Divergence and Redundancy of Transport and Metabolic Rate-Yield Strategies in a SingleEscherichia coliPopulation

Abstract

The energetic efficiency of nutrient uptake and conversion into biomass is a key factor in the ecological behavior of microorganisms. The constraints shaping the metabolic rate-yield trade-off in bacteria are not well understood. To examine whether metabolic rate-yield settings and physiological strategies evolve toward a particular optimum in a constant environment, we studied multiple Escherichia coli isolates evolving in a glucose-limited chemostat population. A major divergence in transport and metabolic strategies was observed, and the isolates included inefficient rate strategists (polluters or cheaters) and yield strategists (conservationists), as well as various hybrid rate-yield strategists and alternative ecotypes (dropouts). Sugar transport assays, strain comparisons based on metabolomics, and Biolog profiling revealed variance to the point of individuality within an evolving population. Only 68 of 177 metabolites assayed were not affected in 10 clonally related strains. The parallel enrichment of rate and yield strategists and the divergence in metabolic phylogenies indicate that bacteria do not converge on a particular rate-yield balance or unique evolutionary solutions. Redundancies in transport and metabolic pathways are proposed to have laid the framework for the multiplicity of bacterial adaptations.Microorganisms exhibit an immense range of metabolic capabilities, and there are extensive metabolic differences between members of a single bacterial species (29). Metabolic capabilities and the efficiency of metabolism are important in the ecological specialization of all organisms (1). Well-known nutritional strategies involving r-and K-adapted organisms differ in terms of their metabolic rate-yield balances (24). Metabolic efficiency is affected by the energetics of nutrient uptake (31) and is also thought to be governed by the trade-off between the rate and yield of energy metabolism (35). Shifts in this trade-off are poorly documented. Information on what determines metabolic efficiency would help to underpin analyses of the complex architecture of metabolic networks and to determine why, for example, systems biology models of extant organisms exhibit multiple metabolic flux distributions that are equally optimal (26,38). Advances in modeling the systems biology of bacteria are being made (16), but many important questions still remain. Does metabolic plasticity extend to the rate-yield balance of organisms? How do the environment and evolutionary selection determine the overall efficiency of metabolism? How is the yield-rate trade-off shifted with prolonged nutrient limitation? In this study we examined these questions after perturbing metabolism through continuous culture of Escherichia coli in a glucose-limited environment.Highly relevant to the questions posed above is that, perhaps paradoxically, one characteristic of bacteria is that microbial growth yields are often 50% less than the optimal yield (48). It is not clear why free-living bacteria like E. coli, which often grow and compete i...

Culture History and Population Heterogeneity as Determinants of Bacterial Adaptation: the Adaptomics of a Single Environmental Transition

“…Some, like coexistence based on trade-offs (127), do contribute to the diversity in E. coli chemostat culture populations (199), and negative frequency dependence is also shown by some isolates in the same environment (200). Further experimental evidence for coexistence based on cannibalism or cross feeding also exists (158,284).…”

Genomic Identification of a Novel Mutation in hfq That Provides Multiple Benefits in Evolving Glucose-Limited Populations of Escherichia coli

“…(A) The outer membrane proteins were extracted from bacterial cells grown under glucose limitation in a chemostat and separated by urea-SDS electrophoresis using procedures described previously (18). The major protein bands are labeled.…”

“…In addition to the rpoS lineages, we previously found separate, coexisting rpoS ϩ isolates in the same glucoselimited populations (18,19), with undefined mutations and fitness properties. Here we report on the mutational adaptation and fitness characteristics of one such strain, E. coli BW4001, that has a complex and previously unexplained series of adaptations under glucose limitation (18).…”

“…A single SNP was unexpected, given the high number of both metabolic and physiological differences between BW4001 and its ancestor ( Fig. 1 and 2) (18,19) and the presence of at least three mutations, in rpoS, mglD (or mglO), and malT (or mlc), in the previously characterized clones from the rpoS lineages sampled at the same time point as BW4001 (23,24,26). To confirm that the single mutation was responsible for most or all evolved phenotypes of BW4001, the hfq mutation was transferred into the ancestral genetic background by cotransduction with purA::tet as a selectable marker.…”

Metabolic trade-offs and the maintenance of the fittest and the flattest

“…With evidence that within--chemostat diversity may not be maintained by frequency--dependent selection 2 and that types differ in fitness 7 , it is classically supposed 10,11,12 that diversity must be transitory. Seeking a different explanation, we ask what conditions permit the stable maintenance of a diversity of simple organisms in a simple environment.…”