.6538	by_group_JB1_JB2
	Acremonium	0.343	0.152	2.26	0.0434	by_group_JB5_JB6_JB7
	Exophiala	−0.108	0.129	−0.84	0.4096	main_effect
	Pseudoechria	0.070	0.086	0.82	0.4201	main_effect
Biocontrol Agents / Beneficial Fungi	Clonostachys	0.021	0.109	0.20	0.8465	main_effect
	Trichoderma	−0.022	0.069	−0.32	0.7532	main_effect
	Mortierella	−0.070	0.138	−0.51	0.6145	main_effect
	Penicillium	0.167	0.201	0.83	0.4143	main_effect
	Aspergillus	0.203	0.089	2.28	0.0307	main_effect
Unclassified	Solicoccozyma	−0.185	0.197	−0.94	0.3570	main_effect
	Nadsonia	0.222	0.403	0.55	0.5853	main_effect
	Apiotrichum	0.056	0.192	0.29	0.7726	main_effect
	Saitozyma	−0.130	0.232	−0.56	0.5802	main_effect
	Triangularia	0.068	0.142	0.48	0.6361	main_effect
	Enterocarpus	−0.124	0.166	−0.75	0.4599	main_effect
	Hymenoscyphus	−0.271	0.237	−1.15	0.2614	main_effect
	Linnemannia	0.032	0.139	0.23	0.8228	main_effect
	Aaosphaeria	−0.007	0.100	−0.07	0.9413	main_effect
	Dendryphion	−0.094	0.087	−1.08	0.2895	main_effect
	Pleotrichocladium	0.058	0.082	0.71	0.4837	main_effect
	Arthrographis	−0.495	0.199	−2.48	0.0199	interaction
	Arthrographis	0.027	0.107	0.25	0.8027	by_group_JB1_JB2
	Arthrographis	−0.467	0.140	−3.33	0.0060	by_group_JB5_JB6_JB7
	Atractospora	0.086	0.134	0.64	0.5258	main_effect
	Arachniotus	−0.016	0.066	−0.24	0.8123	main_effect
	Myrmecridium	−0.045	0.087	−0.52	0.6075	main_effect
	Chaetasbolisia	−0.787	0.206	−3.83	0.0007	interaction
	Chaetasbolisia	0.196	0.103	1.90	0.0779	by_group_JB1_JB2
	Chaetasbolisia	−0.590	0.165	−3.58	0.0038	by_group_JB5_JB6_JB7
	Trichosporiella	−0.074	0.075	−0.99	0.3287	main_effect
	Tetracladium	−0.424	0.181	−2.35	0.0267	interaction
	Tetracladium	0.005	0.072	0.07	0.9420	by_group_JB1_JB2
	Tetracladium	−0.419	0.184	−2.27	0.0422	by_group_JB5_JB6_JB7
Uncertain	Gliomastix	−0.040	0.074	−0.54	0.5947	main_effect
	Podila	0.045	0.161	0.28	0.7813	main_effect
	Keithomyces	0.591	0.230	2.57	0.0163	interaction
	Keithomyces	−0.141	0.131	−1.08	0.2991	by_group_JB1_JB2
	Keithomyces	0.449	0.135	3.33	0.0060	by_group_JB5_JB6_JB7
	Fusicolla	−0.073	0.073	−1.01	0.3213	main_effect
	Paraphaeosphaeria	−0.096	0.167	−0.58	0.5695	main_effect

Table 36: Summary statistics for each core fungal genus. The table shows the summary statistics for the analysis of the metadata variable and each core fungi (genus 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	Genus	Estimate	SE	t	p-value	Model
Ectomycorrhizal Symbionts	Cortinarius	−0.001	0.001	−2.16	0.0398	interaction
	Cortinarius	0.001	0.000	2.71	0.0170	by_group_JB1_JB2
	Cortinarius	0.000	0.000	−0.31	0.7604	by_group_JB5_JB6_JB7
Fungal Saprotrophs	Gibellulopsis	−0.001	0.001	−0.57	0.5751	main_effect
	Cladosporium	0.000	0.001	−0.22	0.8299	main_effect
	Cheilymenia	−0.003	0.002	−1.73	0.0951	main_effect
	Thelebolus	0.000	0.001	0.09	0.9294	main_effect
	Penicillium	0.001	0.001	0.99	0.3327	main_effect
	Preussia	0.000	0.001	0.24	0.8140	main_effect
	Mortierella	0.000	0.001	0.55	0.5884	main_effect
	Pseudeurotium	−0.006	0.003	−2.07	0.0486	interaction
	Pseudeurotium	0.003	0.002	1.61	0.1297	by_group_JB1_JB2
	Pseudeurotium	−0.003	0.002	−1.41	0.1825	by_group_JB5_JB6_JB7
	Podospora	0.000	0.001	0.24	0.8099	main_effect
	Cercophora	0.000	0.000	−0.04	0.9703	main_effect
	Papulaspora	0.000	0.000	0.14	0.8916	main_effect
	Aspergillus	0.000	0.001	0.41	0.6851	main_effect
	Gliomastix	0.000	0.000	1.03	0.3107	main_effect
	Podila	0.000	0.001	0.54	0.5958	main_effect
Plant Pathogens	Fusarium	0.001	0.001	0.59	0.5576	main_effect
	Boeremia	0.000	0.001	0.18	0.8598	main_effect
	Dactylonectria	0.002	0.001	2.25	0.0329	interaction
	Dactylonectria	−0.002	0.001	−3.50	0.0035	by_group_JB1_JB2
	Dactylonectria	0.000	0.001	0.17	0.8677	by_group_JB5_JB6_JB7
	Plectosphaerella	0.000	0.001	−0.38	0.7066	main_effect
	Pyrenochaetopsis	−0.002	0.001	−3.18	0.0036	main_effect
	Ophiosphaerella	−0.001	0.000	−2.77	0.0099	main_effect
	Acremonium	0.000	0.000	−0.60	0.5518	main_effect
	Exophiala	−0.001	0.001	−0.94	0.3557	main_effect
	Pseudoechria	−0.001	0.000	−1.52	0.1405	main_effect
Biocontrol Agents / Beneficial Fungi	Clonostachys	0.000	0.001	0.00	0.9974	main_effect
	Trichoderma	0.001	0.000	1.88	0.0705	main_effect
	Mortierella	0.000	0.001	0.55	0.5884	main_effect
	Penicillium	0.001	0.001	0.99	0.3327	main_effect
	Aspergillus	0.000	0.001	0.41	0.6851	main_effect
Unclassified	Solicoccozyma	−0.001	0.001	−1.31	0.2012	main_effect
	Nadsonia	−0.001	0.002	−0.35	0.7259	main_effect
	Apiotrichum	−0.001	0.001	−0.79	0.4338	main_effect
	Saitozyma	0.001	0.001	0.68	0.5030	main_effect
	Triangularia	−0.001	0.001	−1.23	0.2301	main_effect
	Enterocarpus	−0.001	0.001	−1.25	0.2226	main_effect
	Hymenoscyphus	−0.001	0.001	−1.06	0.3003	main_effect
	Linnemannia	−0.001	0.001	−0.76	0.4531	main_effect
	Aaosphaeria	0.001	0.000	1.93	0.0637	main_effect
	Dendryphion	0.000	0.000	−1.00	0.3276	main_effect
	Pleotrichocladium	0.000	0.000	−0.68	0.5051	main_effect
	Arthrographis	0.000	0.000	−0.14	0.8906	main_effect
	Atractospora	0.000	0.001	−0.23	0.8227	main_effect
	Arachniotus	0.000	0.000	0.58	0.5693	main_effect
	Myrmecridium	−0.001	0.000	−1.62	0.1155	main_effect
	Chaetasbolisia	0.000	0.001	−0.42	0.6813	main_effect
	Trichosporiella	0.000	0.000	0.07	0.9454	main_effect
	Tetracladium	0.000	0.000	−0.53	0.5997	main_effect
Uncertain	Gliomastix	0.000	0.000	1.03	0.3107	main_effect
	Podila	0.000	0.001	0.54	0.5958	main_effect
	Keithomyces	0.000	0.001	0.04	0.9683	main_effect
	Fusicolla	0.000	0.000	−0.38	0.7100	main_effect
	Paraphaeosphaeria	0.000	0.001	0.29	0.7730	main_effect

