Multiple long-term, experimentally-evolved populations of Escherichia coli acquire dependence upon citrate as an iron chelator for optimal growth on glucose

ABSTRACT: BACKGROUND: Specialization for ecological niches is a balance of evolutionary adaptation and its accompanying tradeoffs. Here we focus on the Lenski Long-Term Evolution Experiment, which has maintained cultures of Escherichia coli in the same, defined seasonal environment for 50,000 generations. Over this time, much adaptation and specialization to the environment has occurred. The presence of citrate in the growth media selected one lineage to gain the novel ability to utilize citrate as a carbon source after 31,000 generations. Here we test whether other strains have specialized to rely on citrate after 50,000 generations. RESULTS: We show that in addition to the citrate-catabolizing strain, three other lineages evolving in parallel have acquired a dependence on citrate for optimal growth on glucose. None of these strains were stimulated indirectly by the sodium present in disodium citrate, nor exhibited even partial utilization of citrate as a carbon source. Instead, all three of these citrate-stimulated populations appear to rely on it as a chelator of iron. CONCLUSIONS: The strains we examine here have evolved specialization to their environment through apparent loss of function. Our results are most consistent with the accumulation of mutations in iron transport genes that were obviated by abundant citrate. The results present another example where a subtle decision in the design of an evolution experiment led to unexpected evolutionary outcomes.     

Experimental adaptation of Salmonella typhimurium to mice

Experimental evolution is a powerful approach to study the dynamics and mechanisms of bacterial niche specialization. By serial passage in mice, we evolved 18 independent lineages of Salmonella typhimurium LT2 and examined the rate and extent of adaptation to a mainly reticuloendothelial host environment. Bacterial mutation rates and population sizes were varied by using wild-type and DNA repair-defective mutator (mutS) strains with normal and high mutation rates, respectively, and by varying the number of bacteria intraperitoneally injected into mice. After <200 generations of adaptation all lineages showed an increased fitness as measured by a faster growth rate in mice (selection coefficients 0.11-0.58). Using a generally applicable mathematical model we calculated the adaptive mutation rate for the wild-type bacterium to be >10(-6)/cell/generation, suggesting that the majority of adaptive mutations are not simple point mutations. For the mutator lineages, adaptation to mice was associated with a loss of fitness in secondary environments as seen by a reduced metabolic capability. During adaptation there was no indication that a high mutation rate was counterselected. These data show that S. typhimurium can rapidly and extensively increase its fitness in mice but this niche specialization is, at least in mutators, associated with a cost.     

Experimental evolution of the grain of metabolic specialization in yeast

Adaptation to any given environment may be accompanied by a cost in terms of reduced growth in the ancestral or some alternative environment. Ecologists explain the cost of adaptation through the concept of a trade‐off, by which gaining a new trait involves losing another trait. Two mechanisms have been invoked to explain the evolution of trade‐offs in ecological systems, mutational degradation, and functional interference. Mutational degradation occurs when a gene coding a specific trait is not under selection in the resident environment; therefore, it may be degraded through the accumulation of mutations that are neutral in the resident environment but deleterious in an alternative environment. Functional interference evolves if the gene or a set of genes have antagonistic effects in two or more ecologically different traits. Both mechanisms pertain to a situation where the selection and the alternative environments are ecologically different. To test this hypothesis, we conducted an experiment in which 12 experimental populations of wild yeast were each grown in a minimal medium supplemented with a single substrate. We chose 12 different carbon substrates that were metabolized through similar and different pathways in order to represent a wide range of ecological conditions. We found no evidence for trade‐offs between substrates on the same pathway. The indirect response of substrates on other pathways, however, was consistently negative, with little correlation between the direct and indirect responses. We conclude that the grain of specialization in this case is the metabolic pathway and that specialization appears to evolve through mutational degradation.     

