AUTHOR=Allenby Alexander , Cunningham Mark R. , Hillebrand-Voiculescu Alexandra , Comte Jean-Christophe , Doherty Rory , Kumaresan Deepak 

TITLE=Occurrence of methane-oxidizing bacteria and methanogenic archaea in earth’s cave systems—A metagenomic analysis

JOURNAL=Frontiers in Ecology and Evolution

VOLUME=10

YEAR=2022

URL=https://www.frontiersin.org/journals/ecology-and-evolution/articles/10.3389/fevo.2022.909865

DOI=10.3389/fevo.2022.909865

ISSN=2296-701X

ABSTRACT=<p>Karst ecosystems represent up to 25% of the land surface and recent studies highlight their potential role as a sink for atmospheric methane. Despite this, there is limited knowledge of the diversity and distribution of methane-oxidizing bacteria (MOB) or methanogens in karst caves and the sub-surface environment in general. Here, we performed a survey of 14 shotgun metagenomes from cave ecosystems covering a broad set of environmental conditions, to compare the relative abundance and phylogenetic diversity of MOB and methanogens, targeting biomarker genes for methane monooxygenase (<italic>pmoA</italic> and <italic>mmoX</italic>) and methyl-coenzyme M reductase (<italic>mcrA</italic>). Taxonomic analysis of metagenomes showed 0.02–1.28% of classified reads were related to known MOB, of which <italic>Gammaproteobacterial</italic> MOB were the most abundant making up on average 70% of the surveyed caves’ MOB community. Potential for biogenic methane production in caves was also observed, with 0.008–0.39% of reads classified to methanogens and was dominated by sequences related to <italic>Methanosarcina</italic>. We have also generated a cave ecosystems protein database (CEPD) based on protein level assembly of cave metagenomes that can be used to profile genes of interest.</p>