Spatially mediated interactions shape founder-cell fitness and community assembly in multi-species soil bacteria

Abstract

Microbial communities spontaneously colonize pristine environments, yet how species growth kinetics and individual cell variation shape community assembly remains poorly understood. Here, we use time-lapse microscopy imaging to track the division of individual founder cells in communities composed of up to seven soil bacterial isolates grown on nutrient surfaces. With cell lineage tracking, we quantify species-specific absolute biomass formation and growth kinetics from early growth through stationary phase. The reproductive success of individual founder cells depended on the timing of their first cell division, which determined their access to the primary substrate and their maximum growth rates. In mixed-species communities, founder cell success also depended on species-specific, substrate-dependent growth rates and yields. In addition, spatial factors - such as cells positioning, distances to non-kin neighbours, and identities of co-occurring species - further influenced outcomes. In spatially structured communities, interspecific interactions were globally governed by competition for primary substrates. We also observed cross-feeding of leaked metabolites, reflected in fluctuating paired interaction strengths and interaction signs. Species-pair interactions differed locally, with cells within distances of less than 15 {micro}m exhibiting opposite interaction behaviours. Global pairwise interactions predicted from monoculture growth kinetics were observed in approximately half of the measured pairs, whereas measured paired interactions generally weakened in combinations of three or more species. Using a spatially explicit agent-based Monod growth model that includes interspecific interactions, we accurately predicted the compositions of seven-member communities. Overall, our results indicate that emergent, spatially mediated interspecific interactions between cells of different bacterial species primarily drive local and temporal changes in individual cell growth rates, which in turn determine final biomass formation. Because most natural microbial habitats are spatially structured, stochastic founder-cell positioning and fitness differences are key determinants of locally formed interaction patterns and species coexistence.