Table 37: Summary statistics for each core fungal genus. The table shows the summary statistics for the analysis of the metadata variable and each core fungi (genus 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	Genus	Estimate	SE	t	p-value	Model
Ectomycorrhizal Symbionts	Cortinarius	0.002	0.000	5.02	0.0000	main_effect
Fungal Saprotrophs	Gibellulopsis	0.015	0.006	2.46	0.0207	interaction
	Gibellulopsis	0.000	0.002	−0.20	0.8432	by_group_JB1_JB2
	Gibellulopsis	0.014	0.004	3.30	0.0063	by_group_JB5_JB6_JB7
	Cladosporium	−0.001	0.002	−0.70	0.4868	main_effect
	Cheilymenia	−0.005	0.002	−2.30	0.0293	main_effect
	Thelebolus	−0.012	0.004	−2.94	0.0068	interaction
	Thelebolus	−0.004	0.001	−3.19	0.0065	by_group_JB1_JB2
	Thelebolus	−0.015	0.004	−3.58	0.0038	by_group_JB5_JB6_JB7
	Penicillium	0.000	0.002	−0.02	0.9816	main_effect
	Preussia	0.002	0.001	1.37	0.1806	main_effect
	Mortierella	0.001	0.001	0.52	0.6040	main_effect
	Pseudeurotium	0.007	0.002	4.56	0.0001	main_effect
	Podospora	0.000	0.002	0.13	0.8985	main_effect
	Cercophora	−0.001	0.001	−0.88	0.3883	main_effect
	Papulaspora	0.000	0.001	−0.05	0.9632	main_effect
	Aspergillus	0.002	0.001	2.39	0.0240	main_effect
	Gliomastix	0.000	0.001	0.58	0.5639	main_effect
	Podila	−0.002	0.001	−1.30	0.2049	main_effect
Plant Pathogens	Fusarium	0.002	0.001	1.67	0.1058	main_effect
	Boeremia	−0.002	0.001	−1.32	0.1982	main_effect
	Dactylonectria	−0.002	0.001	−3.79	0.0007	main_effect
	Plectosphaerella	−0.001	0.001	−0.69	0.4933	main_effect
	Pyrenochaetopsis	−0.001	0.001	−0.85	0.4019	main_effect
	Ophiosphaerella	−0.002	0.001	−3.14	0.0040	main_effect
	Acremonium	0.000	0.001	−0.57	0.5757	main_effect
	Exophiala	−0.002	0.001	−2.66	0.0127	main_effect
	Pseudoechria	0.000	0.001	−0.40	0.6943	main_effect
Biocontrol Agents / Beneficial Fungi	Clonostachys	−0.001	0.001	−1.01	0.3211	main_effect
	Trichoderma	0.001	0.000	1.82	0.0792	main_effect
	Mortierella	0.001	0.001	0.52	0.6040	main_effect
	Penicillium	0.000	0.002	−0.02	0.9816	main_effect
	Aspergillus	0.002	0.001	2.39	0.0240	main_effect
Unclassified	Solicoccozyma	−0.004	0.001	−2.91	0.0070	main_effect
	Nadsonia	−0.005	0.003	−1.73	0.0942	main_effect
	Apiotrichum	−0.002	0.001	−1.25	0.2209	main_effect
	Saitozyma	0.015	0.005	3.26	0.0031	interaction
	Saitozyma	0.003	0.001	2.23	0.0424	by_group_JB1_JB2
	Saitozyma	0.018	0.005	3.50	0.0044	by_group_JB5_JB6_JB7
	Triangularia	−0.003	0.001	−3.24	0.0031	main_effect
	Enterocarpus	−0.002	0.001	−1.29	0.2068	main_effect
	Hymenoscyphus	0.000	0.002	0.11	0.9150	main_effect
	Linnemannia	−0.003	0.001	−3.30	0.0027	main_effect
	Aaosphaeria	0.000	0.001	0.23	0.8203	main_effect
	Dendryphion	−0.001	0.001	−1.58	0.1257	main_effect
	Pleotrichocladium	0.004	0.002	2.12	0.0436	interaction
	Pleotrichocladium	0.000	0.001	−0.66	0.5223	by_group_JB1_JB2
	Pleotrichocladium	0.004	0.002	1.93	0.0776	by_group_JB5_JB6_JB7
	Arthrographis	−0.001	0.001	−1.11	0.2744	main_effect
	Atractospora	0.011	0.003	4.11	0.0004	interaction
	Atractospora	−0.002	0.001	−3.00	0.0096	by_group_JB1_JB2
	Atractospora	0.009	0.003	2.88	0.0140	by_group_JB5_JB6_JB7
	Arachniotus	0.000	0.000	0.38	0.7060	main_effect
	Myrmecridium	−0.001	0.001	−0.95	0.3489	main_effect
	Chaetasbolisia	−0.002	0.001	−3.04	0.0051	main_effect
	Trichosporiella	0.000	0.001	0.00	0.9989	main_effect
	Tetracladium	−0.001	0.001	−1.83	0.0775	main_effect
Uncertain	Gliomastix	0.000	0.001	0.58	0.5639	main_effect
	Podila	−0.002	0.001	−1.30	0.2049	main_effect
	Keithomyces	−0.001	0.001	−0.72	0.4804	main_effect
	Fusicolla	0.000	0.001	0.13	0.8985	main_effect
	Paraphaeosphaeria	0.008	0.004	2.34	0.0275	interaction
	Paraphaeosphaeria	0.002	0.001	1.74	0.1038	by_group_JB1_JB2
	Paraphaeosphaeria	0.011	0.003	3.14	0.0085	by_group_JB5_JB6_JB7

