Lack of Ecological and Life History Context Can Create the Illusion of Social Interactions in Dictyostelium discoideum

Reduced social function in experimentally evolved Dictyostelium discoideum implies selection for social conflict in nature

Many microbes interact with one another, but the difficulty of directly observing these interactions in nature makes interpreting their adaptive value complicated. The social amoeba Dictyostelium discoideum forms aggregates wherein some cells are sacrificed for the benefit of others. Within chimaeric aggregates containing multiple unrelated lineages, cheaters can gain an advantage by undercontributing, but the extent to which wild D. discoideum has adapted to cheat is not fully clear. In this study, we experimentally evolved D. discoideum in an environment where there were no selective pressures to cheat or resist cheating in chimaeras. Dictyostelium discoideum lines grown in this environment evolved reduced competitiveness within chimaeric aggregates and reduced ability to migrate during the slug stage. By contrast, we did not observe a reduction in cell number, a trait for which selection was not relaxed. The observed loss of traits that our laboratory conditions had made irrelevant suggests that these traits were adaptations driven and maintained by selective pressures D. discoideum faces in its natural environment. Our results suggest that D. discoideum faces social conflict in nature, and illustrate a general approach that could be applied to searching for social or non-social adaptations in other microbes.

Single-cell phenotypic plasticity modulates social behavior in Dictyostelium discoideum

In Dictyostelium chimeras, "cheaters" are strains that positively bias their contribution to the pool of spores, i.e., the reproductive cells resulting from development. On evolutionary time scales, the selective advantage; thus, gained by cheaters is predicted to undermine collective functions whenever social behaviors are genetically determined. Genotypes; however, are not the sole determinant of spore bias, but the relative role of genetic and plastic differences in evolutionary success is unclear. Here, we study chimeras composed of cells harvested in different phases of population growth. We show that such heterogeneity induces frequency-dependent, plastic variation in spore bias. In genetic chimeras, the magnitude of such variation is not negligible and can even reverse the classification of a strain's social behavior. Our results suggest that differential cell mechanical properties can underpin, through biases emerging during aggregation, a "lottery" in strains' reproductive success that may counter the evolution of cheating.

Heterogeneous individual motility biases group composition in a model of aggregating cells

Aggregative life cycles are characterized by alternating phases of unicellular growth and multicellular development. Their multiple, independent evolutionary emergence suggests that they may have coopted pervasive properties of single-celled ancestors. Primitive multicellular aggregates, where coordination mechanisms were less efficient than in extant aggregative microbes, must have faced high levels of conflict between different co-aggregating populations. Such conflicts within a multicellular body manifest in the differential reproductive output of cells of different types. Here, we study how heterogeneity in cell motility affects the aggregation process and creates a mismatch between the composition of the population and that of self-organized groups of active adhesive particles. We model cells as self-propelled particles and describe aggregation in a plane starting from a dispersed configuration. Inspired by the life cycle of aggregative model organisms such as Dictyostelium discoideum or Myxococcus xanthus, whose cells interact for a fixed duration before the onset of chimeric multicellular development, we study finite-time configurations for identical particles and in binary mixes. We show that co-aggregation results in three different types of frequency-dependent biases, one of which is associated to evolutionarily stable coexistence of particles with different motility. We propose a heuristic explanation of such observations, based on the competition between delayed aggregation of slower particles and detachment of faster particles. Unexpectedly, despite the complexity and non-linearity of the system, biases can be largely predicted from the behavior of the two corresponding homogenous populations. This model points to differential motility as a possibly important factor in driving the evolutionary emergence of facultatively multicellular life-cycles.

Species exclusion and coexistence in a noisy voter model with a competition-colonization tradeoff

We introduce an asymmetric noisy voter model to study the joint effect of immigration and a competition-dispersal tradeoff in the dynamics of two species competing for space in regular lattices. Individuals of one species can invade a nearest-neighbor site in the lattice, while individuals of the other species are able to invade sites at any distance but are less competitive locally, i.e., they establish with a probability g≤1. The model also accounts for immigration, modeled as an external noise that may spontaneously replace an individual at a lattice site by another individual of the other species. This combination of mechanisms gives rise to a rich variety of outcomes for species competition, including exclusion of either species, monostable coexistence of both species at different population proportions, and bistable coexistence with proportions of populations that depend on the initial condition. Remarkably, in the bistable phase, the system undergoes a discontinuous transition as the intensity of immigration overcomes a threshold, leading to a half loop dynamics associated to a cusp catastrophe, which causes the irreversible loss of the species with the shortest dispersal range.

