Modeling cross-feeding interactions reveals the roles of microbial dark matter in coastal terrestrial organic carbon coversion

Lignin is the most abundant aromatic carbon polymer on earth. Its bioconversion is essential for the global carbon cycle and bioenergy production. Microbial communities, with their versatile enzymes and pathways, play a vital role in lignin biodegradation. The interactions among the members of a community greatly affect the performance outcome, yet it is a significant challenge to mechanistically unravel such complex interactions. Here, we developed a marine lignin degrading bacterial consortium (LD), through “top-down” enrichment. High-throughput sequencing revealed that LD is dominated by Pluralibacter gergoviae (>98%), an only identified lignin degrader, with additional rare non-degraders, e.g., Vibrio alginolyticus, Aeromonas hydrophila and Shewanella putrefaciens. Interestingly, physiological analyses suggested that the LD consortium significantly enhanced growth/degradation than the P. gergoviae alone. Thus, the additional outliers, overshadowed by P. gergoviae, are considered to be microbial “dark matter” without definitely roles in lignin degradation. Genome-scale metabolic models were constructed for P. gergoviae and three non-lignin degrading species. An integrated in silico simulation predicted that growth/degradation is boosted by metabolic exchanges between members. The metabolic profiling and culture experiments validated the predication and revealed that the non-degraders survived on metabolic intermediates from P. gergoviae, including succinate, malate, serine and PCA derivates. In return, the non-degraders fed back glycerol, aspartate, alanine, fumarate to P. gergoviae to stimulate its growth and further enhance lignin degradation. Our study revealed the inner workings of the black-box of the LD consortium, in which the microbial dark matter interacts to form a syntrophic community with P. gergoviae for lignin catabolism. Our study highlights the unrecognized role of outliers in lignin degradation, providing a valuable step forward in manipulating microbiomes for biotechnology development.