Metabolic dependencies drive species co-occurrence in diverse microbial communities

Abstract

The association between metabolic interactions and co-occurrence in microbial communities has been addressed in a previous study (40). That study, based on models of binary communities, found that co-occurring communities could be distinguished from the niche-associated ones by increased competition, but not by cooperation. In contrast, we show, by simulating higher-order communities (to better represent ecological complexity) and without resorting to a growth optimality assumption (for which there is yet little evidence), that metabolic dependency is a hallmark of species co-occurrence. The distinction of co-occurring groups is evident in comparison to random assemblies as well as to habitatfiltered background. This further allowed us to carry out comprehensive simulations identifying metabolites that preferentially connect co-occurring species."The complete reference appears below. www.pnas.org/cgi

Microbial mutualism dynamics governed by dose-dependent toxicity of cross-fed nutrients

“…Development of an ecological model capable of predicting coculture behavior Mathematical modeling of synthetic communities is a powerful tool for generating experimentallytestable predictions of what controls mutualism dynamics and stability (Klitgord and Segrè, 2010;Mee et al, 2014;Zomorrodi and Segrè, 2015;Zelezniak et al, 2015). We therefore developed an ecological model (Figure 4) based on previously described interactions for mutualistic systems with Monod uptake kinetics (Meyer et al, 1975;Lee et al, 1976).…”

“…One factor that can promote cross-feeding in natural ecosystems is nutrient limitation, as crossfeeding can be a means by which to acquire scarce key nutrients (Shou et al, 2007;Klitgord and Segrè, 2010;Hom and Murray, 2014;Zelezniak et al, 2015). Limitation of bacterial growth is most commonly considered to result from nutrient deficiency; however, growth can also be influenced by diverse compounds that are inhibitory when abundant but serve as nutrients at lower concentrations (Abbott, 1973;Kunz et al, 1992;Alvarez et al, 2009;Barnhill et al, 2010).…”

Beyond the Black Queen Hypothesis

“…The dynamics of the loss-of-function mutant and extinction of the original population will thus be dependent on such life history traits to reach a steady state. Metabolic dependencies are potentially a major driver of species co-occurrence (Zelezniak et al, 2015). Until recently, the repercussions of such evolution at the community level were mostly overlooked, whereas it is now becoming evident that they are an integral part of community systems (Hairston et al, 2005;Johnson and Stinchcombe, 2007;Schoener, 2011) implying that evolutionary dynamics should systematically be taken into account when characterizing communities.…”

Segregating metabolic processes into different microbial cells accelerates the consumption of inhibitory substrates

“…Different metabolic processes are often segregated into different microbial cell types (Costa et al, 2006;Johnson et al, 2012;Zelezniak et al, 2015). A canonical example is substrate cross-feeding.…”