DOI: 10.5061/dryad.0k6djhb4z
title: Consistent predictors of microbial community composition across spatial scales in grasslands reveal low context-dependency

description: Environmental circumstances shaping soil microbial communities have been
 studied extensively. However, due to disparate study designs, it has been
 difficult to resolve whether a globally consistent set of predictors
 exists, or context-dependency prevails. Here, we used a network of 18
 grassland sites (11 of those containing regional plant productivity
 gradients) to examine i) if similar abiotic or biotic factors predict both
 large-scale (across sites) and regional-scale (within sites) patterns in
 bacterial and fungal community composition, and ii) if microbial community
 composition differs consistently at two levels of regional plant
 productivity (low vs high). We found that bacteria were consistently
 associated with certain soil properties and both bacteria and fungi were
 consistently associated with plant community composition within different
 sites. Moreover, there was a microbial community signal that clearly
 distinguished high and low-productivity soils that was shared across
 different grasslands independent of their location in the world. In this
 study, we show that there is high congruence between predictors of
 bacterial and fungal community composition at different spatial scales and
 that regional productivity differences are typified by characteristic soil
 microbial communities across the grassland biome. These results suggest
 that it might be feasible to predict the overall effects of global changes
 on soil microbial community composition in different grasslands, as well
 as to discriminate fertile from infertile systems using generally
 applicable microbial indicators.
description: Data were collected from 18
 Herbaceous Diversity Network (HerbDivNet) grassland sites located in 12
 countries. Each of the 18 sites
 contained between two and six 8 × 8 m plots: 11 sites contained six plots,
 one site contained four plots, one site three plots and five sites
 contained two plots; giving a total of 83 plots. Most sites were chosen to
 represent a site-specific gradient in productivity based on their plant
 biomass production; with six plots (two replicates of low, medium and high
 productivity) located within the same region with little to no variation
 in climatic conditions. However, some sites contained fewer plots and did
 not show a prominent productivity gradient. A clear gradient in biomass
 production was captured in 11 sites. For each plot within a site, five
 soil subsamples to a depth of 10 cm were taken from four corners and the
 centre of the plot. Subsamples for microbial analyses were analysed
 separately, and soil properties were analysed from one composite sample
 per plot (n=83). Plant species presence and total
 aboveground biomass were measured from each m<sup>2</sup> of
 each 64 m<sup>2</sup> plot in a single event at the peak of
 the growing season. Mean annual
 precipitation (MAP) and temperature (MAT) were derived from the CHELSA
 database on the geographical position (latitude and longitude) of each
 plot. Data on total inorganic nitrogen deposition [kg/ha/yr] were derived
 from Ackerman et al. (2018). We analysed 14 soil properties: soil organic
 matter (SOM), total nitrogen (N), total carbon (C), total phosphorus (P),
 available P, base saturation (BS), cation exchange capacity (CEC), pH,
 soil texture (sand, clay, silt), extractable Ca, Mg and K. The bacterial
 16S V4 region was amplified using the 515F-806R primer pair and the fungal
 ITS1 region was amplified using general fungal primers ITS1 and ITS2. The
 abundance of bacterial and fungal gene copies per sample was quantified
 using qPCR targeting the 16s V4 region for bacteria and the 18s region for
 fungi.
description: # Consistent predictors of microbial community composition across spatial
 scales in grasslands reveal low context-dependency Summary of methods:
 Data were collected from 18 Herbaceous Diversity Network (HerbDivNet)
 grassland sites located in 12 countries. Each of the 18 sites contained
 between two and six 8 × 8 m plots: 11 sites contained six plots, one site
 contained four plots, one site three plots and five sites contained two
 plots; giving a total of 83 plots. Most sites were chosen to represent a
 site-specific gradient in productivity based on their plant biomass
 production; A clear gradient in biomass production (low vs. high) was
 captured in 11 sites. For each plot within a site, five soil subsamples to
 a depth of 10 cm were taken from four corners and the centre of the plot.
 Subsamples for microbial analyses were analysed separately (83 x 5), and
 soil properties were analysed from one composite sample per plot (n = 83).
 The dataset includes the following files: 1. otu\_b.txt - rarefied OTU
 table for bacterial communities (with 5 samples per plot) 2. map\_b.txt -
 metadata file linked to the bacterial OTU table 3. tax\_b.txt - table
 containing taxonomic information for bacterial OTUs 4. otu\_f.txt -
 rarefied OTU table for fungal communities (with 5 samples per plot) 5.
 map\_f.txt - metadata file linked to the fungal OTU table 6. tax\_f.txt -
 table containing taxonomic information for fungal OTUs 7.
