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TOWARD AN ECOLOGICAL CLASSIFICATION OF SOIL BACTERIA

TOWARD AN ECOLOGICAL CLASSIFICATION OF SOIL BACTERIA Although researchers have begun cataloging the incredible diversity of bacteria found in soil, we are largely unable to interpret this information in an ecological context, including which groups of bacteria are most abundant in different soils and why. With this study, we examined how the abundances of major soil bacterial phyla correspond to the biotic and abiotic characteristics of the soil environment to determine if they can be divided into ecologically meaningful categories. To do this, we collected 71 unique soil samples from a wide range of ecosystems across North America and looked for relationships between soil properties and the relative abundances of six dominant bacterial phyla (Acidobacteria, Bacteroidetes, Firmicutes, Actinobacteria, αα-Proteobacteria, and the ββ-Proteobacteria). Of the soil properties measured, net carbon (C) mineralization rate (an index of C availability) was the best predictor of phylum-level abundances. There was a negative correlation between Acidobacteria abundance and C mineralization rates ( r 2 == 0.26, P < 0.001), while the abundances of ββ-Proteobacteria and Bacteroidetes were positively correlated with C mineralization rates ( r 2 == 0.35, P < 0.001 and r 2 == 0.34, P < 0.001, respectively). These patterns were explored further using both experimental and meta-analytical approaches. We amended soil cores from a specific site with varying levels of sucrose over a 12-month period to maintain a gradient of elevated C availabilities. This experiment confirmed our survey results: there was a negative relationship between C amendment level and the abundance of Acidobacteria ( r 2 == 0.42, P < 0.01) and a positive relationship for both Bacteroidetes and ββ-Proteobacteria ( r 2 == 0.38 and 0.70, respectively; P < 0.01 for each). Further support for a relationship between the relative abundances of these bacterial phyla and C availability was garnered from an analysis of published bacterial clone libraries from bulk and rhizosphere soils. Together our survey, experimental, and meta-analytical results suggest that certain bacterial phyla can be differentiated into copiotrophic and oligotrophic categories that correspond to the r - and K -selected categories used to describe the ecological attributes of plants and animals. By applying the copiotroph––oligotroph concept to soil microorganisms we can make specific predictions about the ecological attributes of various bacterial taxa and better understand the structure and function of soil bacterial communities. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Ecology Ecological Society of America

TOWARD AN ECOLOGICAL CLASSIFICATION OF SOIL BACTERIA

Fierer, Noah; Bradford, Mark A.; Jackson, Robert B.
Ecology , Volume 88 (6) – Jun 1, 2007
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References (63)

Publisher
Ecological Society of America
Copyright
Copyright © 2007 by the Ecological Society of America
Subject
Special Feature——New Directions in Microbial Ecology
ISSN
0012-9658
DOI
10.1890/05-1839
Publisher site
See Article on Publisher Site

Abstract

Although researchers have begun cataloging the incredible diversity of bacteria found in soil, we are largely unable to interpret this information in an ecological context, including which groups of bacteria are most abundant in different soils and why. With this study, we examined how the abundances of major soil bacterial phyla correspond to the biotic and abiotic characteristics of the soil environment to determine if they can be divided into ecologically meaningful categories. To do this, we collected 71 unique soil samples from a wide range of ecosystems across North America and looked for relationships between soil properties and the relative abundances of six dominant bacterial phyla (Acidobacteria, Bacteroidetes, Firmicutes, Actinobacteria, αα-Proteobacteria, and the ββ-Proteobacteria). Of the soil properties measured, net carbon (C) mineralization rate (an index of C availability) was the best predictor of phylum-level abundances. There was a negative correlation between Acidobacteria abundance and C mineralization rates ( r 2 == 0.26, P < 0.001), while the abundances of ββ-Proteobacteria and Bacteroidetes were positively correlated with C mineralization rates ( r 2 == 0.35, P < 0.001 and r 2 == 0.34, P < 0.001, respectively). These patterns were explored further using both experimental and meta-analytical approaches. We amended soil cores from a specific site with varying levels of sucrose over a 12-month period to maintain a gradient of elevated C availabilities. This experiment confirmed our survey results: there was a negative relationship between C amendment level and the abundance of Acidobacteria ( r 2 == 0.42, P < 0.01) and a positive relationship for both Bacteroidetes and ββ-Proteobacteria ( r 2 == 0.38 and 0.70, respectively; P < 0.01 for each). Further support for a relationship between the relative abundances of these bacterial phyla and C availability was garnered from an analysis of published bacterial clone libraries from bulk and rhizosphere soils. Together our survey, experimental, and meta-analytical results suggest that certain bacterial phyla can be differentiated into copiotrophic and oligotrophic categories that correspond to the r - and K -selected categories used to describe the ecological attributes of plants and animals. By applying the copiotroph––oligotroph concept to soil microorganisms we can make specific predictions about the ecological attributes of various bacterial taxa and better understand the structure and function of soil bacterial communities.

Journal

Ecology – Ecological Society of America

Published: Jun 1, 2007

Keywords: Acidobacteria ; copiotroph ; K-selection ; microbial diversity ; oligotroph ; Proteobacteria ; quantitative PCR ; real-time PCR ; r-selection ; soil carbon

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