Table 38: Summary statistics for each core fungal genus. The table shows the summary statistics for the analysis of the metadata variable and each core fungi (genus 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	Genus	Estimate	SE	t	p-value	Model
Ectomycorrhizal Symbionts	Cortinarius	−0.009	0.009	−0.99	0.3317	main_effect
Fungal Saprotrophs	Gibellulopsis	0.022	0.034	0.65	0.5198	main_effect
	Cladosporium	−0.033	0.026	−1.28	0.2102	main_effect
	Cheilymenia	0.002	0.039	0.06	0.9515	main_effect
	Thelebolus	−0.036	0.025	−1.46	0.1554	main_effect
	Penicillium	−0.113	0.048	−2.34	0.0272	interaction
	Penicillium	0.087	0.030	2.86	0.0126	by_group_JB1_JB2
	Penicillium	−0.026	0.032	−0.81	0.4353	by_group_JB5_JB6_JB7
	Preussia	0.026	0.021	1.27	0.2145	main_effect
	Mortierella	−0.004	0.017	−0.25	0.8082	main_effect
	Pseudeurotium	0.025	0.033	0.77	0.4449	main_effect
	Podospora	−0.033	0.024	−1.40	0.1729	main_effect
	Cercophora	−0.007	0.011	−0.66	0.5169	main_effect
	Papulaspora	0.011	0.010	1.08	0.2878	main_effect
	Aspergillus	−0.015	0.012	−1.33	0.1955	main_effect
	Gliomastix	−0.004	0.009	−0.39	0.6994	main_effect
	Podila	0.034	0.019	1.80	0.0820	main_effect
Plant Pathogens	Fusarium	−0.028	0.020	−1.41	0.1707	main_effect
	Boeremia	0.003	0.021	0.12	0.9016	main_effect
	Dactylonectria	0.029	0.011	2.76	0.0100	main_effect
	Plectosphaerella	0.001	0.018	0.08	0.9406	main_effect
	Pyrenochaetopsis	−0.018	0.013	−1.34	0.1925	main_effect
	Ophiosphaerella	0.013	0.010	1.30	0.2049	main_effect
	Acremonium	0.006	0.009	0.64	0.5257	main_effect
	Exophiala	−0.001	0.016	−0.03	0.9728	main_effect
	Pseudoechria	0.017	0.010	1.69	0.1012	main_effect
Biocontrol Agents / Beneficial Fungi	Clonostachys	0.023	0.013	1.83	0.0779	main_effect
	Trichoderma	−0.003	0.008	−0.39	0.6967	main_effect
	Mortierella	−0.004	0.017	−0.25	0.8082	main_effect
	Penicillium	−0.113	0.048	−2.34	0.0272	interaction
	Penicillium	0.087	0.030	2.86	0.0126	by_group_JB1_JB2
	Penicillium	−0.026	0.032	−0.81	0.4353	by_group_JB5_JB6_JB7
	Aspergillus	−0.015	0.012	−1.33	0.1955	main_effect
Unclassified	Solicoccozyma	0.016	0.024	0.68	0.5049	main_effect
	Nadsonia	−0.055	0.049	−1.12	0.2714	main_effect
	Apiotrichum	0.051	0.022	2.38	0.0243	main_effect
	Saitozyma	0.048	0.027	1.76	0.0895	main_effect
	Triangularia	−0.025	0.017	−1.46	0.1555	main_effect
	Enterocarpus	−0.047	0.019	−2.54	0.0170	main_effect
	Hymenoscyphus	0.023	0.029	0.79	0.4371	main_effect
	Linnemannia	−0.026	0.016	−1.60	0.1209	main_effect
	Aaosphaeria	−0.014	0.012	−1.15	0.2604	main_effect
	Dendryphion	−0.008	0.011	−0.73	0.4702	main_effect
	Pleotrichocladium	0.007	0.010	0.70	0.4886	main_effect
	Arthrographis	−0.018	0.011	−1.70	0.1003	main_effect
	Atractospora	−0.008	0.017	−0.49	0.6313	main_effect
	Arachniotus	−0.014	0.008	−1.85	0.0744	main_effect
	Myrmecridium	−0.013	0.010	−1.29	0.2091	main_effect
	Chaetasbolisia	0.002	0.012	0.18	0.8574	main_effect
	Trichosporiella	0.011	0.009	1.22	0.2339	main_effect
	Tetracladium	0.007	0.010	0.74	0.4681	main_effect
Uncertain	Gliomastix	−0.004	0.009	−0.39	0.6994	main_effect
	Podila	0.034	0.019	1.80	0.0820	main_effect
	Keithomyces	0.007	0.012	0.59	0.5626	main_effect
	Fusicolla	0.002	0.009	0.19	0.8543	main_effect
	Paraphaeosphaeria	−0.021	0.020	−1.02	0.3162	main_effect

