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

Abstract

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.ImportanceBacteria 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.

Cybergenetic control of microbial community composition

“…Less common methods to measure composition include: dilution plating on different selective medias and counting CFUs (colony forming units) ( Wu et al, 2022 ), which is laborious and slow; qPCR (quantitative Polymerase Chain Reaction) of unique DNA sequences ( Mee et al, 2014 ; Jian et al, 2020 ; Kleyer, Tecon and Or, 2021 ); or RNA sensors on paper-based cell-free systems ( Takahashi et al, 2018 ). qPCR and RNA sensors can be quantitative and cost effective, but typically require primer/RNA sensor design for each species and involve laborious sample extraction and amplification.…”

Genetic, physiological, and cellular heterogeneities of bacterial pathogens in food matrices: Consequences for food safety

“…Within these communities, bacterial pathogens compete with their neighbors for space and resources (Hibbing et al., 2010). Recent reports also demonstrated that life in such structured habitats alters the composition of microbial communities compared to liquid cultures (Kleyer et al., 2021). The recent development of high‐throughput DNA sequencing technologies allows a new approach that is free from the limitations of culture‐dependent experiments and which describes microbial communities in food matrices with unprecedented resolution (Ercolini, 2013).…”