Suffering makes you weaker: Limited evolutionary adaptation in competitively inferior populations.

Interspecific competition can hinder populations from evolutionarily adapting to abiotic environments, particularly by reducing population size and niche space; and feedback may arise between competitive ability and evolutionary adaptation. Here we studied populations of two model bacterial species, Escherichia coli and Pseudomonas fluorescens, that evolved in monocultures and cocultures for approximately 2400 generations at three temperatures. The two species showed a reversal in competitive dominance in cocultures along the temperature gradient. Populations from cocultures where they had been competitively dominant showed the same magnitude of fitness gain as those in monocultures. However, competitively inferior populations in cocultures showed limited abiotic adaptation compared with those in monocultures. The inferior populations in cocultures were also more likely to evolve weaker interspecific competitive ability, or go extinct. The possible competitive ability-adaptation feedback may have crucial consequences for population persistence.

Linking temperature dependence of fitness effects of mutations to thermal niche adaptation.

Fitness effects of mutations may generally depend on temperature that influences all rate-limiting biophysical and biochemical processes. Earlier studies suggested that high temperatures may increase the availability of beneficial mutations ('more beneficial mutations'), or allow beneficial mutations to show stronger fitness effects ('stronger beneficial mutation effects'). The 'more beneficial mutations' scenario would inevitably be associated with increased proportion of conditionally beneficial mutations at higher temperatures. This in turn predicts that populations in warm environments show faster evolutionary adaptation but suffer fitness loss when faced with cold conditions, and those evolving in cold environments become thermal-niche generalists ('hotter is narrower'). Under the 'stronger beneficial mutation effects' scenario, populations evolving in warm environments would show faster adaptation without fitness costs in cold environments, leading to a 'hotter is (universally) better' pattern in thermal niche adaptation. We tested predictions of the two competing hypotheses using an experimental evolution study in which populations of two model bacterial species, Escherichia coli and Pseudomonas fluorescens, evolved for 2400 generations at three experimental temperatures. Results of reciprocal transplant experiments with our P. fluorescens populations were largely consistent with the 'hotter is narrower' prediction. Results from the E. coli populations clearly suggested stronger beneficial mutation effects at higher assay temperatures, but failed to detect faster adaptation in populations evolving in warmer experimental environments (presumably because of limitation in the supply of genetic variation). Our results suggest that the influence of temperature on mutational effects may provide insight into the patterns of thermal niche adaptation and population diversification across thermal conditions.

Fast drug rotation reduces bacterial resistance evolution in a microcosm experiment.

Drug rotation (cycling), in which multiple drugs are administrated alternatively, has the potential for limiting resistance evolution in pathogens. The frequency of drug alternation could be a major factor to determine the effectiveness of drug rotation. Drug rotation practices often have low frequency of drug alternation, with an expectation of resistance reversion. Here we, based on evolutionary rescue and compensatory evolution theories, suggest that fast drug rotation can limit resistance evolution in the first place. This is because fast drug rotation would give little time for the evolutionarily rescued populations to recover in population size and genetic diversity, and thus decrease the chance of future evolutionary rescue under alternate environmental stresses. We experimentally tested this hypothesis using the bacterium Pseudomonas fluorescens and two antibiotics (chloramphenicol and rifampin). Increasing drug rotation frequency reduced the chance of evolutionary rescue, and most of the finally surviving bacterial populations were resistant to both drugs. Drug resistance incurred significant fitness costs, which did not differ among the drug treatment histories. A link between population sizes during the early stages of drug treatment and the end-point fates of populations (extinction vs survival) suggested that population size recovery and compensatory evolution before drug shift increase the chance of population survival. Our results therefore advocate fast drug rotation as a promising approach to reduce bacterial resistance evolution, which in particular could be a substitute for drug combination when the latter has safety risks.

Warmer temperatures enhance beneficial mutation effects.

Temperature determines the rates of all biochemical and biophysical processes, and is also believed to be a key driver of macroevolutionary patterns. It is suggested that physiological constraints at low temperatures may diminish the fitness advantages of otherwise beneficial mutations; by contrast, relatively high, benign, temperatures allow beneficial mutations to efficiently show their phenotypic effects. To experimentally test this "mutational effects" mechanism, we examined the fitness effects of mutations across a temperature gradient using bacterial genotypes from the early stage of a mutation accumulation experiment with Escherichia coli. While the incidence of beneficial mutations did not significantly change across environmental temperatures, the number of mutations that conferred strong beneficial fitness effects was greater at higher temperatures. The results therefore support the hypothesis that warmer temperatures increase the chance and magnitude of positive selection, with implications for explaining the geographic patterns in evolutionary rates and understanding contemporary evolution under global warming.

