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Abstract Microorganisms drive many aspects of organic carbon cycling in thawing permafrost soils, but the compositional trajectory of the post-thaw microbiome and its metabolic activity remain uncertain, which limits our ability to predict permafrost–climate feedbacks in a warming world. Using quantitative metabarcoding and metagenomic sequencing, we determined relative and absolute changes in microbiome composition and functional gene abundance during thaw incubations of wet sedge tundra collected from northern Alaska, USA. Organic soils from the tundra active-layer (0–50 cm), transition-zone (50–70 cm), and permafrost (70+ cm) depths were incubated under reducing conditions at 4 °C for 30 days to mimic an extended thaw duration. Following extended thaw, we found that iron (Fe)-cycling Gammaproteobacteria, specifically the heterotrophic Fe(III)-reducing Rhodoferax sp. and chemoautotrophic Fe(II)-oxidizing Gallionella sp., increased by 3–5 orders of magnitude in absolute abundance within the transition-zone and permafrost microbiomes, accounting for 65% of community abundance. We also found that the abundance of genes for Fe(III) reduction (e.g., MtrE) and Fe(II) oxidation (e.g., Cyc1) increased concurrently with genes for benzoate degradation and pyruvate metabolism, in which pyruvate is used to generate acetate that can be oxidized, along with benzoate, to CO2 when coupled with Fe(III) reduction. Gene abundance for CH4 metabolism decreased following extended thaw, suggesting dissimilatory Fe(III) reduction suppresses acetoclastic methanogenesis under reducing conditions. Our genomic evidence indicates that microbial carbon degradation is dominated by iron redox metabolism via an increase in gene abundance associated with Fe(III) reduction and Fe(II) oxidation during initial permafrost thaw, likely increasing microbial respiration while suppressing methanogenesis in wet sedge tundra.
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This content will become publicly available on November 10, 2026
Consistent microbial responses during the aerobic thaw of Alaskan permafrost soils
Arctic systems are warming at four times the global average, causing permafrost—permanently frozen soil, ice, organic matter, and bedrock—to thaw. Permafrost thaw exposes previously unavailable soil carbon and nutrients to decomposition—a process mediated by microbes—which releases greenhouse gases such as carbon dioxide and methane into the atmosphere. While it is well established that thaw alters the composition and function of the permafrost microbiome, patterns revealing common responses to thaw across different permafrost soil types have not yet emerged. In this study, we address how permafrost thaw impacts microbiome diversity, alters species abundance, and contributes to carbon flux in the Arctic. We sampled peat-like, mineral, and organic-mineral permafrost from three locations in central and northern Alaska. We assessed their abiotic soil properties and microbiome characteristics before and after a 3-month laboratory microcosm incubation. Across all sites, prokaryotic biomass increased following thaw, measured as 16S rRNA gene copy number. This change in biomass was positively correlated with cumulative respiration, indicating an increase in microbial activity post-thaw. We evaluated the thaw response of microbial taxa across three sites, identifying taxa that significantly increased in abundance post-thaw. Common responders shared across all sites belonged to the familiesBeijerinckiaceae,Burkholderiaceae,Clostridiaceae,Oxalobacteraceae,Pseudomonadaceae, andSporichthyaceae, indicating a common set of taxa that consistently respond to thaw regardless of site-specific conditions. Alpha diversity decreased with thaw across all sites, likely reflecting the increased dominance of specific thaw-responsive taxa that may be driving post-thaw biogeochemistry and increased respiration. Taken together, we deepen the understanding of different permafrost microbiomes and their response to thaw, which has implications for the permafrost–climate feedback and enables more accurate predictions of how Arctic ecosystem structure and function respond to change.
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- Award ID(s):
- 2144961
- PAR ID:
- 10674481
- Publisher / Repository:
- Frontiers in Microbiology
- Date Published:
- Journal Name:
- Frontiers in Microbiology
- Volume:
- 16
- ISSN:
- 1664-302X
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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