Functional capacities of microbial communities to carry out large scale geochemical processes are maintained during ex situ anaerobic incubation

Abstract

Mechanisms controlling CO2 and CH4 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 CO2 and CH4 dynamics.

Quantifying the inhibitory impact of soluble phenolics on anaerobic carbon mineralization in a thawing permafrost peatland

“…Methanogen community structure differs significantly among peatland habitats [ 53 – 55 , 57 ]. One could argue that this observation supports explanation 1 (that methanogenic enzymes in the fen could have a limited affinity to bind with soluble phenolics)—as it is feasible that differing methanogenic community structures lead to differing enzyme speciation.…”

“…One could argue that this observation supports explanation 1 (that methanogenic enzymes in the fen could have a limited affinity to bind with soluble phenolics)—as it is feasible that differing methanogenic community structures lead to differing enzyme speciation. However, significantly higher diversity among the methanogen community within fens has been observed relative to bogs [ 53 – 55 ], rendering the possibility that fens do not possess any significant pool of methanogenic enzymes capable of binding to soluble phenolics unlikely.…”

“…Incubations are imperfect representations of in situ phenomena, as perturbations imposed by their sampling, setup, and implementation are inevitable. Thorough analyses—conducted using field and incubation data taken from our study site—have thus been undertaken as a means of quantifying these perturbations [ 55 , 60 ]. Findings demonstrate that the incubations methods employed herein yield C mineralization rates and CO 2 :CH 4 production ratios that are largely consistent with in situ observations [ 60 ].…”

“…First, it has been shown to facilitate consumption of molecular O 2 and reduction of oxidized chemical species [ 48 , 49 ]. Second, it offers a re-acclimation period for the microbial community [ 55 ]. We reference all time points relative to the end of this pre-incubation period such that day 1 corresponds to the first day following the 25-day pre-incubation phase.…”

Carbon Accumulation, Flux, and Fate in Stordalen Mire, a Permafrost Peatland in Transition

“…Decomposition occurs mainly in the acrotelm (the surface peat layer with a fluctuating water table, experiencing occasional to frequent oxic conditions, and living plant roots), but also proceeds in the catotelm (deeper peat that is perennially saturated and generally anoxic), albeit more slowly (Clymo, 1984). Incubation of peat from Stordalen Mire shows that CO 2 production occurs in incubated fen and bog peat from at least as deep as 25-35 cm depth and likely below that depth (Wilson et al, 2019;Wilson, Zayed, et al, 2021). If decomposition is happening deep in the peat profile at the same time that there is high productivity at the top of the peat, the net CO 2 flux that the chambers record would be lower than the accumulation rate estimated by recent aCAR, which measures accumulation near the surface and misses the decomposition of material below.…”