The under-recognized dominance of Verrucomicrobia in soil bacterial communities

By G. Bergmann, S. Bates, Kathryn G. Eilers, C. Lauber, J. Gregory Caporaso, William Walters, Rob Knight, Noah Fierer. Soil Biology and Biochemistry, 2011

699 citations recorded by the source corpus.

Verrucomicrobia are ubiquitous in soil, but members of this bacterial phylum are thought to be present at low frequency in soil, with few studies focusing specifically on verrucomicrobial abundance, diversity, and distribution. Here we used barcoded pyrosequencing to analyze verrucomicrobial communities in surface soils collected across a range of biomes in Antarctica, Europe, and the Americas (112 samples), as well as soils collected from pits dug in a montane coniferous forest (69 samples). Data collected from surface horizons indicate that Verrucomicrobia average 23% of bacterial sequences, making them far more abundant than had been estimated. We show that this underestimation is likely due to primer bias, as many of the commonly used PCR primers appear to exclude verrucomicrobial 16S rRNA genes during amplification. Verrucomicrobia were detected in 180 out of 181 soils examined, with members of the class Spartobacteria dominating verrucomicrobial communities in nearly all biomes and soil depths. The relative abundance of Verrucomicrobia was highest in grasslands and in subsurface soil horizons, where they were often the dominant bacterial phylum. Although their ecology remains poorly understood, Verrucomicrobia appear to be dominant in many soil bacterial communities across the globe, making additional research on their ecology clearly necessary.

Subfields: Ecology

View Paper: https://www.semanticscholar.org/paper/75fc01030fc0d3bcbda8aa40001894cf526388db

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecology

Citations in the corpus

Deciphering the associations between soil microbial diversity and ecosystem multifunctionality driven by long‐term fertilization management (2018, background): “Targeted PCRbased analyses of marker- genes are routinely used to investigate diversity, though this method can be biased against some microbial lineages (Bergmann et al., 2011; Tremblay et al., 2015).”
Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients (2011, methodology): “Amplifications were conducted in triplicate using The ISME Journal the primer set 515f/806r that targets a region of the 16S rRNA gene that yields accurate phylogenetic information (Liu et al., 2007) and should have few biases against any bacterial taxa (Bates et al., 2011; Bergmann et al., 2011).”
Consistent effects of nitrogen amendments on soil microbial communities and processes across biomes (2012, methodology): “A portion of the 16S rRNA gene was ampliﬁed in triplicate PCR reactions using the F515 and R805 primers designed to be universal for bacterial and archaeal taxa (Bates et al. , 2011; Bergmann et al. , 2011).”
The Effect of Tillage System and Crop Rotation on Soil Microbial Diversity and Composition in a Subtropical Acrisol (2012, background): “Studying undisturbed soils from four continents, Bergmann [41] found that 23% of bacterial sequences analyzed belonged to the Verrucomicrobia, which also was often the dominant phylum in these soils with under-recognized dominance in soil.”
Digging deeper to find unique microbial communities: The strong effect of depth on the structure of bacterial and archaeal communities in soil (2012, methodology): “Although Verrucomicrobia are likely to be far more abundant in soil than previous studies would suggest (as most of the commonly-used ‘universal’ bacterial primers are biased against Verrucomicrobia, (Bergmann et al., 2011)) the ecological niches inhabited by soil Verrucomicrobia remain largely unde”
Soil pH Determines Microbial Diversity and Composition in the Park Grass Experiment (2014, result): “This corroborates previous reports [29], which suggested that the phylum is specialized for oligotrophy.”
Microbial Diversity in Caves (2016, background): “They are one of the most abundant bacterial groups present in soils and marine waters (Bergmann et al. 2011; Op den Camp et al. 2009).”
The bacterial community inhabiting temperate deciduous forests is vertically stratified and undergoes seasonal dynamics (2015, background): “Previous studies of the diversity of bacterial communities pointed out a bias in designed 16S rRNA primers against less abundant groups (Bergmann et al., 2011).”
Using network analysis to explore co-occurrence patterns in soil microbial communities (2011, background): “3%) suggesting that, despite being abundant and ubiquitous in soils (Bergmann et al., 2011), they share a specific (and as yet undefined) niche (Figure 4).”
Rate-specific responses of prokaryotic diversity and structure to nitrogen deposition in the Leymus chinensis steppe (2014, background): “Our results confirmed the increase in predicted copiotrophic groups (Proteobacteria and Bacteriodetes) (Goldfarb et al., 2011; Ramirez et al., 2012), and a decrease in predicted oligotrophic groups (Acidobacteria and Nitrospirae) (Jones et al., 2009; Bergmann et al., 2011) with N addition.”
Experimental and analytical tools for studying the human microbiome (2011, background): “Furthermore, a complete bacterial phylum, Verrucomicrobia, is so poorly amplified by the F27–R338 primer set that this group was perceived to be a rare soil microorganism when it is, in fact, a dominant taxon that constitutes more than 20% of soil community member”
Embracing the unknown: disentangling the complexities of the soil microbiome (2017, methodology): “Furthermore, PCR-based marker gene analyses are routinely used to characterize soil microbial diversity, even though we know that they can be biased against some bacterial and archaeal lineages 46,47 .”