Table 39: Summary statistics for each core fungal genus. The table shows the summary statistics for the analysis of the metadata variable and each core fungi (genus 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	Genus	Estimate	SE	t	p-value	Model
Ectomycorrhizal Symbionts	Cortinarius	−0.003	0.008	−0.37	0.7107	main_effect
Fungal Saprotrophs	Gibellulopsis	0.025	0.032	0.79	0.4347	main_effect
	Cladosporium	0.010	0.025	0.41	0.6859	main_effect
	Cheilymenia	−0.017	0.037	−0.47	0.6449	main_effect
	Thelebolus	−0.033	0.024	−1.41	0.1693	main_effect
	Penicillium	−0.025	0.023	−1.07	0.2957	main_effect
	Preussia	0.064	0.016	3.89	0.0006	main_effect
	Mortierella	0.011	0.016	0.71	0.4858	main_effect
	Pseudeurotium	0.045	0.030	1.48	0.1512	main_effect
	Podospora	−0.031	0.023	−1.36	0.1856	main_effect
	Cercophora	−0.004	0.011	−0.37	0.7146	main_effect
	Papulaspora	−0.004	0.010	−0.39	0.6980	main_effect
	Aspergillus	0.012	0.011	1.09	0.2833	main_effect
	Gliomastix	−0.040	0.016	−2.45	0.0211	interaction
	Gliomastix	0.028	0.011	2.59	0.0215	by_group_JB1_JB2
	Gliomastix	−0.012	0.012	−0.97	0.3514	by_group_JB5_JB6_JB7
	Podila	−0.020	0.018	−1.09	0.2864	main_effect
Plant Pathogens	Fusarium	0.026	0.019	1.39	0.1760	main_effect
	Boeremia	−0.071	0.015	−4.81	0.0000	main_effect
	Dactylonectria	−0.007	0.011	−0.63	0.5362	main_effect
	Plectosphaerella	−0.047	0.014	−3.29	0.0027	main_effect
	Pyrenochaetopsis	0.021	0.012	1.70	0.1010	main_effect
	Ophiosphaerella	−0.014	0.009	−1.60	0.1216	main_effect
	Acremonium	0.045	0.015	2.91	0.0073	interaction
	Acremonium	−0.013	0.011	−1.16	0.2671	by_group_JB1_JB2
	Acremonium	0.032	0.010	3.05	0.0101	by_group_JB5_JB6_JB7
	Exophiala	−0.040	0.013	−2.98	0.0060	main_effect
	Pseudoechria	0.005	0.010	0.52	0.6057	main_effect
Biocontrol Agents / Beneficial Fungi	Clonostachys	0.065	0.020	3.31	0.0027	interaction
	Clonostachys	−0.020	0.014	−1.47	0.1624	by_group_JB1_JB2
	Clonostachys	0.045	0.014	3.17	0.0080	by_group_JB5_JB6_JB7
	Trichoderma	0.014	0.008	1.87	0.0719	main_effect
	Mortierella	0.011	0.016	0.71	0.4858	main_effect
	Penicillium	−0.025	0.023	−1.07	0.2957	main_effect
	Aspergillus	0.012	0.011	1.09	0.2833	main_effect
Unclassified	Solicoccozyma	0.004	0.023	0.18	0.8571	main_effect
	Nadsonia	−0.103	0.043	−2.40	0.0235	main_effect
	Apiotrichum	0.017	0.022	0.77	0.4492	main_effect
	Saitozyma	−0.021	0.027	−0.79	0.4366	main_effect
	Triangularia	0.024	0.016	1.48	0.1490	main_effect
	Enterocarpus	0.020	0.019	1.06	0.2990	main_effect
	Hymenoscyphus	0.022	0.028	0.77	0.4484	main_effect
	Linnemannia	−0.008	0.016	−0.50	0.6205	main_effect
	Aaosphaeria	−0.047	0.021	−2.23	0.0343	interaction
	Aaosphaeria	0.034	0.017	1.97	0.0691	by_group_JB1_JB2
	Aaosphaeria	−0.013	0.012	−1.13	0.2789	by_group_JB5_JB6_JB7
	Dendryphion	−0.039	0.007	−5.21	0.0000	main_effect
	Pleotrichocladium	0.015	0.009	1.65	0.1110	main_effect
	Arthrographis	−0.002	0.011	−0.17	0.8642	main_effect
	Atractospora	−0.001	0.016	−0.04	0.9666	main_effect
	Arachniotus	0.006	0.008	0.77	0.4469	main_effect
	Myrmecridium	−0.021	0.009	−2.19	0.0374	main_effect
	Chaetasbolisia	−0.014	0.012	−1.19	0.2454	main_effect
	Trichosporiella	−0.011	0.009	−1.31	0.2018	main_effect
	Tetracladium	−0.032	0.008	−4.22	0.0002	main_effect
Uncertain	Gliomastix	−0.040	0.016	−2.45	0.0211	interaction
	Gliomastix	0.028	0.011	2.59	0.0215	by_group_JB1_JB2
	Gliomastix	−0.012	0.012	−0.97	0.3514	by_group_JB5_JB6_JB7
	Podila	−0.020	0.018	−1.09	0.2864	main_effect
	Keithomyces	0.010	0.012	0.90	0.3749	main_effect
	Fusicolla	−0.005	0.009	−0.57	0.5718	main_effect
	Paraphaeosphaeria	0.013	0.019	0.65	0.5217	main_effect