Mutations in Global Regulators Lead to Metabolic Selection during Adaptation to Complex Environments

Adaptation to ecologically complex environments can provide insights into the evolutionary dynamics and functional constraints encountered by organisms during natural selection. Adaptation to a new environment with abundant and varied resources can be difficult to achieve by small incremental changes if many mutations are required to achieve even modest gains in fitness. Since changing complex environments are quite common in nature, we investigated how such an epistatic bottleneck can be avoided to allow rapid adaptation. We show that adaptive mutations arise repeatedly in independently evolved populations in the context of greatly increased genetic and phenotypic diversity. We go on to show that weak selection requiring substantial metabolic reprogramming can be readily achieved by mutations in the global response regulator arcA and the stress response regulator rpoS. We identified 46 unique single-nucleotide variants of arcA and 18 mutations in rpoS, nine of which resulted in stop codons or large deletions, suggesting that subtle modulations of ArcA function and knockouts of rpoS are largely responsible for the metabolic shifts leading to adaptation. These mutations allow a higher order metabolic selection that eliminates epistatic bottlenecks, which could occur when many changes would be required. Proteomic and carbohydrate analysis of adapting E. coli populations revealed an up-regulation of enzymes associated with the TCA cycle and amino acid metabolism, and an increase in the secretion of putrescine. The overall effect of adaptation across populations is to redirect and efficiently utilize uptake and catabolism of abundant amino acids. Concomitantly, there is a pronounced spread of more ecologically limited strains that results from specialization through metabolic erosion. Remarkably, the global regulators arcA and rpoS can provide a “one-step” mechanism of adaptation to a novel environment, which highlights the importance of global resource management as a powerful strategy to adaptation.     

Metabolic Footprint Analysis Uncovers Strain Specific Overflow Metabolism and D-Isoleucine Production of Staphylococcus Aureus COL and HG001

During infection processes, Staphylococcus aureus is able to survive within the host and to invade tissues and cells. For studying the interaction between the pathogenic bacterium and the host cell, the bacterial growth behaviour and its metabolic adaptation to the host cell environment provides first basic information. In the present study, we therefore cultivated S. aureus COL and HG001 in the eukaryotic cell culture medium RPMI 1640 and analyzed the extracellular metabolic uptake and secretion patterns of both commonly used laboratory strains. Extracellular accumulation of D-isoleucine was detected starting during exponential growth of COL and HG001 in RPMI medium. This non-canonical D-amino acid is known to play a regulatory role in adaptation processes. Moreover, individual uptake of glucose, accumulation of acetate, further overflow metabolites, and intermediates of the branched-chain amino acid metabolism constitute unique metabolic footprints. Altogether these time-resolved footprint analyses give first metabolic insights into staphylococcal growth behaviour in a culture medium used for infection related studies.     

