Evolution of thermal tolerance and phenotypic plasticity under rapid and slow temperature fluctuations.

Global warming is associated with an increase in sea surface temperature and its variability. The consequences of evolving in variable, fluctuating environments are explored by a large body of theory: when populations evolve in fluctuating environments the frequency of fluctuations determines the shapes of tolerance curves (indicative of habitats that organisms can inhabit) and trait reaction norms (the phenotypes that organisms display across these environments). Despite this well-established theoretical backbone, predicting how trait and tolerance curves will evolve in organisms at the foundation of marine ecosystems remains a challenge. Here, we used a globally distributed phytoplankton, Thalassiosira pseudonana, and show that fluctuations in temperature on scales of 3-4 generations rapidly selected for populations with enhanced trait plasticity and elevated thermal tolerance. Fluctuations spanning 30-40 generations selected for the formation of two stable, genetically and physiologically distinct populations, one evolving high trait plasticity and enhanced thermal tolerance, and the other, akin to samples evolved under constant warming, with lower trait plasticity and a smaller increase in thermal tolerance.

Publisher Correction: Environmental fluctuations accelerate molecular evolution of thermal tolerance in a marine diatom.

The PDF version of this Article was updated shortly after publication following an error which resulted in the Φ symbol being omitted from the left hand side of equation 8. The HTML version was correct from the time of publication.

Environmental fluctuations accelerate molecular evolution of thermal tolerance in a marine diatom.

Diatoms contribute roughly 20% of global primary production, but the factors determining their ability to adapt to global warming are unknown. Here we quantify the capacity for adaptation to warming in the marine diatom Thalassiosira pseudonana. We find that evolutionary rescue under severe (32 °C) warming is slow, but adaptation to more realistic scenarios where temperature increases are moderate (26 °C) or fluctuate between benign and severe conditions is rapid and linked to phenotypic changes in metabolic traits and elemental composition. Whole-genome re-sequencing identifies genetic divergence among populations selected in the different warming regimes and between the evolved and ancestral lineages. Consistent with the phenotypic changes, the most rapidly evolving genes are associated with transcriptional regulation, cellular responses to oxidative stress and redox homeostasis. These results demonstrate that the evolution of thermal tolerance in marine diatoms can be rapid, particularly in fluctuating environments, and is underpinned by major genomic and phenotypic change.

Rapid adaptation drives invasion of airway donor microbiota by Pseudomonas after lung transplantation.

In cystic fibrosis (CF) patients, chronic airway infection by Pseudomonas leads to progressive lung destruction ultimately requiring lung transplantation (LT). Following LT, CF-adapted Pseudomonas strains, potentially originating from the sinuses, may seed the allograft leading to infections and reduced allograft survival. We investigated whether CF-adapted Pseudomonas populations invade the donor microbiota and adapt to the non-CF allograft. We collected sequential Pseudomonas isolates and airway samples from a CF-lung transplant recipient during two years, and followed the dynamics of the microbiota and Pseudomonas populations. We show that Pseudomonas invaded the host microbiota within three days post-LT, in association with a reduction in richness and diversity. A dominant mucoid and hypermutator mutL lineage was replaced after 11 days by non-mucoid strains. Despite antibiotic therapy, Pseudomonas dominated the allograft microbiota until day 95. We observed positive selection of pre-LT variants and the appearance of novel mutations. Phenotypic adaptation resulted in increased biofilm formation and swimming motility capacities. Pseudomonas was replaced after 95 days by a microbiota dominated by Actinobacillus. In conclusion, mucoid Pseudomonas adapted to the CF-lung remained able to invade the allograft. Selection of both pre-existing non-mucoid subpopulations and of novel phenotypic traits suggests rapid adaptation of Pseudomonas to the non-CF allograft.

Pre-adapting parasitic phages to a pathogen leads to increased pathogen clearance and lowered resistance evolution with Pseudomonas aeruginosa cystic fibrosis bacterial isolates.

Recent years have seen renewed interest in phage therapy--the use of viruses to specifically kill disease-causing bacteria--because of the alarming rise in antibiotic resistance. However, a major limitation of phage therapy is the ease at with bacteria can evolve resistance to phages. Here, we determined whether in vitro experimental coevolution can increase the efficiency of phage therapy by limiting the resistance evolution of intermittent and chronic cystic fibrosis Pseudomonas aeruginosa lung isolates to four different phages. We first pre-adapted all phage strains against all bacterial strains and then compared the efficacy of pre-adapted and nonadapted phages against ancestral bacterial strains. We found that evolved phages were more efficient in reducing bacterial densities than ancestral phages. This was primarily because only 50% of bacterial strains were able to evolve resistance to evolved phages, whereas all bacteria were able to evolve some level of resistance to ancestral phages. Although the rate of resistance evolution did not differ between intermittent and chronic isolates, it incurred a relatively higher growth cost for chronic isolates when measured in the absence of phages. This is likely to explain why evolved phages were more effective in reducing the densities of chronic isolates. Our data show that pathogen genotypes respond differently to phage pre-adaptation, and as a result, phage therapies might need to be individually adjusted for different patients.

