Ecological and Evolutionary Consequences of Viral Plasticity

Viral plasticity facilitates host diversity in challenging environments

The antagonistic coevolution of microbes and viruses influences fundamentally the diversity of microbial communities. Information on how environmental variables interact with emergent defense-counterdefense strategies and community composition is, however, still scarce. Following biological intuition, diversity should increase with improved growth conditions, which offset evolutionary costs; however, laboratory and regional data suggest that microbial diversity decreases in nutrient-rich conditions. Moreover, global oceanic data show that microbial and viral diversity decline for high latitudes, although the underlying mechanisms are unknown. This article addresses these gaps by introducing an eco-evolutionary model for bacteria-virus antagonistic coevolution. The theory presented here harmonizes the observations above and identifies negative density dependence and viral plasticity (dependence of virus performance on host physiological state) as key drivers: environmental conditions selecting for slow host growth also limit viral performance, facilitating the survival of a diverse host community; host diversity, in turn, enables viral portfolio effects and bet-hedging strategies that sustain viral diversity. From marine microbes to phage therapy against antibiotic-resistant bacteria or cancer cells, the ubiquity of antagonistic coevolution highlights the need to consider eco-evolutionary interactions across a gradient of growth conditions.

Resource asynchrony and landscape homogenization as drivers of virulence evolution: The case of a directly transmitted disease in a social host

Throughout the last decades, the emergence of zoonotic diseases and the frequency of disease outbreaks have increased substantially, fuelled by habitat encroachment and vectors overlapping with more hosts due to global change. The virulence of pathogens is one key trait for successful invasion. In order to understand how global change drivers such as habitat homogenization and climate change drive pathogen virulence evolution, we adapted an established individual-based model of host-pathogen dynamics. Our model simulates a population of social hosts affected by a directly transmitted evolving pathogen in a dynamic landscape. Pathogen virulence evolution results in multiple strains in the model that differ in their transmission capability and lethality. We represent the effects of global change by simulating environmental changes both in time (resource asynchrony) and space (homogenization). We found an increase in pathogenic virulence and a shift in strain dominance with increasing landscape homogenization. Our model further indicated that lower virulence is dominant in fragmented landscapes, although pulses of highly virulent strains emerged under resource asynchrony. While all landscape scenarios favoured co-occurrence of low- and high-virulent strains, the high-virulence strains capitalized on the possibility for transmission when host density increased and were likely to become dominant. With asynchrony likely to occur more often due to global change, our model showed that a subsequent evolution towards lower virulence could lead to some diseases becoming endemic in their host populations.

Single-Cell Approach Reveals Intercellular Heterogeneity in Phage-Producing Capacities

Bacteriophage burst size is the average number of phage virions released from infected bacterial cells, and its magnitude depends on the duration of an intracellular progeny accumulation phase. Burst size is often measured at the population level, not the single-cell level, and consequently, statistical moments are not commonly available. In this study, we estimated the bacteriophage lambda (λ) single-cell burst size mean and variance following different intracellular accumulation period durations by employing Escherichia coli lysogens bearing lysis-deficient λ prophages. Single lysogens can be isolated and chemically lysed at desired times following prophage induction to quantify progeny intracellular accumulation within individual cells. Our data showed that λ phage burst size initially increased exponentially with increased lysis time (i.e., period between induction and chemical lysis) and then saturated at longer lysis times. We also demonstrated that cell-to-cell variation, or "noise," in lysis timing did not contribute significantly to burst size noise. The burst size noise remained constant with increasing mean burst size. The most likely explanation for the experimentally observed constant burst size noise was that cell-to-cell differences in burst size originated from intercellular heterogeneity in cellular capacities to produce phages. The mean burst size measured at different lysis times was positively correlated to cell volume, which may determine the cellular phage production capacity. However, experiments controlling for cell size indicated that there are other factors in addition to cell size that determine this cellular capacity. IMPORTANCE Phages produce offspring by hijacking a cell's replicative machinery. Previously, it was noted that the variation in the number of phages produced by single infected cells far exceeded cell size variation. It was hypothesized that this variation is a consequence of variation in the timing of host cell lysis. Here, we show that cell-to-cell variation in lysis timing does not significantly contribute to the burst size variation. We suggest that the constant burst size variation across different host lysis times results from cell-to-cell differences in capacity to produce phages. We found that the mean burst size measured at different lysis times was positively correlated to cell volume, which may determine the cellular phage production capacity. However, experiments controlling for cell size indicated that there are other factors in addition to cell size that determine this cellular capacity.