The Origins of Specialization: Insights from Bacteria Held 25 Years in Captivity

Examples of ecological specialization abound in nature but the evolutionary and genetic causes of tradeoffs across environments are typically unknown. Natural selection itself may favor traits that improve fitness in one environment but reduce fitness elsewhere. Furthermore, an absence of selection on unused traits renders them susceptible to mutational erosion by genetic drift. Experimental evolution of microbial populations allows these potentially concurrent dynamics to be evaluated directly, rather than by historical inference. The 50,000 generation (and counting) Lenski Long-Term Evolution Experiment (LTEE), in which replicate E. coli populations have been passaged in a simple environment with only glucose for carbon and energy, has inspired multiple studies of their potential specialization. Earlier in this experiment, most changes were the side effects of selection, both broadening growth potential in some conditions and narrowing it in others, particularly in assays of diet breadth and thermotolerance. The fact that replicate populations experienced similar losses suggested they were becoming specialists because of tradeoffs imposed by selection. However a new study in this issue of PLOS Biology by Nicholas Leiby and Christopher Marx revisits these lines with powerful new growth assays and finds a surprising number of functional gains as well as losses, the latter of which were enriched in populations that had evolved higher mutation rates. Thus, these populations are steadily becoming glucose specialists by the relentless pressure of mutation accumulation, which has taken 25 years to detect. More surprising, the unpredictability of functional changes suggests that we still have much to learn about how the best-studied bacterium adapts to grow on the best-studied sugar.The wonder of biological diversity belies a puzzling subtext. Species are defined as much by their limits as their capabilities. Very few species in our common vernacular tolerate life in a wide range of environments, and those that do—the Norway rat, say—are not generally appealing. More often, we celebrate specialization to a particular condition: for example, orchid epiphytes growing tenuously in the cloud forest, only a subtle climate shift from extinction. Even grade school natural history teaches us that species are often unfit when living beyond their natural range.So it comes as a surprise that the causes of this rampant ecological specialization are poorly understood. “Use it or lose it,” but why? One common explanation is that natural selection tends to favor traits that simultaneously enhance fitness in one environment but compromise fitness elsewhere. This selective process is known as “antagonistic pleiotropy.” Another explanation is that a selective shadow falls upon unused traits, rendering them susceptible to mutational erosion by random genetic drift. This neutral process is known as “mutation accumulation” (Figure 1). These processes inevitably co-occur, and can be enhanced by the hybrid dynamic of genetic hitchhiking, in which neutral mutations affecting unused functions become linked to different mutations under positive selection. In most cases, the functional decay of a species can only be studied retrospectively, and distinguishing the roles of antagonistic pleiotropy and mutation accumulation is hampered by weak historical inference. Did selection, or an absence of selection, produce the blind cavefish [1]? There is little controversy that the sum of these dynamics can produce specialists, but their timing and relative importance is an open question.Open in a separate windowFigure 1Hypothetical dynamics of fitness in foreign environments by pleiotropy or mutation accumulation during long-term adaptation.Prolonged adaptation to one environment leads to decelerating fitness gains in the selective environment (solid black line), as beneficial mutations become limiting. Consequences of this adaptation for fitness in other environments may take different forms. No net change may occur if beneficial mutations generate no or inconsistent side effects (neutrality). However, the same mutations responsible for adaptation may also increase fitness in other environments (synergistic pleiotropy, dotted line), may decrease fitness in foreign environments at an equivalent rate if antagonistic effects correlate with selected effects (antagonistic pleiotropy, dotted line), or may decrease fitness at an increasing rate if subsequent mutations generate greater tradeoffs (antagonistic pleiotropy, dashed and dotted line). The uncertainty of the form of pleiotropic effects reflects a general lack of understanding of how mutations interact to affect fitness, particularly over the long term. Mutation accumulation (MA) in traits hidden from selection is expected to reduce fitness randomly but linearly on average, more slowly during evolution at a low mutation rate (MA, low U) or more rapidly at a high mutation rate (MA, high U). Evidence of all processes is now evident in this latest study of the evolution of diet breadth in the LTEE [20].The study of “evolution in action” using model experimental populations of rapidly reproducing organisms allows researchers to quantify both adaptation and any functional declines simultaneously. This approach is especially powerful when samples of evolving populations can be stored inanimate and studied at a later time under various conditions. Perhaps the best example of this approach is Richard Lenski''s Long-Term Evolution Experiment (LTEE), in which 12 populations of E. coli have been grown under simple conditions for more than 25 years and 50,000 generations [2],[3].When as a graduate student I wondered aloud whether the LTEE lines had become specialists, a colleague remarked: “Of course! You''ve selected for streamlined E. coli that have scuttled unused functions.” But with only a small amount of glucose as the sole carbon source available to the ancestor (the innovation by one population of using citrate for growth more than 30,000 generations in the future notwithstanding [4]), all anabolic pathways to construct new cells remain under strong selection to preserve their function. Moreover, because some catabolic reactions use the same intermediates as anabolic pathways (a form of pleiotropy) [5], growth on alternative carbon sources may be nonetheless preserved. Thus, we wondered whether the physiology of E. coli might actually prove to be robust during long-term evolution on glucose alone.Over the first 2,000 generations, the LTEE lines gained more often than lost fitness across a range of different environments [6]. In addition, a high-throughput screen of cellular respiration (Biolog) for the best-studied clone from these lines showed 171 relative gains and only 32 losses [7]. Even these losses in substrate respiration did not translate to reduced fitness versus the ancestor; rather, the evolved clone was simply relatively worse in the foreign resources than in glucose [7]. Evidently, each of the five beneficial mutations