Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses.

BACKGROUND

Current understanding of the carbon cycle in methanogenic environments involves trophic interactions such as interspecies H transfer between organotrophs and methanogens. However, many metabolic processes are thermodynamically sensitive to H accumulation and can be inhibited by H produced from co-occurring metabolisms. Strategies for driving thermodynamically competing metabolisms in methanogenic environments remain unexplored.

RESULTS

To uncover how anaerobes combat this H conflict in situ, we employ metagenomics and metatranscriptomics to revisit a model ecosystem that has inspired many foundational discoveries in anaerobic ecology-methanogenic bioreactors. Through analysis of 17 anaerobic digesters, we recovered 1343 high-quality metagenome-assembled genomes and corresponding gene expression profiles for uncultured lineages spanning 66 phyla and reconstructed their metabolic capacities. We discovered that diverse uncultured populations can drive H-sensitive metabolisms through (i) metabolic coupling with concurrent H-tolerant catabolism, (ii) forgoing H generation in favor of interspecies transfer of formate and electrons (cytochrome- and pili-mediated) to avoid thermodynamic conflict, and (iii) integration of low-concentration O metabolism as an ancillary thermodynamics-enhancing electron sink. Archaeal populations support these processes through unique methanogenic metabolisms-highly favorable H oxidation driven by methyl-reducing methanogenesis and tripartite uptake of formate, electrons, and acetate.

CONCLUSION

Integration of omics and eco-thermodynamics revealed overlooked behavior and interactions of uncultured organisms, including coupling favorable and unfavorable metabolisms, shifting from H to formate transfer, respiring low-concentration O, performing direct interspecies electron transfer, and interacting with high H-affinity methanogenesis. These findings shed light on how microorganisms overcome a critical obstacle in methanogenic carbon cycles we had hitherto disregarded and provide foundational insight into anaerobic microbial ecology. Video Abstract.