The under-recognized dominance of Verrucomicrobia in soil bacterial communities

Abstract

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.

Figure 1

Relative abundance of Verrucomicrobia in soil. A) Percent abundance of Verrucomicrobia in previously published datasets (124 soils; left column) and this study (181 soils in all, including both surface and subsurface samples; right column). B) Percent abundance of Verrucomicrobia for a subset of 55 soils, analyzed using the 27F/338R primer set (Lauber et al., 2009; left column), then reanalyzed in the present study using the 515F/806R primer set (right column). Error bars represent standard error of the mean.

Figure 2

Abundance of Verrucomicrobia by biome. Numbers over each bar represent the number of soil samples for that biome. Total height of each bar represents the mean abundance of Verrucomicrobia (relative to all bacteria) in each biome.

Figure 3

Relative abundance of Verrucomicrobia relative to other bacterial phyla in nine soil pits, ranging in maximum depth from 20 to 170 cm.

Figure 4

Abundance of classes within the phylum Verrucomicrobia in nine soil pits, ranging in maximum depth from 20 to 170 cm. Classes depicted on bar from left to right: Spartobacteria, Subidivision 3, Opitutae, Unassigned, and Verrucomicrobiae.