Table 40: Summary statistics for each core fungal genus. The table shows the summary statistics for the analysis of the metadata variable and each core fungi (genus 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	Genus	Estimate	SE	t	p-value	Model
Ectomycorrhizal Symbionts	Cortinarius	0.009	0.009	1.04	0.3051	main_effect
Fungal Saprotrophs	Gibellulopsis	−0.059	0.034	−1.74	0.0922	main_effect
	Cladosporium	−0.021	0.027	−0.78	0.4440	main_effect
	Cheilymenia	0.014	0.040	0.34	0.7351	main_effect
	Thelebolus	0.015	0.027	0.55	0.5846	main_effect
	Penicillium	0.080	0.021	3.84	0.0006	main_effect
	Preussia	−0.002	0.022	−0.11	0.9124	main_effect
	Mortierella	−0.034	0.016	−2.05	0.0499	main_effect
	Pseudeurotium	−0.017	0.034	−0.49	0.6279	main_effect
	Podospora	0.038	0.024	1.58	0.1256	main_effect
	Cercophora	−0.006	0.011	−0.52	0.6097	main_effect
	Papulaspora	−0.008	0.011	−0.76	0.4532	main_effect
	Aspergillus	0.013	0.012	1.06	0.2995	main_effect
	Gliomastix	0.001	0.009	0.08	0.9345	main_effect
	Podila	0.026	0.020	1.28	0.2094	main_effect
Plant Pathogens	Fusarium	−0.024	0.021	−1.16	0.2553	main_effect
	Boeremia	0.015	0.022	0.70	0.4887	main_effect
	Dactylonectria	0.017	0.012	1.39	0.1756	main_effect
	Plectosphaerella	−0.006	0.018	−0.33	0.7434	main_effect
	Pyrenochaetopsis	−0.027	0.013	−2.10	0.0451	main_effect
	Ophiosphaerella	−0.003	0.010	−0.26	0.7983	main_effect
	Acremonium	−0.007	0.009	−0.73	0.4731	main_effect
	Exophiala	0.024	0.016	1.51	0.1430	main_effect
	Pseudoechria	−0.003	0.011	−0.24	0.8155	main_effect
Biocontrol Agents / Beneficial Fungi	Clonostachys	0.010	0.014	0.71	0.4837	main_effect
	Trichoderma	−0.002	0.009	−0.18	0.8597	main_effect
	Mortierella	−0.034	0.016	−2.05	0.0499	main_effect
	Penicillium	0.080	0.021	3.84	0.0006	main_effect
	Aspergillus	0.013	0.012	1.06	0.2995	main_effect
Unclassified	Solicoccozyma	−0.007	0.025	−0.29	0.7772	main_effect
	Nadsonia	−0.006	0.052	−0.11	0.9099	main_effect
	Apiotrichum	0.021	0.024	0.85	0.4033	main_effect
	Saitozyma	−0.006	0.030	−0.20	0.8392	main_effect
	Triangularia	−0.027	0.017	−1.55	0.1323	main_effect
	Enterocarpus	−0.015	0.021	−0.73	0.4704	main_effect
	Hymenoscyphus	−0.014	0.031	−0.47	0.6423	main_effect
	Linnemannia	0.005	0.018	0.30	0.7698	main_effect
	Aaosphaeria	−0.003	0.013	−0.20	0.8391	main_effect
	Dendryphion	0.016	0.011	1.45	0.1593	main_effect
	Pleotrichocladium	−0.005	0.010	−0.45	0.6575	main_effect
	Arthrographis	0.007	0.012	0.57	0.5755	main_effect
	Atractospora	0.007	0.017	0.42	0.6756	main_effect
	Arachniotus	0.006	0.008	0.73	0.4713	main_effect
	Myrmecridium	0.003	0.011	0.28	0.7796	main_effect
	Chaetasbolisia	0.022	0.012	1.77	0.0872	main_effect
	Trichosporiella	0.013	0.009	1.38	0.1792	main_effect
	Tetracladium	0.015	0.010	1.46	0.1559	main_effect
Uncertain	Gliomastix	0.001	0.009	0.08	0.9345	main_effect
	Podila	0.026	0.020	1.28	0.2094	main_effect
	Keithomyces	0.008	0.013	0.62	0.5407	main_effect
	Fusicolla	0.007	0.009	0.74	0.4669	main_effect
	Paraphaeosphaeria	−0.037	0.020	−1.86	0.0736	main_effect

