Most prevalent phyla.

<p>Taxonomic classification raking the 1^st, 2^nd, and 3^rd most prevalent phylum in each of the six sample sites. Data were classified using mothur’s classify.seqs command and GreenGenes as the reference database (May 2013). In parentheses is the relative abundance of each phylum as a percentage of the total number of sequences within each site.</p><p>Most prevalent phyla.</p

Chao richness estimates of species-level OTUs.

<p><b>(A)</b> Richness level calculated for each of 81 samples, color-coded and grouped by site (INT, TRN, or ORG) and sample type (coffee rhizosphere or soil control) as detailed in the methods. Richness estimates (± 95% confidence intervals) of 97% similarity OTUs calculated in mothur and plotted in R. Black circle indicates number of observed OTUs. <b>(B)</b> Mean Chao richness estimates (± standard error) from individual samples shown in Fig 1A within each sample site and sample type calculated in R.</p

LEfSe discriminatory OTUs among coffee rhizosphere samples.

<p>Heatmap of LEfSe results. The number of discriminatory OTUs in each phylum is shown in corresponding box for each of the three sample sites (INT, TRN, and ORG). Statistic calculated in mothur and results plotted in R.</p

Farm characteristics.

<p>Collected from interviews.</p><p>^a Distance between each coffee tree in a row versus distance between rows (in meter).</p><p>Farm characteristics.</p

Summary data of OTUs, richness, and diversity.

<p>Values shown for each of the six sites (INT, TRN, or ORG) and each sample type (coffee or control) combinations, calculated using mothur. OTUs were clustered at 97% sequence similarity.</p><p>^a CI = confidence interval</p><p>Summary data of OTUs, richness, and diversity.</p