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

By R. Jones, M. Robeson, C. Lauber, Micah Hamady, Rob Knight, Noah Fierer. The ISME Journal, 2009

1,127 citations recorded by the source corpus.

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.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c9f0572c65f905725ac7f958f8d56f4dcea25a33

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Citations in the corpus

Soil pH drives the spatial distribution of bacterial communities along elevation on Changbai Mountain (2013, background): “For instance, the percentage of Acidobacteria has been shown to increase with lower pH (Jones et al., 2009; Dimitriu and Grayston, 2010); subgroups within the Acidobacteria phylum are also shown to be strongly and divergently affected by pH (Jones et al.”
Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale (2009, background): “This was demonstrated in several recent studies (2, 12, 17, 28) that used bar-coded pyrosequencing to simultaneously analyze relatively large numbers of individual samples, surveying the bacterial community in each sample to an extent that would be difficult (or prohibitively expensive) using standa”
Effect of temperature on metabolic activity of intact microbial communities: Evidence for altered metabolic pathway activity but not for increased maintenance respiration and reduced carbon use efficiency (2011, background): “For example, Acidobacteria can make up more than 50% of the microbial community (Fierer et al., 2009; Jones et al., 2009).”
Using network analysis to explore co-occurrence patterns in soil microbial communities (2011, background): “In this case, the pattern is most likely driven by the previously observed phenomenon that soil pH largely governs the distributions of many soil acidobacterial taxa (Jones et al., 2009).”
Comparison of the Levels of Bacterial Diversity in Freshwater, Intertidal Wetland, and Marine Sediments by Using Millions of Illumina Tags (2012, background): “Acidobacteria are ubiquitous and abundant members of soil bacterial communities with a few described strains (14), but their role in freshwater sediment has not been well documented (22).”
Active and total microbial communities in forest soil are largely different and highly stratified during decomposition (2011, background): “In the most abundant phylum, Acidobacteria, the members of Gp1, Gp2 and Gp3 detected were also reported to occur in other low pH soils (Jones et al., 2009).”
The bacterial biogeography of British soils. (2011, background): “…are more abundant at low pH, yet display subgroup differences in response to soil pH: Groups 1 and 2 Acidobacteria were negatively correlated with soil pH, whereas Group 6 Acidobacteria increased in abundance with increasing pH (Lauber et al., 2008; 2009; Jones et al., 2009; Rousk et al., 2010).”
Shifts in bacterial community structure associated with inputs of low molecular weight carbon compounds to soil (2010, background): “the Acidobacteria phylum), cannot be readily isolated and cultivated in the laboratory, the metabolic capabilities of many taxa are not well known (Torsvik and Ovreas, 2002; Jones et al., 2009).”
Members of soil bacterial communities sensitive to tillage and crop rotation (2010, background): “The abundances of Groups 1, 2, 3, 12 and 13 had negative relationships with pH, while groups 4, 6, 7, 10, 11, 16, 17, 18, 22 and 25 had positive correlations with pH (Jones et al., 2009; Lauber et al., 2009).”
Influence of soil pH on the abundance and distribution of core and intact polar lipid-derived branched GDGTs in soil (2010, background): “Indeed, the abundance of Acidobacteria in soil has been shown to increase with decreasing pH (Sait et al., 2006; Männistö et al., 2007; Hartman et al., 2008; Lauber et al., 2009; Jones et al., 2009), similar to the relationship of branched GDGTs with soil pH.”