Keystone taxa drive the synchronous production of methane and refractory dissolved organic matter in inland waters

Inland waters are an important source of greenhouse gas methane (CH₄). The production of CH₄ is influenced by various factors, including the concentration of dissolved organic matter (DOM), redox conditions, and the composition of microbial communities, with clear spatiotemporal heterogeneity in inland waters. Refractory DOM (RDOM) can resist rapid biodegradation and preserve up to thousands of years; therefore, it is important for assessing the natural carbon sequestration potential of aquatic ecosystems. As a critical part of carbon biogeochemical processes in inland waters, the production of CH₄ and RDOM depends on the microbial successive processing of organic carbon. However, it is unclear yet the link of these two processes and the underlying microbial regulation mechanisms. Therefore, a large-scale survey was conducted in China’s inland waters, with the measurement of CH₄ concentrations, DOM chemical composition, microbial community composition, and relative environmental parameters mainly by chromatographic, optical, mass spectrometric, and high-throughput sequencing analyses, to clarify the abovementioned questions. Here, we found a synchronous production of CH₄ and RDOM linked by microbial consortia in inland waters. The increasing microbial cooperation driven by the keystone taxa (mainly Fluviicola and Polynucleobacter) could promote the transformation of labile DOM into RDOM and meanwhile benefit methanogenic microbial communities to produce CH₄. This process was also influenced by environmental factors such as total nitrogen and dissolved oxygen concentrations. Future studies need to combine more field investigations and laboratory control experiments to fully understand these complex processes. This study deepened the understanding of microbial-driven carbon transformation and highlighted the role of microbial keystone taxa in these processes, providing some useful references for the future laboratory control experiments (e.g., the selection of microbial species). Considering that CH₄ emission and RDOM production are closely related to the carbon source-sink relationship, this finding will help to more accurately evaluate the budget in inland aquatic ecosystems.