Enforcing Cooperation in the Social Amoebae

Cooperation has been essential to the evolution of biological complexity, but many societies struggle to overcome internal conflicts and divisions. Dictyostelium discoideum, or the social amoeba, has been a useful model system for exploring these conflicts and how they can be resolved. When starved, these cells communicate, gather into groups, and build themselves into a multicellular fruiting body. Some cells altruistically die to form the rigid stalk, while the remainder sit atop the stalk, become spores, and disperse. Evolutionary theory predicts that conflict will arise over which cells die to form the stalk and which cells become spores and survive. The power of the social amoeba lies in the ability to explore how cooperation and conflict work across multiple levels, ranging from proximate mechanisms (how does it work?) to ultimate evolutionary answers (why does it work?). Recent studies point to solutions to the problem of ensuring fairness, such as the ability to suppress selfishness and to recognize and avoid unrelated individuals. This work confirms a central role for kin selection, but also suggests new explanations for how social amoebae might enforce cooperation. New approaches based on genomics are also enabling researchers to decipher for the first time the evolutionary history of cooperation and conflict and to determine its role in shaping the biology of multicellular organisms.

Nutrient factor-dependent performance of bacterial quorum sensing system during population evolution

Bacterial quorum sensing (QS) system regulates the production of most costly but sharable extracellular products (public goods) in a growth-phase-dependent manner, and the development of this energy-intensive process is susceptible to environmental changes. However, the role of nutrient factors in dominating the QS-mediated cooperative interaction and intracellular metabolism still remains less understood. Here we studied the performance of QS system by growing Pseudomonas aeruginosa under different nutrient and culture conditions. The results of comparative-transcriptomic analyses revealed that carbon source-limitation was the main factor suppressing the activation of QS system, and a substantial number of public-good-encoding genes were induced when phosphorus is limiting in short-term culture. By contrast, although the QS regulation of P. aeruginosa in all the cultures was generally decreased along with the enrichment of QS-deficient individuals during evolution, limitation of different nutrient factors had discrepant effects in directing the formation of population structure by coordinating the production of public goods and primary metabolism, especially the starch and sucrose metabolism. These findings demonstrate the pleiotropy of QS regulation in balancing the development of cooperative behavior and metabolism, and provide a reference for further understanding the role of QS system in causing persistent infections.

Eco-evolutionary significance of "loners"

Loners—individuals out of sync with a coordinated majority—occur frequently in nature. Are loners incidental byproducts of large-scale coordination attempts, or are they part of a mosaic of life-history strategies? Here, we provide empirical evidence of naturally occurring heritable variation in loner behavior in the model social amoeba Dictyostelium discoideum. We propose that Dictyostelium loners—cells that do not join the multicellular life stage—arise from a dynamic population-partitioning process, the result of each cell making a stochastic, signal-based decision. We find evidence that this imperfectly synchronized multicellular development is affected by both abiotic (environmental porosity) and biotic (signaling) factors. Finally, we predict theoretically that when a pair of strains differing in their partitioning behavior coaggregate, cross-signaling impacts slime-mold diversity across spatiotemporal scales. Our findings suggest that loners could be critical to understanding collective and social behaviors, multicellular development, and ecological dynamics in D. discoideum. More broadly, across taxa, imperfect coordination of collective behaviors might be adaptive by enabling diversification of life-history strategies.

Loners (individuals out of sync with a coordinated majority) occur frequently in nature and are generally assumed to be incidental by-products of imperfect coordination attempts. Experimental and theoretical work on the slime mold Dictyostelium discoideum suggests that "lonerism" might actually be an alternative life-history strategy.

