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A continental-scale description of soil bacterial communities and the environmental factors influencing …

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- The diversity and biogeography of soil bacterial communities

The diversity and biogeography of soil bacterial communities

Noah Fierer *, {dagger}, and Robert B. Jackson *, {ddagger}

*Department of Biology and {ddagger}Nicholas School of the Environment and Earth Sciences, Duke University, Durham, NC 27708

Edited by Christopher B. Field, Carnegie Institution of Washington, Stanford, CA, and approved December 5, 2005 (received for review August 29, 2005)


For centuries, biologists have studied patterns of plant and animal diversity at continental scales. Until recently, similar studies were impossible for microorganisms, arguably the most diverse and abundant group of organisms on Earth. Here, we present a continental-scale description of soil bacterial communities and the environmental factors influencing their biodiversity. We collected 98 soil samples from across North and South America and used a ribosomal DNA-fingerprinting method to compare bacterial community composition and diversity quantitatively across sites. Bacterial diversity was unrelated to site temperature, latitude, and other variables that typically predict plant and animal diversity, and community composition was largely independent of geographic distance. The diversity and richness of soil bacterial communities differed by ecosystem type, and these differences could largely be explained by soil pH (r2 = 0.70 and r2 = 0.58, respectively; P was highest in neutral soils and lower in acidic soils, with soils from the Peruvian Amazon the most acidic and least diverse in our study. Our results suggest that microbial biogeography is controlled primarily by edaphic variables and differs fundamentally from the biogeography of "macro" organisms.

biodiversity | microbial ecology | soil bacteria | terminal-restriction fragment length polymorphism

PNAS | January 17, 2006 | vol. 103 | no. 3 | 626-631



Although microorganisms are perhaps the most diverse (1, 2) and abundant (3) type of organism on Earth, the distribution of microbial diversity at continental scales is poorly understood. Ecologists describing microbial biogeography typically invoke Beijerinck (4) from a century ago: "Everything is everywhere, the environment selects." However, few studies have attempted to verify this statement or specify which environmental factors exert the strongest influences on microbial communities in nature (5, 6). With the advent of ribosomal DNA-analysis methods that permit the characterization of bacterial communities without culturing (7, 8), it is now possible to examine the full extent of microbial diversity and describe the biogeographical patterns exhibited by microorganisms at large spatial scales.

Scientific understanding of microbial biogeography is particularly weak for soil bacteria, even though the diversity and composition of soil bacterial communities is thought to have a direct influence on a wide range of ecosystem processes (9, 10). Much of the recent work in soil microbial ecology has focused on cataloging the diversity of soil bacteria and documenting how soil bacterial communities are affected by specific environmental changes or disturbances. As a result, we know that soil bacterial diversity is immense (11, 12) and that the composition and diversity of soil bacterial communities can be influenced by a wide range of biotic and abiotic factors (13). However, almost all of this work has been site-specific, limiting our understanding of the factors that structure soil bacterial communities across biomes and regions.

We hypothesize that soil bacterial communities do exhibit biogeographical patterns at the continental scale of inquiry and that these patterns are predictable. Whereas previous studies have examined the biogeographical distributions of soil fungal communities (14) and individual strains of soil bacteria (15, 16), to our knowledge, no previous study has examined how entire soil bacterial communities are structured across large spatial scales. We hypothesize that the biogeographical patterns exhibited by soil bacteria will be fundamentally similar to the patterns observed with plant and animal taxa and that those variables which are frequently cited as being good predictors of animal and plant diversity, particularly those variables related to energy, water, or the water–energy balance (1719), will also be good predictors of bacterial diversity. To test these hypotheses, we used a ribosomal DNA-fingerprinting method to compare the composition and diversity of bacterial communities in 98 soils collected from across North and South America.

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