细菌群体感应“合作-欺骗”研究进展

细菌利用信号分子进行细胞间的交流即为群体感应.群体感应调控着生物膜形成、公共物质合成、基因水平转移等一系列社会性行为.在群体感应过程中,公共物质分泌后可以被群体中任何个体所使用即合作;亦可以被一些不分泌公共物质的个体所使用形成欺骗.群体感应合作-欺骗既可能在种群中稳定维持,也可能由于欺骗子的快速增长造成种群崩溃.欺骗子致种群崩溃为病原菌控制新策略研发带来了希望,是目前群体感应研究方面的前沿和热点.本文在介绍细菌群体感应合作及欺骗的基础上,分析了群体感应合作-欺骗生态关系形成和发展的影响因素,重点从亲缘选择、谨慎代谢、代谢限制(基因多效型)、群体感应监管等方面探讨了细菌群体感应合作-欺骗的稳定维持机制,并对细菌群体感应合作-欺骗的相关研究进行了问题总结和展望,以期为深入理解群体感应、微生物种群生态提供参考.     

Population dynamics of microbial cross-feeding are determined by co-localization probabilities and cooperation-independent cheater growth

As natural selection acts on individual organisms the evolution of costly cooperation between microorganisms is an intriguing phenomenon. Introduction of spatial structure to privatize exchanged molecules can explain the evolution of cooperation. However, in many natural systems cells can also grow to low cell concentrations in the absence of these exchanged molecules, thus showing “cooperation-independent background growth”. We here serially propagated a synthetic cross-feeding consortium of lactococci in the droplets of a water-in-oil emulsion, essentially mimicking group selection with varying founder population sizes. The results show that when the growth of cheaters completely depends on cooperators, cooperators outcompete cheaters. However, cheaters outcompete cooperators when they can independently grow to only ten percent of the consortium carrying capacity. This result is the consequence of a probabilistic effect, as low founder population sizes in droplets decrease the frequency of cooperator co-localization. Cooperator-enrichment can be recovered by increasing the founder population size in droplets to intermediate values. Together with mathematical modelling our results suggest that co-localization probabilities in a spatially structured environment leave a small window of opportunity for the evolution of cooperation between organisms that do not benefit from their cooperative trait when in isolation or form multispecies aggregates.Subject terms: Community ecology, Microbial ecology, Evolution, Microbial ecology     

Defectors Can Create Conditions That Rescue Cooperation

Cooperation based on the production of costly common goods is observed throughout nature. This is puzzling, as cooperation is vulnerable to exploitation by defectors which enjoy a fitness advantage by consuming the common good without contributing fairly. Depletion of the common good can lead to population collapse and the destruction of cooperation. However, population collapse implies small population size, which, in a structured population, is known to favor cooperation. This happens because small population size increases variability in cooperator frequency across different locations. Since individuals in cooperator-dominated locations (which are most likely cooperators) will grow more than those in defector-dominated locations (which are most likely defectors), cooperators can outgrow defectors globally despite defectors outgrowing cooperators in each location. This raises the possibility that defectors can lead to conditions that sometimes rescue cooperation from defector-induced destruction. We demonstrate multiple mechanisms through which this can occur, using an individual-based approach to model stochastic birth, death, migration, and mutation events. First, during defector-induced population collapse, defectors occasionally go extinct before cooperators by chance, which allows cooperators to grow. Second, empty locations, either preexisting or created by defector-induced population extinction, can favor cooperation because they allow cooperator but not defector migrants to grow. These factors lead to the counterintuitive result that the initial presence of defectors sometimes allows better survival of cooperation compared to when defectors are initially absent. Finally, we find that resource limitation, inducible by defectors, can select for mutations adaptive to resource limitation. When these mutations are initially present at low levels or continuously generated at a moderate rate, they can favor cooperation by further reducing local population size. We predict that in a structured population, small population sizes precipitated by defectors provide a “built-in” mechanism for the persistence of cooperation.     

Emergence and resilience of cooperation in the spatial prisoner's dilemma via a reward mechanism

We study the problem of the emergence of cooperation in the spatial Prisoner's Dilemma. The pioneering work by Nowak and May [1992. Evolutionary games and spatial chaos. Nature 415, 424-426] showed that large initial populations of cooperators can survive and sustain cooperation in a square lattice with imitate-the-best evolutionary dynamics. We revisit this problem in a cost-benefit formulation suitable for a number of biological applications. We show that if a fixed-amount reward is established for cooperators to share, a single cooperator can invade a population of defectors and form structures that are resilient to re-invasion even if the reward mechanism is turned off. We discuss analytically the case of the invasion by a single cooperator and present agent-based simulations for small initial fractions of cooperators. Large cooperation levels, in the sustainability range, are found. In the conclusions we discuss possible applications of this model as well as its connections with other mechanisms proposed to promote the emergence of cooperation.     

