Cooperation Peaks at Intermediate Disturbance

Strain identity effects contribute more to Pseudomonas community functioning than strain interactions

Microbial communities can shape key ecological services, but the determinants of their functioning often remain little understood. While traditional research predominantly focuses on effects related to species identity (community composition and species richness), recent work increasingly explores the impact of species interactions on community functioning. Here, we conducted experiments with replicated small communities of Pseudomonas bacteria to quantify the relative importance of strain identity versus interaction effects on two important functions, community productivity and siderophore production. By combining supernatant and competition assays with an established linear model method, we show that both factors have significant effects on functioning, but identity effects generally outweigh strain interaction effects. These results hold irrespective of whether strain interactions are inferred statistically or approximated experimentally. Our results have implications for microbiome engineering, as the success of approaches aiming to induce beneficial (probiotic) strain interactions will be sensitive to strain identity effects in many communities.

Disturbances can facilitate prior invasions more than subsequent invasions in microbial communities

Invasions are commonly found to benefit from disturbance events. However, the importance of the relative timing of the invasion and disturbance for invader success and impact on community composition remains uncertain. Here, we experimentally test this by invading a five-species bacterial community on eight separate occasions-four before a disturbance and four after. Invader success and impact on community composition was greatest when the invasion immediately followed the disturbance. However, the subsequent invasions had negligible success or impact. Pre-disturbance, invader success and impact was greatest when the invader was added just before the disturbance. Importantly, however, the first three pre-disturbance invasion events had significantly greater success than the last three post-disturbance invasions. Moreover, these findings were consistent across a range of propagule pressures. Overall, we demonstrate that timing is highly important for both the success and impact on community composition of an invader, with both being lower as time since disturbance progresses.

Intermediate Disturbances Enhance Microbial Enzyme Activities in Soil Ecosystems

The Intermediate Disturbance Hypothesis (IDH) posits that maximal plant biodiversity is attained in environments characterized by moderate ecological disturbances. Although the applicability of the IDH to microbial diversity has been explored in a limited number of studies, there is a notable absence of experimental reports on whether soil microbial 'activity' demonstrates a similar response to the frequency or intensity of environmental disturbances. In this investigation, we conducted five distinct experiments employing soils or wetland sediments exposed to varying intensities or frequencies of disturbances, with a specific emphasis on disturbances associated with human activity, such as chemical contamination, hydrologic changes, and forest thinning. Specifically, we examined the effects of bactericide and heavy metal contamination, long-term drainage, tidal flow, and thinning management on microbial enzyme activities in soils. Our findings revealed that microbial enzyme activities were highest at intermediate disturbance levels. Despite the diversity in experiment conditions, each trial consistently demonstrated analogous patterns, suggesting the robustness of the IDH in elucidating microbial activities alongside diversity in soils. These outcomes bear significant implications for ecological restoration and management, as intermediate disturbance may expedite organic matter decomposition and nutrient cycles, crucial for sustaining ecosystem services in soils.

On the possibility of engineering social evolution in microfluidic environments

Many species of microbes cooperate by producing public goods from which they collectively benefit. However, these populations are under the risk of being taken over by cheating mutants that do not contribute to the pool of public goods. Here we present theoretical findings that address how the social evolution of microbes can be manipulated by external perturbations to inhibit or promote the fixation of cheaters. To control social evolution, we determine the effects of fluid-dynamical properties such as flow rate or domain geometry. We also study the social evolutionary consequences of introducing beneficial or harmful chemicals at steady state and in a time-dependent fashion. We show that by modulating the flow rate and by applying pulsed chemical signals, we can modulate the spatial structure and dynamics of the population in a way that can select for more or less cooperative microbial populations.

Interspecific competition prevents the proliferation of social cheaters in an unstructured environment

Bacterial communities are intricate ecosystems in which various members interact, compete for resources, and influence each other's growth. Antibiotics intensify this complexity, posing challenges in maintaining biodiversity. In this study, we delved into the behavior of kin bacterial communities when subjected to antibiotic perturbations, with a particular focus on how interspecific interactions shape these responses. We hypothesized that social cheating-where resistant strains shield both themselves and neighboring cheaters-obstructed coexistence, especially when kin bacteria exhibited varied growth rates and antibiotic sensitivities. To explore potential pathways to coexistence, we incorporated a third bacterial member, anticipating a shift in the dynamics of community coexistence. Simulations and experimental bacterial communities confirmed our predictions, emphasizing the pivotal role of interspecific competition in promoting coexistence under antibiotic interference. These insights are crucial for understanding bacterial ecosystem stability, interpreting drug-microbiome interactions, and predicting bacterial community adaptations to environmental changes.

Coupled environmental and demographic fluctuations shape the evolution of cooperative antimicrobial resistance

There is a pressing need to better understand how microbial populations respond to antimicrobial drugs, and to find mechanisms to possibly eradicate antimicrobial-resistant cells. The inactivation of antimicrobials by resistant microbes can often be viewed as a cooperative behaviour leading to the coexistence of resistant and sensitive cells in large populations and static environments. This picture is, however, greatly altered by the fluctuations arising in volatile environments, in which microbial communities commonly evolve. Here, we study the eco-evolutionary dynamics of a population consisting of an antimicrobial-resistant strain and microbes sensitive to antimicrobial drugs in a time-fluctuating environment, modelled by a carrying capacity randomly switching between states of abundance and scarcity. We assume that antimicrobial resistance (AMR) is a shared public good when the number of resistant cells exceeds a certain threshold. Eco-evolutionary dynamics is thus characterised by demographic noise (birth and death events) coupled to environmental fluctuations which can cause population bottlenecks. By combining analytical and computational means, we determine the environmental conditions for the long-lived coexistence and fixation of both strains, and characterise a fluctuation-driven AMR eradication mechanism, where resistant microbes experience bottlenecks leading to extinction. We also discuss the possible applications of our findings to laboratory-controlled experiments.

