Meta-omics profiling of denitrifying bacterial communities with lignin as carbon source

Lignin is the most abundant renewable source of aromatic carbon and its microbial depolymerization and metabolism under aerobic conditions is well studied. However, lignin breakdown in the absence of oxygen remains poorly understood. Here, we established long-term bacterial enrichment cultures supplied with diverse lignins as the sole carbon source under denitrifying conditions. Denitrification dynamics were followed by monitoring nitrogenous gases. Metagenomics analysis recovered 62 metagenome-assembled genomes (MAGs), several of which encoded enzymes for both denitrification and anaerobic metabolism of aromatic compounds. Quantitative metaproteomics confirmed expression of such enzymes and additionally showed that several MAGs expressed redox-active auxiliary-activity enzymes and other uncharacterised proteins that are potential candidates for involvement in lignin depolymerisation. The detection of several oxygen-dependent oxidoreductases despite anaerobic conditions prompt intriguing discussion of potential mechanistic explanations. This systems-level study expands our understanding of lignin turnover in anaerobic environments by bacteria and suggest enzymatic targets for further exploration of their role in lignin depolymerization under oxygen-limited conditions.