Globally Abundant “ Candidatus Udaeobacter” Benefits from Release of Antibiotics in Soil and Potentially Performs Trace Gas Scavenging

Willms, Inka M.; Rudolph, Anina Y.; Göschel, Isabell; Bolz, Simon H.; Schneider, Dominik; Penone, Caterina; Poehlein, Anja; Schöning, Ingo; Nacke, Heiko; Kent, Angela D. (2020). Globally Abundant “ Candidatus Udaeobacter” Benefits from Release of Antibiotics in Soil and Potentially Performs Trace Gas Scavenging. mSphere, 5(4), p. 186. American Society for Microbiology 10.1128/mSphere.00186-20

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Verrucomicrobia affiliated with “Candidatus Udaeobacter” belong to the most abundant soil bacteria worldwide. Although the synthesis of antibiotics presumably evolved in soil, and environmental pollution with antimicrobials increases, the impact of these complex molecules on “Ca. Udaeobacter” remains to be elucidated. In this study, we demonstrate that “Ca. Udaeobacter” representatives residing in grassland as well as forest soil ecosystems show multidrug resistance and even take advantage of antibiotics release. Soils treated with up to six different antibiotics exhibited a higher “Ca. Udaeobacter” abundance than corresponding controls after 3, 8, and 20 days of incubation. In this context, we provide evidence that “Ca. Udaeobacter” representatives may utilize nutrients which are released due to antibiotic-driven lysis of other soil microbes and thereby reduce energetically expensive synthesis of required biomolecules. Moreover, genomic analysis revealed the presence of genes conferring resistance to multiple classes of antibiotics and indicated that “Ca. Udaeobacter” representatives most likely oxidize the trace gas H2 to generate energy. This energy might be required for long-term persistence in terrestrial habitats, as already suggested for other dominant soil bacteria. Our study illustrates, for the first time, that globally abundant “Ca. Udaeobacter” benefits from release of antibiotics, which confers advantages over other soil bacteria and represents a so-far overlooked fundamental lifestyle feature of this poorly characterized verrucomicrobial genus. Furthermore, our study suggests that “Ca. Udaeobacter” representatives can utilize H2 as an alternative electron donor.

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