Spatial dilemmas of diffusible public goods

Evolutionary graph theory beyond single mutation dynamics: on how network-structured populations cross fitness landscapes

Spatially resolved datasets are revolutionizing knowledge in molecular biology, yet are under-utilized for questions in evolutionary biology. To gain insight from these large-scale datasets of spatial organization, we need mathematical representations and modeling techniques that can both capture their complexity, but also allow for mathematical tractability. Evolutionary graph theory utilizes the mathematical representation of networks as a proxy for heterogeneous population structure and has started to reshape our understanding of how spatial structure can direct evolutionary dynamics. However, previous results are derived for the case of a single new mutation appearing in the population and the role of network structure in shaping fitness landscape crossing is still poorly understood. Here we study how network-structured populations cross fitness landscapes and show that even a simple extension to a two-mutational landscape can exhibit complex evolutionary dynamics that cannot be predicted using previous single-mutation results. We show how our results can be intuitively understood through the lens of how the two main evolutionary properties of a network, the amplification and acceleration factors, change the expected fate of the intermediate mutant in the population and further discuss how to link these models to spatially resolved datasets of cellular organization.

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.

Siderophore-mediated iron partition promotes dynamical coexistence between cooperators and cheaters

Microbes shape their habitats by consuming resources and producing a diverse array of chemicals that can serve as public goods. Despite the risk of exploitation by cheaters, genes encoding sharable molecules like siderophores are widely found in nature, prompting investigations into the mechanisms that allow producers to resist invasion by cheaters. In this work, we presented the chemostat-typed "resource partition model" to demonstrate that dividing the iron resource between private and public siderophores can promote stable or dynamic coexistence between producers and cheaters in a well-mixed environment. Moreover, our analysis shows that when microbes not only consume but also produce resources, chemical innovation leads to stability criteria that differ from those of classical consumer resource models, resulting in more complex dynamics. Our work sheds light on the role of chemical innovations in microbial communities and the potential for resource partition to facilitate dynamical coexistence between cooperative and cheating organisms.

Evolutionary modeling suggests that addictions may be driven by competition-induced microbiome dysbiosis

Recent studies revealed mechanisms by which the microbiome affects its host's brain, behavior and wellbeing, and that dysbiosis - persistent microbiome-imbalance - is associated with the onset and progress of various chronic diseases, including addictive behaviors. Yet, understanding of the ecological and evolutionary processes that shape the host-microbiome ecosystem and affect the host state, is still limited. Here we propose that competition dynamics within the microbiome, associated with host-microbiome mutual regulation, may promote dysbiosis and aggravate addictive behaviors. We construct a mathematical framework, modeling the dynamics of the host-microbiome ecosystem in response to alterations. We find that when this ecosystem is exposed to substantial perturbations, the microbiome may shift towards a composition that reinforces the new host state. Such a positive feedback loop augments post-perturbation imbalances, hindering attempts to return to the initial equilibrium, promoting relapse episodes and prolonging addictions. We show that the initial microbiome composition is a key factor: a diverse microbiome enhances the ecosystem's resilience, whereas lower microbiome diversity is more prone to lead to dysbiosis, exacerbating addictions. This framework provides evolutionary and ecological perspectives on host-microbiome interactions and their implications for host behavior and health, while offering verifiable predictions with potential relevance to clinical treatments.

Evolutionary dynamics within and among competing groups

Biological and social systems are structured at multiple scales, and the incentives of individuals who interact in a group may diverge from the collective incentive of the group as a whole. Mechanisms to resolve this tension are responsible for profound transitions in evolutionary history, including the origin of cellular life, multicellular life, and even societies. Here, we synthesize a growing literature that extends evolutionary game theory to describe multilevel evolutionary dynamics, using nested birth-death processes and partial differential equations to model natural selection acting on competition within and among groups of individuals. We analyze how mechanisms known to promote cooperation within a single group-including assortment, reciprocity, and population structure-alter evolutionary outcomes in the presence of competition among groups. We find that population structures most conducive to cooperation in multiscale systems can differ from those most conducive within a single group. Likewise, for competitive interactions with a continuous range of strategies we find that among-group selection may fail to produce socially optimal outcomes, but it can nonetheless produce second-best solutions that balance individual incentives to defect with the collective incentives for cooperation. We conclude by describing the broad applicability of multiscale evolutionary models to problems ranging from the production of diffusible metabolites in microbes to the management of common-pool resources in human societies.

Predicting partner fitness based on spatial structuring in a light-driven microbial community

Microbial communities have vital roles in systems essential to human health and agriculture, such as gut and soil microbiomes, and there is growing interest in engineering designer consortia for applications in biotechnology (e.g., personalized probiotics, bioproduction of high-value products, biosensing). The capacity to monitor and model metabolite exchange in dynamic microbial consortia can provide foundational information important to understand the community level behaviors that emerge, a requirement for building novel consortia. Where experimental approaches for monitoring metabolic exchange are technologically challenging, computational tools can enable greater access to the fate of both chemicals and microbes within a consortium. In this study, we developed an in-silico model of a synthetic microbial consortia of sucrose-secreting Synechococcus elongatus PCC 7942 and Escherichia coli W. Our model was built on the NUFEB framework for Individual-based Modeling (IbM) and optimized for biological accuracy using experimental data. We showed that the relative level of sucrose secretion regulates not only the steady-state support for heterotrophic biomass, but also the temporal dynamics of consortia growth. In order to determine the importance of spatial organization within the consortium, we fit a regression model to spatial data and used it to accurately predict colony fitness. We found that some of the critical parameters for fitness prediction were inter-colony distance, initial biomass, induction level, and distance from the center of the simulation volume. We anticipate that the synergy between experimental and computational approaches will improve our ability to design consortia with novel function.

The reciprocal changes in dominant species with complete metabolic functions explain the decoupling phenomenon of microbial taxonomic and functional composition in a grassland

The decoupling of microbial functional and taxonomic components refers to the phenomenon that a drastic change in microbial taxonomic composition leads to no or only a gentle change in functional composition. Although many studies have identified this phenomenon, the mechanisms underlying it are still unclear. Here we demonstrate, using metagenomics data from a steppe grassland soil under different grazing and phosphorus addition treatments, that there is no “decoupling” in the variation of taxonomic and metabolic functional composition of the microbial community within functional groups at species level. In contrast, the high consistency and complementarity between the abundance and functional gene diversity of two dominant species made metabolic functions unaffected by grazing and phosphorus addition. This complementarity between the two dominant species shapes a bistability pattern that differs from functional redundancy in that only two species cannot form observable redundancy in a large microbial community. In other words, the “monopoly” of metabolic functions by the two most abundant species leads to the disappearance of functional redundancy. Our findings imply that for soil microbial communities, the impact of species identity on metabolic functions is much greater than that of species diversity, and it is more important to monitor the dynamics of key dominant microorganisms for accurately predicting the changes in the metabolic functions of the ecosystems.

