Diversity and Composition of Methanotroph Communities in Caves

Methane oxidizing microorganisms (methanotrophs) are ubiquitous in the environment and represent a major sink for the greenhouse gas methane (CH₄). Recent studies have demonstrated 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 soils 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 methanotroph community among caves comprised of high-affinity methanotrophs. Although associated with local-scale mineralogy, methanotroph composition did not systematically vary between the entrances and interior of caves, where CH₄ concentrations varied. We also observed methanotrophs are able to disperse readily between cave systems showing these organisms have low barriers to dispersal. Lastly, the relative abundance of methanotrophs was positively correlated with cave-air CH₄ concentrations, suggesting these microorganisms contribute to CH₄ flux in subterranean ecosystems. IMPORTANCE Recent observations have shown 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 represent a potentially important, but overlooked, CH₄ sink. We sampled cave soils to gain a better understand the community composition and structure of cave methanotrophs. Our results show the members of the USC-γ clade are dominant in cave communities and can easily disperse through the environment, methanotroph relative abundance was correlated with local scale mineralogy of soils, and the relative abundance of methanotrophs was positively correlated with CH₄ concentrations in cave air.