Disease-Induced Cooperation Mitigates Populations Against Decline: The Cascade Effect of Cooperation Evolution

Due to density-dependent selection, the ecological factors impacting population dynamics can play an important role in promoting cooperation, and accordingly, benefit a population from the eco-evolutionary feedback. This implies that cooperation between individuals could help resist the attack of infectious diseases. Yet, little is known about how cooperation evolves in response to infections. We here examined theoretically the impact of disease infections with various transmission types on cooperation evolution and its feedback to population dynamics. Results show that infected populations can evolve to be more cooperative, and the level of cooperation increases with the transmission rate, which can protect the population against decline due to infection and prevent population extinction driven by defection. A high transmission rate can stabilize population fluctuation, while a relatively low transmission rate could destabilize population dynamics. We argue that the mechanism underlying such stress-induced cooperation is analogous to the cascade effect of trophic interactions in food webs: reduction in selfishness from environmental stress indirectly relaxes the exploitation of cooperators by defectors. These findings emphasize the role of eco-evolutionary feedback in evolving cooperation and the ecological significance of cooperation evolution for populations withstanding disease infection.

Non-target impacts of fungicide disturbance on phyllosphere yeasts in conventional and no-till management

Fungicides reduce fungal pathogen populations and are essential to food security. Understanding the impacts of fungicides on crop microbiomes is vital to minimizing unintended consequences while maintaining their use for plant protection. However, fungicide disturbance of plant microbiomes has received limited attention, and has not been examined in different agricultural management systems. We used amplicon sequencing of fungi and prokaryotes in maize and soybean microbiomes before and after foliar fungicide application in leaves and roots from plots under long-term no-till and conventional tillage management. We examined fungicide disturbance and resilience, which revealed consistent non-target effects and greater resiliency under no-till management. Fungicides lowered pathogen abundance in maize and soybean and decreased the abundance of Tremellomycetes yeasts, especially Bulleribasidiaceae, including core microbiome members. Fungicide application reduced network complexity in the soybean phyllosphere, which revealed altered co-occurrence patterns between yeast species of Bulleribasidiaceae, and Sphingomonas and Hymenobacter in fungicide treated plots. Results indicate that foliar fungicides lower pathogen and non-target fungal abundance and may impact prokaryotes indirectly. Treatment effects were confined to the phyllosphere and did not impact belowground microbial communities. Overall, these results demonstrate the resilience of no-till management to fungicide disturbance, a potential novel ecosystem service provided by no-till agriculture.

A case for associational resistance: Apparent support for the stress gradient hypothesis varies with study system

According to the stress gradient hypothesis (SGH), ecological interactions between organisms shift positively as environmental stress increases. In the case of associational resistance, habitat is modified to ameliorate stress, benefitting other organisms. The SGH is contentious due to conflicting evidence and theoretical perspectives, so we adopted a meta-analytic approach to determine if it is widely supported across a variety of contexts, including different kingdoms, ecosystems, habitats, interactions, stressors, and life history stages. We developed an extensive list of Boolean search criteria to search the published ecological literature and successfully detect studies that both directly tested the hypothesis, and those that were relevant but never mentioned it. We found that the SGH is well supported by studies that feature bacteria, plants, terrestrial ecosystems, interspecific negative interactions, adults, survival instead of growth or reproduction, and drought, fire, and nutrient stress. We conclude that the SGH is indeed a broadly relevant ecological hypothesis that is currently held back by cross-disciplinary communication barriers. More SGH research is needed beyond the scope of interspecific plant competition, and more SGH research should feature multifactor stress. There remains a need to account for positive interactions in scientific pursuits, such as associational resistance in tests of the SGH.

Population Dynamics in a Changing Environment: Random versus Periodic Switching

Environmental changes greatly influence the evolution of populations. Here, we study the dynamics of a population of two strains, one growing slightly faster than the other, competing for resources in a time-varying binary environment modeled by a carrying capacity switching either randomly or periodically between states of abundance and scarcity. The population dynamics is characterized by demographic noise (birth and death events) coupled to a varying environment. We elucidate the similarities and differences of the evolution subject to a stochastically and periodically varying environment. Importantly, the population size distribution is generally found to be broader under intermediate and fast random switching than under periodic variations, which results in markedly different asymptotic behaviors between the fixation probability of random and periodic switching. We also determine the detailed conditions under which the fixation probability of the slow strain is maximal.

Predicting community dynamics of antibiotic-sensitive and -resistant species in fluctuating environments

Microbes occupy almost every niche within and on their human hosts. Whether colonizing the gut, mouth or bloodstream, microorganisms face temporal fluctuations in resources and stressors within their niche but we still know little of how environmental fluctuations mediate certain microbial phenotypes, notably antimicrobial-resistant ones. For instance, do rapid or slow fluctuations in nutrient and antimicrobial concentrations select for, or against, resistance? We tackle this question using an ecological approach by studying the dynamics of a synthetic and pathogenic microbial community containing two species, one sensitive and the other resistant to an antibiotic drug where the community is exposed to different rates of environmental fluctuation. We provide mathematical models, supported by experimental data, to demonstrate that simple community outcomes, such as competitive exclusion, can shift to coexistence and ecosystem bistability as fluctuation rates vary. Theory gives mechanistic insight into how these dynamical regimes are related. Importantly, our approach highlights a fundamental difference between resistance in single-species populations, the context in which it is usually assayed, and that in communities. While fast environmental changes are known to select against resistance in single-species populations, here we show that they can promote the resistant species in mixed-species communities. Our theoretical observations are verified empirically using a two-species Candida community.

