Mortality causes universal changes in microbial community composition

Abstract

All organisms are sensitive to the abiotic environment, and a deteriorating environment can cause extinction. However, survival in a multispecies community depends upon interactions, and some species may even be favored by a harsh environment that impairs others, leading to potentially surprising community transitions as environments deteriorate. Here we combine theory and laboratory microcosms to predict how simple microbial communities will change under added mortality, controlled by varying dilution. We find that in a two-species coculture, increasing mortality favors the faster grower, confirming a theoretical prediction. Furthermore, if the slower grower dominates under low mortality, the outcome can reverse as mortality increases. We find that this tradeoff between growth and competitive ability is prevalent at low dilution, causing outcomes to shift dramatically as dilution increases, and that these two-species shifts propagate to simple multispecies communities. Our results argue that a bottom-up approach can provide insight into how communities change under stress.

Eco-evolutionary dynamics of nested Darwinian populations and the emergence of community-level heredity

“…When this is not the case, for example when the bottleneck at birth is small, or collective-level generation time too short, evolution of developmental correction will be impeded. The latter favours rapidly growing particles (Abreu et al, 2019) and offers little possibility for the evolution of developmental correction. When the ecological attractor within collectives leads to the extinction of one of the two types, long collectivelevel generation times are incompatible with the maintenance of diversity (van Vliet and Doebeli, 2019).…”

Emergence of alternative stable states in microbial communities in a fluctuating environment

“…To explain a possible origin of this emergent bistability, we employed the Lotka-Volterra (LV) competition model with added mortality, which previously provided powerful insight into how microbial competitive outcomes shift with dilution rate 28 . The two-species LV model with added mortality is: where N i is the abundance of species i normalized by its carrying capacity, r i is the maximum growth rate for species i , α ij is the competition coefficient that determines how strongly species j inhibits species i , and δ is the imposed mortality rate, which is experimentally controlled by the dilution factor, which specifies the fraction of cells discarded per day.…”

“…Given this additional prediction, we sought to experimentally verify that coexistence can also result from time-averaging the dilution factors. Based on results of previous cocultured experiments in a similar growth medium 28 , we chose another fast grower, Enterobacter aerogenes ( Ea ), which is also excluded by the slow-growing Pv at low dilution factor. At intermediate dilution factor Ea and Pv coexist, and Ea dominates at high dilution factor (Fig.…”

Environmental fluctuations reshape an unexpected diversity-disturbance relationship in a microbial community

“…Dilution is perhaps the most common choice for a laboratory disturbance, as it causes species-independent mortality and replenishes the system with fresh nutrients, reminiscent of flow in soil, aquatic, or gut microbiomes. In simple batch culture experiments, where cultures sit undisturbed except for a periodic dilution step, coexistence has been observed at intermediate dilution levels (31,32), though different DDRs arise under different dilution regimes (33), suggesting that the dilution parameter space is vastly under-sampled. For more precise tuning of dilution or other parameters, experimentalists have long relied on continuous culture methods (27,28,34); unfortunately, these systems have traditionally been intractable to large-scale, multidimensional experiments.…”