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

Inferring bacterial interspecific interactions from microcolony growth expansion

Bacterial species interactions significantly shape growth and behavior in communities, determining the emergence of community functions. Typically, these interactions are studied through bulk population measurements, overlooking the role of cell-to-cell variability and spatial context. This study uses real-time surface growth measurements of thousands of sparsely positioned microcolonies to investigate interactions and kinetic variations in monocultures and cocultures of Pseudomonas putida and P. veronii under substrate competition (succinate) or substrate independence (d-mannitol and putrescine). In monoculture, microcolonies exhibited expected substrate-dependent expansion rates, but individual colony sizes were affected by founder cell density, spatial positioning, growth rates, and lag times. In coculture, substrate competition favored P. putida, but unexpectedly, reduced the maximum growth rates of both species. In contrast, 10% of P. veronii microcolonies under competition grew larger than expected, likely due to founder cell phenotypic variation and stochastic spatial positioning. These effects were alleviated under substrate independence. A linear relationship between founder cell ratios and final colony area ratios in local neighborhoods (6.5-65 µm radius) was observed in coculture, with its slope reflecting interaction type and strength. Measured slopes in the P. putida to P. veronii biomass ratio under competition were one-third reduced compared to kinetic predictions using a cell-agent growth model, which exometabolite analysis and simulations suggested may be due to metabolite cross-feeding or inhibitory compound production. This indicates additional factors beyond inherent monoculture growth kinetics driving spatial interactions. Overall, the study demonstrates how microcolony growth experiments offer valuable insights into bacterial interactions, from local to community-level dynamics.

Fragmented micro-growth habitats present opportunities for alternative competitive outcomes

Bacteria in nature often thrive in fragmented environments, like soil pores, plant roots or plant leaves, leading to smaller isolated habitats, shared with fewer species. This spatial fragmentation can significantly influence bacterial interactions, affecting overall community diversity. To investigate this, we contrast paired bacterial growth in tiny picoliter droplets (1-3 cells per 35 pL up to 3-8 cells per species in 268 pL) with larger, uniform liquid cultures (about 2 million cells per 140 µl). We test four interaction scenarios using different bacterial strains: substrate competition, substrate independence, growth inhibition, and cell killing. In fragmented environments, interaction outcomes are more variable and sometimes even reverse compared to larger uniform cultures. Both experiments and simulations show that these differences stem mostly from variation in initial cell population growth phenotypes and their sizes. These effects are most significant with the smallest starting cell populations and lessen as population size increases. Simulations suggest that slower-growing species might survive competition by increasing growth variability. Our findings reveal how microhabitat fragmentation promotes diverse bacterial interaction outcomes, contributing to greater species diversity under competitive conditions.

Niche availability and competitive loss by facilitation control proliferation of bacterial strains intended for soil microbiome interventions

Microbiome engineering - the targeted manipulation of microbial communities - is considered a promising strategy to restore ecosystems, but experimental support and mechanistic understanding are required. Here, we show that bacterial inoculants for soil microbiome engineering may fail to establish because they inadvertently facilitate growth of native resident microbiomes. By generating soil microcosms in presence or absence of standardized soil resident communities, we show how different nutrient availabilities limit outgrowth of focal bacterial inoculants (three Pseudomonads), and how this might be improved by adding an artificial, inoculant-selective nutrient niche. Through random paired interaction assays in agarose micro-beads, we demonstrate that, in addition to direct competition, inoculants lose competitiveness by facilitating growth of resident soil bacteria. Metatranscriptomics experiments with toluene as selective nutrient niche for the inoculant Pseudomonas veronii indicate that this facilitation is due to loss and uptake of excreted metabolites by resident taxa. Generation of selective nutrient niches for inoculants may help to favor their proliferation for the duration of their intended action while limiting their competitive loss.