Wild Dictyostelium discoideum social amoebae show plastic responses to the presence of nonrelatives during multicellular development

When multiple strains of microbes form social groups, such as the multicellular fruiting bodies of Dictyostelium discoideum, conflict can arise regarding cell fate. Both fixed and plastic differences among strains can contribute to cell fate, and plastic responses may be particularly important if social environments frequently change. We used RNA-sequencing and photographic time series analysis to detect possible conflict-induced plastic differences between wild D. discoideum aggregates formed by single strains compared with mixed pairs of strains (chimeras). We found one hundred and two differentially expressed genes that were enriched for biological processes including cytoskeleton organization and cyclic AMP response (up-regulated in chimeras), and DNA replication and cell cycle (down-regulated in chimeras). In addition, our data indicate that in reference to a time series of multicellular development in the laboratory strain AX4, chimeras may be slightly behind clonal aggregates in their development. Finally, phenotypic analysis supported slower splitting of aggregates and a nonsignificant trend for larger group sizes in chimeras. The transcriptomic comparison and phenotypic analyses support discoordination among aggregate group members due to social conflict. These results are consistent with previously observed factors that affect cell fate decision in D. discoideum and provide evidence for plasticity in cAMP signaling and phenotypic coordination during development in response to social conflict in D. discoideum and similar microbial social groups.

Many roads lead to Rome: Neutral phenotypes in microorganisms

John Bonner pointed out that microorganisms differ in several ways, some of which may reflect neutral phenotypic evolution. For making his case, Bonner referred to interspecies differences and morphological traits. Here we consider intraspecies differences and physiological traits. As a case-study, we examine the production of an extracellular cyclic 3 ' ,5 ' monophosphate phosphodiesterase in the cellular slime mold Dictyostelium discoideum. Temporal profiles of phosphodiesterase activity differ significantly between wild-type strains. From that we argue that the inference drawn initially from studies on a single wild-type, namely that the profile displayed by it pointed to an adaptive role, was mistaken. We generalize the conclusion to suggest that physiological differences exhibited by microorganisms of the same species may, but need not, reflect adaptations to different environments. Rather, the differences could be related to the fact that microorganisms live in groups whose composition can vary between homogeneous (clonal) and heterogeneous (polyclonal). More than one physiological profile is consistent with the normal development of the group in a given environment; the alternatives are neutral. When studying microbial physiology and behavior, it is expected that the observations are made on a clonal population; genetic (and so phenotypic) heterogeneity is carefully guarded against. As the example from D. discoideum shows, an unintended consequence of overlooking phenotypic heterogeneity is that one can fall into the trap of accepting a seemingly plausible, but possibly erroneous, adaptive explanation for a "normal" wild-type phenotype.

Cellular allorecognition and its roles in Dictyostelium development and social evolution

The social amoeba Dictyostelium discoideum is a tractable model organism to study cellular allorecognition, which is the ability of a cell to distinguish itself and its genetically similar relatives from more distantly related organisms. Cellular allorecognition is ubiquitous across the tree of life and affects many biological processes. Depending on the biological context, these versatile systems operate both within and between individual organisms, and both promote and constrain functional heterogeneity. Some of the most notable allorecognition systems mediate neural self-avoidance in flies and adaptive immunity in vertebrates. D. discoideum's allorecognition system shares several structures and functions with other allorecognition systems. Structurally, its key regulators reside at a single genomic locus that encodes two highly polymorphic proteins, a transmembrane ligand called TgrC1 and its receptor TgrB1. These proteins exhibit isoform-specific, heterophilic binding across cells. Functionally, this interaction determines the extent to which co-developing D. discoideum strains co-aggregate or segregate during the aggregation phase of multicellular development. The allorecognition system thus affects both development and social evolution, as available evidence suggests that the threat of developmental cheating represents a primary selective force acting on it. Other significant characteristics that may inform the study of allorecognition in general include that D. discoideum's allorecognition system is a continuous and inclusive trait, it is pleiotropic, and it is temporally regulated.

