Permafrost thaw in northern latitudinal peatlands is likely to create a positive feedback to climate change, as previously frozen soil carbon (C) becomes bioavailable and is released to the atmosphere as carbon dioxide (CO2) or methane (CH4). The loss is the result of microbially mediated transformations of “old” permafrost C, “new” C from plant inputs, and intermediate-age C in the seasonally thawed active layer. The microbiome, and its encoded carbon-processing potential, changes with thaw, but the realized effect on substrate utilization and gas emissions has not been characterized.
We, therefore, examined how microbial C cycling changed in two sequential thaw stages (a Sphagnum-dominated bog and a sedge-dominated fen) in Stordalen Mire (68.35°N, 19.05°E), in northern Sweden, using two incubation-based methods. We characterized the diversity and extent of microbial C substrate utilization across a wide range of substrates by Biolog EcoplatesTM, under dilute aerobic conditions. To test specific substrate hypotheses under more field-relevant conditions, with parallel quantification of microbiome shifts and C gas emissions, we amended anaerobic microcosms with selected substrates (glucose, acetate, butyrate, galacturonic acid, and p-hydroxybenzoic acid). The initial and final microbiomes were characterized via 16S rRNA amplicon sequencing. Biolog incubations revealed a higher diversity and faster rate of overall substrate utilization in the fully thawed fen than in the bog, especially in amine, carbohydrate, and carboxylic acid substrate groups. Anaerobic incubations indicated habitat differences in microbial use of key substrates, higher CH4 and CO2 production in the fen compared to the bog, and lower CO2:CH4 ratios in the fen reflecting the greater role of methanogenesis. Changes in the CO2:CH4 ratio with depth were larger in the bog, paralleling its greater microbiome shifts with depth. The substrates that induced the greatest shifts in both gas production and microbiomes were the organic acids. Galacturonic acid increased CO2:CH4 production ratios in both depths of both habitats, driven by a decrease in methane production, suggesting potential inhibition of methanogenesis. P-hydroxybenzoic acid decreased the CO2:CH4 production ratio in both habitats’ mid-depth, driven by a decrease in CO2 and an increase in CH4. In the deep depth of both habitats, however, p-hydroxybenzoic acid dramatically increased the CO2:CH4 production ratio, with lower gas production overall but a stronger decrease in CH4. This suggests inhibition of microbial activity in general, and methanogenesis in particular, at depth.
The organic acids not only shifted the overall microbiome composition the most, but they also produced the most differentially enriched or depleted lineages relative to the controls, as identified by linear discriminant analysis (LEfSe, p < 0.05, LDA > 2.0). Galacturonic acid exhibited the greatest enrichments and depletions of lineages and phylogenetically-inferred metabolisms (via PICRUSt2), in both bog and fen, supporting the literature-reported role of this organic acid as a C source for some lineages and an inhibitor of others. P-hydroxybenzoic acid exhibited a moderate number of enrichments and depletions, with greater depletions in the fen, consistent with the fen microbiome’s lower exposure to this Sphagnum-derived compound. Collectively, these results provide evidence for the importance of aboveground-belowground linkages in substrate supply and microbiome processing in these dynamically changing systems. They also confirm the impact of thaw stages on microbially-mediated C loss to the atmosphere as CO2 or CH4, the ratio of which is a key indicator of the strength of climate feedbacks.