Interaction effects of cell diffusion,cell density and public goods properties on the evolution of cooperation in digital microbes

Microbial cooperation typically consists in the sharing of secreted metabolites (referred to as public goods) within the community. Although public goods generally promote population growth, they are also vulnerable to exploitation by cheating mutants, which no longer contribute, but still benefit from the public goods produced by others. Although previous studies have identified a number of key factors that prevent the spreading of cheaters, little is known about how these factors interact and jointly shape the evolution of microbial cooperation. Here, we address this issue by investigating the interaction effects of cell diffusion, cell density, public good diffusion and durability (factors known to individually influence costs and benefits of public goods production) on selection for cooperation. To be able to quantify these effects across a wide parameter space, we developed an individual‐based simulation platform, consisting of digital cooperator and cheater bacteria inhabiting a finite two‐dimensional continuous toroidal surface. Our simulations, which closely mimic microbial microcolony growth, revealed that: (i) either reduced cell diffusion (which keeps cooperators together) or reduced public good diffusion (which keeps the public goods closer to the producer) is not only essential but also sufficient for cooperation to be promoted; (ii) the sign of selection for or against cooperation can change as a function of cell density and in interaction with diffusion parameters; and (iii) increased public goods durability has opposing effects on the evolution of cooperation depending on the level of cell and public good diffusion. Our work highlights that interactions between key parameters of public goods cooperation give rise to complex fitness landscapes, a finding that calls for multifactorial approaches when studying microbial cooperation in natural systems.     

Adaptive Dynamics of Altruistic Cooperation in a Metapopulation: Evolutionary Emergence of Cooperators and Defectors or Evolutionary Suicide?

We investigate the evolution of public goods cooperation in a metapopulation model with small local populations, where altruistic cooperation can evolve due to assortment and kin selection, and the evolutionary emergence of cooperators and defectors via evolutionary branching is possible. Although evolutionary branching of cooperation has recently been demonstrated in the continuous snowdrift game and in another model of public goods cooperation, the required conditions on the cost and benefit functions are rather restrictive, e.g., altruistic cooperation cannot evolve in a defector population. We also observe selection for too low cooperation, such that the whole metapopulation goes extinct and evolutionary suicide occurs. We observed intuitive effects of various parameters on the numerical value of the monomorphic singular strategy. Their effect on the final coexisting cooperator–defector pair is more complex: changes expected to increase cooperation decrease the strategy value of the cooperator. However, at the same time the population size of the cooperator increases enough such that the average strategy does increase. We also extend the theory of structured metapopulation models by presenting a method to calculate the fitness gradient in a general class of metapopulation models, and try to make a connection with the kin selection approach.     

Negative niche construction favors the evolution of cooperation

By benefitting others at a cost to themselves, cooperators face an ever present threat from defectors—individuals that avail themselves of the cooperative benefit without contributing. A longstanding challenge to evolutionary biology is to understand the mechanisms that support the many instances of cooperation that nevertheless exist. In spatially-structured environments, clustered cooperator populations reach greater densities, which creates more mutational opportunities to gain beneficial non-social adaptations. Hammarlund et al. recently demonstrated that cooperation rises in abundance by hitchhiking with these non-social mutations. However, once adaptive opportunities have been exhausted, the ride abruptly ends as cooperators are displaced by adapted defectors. Using an agent-based model, we demonstrate that the selective feedback that is created as populations construct their local niches can maintain cooperation at high proportions and even allow cooperators to invade. This cooperator success depends specifically on negative niche construction, which acts as a perpetual source of adaptive opportunities. As populations adapt, they alter their environment in ways that reveal additional opportunities for adaptation. Despite being independent of niche construction in our model, cooperation feeds this cycle. By reaching larger densities, populations of cooperators are better able to adapt to changes in their constructed niche and successfully respond to the constant threat posed by defectors. We relate these findings to previous studies from the niche construction literature and discuss how this model could be extended to provide a greater understanding of how cooperation evolves in the complex environments in which it is found.     

