Occurrence of methane oxidizing bacteria and methanogenic archaea in Earth’s cave systems: a metagenomic analysis

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

Research output: Contribution to journalArticlepeer-review


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 (pmoA and mmoX) and methyl-coenzyme M reductase (mcrA). Taxonomic analysis of metagenomes showed 0.02–1.28% of classified reads were related to known MOB, of which Gammaproteobacterial 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 Methanosarcina. 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.
Original languageEnglish
Article number909865
Number of pages14
JournalFrontiers in Ecology and Evolution
Early online date15 Aug 2022
Publication statusPublished - 15 Aug 2022


  • methanotrophs
  • methanogens
  • methane
  • karst cave
  • biogeochemical cycles


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