Evolution of cooperation under a generalized death-birth process

According to the evolutionary death-birth protocol, a player is chosen randomly to die and neighbors compete for the available position proportional to their fitness. Hence, the status of the focal player is completely ignored and has no impact on the strategy update. In this paper, we revisit and generalize this rule by introducing a weight factor to compare the payoff values of the focal and invading neighbors. By means of evolutionary graph theory, we analyze the model on joint transitive graphs to explore the possible consequences of the presence of a weight factor. We find that focal weight always hinders cooperation under weak selection strength. Surprisingly, the results show a nontrivial tipping point of the weight factor where the threshold of cooperation success shifts from positive to negative infinity. Once focal weight exceeds this tipping point, cooperation becomes unreachable. Our theoretical predictions are confirmed by Monte Carlo simulations on a square lattice of different sizes. We also verify the robustness of the conclusions to arbitrary two-player prisoner's dilemmas, to dispersal graphs with arbitrary edge weights, and to interaction and dispersal graphs overlapping arbitrarily.

How public can public goods be? Environmental context shapes the evolutionary ecology of partially private goods

The production of costly public goods (as distinct from metabolic byproducts) has largely been understood through the realization that spatial structure can minimize losses to non-producing "cheaters" by allowing for the positive assortment of producers. In well-mixed systems, where positive assortment is not possible, the stable production of public goods has been proposed to depend on lineages that become indispensable as the sole producers of those goods while their neighbors lose production capacity through genome streamlining (the Black Queen Hypothesis). Here, we develop consumer-resource models motivated by nitrogen-fixing, siderophore-producing bacteria that consider the role of colimitation in shaping eco-evolutionary dynamics. Our models demonstrate that in well-mixed environments, single "public goods" can only be ecologically and evolutionarily stable if they are partially privatized (i.e., if producers reserve a portion of the product pool for private use). Colimitation introduces the possibility of subsidy: strains producing a fully public good can exclude non-producing strains so long as the producing strain derives sufficient benefit from the production of a second partially private good. We derive a lower bound for the degree of privatization necessary for production to be advantageous, which depends on external resource concentrations. Highly privatized, low-investment goods, in environments where the good is limiting, are especially likely to be stably produced. Coexistence emerges more rarely in our mechanistic model of the external environment than in past phenomenological approaches. Broadly, we show that the viability of production depends critically on the environmental context (i.e., external resource concentrations), with production of shared resources favored in environments where a partially-privatized resource is scarce.

Reputation effects drive the joint evolution of cooperation and social rewarding

People routinely cooperate with each other, even when cooperation is costly. To further encourage such pro-social behaviors, recipients often respond by providing additional incentives, for example by offering rewards. Although such incentives facilitate cooperation, the question remains how these incentivizing behaviors themselves evolve, and whether they would always be used responsibly. Herein, we consider a simple model to systematically study the co-evolution of cooperation and different rewarding policies. In our model, both social and antisocial behaviors can be rewarded, but individuals gain a reputation for how they reward others. By characterizing the game’s equilibria and by simulating evolutionary learning processes, we find that reputation effects systematically favor cooperation and social rewarding. While our baseline model applies to pairwise interactions in well-mixed populations, we obtain similar conclusions under assortment, or when individuals interact in larger groups. According to our model, rewards are most effective when they sway others to cooperate. This view is consistent with empirical observations suggesting that people reward others to ultimately benefit themselves.

Rewards can motivate people to cooperate, but the evolution of rewarding behavior is itself poorly understood. Here, a game-theoretic analysis shows that reputation effects facilitate the simultaneous evolution of cooperation and social rewarding policies.

Social evolution of shared biofilm matrix components

Biofilm formation is an important and ubiquitous mode of growth among bacteria. Central to the evolutionary advantage of biofilm formation is cell-cell and cell-surface adhesion achieved by a variety of factors, some of which are diffusible compounds that may operate as classical public goods-factors that are costly to produce but may benefit other cells. An outstanding question is how diffusible matrix production, in general, can be stable over evolutionary timescales. In this work, using Vibrio cholerae as a model, we show that shared diffusible biofilm matrix proteins are indeed susceptible to cheater exploitation and that the evolutionary stability of producing these matrix components fundamentally depends on biofilm spatial structure, intrinsic sharing mechanisms of these components, and flow conditions in the environment. We further show that exploitation of diffusible adhesion proteins is localized within a well-defined spatial range around cell clusters that produce them. Based on this exploitation range and the spatial distribution of cell clusters, we constructed a model of costly diffusible matrix production and related these length scales to the relatedness coefficient in social evolution theory. Our results show that production of diffusible biofilm matrix components is evolutionarily stable under conditions consistent with natural biofilm habitats and host environments. We expect the mechanisms revealed in this study to be relevant to other secreted factors that operate as cooperative public goods in bacterial communities and the concept of exploitation range and the associated analysis tools to be generally applicable.

Ecological modelling approaches for predicting emergent properties in microbial communities

Recent studies have brought forward the critical role of emergent properties in shaping microbial communities and the ecosystems of which they are a part. Emergent properties-patterns or functions that cannot be deduced linearly from the properties of the constituent parts-underlie important ecological characteristics such as resilience, niche expansion and spatial self-organization. While it is clear that emergent properties are a consequence of interactions within the community, their non-linear nature makes mathematical modelling imperative for establishing the quantitative link between community structure and function. As the need for conservation and rational modulation of microbial ecosystems is increasingly apparent, so is the consideration of the benefits and limitations of the approaches to model emergent properties. Here we review ecosystem modelling approaches from the viewpoint of emergent properties. We consider the scope, advantages and limitations of Lotka-Volterra, consumer-resource, trait-based, individual-based and genome-scale metabolic models. Future efforts in this research area would benefit from capitalizing on the complementarity between these approaches towards enabling rational modulation of complex microbial ecosystems.

Slow expanders invade by forming dented fronts in microbial colonies

Living organisms never cease to evolve, so there is a significant interest in predicting and controlling evolution in all branches of life sciences. The most basic question is whether a trait should increase or decrease in a given environment. The answer seems to be trivial for traits such as the growth rate in a bioreactor or the expansion rate of a tumor. Yet, it has been suggested that such traits can decrease, rather than increase, during evolution. Here, we report a mutant that outcompeted the ancestor despite having a slower expansion velocity when in isolation. To explain this observation, we developed and validated a theory that describes spatial competition between organisms with different expansion rates and arbitrary competitive interactions.

Most organisms grow in space, whether they are viruses spreading within a host tissue or invasive species colonizing a new continent. Evolution typically selects for higher expansion rates during spatial growth, but it has been suggested that slower expanders can take over under certain conditions. Here, we report an experimental observation of such population dynamics. We demonstrate that mutants that grow slower in isolation nevertheless win in competition, not only when the two types are intermixed, but also when they are spatially segregated into sectors. The latter was thought to be impossible because previous studies focused exclusively on the global competitions mediated by expansion velocities, but overlooked the local competitions at sector boundaries. Local competition, however, can enhance the velocity of either type at the sector boundary and thus alter expansion dynamics. We developed a theory that accounts for both local and global competitions and describes all possible sector shapes. In particular, the theory predicted that a slower on its own, but more competitive, mutant forms a dented V-shaped sector as it takes over the expansion front. Such sectors were indeed observed experimentally, and their shapes matched quantitatively with the theory. In simulations, we further explored several mechanisms that could provide slow expanders with a local competitive advantage and showed that they are all well-described by our theory. Taken together, our results shed light on previously unexplored outcomes of spatial competition and establish a universal framework to understand evolutionary and ecological dynamics in expanding populations.