Freedom to choose between public resources promotes cooperation

As cooperation incurs a cost to the cooperator for others to benefit, its evolution seems to contradict natural selection. How evolution has resolved this obstacle has been among the most intensely studied questions in evolutionary theory in recent decades. Here, we show that having a choice between different public resources provides a simple mechanism for cooperation to flourish. Such a mechanism can be at work in many biological or social contexts where individuals can form different groups or join different institutions to perform a collective action task, or when they can choose between collective actions with different profitability. As a simple evolutionary model suggests, defectors tend to join the highest quality resource in such a context. This allows cooperators to survive and out-compete defectors by sheltering in a lower quality resource. Cooperation is maximized, however, when the qualities of the two highest quality resources are similar, and thus, they are almost interchangeable.     

The Increased Risk of Joint Venture Promotes Social Cooperation

The joint venture of many members is common both in animal world and human society. In these public enterprizes, highly cooperative groups are more likely to while low cooperative groups are still possible but not probable to succeed. Existent literature mostly focuses on the traditional public goods game, in which cooperators create public wealth unconditionally and benefit all group members unbiasedly. We here institute a model addressing this public goods dilemma with incorporating the public resource foraging failure risk. Risk-averse individuals tend to lead a autarkic life, while risk-preferential ones tend to participate in the risky public goods game. For participants, group''s success relies on its cooperativeness, with increasing contribution leading to increasing success likelihood. We introduce a function with one tunable parameter to describe the risk removal pattern and study in detail three representative classes. Analytical results show that the widely replicated population dynamics of cyclical dominance of loner, cooperator and defector disappear, while most of the time loners act as savors while eventually they also disappear. Depending on the way that group''s success relies on its cooperativeness, either cooperators pervade the entire population or they coexist with defectors. Even in the later case, cooperators still hold salient superiority in number as some defectors also survive by parasitizing. The harder the joint venture succeeds, the higher level of cooperation once cooperators can win the evolutionary race. Our work may enrich the literature concerning the risky public goods games.     

Persistence of the single lineage of transmissible 'social cancer' in an asexual ant

How cooperation can arise and persist, given the threat of cheating phenotypes, is a central problem in evolutionary biology, but the actual significance of cheating in natural populations is still poorly understood. Theories of social evolution predict that cheater lineages are evolutionarily short-lived. However, an exception comes from obligate socially parasitic species, some of which thought to have arisen as cheaters within cooperator colonies and then diverged through sympatric speciation. This process requires the cheater lineage to persist by avoiding rapid extinction that would result from the fact that the cheaters inflict fitness cost on their host. We examined whether this prerequisite is fulfilled, by estimating the persistence time of cheaters in a field population of the parthenogenetic ant Pristomyrmex punctatus. Population genetic analysis found that the cheaters belong to one monophyletic lineage which we infer has persisted for 200-9200 generations. We show that the cheaters migrate and are thus horizontally transmitted between colonies, a trait allowing the lineage to avoid rapid extinction with its host colony. Although horizontal transmission of disruptive cheaters has the potential to induce extinction of the entire population, such collapse is likely averted when there is spatially restricted migration in a structured population, a scenario that matches the observed isolation by distance pattern that we found. We compare our result with other examples of disruptive and horizontally transmissible cheater lineages in nature.     

Evolution of cooperation in patchy habitat under patch decay and isolation

The spatial version of Prisoners Dilemma (PD) is studied, which incorporates habitat decay through change in the mortality parameter and habitat isolation through change in the colonization coefficient. We found four kinds of evolutionary results, which are affected profoundly by the elements of the payoff matrix and the ratio of the colonization coefficient to the mortality parameter: population extinction, a pure cooperator population, coexistence of cooperators and defectors, and a pure defector population. First, the parameter region of cooperation (pure cooperator and coexistence region) shrinks with an increase in the cooperative cost, and that of defection extends. The increase in cooperative reward makes the cooperative region extend and the defector region become small. Second, the cooperative reward can compensate for the extinction risk due to habitat destruction and allow a population to survive even if the colonization coefficient is smaller than the mortality parameter. Third, although habitat destruction (including decay and isolation) increase the extinction risk of a population, moderate external power can push the evolution of cooperation ahead of population extinction, and even make a completely cooperative world come into being. Finally, for certain values of elements of the payoff matrix, the population suffering habitat destruction can maintain a stable population size by regulating the frequencies of cooperators and defectors. This implies that the multi-behavior strategy within a population may be a mechanism to defend against the influences of a changing environment.     

