The tragedy of the commons in microbial populations: insights from theoretical, comparative and experimental studies

First principles of thermodynamics imply that metabolic pathways are faced with a trade-off between the rate and yield of ATP production. Simple evolutionary models argue that this trade-off generates a fundamental social conflict in microbial populations: average fitness in a population is highest if all individuals exploit common resources efficiently, but individual reproductive rate is maximized by consuming common resources at the highest possible rate, a scenario known as the tragedy of the commons. In this paper, I review studies that have addressed two key questions: What is the evidence that the rate-yield trade-off is an evolutionary constraint on metabolic pathways? And, if so, what determines evolutionary outcome of the conflicts generated by this trade-off? Comparative studies and microbial experiments provide evidence that the rate-yield trade-off is an evolutionary constraint that is driven by thermodynamic constraints that are common to all metabolic pathways and pathway-specific constraints that reflect the evolutionary history of populations. Microbial selection experiments show that the evolutionary consequences of this trade-off depend on both kin selection and biochemical constraints. In well-mixed populations with low relatedness, genotypes with rapid and efficient metabolism can coexist as a result of negative frequency-dependent selection generated by density-dependent biochemical costs of rapid metabolism. Kin selection can promote the maintenance of efficient metabolism in structured populations with high relatedness by ensuring that genotypes with efficient metabolic pathways gain an indirect fitness benefit from their competitive restraint. I conclude by suggesting avenues for future research and by discussing the broader implications of this work for microbial social evolution.     

The tragedy of the commons in microbial populations: insights from theoretical, comparative and experimental studies

First principles of thermodynamics imply that metabolic pathways are faced with a trade-off between the rate and yield of ATP production. Simple evolutionary models argue that this trade-off generates a fundamental social conflict in microbial populations: average fitness in a population is highest if all individuals exploit common resources efficiently, but individual reproductive rate is maximized by consuming common resources at the highest possible rate, a scenario known as the tragedy of the commons. In this paper, I review studies that have addressed two key questions: What is the evidence that the rate-yield trade-off is an evolutionary constraint on metabolic pathways? And, if so, what determines evolutionary outcome of the conflicts generated by this trade-off? Comparative studies and microbial experiments provide evidence that the rate-yield trade-off is an evolutionary constraint that is driven by thermodynamic constraints that are common to all metabolic pathways and pathway-specific constraints that reflect the evolutionary history of populations. Microbial selection experiments show that the evolutionary consequences of this trade-off depend on both kin selection and biochemical constraints. In well-mixed populations with low relatedness, genotypes with rapid and efficient metabolism can coexist as a result of negative frequency-dependent selection generated by density-dependent biochemical costs of rapid metabolism. Kin selection can promote the maintenance of efficient metabolism in structured populations with high relatedness by ensuring that genotypes with efficient metabolic pathways gain an indirect fitness benefit from their competitive restraint. I conclude by suggesting avenues for future research and by discussing the broader implications of this work for microbial social evolution.     

Energetics of the smallest: Do bacteria breathe at the same rate as whales?

Power laws describing the dependence of metabolic rate on body mass have been established for many taxa, but not for prokaryotes, despite the ecological dominance of the smallest living beings. Our analysis of 80 prokaryote species with cell volumes ranging more than 1,000,000-fold revealed no significant relationship between mass-specific metabolic rate q and cell mass. By absolute values, mean endogenous mass-specific metabolic rates of non-growing bacteria are similar to basal rates of eukaryote unicells, terrestrial arthropods and mammals. Maximum mass-specific metabolic rates displayed by growing bacteria are close to the record tissue-specific metabolic rates of insects, amphibia, birds and mammals. Minimum mass-specific metabolic rates of prokaryotes coincide with those of larger organisms in various energy-saving regimes: sit-and-wait strategists in arthropods, poikilotherms surviving anoxia, hibernating mammals. These observations suggest a size-independent value around which the mass-specific metabolic rates vary bounded by universal upper and lower limits in all body size intervals.     

Isolation and Characterization of Arsenate-Reducing Bacteria from Arsenic-Contaminated Sites in New Zealand

Two environmental sites in New Zealand were sampled (e.g., water and sediment) for bacterial isolates that could use either arsenite as an electron donor or arsenate as an electron acceptor under aerobic and anaerobic growth conditions, respectively. These two sites were subjected to widespread arsenic contamination from mine tailings generated from historic gold mining activities or from geothermal effluent. No bacteria were isolated from these sites that could utilize arsenite or arsenate under the respective growth conditions tested, but a number of chemoheterotrophic bacteria were isolated that could grow in the presence of high concentrations of arsenic species. In total, 17 morphologically distinct arsenic-resistant heterotrophic bacteria isolates were enriched from the sediment samples, and analysis of the 16S rRNA gene sequence of these bacteria revealed them to be members of the genera Exiguobacterium, Aeromonas, Bacillus, Pseudomonas, Escherichia, and Acinetobacter. Two isolates, Exiguobacterium sp. WK6 and Aeromonas sp. CA1, were of particular interest because they appeared to gain metabolic energy from arsenate under aerobic growth conditions, as demonstrated by an increase in cellular growth yield and growth rate in the presence of arsenate. Both bacteria were capable of reducing arsenate to arsenite via a non-respiratory mechanism. Strain WK6 was positive for arsB, but the pathway of arsenate reduction for isolate CA1 was via a hitherto unknown mechanism. These isolates were not gaining an energetic advantage from arsenate or arsenite utilization, but were instead detoxifying arsenate to arsenite. As a subsidiary process to arsenate reduction, the external pH of the growth medium increased (i.e., became more alkaline), allowing these bacteria to grow for extended periods of time.     