Stochasticity and non-additivity expose hidden evolutionary pathways to cooperation

Cooperation is widespread across the tree of life, with examples ranging from vertebrates to lichens to multispecies biofilms. The initial evolution of such cooperation is likely to involve interactions that produce non-additive fitness effects among small groups of individuals in local populations. However, most models for the evolution of cooperation have focused on genealogically related individuals, assume that the factors influencing individual fitness are deterministic, that populations are very large, and that the benefits of cooperation increase linearly with the number of cooperative interactions. Here we show that stochasticity and non-additive interactions can facilitate the evolution of cooperation in small local groups. We derive a generalized model for the evolution of cooperation and show that if cooperation reduces the variance in individual fitness (separate from its effect on average fitness), this can aid in the evolution of cooperation through directional stochastic effects. In addition, we show that the potential for the evolution of cooperation is influenced by non-additivity in benefits with cooperation being more likely to evolve when the marginal benefit of a cooperative act increases with the number of such acts. Our model compliments traditional cooperation models (kin selection, reciprocal cooperation, green beard effect, etc.) and applies to a broad range of cooperative interactions seen in nature.

Privatization of public goods can cause population decline

Microbes commonly deploy a risky strategy to acquire nutrients from their environment, involving the production of costly public goods that can be exploited by neighbouring individuals. Why engage in such a strategy when an exploitation-free alternative is readily available whereby public goods are kept private? We address this by examining metabolism of Saccharomyces cerevisiae in its native form and by creating a new three-strain synthetic community deploying different strategies of sucrose metabolism. Public-metabolizers digest resources externally, private-metabolizers internalize resources before digestion, and cheats avoid the metabolic costs of digestion but exploit external products generated by competitors. A combination of mathematical modelling and ecological experiments reveal that private-metabolizers invade and take over an otherwise stable community of public-metabolizers and cheats. However, owing to the reduced growth rate of private-metabolizers and population bottlenecks that are frequently associated with microbial communities, privatizing public goods can become unsustainable, leading to population decline.

Intermediate Levels of Antibiotics May Increase Diversity of Colony Size Phenotype in Bacteria

Antibiotics select for resistant bacteria whose existence and emergence is more likely in populations with high phenotypic and genetic diversity. Identifying the mechanisms that generate this diversity can thus have clinical consequences for drug-resistant pathogens. We show here that intermediate levels of antibiotics are associated with higher levels of phenotypic diversity in size of colony forming units (cfus), within a single bacterial population. We examine experimentally thousands of populations of bacteria subjected to different disturbance levels that are created by varying antibiotic concentrations. Based on colony sizes, we find that intermediate levels of antibiotics always result in the highest phenotypic variation of this trait. This result is supported across bacterial densities and in the presence of three different antibiotics with two different mechanisms of action. Our results suggest intermediate levels of a stressor (as opposed to very low or very high levels) could affect the phenotypic diversity of a population, at least with regards to the single trait measured here. While this study is limited to a single phenotypic trait within a single species, the results suggest examining phenotypic and genetic variation created by disturbances and stressors could be a promising way to understand and limit variation in pathogens.

Eco-evolutionary dynamics of a population with randomly switching carrying capacity

Environmental variability greatly influences the eco-evolutionary dynamics of a population, i.e. it affects how its size and composition evolve. Here, we study a well-mixed population of finite and fluctuating size whose growth is limited by a randomly switching carrying capacity. This models the environmental fluctuations between states of resources abundance and scarcity. The population consists of two strains, one growing slightly faster than the other, competing under two scenarios: one in which competition is solely for resources, and one in which the slow (cooperating) strain produces a public good (PG) that benefits also the fast (free-riding) strain. We investigate how the coupling of demographic and environmental (external) noise affects the population's eco-evolutionary dynamics. By analytical and computational means, we study the correlations between the population size and its composition, and discuss the social-dilemma-like 'eco-evolutionary game' characterizing the PG production. We determine in what conditions it is best to produce a PG; when cooperating is beneficial but outcompeted by free riding, and when the PG production is detrimental for cooperators. Within a linear noise approximation to populations of varying size, we also accurately analyse the coupled effects of demographic and environmental noise on the size distribution.

Biofilm formation and toxin production provide a fitness advantage in mixed colonies of environmental yeast isolates

Microbes can engage in social interactions ranging from cooperation to warfare. Biofilms are structured, cooperative microbial communities. Like all cooperative communities, they are susceptible to invasion by selfish individuals who benefit without contributing. However, biofilms are pervasive and ancient, representing the first fossilized life. One hypothesis for the stability of biofilms is spatial structure: Segregated patches of related cooperative cells are able to outcompete unrelated cells. These dynamics have been explored computationally and in bacteria; however, their relevance to eukaryotic microbes remains an open question. The complexity of eukaryotic cell signaling and communication suggests the possibility of different social dynamics. Using the tractable model yeast, Saccharomyces cerevisiae, which can form biofilms, we investigate the interactions of environmental isolates with different social phenotypes. We find that biofilm strains spatially exclude nonbiofilm strains and that biofilm spatial structure confers a consistent and robust fitness advantage in direct competition. Furthermore, biofilms may protect against killer toxin, a warfare phenotype. During biofilm formation, cells are susceptible to toxin from nearby competitors; however, increased spatial use may provide an escape from toxin producers. Our results suggest that yeast biofilms represent a competitive strategy and that principles elucidated for the evolution and stability of bacterial biofilms may apply to more complex eukaryotes.