Feedback between Population and Evolutionary Dynamics Determines the Fate of Social Microbial Populations

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.     

Shape matters: Lifecycle of cooperative patches promotes cooperation in bulky populations

Natural cooperative systems take many forms, ranging from one‐dimensional cyanobacteria arrays to fractal‐like biofilms. We use in silico experimental systems to study a previously overlooked factor in the evolution of cooperation, physical shape of the population. We compare the emergence and maintenance of cooperation in populations of digital organisms that inhabit bulky (100 × 100 cells) or slender (4 × 2500) toroidal grids. Although more isolated subpopulations of secretors in a slender population could be expected to favor cooperation, we find the opposite: secretion evolves to higher levels in bulky populations. We identify the mechanistic explanation for the shape effect by analyzing the lifecycle and dynamics of cooperator patches, from their emergence and growth, to invasion by noncooperators and extinction. Because they are constrained by the population shape, the cooperator patches expand less in slender than in bulky populations, leading to fewer cooperators, less public good secretion, and generally lower cooperation. The patch dynamics and mechanisms of shape effect are robust across several digital cooperation systems and independent of the underlying basis for cooperation (public good secretion or a cooperation game). Our results urge for a greater consideration of population shape in the study of the evolution of cooperation across experimental and modeling systems.     

An evolutionary mechanism for diversity in siderophore-producing bacteria

Bacteria produce a great diversity of siderophores to scavenge for iron in their environment. We suggest that this diversity results from the interplay between siderophore producers (cooperators) and non-producers (cheaters): when there are many cheaters exploiting a siderophore type it is beneficial for a mutant to produce a siderophore unusable by the dominant population. We formulated and analysed a mathematical model for tagged public goods to investigate the potential for the emergence of diversity. We found that, although they are rare most of the time, cheaters play a key role in maintaining diversity by regulating the different populations of cooperators. This threshold-triggered feedback prevents any stain of cooperators from dominating the others. Our study provides a novel general mechanism for the evolution of diversity that may apply to many forms of social behaviour.     

Microbial Communication,Cooperation and Cheating: Quorum Sensing Drives the Evolution of Cooperation in Bacteria

An increasing body of empirical evidence suggests that cooperation among clone-mates is common in bacteria. Bacterial cooperation may take the form of the excretion of “public goods”: exoproducts such as virulence factors, exoenzymes or components of the matrix in biofilms, to yield significant benefit for individuals joining in the common effort of producing them. Supposedly in order to spare unnecessary costs when the population is too sparse to supply the sufficient exoproduct level, many bacteria have evolved a simple chemical communication system called quorum sensing (QS), to “measure” the population density of clone-mates in their close neighborhood. Cooperation genes are expressed only above a threshold rate of QS signal molecule re-capture, i.e., above the local quorum of cooperators. The cooperative population is exposed to exploitation by cheaters, i.e., mutants who contribute less or nil to the effort but fully enjoy the benefits of cooperation. The communication system is also vulnerable to a different type of cheaters (“Liars”) who may produce the QS signal but not the exoproduct, thus ruining the reliability of the signal. Since there is no reason to assume that such cheaters cannot evolve and invade the populations of honestly signaling cooperators, the empirical fact of the existence of both bacterial cooperation and the associated QS communication system seems puzzling. Using a stochastic cellular automaton approach and allowing mutations in an initially non-cooperating, non-communicating strain we show that both cooperation and the associated communication system can evolve, spread and remain persistent. The QS genes help cooperative behavior to invade the population, and vice versa; cooperation and communication might have evolved synergistically in bacteria. Moreover, in good agreement with the empirical data recently available, this synergism opens up a remarkably rich repertoire of social interactions in which cheating and exploitation are commonplace.     

On the dynamic persistence of cooperation: how lower individual fitness induces higher survivability

We study a model in which cooperation and defection coexist in a dynamical steady state. In our model, subpopulations of cooperators and defectors inhabit sites on a lattice. The interactions among the individuals at a site, in the form of a prisoner's dilemma (PD) game, determine their fitnesses. The chosen PD payoff allows cooperators, but not defectors, to maintain a homogeneous population. Individuals mutate between types and migrate to neighboring sites with low probabilities. We consider both density-dependent and density-independent versions of the model. The persistence of cooperation in this model can be explained in terms of the life cycle of a population at a site. This life cycle starts when one cooperator establishes a population. Then defectors invade and eventually take over, resulting finally in the death of the population. During this life cycle, single cooperators migrate to empty neighboring sites to found new cooperator populations. The system can reach a steady state where cooperation prevails if the global "birth" rate of populations is equal to their global "death" rate. The dynamic persistence of cooperation ranges over a large section of the model's parameter space. We compare these dynamics to those from other models for the persistence of altruism and to predator-prey models.     