Experimental Testing of Dispersal Limitation in Soil Bacterial Communities with a Propagule Addition Approach.

The role of dispersal in the assembly of microbial communities remains contentious. This study tested the importance of dispersal limitation for the structuring of local soil bacterial communities using an experimental approach of propagule addition. Microbes extracted from soil pooled from samples collected at 20 localities across ~ 400 km in a temperate steppe were added to microcosms of local soils at three sites; the microcosms were then incubated in situ for 3 months. We then assessed the composition and diversity of bacterial taxa in the soils using 16S rRNA gene amplicon sequencing. The addition of the regional microbial pool did not cause significant changes in the overall composition or diversity of the total bacterial community, although a very small number of individual taxa may have been affected by the addition treatment. Our results suggest a negligible role of dispersal limitation in structuring soil bacterial communities in our study area.

Temperature responses of mutation rate and mutational spectrum in an Escherichia coli strain and the correlation with metabolic rate.

BACKGROUND: Temperature is a major determinant of spontaneous mutation, but the precise mode, and the underlying mechanisms, of the temperature influences remain less clear. Here we used a mutation accumulation approach combined with whole-genome sequencing to investigate the temperature dependence of spontaneous mutation in an Escherichia coli strain. Experiments were performed under aerobic conditions at 25, 28 and 37 °C, three temperatures that were non-stressful for the bacterium but caused significantly different bacterial growth rates. RESULTS: Mutation rate did not differ between 25 and 28 °C, but was higher at 37 °C. Detailed analyses of the molecular spectrum of mutations were performed; and a particularly interesting finding is that higher temperature led to a bias of mutation to coding, relative to noncoding, DNA. Furthermore, the temperature response of mutation rate was extremely similar to that of metabolic rate, consistent with an idea that metabolic rate predicts mutation rate. CONCLUSIONS: Temperature affects mutation rate and the types of mutation supply, both being crucial for the opportunity of natural selection. Our results help understand how temperature drives evolutionary speed of organisms and thus the global patterns of biodiversity. This study also lend support to the metabolic theory of ecology for linking metabolic rate and molecular evolution rate.

Specific adaptation to strong competitors can offset the negative effects of population size reductions.

Competition plays a crucial role in determining adaptation of species, yet we know little as to how adaptation is affected by the strength of competition. On the one hand, strong competition typically results in population size reductions, which can hamper adaptation owing to a shortage of beneficial mutations; on the other hand, specificity of adaptation to competitors may offset the negative evolutionary consequences of such population size effects. Here, we investigate how competition strength affects population fitness in the bacterium Pseudomonas fluorescens Our results demonstrate that strong competition constrains adaptation of focal populations, which can be partially explained by population size reductions. However, fitness assays also reveal specific adaptation of focal populations to particular competitors varying in competitive ability. Additionally, this specific adaptation can offset the negative effects of competitor-mediated population size reductions under strong competition. Our study, therefore, highlights the importance of opposing effects of strong competition on species adaptation, which may lead to different outcomes of colonization under intense and relaxed competitive environments in the context of population dispersal.

Temperature drives diversification in a model adaptive radiation.

The warmer regions harbour more species, attributable to accelerated speciation and increased ecological opportunities for coexistence. While correlations between temperature and energy availability and habitat area have been suggested as major drivers of these biodiversity patterns, temperature can theoretically also have direct effects on the evolution of diversity. Here, we experimentally studied the evolution of diversity in a model adaptive radiation of the bacterium Pseudomonas fluorescens across a temperature gradient. Diversification increased at higher temperatures, driven by both faster generation of genetic variation and stronger diversifying selection. Specifically, low temperatures could limit the generation of diversity, suggested by the observation that supply of genetic variation through immigration increased diversity at low, but not high temperatures. The two major determinants of mutation supply, population size and mutation rate, both showed a positive temperature dependence. Stronger diversifying selection in warmer environments was suggested by promoted coexistence, and further explicitly inferred by the ability of evolved phenotypes to invade the ancestral type from rare. We discuss possible physiological and environmental mechanisms underlying the findings, most of which are likely to be general.

