The Ecology and Evolution of Microbial Competition

Microbes express many competitive phenotypes in the presence of others; exploitative phenotypes include metabolic changes that increase growth rates or molecule secretion to harvest nutrients, while interference competition occurs through antimicrobial secretions or contact-dependent killing. Microbial competition is common, although evidence suggests that, in many environments, interspecies interactions are weak. Competition is expected on first encounter, but can be reduced over time through competitive exclusion, or niche partitioning via resource or spatial separation, leading to communities with a reduced local diversity of strains and species that can nevertheless coexist stably. Many complementary methods exist for studying microbial communities. Combining them to analyse a simple community would reveal a more complete picture. Microbes are typically surrounded by different strains and species with whom they compete for scarce nutrients and limited space. Given such challenging living conditions, microbes have evolved many phenotypes with which they can outcompete and displace their neighbours: secretions to harvest resources, loss of costly genes whose products can be obtained from others, stabbing and poisoning neighbouring cells, or colonising spaces while preventing others from doing so. These competitive phenotypes appear to be common, although evidence suggests that, over time, competition dies down locally, often leading to stable coexistence of genetically distinct lineages. Nevertheless, the selective forces acting on competition and the resulting evolutionary fates of the different players depend on ecological conditions in a way that is not yet well understood. Here, we highlight open questions and theoretical predictions of the long-term dynamics of competition that remain to be tested. Establishing a clearer understanding of microbial competition will allow us to better predict the behaviour of microbes, and to control and manipulate microbial communities for industrial, environmental, and medical purposes. Microbes are typically surrounded by different strains and species with whom they compete for scarce nutrients and limited space. Given such challenging living conditions, microbes have evolved many phenotypes with which they can outcompete and displace their neighbours: secretions to harvest resources, loss of costly genes whose products can be obtained from others, stabbing and poisoning neighbouring cells, or colonising spaces while preventing others from doing so. These competitive phenotypes appear to be common, although evidence suggests that, over time, competition dies down locally, often leading to stable coexistence of genetically distinct lineages. Nevertheless, the selective forces acting on competition and the resulting evolutionary fates of the different players depend on ecological conditions in a way that is not yet well understood. Here, we highlight open questions and theoretical predictions of the long-term dynamics of competition that remain to be tested. Establishing a clearer understanding of microbial competition will allow us to better predict the behaviour of microbes, and to control and manipulate microbial communities for industrial, environmental, and medical purposes. consider two strains A and B that differ on one or more loci. Strain A is a competitor of B if (a) B has a lower fitness in A's presence relative to its absence; (b) the phenotype in A resulting in a fitness change in B occurs in the long- or short-term presence of B; and (c) A and B require similar nutrients and space. Note that this definition is context-dependent. Furthermore, even if a phenotype did not evolve due to biotic competition, it may nevertheless result in a competitive advantage. the number of strains or species in a community (however they may be distinguished, e.g., Operational Taxonomic Units (OTUs) at 97%, or differentially labelled strains; a community also needs to be spatially delimited, e.g., a microbial colony, or strains living in the human oral tract). the probability that a community will return to its previous state following a small perturbation. We use this definition broadly to include measures such as resilience (the speed at which a community returns to its previous state) and permanence (all original species are maintained in the community) [62Coyte K.Z. et al.The ecology of the microbiome: Networks, competition, and stability.Science. 2015; 350: 663-666Crossref PubMed Scopus (130) Google Scholar]. evolutionary stability refers to evolutionary stable strategies (ESS), a game-theoretic concept whereby a population maintaining that strategy cannot be invaded by any alternative strategy that is initially rare [136Maynard Smith J. Evolution and the Theory of Games. Cambridge University Press, 1982Crossref Google Scholar]. here we use fitness as a proxy for the rate of division and survival relative to the interacting competitors’ division and survival. a principle which predicts that phylogenetically similar species will tend to co-occur because the environment selects for species that are adapted to it. a system of differential equations that describes the population dynamics of two or more interacting groups (typically species). this theory states that a species in a community that is able to survive on the lowest abundance of a given nutrient will dominate the community if it is limiting. In the presence of two limiting nutrients, it predicts that two species may coexist, provided that each is limited by one of the nutrients.