Phenotypic flux: The role of physiology in explaining the conundrum of bacterial persistence amid phage attack

Bacteriophages, the viruses of bacteria, have been studied for over a century. They were not only instrumental in laying the foundations of molecular biology, but they are also likely to play crucial roles in shaping our biosphere and may offer a solution to the control of drug-resistant bacterial infections. However, it remains challenging to predict the conditions for bacterial eradication by phage predation, sometimes even under well-defined laboratory conditions, and, most curiously, if the majority of surviving cells are genetically phage-susceptible. Here, I propose that even clonal phage and bacterial populations are generally in a state of continuous 'phenotypic flux', which is caused by transient and nongenetic variation in phage and bacterial physiology. Phenotypic flux can shape phage infection dynamics by reducing the force of infection to an extent that allows for coexistence between phages and susceptible bacteria. Understanding the mechanisms and impact of phenotypic flux may be key to providing a complete picture of phage-bacteria coexistence. I review the empirical evidence for phenotypic variation in phage and bacterial physiology together with the ways they have been modeled and discuss the potential implications of phenotypic flux for ecological and evolutionary dynamics between phages and bacteria, as well as for phage therapy.

Assessment of Explicit Representation of Dynamic Viral Processes in Regional Marine Ecological Models

Viruses, the most abundant microorganisms in the ocean, play important roles in marine ecosystems, mainly by killing their hosts and contributing to nutrient recycling. However, in models simulating ecosystems in real marine environments, the virus-mediated mortality (VMM) rates of their hosts are implicitly represented by constant parameters, thus ignoring the dynamics caused by interactions between viruses and hosts. Here, we construct a model explicitly representing marine viruses and the VMM rates of major hosts, heterotrophic bacteria, and apply it to two sites in the oligotrophic North Pacific and the more productive Arabian Sea. The impacts of the viral processes were assessed by comparing model results with the viral processes enabled and disabled. For reliable assessments, a data assimilation method was used to objectively optimize the model parameters in each run. The model generated spatiotemporally variable VMM rates, generally decreasing in the subsurface but increasing at the surface. Although the dynamics introduced by viruses could be partly stabilized by the ecosystems, they still caused substantial changes to the bacterial abundance, primary production and carbon export, with the changes greater at the more productive site. Our modeling experiments reveal the importance of explicitly simulating dynamic viral processes in marine ecological models.

An Optimal Lysis Time Maximizes Bacteriophage Fitness in Quasi-Continuous Culture

Optimality models have a checkered history in evolutionary biology. While optimality models have been successful in providing valuable insight into the evolution of a wide variety of biological traits, a common objection is that optimality models are overly simplistic and ignore organismal genetics. We revisit evolutionary optimization in the context of a major bacteriophage life history trait, lysis time. Lysis time refers to the period spanning phage infection of a host cell and its lysis, whereupon phage progenies are released. Lysis time, therefore, directly determines phage fecundity assuming progeny assembly does not exhaust host resources prior to lysis. Noting that previous tests of lysis time optimality rely on batch culture, we implemented a quasi-continuous culture system to observe productivity of a panel of isogenic phage λ genotypes differing in lysis time. We report that under our experimental conditions, λ phage productivity is maximized around optimal lysis times ranging from 60 to 100 min, and λ wildtype strain falls within this range. It would appear that natural selection on phage λ lysis time uncovered a set of genetic solutions that optimized progeny production in its ecological milieu relative to alternative genotypes. We discuss this finding in light of recent results that lysis time variation is also minimized in the strains with lysis times closer to the λ wild-type strain. IMPORTANCE Optimality theory presents the idea that natural selection acts on organismal traits to produce genotypes that maximize organismal survival and reproduction. As such, optimality theory is a valuable tool in guiding our understanding of the genetic constraints and tradeoffs organisms experience as their genotypes are selected to produce optimal solutions to biological problems. However, optimality theory is often critiqued as being overly simplistic and ignoring the roles of chance and history in the evolution of organismal traits. We show here that the wild-type genotype of a popular laboratory model organism, the bacteriophage λ, produces a phenotype for a major life history trait, lysis time, that maximizes the reproductive success of bearers of that genotype relative to other possible genotypes. This result demonstrates, as is rarely shown experimentally, that natural selection can achieve optimal solutions to ecological challenges.