Migration highways and migration barriers created by host-parasite interactions.

Co-evolving parasites may play a key role in host migration and population structure. Using co-evolving bacteria and viruses, we test general hypotheses as to how co-evolving parasites affect the success of passive host migration between habitats that can support different intensities of host-parasite interactions. First, we show that parasites aid migration from areas of intense to weak co-evolutionary interactions and impede migration in the opposite direction, as a result of intraspecific apparent competition mediated via parasites. Second, when habitats show qualitative difference such that some environments support parasite persistence while others do not, different population regulation forces (either parasitism or competitive exclusion) will reduce the success of migration in both directions. Our study shows that co-evolution with parasites can predictably homogenises or isolates host populations, depending on heterogeneity of abiotic conditions, with the second scenario constituting a novel type of 'isolation by adaptation'.

Resource-dependent antagonistic coevolution leads to a new paradox of enrichment.

The classical, ecological, paradox of enrichment describes a phenomenon that resource enrichment destabilizes predator-prey systems by exacerbating population oscillations. Here we suggest a new, evolutionary, paradox of enrichment. Resource enrichment can lead to more asymmetrical predator-prey coevolution (i.e., extremely high levels of prey defenses against predators) that decreases predator abundances and increases predator extinction risk. A major reason for this is that high resource availability can reduce fitness costs associated with prey defenses. In our experiments with a bacterium and its lytic phage, nutrient-balanced resource enrichment led to patterns in population demography and coevolutionary dynamics consistent with this coevolution-based paradox of enrichment; in particular, phage population extinction events were observed under nutrient-rich, not nutrient-poor, conditions. Consistent with ecological studies, carbon-biased resource enrichment (with carbon availability disproportionately increased relative to other nutrients) did not destabilize dynamics, and the asymmetry of coevolution was not altered in this context. Our work highlights the importance of integrating ecological and evolutionary thinking for studies of the consequences of nutrient pollution and other types of environmental changes.

Evolutionary rescue can be impeded by temporary environmental amelioration.

Rapid evolutionary adaptation has the potential to rescue from extinction populations experiencing environmental changes. Little is known, however, about the impact of short-term environmental fluctuations during long-term environmental deterioration, an intrinsic property of realistic environmental changes. Temporary environmental amelioration arising from such fluctuations could either facilitate evolutionary rescue by allowing population recovery (a positive demographic effect) or impede it by relaxing selection for beneficial mutations required for future survival (a negative population genetic effect). We address this uncertainty in an experiment with populations of a bacteriophage virus that evolved under deteriorating conditions (gradually increasing temperature). Periodic environmental amelioration (short periods of reduced temperature) caused demographic recovery during the early phase of the experiment, but ultimately reduced the frequency of evolutionary rescue. These experimental results suggest that environmental fluctuations could reduce the potential of evolutionary rescue.

Loss and recovery of ecological diversity associated with evolutionary rescue in abruptly and gradually deteriorating environments.

Populations may survive environmental deterioration by evolutionary adaptation. However, such evolutionary rescue events may be associated with ecological costs, such as reduction in growth performance and loss of ecologically important genetic diversity. Those negative ecological consequences may be mitigated by additional adaptive evolution. Both the ecological costs and the opportunities for additional evolution are contingent on the severity of environmental deterioration. Here, we hypothesize that populations evolutionarily rescued from faster, relative to slow, environmental deterioration suffer more severe long-term fitness decline and diversity loss. An experiment with the model adaptive radiation of bacterium Pseudomonas fluorescens exposed to abruptly or gradually increased antibiotic stress supported our hypothesis. The effect of additional adaptive evolution in recovering population size and ecological diversity was far from perfect. Cautions are therefore needed in predicting the role of rapid evolution for mitigating the impacts of environmental changes, in particular very fast environmental deterioration. We also found that bacterial populations rescued from gradually increased antibiotic stress evolved higher levels of antibiotic resistance, lending more support to aggressive chemotherapy in pathogen control.

A two-dimensional mass transfer model for an annular bioreactor using immobilized photosynthetic bacteria for hydrogen production.

