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

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Results and Discussion
- The diversity and biogeography of soil bacterial communities


Soil bacterial diversity, as estimated by phylotype richness and diversity (Shannon index) (20), varied across ecosystem types (Fig. 1). Of all soil and site variables examined, soil pH was, by far, the best predictor of both soil bacterial diversity (r2 = 0.70, P Table 1 and Fig. 1 A) and richness (r2 = 0.58, P Fig. 1B) with the lowest levels of diversity and richness observed in acid soils (Fig. 1). Because soils with pH levels >8.5 are rare, it is not clear whether the relationship between bacterial diversity is truly unimodal, as indicated in Fig. 1, or whether diversity simply plateaus in soils with near-neutral pHs. Likewise, because our fingerprinting method underestimates total bacterial diversity (see Methods), we cannot predict how the absolute diversity of bacteria changes across the pH gradient. When we compare paired sampling locations with similar vegetation and climate but very different soil pHs, we find evidence for the strong correlation between bacterial diversity and soil pH at the local scale. For example, two deciduous forest soils collected in the Duke Forest, North Carolina (see Table 3, which is published as supporting information on the PNAS web site), showed that the soil with the higher pH (DF2, pH = 6.8) had an estimated bacterial richness 60% higher than the more acidic soil (DF3, pH = 5.1). Similarly for two tropical forest soils collected the soil with the higher pH (PE8, pH = 5.5) had an estimated bacterial richness 26% higher than the more acidic soil (PE7, pH = 4.1).

Qualitatively, there was no clear relationship between soil bacterial diversity and plant diversity at the continental scale. Although plant diversity was not determined at each sampling site, ecosystems with the highest levels of bacterial diversity (semiarid ecosystems in the continental U.S.) have relatively low levels of plant diversity (21). Likewise, soils from terra firme sites in the Peruvian Amazon in our analysis had relatively low levels of bacterial diversity (H' = 2.5–2.7), but these sites have some of the highest recorded levels of plant diversity on Earth (22). In fact, we added the tropical sites at Manu National Park, Peru (PE, Table 3) and Missiones, Argentina (AR, Table 3) to test our initial relationship and to contrast microbial diversity at two tropical sites with high plant diversity but contrasting soil pH.

There was also no apparent latitudinal gradient in diversity (Table 1 and Fig. 2), unlike diversity observations for plants and animals (18). Consequently, the environmental factors frequently cited as good predictors of plant and animal diversity at continental scales, particularly mean annual temperature (MAT) and potential evapotranspiration (PET) (1719), had little effect on measured soil bacterial diversity (Fig. 2). Sampling resolution can have an important influence on the assessment of diversity patterns (23, 24), and, in this study, soils were collected from plots of {approx}100 m2 that are smaller in size than those commonly used to quantify large-scale patterns of plant and animal diversity (17). However, because individual soil bacteria are many orders-of-magnitude smaller than individual plants or animals (25), the number of individuals per plot may be directly comparable. It is also possible that the small size of our plots causes us to overestimate the importance of local parameters, such as soil pH, on bacterial community composition and underestimate the importance of parameters, such as PET and MAT, which are more regional in scale. Nonetheless, our results do suggest that the biogeographical patterns observed in soil bacterial communities are fundamentally different from those observed in well studied plant and animal communities that have provided the foundation for biogeographical theory to date.

Not only did we observe that soil pH was the best predictor of bacterial richness and diversity, it was also the strongest predictor of overall community composition (Fig. 3). We observed a general clustering of soil bacterial communities within ecosystems that corresponded to the observed pattern with pH across systems (Fig. 3). For example, the bacterial communities found in soils of arid and semiarid ecosystems, which generally have near-neutral pHs, cluster together, as do bacterial communities from temperate and tropical forest ecosystems, which generally have acidic soils. Of all of the soil and site characteristics examined, soil pH was the best predictor of soil microbial community composition at the continental scale (Table 2), and there was a strong correlation between the primary axis of Fig. 3, which describes 73% of the variation among soil communities, and soil pH (r2 = 0.83 for Axis 1, P pH and a number of other soil properties including soil moisture deficit (r = 0.68), soil organic C content (r = –0.53), and soil C:N ratio (r = –0.51), but the differences in bacterial community composition across ecosystems could largely be explained by differences in soil pH alone (rMantel = 0.75, r2 = 0.56, P affected by variation in sampling times, because all soils were collected near the height of the plant growing season at each site and the intrasite variability in bacterial community structure for soils collected at the same location 6 months apart was less than the intersite variability in bacterial community structure (see Fig. 4, which is published as supporting information on the PNAS website).

Whereas vegetation type, carbon availability, nutrient availability, and soil moisture may influence microbial community composition at local scales (13), soil pH was a better predictor of community structure at the continental scale (Table 2). The strong correlation between soil pH and microbial community structure could be a result of soil pH integrating a number of other individual soil and site variables. However, we would also expect soil pH to be an independent driver of soil bacterial diversity, because the intracellular pH of most microorganisms is usually within 1 pH unit of neutral (26). Moreover, any significant deviation in environmental (extracellular) pH should impose stress on single-celled organisms. The stress of residing in suboptimal pH environments has been shown to have a significant effect on the overall diversity and composition of microbial communities in a range of terrestrial and aquatic environments (2729).

The degree of similarity between soil bacterial communities was largely unrelated to geographic distance. For example, forest soils from the Northeast U.S., Northwest U.S., boreal, and tropical regions had bacterial communities that were relatively similar in composition. Once the soil environmental variables listed in Table 2 were taken into account, geographic distance was found to be a poor predictor of the degree of similarity in bacterial communities (rMantel = 0.13, r2 = 0.02, P = 0.15), suggesting that soils with similar environmental characteristics have similar bacterial communities regardless of geographic distance. We estimated the relationship between the number of unique taxa (phylotypes) and area sampled using the distance-decay approach (14, 30, 31). Our estimated z value, the rate of turnover of unique phylotypes across space, is 0.03 (95% confidence interval: 0.02 to 0.04, P z values reported for other microbial groups (14, 31) and much lower than z values commonly reported for plant and animal taxa (32). As suggested in refs. 14 and 31, the low z values reported for microbial taxa may be related, in part, to the discontinuous nature of the microbial habitats surveyed and the relatively low taxonomic resolution of the rDNA-based methodology used in this study. Nevertheless, our results provide strong evidence that environmental factors, such as soil pH, are more important than geographic distance in influencing the continental-scale spatial structuring of microbial communities at higher taxonomic levels. In the soil environment, the distribution and structure of bacterial communities can largely be understood in terms of habitat properties alone.

Here, we show that the structure of soil bacterial communities is not random at the continental scale and that the diversity and composition of soil bacterial communities at large spatial scales can largely be predicted with a single variable, soil pH. These results suggest that, to some degree, the large-scale biogeographical patterns observed in soil microorganisms are fundamentally distinct from those observed in well studied plant and animal taxa. Although the biogeography of microorganisms remains poorly understood, and many questions remain unanswered, a thorough integration of microbial ecology into the field of biogeography is likely to provide a more comprehensive understanding of the factors controlling the Earth's biodiversity and biogeochemistry.

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