Unconstrained coevolution of bacterial size and the latent period of plastic phage

Viruses play critical roles in the dynamics of microbial communities. Lytic viruses, for example, kill significant fractions of autotrophic and heterotrophic microbes daily. The dynamic interplay between viruses and microbes results from an overlap of physiological, ecological, and evolutionary responses: environmental changes trigger host physiological changes, affecting the ecological interactions of host and virus and, ultimately, the evolutionary pressures influencing the two populations. Recent theoretical work studied how the dependence of viral traits on host physiology (viral plasticity) affects the evolutionarily stable host cell size and viral infection time emerging from coevolution. Here, we broaden the scope of the framework to consider any coevolutionary outcome, including potential evolutionary collapses of the system. We used the case study of Escherichia coli and T-like viruses under chemostat conditions, but the framework can be adapted to any microbe-virus system. Oligotrophic conditions led to smaller, lower-quality but more abundant hosts, and infections that were longer but produced a reduced viral offspring. Conversely, eutrophic conditions resulted in fewer but larger higher-quality hosts, and shorter but more productive infections. The virus influenced host evolution decreasing host size more noticeably for low than for high dilution rates, and for high than for low nutrient input concentration. For low dilution rates, the emergent infection time minimized host need/use, but higher dilution led to an opportunistic strategy that shortened the duration of infections. System collapses driven by evolution resulted from host failure to adapt quickly enough to the evolving virus. Our results contribute to understanding the eco-evolutionary dynamics of microbes and virus, and to improving the predictability of current models for host-virus interactions. The large quantitative and qualitative differences observed with respect to a classic description (in which viral traits are assumed to be constant) highlights the importance of including viral plasticity in theories describing short- and long-term host-virus dynamics.

Delayed Lysis Time at High Multiplicities of Particles in a Chlorovirus-Chlorella Interaction

When viruses infect microbial cells, their phenotypes depend on the host's genotype and on the environmental conditions. Here we describe such an effect in laboratory strains of the chlorovirus PBCV-1 and its algal host Chlorella variabilis. We studied the growth of six virus isolates, and found that the mean lysis time was 1.34±0.05 times longer at multiplicity of particles (MOP) 10 than at MOP 1. We could not detect any associated changes in burst size. This is a novel plastic trait for chloroviruses, and we hypothesize that it is caused by our specific laboratory algae.

Filamentous Bacteriophages and the Competitive Interaction between Pseudomonas aeruginosa Strains under Antibiotic Treatment: a Modeling Study