Energy Availability Determines Strategy of Microbial Amino Acid Synthesis in Volatile Fatty Acid-Fed Anaerobic Methanogenic Chemostats

In natural communities, microbes exchange a variety of metabolites (public goods) with each other, which drives the evolution of auxotroph and shapes interdependent patterns at community-level. However, factors that determine the strategy of public goods synthesis for a given community member still remains to be elucidated. In anaerobic methanogenic communities, energy availability of different community members is largely varied. We hypothesized that this uneven energy availability contributed to the heterogeneity of public goods synthesis ability among the members in these communities. We tested this hypothesis by analyzing the synthetic strategy of amino acids of the bacterial and archaeal members involved in four previously enriched anaerobic methanogenic communities residing in thermophilic chemostats. Our analyses indicate that most of the members in the communities did not possess ability to synthesize all the essential amino acids, suggesting they exchanged these essential public goods to establish interdependent patterns for survival. Importantly, we found that the amino acid synthesis ability of a functional group was largely determined by how much energy it could obtain from its metabolism in the given environmental condition. Moreover, members within a functional group also possessed different amino acid synthesis abilities, which are related to their features of energy metabolism. Our study reveals that energy availability is a key driver of microbial evolution in presence of metabolic specialization at community level and suggests the feasibility of managing anaerobic methanogenic communities for better performance through controlling the metabolic interactions involved.

Spatial segregation and cooperation in radially expanding microbial colonies under antibiotic stress

Antibiotic resistance in microbial communities reflects a combination of processes operating at different scales. In this work, we investigate the spatiotemporal dynamics of bacterial colonies comprised of drug-resistant and drug-sensitive cells undergoing range expansion under antibiotic stress. Using the opportunistic pathogen Enterococcus faecalis with plasmid-encoded β-lactamase, we track colony expansion dynamics and visualize spatial patterns in fluorescently labeled populations exposed to antibiotics. We find that the radial expansion rate of mixed communities is approximately constant over a wide range of drug concentrations and initial population compositions. Imaging of the final populations shows that resistance to ampicillin is cooperative, with sensitive cells surviving in the presence of resistant cells at otherwise lethal concentrations. The populations exhibit a diverse range of spatial segregation patterns that depend on drug concentration and initial conditions. Mathematical models indicate that the observed dynamics are consistent with global cooperation, despite the fact that β-lactamase remains cell-associated. Experiments confirm that resistant colonies provide a protective effect to sensitive cells on length scales multiple times the size of a single colony, and populations seeded with (on average) no more than a single resistant cell can produce mixed communities in the presence of the drug. While biophysical models of drug degradation suggest that individual resistant cells offer only short-range protection to neighboring cells, we show that long-range protection may arise from synergistic effects of multiple resistant cells, providing surprisingly large protection zones even at small population fractions.

Life in a Droplet: Microbial Ecology in Microscopic Surface Wetness

While many natural and artificial surfaces may appear dry, they are in fact covered by thin liquid films and microdroplets invisible to the naked eye known as microscopic surface wetness (MSW). Central to the formation and the retention of MSW are the deliquescent properties of hygroscopic salts that prevent complete drying of wet surfaces or that drive the absorption of water until dissolution when the relative humidity is above a salt-specific level. As salts are ubiquitous, MSW occurs in many microbial habitats, such as soil, rocks, plant leaf, and root surfaces, the built environment, and human and animal skin. While key properties of MSW, including very high salinity and segregation into droplets, greatly affect microbial life therein, it has been scarcely studied, and systematic studies are only in their beginnings. Based on recent findings, we propose that the harsh micro-environment that MSW imposes, which is very different from bulk liquid, affects key aspects of bacterial ecology including survival traits, antibiotic response, competition, motility, communication, and exchange of genetic material. Further research is required to uncover the fundamental principles that govern microbial life and ecology in MSW. Such research will require multidisciplinary science cutting across biology, physics, and chemistry, while incorporating approaches from microbiology, genomics, microscopy, and computational modeling. The results of such research will be critical to understand microbial ecology in vast terrestrial habitats, affecting global biogeochemical cycles, as well as plant, animal, and human health.

Social efficiency deficit deciphers social dilemmas

What do corruption, resource overexploitation, climate inaction, vaccine hesitancy, traffic congestion, and even cancer metastasis have in common? All these socioeconomic and sociobiological phenomena are known as social dilemmas because they embody in one form or another a fundamental conflict between immediate self-interest and long-term collective interest. A shortcut to the resolution of social dilemmas has thus far been reserved solely for highly stylised cases reducible to dyadic games (e.g., the Prisoner’s Dilemma), whose nature and outcome coalesce in the concept of dilemma strength. We show that a social efficiency deficit, measuring an actor’s potential gain in utility or fitness by switching from an evolutionary equilibrium to a social optimum, generalises dilemma strength irrespective of the underlying social dilemma’s complexity. We progressively build from the simplicity of dyadic games for which the social efficiency deficit and dilemma strength are mathematical duals, to the complexity of carcinogenesis and a vaccination dilemma for which only the social efficiency deficit is numerically calculable. The results send a clear message to policymakers to enact measures that increase the social efficiency deficit until the strain between what is and what could be incentivises society to switch to a more desirable state.

A multi-scale eco-evolutionary model of cooperation reveals how microbial adaptation influences soil decomposition

The decomposition of soil organic matter (SOM) is a critical process in global terrestrial ecosystems. SOM decomposition is driven by micro-organisms that cooperate by secreting costly extracellular (exo-)enzymes. This raises a fundamental puzzle: the stability of microbial decomposition in spite of its evolutionary vulnerability to “cheaters”—mutant strains that reap the benefits of cooperation while paying a lower cost. Resolving this puzzle requires a multi-scale eco-evolutionary model that captures the spatio-temporal dynamics of molecule-molecule, molecule-cell, and cell-cell interactions. The analysis of such a model reveals local extinctions, microbial dispersal, and limited soil diffusivity as key factors of the evolutionary stability of microbial decomposition. At the scale of whole-ecosystem function, soil diffusivity influences the evolution of exo-enzyme production, which feeds back to the average SOM decomposition rate and stock. Microbial adaptive evolution may thus be an important factor in the response of soil carbon fluxes to global environmental change.

Abs et al. develop a multi-scale model to explain the evolution of microbial cooperation driving the decomposition of soil organic matter. Their model shows that the evolutionary stability of decomposition depends on a combination of local extinctions, microbial dispersal, and limited soil diffusivity.

A Glance on the Role of Bacterial Siderophore from the Perspectives of Medical and Biotechnological Approaches

Iron, which is described as the most basic component found in nature, is hard to be assimilated by microorganisms. It has become increasingly complicated to obtain iron from nature as iron (II) in the presence of oxygen oxidized to press (III) oxide and hydroxide, becoming unsolvable at neutral pH. Microorganisms appeared to produce organic molecules known as siderophores in order to overcome this condition. Siderophore's essential function is to connect with iron (II) and make it dissolvable and enable cell absorption. These siderophores, apart from iron particles, have the ability to chelate various other metal particles that have collocated away to focus the use of siderophores on wound care items. There is a severe clash between the host and the bacterial pathogens during infection. By producing siderophores, small ferric iron-binding molecules, microorganisms obtain iron. In response, host immune cells produce lipocalin 2 to prevent bacterial reuptake of siderophores loaded with iron. Some bacteria are thought to produce lipocalin 2-resistant siderophores to counter this risk. The aim of this article is to discuss the recently described roles and applications of bacterial siderophore.