Cooperation-based branching as a mechanism of evolutionary speciation

When performing complex tasks, coexistence of organisms in a shared environment can be achieved by means of different strategies. For example, individuals can evolve to complete all parts of the complex task, choosing self-sufficiency over cooperation. On the other hand, they may choose to split parts of the task and share the products for mutual benefit, such that distinct groups of the organisms specialize on a subset of elementary tasks. In contrast to the existing theory of specialization and task sharing for cells in multicellular organisms (or colonies of social insects), here we describe a mechanism of evolutionary branching which is based on cooperation and division of labor, and where selection happens at the individual level. Using a class of mathematical models and the methodology of adaptive dynamics, we investigate the conditions for such branching into distinct cooperating subgroups to occur. We show that, as long as performing multiple tasks is associated with additional cost, branching occurs for a wide parameter range, and this scenario is stable against the invasion of cheaters. We hypothesize that over time, this can lead to evolutionary speciation. Examples from bacterial evolution and the connection with the Black Queen Hypothesis are discussed. It is our hope that the theory of diversification rooted in cooperation may inspire further ecological research to identify more evolutionary examples consistent with this speciation mechanism.

Clonal yeast biofilms can reap competitive advantages through cell differentiation without being obligatorily multicellular

How differentiation between cell types evolved is a fundamental question in biology, but few studies have explored single-gene phenotypes that mediate first steps towards division of labour with selective advantage for groups of cells. Here, we show that differential expression of the FLO11 gene produces stable fractions of Flo11⁺ and Flo11^- cells in clonal Saccharomyces cerevisiae biofilm colonies on medium with intermediate viscosity. Differentiated Flo11^+/- colonies, consisting of adhesive and non-adhesive cells, obtain a fourfold growth advantage over undifferentiated colonies by overgrowing glucose resources before depleting them, rather than depleting them while they grow as undifferentiated Flo11^- colonies do. Flo11^+/- colonies maintain their structure and differentiated state by switching non-adhesive cells to adhesive cells with predictable probability. Mixtures of Flo11⁺ and Flo11^- cells from mutant strains that are unable to use this epigenetic switch mechanism produced neither integrated colonies nor growth advantages, so the condition-dependent selective advantages of differentiated FLO11 expression can only be reaped by clone-mate cells. Our results show that selection for cell differentiation in clonal eukaryotes can evolve before the establishment of obligate undifferentiated multicellularity, and without necessarily leading to more advanced organizational complexity.

Phylogenetic context determines the role of competition in adaptive radiation

Understanding ecological mechanisms regulating the evolution of biodiversity is of much interest to ecologists and evolutionary biologists. Adaptive radiation constitutes an important evolutionary process that generates biodiversity. Competition has long been thought to influence adaptive radiation, but the directionality of its effect and associated mechanisms remain ambiguous. Here, we report a rigorous experimental test of the role of competition on adaptive radiation using the rapidly evolving bacterium Pseudomonas fluorescens SBW25 interacting with multiple bacterial species that differed in their phylogenetic distance to the diversifying bacterium. We showed that the inhibitive effect of competitors on the adaptive radiation of P. fluorescens decreased as their phylogenetic distance increased. To explain this phylogenetic dependency of adaptive radiation, we linked the phylogenetic distance between P. fluorescens and its competitors to their niche and competitive fitness differences. Competitive fitness differences, which showed weak phylogenetic signal, reduced P. fluorescens abundance and thus diversification, whereas phylogenetically conserved niche differences promoted diversification. These results demonstrate the context dependency of competitive effects on adaptive radiation, and highlight the importance of past evolutionary history for ongoing evolutionary processes.

Evolution of a Fluctuating Population in a Randomly Switching Environment

Environment plays a fundamental role in the competition for resources, and hence in the evolution of populations. Here, we study a well-mixed, finite population consisting of two strains competing for the limited resources provided by an environment that randomly switches between states of abundance and scarcity. Assuming that one strain grows slightly faster than the other, we consider two scenarios-one of pure resource competition, and one in which one strain provides a public good-and investigate how environmental randomness (external noise) coupled to demographic (internal) noise determines the population's fixation properties and size distribution. By analytical means and simulations, we show that these coupled sources of noise can significantly enhance the fixation probability of the slower-growing species. We also show that the population size distribution can be unimodal, bimodal, or multimodal and undergoes noise-induced transitions between these regimes when the rate of switching matches the population's growth rate.

Basic Processes in Salmonella-Host Interactions: Within-Host Evolution and the Transmission of the Virulent Genotype

Transmission and virulence are central aspects of pathogen evolution. However, in many cases their interconnection has proven difficult to assess by experimentation. Here we discuss recent advances from a mouse model for Salmonella diarrhea. Mouse models mimic the enhanced susceptibility of antibiotic-treated individuals to nontyphoidal salmonellosis. In streptomycin-pretreated mice, Salmonella enterica subspecies 1 serovar Typhimurium efficiently colonizes the gut lumen and elicits pronounced enteropathy. In the host's gut, S. Typhimurium forms two subpopulations that cooperate to elicit disease and optimize transmission. The disease-causing subpopulation expresses a set of dedicated virulence factors (the type 3 secretion system 1 [TTSS-1]) that drive gut tissue invasion. The virulence factor expression is "costly" by retarding the growth rate and exposing the pathogen to innate immune defenses within the gut tissue. These costs are compensated by the gut inflammation (a "public good") that is induced by the invading subpopulation. The inflamed gut lumen fuels S. Typhimurium growth, in particular that of the TTSS-1 "off" subpopulation. The latter grows up to very high densities and promotes transmission. Thus, both phenotypes cooperate to elicit disease and ensure transmission. This system has provided an experimental framework for studying within-host evolution of pathogen virulence, how cooperative virulence is stabilized, and how environmental changes (e.g., antibiotic therapy) affect the transmission of the virulent genotype.