Table 41: Summary statistics for each core fungal genus. The table shows the summary statistics for the analysis of the metadata variable and each core fungi (genus 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	Genus	Estimate	SE	t	p-value	Model
Ectomycorrhizal Symbionts	Cortinarius	0.015	0.008	1.84	0.0758	main_effect
Fungal Saprotrophs	Gibellulopsis	−0.031	0.033	−0.94	0.3535	main_effect
	Cladosporium	−0.016	0.026	−0.62	0.5419	main_effect
	Cheilymenia	−0.049	0.037	−1.33	0.1947	main_effect
	Thelebolus	−0.045	0.024	−1.89	0.0691	main_effect
	Penicillium	0.065	0.021	3.08	0.0046	main_effect
	Preussia	0.044	0.019	2.29	0.0299	main_effect
	Mortierella	−0.010	0.016	−0.64	0.5286	main_effect
	Pseudeurotium	0.013	0.032	0.41	0.6835	main_effect
	Podospora	−0.108	0.043	−2.50	0.0190	interaction
	Podospora	0.065	0.031	2.11	0.0529	by_group_JB1_JB2
	Podospora	−0.043	0.030	−1.43	0.1787	by_group_JB5_JB6_JB7
	Cercophora	−0.031	0.009	−3.46	0.0017	main_effect
	Papulaspora	−0.010	0.010	−1.02	0.3172	main_effect
	Aspergillus	0.024	0.011	2.29	0.0300	main_effect
	Gliomastix	0.009	0.009	1.09	0.2853	main_effect
	Podila	0.011	0.019	0.56	0.5822	main_effect
Plant Pathogens	Fusarium	0.008	0.020	0.41	0.6848	main_effect
	Boeremia	−0.051	0.018	−2.81	0.0089	main_effect
	Dactylonectria	0.009	0.012	0.78	0.4431	main_effect
	Plectosphaerella	−0.061	0.013	−4.82	0.0000	main_effect
	Pyrenochaetopsis	−0.022	0.013	−1.73	0.0939	main_effect
	Ophiosphaerella	−0.017	0.009	−1.81	0.0811	main_effect
	Acremonium	0.053	0.015	3.58	0.0014	interaction
	Acremonium	−0.022	0.010	−2.13	0.0517	by_group_JB1_JB2
	Acremonium	0.032	0.011	2.91	0.0132	by_group_JB5_JB6_JB7
	Exophiala	−0.001	0.016	−0.06	0.9560	main_effect
	Pseudoechria	0.009	0.010	0.88	0.3884	main_effect
Biocontrol Agents / Beneficial Fungi	Clonostachys	0.053	0.020	2.65	0.0134	interaction
	Clonostachys	−0.001	0.015	−0.09	0.9259	by_group_JB1_JB2
	Clonostachys	0.051	0.013	3.89	0.0021	by_group_JB5_JB6_JB7
	Trichoderma	0.016	0.008	2.11	0.0440	main_effect
	Mortierella	−0.010	0.016	−0.64	0.5286	main_effect
	Penicillium	0.065	0.021	3.08	0.0046	main_effect
	Aspergillus	0.024	0.011	2.29	0.0300	main_effect
Unclassified	Solicoccozyma	−0.013	0.024	−0.54	0.5931	main_effect
	Nadsonia	−0.086	0.046	−1.89	0.0694	main_effect
	Apiotrichum	0.036	0.022	1.62	0.1165	main_effect
	Saitozyma	0.022	0.028	0.79	0.4339	main_effect
	Triangularia	−0.019	0.017	−1.12	0.2742	main_effect
	Enterocarpus	−0.038	0.019	−2.04	0.0511	main_effect
	Hymenoscyphus	0.021	0.029	0.74	0.4628	main_effect
	Linnemannia	−0.005	0.017	−0.30	0.7665	main_effect
	Aaosphaeria	−0.004	0.012	−0.31	0.7561	main_effect
	Dendryphion	−0.025	0.010	−2.58	0.0154	main_effect
	Pleotrichocladium	0.009	0.010	0.90	0.3754	main_effect
	Arthrographis	−0.015	0.011	−1.41	0.1691	main_effect
	Atractospora	0.008	0.016	0.51	0.6107	main_effect
	Arachniotus	−0.001	0.008	−0.11	0.9171	main_effect
	Myrmecridium	−0.027	0.009	−2.91	0.0069	main_effect
	Chaetasbolisia	−0.002	0.012	−0.17	0.8637	main_effect
	Trichosporiella	0.004	0.009	0.47	0.6440	main_effect
	Tetracladium	−0.006	0.010	−0.66	0.5165	main_effect
Uncertain	Gliomastix	0.009	0.009	1.09	0.2853	main_effect
	Podila	0.011	0.019	0.56	0.5822	main_effect
	Keithomyces	0.015	0.012	1.27	0.2132	main_effect
	Fusicolla	−0.001	0.009	−0.14	0.8930	main_effect
	Paraphaeosphaeria	−0.025	0.019	−1.29	0.2092	main_effect

Table 42: Summary statistics for each core fungal genus. The table shows the summary statistics for the analysis of the metadata variable and each core fungi (genus 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	Genus	Estimate	SE	t	p-value	Model
Ectomycorrhizal Symbionts	Cortinarius	−0.006	0.010	−0.65	0.5201	main_effect
Fungal Saprotrophs	Gibellulopsis	−0.015	0.037	−0.41	0.6868	main_effect
	Cladosporium	0.070	0.026	2.71	0.0112	main_effect
	Cheilymenia	0.024	0.042	0.57	0.5753	main_effect
	Thelebolus	0.020	0.028	0.72	0.4779	main_effect
	Penicillium	−0.030	0.026	−1.12	0.2738	main_effect
	Preussia	−0.040	0.022	−1.80	0.0824	main_effect
	Mortierella	0.033	0.017	1.92	0.0653	main_effect
	Pseudeurotium	−0.037	0.035	−1.04	0.3071	main_effect
	Podospora	0.012	0.026	0.45	0.6588	main_effect
	Cercophora	0.023	0.011	2.09	0.0459	main_effect
	Papulaspora	0.005	0.011	0.46	0.6466	main_effect
	Aspergillus	−0.016	0.013	−1.28	0.2121	main_effect
	Gliomastix	−0.001	0.010	−0.13	0.8967	main_effect
	Podila	−0.001	0.021	−0.06	0.9504	main_effect
Plant Pathogens	Fusarium	0.023	0.022	1.03	0.3097	main_effect
	Boeremia	0.018	0.023	0.80	0.4298	main_effect
	Dactylonectria	−0.019	0.013	−1.50	0.1435	main_effect
	Plectosphaerella	0.000	0.019	−0.01	0.9895	main_effect
	Pyrenochaetopsis	−0.005	0.015	−0.35	0.7282	main_effect
	Ophiosphaerella	0.006	0.011	0.53	0.6001	main_effect
	Acremonium	−0.016	0.010	−1.65	0.1099	main_effect
	Exophiala	−0.007	0.017	−0.39	0.7000	main_effect
	Pseudoechria	−0.006	0.011	−0.53	0.5993	main_effect
Biocontrol Agents / Beneficial Fungi	Clonostachys	0.057	0.024	2.37	0.0252	interaction
	Clonostachys	−0.039	0.012	−3.31	0.0051	by_group_JB1_JB2
	Clonostachys	0.019	0.022	0.83	0.4250	by_group_JB5_JB6_JB7
	Trichoderma	0.000	0.009	0.01	0.9897	main_effect
	Mortierella	0.033	0.017	1.92	0.0653	main_effect
	Penicillium	−0.030	0.026	−1.12	0.2738	main_effect
	Aspergillus	−0.016	0.013	−1.28	0.2121	main_effect
Unclassified	Solicoccozyma	0.009	0.027	0.32	0.7505	main_effect
	Nadsonia	−0.002	0.054	−0.04	0.9659	main_effect
	Apiotrichum	−0.013	0.026	−0.51	0.6138	main_effect
	Saitozyma	−0.032	0.030	−1.06	0.2970	main_effect
	Triangularia	0.006	0.019	0.34	0.7351	main_effect
	Enterocarpus	0.037	0.021	1.74	0.0921	main_effect
	Hymenoscyphus	0.008	0.032	0.25	0.8060	main_effect
	Linnemannia	0.024	0.018	1.33	0.1931	main_effect
	Aaosphaeria	0.019	0.013	1.51	0.1413	main_effect
	Dendryphion	0.004	0.012	0.31	0.7599	main_effect
	Pleotrichocladium	−0.020	0.010	−1.97	0.0593	main_effect
	Arthrographis	0.019	0.012	1.65	0.1104	main_effect
	Atractospora	0.007	0.018	0.37	0.7118	main_effect
	Arachniotus	0.001	0.009	0.11	0.9136	main_effect
	Myrmecridium	0.005	0.012	0.41	0.6820	main_effect
	Chaetasbolisia	0.066	0.024	2.69	0.0123	interaction
	Chaetasbolisia	−0.017	0.017	−1.01	0.3306	by_group_JB1_JB2
	Chaetasbolisia	0.048	0.017	2.88	0.0139	by_group_JB5_JB6_JB7
	Trichosporiella	0.000	0.010	−0.02	0.9828	main_effect
	Tetracladium	0.012	0.011	1.08	0.2879	main_effect
Uncertain	Gliomastix	−0.001	0.010	−0.13	0.8967	main_effect
	Podila	−0.001	0.021	−0.06	0.9504	main_effect
	Keithomyces	−0.012	0.013	−0.91	0.3718	main_effect
	Fusicolla	0.008	0.010	0.81	0.4252	main_effect
	Paraphaeosphaeria	−0.005	0.022	−0.23	0.8210	main_effect

