A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses

Abstract

Acidobacteria are ubiquitous and abundant members of soil bacterial communities. However, an ecological understanding of this important phylum has remained elusive because its members have been difficult to culture and few molecular investigations have focused exclusively on this group. We generated an unprecedented number of acidobacterial DNA sequence data using pyrosequencing and clone libraries (39,707 and 1787 sequences, respectively) to characterize the relative abundance, diversity and composition of acidobacterial communities across a range of soil types. To gain insight into the ecological characteristics of acidobacterial taxa, we investigated the large-scale biogeographic patterns exhibited by acidobacterial communities, and related soil and site characteristics to acidobacterial community assemblage patterns. The 87 soils analyzed by pyrosequencing contained more than 8600 unique acidobacterial phylotypes (at the 97% sequence similarity level). One phylotype belonging to Acidobacteria subgroup 1, but not closely related to any cultured representatives, was particularly abundant, accounting for 7.4% of bacterial sequences and 17.6% of acidobacterial sequences, on average, across the soils. The abundance of Acidobacteria relative to other bacterial taxa was highly variable across the soils examined, but correlated strongly with soil pH (R=-0.80, P<0.001). Soil pH was also the best predictor of acidobacterial community composition, regardless of how the communities were characterized, and the relative abundances of the dominant Acidobacteria subgroups were readily predictable. Acidobacterial communities were more phylogenetically clustered as soil pH departed from neutrality, suggesting that pH is an effective habitat filter, restricting community membership to progressively more narrowly defined lineages as pH deviates from neutrality.

Figure 1

Relationship between pH and the relative abundance of Acidobacteria in 87 soil bacterial communities using pyrosequencing data. Abundance of Acidobacteria is strongly and negatively correlated o with pH (Spearman's rank correlation: R=−0.80, P<0.001).

Figure 2

Effect of pH on abundance of Acidobacteria subgroups (1–7 and 16) relative to all Acidobacteria using pyrosequencing and clone library data. Triangles (black) represent pyrosequencing data; circles (grey) represent clone library data. Spearman's rank correlations between subgroup abundance and pH are depicted. NS, not significant; ND, not detected. *P<0.05; **P<0.001.

Figure 3

The net relatedness index (NRI) measures phylogenetic evenness. Positive NRI values indicate that communities are phylogenetically clustered and negative values indicate phylogenetic evenness. Here, phylogenetic clustering is positively correlated with departure from neutral pH (R²=0.229, P<0.05); the more the soil pH departs from neutrality, the more the communities are phylogenetically clustered. Median NRI values are plotted.

Figure 4

Non-metric multi-dimensional scaling plot of soil community assembly patterns (using Bray–Curtis-transformed pyrosequencing data) as related to soil pH. The first principal axis is dominated by soil pH effects, showing the key effect of pH on acidobacterial community assembly.

Figure 5

Relative abundances of the 20 most abundant phylotypes (97% OTU designation) in individual soil samples using clone library data. Subgroups are indicated over phylotypes. Soils are arranged from lowest pH (CF2) to highest pH (SA2). Phylotypes with asterisks share >97.0% sequence similarity with a cultured isolate. Percentages at bottom indicate the abundance of each phylotype relative to all detected acidobacterial sequences (values corrected for acidobacterial-specific primers not detecting certain subgroups; see text).