Pseudomonas aeruginosa (Pa) is a major bacterial pathogen responsible for chronic lung infections in cystic fibrosis patients. Recent work has implicated Pf bacteriophages, nonlytic filamentous viruses produced by Pa, in the chronicity and severity of Pa infections. Pf phages act as structural elements in Pa biofilms and sequester aerosolized antibiotics, thereby contributing to antibiotic tolerance. Consistent with a selective advantage in this setting, the prevalence of Pf-positive (Pf+) bacteria increases over time in these patients. However, the production of Pf phages comes at a metabolic cost to bacteria, such that Pf+ strains grow more slowly than Pf-negative (Pf-) strains in vitro. Here, we use a mathematical model to investigate how these competing pressures might influence the relative abundance of Pf+ versus Pf- strains in different settings. Our model suggests that Pf+ strains of Pa cannot outcompete Pf- strains if the benefits of phage production falls onto both Pf+ and Pf- strains for a majority of parameter combinations. Further, phage production leads to a net positive gain in fitness only at antibiotic concentrations slightly above the MIC (i.e., concentrations for which the benefits of antibiotic sequestration outweigh the metabolic cost of phage production) but which are not lethal for Pf+ strains. As a result, our model suggests that frequent administration of intermediate doses of antibiotics with low decay rates and high killing rates favors Pf+ over Pf- strains. These models inform our understanding of the ecology of Pf phages and suggest potential treatment strategies for Pf+ Pa infections. IMPORTANCE Filamentous phages are a frontier in bacterial pathogenesis, but the impact of these phages on bacterial fitness is unclear. In particular, Pf phages produced by Pa promote antibiotic tolerance but are metabolically expensive to produce, suggesting that competing pressures may influence the prevalence of Pf+ versus Pf- strains of Pa in different settings. Our results identify conditions likely to favor Pf+ strains and thus antibiotic tolerance. This study contributes to a better understanding of the unique ecology of filamentous phages in both environmental and clinical settings and may facilitate improved treatment strategies for combating antibiotic tolerance.

Evolutionarily Stable Coevolution Between a Plastic Lytic Virus and Its Microbial Host

Hosts influence and are influenced by viral replication. Cell size, for example, is a fundamental trait for microbial hosts that can not only alter the probability of viral adsorption, but also constrain the host physiological processes that the virus relies on to replicate. This intrinsic connection can affect the fitness of both host and virus, and therefore their mutual evolution. Here, we study the coevolution of bacterial hosts and their viruses by considering the dependence of viral performance on the host physiological state (viral plasticity). To this end, we modified a standard host-lytic phage model to include viral plasticity, and compared the coevolutionary strategies emerging under different scenarios, including cases in which only the virus or the host evolve. For all cases, we also obtained the evolutionary prediction of the traditional version of the model, which assumes a non-plastic virus. Our results reveal that the presence of the virus leads to an increase in host size and growth rate in the long term, which benefits both interacting populations. Our results also show that viral plasticity and evolution influence the classic host quality-quantity trade-off. Poor nutrient environments lead to abundant low-quality hosts, which tends to increase viral infection time. Conversely, richer nutrient environments lead to fewer but high-quality hosts, which decrease viral infection time. Our results can contribute to advancing our understanding of the microbial response to changing environments. For instance, both cell size and viral-induced mortality are essential factors that determine the structure and dynamics of the marine microbial community, and therefore our study can improve predictions of how marine ecosystems respond to environmental change. Our study can also help devise more reliable strategies to use phage to, for example, fight bacterial infections.

Temperate infection in a virus-host system previously known for virulent dynamics

The blooming cosmopolitan coccolithophore Emiliania huxleyi and its viruses (EhVs) are a model for density-dependent virulent dynamics. EhVs commonly exhibit rapid viral reproduction and drive host death in high-density laboratory cultures and mesocosms that simulate blooms. Here we show that this system exhibits physiology-dependent temperate dynamics at environmentally relevant E. huxleyi host densities rather than virulent dynamics, with viruses switching from a long-term non-lethal temperate phase in healthy hosts to a lethal lytic stage as host cells become physiologically stressed. Using this system as a model for temperate infection dynamics, we present a template to diagnose temperate infection in other virus-host systems by integrating experimental, theoretical, and environmental approaches. Finding temperate dynamics in such an established virulent host-virus model system indicates that temperateness may be more pervasive than previously considered, and that the role of viruses in bloom formation and decline may be governed by host physiology rather than by host-virus densities.