Genetic signatures of microbial altruism and cheating in social amoebas in the wild

Many microbes engage in social interactions. Some of these have come to play an important role in the study of cooperation and conflict, largely because, unlike most animals, they can be genetically manipulated and experimentally evolved. However, whereas animal social behavior can be observed and assessed in natural environments, microbes usually cannot, so we know little about microbial social adaptations in nature. This has led to some difficult-to-resolve controversies about social adaptation even for well-studied traits such as bacterial quorum sensing, siderophore production, and biofilms. Here we use molecular signatures of population genetics and molecular evolution to address controversies over the existence of altruism and cheating in social amoebas. First, we find signatures of rapid adaptive molecular evolution that are consistent with social conflict being a significant force in nature. Second, we find population-genetic signatures of purifying selection to support the hypothesis that the cells that form the sterile stalk evolve primarily through altruistic kin selection rather than through selfish direct reproduction. Our results show how molecular signatures can provide insight into social adaptations that cannot be observed in their natural context, and they support the hypotheses that social amoebas in the wild are both altruists and cheaters.

Seasonality can induce coexistence of multiple bet-hedging strategies in Dictyostelium discoideum via storage effect

The social amoeba Dictyostelium discoideum has been recently suggested as an example of bet-hedging in microbes. In the presence of resources, amoebae reproduce as unicellular organisms. Resource depletion, however, leads to a starvation phase in which the population splits between aggregators, which form a fruiting body made of a stalk and resistant spores, and non-aggregators, which remain as vegetative cells. Spores are favored when starvation periods are long, but vegetative cells can exploit resources in environments where food replenishes quickly. The investment in aggregators versus non-aggregators can therefore be understood as a bet-hedging strategy that evolves in response to stochastic starvation times. A genotype (or strategy) is defined by the balance between each type of cells. In this framework, if the ecological conditions on a patch are defined in terms of the mean starvation time (i.e. time between the onset of starvation and the arrival of a new food pulse), a single genotype dominates each environment, which is inconsistent with the huge genetic diversity observed in nature. Here we investigate whether seasonality, represented by a periodic, wet-dry alternation in the mean starvation times, allows the coexistence of several strategies in a single patch. We study this question in a non-spatial (well-mixed) setting in which different strains compete for a common pool of resources over a sequence of growth-starvation cycles. We find that seasonality induces a temporal storage effect that can promote the stable coexistence of multiple genotypes. Two conditions need to be met in our model. First, there has to be a temporal niche partitioning (two well-differentiated habitats within the year), which requires not only different mean starvation times between seasons but also low variance within each season. Second, each season's well-adapted strain has to grow and create a large enough population that permits its survival during the subsequent unfavorable season, which requires the number of growth-starvation cycles within each season to be sufficiently large. These conditions allow the coexistence of two bet-hedging strategies. Additional tradeoffs among life-history traits can expand the range of coexistence and increase the number of coexisting strategies, contributing toward explaining the genetic diversity observed in D. discoideum. Although focused on this cellular slime mold, our results are general and may be easily extended to other microbes.

Understanding Microbial Divisions of Labor

Divisions of labor are ubiquitous in nature and can be found at nearly every level of biological organization, from the individuals of a shared society to the cells of a single multicellular organism. Many different types of microbes have also evolved a division of labor among its colony members. Here we review several examples of microbial divisions of labor, including cases from both multicellular and unicellular microbes. We first discuss evolutionary arguments, derived from kin selection, that allow divisions of labor to be maintained in the face of non-cooperative cheater cells. Next we examine the widespread natural variation within species in their expression of divisions of labor and compare this to the idea of optimal caste ratios in social insects. We highlight gaps in our understanding of microbial caste ratios and argue for a shift in emphasis from understanding the maintenance of divisions of labor, generally, to instead focusing on its specific ecological benefits for microbial genotypes and colonies. Thus, in addition to the canonical divisions of labor between, e.g., reproductive and vegetative tasks, we may also anticipate divisions of labor to evolve to reduce the costly production of secondary metabolites or secreted enzymes, ideas we consider in the context of streptomycetes. The study of microbial divisions of labor offers opportunities for new experimental and molecular insights across both well-studied and novel model systems.