Dynamic responses of percolation fen microbiome activity to organic matter and oxygen availability

In peatlands, as predominantly waterlogged and thus anoxic ecosystems, incomplete and limited decomposition of organic matter leads to accumulation of peat, while ongoing, albeit slow decomposition releases greenhouse gases (CO₂, CH₄, and N₂O) into the atmosphere. Thus, peatlands function simultaneously as major global carbon sinks and reservoirs and as active sources of greenhouse gases. Diverse microbial communities, characterized by a wide range of metabolic capabilities, regulate organic matter decomposition under both oxic and anoxic conditions, along with thermodynamic and transport related constraints. Decomposition under anoxic conditions is a process that often represents the main bottleneck in carbon mineralization in peatlands. However, the functional role of percolation fen microbiomes in organic matter decomposition and carbon mineralization under varying environmental conditions remains poorly understood.

We investigated the effects of ten key organic model substrates with different molecular complexity and three aeration regimes (oxic, anoxic, and oxic–anoxic shift) on microbial CO₂ and CH₄ production as an indicator of potential carbon mineralization over a 56-day incubation time series. We also evaluated inorganic and organic terminal electron acceptor availability by measuring electron-accepting (EAC) and electron-donating capacities (EDC) and other geochemical parameters (e.g., pH, DOC, trace metals, major ions, and NH⁴⁺) in relation to microbial respiration.

Our results showed that CO₂ and CH₄ production were highly substrate-specific. Each complex substrate, including plant tissues (e.g., Carex spp., Typha spp., Alnus spp.), lignin, cellulose, and chitin exhibited a distinct temporal pattern of CO₂ and CH₄ production throughout the incubation period. In contrast, simple substrates (e.g., artificial root exudate, acetate, tannic acid, and cyanin) showed similar patterns as observed in the non-amended control sample. Similar substrate-specific trends were observed for EAC and EDC. The oxic–anoxic shift condition resulted in the highest CO₂ production while CH₄ production remained suppressed as compared to continuously anoxic conditions. Despite this, EAC did not increase under the oxic–anoxic shift; rather, its pattern closely resembled the permanently anoxic treatment, indicating that the brief oxygen exposure was insufficient to recharge EAC and that microbes consumed the O₂ faster than regeneration of organic matter EAC by O₂ could occur. Furthermore, our multivariate analysis of aeration conditions and substrates using PERMANOVA showed a significant effect of O₂ availability throughout the incubation period (p = 0.001, R² = 0.62). While microbial responses and geochemical parameters did not differ among aeration conditions at early stage of incubation, but clear separation emerged in the second half of the incubation period, driven primarily by divergence in the oxic condition, while the anoxic and oxic–anoxic conditions remained similar to each other.

Our study demonstrates that aeration regimes and substrate quality strongly influence microbiome-driven biomass turnover in fen peatlands. Notably, microbial communities exhibit a more rapid response to O₂ availability than terminal electron acceptors, even following brief oxygen exposure. Furthermore, microbial organic matter decomposition patterns shift over time in accordance with the complexity of each substrate. We are currently performing metagenomic and proteomic analyses to elucidate the fen peatland microbial community functional structures involved in these diverging responses.