Diversity and composition of cave methanotrophic communities

Abstract

ABSTRACTMethane oxidizing bacteria (methanotrophs) are a ubiquitous group of microorganisms that represent a major sink for the greenhouse gas methane (CH4). Recent studies have demonstrated that methanotrophs are abundant and contribute to CH4 dynamics in caves. However, very little is known about what controls the distribution and abundance of methanotrophs in subterranean ecosystems. Here, we report a survey of sediments collected from >20 caves in North America to elucidate the factors shaping cave methanotroph communities. Using 16S rRNA sequencing, we recovered methanotrophs from nearly all (98 %) of the samples, including cave sites where CH4 concentrations were at or below detection limits (≤ 0.3 ppmv). We identified a core microbiome among caves that was dominated by members of the USC-γ clade, which are recognized as high-affinity methanotrophs. Although methanotrophs were associated with local-scale mineralogy, their community composition did not systematically vary between the entrances and interior of caves, where CH4 concentrations varied. However, we did detect a decay in compositional similarity of methanotrophic community composition with geographic distance. This biogeographic pattern is consistent with dispersal limitation perhaps due to the insular nature of cave ecosystems. Last, the relative abundance of methanotrophs was positively correlated with cave-air CH4 concentrations—suggesting that these microorganisms contribute to CH4 flux in subterranean ecosystems.IMPORTANCERecent observations have shown that the atmospheric greenhouse gas methane (CH4) is consumed by microorganisms (methanotrophs) in caves at rates comparable to CH4 oxidation in surface soils. Caves are abundant in karst landscapes that comprise 14 % of Earth’s land surface area, and therefore may be acting as a substantial CH4 sink. A detailed ecological understanding of the forces that shape methanotrophic communities in caves is lacking. We sampled cave sediments to better understand the community composition and structure of cave methanotrophs. Our results show that the members of the USC- γ clade are dominant in cave communities, that the relative abundance of methanotrophs was positively correlated with CH4 concentrations in cave air, and that methanotroph relative abundance was correlated with local scale mineralogy of soils.