Spatial heterogeneity lowers rather than increases host-parasite specialization.

Abiotic environmental heterogeneity can promote the evolution of diverse resource specialists, which in turn may increase the degree of host-parasite specialization. We coevolved Pseudomonas fluorescens and lytic phage ϕ2 in spatially structured populations, each consisting of two interconnected subpopulations evolving in the same or different nutrient media (homogeneous and heterogeneous environments, respectively). Counter to the normal expectation, host-parasite specialization was significantly lower in heterogeneous compared with homogeneous environments. This result could not be explained by dispersal homogenizing populations, as this would have resulted in the heterogeneous treatments having levels of specialization equal to or greater than that of the homogeneous environments. We argue that selection for costly generalists is greatest when the coevolving species are exposed to diverse environmental conditions and that this can provide an explanation for our results. A simple coevolutionary model of this process suggests that this can be a general mechanism by which environmental heterogeneity can reduce rather than increase host-parasite specialization.

Parasite host range and the evolution of host resistance.

Parasite host range plays a pivotal role in the evolution and ecology of hosts and the emergence of infectious disease. Although the factors that promote host range and the epidemiological consequences of variation in host range are relatively well characterized, the effect of parasite host range on host resistance evolution is less well understood. In this study, we tested the impact of parasite host range on host resistance evolution. To do so, we used the host bacterium Pseudomonas fluorescens SBW25 and a diverse suite of coevolved viral parasites (lytic bacteriophage Φ2) with variable host ranges (defined here as the number of host genotypes that can be infected) as our experimental model organisms. Our results show that resistance evolution to coevolved phages occurred at a much lower rate than to ancestral phage (approximately 50% vs. 100%), but the host range of coevolved phages did not influence the likelihood of resistance evolution. We also show that the host range of both single parasites and populations of parasites does not affect the breadth of the resulting resistance range in a naïve host but that hosts that evolve resistance to single parasites are more likely to resist other (genetically) more closely related parasites as a correlated response. These findings have important implications for our understanding of resistance evolution in natural populations of bacteria and viruses and other host-parasite combinations with similar underlying infection genetics, as well as the development of phage therapy.

Rapid prey evolution can alter the structure of predator-prey communities.

Although microevolution has been shown to play an important role in pairwise antagonistic species interactions, its importance in more complex communities has received little attention. Here, we used two Pseudomonas fluorescens prey bacterial strains (SBW25 and F113) and Tetrahymena thermophila protist predator to study how rapid evolution affects the structuring of predator-prey communities. Both bacterial strains coexisted in the absence of predation, and F113 was competitively excluded in the presence of both SBW25 and predator during the 24-day experiment, an initially surprising result given that F113 was originally poorer at growing, but more resistant to predation. However, this can be explained by SBW25 evolving greater antipredatory defence with a lower growth cost than F113. These results show that rapid prey evolution can alter the structure of predator-prey communities, having different effects depending on the initial composition of the evolving community. From a more applied perspective, our results suggest that the effectiveness of biocontrol bacteria, such as F113, could be weaker in communities characterized by intense bacterial competition and protist predation.

The social evolution of dispersal with public goods cooperation.

Selection can favour the evolution of individually costly dispersal if this alleviates competition between relatives. However, conditions that favour altruistic dispersal also mediate selection for other social behaviours, such as public goods cooperation, which in turn is likely to mediate dispersal evolution. Here, we investigate - both experimentally (using bacteria) and theoretically - how social habitat heterogeneity (i.e. the distribution of public goods cooperators and cheats) affects the evolution of dispersal. In addition to recovering the well-known theoretical result that the optimal level of dispersal increases with genetic relatedness of patch mates, we find both mathematically and experimentally that dispersal is always favoured when average patch occupancy is low, but when average patch occupancy is high, the presence of public goods cheats greatly alters selection for dispersal. Specifically, when public goods cheats are localized to the home patch, higher dispersal rates are favoured, but when cheats are present throughout available patches, lower dispersal rates are favoured. These results highlight the importance of other social traits in driving dispersal evolution.

Bacterial motility confers fitness advantage in the presence of phages.

