Would that it were so simple: Interactions between multiple traits undermine classical single-trait-based predictions of microbial community function and evolution

Review on computer-assisted biosynthetic capacities elucidation to assess metabolic interactions and communication within microbial communities

Microbial communities thrive through interactions and communication, which are challenging to study as most microorganisms are not cultivable. To address this challenge, researchers focus on the extracellular space where communication events occur. Exometabolomics and interactome analysis provide insights into the molecules involved in communication and the dynamics of their interactions. Advances in sequencing technologies and computational methods enable the reconstruction of taxonomic and functional profiles of microbial communities using high-throughput multi-omics data. Network-based approaches, including community flux balance analysis, aim to model molecular interactions within and between communities. Despite these advances, challenges remain in computer-assisted biosynthetic capacities elucidation, requiring continued innovation and collaboration among diverse scientists. This review provides insights into the current state and future directions of computer-assisted biosynthetic capacities elucidation in studying microbial communities.

Engineering multifunctional rhizosphere probiotics using consortia of Bacillus amyloliquefaciens transposon insertion mutants

While bacterial diversity is beneficial for the functioning of rhizosphere microbiomes, multi-species bioinoculants often fail to promote plant growth. One potential reason for this is that competition between different species of inoculated consortia members creates conflicts for their survival and functioning. To circumvent this, we used transposon insertion mutagenesis to increase the functional diversity within Bacillus amyloliquefaciens bacterial species and tested if we could improve plant growth promotion by assembling consortia of highly clonal but phenotypically dissimilar mutants. While most insertion mutations were harmful, some significantly improved B. amyloliquefaciens plant growth promotion traits relative to the wild-type strain. Eight phenotypically distinct mutants were selected to test if their functioning could be improved by applying them as multifunctional consortia. We found that B. amyloliquefaciens consortium richness correlated positively with plant root colonization and protection from Ralstonia solanacearum phytopathogenic bacterium. Crucially, 8-mutant consortium consisting of phenotypically dissimilar mutants performed better than randomly assembled 8-mutant consortia, suggesting that improvements were likely driven by consortia multifunctionality instead of consortia richness. Together, our results suggest that increasing intra-species phenotypic diversity could be an effective way to improve probiotic consortium functioning and plant growth promotion in agricultural systems.

Metabolic efficiency reshapes the seminal relationship between pathogen growth rate and virulence

A cornerstone of classical virulence evolution theories is the assumption that pathogen growth rate is positively correlated with virulence, the amount of damage pathogens inflict on their hosts. Such theories are key for incorporating evolutionary principles into sustainable disease management strategies. Yet, empirical evidence raises doubts over this central assumption underpinning classical theories, thus undermining their generality and predictive power. In this paper, we identify a key component missing from current theories which redefines the growth-virulence relationship in a way that is consistent with data. By modifying the activity of a single metabolic gene, we engineered strains of Magnaporthe oryzae with different nutrient acquisition and growth rates. We conducted in planta infection studies and uncovered an unexpected non-monotonic relationship between growth rate and virulence that is jointly shaped by how growth rate and metabolic efficiency interact. This novel mechanistic framework paves the way for a much-needed new suite of virulence evolution theories.

Cheating Promotes Coexistence in a Two-Species One-Substrate Culture Model

Cheating in microbial communities is often regarded as a precursor to a “tragedy of the commons,” ultimately leading to over-exploitation by a few species and destabilization of the community. While current evidence suggests that cheaters are evolutionarily and ecologically abundant, they can also play important roles in communities, such as promoting cooperative behaviors of other species. We developed a closed culture model with two microbial species and a single, complex nutrient substrate (the metaphorical “common”). One of the organisms, an enzyme producer, degrades the substrate, releasing an essential and limiting resource that it can use both to grow and produce more enzymes, but at a cost. The second organism, a cheater, does not produce the enzyme but can access the diffused resource produced by the other species, allowing it to benefit from the public good without contributing to it. We investigated evolutionarily stable states of coexistence between the two organisms and described how enzyme production rates and resource diffusion influence organism abundances. Our model shows that, in the long-term evolutionary scale, monocultures of the producer species drive themselves extinct because selection always favors mutant invaders that invest less in enzyme production, ultimately driving down the release of resources. However, the presence of a cheater buffers this process by reducing the fitness advantage of lower enzyme production, thereby preventing runaway selection in the producer, and promoting coexistence. Resource diffusion rate controls cheater growth, preventing it from outcompeting the producer. These results show that competition from cheaters can force producers to maintain adequate enzyme production to sustain both itself and the cheater. This is similar to what is known in evolutionary game theory as a “snowdrift game” – a metaphor describing a snow shoveler and a cheater following in their clean tracks. We move further to show that cheating can stabilize communities and possibly be a precursor to cooperation, rather than extinction.