Bacterial community response to species overrepresentation or omission is strongly influenced by life in spatially structured habitats

Variations in type and strength of interspecific interactions in natural bacterial communities (e.g., synergistic to inhibitory) affect species composition and community functioning. The extent of interspecific interactions is often modulated by environmental factors that constrain diffusion pathways and cell mobility and limit community spatial arrangement. We studied how spatially structured habitats affect interspecific interactions and influence the resulting bacterial community composition. We used a bacterial community made of 11 well-characterized species that grew in porous habitats (comprised of glass beads) under controlled hydration conditions or in liquid habitats. We manipulated the initial community composition by overrepresenting or removing selected members, and observed community composition over time. Life in porous media reduced the number and strength of interspecific interactions compared to mixed liquid culture, likely due to spatial niche partitioning in porous habitats. The community converged to similar species composition irrespective of the initial species mix, however, the dominant bacterial species was markedly different between liquid culture and structured porous habitats. Moreover, differences in water saturation levels of the porous medium affected community assembly highlighting the need to account for habitat structure and physical conditions to better understand and interpret assembly of bacterial communities. We point at the modulation of bacterial interactions due to spatial structuring as a potential mechanism for promoting community stability and species coexistence, as observed in various natural environments such as soil or human gut. Importance Bacteria live as complex multispecies communities essential for healthy and functioning ecosystems ranging from soil to the human gut. The bacterial species that form these communities can have positive or negative impact on each other, promoting or inhibiting each other’s growth. Yet, the factors controlling the balance of such interactions in nature, and how these influence the community, are not fully understood. Here, we show that bacterial interactions are modified by life in spatially structured bacterial habitats. These conditions exert important control over the resulting bacterial community regardless of initial species composition. The study demonstrates limitations of inferences from bacterial communities grown in liquid culture relative to behaviour in structured natural habitats such as soil.