52 / 2025-03-29 16:57:15

The importance of outliers in the lignin degrading consortium

Microbial interactions, Cross-feeding, Genome-scale metabolic model, Auxiliary enzymes, Lignin degradation

Theme 2: Geobiology of Modern Habitable Earth > Session 2a: Microbe-mediated Carbon Cycling on Modern Earth

Lignin, as the abundant carbon polymer, is essential for carbon cycle and biorefinery. Microorganisms interact to form communities for lignin biodegradation, yet it is a challenge to understand such complex interactions. Here, we develop a coastal lignin degrading bacterial consortium (LD), through “top-down” enrichment. Sequencing and physiological analyses reveal that LD is dominated by the lignin degrader Pluralibacter gergoviae (> 98%), with additional rare non-degraders. Interestingly, LD, cultured in lignin-MB medium, significantly enhances cell growth and lignin degradation as compared to P. gergoviae alone, implying a role of additional outliers. Using genome-scale metabolic models, metabolic profiling and culture experiments, modeling of inter-species interactions between P. gergoviae, Vibrio alginolyticus, Aeromonas hydrophila and Shewanella putrefaciens, unravels cross-feeding of amino acids, organic acids and alcohols between the degrader and non-degraders. Furthermore, the sub-population ratio is essential to enforce the synergy. In addition, lignin degradation involves synergy between ligninases and auxiliary enzymes. However, auxiliary enzymes, which are composed of thousands of enzymes, remain enigmatic, although several ligninolytic enzymes have been well-characterized. This study uncovers bacterial accessory enzymes for B-type dye-decolorizing peroxidases (DypBs). The catalytic network of the DypBs-based multi-enzyme complex is characterized. DypBs couple with quinone reductases and nitroreductase to participate in quinone redox cycling. They work with superoxide dismutase to induce Fenton reaction for lignin oxidation. Our study highlights the unrecognized role of outliers in lignin degradation and advances the knowledge of bacterial lignin degrading multi-enzymes.