Mutual cross-feeding drives marine biofilm assembly on various carbon sources

Abstract A major factor affecting the assembly of microbial community is environmental carbon source. It is still unclear, however, to which extent the community structure is determined by the type of carbon source, especially for marine microbiota with high diversity. Here, this research question has been systematically addressed by enrichment culture of a marine biofilm community with 69 different carbon sources, under both aerobic and anaerobic conditions, followed by analysis of 3.2 Tb of metagenomic datasets. The finding revealed that the taxonomic composition of the enrichment cultured communities is not primarily determined by carbon source. Analysis of 535 high-quality metagenome-assembled genomes revealed strong microbial coexistence across different carbon sources. Moreover, co-culture experiments with isolated strains suggested extensive microbial cooperation, which expands the range of available carbon sources. Furthermore, co-culture metabolomics and transcriptomics indicated the presence of an extracellular amino acid pool that facilitate cross-feeding, which is probably regulated by complementary gene expression. Altogether, cross-feeding based on the metabolism of essential elements (e.g., amino acids) lays the foundation of microbial cooperation, diminishing the influence of carbon source on community assembly.