Comparison of the regions considered on the basis of their soil habitats.

<p>A. Soil average dissimilarity of soil habitat for the different regions (number linked to the corresponding region) and position of sites; B. Between group analysis of soil habitats according to the region; C. Correlation circle of the variables defining soil habitat in the between group analysis. The length of the arrow corresponds to the Pearson’s correlation coefficient for quantitative variables and to the correlation ratio for qualitative variables. Symbols: Alt.: Elevation; T°C: Sum of annual temperatures; P_ass: Assimilable P; C:N: Carbon to Nitrogen ratio; C_org: Organic Carbon content.</p

Similar Processes but Different Environmental Filters for Soil Bacterial and Fungal Community Composition Turnover on a Broad Spatial Scale

<div><p>Spatial scaling of microorganisms has been demonstrated over the last decade. However, the processes and environmental filters shaping soil microbial community structure on a broad spatial scale still need to be refined and ranked. Here, we compared bacterial and fungal community composition turnovers through a biogeographical approach on the same soil sampling design at a broad spatial scale (area range: 13300 to 31000 km²): i) to examine their spatial structuring; ii) to investigate the relative importance of environmental selection and spatial autocorrelation in determining their community composition turnover; and iii) to identify and rank the relevant environmental filters and scales involved in their spatial variations. Molecular fingerprinting of soil bacterial and fungal communities was performed on 413 soils from four French regions of contrasting environmental heterogeneity (Landes</p></div

Variance partitioning of bacterial and fungal community composition.

<p>The number indicated in brackets corresponds to the number of samples for the region. Significance levels: ns: not significant; P<0.05: *; P<0.01: **, P<0.001: ***.</p

Distance-Decay Relationships for bacteria and fungi.

<p>Each panel correspond to a region: Brittany (A), Burgundy (B), Landes (C) and South-East (D) Points the average Sørensen’s similarity between sites for each distance class. Lines represent the regression model based on the whole set of paired comparisons; for bacteria (grey) and fungi (black). The equations for the regression models were as follows: (<b>A</b>) Brittany: Bacteria***: log10(Sørensen’s similarity) = −0.014×log10(geographic distance)−0.156; Fungi***: log10(Sørensen’s similarity) = −0.017×log10(geographic distance)−0.350; (<b>B</b>) Burgundy: Bacteria*** log10(Sørensen’s similarity) = −0.018×log10(geographic distance)−0.144; Fungi***: log10(Sørensen’s similarity) = −0.015×log10(geographic distance)−0.316; (<b>C</b>) Landes: Bacteria*: log10(Sørensen’s similarity) = −0.017×log10(geographic distance)−0.198; Fungi ^ns: log10(Sørensen’s similarity) = −0.012×log10(geographic distance)−0.357; (<b>D</b>) South-East: Bacteria***: log10(Sørensen’s similarity) = −0.027×log10(geographic distance)−0.101; Fungi***: log10(Sørensen’s similarity) = −0.019×log10(geographic distance)−0.298. A graph with points representing all paired-comparisions between sites as points can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111667#pone.0111667.s002" target="_blank">Figure S2</a>. Significance of the model is indicated as an exponent for each organism: ns: not significant; P<0.05: *; P<0.01: **, P<0.001: ***.</p

Variations of microbial communities partitionned according to edaphic variables and space.

<p>For each organism and region, only variables retained in the most parsimonious model are presented and their pure effect is tested by a permutation test. Significance levels are: P<0.05: *; P<0.01: **, P<0.001: ***. Missing values or variables indicate that the variable was not retained in the model. Sand was removed prior to model evaluation since it was represented by the opposite of the sum of silt and clay content. Rainfall: Sum of annual rainfall (mm). Temperature: Sum of annual temperature (°C). Spatial components were summarized according to the scale considered: trend (x, y and z coordinates), coarse, medium or fine. The interval in brackets indicates the numbers of PCNMs retained in the model for each scale. The proportion of variance for each scale was determined as the sum of the pure effects of each PCNM when these were significant. Coarse, medium and fine scales correspond to PCNM with a spatial range of 80 to 120 km, 40 to 65 km and less than 40 km; respectively.</p

Regression parameters of the Distance-Decay Relationships for Bacteria and Fungi.

<p>The number of observations per region is provided in brackets beside the name of the region. The community composition turnover rate (z) and the initial similarity are derived from the slope of the regression (−2z) and the mean of similarity at 16 km; respectively. The statistical comparison between region and organism was performed by examining the overlap of the 95% confidence intervals of turnover rates or initial similarities.</p><p>Regression parameters of the Distance-Decay Relationships for Bacteria and Fungi.</p

PerMANOVA analyses of microbial communities t-RFLP profiles : influence of extraction method and soil type.

<p>PerMANOVA analysis showing the influence of extraction method and soil type in explaining overall variance in microbial communities.</p>*<p>denotes significance (<i>p</i><0.01).</p

Quantifications of crude extracted DNA and microbial abundances according to extraction procedures in different soils.

<p>Quantification of (A) crude extracted DNA, (B) 16S rRNA genes, (C) 18S rRNA genes, (D) archaeal 16S rRNA genes according to three different extraction procedures (ISO, GnS-GII and ISOm) in five different soils (C, E, F, L, R). Bars correspond to averages of three replicates ± SD (n = 3). Within each soil, bars topped by the same letter are not significantly different at <i>p</i><0.05.</p

Principal component analysis of microbial communities t-RFLP profiles according to DNA extraction procedures.

<p>Principal component analysis of t-RFLP profiles of (A) bacterial communities, (B) archaeal communities, and (C) fungal communities, coming from five different soils (C, E, F, L, R) according to three different extraction procedures (ISO, GnS-GII and ISOm).</p