Hitchhiking, collapse, and contingency in phage infections of migrating bacterial populations

Natural bacterial populations are subjected to constant predation pressure by bacteriophages. Bacteria use a variety of molecular mechanisms to defend themselves from phage predation. However, since phages are nonmotile, perhaps the simplest defense against phage is for bacteria to move faster than phages. In particular, chemotaxis, the active migration of bacteria up attractant gradients, may help the bacteria escape slowly diffusing phages. Here we study phage infection dynamics in migrating bacterial populations driven by chemotaxis through low viscosity agar plates. We find that expanding phage-bacteria populations supports two moving fronts, an outermost bacterial front driven by nutrient uptake and chemotaxis and an inner phage front at which the bacterial population collapses due to phage predation. We show that with increasing adsorption rate and initial phage population, the speed of the moving phage front increases, eventually overtaking the bacterial front and driving the system across a transition from a regime where bacterial front speed exceeds that of the phage front to one where bacteria must evolve phage resistance to survive. Our data support the claim that this process requires phage to hitchhike with moving bacteria. A deterministic model recapitulates the transition under the assumption that phage virulence declines with host growth rate which we confirm experimentally. Finally, near the transition between regimes we observe macroscopic fluctuations in bacterial densities at the phage front. Our work opens a new, spatio-temporal, line of investigation into the eco-evolutionary struggle between bacteria and phage.

The effect of viral plasticity on the persistence of host-virus systems

Phenotypic plasticity plays an important role in the survival of individuals. In microbial host-virus systems, previous studies have shown the stabilizing effect that host plasticity has on the coexistence of the system. By contrast, it remains uncertain how the dependence of the virus on the metabolism of the host (i.e. "viral plasticity") shapes bacteria-phage population dynamics in general, or the stability of the system in particular. Moreover, bacteria-phage models that do not consider viral plasticity are now recognised as overly simplistic. For these reasons, here we focus on the effect of viral plasticity on the stability of the system under different environmental conditions. We compared the predictions from a standard bacteria-phage model, which neglects plasticity, with those of a modification that includes viral plasticity. We investigated under which conditions viral plasticity promotes coexistence, with or without oscillatory dynamics. Our analysis shows that including viral plasticity reveals coexistence in regions of the parameter space where models without plasticity predict a collapse of the system. We also show that viral plasticity tends to reduce population oscillations, although this stabilizing effect is not consistently observed across environmental conditions: plasticity may instead reinforce dynamic feedbacks between the host, the virus, and the environment, which leads to wider oscillations. Our results contribute to a deeper understanding of the dynamic control of bacteriophage on host populations observed in nature.

Impact of Lytic Phages on Phosphorus- vs. Nitrogen-Limited Marine Microbes

Lytic viruses kill almost 20% of marine bacteria every day, re-routing nutrients away from the higher trophic levels of the marine food web and back in the microbial loop. Importantly, the effect of this inflow of key elements on the ecosystem depends on the nutrient requirements of bacteria as well as on the elemental composition of the viruses that infect them. Therefore, the influence of viruses on the ecosystem could vary depending on which nutrient is limiting. In this paper, we considered an existing multitrophic model (nutrient, bacteria, zooplankton, and viruses) that accounts for nitrogen limitation, and developed a phosphorus-limited version to assess whether the limiting nutrient alters the role of viruses in the ecosystem. For both versions, we evaluated the stationary state of the system with and without viruses. In agreement with existing results, nutrient release increased with viruses for nitrogen–limited systems, while zooplankton abundance and export to higher trophic levels decreased. We found this to be true also for phosphorus-limited systems, although nutrient release increased less than in nitrogen-limited systems. The latter supports a nutrient-specific response of the ecosystem to viruses. Bacterial concentration decreased in the phosphorus-limited system but increased in most nitrogen-limited cases due to a switch from mostly bottom-up to entirely top-down control by viruses. Our results also show that viral concentration is best predicted by a power-law of bacterial concentration with exponent different from 1. Finally, we found a positive correlation between carbon export and viruses regardless of the limiting nutrient, which led us to suggest viral abundance as a predictor of carbon sink.

Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems

Ecosystems are controlled by 'bottom-up' (resources) and 'top-down' (predation) forces. Viral infection is now recognized as a ubiquitous top-down control of microbial growth across ecosystems but, at the same time, cell death by viral predation influences, and is influenced by, resource availability. In this Review, we discuss recent advances in understanding the biogeochemical impact of viruses, focusing on how metabolic reprogramming of host cells during lytic viral infection alters the flow of energy and nutrients in aquatic ecosystems. Our synthesis revealed several emerging themes. First, viral infection transforms host metabolism, in part through virus-encoded metabolic genes; the functions performed by these genes appear to alleviate energetic and biosynthetic bottlenecks to viral production. Second, viral infection depends on the physiological state of the host cell and on environmental conditions, which are challenging to replicate in the laboratory. Last, metabolic reprogramming of infected cells and viral lysis alter nutrient cycling and carbon export in the oceans, although the net impacts remain uncertain. This Review highlights the need for understanding viral infection dynamics in realistic physiological and environmental contexts to better predict their biogeochemical consequences.