A two-dimensional model for substrate transfer and biodegradation in a novel, annular fiber-illuminating bioreactor (AFIBR) is proposed in which photosynthetic bacteria are immobilized on the surface of a side-glowing optical fiber to form a stable biofilm. When excited by light, the desired intensity and uniform light distribution can be obtained within the biofilm zone in bioreactor and then realize continuous hydrogen production. Substrate transfer and biodegradation within the biofilm zone, as well as substrate diffusion and convection within bulk fluid regions are considered simultaneously in this model. The validity of the model is verified experimentally. Based on the model analysis, influences of flow rate and light intensity on the substrate consumption rate and substrate degradation efficiency were investigated. The simulation results show that the optimum operational conditions for the substrate degradation within the AFIBR are: flow rate 100 ml h(-1) and light intensity 14.6 µmol photons m(-2 )s(-1).

The effectiveness of artificial microbial community selection: a conceptual framework and a meta-analysis.

The potential for artificial selection at the community level to improve ecosystem functions has received much attention in applied microbiology. However, we do not yet understand what conditions in general allow for successful artificial community selection. Here we propose six hypotheses about factors that determine the effectiveness of artificial microbial community selection, based on previous studies in this field and those on multilevel selection. In particular, we emphasize selection strategies that increase the variance among communities. We then report a meta-analysis of published artificial microbial community selection experiments. The reported responses to community selection were highly variable among experiments; and the overall effect size was not significantly different from zero. The effectiveness of artificial community selection was greater when there was no migration among communities, and when the number of replicated communities subjected to selection was larger. The meta-analysis also suggests that the success of artificial community selection may be contingent on multiple necessary conditions. We argue that artificial community selection can be a promising approach, and suggest some strategies for improving the performance of artificial community selection programs.

Source-sink migration of natural enemies drives maladaptation of victim populations in sink habitats.

Natural enemies are critical drivers of species biogeography, and they may often limit the evolutionary adaptation and persistence of victim populations in sink habitats. Source-sink migration is also a major determinant of adaptation in sink habitats. Here, we specifically suggest that source-sink migration of enemies reduces evolutionary adaptation of victim populations in sink habitats. The underlying mechanisms may include depressed population size (which limits the supply of genetic variation) and enforced resistance evolution in victims (which shows a trade-off with growth performance). We experimentally tested this hypothesis using a model microbial system, bacterium Pseudomonas fluorescens (victim) and its lytic bacteriophage (enemy). The ancestral bacterial strain had lower growth performance at a cold temperature (10 °C, considered as sink habitat) than at its optimal temperature (28 °C, source habitat). Evolutionary adaptation took place in bacterial populations that evolved alone in the cold environment. When phages were present, no significant abiotic adaptation was observed. Crucially, phage immigration from source populations caused maladaptation, i.e., decreased growth performance relative to the ancestral genotype, although this was not the case when there was simultaneous immigration of phage and bacteria. Therefore, enemy-mediated intraspecific apparent competition could lead to prosperity in core habitats causing hardship in edge habitats.

Antagonistic coevolution limits population persistence of a virus in a thermally deteriorating environment.

Understanding the conditions under which rapid evolutionary adaptation can prevent population extinction in deteriorating environments (i.e. evolutionary rescue) is a crucial aim in the face of global climate change. Despite a rapidly growing body of work in this area, little attention has been paid to the importance of interspecific coevolutionary interactions. Antagonistic coevolution commonly observed between hosts and parasites is likely to retard evolutionary rescue because it often reduces population sizes, and results in the evolution of costly host defence and parasite counter-defence. We used experimental populations of a bacterium Pseudomonas fluorescens SBW25 and a bacteriophage virus (SBW25Φ2), to study how host-parasite coevolution impacts viral population persistence in the face of gradually increasing temperature, an environmental stress for the virus but not the bacterium. The virus persisted much longer when it evolved in the presence of an evolutionarily constant host genotype (i.e. in the absence of coevolution) than when the bacterium and virus coevolved. Further experiments suggest that both a reduction in population size and costly infectivity strategies contributed to viral extinction as a result of coevolution. The results highlight the importance of interspecific evolutionary interactions for the evolutionary responses of populations to global climate change.

Overcoming the growth-infectivity trade-off in a bacteriophage slows bacterial resistance evolution.