Dispersal provides the opportunity to escape harm and colonize new patches, enabling populations to expand and persist. However, the benefits of dispersal associated with escaping harm will be dependent on the structure of the environment and the likelihood of escape. Here, we empirically investigate how the spatial distribution of a parasite influences the evolution of host dispersal. Bacteriophages are a strong and common threat for bacteria in natural environments and offer a good system with which to explore parasite-mediated selection on host dispersal. We used two transposon mutants of the opportunistic bacteria, Pseudomonas aeruginosa, which varied in their motility (a disperser and a nondisperser), and the lytic bacteriophage ФKZ. The phage was distributed either in the central point of colony inoculation only, thus offering an escape route for the dispersing bacteria; or, present throughout the agar, where benefits of dispersal might be lost. Surprisingly, we found dispersal to be equally advantageous under both phage conditions relative to when phages were absent. A general explanation is that dispersal decreased the spatial structuring of host population, reducing opportunities for parasite transmission, but other more idiosyncratic mechanisms may also have contributed. This study highlights the crucial role the parasites can play on the evolution of dispersal and, more specifically, that bacteriophages, which are ubiquitous, are likely to select for bacterial motility.

No effect of host-parasite co-evolution on host range expansion.

Antagonistic co-evolution between hosts and parasites (reciprocal selection for resistance and infectivity) is hypothesized to play an important role in host range expansion by selecting for novel infectivity alleles, but tests are lacking. Here, we determine whether experimental co-evolution between a bacterium (Pseudomonas fluorescens SBW25) and a phage (SBW25Φ2) affects interstrain host range: the ability to infect different strains of P. fluorescens other than SBW25. We identified and tested a genetically and phenotypically diverse suite of co-evolved phage variants of SBW25Φ2 against both sympatric and allopatric co-evolving hosts (P. fluorescens SBW25) and a large set of other P. fluorescens strains. Although all co-evolved phage had a greater host range than the ancestral phage and could differentially infect co-evolved variants of P. fluorescens SBW25, none could infect any of the alternative P. fluorescens strains. Thus, parasite generalism at one genetic scale does not appear to affect generalism at other scales, suggesting fundamental genetic constraints on parasite adaptation for this virus.

Multiplicity of infection does not accelerate infectivity evolution of viral parasites in laboratory microcosms.

Coinfection with multiple parasite genotypes [multiplicity of infection (MOI)] creates within-host competition and opportunities for parasite recombination and is therefore predicted to be important for both parasite and host evolution. We tested for a difference in the infectivity of viral parasites (lytic phage Φ2) and resistance of their bacterial hosts (Pseudomonas fluorescens SBW25) under both high and low MOI during coevolution in laboratory microcosms. Results show that MOI has no effect on infectivity and resistance evolution during coevolution over ∼80 generations of host growth, and this is true when the experiment is initiated with wild-type viruses and hosts, or with viruses and hosts that have already been coevolving for ∼330 generations. This suggests that MOI does not have a net effect of accelerating parasite adaptation to hosts through recombination, or slowing adaptation to hosts through between-parasite conflict in this system.

Abiotic heterogeneity drives parasite local adaptation in coevolving bacteria and phages.

Spatial abiotic heterogeneity can result in divergent selection, hence might increase the magnitude of host-parasite local adaptation (the mean difference in fitness of sympatric vs. allopatric host-parasite combinations). We explicitly tested this hypothesis by measuring local adaptation in experimentally coevolved populations of bacteria and viruses evolved in the same or different nutrient media. Consistent with previous work, we found that mean levels of evolved phage infectivity and bacteria resistance varied with nutrient concentration, with maximal levels at nutrient concentrations that supported the greatest densities of bacteria. Despite this variation in evolved mean infectivity and resistance between treatments, we found that parasite local adaptation was greatly increased when measured between populations evolved in different, compared with the same, media. This pattern is likely to have resulted from different media imposing divergent selection on bacterial hosts, and phages in turn adapting to their local hosts. These results demonstrate that the abiotic environment can play a strong and predictable role in driving patterns of local adaptation.

In vitro tests of natural allelic variation of innate immune genes (avian ß-defensins) reveal functional differences in microbial inhibition.

Allelic variation in immune genes might result from, and contribute to, host-pathogen evolution. Functional allelic variation in the innate immune system has received little attention. Here, we investigate whether naturally occurring allelic variation within the avian innate immune system (ß-defensins) is associated with variation in antimicrobial activity. We tested differences in in vitro antimicrobial properties of the synthesized products of two alleles of avian ß-defensin 7, both of which occur at high frequency in natural populations of the great tit (Parus major). Only one allele strongly inhibited the growth of the gram-positive bacterium Staphylococcus aureus, but both alleles strongly inhibited growth of the gram-negative bacterium Escherechia coli. Our data demonstrate functional allelic variation in natural defensin genes, and we discuss how differences in efficacy against microbial species might contribute to maintaining this variation.

Antagonistic coevolution across productivity gradients: an experimental test of the effects of dispersal.