Cooperation as a volunteer’s dilemma and the strategy of conflict in public goods games

Conflict and cooperation for the exploitation of public goods are usually modelled as an N‐person prisoner’s dilemma. Many social dilemmas, however, would be described more properly as a volunteer’s dilemma, in which a certain number of individuals are necessary to produce a public good. If volunteering is costly, but so is failure to produce the public good, cheaters can invade and form a stable mixed equilibrium with cooperators. The dilemma is that the benefit for the group decreases with group size because the larger the group is, the less likely it is that someone volunteers. This problem persists even in the presence of a high degree of relatedness between group members. This model provides precise, testable predictions for the stability of cooperation. It also suggests a counterintuitive but practical solution for this kind of social dilemmas: increasing the damage resulting from the failure to produce the public good increases the probability that the public good is actually produced. Adopting a strategy that entails a deliberate risk (brinkmanship), therefore, can lead to a benefit for the society without being detrimental for the individual.     

Resource abundance and the critical transition to cooperation

Cooperation is abundant in nature, occurring at all levels of biological complexity. Yet cooperation is continually threatened by subversion from noncooperating cheaters. Previous studies have shown that cooperation can nevertheless be maintained when the benefits that cooperation provides to relatives outweigh the associated costs. These fitness costs and benefits are not fixed properties, but can be affected by the environment in which populations reside. Here, we describe how one environmental factor, resource abundance, decisively affects the evolution of cooperative public goods production in two independent evolving systems. In the Avida digital evolution platform, populations evolved in environments with different levels of a required resource, whereas populations of Vibrio cholerae evolved in the presence of different nutrient concentrations. In both systems, cooperators and cheaters co‐existed stably in resource‐rich environments, whereas cheaters dominated in resource‐poor environments. These two outcomes were separated by a sharp transition that occurred at a critical level of resource. These results offer new insights into how the environment affects the evolution of cooperation and highlight the challenges that populations of cooperators face when they experience environmental change.     

A general model for the evolution of mutualisms

The evolution of mutualisms presents a puzzle. Why does selection favour cooperation among species rather than cheaters that accept benefits but provide nothing in return? Here we present a general model that predicts three key factors will be important in mutualism evolution: (i) high benefit to cost ratio, (ii) high within‐species relatedness and (iii) high between‐species fidelity. These factors operate by moderating three types of feedback benefit from mutualism: cooperator association, partner‐fidelity feedback and partner choice. In defining the relationship between these processes, our model also allows an assessment of their relative importance. Importantly, the model suggests that phenotypic feedbacks (partner‐fidelity feedback, partner choice) are a more important explanation for between‐species cooperation than the development of genetic correlations among species (cooperator association). We explain the relationship of our model to existing theories and discuss the empirical evidence for our predictions.     

Frequency dependence and cooperation: theory and a test with bacteria

Hamilton's inclusive fitness theory provides a leading explanation for the problem of cooperation. A general result from inclusive fitness theory is that, except under restrictive conditions, cooperation should not be subject to frequency-dependent selection. However, several recent studies in microbial systems have demonstrated that the relative fitness of cheaters, which do not cooperate, is greater when cheaters are rarer. Here we demonstrate theoretically that such frequency-dependent selection can occur in microbes when there is (1) sufficient population structuring or (2) an association between the level of cooperation and total population growth. We test prediction (2) and its underlying assumption, using the pathogenic bacterium Pseudomonas aeruginosa, by competing strains that produce iron-scavenging siderophore molecules (cooperators) with nonproducers (cheaters) at various ratios, under conditions that minimize population structuring. We found that both the relative fitness of cheaters and the productivity of the mixed culture were significantly negatively related to initial cheater frequency. Furthermore, when the period of population growth was experimentally shortened, the strength of frequency dependence was reduced. More generally, we argue that frequency-dependent selection on cooperative traits may be more common in microbes than in metazoans because strong selection, structuring, and cooperation-dependent growth will be more common in microbial populations.