Table 43: Summary statistics for each core fungal genus. The table shows the summary statistics for the analysis of the metadata variable and each core fungi (genus 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	Genus	Estimate	SE	t	p-value	Model
Ectomycorrhizal Symbionts	Cortinarius	−0.017	0.008	−2.13	0.0418	main_effect
Fungal Saprotrophs	Gibellulopsis	−0.005	0.032	−0.16	0.8751	main_effect
	Cladosporium	0.022	0.025	0.88	0.3841	main_effect
	Cheilymenia	0.126	0.028	4.45	0.0001	main_effect
	Thelebolus	0.046	0.023	1.99	0.0569	main_effect
	Penicillium	−0.055	0.021	−2.57	0.0159	main_effect
	Preussia	−0.014	0.020	−0.71	0.4845	main_effect
	Mortierella	−0.004	0.016	−0.28	0.7847	main_effect
	Pseudeurotium	−0.037	0.031	−1.21	0.2359	main_effect
	Podospora	0.020	0.023	0.87	0.3927	main_effect
	Cercophora	0.012	0.010	1.12	0.2702	main_effect
	Papulaspora	−0.024	0.009	−2.76	0.0100	main_effect
	Aspergillus	−0.010	0.011	−0.90	0.3750	main_effect
	Gliomastix	0.000	0.009	−0.01	0.9952	main_effect
	Podila	−0.008	0.019	−0.44	0.6634	main_effect
Plant Pathogens	Fusarium	−0.021	0.019	−1.11	0.2763	main_effect
	Boeremia	0.019	0.020	0.97	0.3399	main_effect
	Dactylonectria	0.006	0.011	0.56	0.5828	main_effect
	Plectosphaerella	0.011	0.017	0.67	0.5087	main_effect
	Pyrenochaetopsis	0.023	0.012	1.93	0.0637	main_effect
	Ophiosphaerella	0.009	0.009	1.00	0.3245	main_effect
	Acremonium	−0.003	0.009	−0.31	0.7574	main_effect
	Exophiala	0.003	0.015	0.20	0.8421	main_effect
	Pseudoechria	−0.002	0.010	−0.21	0.8382	main_effect
Biocontrol Agents / Beneficial Fungi	Clonostachys	−0.005	0.013	−0.36	0.7185	main_effect
	Trichoderma	−0.004	0.008	−0.48	0.6351	main_effect
	Mortierella	−0.004	0.016	−0.28	0.7847	main_effect
	Penicillium	−0.055	0.021	−2.57	0.0159	main_effect
	Aspergillus	−0.010	0.011	−0.90	0.3750	main_effect
Unclassified	Solicoccozyma	0.018	0.023	0.78	0.4436	main_effect
	Nadsonia	0.081	0.045	1.81	0.0818	main_effect
	Apiotrichum	−0.027	0.022	−1.22	0.2326	main_effect
	Saitozyma	−0.090	0.021	−4.26	0.0002	main_effect
	Triangularia	0.045	0.014	3.10	0.0043	main_effect
	Enterocarpus	0.049	0.017	2.86	0.0078	main_effect
	Hymenoscyphus	0.001	0.028	0.05	0.9603	main_effect
	Linnemannia	0.031	0.015	2.03	0.0517	main_effect
	Aaosphaeria	0.004	0.012	0.33	0.7457	main_effect
	Dendryphion	0.007	0.010	0.72	0.4759	main_effect
	Pleotrichocladium	−0.007	0.010	−0.76	0.4521	main_effect
	Arthrographis	0.008	0.011	0.74	0.4628	main_effect
	Atractospora	0.023	0.015	1.52	0.1393	main_effect
	Arachniotus	0.009	0.007	1.17	0.2535	main_effect
	Myrmecridium	0.010	0.010	1.00	0.3242	main_effect
	Chaetasbolisia	0.004	0.012	0.32	0.7515	main_effect
	Trichosporiella	−0.012	0.009	−1.45	0.1576	main_effect
	Tetracladium	0.004	0.010	0.45	0.6541	main_effect
Uncertain	Gliomastix	0.000	0.009	−0.01	0.9952	main_effect
	Podila	−0.008	0.019	−0.44	0.6634	main_effect
	Keithomyces	−0.001	0.012	−0.05	0.9576	main_effect
	Fusicolla	−0.009	0.008	−1.12	0.2730	main_effect
	Paraphaeosphaeria	−0.004	0.020	−0.21	0.8339	main_effect