found in this early clone was broadly beneficial and imparted few tradeoffs [8]. Generalists rather than specialists were the rule.Between 2,000 and 20,000 generations, fitness losses in foreign conditions became more obvious but not always consistent. Some lines became less fit than the ancestor in a dilute complex medium (LB) [9], all lines grew worse at high (>40°C) and low (<20°C) temperature [10], and all lines became sensitive to the resource concentration in their environment, even for glucose [9]. Did subsequent beneficial mutations cause these tradeoffs (antagonistic pleiotropy), or did other, neutral or slightly harmful mutations accumulate by drift (Figure 1)? We must consider the population genetic dynamics of these LTEE populations. The hallmark of neutral theory [11] is that mutations with no effect in the selective environment should become fixed in the population at the rate of mutation. For the ancestor of this experiment, the mutation rate is ∼10⁻³ per genome per generation [12],[13], so only a handful of neutral mutations would have fixed by the time tradeoffs became evident, and would not likely explain the early specialization.However, an important extension of neutral theory is that slightly harmful mutations—those whose effects are roughly the inverse of the population size or below, 1/N—can also be fixed by drift [14]. Millions of slightly deleterious mutations were produced in these populations, which cycled between 5×10⁶ and 5×10⁸ cells each day. Might these mutations account for tradeoffs over the first 10–20,000 generations? In small populations, the effect of these mutations can be substantial, which explains why bottlenecked populations may experience fitness declines or even the genome erosion frequently seen in bacterial endosymbionts [15]. But in the large LTEE populations, most deleterious mutations are weeded out by selection and only those with the slightest effects may accumulate over very long time scales. Thus, because these early losses tended to occur when adaptation in the selective environment was most rapid, and because the randomness and rarity of mutation accumulation should not produce parallel changes over these time scales, early specialization is best explained by antagonistic pleiotropy [9],[10].Later in the LTEE, elevated mutation rates began to evolve in certain lines, resulting in a fundamental change in the population genetic environment [16],[17] that should increase the rate of functional decay in unused, essentially neutral functions. These mutator populations tended to perform worse in multiple environments, and in theory should continue to specialize more rapidly by accelerated mutation accumulation. As a first test, we used Biolog plates to assay respiration on 95 different carbon sources over the first 20,000 generations [18]. Although mutators tended to exhibit a reduced breadth of function in this assay, the difference was not statistically significant [18]. Rather, a surprising number of losses of function were shared among replicate lines, and we took this parallelism as further support of antagonistic pleiotropy driven by selection for common sets of adaptive mutations.Here the LTEE offers its greatest advantage: more time, both for evolution and innovative research. Over subsequent generations, mutator lines should continue to accumulate greater mutational load by drift and hence become more specialized than lines retaining the low ancestral rate. Genomic sequences of the evolved lines now have confirmed this increased mutational load [3],[19] in the six of 12 lines that are now mutators [16]. In this issue, Leiby and Marx [20] have readdressed these questions by retracing old steps, applying the prior Biolog assays to lines spanning 50,000 generations of evolution, and by pioneering new high-throughput assays of fitness in many resources. Somewhat surprisingly, these methods disagree and challenge the reliability of Biolog data as a fitness proxy. As a proprietary measure of cellular respiration, it can demonstrate major functional shifts but is less reliable than growth rate as a fitness parameter.More importantly, Leiby and Marx provide clear evidence that niche breadth in the LTEE was shaped by both mutation accumulation and pleiotropy. Growth rates actually increased on several resources, and hence the pleiotropic effects of adaptation to glucose were synergistic, broadening functionality particularly over the first 20,000 generations, as well as antagonistic, producing fewer tradeoffs than previously thought [20]. Pleiotropic effects were also somewhat unpredictable: a sophisticated flux-balance analysis [21] of foreign substrates did not reveal more gains for resources similar to glucose or losses for dissimilar resources. Some early losses linked to selection (maltose, galactose, serine) [6] became complete, but also subtle gains of function for dicarboxylic acid metabolism, perhaps related to growth on metabolic byproducts, became amplified. The most striking pattern was that mutator populations became specialists, diminished for many functions owing to their greater mutational burden, and this only became evident after 50,000 generations in a single resource. These convergent functional losses were not caused by selection, as is often argued, but rather by an absence of selection in the face of mutational pressure. Mutational decay by genetic drift takes a long time, and it will take much longer for the non-mutator lines, it seems.Although Leiby and Marx [20] correctly emphasize the importance of truly long-term selection combined with deficient DNA repair to reveal effects of mutation accumulation, decay has been witnessed in other systems undergoing regular population bottlenecks over shorter time scales [22],[23]. Antagonistic pleiotropy can also reveal its effects much more rapidly than was seen in the LTEE, especially when selection discriminates among discrete fitness features in a heterogeneous environment, such as in the colonization of a new landscape [24],[25]. What this study uniquely illustrates is the unpredictability of pleiotropic effects of adaptation to a simple environment, which in turn shows how chance draws from a distribution of contending beneficial mutations may produce divergent outcomes, ranging from generalists to specialists. A sample of the first mutants competing to prevail in the LTEE system showed variable niche breadth [26] so perhaps we should not be surprised that the footprints of these large-effect mutations endure. Further study of the precise mechanisms by which different mutations produce more fit offspring will teach us more about the origins of diversity that beguile us. We can also gain a broader perspective on the longstanding tension between chance and necessity [27]—a motivator of the LTEE—by focusing more on what is unnecessary, such as how organisms grow in foreign environments. Often insight comes from studying at the margins of a problem, and here, the limits to the growth of these bacteria have allowed us to focus more on how exactly they have accomplished their most essential tasks.     

