Microbes in porous environments: from active interactions to emergent feedback

Recent studies have shown thatEscherichia coliin highly confined porous media exhibit extended periods of `trapping' punctuated by forward `hops', a significant restructuring of the classical run-and-tumble model of motility. However, bacterial species must navigate a diverse range of complex habitats, such as biological tissues, soil, and sediments. These natural environments display varying levels of both (1) packing density (i.e., confinement) and (2) packing structure (i.e., disorder). Here, we introduce a microfluidic device that enables precise tuning of these environmental parameters, allowing for a more systematic exploration of bacterial motility bridging the extremes of unconfined and highly confined conditions. We observe that motility patterns characteristic of both hop-and-trap and run-and-tumble models coexist in nearly all environments tested, with ensemble dynamics transitioning between these behaviors as both confinement and disorder increase. We demonstrate that dynamics expected from the hop-and-trap model emerge naturally from a slightly modified run-and-tumble model under specific environmental constraints. Our results suggest that bacterial motility patterns lie along a continuum, rather than being confined to a small set of discrete locomotive modes.

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Environmental matrix and moisture are key determinants of microbial phenotypes expressed in a reduced complexity soil-analog

Rodríguez-Ramos,

Sadler,

Zegeye

et al. 2024

Preprint

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Soil moisture and porosity regulate microbial metabolism by influencing factors such as redox conditions, substrate availability, and soil connectivity. However, the inherent biological, chemical, and physical heterogeneity of soil complicates laboratory investigations into microbial phenotypes that mediate community metabolism. This difficulty arises from challenges in accurately representing the soil environment and in establishing a tractable microbial community that limits confounding variables. To address these challenges in our investigation of community metabolism, we use a reduced-complexity microbial consortium grown in a soil analog using a glass-bead matrix amended with chitin. Long-read and short-read metagenomes, metatranscriptomes, metaproteomes, and metabolomes were analyzed to test the effects of soil structure and moisture on chitin degradation. Our soil structure analog system greatly altered microbial expression profiles compared to the liquid-only incubations, emphasizing the importance of incorporating environmental parameters, like pores and surfaces, for understanding microbial phenotypes relevant to soil ecosystems. These changes were mainly driven by differences in overall expression of chitin-degrading Streptomyces species and stress-tolerant Ensifer. Our findings suggest that the success of Ensifer in a structured environment is likely related to its ability to repurpose carbon via the glyoxylate shunt while potentially using polyhydroxyalkanoate granules as a C source. We also identified traits like motility, stress resistance, and biofilm formation that underlie the degradation of chitin across our treatments and inform how they may ultimately alter carbon use efficiency. Together our results demonstrate that community functions like decomposition are sensitive to environmental conditions and more complex than the multi-enzyme pathways involved in depolymerization.

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Microbes in porous environments: from active interactions to emergent feedback

Cited by 5 publications

References 181 publications

Biophysical Reviews: a transition in the journal

Biophysical Reviews: a transition in the journal

Bacterial motility patterns adapt smoothly in response to spatial confinement and disorder

Environmental matrix and moisture are key determinants of microbial phenotypes expressed in a reduced complexity soil-analog

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