The use of lytic bacteriophages for treating harmful bacteria (phage therapy) is faced with the challenge of bacterial resistance evolution. Phage strains with certain traits, for example, rapid growth and relatively broad infectivity ranges, may enjoy an advantage in slowing bacterial resistance evolution. Here, we show the possibility for laboratory selection programs ("evolutionary training") to yield phage genotypes with both high growth rate and broad infectivity, traits between which a trade-off has been assumed. We worked with a lytic phage that infects the bacterium Pseudomonas fluorescens and adopted three types of training strategies: evolution on susceptible bacteria, coevolution with bacteria, and rotation between evolution and coevolution phases. Overall, there was a trade-off between growth rate and infectivity range in the evolved phage isolates, including those from the rotation training programs. A small number of phages had both high growth rate and broad infectivity, and those trade-off-overcoming phages could slow or even completely prevent resistance evolution in initially susceptible bacterial populations. Our findings show the promise of well-designed evolutionary training programs, in particular an evolution/coevolution rotation selection regime, for obtaining therapeutically useful phage materials.

Compensatory adaptation and diversification subsequent to evolutionary rescue in a model adaptive radiation.

Biological populations may survive lethal environmental stress through evolutionary rescue. The rescued populations typically suffer a reduction in growth performance and harbor very low genetic diversity compared with their parental populations. The present study addresses how population size and within-population diversity may recover through compensatory evolution, using the experimental adaptive radiation of bacterium Pseudomonas fluorescens. We exposed bacterial populations to an antibiotic treatment and then imposed a one-individual-size population bottleneck on those surviving the antibiotic stress. During the subsequent compensatory evolution, population size increased and leveled off very rapidly. The increase of diversity was of slower paces and persisted longer. In the very early stage of compensatory evolution, populations of large sizes had a greater chance to diversify; however, this productivity-diversification relationship was not observed in later stages. Population size and diversity from the end of the compensatory evolution was not contingent on initial population growth performance. We discussed the possibility that our results be explained by the emergence of a "holey" fitness landscape under the antibiotic stress.

Consequences of mutation accumulation for growth performance are more likely to be resource-dependent at higher temperatures.

BACKGROUND: Mutation accumulation (MA) has profound ecological and evolutionary consequences. One example is that accumulation of conditionally neutral mutations leads to fitness trade-offs among heterogenous habitats which cause population divergence. Here we suggest that temperature, which controls the rates of all biochemical and biophysical processes, should play a crucial role for determining mutational effects. Particularly, warmer temperatures may mitigate the effects of some, not all, deleterious mutations and cause stronger environmental dependence in MA effects. RESULTS: We experimentally tested the above hypothesis by measuring the growth performance of ten Escherichia coli genotypes on six carbon resources across ten temperatures, where the ten genotypes were derived from a single ancestral strain and accumulated spontaneous mutations. We analyzed resource dependence of MA consequences for growth yields. The MA genotypes typically showed reduced growth yields relative to the ancestral type; and the magnitude of reduction was smaller at intermediate temperatures. Stronger resource dependence in MA consequences for growth performance was observed at higher temperatures. Specifically, the MA genotypes were more likely to show impaired growth performance on all the six carbon resources when grown at lower temperatures; but suffered growth performance loss only on some, not all the six, carbon substrates at higher temperatures. CONCLUSIONS: Higher temperatures increase the chance that MA causes conditionally neutral fitness effects while MA is more likely to cause fitness loss regardless of available resources at lower temperatures. This finding has implications for understanding how geographic patterns in population divergence may emerge, and how conservation practices, particularly protection of diverse microhabitats, may mitigate the impacts of global warming.

Interspecific Niche Competition Increases Morphological Diversity in Multi-Species Microbial Communities.

Intraspecific competition for limited niches has been recognized as a driving force for adaptive radiation, but results for the role of interspecific competition have been mixed. Here, we report the adaptive diversification of the model bacteria Pseudomonas fluorescens in the presence of different numbers and combinations of four competing bacterial species. Increasing the diversity of competitive community increased the morphological diversity of focal species, which is caused by impeding the domination of a single morphotype. Specifically, this pattern was driven by more diverse communities being more likely to contain key species that occupy the same niche as otherwise competitively superior morphotype, and thus preventing competitive exclusion within the focal species. Our results suggest that sympatric adaptive radiation is driven by the presence or absence of niche-specific competitors.