Phenotypic suppression of a fructose-1,6-diphosphate aldolase mutation in Escherichia coli

Strain NP 315 of Escherichia coli possesses a thermolabile fructose-1, 6-diphosphate (FDP) aldolase; its growth on carbohydrate substrates is inhibited probably as a consequence of the accumulation of high intracellular levels of FDP. Studies of one class of phenotypic revertants of strain NP 315 which have regained their ability to grow on C(6) substrates at 40 C showed that in these strains the buildup of the inhibitory FDP pool is prevented by additional mutations in enzymes catalyzing the conversion of the substrate offered in the medium to FDP. For example, mutations affecting 6-phosphogluconate dehydrogenase activity (gnd(-)) may be selected in great number without any mutagenesis and enrichment simply by isolating revertants of strain NP 315 able to grow on gluconate at 40 C. Similarly, an additional mutation in phosphoglucose isomerase (pgi(-)) restores the ability of these fda(-)gnd(-) strains to grow on glucose at 40 C. Glucose metabolism of these fda(-)gnd(-)pgi(-) strains was investigated. The enzymes of the Entner-Doudoroff pathway are induced to an appreciable extent upon growth of these mutants on glucose medium; further evidence for glucose degradation via this route (which normally is induced only in the presence of gluconate) was provided by following the fate of the C1 label of radioactive glucose in l-alanine. Predominant labeling of the carboxyl-carbon of l-alanine was observed, inciating a major contribution of the Entner-Doudoroff path to pyruvate formation from glucose. Chromatographic analysis of the intermediates of glucose metabolism showed further that glucose apparently is at least partly metabolized via a bypass consisting of the accumulation of extracellular gluconic acid which arises by dephosphorylation of 6-phosphogluconolactone and possibly of 6-phosphogluconate. This extracellular gluconate is then taken up and metabolized in the normal manner via the Entner-Doudoroff enzymes.     

THE ADAPTATION RATE OF ASEXUALS: DELETERIOUS MUTATIONS,CLONAL INTERFERENCE AND POPULATION BOTTLENECKS

The rate at which a population adapts to its environment is a cornerstone of evolutionary theory, and recent experimental advances in microbial populations have renewed interest in predicting and testing this rate. Efforts to understand the adaptation rate theoretically are complicated by high mutation rates, to both beneficial and deleterious mutations, and by the fact that beneficial mutations compete with each other in asexual populations (clonal interference). Testable predictions must also include the effects of population bottlenecks, repeated reductions in population size imposed by the experimental protocol. In this contribution, we integrate previous work that addresses each of these issues, developing an overall prediction for the adaptation rate that includes: beneficial mutations with probabilistically distributed effects, deleterious mutations of arbitrary effect, population bottlenecks, and clonal interference.     

ASYMMETRIC, BIMODAL TRADE-OFFS DURING ADAPTATION OF METHYLOBACTERIUM TO DISTINCT GROWTH SUBSTRATES

Trade-offs between selected and nonselected environments are often assumed to exist during adaptation. This phenomenon is prevalent in microbial metabolism, where many organisms have come to specialize on a narrow breadth of substrates. One well-studied example is methylotrophic bacteria that can use single-carbon (C₁) compounds as their sole source of carbon and energy, but generally use few, if any, multi-C compounds. Here, we use adaptation of experimental populations of the model methylotroph, Methylobacterium extorquens AM1, to C₁ (methanol) or multi-C (succinate) compounds to investigate specialization and trade-offs between these two metabolic lifestyles. We found a general trend toward trade-offs during adaptation to succinate, but this was neither universal nor showed a quantitative relationship with the extent of adaptation. After 1500 generations, succinate-evolved strains had a remarkably bimodal distribution of fitness values on methanol: either an improvement comparable to the strains adapted on methanol or the complete loss of the ability to grow on C₁ compounds. In contrast, adaptation to methanol resulted in no such trade-offs. Based on the substantial, asymmetric loss of C₁ growth during growth on succinate, we suggest that the long-term maintenance of C₁ metabolism across the genus Methylobacterium requires relatively frequent use of C₁ compounds to prevent rapid loss.     