Table 44: Summary statistics for each core fungal genus. The table shows the summary statistics for the analysis of the metadata variable and each core fungi (genus 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	Genus	Estimate	SE	t	p-value	Model
Ectomycorrhizal Symbionts	Cortinarius	0.007	0.011	0.68	0.5042	main_effect
Fungal Saprotrophs	Gibellulopsis	−0.056	0.041	−1.37	0.1806	main_effect
	Cladosporium	−0.041	0.032	−1.29	0.2075	main_effect
	Cheilymenia	−0.045	0.047	−0.96	0.3471	main_effect
	Thelebolus	0.034	0.031	1.09	0.2844	main_effect
	Penicillium	0.059	0.029	2.05	0.0498	main_effect
	Preussia	−0.043	0.025	−1.71	0.0979	main_effect
	Mortierella	0.019	0.021	0.93	0.3602	main_effect
	Pseudeurotium	−0.074	0.038	−1.93	0.0639	main_effect
	Podospora	0.010	0.030	0.32	0.7484	main_effect
	Cercophora	0.000	0.014	0.02	0.9856	main_effect
	Papulaspora	0.019	0.012	1.54	0.1342	main_effect
	Aspergillus	−0.001	0.015	−0.05	0.9618	main_effect
	Gliomastix	0.003	0.011	0.30	0.7675	main_effect
	Podila	0.029	0.024	1.23	0.2283	main_effect
Plant Pathogens	Fusarium	−0.053	0.023	−2.26	0.0315	main_effect
	Boeremia	0.003	0.026	0.11	0.9148	main_effect
	Dactylonectria	−0.001	0.015	−0.10	0.9238	main_effect
	Plectosphaerella	0.004	0.022	0.19	0.8476	main_effect
	Pyrenochaetopsis	−0.037	0.015	−2.41	0.0229	main_effect
	Ophiosphaerella	−0.013	0.012	−1.12	0.2739	main_effect
	Acremonium	−0.007	0.011	−0.66	0.5123	main_effect
	Exophiala	0.024	0.019	1.23	0.2275	main_effect
	Pseudoechria	−0.003	0.013	−0.26	0.7955	main_effect
Biocontrol Agents / Beneficial Fungi	Clonostachys	−0.007	0.016	−0.45	0.6596	main_effect
	Trichoderma	0.001	0.010	0.14	0.8881	main_effect
	Mortierella	0.019	0.021	0.93	0.3602	main_effect
	Penicillium	0.059	0.029	2.05	0.0498	main_effect
	Aspergillus	−0.001	0.015	−0.05	0.9618	main_effect
Unclassified	Solicoccozyma	−0.027	0.030	−0.89	0.3796	main_effect
	Nadsonia	−0.002	0.061	−0.04	0.9715	main_effect
	Apiotrichum	0.017	0.029	0.58	0.5661	main_effect
	Saitozyma	−0.011	0.035	−0.32	0.7534	main_effect
	Triangularia	−0.012	0.021	−0.56	0.5782	main_effect
	Enterocarpus	−0.015	0.025	−0.60	0.5557	main_effect
	Hymenoscyphus	−0.027	0.036	−0.75	0.4573	main_effect
	Linnemannia	0.032	0.020	1.58	0.1250	main_effect
	Aaosphaeria	0.030	0.014	2.19	0.0374	main_effect
	Dendryphion	0.018	0.013	1.40	0.1735	main_effect
	Pleotrichocladium	0.003	0.012	0.25	0.8027	main_effect
	Arthrographis	0.021	0.013	1.59	0.1223	main_effect
	Atractospora	0.033	0.019	1.69	0.1014	main_effect
	Arachniotus	−0.009	0.010	−0.91	0.3683	main_effect
	Myrmecridium	−0.002	0.013	−0.13	0.8985	main_effect
	Chaetasbolisia	0.017	0.015	1.13	0.2696	main_effect
	Trichosporiella	−0.001	0.011	−0.06	0.9530	main_effect
	Tetracladium	0.002	0.012	0.16	0.8774	main_effect
Uncertain	Gliomastix	0.003	0.011	0.30	0.7675	main_effect
	Podila	0.029	0.024	1.23	0.2283	main_effect
	Keithomyces	0.034	0.014	2.50	0.0187	main_effect
	Fusicolla	−0.003	0.011	−0.24	0.8140	main_effect
	Paraphaeosphaeria	−0.047	0.024	−1.97	0.0589	main_effect

Table 45: Summary statistics for each core fungal genus. The table shows the summary statistics for the analysis of the metadata variable and each core fungi (genus 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

Statistical Analysis Report

Fungal profile from metabarcoding (dataset 2024)

Biomcare ApS

11/06/2025

Introduction to the biostatistical analysis

Overview of metadata variables

Geography

JB value

Grazed

Harvested

Clovergrass within 3 years

Biodynamic farm

Years since turning organic

Evaluation of overall microbiome profiles

Core fungi

Biodynamic farm

soil tmp.

Years since plowing

Rt

Phosphorus

Potassium

Magnesium

Cobber

Organic material (perc)

Clay (perc)

Nitrogen (perc)

Years since turning organic

Years since turning biodynamic

Field keep water

Grazed

Harvested

Clovergrass (within 3 years)

Organic material (factor)

Livestock manure

Degassed fertilizer

Version information