Unique high Arctic methane metabolizing community revealed through in situ (13)CH(4)-DNA-SIP enrichment in concert with genome binning

• Published in: Scientific Reports
• Main Authors: Altshuler, Ianina, Raymond-Bouchard, Isabelle, Magnuson, Elisse, Tremblay, Julien, Greer, Charles W., Whyte, Lyle G.
• Format: Text
• Language: English
• Published: Nature Publishing Group UK 2022
• Subjects: Article; Arctic; arctic methane; permafrost
• Online Access: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8782848/; http://www.ncbi.nlm.nih.gov/pubmed/35064149; https://doi.org/10.1038/s41598-021-04486-z

Greenhouse gas (GHG) emissions from Arctic permafrost soils create a positive feedback loop of climate warming and further GHG emissions. Active methane uptake in these soils can reduce the impact of GHG on future Arctic warming potential. Aerobic methane oxidizers are thought to be responsible for this apparent methane sink, though Arctic representatives of these organisms have resisted culturing efforts. Here, we first used in situ gas flux measurements and qPCR to identify relative methane sink hotspots at a high Arctic cytosol site, we then labeled the active microbiome in situ using DNA Stable Isotope Probing (SIP) with heavy (13)CH(4) (at 100 ppm and 1000 ppm). This was followed by amplicon and metagenome sequencing to identify active organisms involved in CH(4) metabolism in these high Arctic cryosols. Sequencing of (13)C-labeled pmoA genes demonstrated that type II methanotrophs (Methylocapsa) were overall the dominant active methane oxidizers in these mineral cryosols, while type I methanotrophs (Methylomarinovum) were only detected in the 100 ppm SIP treatment. From the SIP-(13)C-labeled DNA, we retrieved nine high to intermediate quality metagenome-assembled genomes (MAGs) belonging to the Proteobacteria, Gemmatimonadetes, and Chloroflexi, with three of these MAGs containing genes associated with methanotrophy. A novel Chloroflexi MAG contained a mmoX gene along with other methane oxidation pathway genes, identifying it as a potential uncultured methane oxidizer. This MAG also contained genes for copper import, synthesis of biopolymers, mercury detoxification, and ammonia uptake, indicating that this bacterium is strongly adapted to conditions in active layer permafrost and providing new insights into methane biogeochemical cycling. In addition, Betaproteobacterial MAGs were also identified as potential cross-feeders with methanotrophs in these Arctic cryosols. Overall, in situ SIP labeling combined with metagenomics and genome binning demonstrated to be a useful tool for discovering and ...