GENETIC LOAD OF THE YEAST SACCHAROMYCES CEREVISIAE UNDER DIVERSE ENVIRONMENTAL CONDITIONS

Fitness effect of spontaneous mutations accumulated in mismatch-repair deficient strains of yeast was estimated by measuring their maximum growth rate. Several environments with different energetic substrates, nutritional conditions, and temperature were tested. Genetic load of haploid strains was about 20–30% under most of these conditions. Because such a pronounced effect was caused by relatively small lesions (point mutations) affecting probably less than 1% of genes, resistance of the yeast genome to DNA damage appears to be rather limited. Fitness transitions among environments were orderly, in the sense that some strains tended to be more or less fit than others in all circumstances. One of the environments (an extremely high temperature, 38°C) was stressful to the strains that accumulated mutations, as some of them stopped to grow, whereas the mutation-free strains were only moderately affected. These results imply that the impact of random point mutations is substantial and generally not dependent on a particular environment. Under stressful conditions, however, natural selection may be especially effective in purging mutations that, if commonly met, could slow down the rate of mutation accumulation.     

The cost of evolved constitutive lac gene expression is usually,but not always,maintained during evolution of generalist populations

Beneficial mutations can become costly following an environmental change. Compensatory mutations can relieve these costs, while not affecting the selected function, so that the benefits are retained if the environment shifts back to be similar to the one in which the beneficial mutation was originally selected. Compensatory mutations have been extensively studied in the context of antibiotic resistance, responses to specific genetic perturbations, and in the determination of interacting gene network components. Few studies have focused on the role of compensatory mutations during more general adaptation, especially as the result of selection in fluctuating environments where adaptations to different environment components may often involve trade‐offs. We examine whether costs of a mutation in lacI, which deregulated the expression of the lac operon in evolving populations of Escherichia coli bacteria, were compensated. This mutation occurred in multiple replicate populations selected in environments that fluctuated between growth on lactose, where the mutation was beneficial, and on glucose, where it was deleterious. We found that compensation for the cost of the lacI mutation was rare, but, when it did occur, it did not negatively affect the selected benefit. Compensation was not more likely to occur in a particular evolution environment. Compensation has the potential to remove pleiotropic costs of adaptation, but its rarity indicates that the circumstances to bring about the phenomenon may be peculiar to each individual or impeded by other selected mutations.     

MUTATIONAL MELTDOWN IN LABORATORY YEAST POPULATIONS

Abstract.— In small or repeatedly bottlenecked populations, mutations are expected to accumulate by genetic drift, causing fitness declines. In mutational meltdown models, such fitness declines further reduce population size, thus accelerating additional mutation accumulation and leading to extinction. Because the rate of mutation accumulation is determined partly by the mutation rate, the risk and rate of meltdown are predicted to increase with increasing mutation rate. We established 12 replicate populations of Saccharomyces cerevisiae from each of two isogenic strains whose genomewide mutation rates differ by approximately two orders of magnitude. Each population was transferred daily by a fixed dilution that resulted in an effective population size near 250. Fitness declines that reduce growth rates were expected to reduce the numbers of cells transferred after dilution, thus reducing population size and leading to mutational meltdown. Through 175 daily transfers and approximately 2900 generations, two extinctions occurred, both in populations with elevated mutation rates. For one of these populations there is direct evidence that extinction resulted from mutational meltdown: Extinction immediately followed a major fitness decline, and it recurred consistently in replicate populations reestablished from a sample frozen after this fitness decline, but not in populations founded from a predecline sample. Wild‐type populations showed no trend to decrease in size and, on average, they increased in fitness.     

