Barrier-Free Microhabitats: Self-Organized Seclusion in Microbial Communities

Abstract: Bacteria frequently colonize natural microcavities such as gut crypts, plant apoplasts, and soil pores. Recent studies have shown that the physical structure of these spaces plays a crucial role in shaping the stability and resilience of microbial populations (Karita et al., PNAS 2022, Postek et al. PNAS 2024). Here, we demonstrate that protected microhabitats can emerge dynamically, even in the absence of physical barriers. Interactions with surface features -- such as roughness or friction -- lead microbial populations to self-organize into effectively segregated subpopulations. Our numerical and analytical models reveal that this self-organization persists even when strains have different growth rates, allowing slower-growing strains to avoid competitive exclusion. These findings suggest that emergent spatial structuring can serve as a fundamental mechanism for maintaining microbial diversity, despite selection pressures, competition, and genetic drift.