Expansion, Exploitation and Extinction: Niche Construction in Ephemeral Landscapes

We aim to understand general consequences of niche construction on metapopulation dynamics in ephemeral landscapes. To this effect, a contact process-like stochastic spatial model is introduced where local populations colonize and go extinct on a dynamic landscape of habitable and destroyed patches. In contrast to previous models, where the extinction threshold is a consequence of available niche rendered by global rates of patch destruction/renewal, here we investigate how the metapopulation persists when they are the sole generators of their own niche. Niche construction is full-filled by localized populations through the transformation of destroyed patches in their neighborhood to viable habitat for future colonization. With this theoretical framework we are able to address the dual nature of niche construction by investigating the ephemerality of the landscape (destruction rate) and the continuum of population level strategies, where construction comes at a cost to colonization. Using mean field theory and Monte Carlo simulations of the model, we are able to quantify optimal population level strategies in a wide range of ephemeral landscapes. Interestingly, we observe qualitative differences at the extinction threshold between analytic and numeric results. Investigating this discrepancy further, we find that increasing niche construction neighborhood in the spatial model leads to two interrelated effects i) an increased rate in range expansion ii) a loss in resiliency and return of the discontinuous transition at the extinction threshold. Furthermore, in the discontinuous regime of the model, spatial clustering prior to a critical transition disappears. This is a significant finding as spatial clustering has been considered to be an early warning signal before ecosystems reach their 'tipping point'. In addition to maintaining stability, we find local niche construction strategies have an advantage when in scramble competition with an exploiter strategy because of their ability to monopolize the constructed niche due to spatial adjacency. As the niche construction neighborhood expands this advantage disappears and the exploiter strategy out-competes the niche constructor. In some cases the exploiter pushes the niche constructor to extinction, thus a tragedy of the commons ensues leading to 'ecological suicide' and a collapse of the niche.

Spatial reciprocity in the evolution of cooperation

Cooperation is key to the survival of all biological systems. The spatial structure of a system constrains who interacts with whom (interaction partner) and who acquires new traits from whom (role model). Understanding when and to what degree a spatial structure affects the evolution of cooperation is an important and challenging topic. Here, we provide an analytical formula to predict when natural selection favours cooperation where the effects of a spatial structure are described by a single parameter. We find that a spatial structure promotes cooperation (spatial reciprocity) when interaction partners overlap role models. When they do not, spatial structure inhibits cooperation even without cooperation dilemmas. Furthermore, a spatial structure in which individuals interact with their role models more often shows stronger reciprocity. Thus, imitating individuals with frequent interactions facilitates cooperation. Our findings are applicable to both pairwise and group interactions and show that strong social ties might hinder, while asymmetric spatial structures for interaction and trait dispersal could promote cooperation.

Bacterial siderophores in community and host interactions

Iron is an essential trace element for most organisms. A common way for bacteria to acquire this nutrient is through the secretion of siderophores, which are secondary metabolites that scavenge iron from environmental stocks and deliver it to cells via specific receptors. While there has been tremendous interest in understanding the molecular basis of siderophore synthesis, uptake and regulation, questions about the ecological and evolutionary consequences of siderophore secretion have only recently received increasing attention. In this Review, we outline how eco-evolutionary questions can complement the mechanistic perspective and help to obtain a more integrated view of siderophores. In particular, we explain how secreted diffusible siderophores can affect other community members, leading to cooperative, exploitative and competitive interactions between individuals. These social interactions in turn can spur co-evolutionary arms races between strains and species, lead to ecological dependencies between them and potentially contribute to the formation of stable communities. In brief, this Review shows that siderophores are much more than just iron carriers: they are important mediators of interactions between members of microbial assemblies and the eukaryotic hosts they inhabit.

Why microbes secrete molecules to modify their environment: the case of iron-chelating siderophores

Many microorganisms secrete molecules that interact with resources outside of the cell. This includes, for example, enzymes that degrade polymers like chitin, and chelators that bind trace metals like iron. In contrast to direct uptake via the cell surface, such release strategies entail the risk of losing the secreted molecules to environmental sinks, including 'cheating' genotypes. Nevertheless, such secretion strategies are widespread, even in the well-mixed marine environment. Here, we investigate the benefits of a release strategy whose efficiency has frequently been questioned: iron uptake in the ocean by secretion of iron chelators called siderophores. We asked the question whether the release itself is essential for the function of siderophores, which could explain why this risky release strategy is widespread. We developed a reaction-diffusion model to determine the impact of siderophore release on iron uptake from the predominant iron sources in marine environments, colloidal or particulate iron, formed due to poor iron solubility. We found that release of siderophores is essential to accelerate iron uptake, as secreted siderophores transform slowly diffusing large iron particles to small, quickly diffusing iron-siderophore complexes. In addition, we found that cells can synergistically share their siderophores, depending on their distance and the size of the iron sources. Our study helps understand why release of siderophores is so widespread: even though a large fraction of siderophores is lost, the solubilization of iron through secreted siderophores can efficiently increase iron uptake, especially if siderophores are produced cooperatively by several cells. Overall, resource uptake mediated via release of molecules transforming their substrate could be essential to overcome diffusion limitation specifically in the cases of large, aggregated resources. In addition, we find that including the reaction of the released molecule with the substrate can impact the result of cooperative and competitive interactions, making our model also relevant for release-based uptake of other substrates.

Persistence of cooperation in diffusive public goods games

Diffusive public goods (PG) games are difficult to analyze due to population assortment affecting growth rates of cooperators (producers) and free-riders. We study these growth rates using spectral decomposition of cellular densities and derive a finite cell-size correction of the growth rate advantage which exactly describes the dynamics of a randomly assorted population and approximates the dynamics under limited dispersal. The resulting effective benefit-to-cost ratio relates the physical parameters of PG dynamics to the persistence of cooperation, and our findings provide a powerful tool for the analysis of diffusive PG games, explaining commonly observed patterns of cooperation.

Biofilm formation as a microbial strategy to assimilate particulate substrates

In most ecosystems, a large part of the organic carbon is not solubilized in the water phase. Rather, it occurs as particles made of aggregated hydrophobic and/or polymeric natural or man-made organic compounds. These particulate substrates are degraded by extracellular digestion/solubilization implemented by heterotrophic bacteria that form biofilms on them. Organic particle-degrading biofilms are widespread and have been observed in aquatic and terrestrial natural ecosystems, in polluted and man-driven environments and in the digestive tracts of animals. They have central ecological functions as they are major players in carbon recycling and pollution removal. The aim of this review is to highlight bacterial adhesion and biofilm formation as central mechanisms to exploit the nutritive potential of organic particles. It focuses on the mechanisms that allow access and assimilation of non-dissolved organic carbon, and considers the advantage provided by biofilms for gaining a net benefit from feeding on particulate substrates. Cooperative and competitive interactions taking place in biofilms feeding on particulate substrates are also discussed.