Genetic basis of growth adaptation of Escherichia coli after deletion of pgi, a major metabolic gene

Bacterial survival requires adaptation to different environmental perturbations such as exposure to antibiotics, changes in temperature or oxygen levels, DNA damage, and alternative nutrient sources. During adaptation, bacteria often develop beneficial mutations that confer increased fitness in the new environment. Adaptation to the loss of a major non-essential gene product that cripples growth, however, has not been studied at the whole-genome level. We investigated the ability of Escherichia coli K-12 MG1655 to overcome the loss of phosphoglucose isomerase (pgi) by adaptively evolving ten replicates of E. coli lacking pgi for 50 days in glucose M9 minimal medium and by characterizing endpoint clones through whole-genome re-sequencing and phenotype profiling. We found that 1) the growth rates for all ten endpoint clones increased approximately 3-fold over the 50-day period; 2) two to five mutations arose during adaptation, most frequently in the NADH/NADPH transhydrogenases udhA and pntAB and in the stress-associated sigma factor rpoS; and 3) despite similar growth rates, at least three distinct endpoint phenotypes developed as defined by different rates of acetate and formate secretion. These results demonstrate that E. coli can adapt to the loss of a major metabolic gene product with only a handful of mutations and that adaptation can result in multiple, alternative phenotypes.     

Metabolic specialization and the assembly of microbial communities

Metabolic specialization is a general biological principle that shapes the assembly of microbial communities. Individual cell types rarely metabolize a wide range of substrates within their environment. Instead, different cell types often specialize at metabolizing only subsets of the available substrates. What is the advantage of metabolizing subsets of the available substrates rather than all of them? In this perspective piece, we argue that biochemical conflicts between different metabolic processes can promote metabolic specialization and that a better understanding of these conflicts is therefore important for revealing the general principles and rules that govern the assembly of microbial communities. We first discuss three types of biochemical conflicts that could promote metabolic specialization. Next, we demonstrate how knowledge about the consequences of biochemical conflicts can be used to predict whether different metabolic processes are likely to be performed by the same cell type or by different cell types. We then discuss the major challenges in identifying and assessing biochemical conflicts between different metabolic processes and propose several approaches for their measurement. Finally, we argue that a deeper understanding of the biochemical causes of metabolic specialization could serve as a foundation for the field of synthetic ecology, where the objective would be to rationally engineer the assembly of a microbial community to perform a desired biotransformation.     

Understanding the evolutionary fate of finite populations: the dynamics of mutational effects

The most consistent result in more than two decades of experimental evolution is that the fitness of populations adapting to a constant environment does not increase indefinitely, but reaches a plateau. Using experimental evolution with bacteriophage, we show here that the converse is also true. In populations small enough such that drift overwhelms selection and causes fitness to decrease, fitness declines down to a plateau. We demonstrate theoretically that both of these phenomena must be due either to changes in the ratio of beneficial to deleterious mutations, the size of mutational effects, or both. We use mutation accumulation experiments and molecular data from experimental evolution to show that the most significant change in mutational effects is a drastic increase in the rate of beneficial mutation as fitness decreases. In contrast, the size of mutational effects changes little even as organismal fitness changes over several orders of magnitude. These findings have significant implications for the dynamics of adaptation.     

Pleiotropic effects of beneficial mutations in Escherichia coli

Micromutational models of adaptation have placed considerable weight on antagonistic pleiotropy as a mechanism that prevents mutations of large effect from achieving fixation. However, there are few empirical studies of the distribution of pleiotropic effects, and no studies that have examined this distribution for a large number of adaptive mutations. Here we examine the form and extent of pleiotropy associated with beneficial mutations in Escherichia coli. To do so, we used a collection of independently evolved genotypes, each of which contains a beneficial mutation that confers increased fitness in a glucose-limited environment. To determine the pleiotropic effects of these mutations, we examined the fitnesses of the mutants in five novel resource environments. Our results show that the majority of mutations had significant fitness effects in alternative resources, such that pleiotropy was common. The predominant form of this pleiotropy was positive--that is, most mutations that conferred increased fitness in glucose also conferred increased fitness in novel resources. We did detect some deleterious pleiotropic effects, but they were primarily limited to one of the five resources, and within this resource, to only a subset of mutants. Although pleiotropic effects were generally positive, fitness levels were lower and more variable on resources that differed most in their mechanisms of uptake and catabolism from that of glucose. Positive pleiotropic effects were strongly correlated in magnitude with their direct effects, but no such correlation was found among mutants with deleterious pleiotropic effects. Whereas previous studies of populations evolved on glucose for longer periods of time showed consistent declines on some of the resources used here, our results suggest that deleterious pleiotropic effects were limited to only a subset of the beneficial mutations available.     

