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 largescale 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 ¼ À0.80, Po0.001). 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.

Seasonality and resource availability control bacterial and archaeal communities in soils of a temperate beech forest

“…Several members of this phylum have been evidenced to be facultative or obligatory anaerobic organotrophs (Jones et al, 2009;Fierer et al, 2007). Hence, their abundance may be particularly favored by high soil moisture together with effects on community structure, as we found in the present field study and was proven by other reports (for example, Janssen, 2006).…”

Illumina MiSeq sequencing investigation on the contrasting soil bacterial community structures in different iron mining areas

“…PCA at all levels demonstrated that the large gap between CV and the other regions in the unpolluted area was in accordance with the fact that the predominance of Acidobacteria in CV was closely related with the strong acidic nature of the site. Many research studies have confirmed that this phenomenon had close relationship with the strong acidic nature of soil (Jones et al 2009). …”

Examining the global distribution of dominant archaeal populations in soil

“…With this level of coverage, the full extent of microbial diversity has not been surveyed; however, previous work (Fierer et al, 2008;Jones et al, 2009;Lauber et al, 2009;Miller et al, 2009) has shown that patterns of beta diversity and overall taxon relative abundances of dominant lineages can be accurately inferred with this depth of sequencing. Of these reads, 159 618 (99%) could be confidently identified, the majority to the level of family or genus.…”