Evolutionary games on isothermal graphs

Population structure affects the outcome of natural selection. These effects can be modeled using evolutionary games on graphs. Recently, conditions were derived for a trait to be favored under weak selection, on any weighted graph, in terms of coalescence times of random walks. Here we consider isothermal graphs, which have the same total edge weight at each node. The conditions for success on isothermal graphs take a simple form, in which the effects of graph structure are captured in the ‘effective degree’—a measure of the effective number of neighbors per individual. For two update rules (death-Birth and birth-Death), cooperative behavior is favored on a large isothermal graph if the benefit-to-cost ratio exceeds the effective degree. For two other update rules (Birth-death and Death-birth), cooperation is never favored. We relate the effective degree of a graph to its spectral gap, thereby linking evolutionary dynamics to the theory of expander graphs. Surprisingly, we find graphs of infinite average degree that nonetheless provide strong support for cooperation.

The spatial structure of a population is often critical for the evolution of cooperation. Here, Allen and colleagues show that when spatial structure is represented by an isothermal graph, the effective number of neighbors per individual determines whether or not cooperation can evolve.

Evolutionary multiplayer games on graphs with edge diversity

Evolutionary game dynamics in structured populations has been extensively explored in past decades. However, most previous studies assume that payoffs of individuals are fully determined by the strategic behaviors of interacting parties, and social ties between them only serve as the indicator of the existence of interactions. This assumption neglects important information carried by inter-personal social ties such as genetic similarity, geographic proximity, and social closeness, which may crucially affect the outcome of interactions. To model these situations, we present a framework of evolutionary multiplayer games on graphs with edge diversity, where different types of edges describe diverse social ties. Strategic behaviors together with social ties determine the resulting payoffs of interactants. Under weak selection, we provide a general formula to predict the success of one behavior over the other. We apply this formula to various examples which cannot be dealt with using previous models, including the division of labor and relationship- or edge-dependent games. We find that labor division can promote collective cooperation markedly. The evolutionary process based on relationship-dependent games can be approximated by interactions under a transformed and unified game. Our work stresses the importance of social ties and provides effective methods to reduce the calculating complexity in analyzing the evolution of realistic systems.

Is "Wolf-Pack" Predation by Antimicrobial Bacteria Cooperative? Cell Behaviour and Predatory Mechanisms Indicate Profound Selfishness, Even when Working Alongside Kin

For decades, myxobacteria have been spotlighted as exemplars of social "wolf-pack" predation, communally secreting antimicrobial substances into the shared public milieu. This behavior has been described as cooperative, becoming more efficient if performed by more cells. However, laboratory evidence for cooperativity is limited and of little relevance to predation in a natural setting. In contrast, there is accumulating evidence for predatory mechanisms promoting "selfish" behavior during predation, which together with conflicting definitions of cooperativity, casts doubt on whether microbial "wolf-pack" predation really is cooperative. Here, it is hypothesized that public-goods-mediated predation is not cooperative, and it is argued that a holistic model of microbial predation is needed, accounting for predator and prey relatedness, social phenotypes, spatial organization, activity/specificity/transport of secreted toxins, and prey resistance mechanisms. Filling such gaps in our knowledge is vital if the evolutionary benefits of potentially costly microbial behaviors mediated by public goods are to be properly understood.

Social Behavior of Antibiotic Resistant Mutants Within Pseudomonas aeruginosa Biofilm Communities

The complex spatial structure and the heterogeneity within biofilms lead to the emergence of specific social behaviors. However, the impact of resistant mutants within bacterial communities is still mostly unknown. Thus, we determined whether antibiotic resistant mutants display selfish or altruistic behaviors in mixed Pseudomonas aeruginosa biofilms exposed to antibiotics. ECFP-tagged P. aeruginosa strain PAO1 and its EYFP-tagged derivatives hyperproducing the β-lactamase AmpC or the efflux pump MexAB-OprM were used to develop single or mixed biofilms. Mature biofilms were challenged with different concentrations of β-lactams to monitor biofilm structural dynamics, using confocal laser scanning microscopy (CLSM), and population dynamics, through enumeration of viable cells. While exposure of single wild-type PAO1 biofilms to β-lactams lead to a major reduction in bacterial load, it had little effect on biofilms formed by the resistant mutants. However, the most reveling finding was that bacterial load of wild-type PAO1 was significantly increased when growing in mixed biofilms compared to single biofilms. In agreement with CFU enumeration data, CLSM images revealed the amplification of the resistant mutants and their protection of susceptible populations. These findings show that mutants expressing diverse resistance mechanisms, including β-lactamases, but also, as evidenced for the first time, efflux pumps, protect the whole biofilm community, preserving susceptible populations from the effect of antibiotics. Thus, these results are a step forward to understanding antibiotic resistance dynamics in biofilms, as well as the population biology of bacterial pathogens in chronic infections, where the coexistence of susceptible and resistant variants is a hallmark.

Aggregate Filamentous Growth Responses in Yeast

Filamentous growth is a fungal morphogenetic response that is critical for virulence in some fungal species. Many aspects of filamentous growth remain poorly understood. We have identified an aspect of filamentous growth in the budding yeast Saccharomyces cerevisiae and the human pathogen Candida albicans where cells behave collectively to invade surfaces in aggregates. These responses may reflect an extension of normal filamentous growth, as they share the same signaling pathways and effector processes. Aggregate responses may involve cooperation among individual cells, because aggregation was stimulated by cell adhesion molecules, secreted enzymes, and diffusible molecules that promote quorum sensing. Our study may provide insights into the genetic basis of collective cellular responses in fungi. The study may have ramifications in fungal pathogenesis, in situations where collective responses occur to promote virulence.

Many fungal species, including pathogens, undergo a morphogenetic response called filamentous growth, where cells differentiate into a specialized cell type to promote nutrient foraging and surface colonization. Despite the fact that filamentous growth is required for virulence in some plant and animal pathogens, certain aspects of this behavior remain poorly understood. By examining filamentous growth in the budding yeast Saccharomyces cerevisiae and the opportunistic pathogen Candida albicans, we identify responses where cells undergo filamentous growth in groups of cells or aggregates. In S. cerevisiae, aggregate invasive growth was regulated by signaling pathways that control normal filamentous growth. These pathways promoted aggregation in part by fostering aspects of microbial cooperation. For example, aggregate invasive growth required cellular contacts mediated by the flocculin Flo11p, which was produced at higher levels in aggregates than cells undergoing regular invasive growth. Aggregate invasive growth was also stimulated by secreted enzymes, like invertase, which produce metabolites that are shared among cells. Aggregate invasive growth was also induced by alcohols that promote density-dependent filamentous growth in yeast. Aggregate invasive growth also required highly polarized cell morphologies, which may affect the packing or organization of cells. A directed selection experiment for aggregating phenotypes uncovered roles for the fMAPK and RAS pathways, which indicates that these pathways play a general role in regulating aggregate-based responses in yeast. Our study extends the range of responses controlled by filamentation regulatory pathways and has implications in understanding aspects of fungal biology that may be relevant to fungal pathogenesis.

