Mechanistic Modelling of Wetland Methane Dynamics in the JULES Land Surface Model: Representing Redox-Driven Substrate Dynamics and Microbial Switching

Wetlands, as the largest natural source of methane (CH₄) emissions, have received increasing attention in climate modelling. Recognising that methanogenesis is governed by anaerobic microbial processes, some models explicitly represent methanogen activity to simulate CH₄ emissions from permanently inundated wetlands. In such models, CH₄ emissions from seasonally flooded wetlands are usually estimated using an empirical oxidation factor to represent methanotrophic consumption. However, this approach neglects an additional important effect of atmospheric oxygen ingress during hydrological drawdown: the stimulation of organic matter decomposition upon rewetting, analogous to the Birch effect in seasonally dry ecosystems.

Despite the high annual methane emissions from permanently inundated sites, some of the highest intensity CH₄ emission spikes throughout the year are exhibited by seasonally inundated systems, such as freshwater marshes, floodplain wetlands and fens. Consequently, improved mechanistic representation of biogeochemical processes in seasonally inundated wetlands is needed to robustly assess global wetland greenhouse gas contribution.

This study presents a process-based wetland biogeochemical model that explicitly represents oxygen-stimulated substrate dynamics and microbial functional differentiation. Dissolved organic carbon (DOC) is partitioned into a “dry DOC” pool that accumulates during dry periods, and a “wet DOC” pool that is replenished upon rewetting. Microbial processes include distinct aerobic and anaerobic pools, whose activities are regulated by soil water content (SWC). Aerobic microbial activity follows a Gaussian response to SWC, reflecting optimal activity under intermediate moisture conditions. Water table depth (WTD), a relatively commonly measured wetland metric, is used to infer vertical SWC profiles in the soil column through a fitted van Genuchten soil water retention curve.

The microbial-DOC framework is coupled with the Joint UK Land Environment Simulator (JULES), a community land-surface model simulating the exchanges of energy, water and carbon between the land surface and the atmosphere, which can also be used as the land surface scheme of the UK Earth System Model (UKESM). JULES drives the microbial-DOC module by providing partitioned pools of litter, soil organic carbon, and root exudates, each characterised by distinct turnover kinetics. Temperature sensitivity is represented using Arrhenius kinetics, while substrate and microbial limitations are described using Michaelis–Menten formulations. Model parameters are constrained using methane and carbon dioxide flux measurements, alongside methanogen abundance data, from flooded hardwood and palm forests in Panama.

Resolving oxygen-mediated substrate priming and microbial responses, the framework moves beyond oxidation-only representations and improves estimates of wetland carbon source–sink dynamics under climate change.