Hyphal growth determines spatial organization and coexistence in a pathogenic polymicrobial community in a spatially structured environment

The bodies of macroorganisms host microbes living in multispecies communities. Sequencing approaches have revealed that different organs host different microbiota and tend to be infected by different pathogens, drawing correlations between environmental parameters at the organ level and microbial composition. However, less is known about the microscale dimension of microbial ecology, particularly during infection. In this study, we focus on the role of microscale spatial structure, studying its influence on the ecology of a polymicrobial infection of Pseudomonas aeruginosa, Staphylococcus aureus, and Candida albicans. Although these pathogens are commonly found together in the lungs of chronically ill patients, it is unclear whether they coexist or compete and segregate in different niches. We find that, whereas P. aeruginosa quickly outcompetes C. albicans and S. aureus on large surfaces, robust spatial organization and coexistence emerges in spatially structured microenvironments. In confined spaces, slowly growing C. albicans is able to leverage rapid radial hyphal growth to conquer boundaries, where it establishes itself displacing the other pathogens. Similar outcomes are observed when the P. aeruginosa strain carries mexT-inactivating mutations, which are often found in clinical isolates. The observed spatial organization enables coexistence and potentially determines infection severity and outcomes. Our findings reveal a previously unrecognized role of mechanical forces in shaping infection dynamics, suggesting that microenvironmental structure might be a critical determinant of pathogen coexistence, virulence, and treatment outcomes. Because adaptations, such as changes in morphology, are widespread among microbes, these results are generalizable to other ecologies and environments.