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Mechanisms controlling CO 2 and CH 4 production in wetlands are central to understanding carbon cycling and greenhouse gas exchange. However, the volatility of these respiration products complicates quantifying their rates of production in the field. Attempts to circumvent the challenges through closed system incubations, from which gases cannot escape, have been used to investigate bulk in situ geochemistry. Efforts towards mapping mechanistic linkages between geochemistry and microbiology have raised concern regarding sampling and incubation-induced perturbations. Microorganisms are impacted by oxygen exposure, increased temperatures and accumulation of metabolic products during handling, storage, and incubation. We probed the extent of these perturbations, and their influence on incubation results, using high-resolution geochemical and microbial gene-based community profiling of anaerobically incubated material from three wetland habitats across a permafrost peatland. We compared the original field samples to the material anaerobically incubated over 50 days. Bulk geochemistry and phylum-level microbiota in incubations largely reflected field observations, but divergence between field and incubations occurred in both geochemistry and lineage-level microbial composition when examined at closer resolution. Despite the changes in representative lineages over time, inferred metabolic function with regards to carbon cycling largely reproduced field results suggesting functional consistency. Habitat differences among the source materials remained the largest driver of variation in geochemical and microbial differences among the samples in both incubations and field results. While incubations may have limited usefulness for identifying specific mechanisms, they remain a viable tool for probing bulk-scale questions related to anaerobic C cycling, including CO 2 and CH 4 dynamics. 

Stordalen Mire is a peatland in the discontinuous permafrost zone in arctic Sweden that exhibits a habitat gradient from permafrost palsa, toSphagnumbog underlain by permafrost, toEriophorum‐dominated fully thawed fen. We used three independent approaches to evaluate the annual, multi‐decadal, and millennial apparent carbon accumulation rates (aCAR) across this gradient: seven years of direct semi‐continuous measurement of CO₂and CH₄exchange, and 21 core profiles for²¹⁰Pb and¹⁴C peat dating. Year‐round chamber measurements indicated net carbon balance of −13 ± 8, −49 ± 15, and −91 ± 43 g C m⁻² y⁻¹for the years 2012–2018 in palsa, bog, and fen, respectively. Methane emission offset 2%, 7%, and 17% of the CO₂uptake rate across this gradient. Recent aCAR indicates higher C accumulation rates in surface peats in the palsa and bog compared to current CO₂fluxes, but these assessments are more similar in the fen. aCAR increased from low millennial‐scale levels (17–29 g C m⁻² y⁻¹) to moderate aCAR of the past century (72–81 g C m⁻² y⁻¹) to higher recent aCAR of 90–147 g C m⁻² y⁻¹. Recent permafrost collapse, greater inundation and vegetation response has made the landscape a stronger CO₂sink, but this CO₂sink is increasingly offset by rising CH₄emissions, dominated by modern carbon as determined by¹⁴C. The higher CH₄emissions result in higher net CO_{2‐equivalent}emissions, indicating that radiative forcing of this mire and similar permafrost ecosystems will exert a warming influence on future climate.