Aerobic methanotrophs in anoxic soils: comparing peatland, rice paddy and thawing permafrost methanotrophs and their respective metabolisms

Soil microbial communities often get sequenced using general primers that allow the detection of a wide range of microbial species. This sometimes leads to unexpected finds in sequencing data. We noticed the presence of sequences attributed to aerobic methanotrophs in multiple field sites. These were all carbon rich, water saturated, anoxic soils that were known for their high methane emission potential. Using qPCR, we found pmoA to be abundant deep in the anoxic layer of these soils. Although aerobic methanotrophs have been found in anoxic locations before, they are often dismissed as inactive or as purely a remnant of past oxic conditions. We aimed to discover whether these methane oxidizing bacteria could play a significant role in in situ methane oxidation and in mediating methane emissions.

Using samples from these locations, we created oxic enrichment cultures that rapidly became dominated by methanotrophic bacteria, the same that were detected in the initial anoxic soil sample sequencing results. These enrichment cultures were dominated by methanotrophs of the genera Methylobacter (thawed permafrost soil), Methylotetracoccus (rice paddy) and Methylovulum (alpine peatland). Although some species of these genera have been detected in anoxic locations before, and certain species are known to have the genetic capability to perform fermentation, it is unknown which electron acceptor these methanotrophs rely on in anoxic or hypoxic conditions. We perform culture experiments with iron, nitrate and organic compounds as electron acceptors, to elucidate the pathways used by these methanotrophs. We also added enriched methanotrophs to natural soil samples of the same locations, to test whether these methanotrophs were able to enhance methane removal from the original sampling locations.