EVOLUTION OF THERMAL DEPENDENCE OF GROWTH RATE OF ESCHERICHIA COLI POPULATIONS DURING 20,000 GENERATIONS IN A CONSTANT ENVIRONMENT

Abstract.— Twelve experimental populations of the bacterium Escherichia coli evolved for 20,000 generations in a defined medium at 37°C. We measured their maximum growth rates across a broad range of temperatures and at several evolutionary time points to quantify the extent to which they became thermal specialists with diminished performance at other temperatures. We also sought to determine whether antagonistic pleiotropy (genetic trade‐offs) or mutation accumulation (drift decay) was primarily responsible for any thermal specialization. Populations showed consistent improvement in growth rate at moderate temperatures (27–39°C), but tended to have decreased growth rate at both low (20°C) and high (41–42°C) temperatures. Most loss occurred early in the experiment, when adaptation was most rapid. This dynamic is predicted by antagonistic pleiotropy but not by mutation accumulation. Several populations evolved high mutation rates due to defects in their DNA repair, but they did not subsequently undergo a greater decrease in growth rate at thermal extremes than populations that retained low mutation rates, contrary to the acceleration of decay predicted by mutation accumulation. Antagonistic pleiotropy therefore is more likely to be responsible for the evolution of thermal specialization observed in maximum growth rate.     

Ploidy controls the success of mutators and nature of mutations during budding yeast evolution

BACKGROUND: We used the budding yeast Saccharomyces cerevisiae to ask how elevated mutation rates affect the evolution of asexual eukaryotic populations. Mismatch repair defective and nonmutator strains were competed during adaptation to four laboratory environments (rich medium, low glucose, high salt, and a nonfermentable carbon source). RESULTS: In diploids, mutators have an advantage over nonmutators in all conditions, and mutators that win competitions are on average fitter than nonmutator winners. In contrast, haploid mutators have no advantage when competed against haploid nonmutators, and haploid mutator winners are less fit than nonmutator winners. The diploid mutator winners were all superior to their ancestors both in the condition they had adapted to, and in two of the other conditions. This phenotype was due to a mutation or class of mutations that confers a large growth advantage during the respiratory phase of yeast cultures that precedes stationary phase. This generalist mutation(s) was not selected in diploid nonmutator strains or in haploid strains, which adapt primarily by fixing specialist (condition-specific) mutations. In diploid mutators, such mutations also occur, and the majority accumulates after the fixation of the generalist mutation. CONCLUSIONS: We conclude that the advantage of mutators depends on ploidy and that diploid mutators can give rise to beneficial mutations that are inaccessible to nonmutators and haploid mutators.     

Disentangling genetic and epigenetic determinants of ultrafast adaptation

A major rationale for the advocacy of epigenetically mediated adaptive responses is that they facilitate faster adaptation to environmental challenges. This motivated us to develop a theoretical–experimental framework for disclosing the presence of such adaptation‐speeding mechanisms in an experimental evolution setting circumventing the need for pursuing costly mutation–accumulation experiments. To this end, we exposed clonal populations of budding yeast to a whole range of stressors. By growth phenotyping, we found that almost complete adaptation to arsenic emerged after a few mitotic cell divisions without involving any phenotypic plasticity. Causative mutations were identified by deep sequencing of the arsenic‐adapted populations and reconstructed for validation. Mutation effects on growth phenotypes, and the associated mutational target sizes were quantified and embedded in data‐driven individual‐based evolutionary population models. We found that the experimentally observed homogeneity of adaptation speed and heterogeneity of molecular solutions could only be accounted for if the mutation rate had been near estimates of the basal mutation rate. The ultrafast adaptation could be fully explained by extensive positive pleiotropy such that all beneficial mutations dramatically enhanced multiple fitness components in concert. As our approach can be exploited across a range of model organisms exposed to a variety of environmental challenges, it may be used for determining the importance of epigenetic adaptation‐speeding mechanisms in general.