IMPORTANCE Filamentous growth is a fungal morphogenetic response that is critical for virulence in some fungal species. Many aspects of filamentous growth remain poorly understood. We have identified an aspect of filamentous growth in the budding yeast Saccharomyces cerevisiae and the human pathogen Candida albicans where cells behave collectively to invade surfaces in aggregates. These responses may reflect an extension of normal filamentous growth, as they share the same signaling pathways and effector processes. Aggregate responses may involve cooperation among individual cells, because aggregation was stimulated by cell adhesion molecules, secreted enzymes, and diffusible molecules that promote quorum sensing. Our study may provide insights into the genetic basis of collective cellular responses in fungi. The study may have ramifications in fungal pathogenesis, in situations where collective responses occur to promote virulence.

Dynamics of multiplayer games on complex networks using territorial interactions

The modeling of evolution in structured populations has been significantly advanced by evolutionary graph theory, which incorporates pairwise relationships between individuals on a network. More recently, a new framework has been developed to allow for multiplayer interactions of variable size in more flexible and potentially changing population structures. While the theory within this framework has been developed and simple structures considered, there has been no systematic consideration of a large range of different population structures, which is the subject of this paper. We consider a large range of underlying graphical structures for the territorial raider model, the most commonly used model in the new structure, and consider a variety of important properties of our structures with the aim of finding factors that determine the fixation probability of mutants. We find that the graphical temperature and the average group size, as previously defined, are strong predictors of fixation probability, while all other properties considered are poor predictors, although the clustering coefficient is a useful secondary predictor when combined with either temperature or group size. The relationship between temperature or average group size and fixation probability is sometimes, however, nonmonotonic, with a directional reverse occurring around the temperature associated with what we term "completely mixed" populations in the case of the hawk-dove game, but not the public goods game.

Individual- versus group-optimality in the production of secreted bacterial compounds

How unicellular organisms optimize the production of compounds is a fundamental biological question. While it is typically thought that production is optimized at the individual-cell level, secreted compounds could also allow for optimization at the group level, leading to a division of labor where a subset of cells produces and shares the compound with everyone. Using mathematical modeling, we show that the evolution of such division of labor depends on the cost function of compound production. Specifically, for any trait with saturating benefits, linear costs promote the evolution of uniform production levels across cells. Conversely, production costs that diminish with higher output levels favor the evolution of specialization-especially when compound shareability is high. When experimentally testing these predictions with pyoverdine, a secreted iron-scavenging compound produced by Pseudomonas aeruginosa, we found linear costs and, consistent with our model, detected uniform pyoverdine production levels across cells. We conclude that for shared compounds with saturating benefits, the evolution of division of labor is facilitated by a diminishing cost function. More generally, we note that shifts in the level of selection from individuals to groups do not solely require cooperation, but critically depend on mechanistic factors, including the distribution of compound synthesis costs.

Neighborhood size-effects shape growing population dynamics in evolutionary public goods games

An evolutionary game emerges when a subset of individuals incur costs to provide benefits to all individuals. Public goods games (PGG) cover the essence of such dilemmas in which cooperators are prone to exploitation by defectors. We model the population dynamics of a non-linear PGG and consider density-dependence on the global level, while the game occurs within local neighborhoods. At low cooperation, increases in the public good provide increasing returns. At high cooperation, increases provide diminishing returns. This mechanism leads to diverse evolutionarily stable strategies, including monomorphic and polymorphic populations, and neighborhood-size-driven state changes, resulting in hysteresis between equilibria. Stochastic or strategy-dependent variations in neighborhood sizes favor coexistence by destabilizing monomorphic states. We integrate our model with experiments of cancer cell growth and confirm that our framework describes PGG dynamics observed in cellular populations. Our findings advance the understanding of how neighborhood-size effects in PGG shape the dynamics of growing populations.

Share, but unequally: a plausible mechanism for emergence and maintenance of intratumour heterogeneity

Intratumour heterogeneity (ITH), referring to the coexistence of different cell subpopulations in a single tumour, has been a major puzzle in cancer research for almost half a century. The lack of understanding of the underlying mechanism of ITH hinders progress in developing effective therapies for cancers. Based on the findings in a recent quantitative experiment on pancreatic cancer, we developed a general evolutionary model for one type of cancer, accounting for interactions between different cell populations through paracrine or juxtacrine factors. We show that the emergence of a stable heterogeneous state in a tumour requires an unequal allocation of paracrine growth factors (public goods) between cells that produce them and those that merely consume them. Our model provides a quantitative explanation of recent in vitro experimental studies in pancreatic cancer in which insulin-like growth factor II (IGF-II) plays the role of public goods. The calculated phase diagrams as a function of exogenous resources and fraction of growth factor producing cells show ITH persists only in a narrow range of concentration of exogenous IGF-II. Remarkably, maintenance of ITH requires cooperation among tumour cell subpopulations in harsh conditions, specified by lack of exogenous IGF-II, whereas surplus exogenous IGF-II elicits competition. Our theory also quantitatively accounts for measured in vivo tumour growth in glioblastoma multiforme (GBM). The predictions for GBM tumour growth as a function of the fraction of tumour cells are amenable to experimental tests. The mechanism for ITH also provides hints for devising efficacious therapies.

Manganese Oxide Biomineralization Provides Protection against Nitrite Toxicity in a Cell-Density-Dependent Manner

Manganese biomineralization is a widespread process among bacteria and fungi. To date, there is no conclusive experimental evidence for how and if this process impacts microbial fitness in the environment. Here, we show how a model organism for manganese oxidation is growth inhibited by nitrite, and that this inhibition is mitigated in the presence of manganese. We show that such manganese-mediated mitigation of nitrite inhibition is dependent on the culture inoculum size, and that manganese oxide (MnOX) forms granular precipitates in the culture, rather than sheaths around individual cells. We provide evidence that MnOX protection involves both its ability to catalyze nitrite oxidation into (nontoxic) nitrate under physiological conditions and its potential role in influencing processes involving reactive oxygen species (ROS). Taken together, these results demonstrate improved microbial fitness through MnOX deposition in an ecological setting, i.e., mitigation of nitrite toxicity, and point to a key role of MnOX in handling stresses arising from ROS.IMPORTANCE We present here a direct fitness benefit (i.e., growth advantage) for manganese oxide biomineralization activity in Roseobacter sp. strain AzwK-3b, a model organism used to study this process. We find that strain AzwK-3b in a laboratory culture experiment is growth inhibited by nitrite in manganese-free cultures, while the inhibition is considerably relieved by manganese supplementation and manganese oxide (MnOX) formation. We show that biogenic MnOX interacts directly with nitrite and possibly with reactive oxygen species and find that its beneficial effects are established through formation of dispersed MnOX granules in a manner dependent on the population size. These experiments raise the possibility that manganese biomineralization could confer protection against nitrite toxicity to a population of cells. They open up new avenues of interrogating this process in other species and provide possible routes to their biotechnological applications, including in metal recovery, biomaterials production, and synthetic community engineering.

