Fitness and Productivity Increase with Ecotypic Diversity among Escherichia coli Strains That Coevolved in a Simple, Constant Environment

Abstract

The productivity of a biological community often correlates with its diversity. In the microbial world this phenomenon can sometimes be explained by positive, density-dependent interactions such as cross-feeding and syntrophy. These metabolic interactions help account for the astonishing variety of microbial life and drive many of the biogeochemical cycles without which life as we know it could not exist. While it is difficult to recapitulate experimentally how these interactions evolved among multiple taxa, we can explore in the laboratory how they arise within one. These experiments provide insight into how different bacterial ecotypes evolve and from these, possibly new “species.” We have previously shown that in a simple, constant environment a single clone of Escherichia coli can give rise to a consortium of genetically and phenotypically differentiated strains, in effect, a set of ecotypes, that coexist by cross-feeding. We marked these different ecotypes and their shared ancestor by integrating fluorescent protein into their genomes and then used flow cytometry to show that each evolved strain is more fit than the shared ancestor, that pairs of evolved strains are fitter still, and that the entire consortium is the fittest of all. We further demonstrate that the rank order of fitness values agrees with estimates of yield, indicating that an experimentally evolved consortium more efficiently converts primary and secondary resources to offspring than its ancestor or any member acting in isolation. IMPORTANCE Polymicrobial consortia occur in both environmental and clinical settings. In many cases, diversity and productivity correlate in these consortia, especially when sustained by positive, density-dependent interactions. However, the evolutionary history of such entities is typically obscure, making it difficult to establish the relative fitness of consortium partners and to use those data to illuminate the diversity-productivity relationship. Here, we dissect an Escherichia coli consortium that evolved under continuous glucose limitation in the laboratory from a single common ancestor. We show that a partnership consisting of cross-feeding ecotypes is better able to secure primary and secondary resources and to convert those resources to offspring than the ancestral clone. Such interactions may be a prelude to a special form of syntrophy and are likely determinants of microbial community structure in nature, including those having clinical significance such as chronic infections.

Contingent evolution of alternative metabolic network topologies determines whether cross-feeding evolves

“…Another suggested driver for the evolution of cross-feeding is that the collective exploitation of resources can be more efficient or productive than individual-based solutions 19,26,53,54 . In our simulations, autonomous mutants in cross-feeding communities are indeed less productive than the resident cross-feeders ( Fig.…”

Evolutionary dynamics and structural consequences of de novo beneficial mutations and mutant lineages arising in a constant environment

“…Subtle differences in either of these parameters may account for the apparent absence of the interaction. It is noteworthy that we detected no mutations at any of the loci previously implicated in cross-feeding evolution, e.g., acs, lpd, and ptsI [34,120].…”

“…Classic studies by Adams and colleagues showed that populations originating from the same ancestor used in our experiments could evolve into consortia consisting of ecotypes that co-exist via cross-feeding [35,36] and relief from product inhibition [37]. Recent data have shown that such consortia can be more fit and are more productive than either their ancestor or clones representing each ecotype [120]. By contrast, in the populations described here, neither the observed spectrum of mutations nor the structure of clone phylogenies suggest trophic interactions that could be construed as clonal reinforcement.…”

“…Thus, evolutionary dynamics in these populations is governed by clonal interference and not by clonal replacement or clonal reinforcement. This conclusion is reinforced by lack of evidence for mutations that support interactions which give cross-feeding consortia higher fitness and productivity than any consortium member by itself [120]. The dynamics of galS replacement illustrates the effect that clonal interference can have on the fate of different alleles.…”

Experimental and computational approaches to unravel microbial community assembly

“…The approach also offers the possibility, depending on the experimental settings, of non-destructively imaging the communities and thus observing assembly in real time. However, it has been observed that the burden of fluorescent protein expression can alter fitness values [33] , and thus could bias the resulting assembly patterns. On the other hand, FISH can be employed destructively with non-genetically modified strains, commonly allowing the visualization of very few phylotypes in a sample at a time [34] , [35] .…”