 plant\_genera\_abundance.txt - table with the abundances of plant genera
 per plot 8. map\_general.txt - an overall map data table with information
 about sites, soil properties, climate, biomass, coordinates, bacterial and
 fungal biomass per plot 9. map\_prod\_levels.txt - a map data table with
 the same information as before, specifically for the sites that contain
 plant productivity gradient 10. R\_script\_full - R script describing the
 steps taken in the analyses Missing data codes: NA ## Description of the
 data and file structure 1. Data-specific information for otu\_b.txt \-
 Number of rows = 485 \(5 replicate samples collected from 83 plots
 including technical replicates and failed/repeated samples\) \- Number of
 columns = 19248 \(bacterial OTUs\) 2. Data-specific information for
 map\_b.txt \- Number of rows = 461 \(5 replicate samples collected from 83
 plots including technical replicates\) \- row names to be matched with row
 names of otu\_b\.txt \- Number of columns = 9 continent - where the sites
 are located short\_site - short names of the site plot - the number of the
 plot within the site site\_plot - combination of the site name and plot
 number sample - 1 to 5 samples taken per plot rep - 1 = used in the
 analysis, r = technical replicate (not used in the analyses) real - 1 =
 samples used in the analyses, 2 = samples not used in the analyses upsam -
 samples that were upsampled during rarefaction (yes), and the other
 samples (no) site\_long - full name of the countries where the sites were
 located 3. Data-specific information for tax\_b.txt \- Number of rows =
 19248 \(OTUs\) \- to be matched with otu\_b\.txt \- Number of columns = 7
 Domain Phylum Class Order Family Genus Species 4. Data-specific
 information for otu\_f.txt \- Number of rows = 462 \(5 replicate samples
 collected from 83 plots including technical replicates and failed/repeated
 samples\) \- Number of columns = 13967 \(fungal OTUs\) 5. Data-specific
 information for map\_f.txt \- Number of rows = 451 \(5 replicate samples
 collected from 83 plots including technical replicates\) \- row names to
 be matched with otu\_f\.txt \- Number of columns = 8 continent - where the
 sites are located short\_site - short names of the site plot - the number
 of the plot within the site site\_plot - combination of the site name and
 plot number sample - 1 to 5 samples taken per plot rep - 1 = used in the
 analysis, r = technical replicate (not used in the analyses) real - 1 =
 samples used in the analyses, 2 = samples not used in the analyses
 site\_long - full name of the countries where the sites were located 6.
 Data-specific information for tax\_f.txt \- Number of rows = 13967
 \(OTUs\) \- to be matched with otu\_f\.txt \- Number of columns = 12 OTU
 phylum class order family genus species trophicMode - possible trophic
 status (includes combinations of different possibilities) troph1 - the
 first possible trophic status (used in the study) troph2 - the second
 possible trophic status guild guild\_long 7. Data-specific information for
 plant\_genera\_abundance.txt \- Number of rows = 83 \- row names to be
 matched with plot aggregated data of otu\_b\, otu\_f \(site\_short\) and
 site\_short of map\_general\.txt \- Number of columns = 566 \- plant
 genera 8. Data-specific information for map\_general.txt \- Number of rows
 = 83 \- Number of columns = 38 site\_short - short names of the site plot
 - the number of the plot within the site site\_plot - combination of the
 site name and plot number Ndep - atmospheric nitrogen deposition derived
 from Ackerman et al. (2018). [kg/ha/yr] Biomass - average peak biomass
 production per plot [g/m2] Litter - per plot [g/m2] Total\_biomass - per
 plot [g/m2] Sp\_richness - species richness per plot Latitude - plot
 latitude [decimal degrees] Longitude - plot longitude [decimal degrees]
 Elevation [m] prec - mean annual precipitation [mm/year] derived from the
 CHELSA database temp - mean annual temperature [°C] derived from the
 CHELSA database ph\_KCl - pH measured in KCl H - hydrogen H+ [meq/100g] Ca
 - calcium [meq/100g] K - potassium [meq/100g] Mg - magnesium [meq/100g] Na
 -sodium [meq/100g] Al - aluminium [meq/100g] Fe - iron [meq/100g] Mn -
 manganese [meq/100g] CEC - cation exchange capacity [meq/100g] BS - base
 saturation [%] P\_Olsen - extractable phosphorus Olsen [mg/kg - ppm]
 P\_Bray - extractable phosphorus Bray [mg/kg - ppm] P - total phosphorus
 [mg/kg - ppm] N - total nitrogen [%] C - total carbon [%] CN\_ratio - C:N
 SOM - soil organic matter [%] BD - bulk density [kg/m3] Sand [%] Clay [%]
 Silt [%] Fcopies\_g - number of fungal gene copies per gram of dry soil
 Bcopies\_g - number of bacterial gene copies per gram of dry soil F\_B -
 ratio of fungal to bacterial copies 9. Data-specific information for
 map\_prod\_levels.txt \- Number of rows = 44 \- Number of columns = 38
 contains the same variables as in the previous file f\_group -
 productivity level (l-low, h-high) ## Sharing/Access information Links to
 other publicly accessible locations of the data: NA Data was derived from
 the following sources: * N deposition:
 https://doi.org/10.1029/2018GB005990 * Climatic variables:
 https://chelsa-climate.org/ * Plant biomass and richness: DOI:
 10.1126/science.aab3916 ## Code/Software NA