Cooperation and competition shape ecological resistance during periodic spatial disturbance of engineered bacteria

Cooperation is fundamental to the survival of many bacterial species. Previous studies have shown that spatial structure can both promote and suppress cooperation. Most environments where bacteria are found are periodically disturbed, which can affect the spatial structure of the population. Despite the important role that spatial disturbances play in maintaining ecological relationships, it remains unclear as to how periodic spatial disturbances affect bacteria dependent on cooperation for survival. Here, we use bacteria engineered with a strong Allee effect to investigate how the frequency of periodic spatial disturbances affects cooperation. We show that at intermediate frequencies of spatial disturbance, the ability of the bacterial population to cooperate is perturbed. A mathematical model demonstrates that periodic spatial disturbance leads to a tradeoff between accessing an autoinducer and accessing nutrients, which determines the ability of the bacteria to cooperate. Based on this relationship, we alter the ability of the bacteria to access an autoinducer. We show that increased access to an autoinducer can enhance cooperation, but can also reduce ecological resistance, defined as the ability of a population to resist changes due to disturbance. Our results may have implications in maintaining stability of microbial communities and in the treatment of infectious diseases.

Asymmetry within social groups: division of labour and intergroup competition

Social animals vary in their ability to compete with group members over shared resources and also vary in their cooperative efforts to produce these resources. Competition among groups can promote within-group cooperation, but many existing models of intergroup cooperation do not explicitly account for observations that group members invest differentially in cooperation and that there are often within-group competitive or power asymmetries. We present a game theoretic model of intergroup competition that investigates how such asymmetries affect within-group cooperation. In this model, group members adopt one of two roles, with relative competitive efficiency and the number of individuals varying between roles. Players in each role make simultaneous, coevolving decisions. The model predicts that although intergroup competition increases cooperative contributions to group resources by both roles, contributions are predominantly from individuals in the less competitively efficient role, whereas individuals in the more competitively efficient role generally gain the larger share of these resources. When asymmetry in relative competitive efficiency is greater, a group's per capita cooperation (averaged across both roles) is higher, due to increased cooperation from the competitively inferior individuals. For extreme asymmetry in relative competitive efficiency, per capita cooperation is highest in groups with a single competitively superior individual and many competitively inferior individuals, because the latter acquiesce and invest in cooperation rather than within-group competition. These predictions are consistent with observed features of many societies, such as monogynous Hymenoptera with many workers and caste dimorphism.

Rethinking evolutionary individuality

This paper considers whether multispecies biofilms are evolutionary individuals. Numerous multispecies biofilms have characteristics associated with individuality, such as internal integrity, division of labor, coordination among parts, and heritable adaptive traits. However, such multispecies biofilms often fail standard reproductive criteria for individuality: they lack reproductive bottlenecks, are comprised of multiple species, do not form unified reproductive lineages, and fail to have a significant division of reproductive labor among their parts. If such biofilms are good candidates for evolutionary individuals, then evolutionary individuality is achieved through other means than frequently cited reproductive processes. The case of multispecies biofilms suggests that standard reproductive requirements placed on individuality should be reconsidered. More generally, the case of multispecies biofilms indicates that accounts of individuality that focus on single-species eukaryotes are too restrictive and that a pluralistic and open-ended account of evolutionary individuality is needed.

A Synthetic Quorum Sensing System Reveals a Potential Private Benefit for Public Good Production in a Biofilm

Bacteria predominantly reside in microbial communities known as biofilms, where cells are encapsulated and protected by the extracellular matrix (ECM). While all biofilm cells benefit from the ECM, only a subgroup of cells carries the burden of producing this public good. This dilemma provokes the question of how these cells balance the cost of ECM production. Here we show that ECM producing cells have a higher gene expression response to quorum sensing (QS) signals, which can lead to a private benefit. Specifically, we constructed a synthetic quorum-sensing system with designated “Sender” and “Receiver” cells in Bacillus subtilis. This synthetic QS system allowed us to uncouple and independently investigate ECM production and QS in both biofilms and single cells. Results revealed that ECM production directly enhances the response to QS signals, which may offset the cost of ECM production.

The emergence of cooperation from a single mutant during microbial life cycles

Cooperative behaviour is widespread in nature, even though cooperating individuals always run the risk of being exploited by free-riders. Population structure effectively promotes cooperation given that a threshold in the level of cooperation was already reached. However, the question how cooperation can emerge from a single mutant, which cannot rely on a benefit provided by other cooperators, is still puzzling. Here, we investigate this question for a well-defined but generic situation based on typical life cycles of microbial populations where individuals regularly form new colonies followed by growth phases. We analyse two evolutionary mechanisms favouring cooperative behaviour and study their strength depending on the inoculation size and the length of a life cycle. In particular, we find that population bottlenecks followed by exponential growth phases strongly increase the survival and fixation probabilities of a single cooperator in a free-riding population.