Coevolution commonly occurs in spatially heterogeneous environments, resulting in variable selection pressures acting on coevolving species. Dispersal across such environments is predicted to have a major impact on local coevolutionary dynamics. Here, we address how co-dispersal of coevolving populations of host and parasite across an environmental productivity gradient affected coevolution in experimental populations of bacteria and their parasitic viruses (phages). The rate of coevolution between bacteria and phages was greater in high-productivity environments. High-productivity immigrants ( approximately 2% of the recipient population) caused coevolutionary dynamics (rates of coevolution and degree of generalist evolution) in low-productivity environments to be largely indistinguishable from high-productivity environments, whereas immigration from low-productivity environments ( approximately 0.5% of the population) had no discernable impact. These results could not be explained by demography alone, but rather high-productivity immigrants had a selective advantage in low-productivity environments, but not vice versa. Coevolutionary interactions in high-productivity environments are therefore likely to have a disproportionate impact on coevolution across the landscape as a whole.

Persistence of costly novel genes in the absence of positive selection.

Many genetic changes that ultimately lead to adaptive evolution come with a short-term cost expressed in terms of reduced survival and reproduction. In the absence of genetic drift, it is unclear how such costly mutations may persist. Here we experimentally demonstrate that parasites can promote the persistence of costly genetic variants. We employed a genetically engineered strain (GMMO) of the bacterium Pseudomonas fluorescens as a model of the acquisition of a new gene either through a major mutation or through horizontal transfer, and examined its persistence in different evolving communities comprising an ancestral strain and a lytic bacteriophage. Whereas competition resulted in the elimination of the GMMO, inclusion of the phage promoted GMMO persistence. We provide evidence for why this effect is due to the differential susceptibility of GMMO and ancestral bacteria to phage.

Effects of antagonistic coevolution on parasite-mediated host coexistence.

Parasites can promote diversity by mediating coexistence between a poorer and superior competitor, if the superior competitor is more susceptible to parasitism. However, hosts and parasites frequently undergo antagonistic coevolution. This process may result in the accumulation of pleiotropic fitness costs associated with host resistance, and could breakdown coexistence. We experimentally investigated parasite-mediated coexistence of two genotypes of the bacterium Pseudomonas fluorescens, where one genotype underwent coevolution with a parasite (a virulent bacteriophage), whereas the other genotype was resistant to the evolving phages at all time points, but a poorer competitor. In the absence of phages, the resistant genotype was rapidly driven extinct in all populations. In the presence of the phages, the resistant genotype persisted in four of six populations and eventually reached higher frequencies than the sensitive genotype. The coevolving genotype showed a reduction in the growth rate, consistent with a cost of resistance, which may be responsible for a decline in its relative fitness. These results demonstrate that the stability of parasite-mediated coexistence of resistant and susceptible species or genotypes is likely to be affected if parasites and susceptible hosts coevolve.

Host-parasite coevolution and patterns of adaptation across time and space.

The description of coevolutionary dynamics requires a characterization of the evolutionary dynamics of both the parasite and its host. However, a thorough description of the underlying genetics of the coevolutionary process is often extremely difficult to carry out. We propose that measures of adaptation (mean population fitness) across time or space may represent a feasible alternative approach for characterizing important features of the coevolutionary process. We discuss recent experimental work in the light of simple mathematical models of coevolution to demonstrate the potential power of this phenotypic experimental approach.

The rate of environmental change drives adaptation to an antibiotic sink.

Recent accelerated trends of human-induced global changes are providing many examples of adaptation to novel environments. Although the rate of environmental change can vary dramatically, its effect on evolving populations is unknown. A crucial feature explaining the adaptation to harsh environments is the supply of beneficial mutations via immigration from a 'source' population. In this study, we tested the effect of immigration on adaptation to increasing concentrations of antibiotics. Using experimental population of Pseudomonas aeruginosa, a pathogenic bacterium, we show that higher immigration rates and a slow increase in antibiotic concentration result in a more rapid evolution of resistance; however, a high immigration rate combined with rapid increases in concentration resulted in higher maximal levels of resistance. These findings, which support recent theoretical work, have important implications for the control of antibiotic resistance because they show that rapid rates of change can produce variants with the ability to resist future treatments.

Increasing productivity accelerates host-parasite coevolution.

Host-parasite coevolution is believed to influence a range of evolutionary and ecological processes, including population dynamics, evolution of diversity, sexual reproduction and parasite virulence. The impact of coevolution on these processes will depend on its rate, which is likely to be affected by the energy flowing through an ecosystem, or productivity. We addressed how productivity affected rates of coevolution during a coevolutionary arms race between experimental populations of bacteria and their parasitic viruses (phages). As hypothesized, the rate of coevolution between bacterial resistance and phage infectivity increased with increased productivity. This relationship can in part be explained by reduced competitiveness of resistant bacteria in low compared with high productivity environments, leading to weaker selection for resistance in the former. The data further suggest that variation in productivity can generate variation in selection for resistance across landscapes, a result that is crucial to the geographic mosaic theory of coevolution.