The diversity and biogeography of soil bacterial communities

Abstract

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 (r(2) = 0.70 and r(2) = 0.58, respectively; P < 0.0001 in both cases). Bacterial diversity 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.

Fig. 1.

The relationship between soil pH and bacterial phylotype diversity (A) and phylotype richness (B), defined as the number of unique phylotypes. Diversity was estimated by using the Shannon index, a summary variable that incorporates the richness and evenness of phylotypes (20). Symbols correspond to general ecosystem categories, and labels denote individual soils (see Table 3). Detailed information on the individual soils is provided in Table 3. Both quadratic regressions (H′=–0.08pH² + 1.12 pH – 0.5, r² = 0.70 for A and Richness =–1.65pH² + 23.2pH – 42.3, r² = 0.58 for B) were statistically significant (P < 0.0001). There was no significant correlation between the residuals of the two regressions shown here and any of the other soil and site variables listed in Table 1 (P > 0.25 in all cases).

Fig. 2.

Relationships between phylotype diversity (Shannon index) and MAT, latitude, PET, and soil pH (as in Fig. 1 A). MAT, PET, and latitude are typically good predictors of animal and plant diversity at the continental scale (17, 18). In contrast, soil pH is the best predictor of bacterial diversity. The r² values for the MAT, latitude, PET, and pH regressions are 0.01, 0.16, 0.02, and 0.70, respectively (see Table 1 for complete regression statistics).

Fig. 3.

Nonmetric multidimensional scaling plots of soil bacterial communities, showing the relative differences in community composition. Plots A and B are identical except that A is overlayed with general ecosystem type and B is overlayed with pH category. The r² values between ordination distance and distance in the original space are 0.73 and 0.16 for axis 1 and axis 2, respectively. Soil pH explains 83% of the variability along the primary axis, axis 1 (see text). The addition of more than two dimensions did not lead to a significant increase in the explanatory power of the ordination. The Sorensen distance metric (44) was used to quantify the similarity between phylotype patterns.