Non-metric multidimensional scaling of phylogeny-based composition of denitrifying communities.

<p>The distance matrix was based on pairwise differences in the unique fraction of branches shared (UniFrac) for each soil community replicate in the maximum likelihood phylogentic tree of 400 <i>nos</i>Z gene sequences. Vectors indicate diversity metrics and modeled rate parameters that were significantly correlated with the ordination (<i>P</i><0.1): Chao richness index, Shannon’s diversity index (<i>H´</i>), phylogenetic diversity (PD), width of the modeled temperature gradient curve (<i>w</i>), denitrifiction rate at temperature optimum (<i>T_m</i>), salt concentration when denitrification rate was zero (SA0) and salt concentration at the initiation of rate inhibition (SAI). Stress was 12.0.</p

Model parameters representing the functional operating range for potential denitrification rates in assembled soil communities under temperature and salt concentration gradients modeled using a Gaussian function and power equation, respectively.

<p>Mean values of three field replicates of the soil communities are shown with standard deviations (±SD). Values followed by the same letter indicate treatments without significant differences (<i>p</i><0.1).</p>†<p>Gaussian function: Denitrification rate = <i>V_max</i> * e^{–(<i>T-Tm</i>)²^{/(2*<i>w</i>²⁾ where <i>V_ma</i>_x = maximum denitrification rate, <i>T</i> = tested temperature, <i>T_m</i> = optimum temperature and <i>w</i> = measure of the width of the curve.}}</p>§<p>Power equation: Denitrification rate = <i>k</i>/√(<i>c</i>) - <i>a</i>, where <i>k</i> = slope, <i>c</i> = % salt concentration and <i>a</i> = intercept. From the equation, the salt concentration when denitrification begins to be inhibited (SAI) and when the rate reaches zero (SA0) were calculated.</p

Normalized denitrification rates at different temperatures and salt concentrations.

<p>The rates are normalized by percent of the maximum rate within each soil community replicate and modeled using a Gaussian function and a power equation for temperature (a) and salt concentration (b) gradients, respectively. The fitted curves and data points are colored by community and soil treatment: Red, community A, fallow; Green, community B, unfertilized; Blue, community C, nitrate fertilized; and Black, community J, cattle manure fertilized. Each field replicate within a treatment/community is represented by different symbols.</p

Venn diagram representing shared and unique restriction fragment length polymorphisms (RFLP) groups for denitrifying communities.

<p>The groups were detected by screening ∼100 <i>nosZ</i> gene clones retrived from soil communities A–C and J. Community A had 30, B had 34, C had 23 and J had 44 of the 64 groups in total.</p

Diversity indices of denitrifying bacterial communities determined from RFLP group membership using Chao and Shannon (<i>H</i>') metrics or by comparative sequence analysis for phylogenetic diversity (PD), net relatedness index (NRI), and nearest taxon index (NTI) based on <i>nosZ</i> gene clones from each soil community (n = 3).

<p>Values in parentheses indicate the lower and upper 95% confidence intervals <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0051962#pone.0051962-Schloss1" target="_blank">[27]</a> and * indicate values significantly different from the null (<i>p</i><0.05).</p

Field, Experimental plot, and AOB data for JEcol-2015-0504.R1

Microsoft Excel file, multiple tabs. Includes all all field collected, experimental plot, and AOB data for JEcol-2015-0504.R1

Appendix A. Between-group analysis describing the structure of bacterial communities for all the studied plant species.

Between-group analysis describing the structure of bacterial communities for all the studied plant species