Nutrient environments shape amino acid auxotrophy and cross-feeding

Abstract

Auxotrophy, the absence of biosynthetic capacity for essential metabolites, is widespread in microbes and is thought to shape interactions within communities. Auxotrophies are often treated as fixed properties of organisms; however, evidence indicates that auxotrophic phenotypes can depend on environmental context, thereby affecting community assembly by cross-feeding. Here, we systematically quantify how nutrient environments shape both auxotrophy and cross-feeding. Using matched sets of six amino acid auxotrophs in Escherichia coli and Bacillus subtilis, we measured monoculture and pairwise coculture growth across 40 carbon and nitrogen environments. We find that auxotrophy itself is highly environment dependent, with strains growing in a substantial fraction of amino acid-free conditions despite lacking key biosynthetic enzymes. Cross-feeding likewise varies widely across species, environments, and auxotroph pairs. Despite this variability, cross-feeding outcomes exhibit consistent patterns within and across species. In particular, B. subtilis cross-feeds better overall and cross-feeding growth is better predicted by auxotroph type (i.e., which amino acids the strain cannot produce) than by environmental context. A machine-learning model recapitulates this pattern, identifying auxotroph type as the strongest predictor of cross-feeding growth, similar to species identity, exceeding the contributions of nutrient environment and prototroph growth. Together, these results show that environmental context reshapes both metabolic need and exchange, yet cross-feeding follows emergent patterns linked to the species and auxotrophy type, with implications for predicting community assemblies and the evolution of gene loss.