Cancer: an emergent property of disturbed resource-rich environments? Ecology meets personalized medicine

For an increasing number of biologists, cancer is viewed as a dynamic system governed by evolutionary and ecological principles. Throughout most of human history, cancer was an uncommon cause of death and it is generally accepted that common components of modern culture, including increased physiological stresses and caloric intake, favor cancer development. However, the precise mechanisms for this linkage are not well understood. Here, we examine the roles of ecological and physiological disturbances and resource availability on the emergence of cancer in multicellular organisms. We argue that proliferation of 'profiteering phenotypes' is often an emergent property of disturbed, resource-rich environments at all scales of biological organization. We review the evidence for this phenomenon, explore it within the context of malignancy, and discuss how this ecological framework may offer a theoretical background for novel strategies of cancer prevention. This work provides a compelling argument that the traditional separation between medicine and evolutionary ecology remains a fundamental limitation that needs to be overcome if complex processes, such as oncogenesis, are to be completely understood.

Experimental evolution can unravel the complex causes of natural selection in clinical infections

It is increasingly clear that rapid evolutionary dynamics are an important process in microbial ecology. Experimental evolution, wherein microbial evolution is observed in real-time, has revealed many instances of appreciable evolutionary change occurring on very short timescales of a few days or weeks in response to a variety of biotic and abiotic selection pressures. From clinical infections, including the chronic bacterial lung infections associated with cystic fibrosis that form a focus of my research, there is now abundant evidence suggesting that rapid evolution by infecting microbes contributes to host adaptation, treatment failure and worsening patient prognosis. However, disentangling the drivers of natural selection in complex infection environments is extremely challenging and limits our understanding of the selective pressures acting upon microbes in infections. Controlled evolution experiments can make a vital contribution to this by determining the causal links between predicted drivers of natural selection and the evolutionary responses of microbes. Integration of experimental evolution into studies of clinical infections is a key next step towards a better understanding of the causes and consequences of rapid microbial evolution in infections, and discovering how these evolutionary processes might be influenced to improve patient health.A video of this Prize Lecture, presented at the Society for General Microbiology Annual Conference 2015, can be viewed via this link: Michael A. Brockhurst https://www.youtube.com/watch?v=N1bodVSl27E.

One pot synthesis and anti-biofilm potential of copper nanoparticles (CuNPs) against clinical strains of Pseudomonas aeruginosa

Pseudomonas aeruginosa, an opportunistic pathogen frequently associated with nosocomial infections, is emerging as a serious threat due to its resistance to broad spectrum antimicrobials. The biofilm mode of growth confers resistance to antibiotics and novel anti-biofilm agents are urgently needed. Nanoparticle based treatments and therapies have been of recent interest because of their versatile applications. This study investigates the anti-biofilm activity of copper nanoparticles (CuNPs) synthesized by the one pot method against P. aeruginosa. Standard physical techniques including UV-visible and Fourier transform infrared spectroscopy, X-ray diffraction and transmission electron microscopy were used to characterize the synthesized CuNPs. CuNP treatments at 100 ng ml(-1) resulted in a 94, 89 and 92% reduction in biofilm, cell surface hydrophobicity and exopolysaccharides respectively, without bactericidal activity. Evidence of biofilm inhibition was also seen with light and confocal microscope analysis. This study highlights the anti-biofilm potential of CuNPs, which could be utilized as coating agents on surgical devices and medical implants to manage biofilm associated infections.

A microbial model of economic trading and comparative advantage

The economic theory of comparative advantage postulates that beneficial trading relationships can be arrived at by two self-interested entities producing the same goods as long as they have opposing relative efficiencies in producing those goods. The theory predicts that upon entering trade, in order to maximize consumption both entities will specialize in producing the good they can produce at higher efficiency, that the weaker entity will specialize more completely than the stronger entity, and that both will be able to consume more goods as a result of trade than either would be able to alone. We extend this theory to the realm of unicellular organisms by developing mathematical models of genetic circuits that allow trading of a common good (specifically, signaling molecules) required for growth in bacteria in order to demonstrate comparative advantage interactions. In Conception 1, the experimenter controls production rates via exogenous inducers, allowing exploration of the parameter space of specialization. In Conception 2, the circuits self-regulate via feedback mechanisms. Our models indicate that these genetic circuits can demonstrate comparative advantage, and that cooperation in such a manner is particularly favored under stringent external conditions and when the cost of production is not overly high. Further work could involve implementing the models in living bacteria and searching for naturally occurring cooperative relationships between bacteria that conform to the principles of comparative advantage.

Rapid evolution of cooperation in group-living animals

BACKGROUND

It is often assumed that evolution takes place on very large timescales. Countering this assumption, rapid evolutionary dynamics are increasingly documented in biological systems, e.g. in the context of predator-prey interactions, species coexistence and invasion. It has also been shown that rapid evolution can facilitate the evolution of cooperation. In this context often evolutionary dynamics influence population dynamics, but in spatial models rapid evolutionary dynamics also emerge with constant population sizes. Currently it is not clear how well these spatial models apply to species in which individuals are not embedded in fixed spatial structures. To address this issue we employ an agent-based model of group living individuals. We investigate how positive assortment between cooperators and defectors and pay-off differences between cooperators and defectors depend on the occurrence of evolutionary dynamics.

