The chosen few\u2014variations in common and rare soil bacteria across biomes

Samuel Bickel,Dani Or

doi:10.1038/s41396-021-00981-3

Abstract

Soil bacterial communities are dominated by a few abundant species, while their richness is associated with rare species with largely unknown ecological roles and biogeography. Analyses of previously published soil bacterial community data using a novel classification of common and rare bacteria indicate that only 0.4% of bacterial species can be considered common and are prevalent across biomes. The remaining bacterial species designated as rare are endemic with low relative abundances. Observations coupled with mechanistic models highlight the central role of soil wetness in shaping bacterial rarity. An individual-based model reveals systematic shifts in community composition induced by low carbon inputs in drier soils that deprive common species of exhibiting physiological advantages relative to other species. We find that only a “chosen few” common species shape bacterial communities across biomes; however, their contributions are curtailed in resource-limited environments where a larger number of rare species constitutes the soil microbiome.

Highlights

Bacterial communities are characterized by strongly skewed relative abundance distributions (RADs) with most phylotypes present at low relative abundances [1]
The classification of common and rare species was achieved by using a global threshold of relative abundance based on minimizing cross-entropy [33], i.e., a threshold that minimizes the amount of information needed to reconstruct the RAD given the binary classification of common and rare species (Fig. 2a)
The resulting threshold to delineate the relative abundance of common species was remarkably consistent (0.019 ± 0.002%, bootstrap mean ± SD; Table S2) and comparable to previous, empirical, or operationally defined thresholds based on relative abundance [12, 17, 20]

Summary

Introduction

Bacterial communities are characterized by strongly skewed relative abundance distributions (RADs) with most phylotypes (or “species” for simplicity) present at low relative abundances [1] These rare bacterial species are considered ecologically important [2]. Despite the high functional potential of the soil microbiome and its diverse genetic composition [5, 11], only a few bacterial species appear to be prevalent across soils from different environments [12, 13]. The processes that affect rare bacterial species remain largely unknown [16, 19, 20] or are overlooked [21]

Methods

Results

Conclusion