The ubiquitous soil verrucomicrobial clade 'Candidatus Udaeobacter' shows preferences for acidic pH

Members of the verrucomicrobial clade 'Candidatus Udaeobacter' rank among the most dominant bacterial phylotypes in soil. Nevertheless, despite this global prevalence, in-depth analyses with respect to pH preferences of 'Ca. Udaeobacter' representatives are still lacking. Here, we utilized a recently designed primer pair, specifically targeting 'Ca. Udaeobacter', to investigate links between soil pH and the abundance as well as phylotype composition of this largely unexplored verrucomicrobial clade. Based on 150 forest and 150 grassland soils, comprising a broad pH range, we determined the highest total abundance of 'Ca. Udaeobacter' in strongly acidic soil (pH, ~5.1) and, noteworthy, in ultra-acidic soil (pH < 3.5) and at a pH ≥ 7, its abundance drastically declined. When we analysed the six most dominant amplicon sequence variants affiliated with 'Ca. Udaeobacter' separately, their abundances peaked within a pH range of approximately 4.7-5.2, and only in one case at slightly acidic soil pH (pH, 6.1). Our study benefits from a combination of quantitative real-time PCR and high-throughput amplicon sequencing, enabling for the first time a highly specific abundance analysis of representatives affiliated with 'Ca. Udaeobacter', which revealed that this globally abundant verrucomicrobial clade shows preferences for acidic soil.