Lysogeny in the Lactic Acid Bacterium Oenococcus oeni Is Responsible for Modified Colony Morphology on Red Grape Juice Agar

Oenococcus oeni is the lactic acid bacterium (LAB) that most commonly drives malolactic fermentation in wine. Although oenococcal prophages are highly prevalent, their implications on bacterial fitness have remained unexplored and more research is required in this field. An important step toward achieving this goal is the ability to produce isogenic pairs of strains that differ only by the lysogenic presence of a given prophage, allowing further comparisons of different phenotypic traits. A novel protocol for the rapid isolation of lysogens is presented. Bacteria were first picked from the center of turbid plaques produced by temperate oenophages on a sensitive nonlysogenic host. When streaked onto an agar medium containing red grape juice (RGJ), cells segregated into white and red colonies. PCR amplifications with phage-specific primers demonstrated that only lysogens underwent white-red morphotypic switching. The method proved successful for various oenophages irrespective of their genomic content and attachment site used for site-specific recombination in the bacterial chromosome. The color switch was also observed when a sensitive nonlysogenic strain was infected with an exogenously provided lytic phage, suggesting that intracolonial lysis triggers the change. Last, lysogens also produced red colonies on white grape juice agar supplemented with polyphenolic compounds. We posit that spontaneous prophage excision produces cell lysis events in lysogenic colonies growing on RGJ agar, which, in turn, foster interactions between lysed materials and polyphenolic compounds to yield colonies easily distinguishable by their red color. Furthermore, the technique was used successfully with other species of LAB.IMPORTANCE The presence of white and red colonies on red grape juice (RGJ) agar during enumeration of Oenococcus oeni in wine samples is frequently observed by stakeholders in the wine industry. Our study brings an explanation for this intriguing phenomenon and establishes a link between the white-red color switch and the lysogenic state of O. oeni It also provides a simple and inexpensive method to distinguish between lysogenic and nonlysogenic derivatives in O. oeni with a minimum of expended time and effort. Noteworthy, the protocol could be adapted to two other species of LAB, namely, Leuconostoc citreum and Lactobacillus plantarum It could be an effective tool to provide genetic, ecological, and functional insights into lysogeny and aid in improving biotechnological processes involving members of the lactic acid bacterium (LAB) family.

Closely related viruses of the marine picoeukaryotic alga Ostreococcus lucimarinus exhibit different ecological strategies

In marine ecosystems, viruses are major disrupters of the direct flow of carbon and nutrients to higher trophic levels. Although the genetic diversity of several eukaryotic phytoplankton virus groups has been characterized, their infection dynamics are less understood, such that the physiological and ecological implications of their diversity remain unclear. We compared genomes and infection phenotypes of the two most closely related cultured phycodnaviruses infecting the widespread picoprasinophyte Ostreococcus lucimarinus under standard- (1.3 divisions per day) and limited-light (0.41 divisions per day) nutrient replete conditions. OlV7 infection caused early arrest of the host cell cycle, coinciding with a significantly higher proportion of infected cells than OlV1-amended treatments, regardless of host growth rate. OlV7 treatments showed a near-50-fold increase of progeny virions at the higher host growth rate, contrasting with OlV1's 16-fold increase. However, production of OlV7 virions was more sensitive than OlV1 production to reduced host growth rate, suggesting fitness trade-offs between infection efficiency and resilience to host physiology. Moreover, although organic matter released from OlV1- and OlV7-infected hosts had broadly similar chemical composition, some distinct molecular signatures were observed. Collectively, these results suggest that current views on viral relatedness through marker and core gene analyses underplay operational divergence and consequences for host ecology.