Batsch, M. | Search bioRxiv

bioRxiv2026

Habitat fragmentation controls bacterial community composition outcomes

Natural habitats of bacteria are often highly structured in space, but how this affects their interactions and community composition outcomes is poorly understood. To address this gap, we studied the development of a synthetic soil community of 21 bacterial strains under a gradient of habitat fragmentation on single or mixed-substrate conditions. Fragmentation was produced by random microfluidic seeding of the mixed inoculum into culture medium droplets of variable volume (30-150 pL), targeting mean starting densities between 1 and 27 founder cells comprising 1-2, 7 or 14 taxa per droplet. Across all droplets for each of the fragmented states, globally different community compositions arose, suggesting variable individual taxa strategies and adaptation to differences in habitat fragmentation. In comparison to the same mixed inoculum growing under the same nutrient conditions in bulk culture, the more fragmented conditions allowed higher cell density and diversity, with less overgrowth by a few strains. Community evenness was highest when inocula were dispersed into individual taxon (1-2 taxa) or low-order combinations (7 taxa per droplet), but individual dispersion reduced the productivity of the meta-community across droplets. Monod-type simulations suggested that most community composition could be explained by the inherent individual kinetic properties and dispersal constraint effects of the fragmented habitat, with smaller effects from emerging interspecific interactions. Overall, our results show the strong effect of habitat structure on community outcomes, with higher fragmentation states favoring more even species coexistence. TEASERHabitat fragmentation results in the formation of locally isolated, smaller communities with varying richness and interactions, which altogether contribute positively to the maintenance of prokaryotic species diversity.

microbiology↗

bioRxiv2024

Fragmented micro-growth habitats present opportunities for alternative competitive outcomes

Bacteria in nature often proliferate in highly patchy environments, such as soil pores, particles, plant roots or leaves. The resulting spatial fragmentation leads to cells being constrained to smaller habitats, shared with potentially fewer other species. The effects of microhabitats on the emergence of bacterial interspecific interactions are poorly understood, but potentially important for the maintenance of diversity at a larger scale. To study this more in-depth, we contrasted paired species-growth in picoliter droplets at low population census with that in large (macro) population liquid suspended cultures. Four interaction scenarios were imposed by using different bacterial strain combinations and media: substrate competition, substrate independence, growth inhibition, and cell killing by tailocins. In contrast to macro-level culturing, we observed that fragmented growth in picoliter droplets in all cases yielded more variable outcomes, and even reversing the macro-level assumed interaction type in a small proportion of droplet habitats. Timelapse imaging and mathematical simulations indicated that the variable and alternative interaction outcomes are a consequence of founder cell phenotypic variation and small founder population sizes. Simulations further suggested that increased growth kinetic variation may be a crucial selectable property for slower-growing bacterial species to survive competition. Our results thus demonstrate how microhabitat fragmentation enables the proliferation of alternative interaction trajectories and contributes to the maintenance of higher species diversity under substrate competition.

microbiology↗

bioRxiv2023

Regulated bacterial interaction networks: A mathematical framework to describe competitive growth under inclusion of metabolite cross-feeding

When bacterial species with the same resource preferences share the same growth environment, it is commonly believed that direct competition will arise. A large variety of competition and more general interaction models have been formulated, but what is currently lacking are models that link mono-culture growth kinetics and community growth under inclusion of emerging biological interactions, such as metabolite cross-feeding. In order to understand and mathematically describe the nature of potential cross-feeding interactions, we design experiments where two bacterial species Pseudomonas putida and Pseudomonas veronii grow in liquid medium either in mono- or as co-culture in a resource-limited environment. We measure population growth under single substrate competition or with double species-specific substrates (substrate indifference), and starting from varying cell ratios of either species. Using experimental data as input, we first consider a mean-field model of resource-based competition, which captures well the empirically observed growth rates for mono-cultures, but fails to correctly predict growth rates in co-culture mixtures, in particular for skewed starting species ratios. Based on this, we extend the model by cross-feeding interactions where the consumption of substrate by one consumer produces metabolites that in turn are resources for the other consumer, thus leading to positive feedback loops in the species system. Two different cross-feeding options were considered, which either lead to constant metabolite cross-feeding, or to a regulated form, where metabolite utilization is activated with rates according to either a threshold or a Hill function, dependent on metabolite concentration. Both mathematical proof and experimental data indicate regulated cross-feeding to be the preferred model over constant metabolite utilization, with best co-culture growth predictions in case of high Hill coefficients, close to binary (on/off) activation states. This suggests that species use the appearing metabolite concentrations only when they are becoming high enough; possibly as a consequence of their lower energetic content than the primary substrate. Metabolite sharing was particularly relevant at unbalanced starting cell ratios, causing the minority partner to proliferate more than expected from the competitive substrate because of metabolite release from the majority partner. This effect thus likely quells immediate substrate competition and may be important in natural communities with typical very skewed relative taxa abundances and slower-growing taxa. In conclusion, the regulated bacterial interaction network correctly describes species substrate growth reactions in mixtures with few kinetic parameters that can be obtained from mono-culture growth experiments. 1 Author summaryCorrectly predicting growth of communities of diverse bacterial taxa remains a challenge, because of the very different growth properties of individual members and their myriads of interactions that can influence growth. Here we tried to improve and empirically validate mathematical models that combine theory of bacterial growth kinetics (i.e., Monod models) with mathematical definition of interaction parameters. We focused in particular on common cases of shared primary substrates (i.e., competition) and independent substrates (i.e., indifference) in an experimental system consisting of one fast-growing and one slower growing Pseudomonas species. Growth kinetic parameters derived from mono-culture experiments included in a Monod-type consumer-resource model explained some 75% of biomass formation of either species in co-culture, but underestimated the observed growth improvement when either of the species started as a minority compared to the other. This suggested an in important role of cross-feeding, whereby released metabolites from one of the partners is utilized by the other. Inclusion of cross-feeding feedback in the two-species Monod growth model largely explained empirical data at all species-starting ratios, in particular when cross-feeding is activated in almost binary manner as a function of metabolite concentration. Our results also indicate the importance of cross-feeding for minority taxa, which can explain their survival despite being poorly competitive.

microbiology↗