Soil Bacterial Communities Exhibit Strong Biogeographic Patterns at Fine Taxonomic Resolution

MSystems
Sean K BayChris Greening

Abstract

Bacteria have been inferred to exhibit relatively weak biogeographic patterns. To what extent such findings reflect true biological phenomena or methodological artifacts remains unclear. Here, we addressed this question by analyzing the turnover of soil bacterial communities from three data sets. We applied three methodological innovations: (i) design of a hierarchical sampling scheme to disentangle environmental from spatial factors driving turnover; (ii) resolution of 16S rRNA gene amplicon sequence variants to enable higher-resolution community profiling; and (iii) application of the new metric zeta diversity to analyze multisite turnover and drivers. At fine taxonomic resolution, rapid compositional turnover was observed across multiple spatial scales. Turnover was overwhelmingly driven by deterministic processes and influenced by the rare biosphere. The communities also exhibited strong distance decay patterns and taxon-area relationships, with z values within the interquartile range reported for macroorganisms. These biogeographical patterns were weakened upon applying two standard approaches to process community sequencing data: clustering sequences at 97% identity threshold and/or filtering the rare biosphere (sequences...Continue Reading

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Methods Mentioned

BETA
amplicon sequencing
electrophoresis
amplicon and shotgun sequencing

Software Mentioned

hmmsearch HMMER
MAFFT
vegan
BBTools
ggplot2
zetadiv
deblur
R
q2
GraftM

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