Delays in Fitness Adjustment Can Lead to Coexistence of Hierarchically Interacting Species

Organisms that exploit different environments may experience a stochastic delay in adjusting their fitness when they switch habitats. We study two such organisms whose fitness is determined by the species composition of the local environment, as they interact through a public good. We show that a delay in the fitness adjustment can lead to the coexistence of the two species in a metapopulation, although the faster-growing species always wins in well-mixed competition experiments. Coexistence is favored over wide parameter ranges and is independent of spatial clustering. It arises when species are heterogeneous in their fitness and can keep each other balanced.

Selection for synchronized cell division in simple multicellular organisms

The evolution of multicellularity was a major transition in the history of life on earth. Conditions under which multicellularity is favored have been studied theoretically and experimentally. But since the construction of a multicellular organism requires multiple rounds of cell division, a natural question is whether these cell divisions should be synchronous or not. We study a population model in which there compete simple multicellular organisms that grow by either synchronous or asynchronous cell divisions. We demonstrate that natural selection can act differently on synchronous and asynchronous cell division, and we offer intuition for why these phenotypes are generally not neutral variants of each other.

Model of bacterial toxin-dependent pathogenesis explains infective dose

The initial amount of pathogens required to start an infection within a susceptible host is called the infective dose and is known to vary to a large extent between different pathogen species. We investigate the hypothesis that the differences in infective doses are explained by the mode of action in the underlying mechanism of pathogenesis: Pathogens with locally acting mechanisms tend to have smaller infective doses than pathogens with distantly acting mechanisms. While empirical evidence tends to support the hypothesis, a formal theoretical explanation has been lacking. We give simple analytical models to gain insight into this phenomenon and also investigate a stochastic, spatially explicit, mechanistic within-host model for toxin-dependent bacterial infections. The model shows that pathogens secreting locally acting toxins have smaller infective doses than pathogens secreting diffusive toxins, as hypothesized. While local pathogenetic mechanisms require smaller infective doses, pathogens with distantly acting toxins tend to spread faster and may cause more damage to the host. The proposed model can serve as a basis for the spatially explicit analysis of various virulence factors also in the context of other problems in infection dynamics.

Division of Labor during Biofilm Matrix Production

Organisms as simple as bacteria can engage in complex collective actions, such as group motility and fruiting body formation. Some of these actions involve a division of labor, where phenotypically specialized clonal subpopulations or genetically distinct lineages cooperate with each other by performing complementary tasks. Here, we combine experimental and computational approaches to investigate potential benefits arising from division of labor during biofilm matrix production. We show that both phenotypic and genetic strategies for a division of labor can promote collective biofilm formation in the soil bacterium Bacillus subtilis. In this species, biofilm matrix consists of two major components, exopolysaccharides (EPSs) and TasA. We observed that clonal groups of B. subtilis phenotypically segregate into three subpopulations composed of matrix non-producers, EPS producers, and generalists, which produce both EPSs and TasA. This incomplete phenotypic specialization was outperformed by a genetic division of labor, where two mutants, engineered as specialists, complemented each other by exchanging EPSs and TasA. The relative fitness of the two mutants displayed a negative frequency dependence both in vitro and on plant roots, with strain frequency reaching a stable equilibrium at 30% TasA producers, corresponding exactly to the population composition where group productivity is maximized. Using individual-based modeling, we show that asymmetries in strain ratio can arise due to differences in the relative benefits that matrix compounds generate for the collective and that genetic division of labor can be favored when it breaks metabolic constraints associated with the simultaneous production of two matrix components.

Shearing in flow environment promotes evolution of social behavior in microbial populations

How producers of public goods persist in microbial communities is a major question in evolutionary biology. Cooperation is evolutionarily unstable, since cheating strains can reproduce quicker and take over. Spatial structure has been shown to be a robust mechanism for the evolution of cooperation. Here we study how spatial assortment might emerge from native dynamics and show that fluid flow shear promotes cooperative behavior. Social structures arise naturally from our advection-diffusion-reaction model as self-reproducing Turing patterns. We computationally study the effects of fluid advection on these patterns as a mechanism to enable or enhance social behavior. Our central finding is that flow shear enables and promotes social behavior in microbes by increasing the group fragmentation rate and thereby limiting the spread of cheating strains. Regions of the flow domain with higher shear admit high cooperativity and large population density, whereas low shear regions are devoid of life due to opportunistic mutations.

According to the principle of the ‘survival of the fittest’, selfish individuals should be better off compared to peers that cooperate with each other. Indeed, even though a population of organisms benefits from working together, selfish members can exploit the cooperative behavior of others without doing their part. These ‘cheaters’ then use their advantage to reproduce faster and take over the population.

Yet, social cooperation is widespread in the natural world, and occurs in creatures as diverse as bacteria and whales. How can it arise and persist then? One idea is that when individuals form distinct groups, the ones with cheaters will perish. Even though a selfish individual will fare better than the rest of its team, overall, cooperating groups will survive more and reproduce faster; ultimately, they will be favored by evolution. This is called group selection.

Here, Uppal and Vural examine how the physical properties of the environment can influence the evolution of social interactions between bacteria. To this end, mathematical models are used to simulate how bacteria grow, evolve and drift in a flowing fluid. These are based on equations worked out from the behavior of real-life populations.

The results show that flow patterns in a fluid habitat govern the social behavior of bacteria. When different regions of the fluid are moving at different speeds, ‘shear forces’ are created that cause bacterial colonies to distort and occasionally break apart to form two groups. As such, cooperative groups will rapidly form new cooperating colonies, whereas groups with cheaters will reproduce slower or perish.

Furthermore, results show that when different areas of the fluid have different shear forces, social cooperation will only prevail in certain places. This makes it possible to use flow patterns to fine tune social evolution so that cooperating bacteria will be confined in a certain region. Outside of this area, these bacteria would be taken over by cheaters and go extinct.

Bacteria are both useful and dangerous to humans: for example, certain species can break down pollutants in the water, when others cause deadly infections. These results show it could be possible to control the activity of these microorganisms to our advantage by changing the flow of the fluids in which they live. More broadly, the simulations developed by Uppal and Vural can be applied to a variety of ecosystems where microscopic organisms inhabit fluids, such as plankton flowing in oceanic currents.

Fast cheater migration stabilizes coexistence in a public goods dilemma on networks

Through the lens of game theory, cooperation is frequently considered an unsustainable strategy: if an entire population is cooperating, each individual can increase its overall fitness by choosing not to cooperate, thereby still receiving all the benefit of its cooperating neighbors while no longer expending its own energy. Observable cooperation in naturally-occurring public goods games is consequently of great interest, as such systems offer insight into both the emergence and sustainability of cooperation. Here we consider a population that obeys a public goods game on a network of discrete regions (that we call colonies), between any two of which individuals are free to migrate. We construct a system of piecewise-smooth ordinary differential equations that couple the within-colony population dynamics and the between-colony migratory dynamics. Through a combination of analytical and numerical methods, we show that if the workers within the population migrate sufficiently fast relative to the cheaters, the network loses stability first through a Hopf bifurcation, then a torus bifurcation, after which one or more colonies collapse. Our results indicate that fast moving cheaters can act to stabilize worker-cheatercoexistence within network that would otherwise collapse. We end with a comparison of our results with the dynamics observed in colonies of the ant species Pristomyrmex punctatus, and argue that they qualitatively agree.

