Experimental mapping of bacterial fitness landscapes reveals eco-evolutionary fingerprints

Understanding microbial dynamics in natural environments remains a significant challenge. As an alternative approach, studying model bacterial strains under well-defined laboratory conditions can reveal ecological niche patterns and evolutionary consequences in a controlled setting. Here, we evaluated bacterial growth dynamics to map fitness landscapes that may reflect natural processes experimentally. Six bacterial strains from a broad phylogenetic range were cultured individually across 195 distinct media, comprising 30 components, including both pure chemical compounds and natural ingredients. This approach generated 4,680 growth rate (r) and carrying capacity (K) pairs derived from growth curves spanning a broad range of nutritional conditions. Despite variations in growth profiles among strains, both positive and negative correlations in growth were observed across different media types. Notably, patterns of growth profiles showed strong concordance with known eco-evolutionary relationships, such as phylogenetic affiliations and biogeographic traits, suggesting that microbial responses to nutrient environments are evolutionarily conserved rather than arbitrary. Moreover, the medium components influencing r and K exhibited distinct patterns of generality and specificity, independently of their chemical properties or nutritional categories. These results demonstrate that bacterial fitness landscapes, reconstructed in laboratory conditions, serve as eco-evolutionary fingerprints, offering a proof-of-concept for experimental ecology. Our findings suggest that functional traits, such as growth, can provide a framework to explore trait-phylogeny relationships and offer insights that may inform future microbial design.