Dynamic Methanogens – Persistent Methanotrophs: Shedding Light on Microbial Communities of the Methane Cycle Across Seasons in Permafrost-Affected Soils in West Greenland

About 15 % of the northern hemisphere is covered by permafrost, which is subjected to climate change and therefore drastically changing conditions for soil microorganisms. Progressing permafrost thaw could enable formerly inactive microorganisms to (re)gain activity and metabolize carbon. Methane (CH4) is a biogenic greenhouse gas (GHG) that is approximately 28 times more potent than carbon dioxide (CO2) on a 100-year time horizon. It is currently not well understood how the emissions of this potent GHG from permafrost-affected soils will be changing under the effects of climate change.

It was suggested that during freeze-thaw-cycles and even during winter, Arctic tundra soils emit substantial amounts of methane but since sampling in permafrost regions is logistically intricate, there is a low study coverage. Here, we present molecular data of four distinct field campaigns on Disko Island, West Greenland. The studies encompass three years (2022 to 2024) and three different seasons: September – time of maximum active layer depth, July – initial annual thawing period, and April – completely frozen soil with snow cover. We sampled two moisture transects in permafrost-affected soils, each from higher elevation with dry soil towards lower elevation, with soil almost completely water saturated. The soil moisture gradients were chosen, because they are potentially important drivers of the ratio between CH4 oxidation vs. production throughout the seasons. Each plot was sampled in triplicates to varying depths of 10 cm to up to 90 cm. The samples were taken from identified soil horizons and DNA for metagenome analysis was extracted. The resulting total of 235 samples over all four sampling seasons were used for 16S rRNA gene metabarcoding (Illumina) to investigate the microbial community diversity over the different sampling seasons.

Methane oxidizers (methanotrophs) were constantly abundant but accounted for less than 1 % of the relative abundance across the samples. The abundance of methane producers (methanogens), mostly Methanobacterium spp., substantially changed throughout the different time points, locations and depths, and accounted at times for over 20 % of relative abundance of all prokaryotes while being completely absent in other samples.

Additional quantitative PCR (qPCR) analyses have revealed distinct distributions of both pmoA (gene for a membrane-bound enzyme for oxidizing methane) and mcrA (gene for the final step of biological methane production) for September 2022, with a higher methanogenic gene abundance in deep and wet samples. This was confirmed through incubation experiments and subsequent gas analyses in the laboratory. Further qPCR will reveal the CH4-oxidation and -production potential for the other time points. Accompanying to this, other environmental parameters (H2O content, season, pH) will allow to assess potential key factors for methanogenesis vs. methanotrophy in a final correlation approach.

Our results show that permafrost-affected soils harbor a surprisingly large spatiotemporal variability in community composition and abundance of methanogens while the methanotroph community seems to be comparably stable. These findings have implications for future GHG budget calculations of the Earth, as this suggests that methanotrophs and methanogens would react very differently to Earth’s changing climate and resulting environmental changes, such as water saturation of soils.