RESULTS

We find that positive assortment and pay-off differences between cooperators and defectors differ when comparing scenarios with and without selection, which indicates that rapid evolutionary dynamics are occurring in the selection scenarios. Specifically, rapid evolution occurs because changes in positive assortment feed back on evolutionary dynamics, which crucially impacts the evolution of cooperation. At high frequencies of cooperators these feedback dynamics increase positive assortment facilitating the evolution of cooperation. In contrast, at low frequencies of cooperators rapid evolutionary dynamics lead to a decrease in assortment, which acts against the evolution of cooperation. The contrasting dynamics at low and high frequencies of cooperators create positive frequency-dependent selection.

CONCLUSIONS

Rapid evolutionary dynamics can influence the evolution of cooperation in group-living species and lead to positive frequency-dependent selection even if population size and maximum group-size are not affected by evolutionary dynamics. Rapid evolutionary dynamics can emerge in this case because sufficiently strong selective pressures allow evolutionary and demographic dynamics, and consequently also feedback between assortment and evolution, to occur on the same timescale. In particular, emerging positive frequency-dependent selection could be an important explanation for differences in cooperative behaviors among different species with similar population structures such as humans and chimpanzees.

The genotypic view of social interactions in microbial communities

Dense and diverse microbial communities are found in many environments. Disentangling the social interactions between strains and species is central to understanding microbes and how they respond to perturbations. However, the study of social evolution in microbes tends to focus on single species. Here, we broaden this perspective and review evolutionary and ecological theory relevant to microbial interactions across all phylogenetic scales. Despite increased complexity, we reduce the theory to a simple null model that we call the genotypic view. This states that cooperation will occur when cells are surrounded by identical genotypes at the loci that drive interactions, with genetic identity coming from recent clonal growth or horizontal gene transfer (HGT). In contrast, because cooperation is only expected to evolve between different genotypes under restrictive ecological conditions, different genotypes will typically compete. Competition between two genotypes includes mutual harm but, importantly, also many interactions that are beneficial to one of the two genotypes, such as predation. The literature offers support for the genotypic view with relatively few examples of cooperation between genotypes. However, the study of microbial interactions is still at an early stage. We outline the logic and methods that help to better evaluate our perspective and move us toward rationally engineering microbial communities to our own advantage.

feedback between population and evolutionary dynamics determines the fate of social microbial populations

A new study finds that the evolution of social genes may be coupled with population dynamics, and may dramatically affect ecological resilience, particularly in the face of rapidly deteriorating environments.

The evolutionary spread of cheater strategies can destabilize populations engaging in social cooperative behaviors, thus demonstrating that evolutionary changes can have profound implications for population dynamics. At the same time, the relative fitness of cooperative traits often depends upon population density, thus leading to the potential for bi-directional coupling between population density and the evolution of a cooperative trait. Despite the potential importance of these eco-evolutionary feedback loops in social species, they have not yet been demonstrated experimentally and their ecological implications are poorly understood. Here, we demonstrate the presence of a strong feedback loop between population dynamics and the evolutionary dynamics of a social microbial gene, SUC2, in laboratory yeast populations whose cooperative growth is mediated by the SUC2 gene. We directly visualize eco-evolutionary trajectories of hundreds of populations over 50–100 generations, allowing us to characterize the phase space describing the interplay of evolution and ecology in this system. Small populations collapse despite continual evolution towards increased cooperative allele frequencies; large populations with a sufficient number of cooperators “spiral” to a stable state of coexistence between cooperator and cheater strategies. The presence of cheaters does not significantly affect the equilibrium population density, but it does reduce the resilience of the population as well as its ability to adapt to a rapidly deteriorating environment. Our results demonstrate the potential ecological importance of coupling between evolutionary dynamics and the population dynamics of cooperatively growing organisms, particularly in microbes. Our study suggests that this interaction may need to be considered in order to explain intraspecific variability in cooperative behaviors, and also that this feedback between evolution and ecology can critically affect the demographic fate of those species that rely on cooperation for their survival.

The fact that rapid evolution within a species can cause dramatic ecological changes has only recently begun to be appreciated. In particular, it has often been assumed that population dynamics, controlled by ecological circumstances such as the presence of predators or disease, occur at such different timescales compared with evolutionary dynamics that they are effectively de-coupled. Recent studies, however, have found that evolution can occur over ecological timescales and thus may have important effects on ecological dynamics. Here, we demonstrate the presence of a tight coupling between population dynamics and the evolutionary dynamics of a “social” microbial gene, which allows a laboratory population of budding yeast to cooperatively break down sucrose and grow on the simpler sugars released from it. In such cooperative populations, evolution may favor non-cooperative, or “cheater” individuals that do not contribute to the public good (in this case, the products of sucrose break down), but still use that public good to grow at the expense of the individuals that do cooperate. Our study shows that a population of cooperators that is invaded by cheaters does not collapse as a result of cheater proliferation but can evolve to a viable equilibrium. However, the coexisting population is less resilient to perturbations.

Range expansion promotes cooperation in an experimental microbial metapopulation

Natural populations throughout the tree of life undergo range expansions in response to changes in the environment. Recent theoretical work suggests that range expansions can have a strong effect on evolution, even leading to the fixation of deleterious alleles that would normally be outcompeted in the absence of migration. However, little is known about how range expansions might influence alleles under frequency- or density-dependent selection. Moreover, there is very little experimental evidence to complement existing theory, since expanding populations are difficult to study in the natural environment. In this study, we have used a yeast experimental system to explore the effect of range expansions on the maintenance of cooperative behaviors, which commonly display frequency- and density-dependent selection and are widespread in nature. We found that range expansions favor the maintenance of cooperation in two ways: (i) through the enrichment of cooperators at the front of the expanding population and (ii) by allowing cooperators to "outrun" an invading wave of defectors. In this system, cooperation is enhanced through the coupling of population ecology and evolutionary dynamics in expanding populations, thus providing experimental evidence for a unique mechanism through which cooperative behaviors could be maintained in nature.

