Single-cell assembled genomes predict enhanced bacterial metabolic cross-feeding potential in carbon-enriched soils

Abstract

Carbon availability is a key determinant of soil microbial community structure and function, shaping their metabolic activities and interactions. However, the mechanisms driving these interactions and their ecological and evolutionary implications remain poorly understood. Here, we integrated single-cell Cell Sorting and Sequencing (scCS-seq) technologies with community metabolic modeling to investigate the genomic traits and metabolic interactions of microorganisms in soils with different carbon availability. We find that microorganisms in carbon-enriched soils exhibit larger genomes with more coding sequences and enrichment of biosynthesis-related CAZyme families (e.g. GT83, GT44), whereas those in carbon-depleted soils adapt to resource scarcity with streamlined genomes and higher GC content. Our metabolic modeling predicts a stronger potential for cross-feeding in carbon-enriched soils, with amino acids and aromatic compounds identified as preferentially exchanged metabolites. This enhanced cross-feeding potential may promote resource sharing and functional complementarity among soil microorganisms. These findings highlight the role of microbial metabolic interactions as fundamental drivers of community assembly and ecosystem functioning, providing new insights into the ecological and evolutionary principles that structure soil microbiomes.