Microbial mutualism at a distance: The role of geometry in diffusive exchanges

The exchange of diffusive metabolites is known to control the spatial patterns formed by microbial populations, as revealed by recent studies in the laboratory. However, the matrices used, such as agarose pads, lack the structured geometry of many natural microbial habitats, including in the soil or on the surfaces of plants or animals. Here we address the important question of how such geometry may control diffusive exchanges and microbial interaction. We model mathematically mutualistic interactions within a minimal unit of structure: two growing reservoirs linked by a diffusive channel through which metabolites are exchanged. The model is applied to study a synthetic mutualism, experimentally parametrized on a model algal-bacterial co-culture. Analytical and numerical solutions of the model predict conditions for the successful establishment of remote mutualisms, and how this depends, often counterintuitively, on diffusion geometry. We connect our findings to understanding complex behavior in synthetic and naturally occurring microbial communities.

The spatial and metabolic basis of colony size variation

Spatial structure impacts microbial growth and interactions, with ecological and evolutionary consequences. It is therefore important to quantitatively understand how spatial proximity affects interactions in different environments. We tested how proximity influences colony size when either Escherichia coli or Salmonella enterica are grown on various carbon sources. The importance of colony location changed with species and carbon source. Spatially explicit, genome-scale metabolic modeling recapitulated observed colony size variation. Competitors that determine territory size, according to Voronoi diagrams, were the most important drivers of variation in colony size. However, the relative importance of different competitors changed through time. Further, the effect of location increased when colonies took up resources quickly relative to the diffusion of limiting resources. These analyses made it apparent that the importance of location was smaller than expected for experiments with S. enterica growing on glucose. The accumulation of toxic byproducts appeared to limit the growth of large colonies and reduced variation in colony size. Our work provides an experimentally and theoretically grounded understanding of how location interacts with metabolism and diffusion to influence microbial interactions.

Microbial expansion-collision dynamics promote cooperation and coexistence on surfaces

Microbes colonizing a surface often experience colony growth dynamics characterized by an initial phase of spatial clonal expansion followed by collision between neighboring colonies to form potentially genetically heterogeneous boundaries. For species with life cycles consisting of repeated surface colonization and dispersal, these spatially explicit "expansion-collision dynamics" generate periodic transitions between two distinct selective regimes, "expansion competition" and "boundary competition," each one favoring a different growth strategy. We hypothesized that this dynamic could promote stable coexistence of expansion- and boundary-competition specialists by generating time-varying, negative frequency-dependent selection that insulates both types from extinction. We tested this experimentally in budding yeast by competing an exoenzyme secreting "cooperator" strain (expansion-competition specialists) against nonsecreting "defectors" (boundary-competition specialists). As predicted, we observed cooperator-defector coexistence or cooperator dominance with expansion-collision dynamics, but only defector dominance otherwise. Also as predicted, the steady-state frequency of cooperators was determined by colonization density (the average initial cell-cell distance) and cost of cooperation. Lattice-based spatial simulations give good qualitative agreement with experiments, supporting our hypothesis that expansion-collision dynamics with costly public goods production is sufficient to generate stable cooperator-defector coexistence. This mechanism may be important for maintaining public-goods cooperation and conflict in microbial pioneer species living on surfaces.

Evolutionary dynamics on any population structure

Evolution occurs in populations of reproducing individuals. The structure of a population can affect which traits evolve. Understanding evolutionary game dynamics in structured populations remains difficult. Mathematical results are known for special structures in which all individuals have the same number of neighbours. The general case, in which the number of neighbours can vary, has remained open. For arbitrary selection intensity, the problem is in a computational complexity class that suggests there is no efficient algorithm. Whether a simple solution for weak selection exists has remained unanswered. Here we provide a solution for weak selection that applies to any graph or network. Our method relies on calculating the coalescence times of random walks. We evaluate large numbers of diverse population structures for their propensity to favour cooperation. We study how small changes in population structure-graph surgery-affect evolutionary outcomes. We find that cooperation flourishes most in societies that are based on strong pairwise ties.

Antibiotic stress selects against cooperation in the pathogenic bacterium Pseudomonas aeruginosa

Cheats are a pervasive threat to public goods production in natural and human communities, as they benefit from the commons without contributing to it. Although ecological antagonisms such as predation, parasitism, competition, and abiotic environmental stress play key roles in shaping population biology, it is unknown how such stresses generally affect the ability of cheats to undermine cooperation. We used theory and experiments to address this question in the pathogenic bacterium, Pseudomonas aeruginosa Although public goods producers were selected against in all populations, our competition experiments showed that antibiotics significantly increased the advantage of nonproducers. Moreover, the dominance of nonproducers in mixed cultures was associated with higher resistance to antibiotics than in either monoculture. Mathematical modeling indicates that accentuated costs to producer phenotypes underlie the observed patterns. Mathematical analysis further shows how these patterns should generalize to other taxa with public goods behaviors. Our findings suggest that explaining the maintenance of cooperative public goods behaviors in certain natural systems will be more challenging than previously thought. Our results also have specific implications for the control of pathogenic bacteria using antibiotics and for understanding natural bacterial ecosystems, where subinhibitory concentrations of antimicrobials frequently occur.

The ecology and evolution of social behavior in microbes

Cooperation has been studied extensively across the tree of life, from eusociality in insects to social behavior in humans, but it is only recently that a social dimension has been recognized and extensively explored for microbes. Research into microbial cooperation has accelerated dramatically and microbes have become a favorite system because of their fast evolution, their convenience as lab study systems and the opportunity for molecular investigations. However, the study of microbes also poses significant challenges, such as a lack of knowledge and an inaccessibility of the ecological context (used here to include both the abiotic and the biotic environment) under which the trait deemed cooperative has evolved and is maintained. I review the experimental and theoretical evidence in support of the limitations of the study of social behavior in microbes in the absence of an ecological context. I discuss both the need and the opportunities for experimental investigations that can inform a theoretical framework able to reframe the general questions of social behavior in a clear ecological context and to account for eco-evolutionary feedback.

Proto-cooperation: group hunting sailfish improve hunting success by alternating attacks on grouping prey

We present evidence of a novel form of group hunting. Individual sailfish (Istiophorus platypterus) alternate attacks with other group members on their schooling prey (Sardinella aurita). While only 24% of attacks result in prey capture, multiple prey are injured in 95% of attacks, resulting in an increase of injured fish in the school with the number of attacks. How quickly prey are captured is positively correlated with the level of injury of the school, suggesting that hunters can benefit from other conspecifics' attacks on the prey. To explore this, we built a mathematical model capturing the dynamics of the hunt. We show that group hunting provides major efficiency gains (prey caught per unit time) for individuals in groups of up to 70 members. We also demonstrate that a free riding strategy, where some individuals wait until the prey are sufficiently injured before attacking, is only beneficial if the cost of attacking is high, and only then when waiting times are short. Our findings provide evidence that cooperative benefits can be realized through the facilitative effects of individuals' hunting actions without spatial coordination of attacks. Such 'proto-cooperation' may be the pre-cursor to more complex group-hunting strategies.