From metabolism to ecology: cross-feeding interactions shape the balance between polymicrobial conflict and mutualism

Polymicrobial interactions are widespread in nature and play a major role in maintaining human health and ecosystems. Whenever one organism uses metabolites produced by another organism as energy or nutrient sources, it is called cross-feeding. The ecological outcomes of cross-feeding interactions are poorly understood and potentially diverse: mutualism, competition, exploitation, or commensalism. A major reason for this uncertainty is the lack of theoretical approaches linking microbial metabolism to microbial ecology. To address this issue, we explore the dynamics of a one-way interspecific cross-feeding interaction in which food can be traded for a service (detoxification). Our results show that diverse ecological interactions (competition, mutualism, exploitation) can emerge from this simple cross-feeding interaction and can be predicted by the metabolic, demographic, and environmental parameters that govern the balance of the costs and benefits of association. In particular, our model predicts stronger mutualism for intermediate by-product toxicity because the resource-service exchange is constrained to the service being neither too vital (high toxicity impairs resource provision) nor dispensable (low toxicity reduces need for service). These results support the idea that bridging microbial ecology and metabolism is a critical step toward a better understanding of the factors governing the emergence and dynamics of polymicrobial interactions.

Cellular cooperation: insights from microbes

Cooperation between cells is a widespread phenomenon in nature, found across diverse systems ranging from microbial populations to multicellular organisms. For cooperation to evolve and be maintained within a population of cells, costs due to competition have to be outweighed by the benefits gained through cooperative actions. Because cooperation generally confers a cost to the cooperating cells, defector cells that do not cooperate but reap the benefits of cooperation can thrive and eventually drive the cooperating phenotypes to extinction. Here we summarize recent advances made in understanding how cooperation and multicellularity can evolve in microbial populations in the face of such conflicts and discuss parallels with cell populations within multicellular organisms.

Unfavourable environment limits social conflict in Yuhina brunneiceps

Identifying the factors that modulate cooperative and competitive behaviours is the key to understanding social evolution. However, how ecological factors affect social conflict and their fitness consequences remain relatively unexplored. Here, using both a game-theoretical model and empirical data, we show that Taiwan yuhinas (Yuhina brunneiceps)--a joint-nesting species in which group members are unrelated--employ more cooperative strategies in unfavourable environmental conditions. Fighting duration was lower, fewer total eggs were laid and incubation was more likely to start after all females completed egg laying (which causes more synchronous egg hatching). Surprisingly, as a consequence, there were more surviving offspring in unfavourable conditions because the cooperative strategies resulted in fewer dead nestlings. To our knowledge, this study is the first theoretical analysis and empirical study demonstrating that an unfavourable environment reduces social conflict and results in better fitness consequences in social vertebrates.

Selection on non-social traits limits the invasion of social cheats

While the conditions that favour the maintenance of cooperation have been extensively investigated, the significance of non-social selection pressures on social behaviours has received little attention. In the absence of non-social selection pressures, patches of cooperators are vulnerable to invasion by cheats. However, we show both theoretically, and experimentally with the bacterium Pseudomonas fluorescens, that cheats may be unable to invade patches of cooperators under strong non-social selection (both a novel abiotic environment and to a lesser extent, the presence of a virulent parasite). This is because beneficial mutations are most likely to arise in the numerically dominant cooperator population. Given the ubiquity of novel selection pressures on microbes, these results may help to explain why cooperation is the norm in natural populations of microbes.

Diversity-disturbance relationships: frequency and intensity interact

An influential ecological theory, the intermediate disturbance hypothesis (IDH), predicts that intermediate levels of disturbance will maximize species diversity. Empirical studies, however, have described a wide variety of diversity-disturbance relationships (DDRs). Using experimental populations of microbes, we show that the form of the DDR depends on an interaction between disturbance frequency and intensity. We find that diversity shows a monotonically increasing, unimodal or flat relationship with disturbance, depending on the values of the disturbance aspects considered. These results confirm recent theoretical predictions, and potentially reconcile the conflicting body of empirical evidence on DDRs.

The quorum sensing diversity within and between ecotypes of Bacillus subtilis

Ecological sociobiology is an emerging field that aims to frame social evolution in terms of ecological adaptation. Here we explore the ecological context for evolution of quorum sensing diversity in bacteria, where social communication is limited to members of the same quorum sensing type (pherotype). We sampled isolates of Bacillus subtilis from soil on a microgeographical scale and identified three ecologically distinct phylogenetic groups (ecotypes) and three pherotypes. Each pherotype was strongly associated with a different ecotype, suggesting that it is usually not adaptive for one ecotype to 'listen' to the signalling of another. Each ecotype, however, contained one or more minority pherotypes shared with the other B. subtilis ecotypes and with more distantly related species taxa. The pherotype diversity within ecotypes is consistent with two models: first, a pherotype cycling model, whereby minority pherotypes enter a population through horizontal genetic transfer and increase in frequency through cheating the social interaction; and second, an occasional advantage model, such that when two ecotypes are each below their quorum densities, they may benefit from listening to one another. This is the first survey of pherotype diversity in relation to ecotypes and it will be interesting to further test the hypotheses raised and supported here, and to explore other bacterial systems for the role of ecological divergence in fostering pherotype diversity.