Human male mating strategies: II. Moral codes of “quality” and “quantity” strategists

Men following quality and quantity strategies (pair bond with paternal investment/short-term sexual bonds) should have different, self-serving moral codes. If so, the different strategists should rate dating behaviors differently on ethical (honest and exploitative) and usage (by quality and quantity courters) scales. Quality strategists, who use honest advertisement, should promote their honest behavior by sharp distinctions between what is honest and exploitative and between what men like themselves and others (quantity strategists) do. Quantity strategists, who may exploit (e.g., verbal or physical coercion), should blur these distinctions. Their interests are served by the belief that all men are alike and not morally distinguishable. The companion study obtained men's ratings of quality-strategy behaviors (honest) and quantity-strategy behaviors (exploitative) on ethical and usage scales. Correlations were obtained between those ratings and the same men's scores on bipolar dimensions distinguishing quality from quantity strategists: sexual history, adult characteristics associated with female mate preference, and certain childhood experiences. The correlations supported the hypotheses with two exceptions. First, socioeconomic status and endorsement of a foraging tactic (leave if sexual relations do not start quickly) predicted ratings for quality-strategy behaviors, but did not predict ratings for quantity-strategy behaviors. Sexual history items and childhood experiences related to perceptions of relationships predicted only the ratings for quantity-strategy behaviors. Second, ratings of the lack of honesty in exploitative behavior and its lack of usage by quality courters did not distinguish the strategists. Three conclusions followed. One, there are two kinds of quantity strategists: commodifiers who trade resources for sex and predators who exploit. Two, quantity strategists are mixed strategists while some men follow only a quality strategy. Three, quantity strategists deceive themselves about the exploitative character of their behavior. The data fit evolutionary analyses of human morality and, with a few exceptions, current views of contextual factors governing adoption of different reproductive strategies.     

Migration highways and migration barriers created by host–parasite interactions

Co‐evolving parasites may play a key role in host migration and population structure. Using co‐evolving bacteria and viruses, we test general hypotheses as to how co‐evolving parasites affect the success of passive host migration between habitats that can support different intensities of host–parasite interactions. First, we show that parasites aid migration from areas of intense to weak co‐evolutionary interactions and impede migration in the opposite direction, as a result of intraspecific apparent competition mediated via parasites. Second, when habitats show qualitative difference such that some environments support parasite persistence while others do not, different population regulation forces (either parasitism or competitive exclusion) will reduce the success of migration in both directions. Our study shows that co‐evolution with parasites can predictably homogenises or isolates host populations, depending on heterogeneity of abiotic conditions, with the second scenario constituting a novel type of ‘isolation by adaptation’.     

A spore quality–quantity tradeoff favors diverse sporulation strategies in Bacillus subtilis

Quality–quantity tradeoffs govern the production of propagules across taxa and can explain variability in life-history traits in higher organisms. A quality–quantity tradeoff was recently discovered in spore forming bacteria, but whether it impacts fitness is unclear. Here we show both theoretically and experimentally that the nutrient supply during spore revival determines the fitness advantage associated with different sporulation behaviors in Bacillus subtilis. By tuning sporulation rates we generate spore-yield and spore-quality strategists that compete with each other in a microscopic life-cycle assay. The quality (yield) strategist is favored when spore revival is triggered by poor (rich) nutrients. We also show that natural isolates from the gut and soil employ different life-cycle strategies that result from genomic variations in the number of rap-phr signaling systems. Taken together, our results suggest that a spore quality–quantity tradeoff contributes to the evolutionary adaptation of sporulating bacteria.Subject terms: Bacterial genetics, Biological sciences, Bacterial evolution     

Effects of dispersal plasticity on population divergence and speciation

Phenotypic plasticity is thought to have a role in driving population establishment, local adaptation and speciation. However, dispersal plasticity has been underappreciated in this literature. Plasticity in the decision to disperse is taxonomically widespread and I provide examples for insects, molluscs, polychaetes, vertebrates and flowering plants. Theoretical work is limited but indicates an interaction between dispersal distance and plasticity in the decision to disperse. When dispersal is confined to adjacent patches, dispersal plasticity may enhance local adaptation over unconditional (non-plastic) dispersal. However, when dispersal distances are greater, plasticity in dispersal decisions strongly reduces the potential for local adaptation and population divergence. Upon dispersal, settlement may be random, biased but genetically determined, or biased but plastically determined. Theory shows that biased settlement of either type increases population divergence over random settlement. One model suggests that plasticity further enhances chances of speciation. However, there are many strategies for deciding on where to settle such as a best-of-N strategy, sequential sampling with a threshold for acceptance or matching with natal habitat. To date, these strategies do not seem to have been compared within a single model. Although we are just beginning to explore evolutionary effects of dispersal plasticity, it clearly has the potential to enhance as well as inhibit population divergence. Additional work should pay particular attention to dispersal distance and the strategy used to decide on where to settle.     

The extent of variation in male song, wing and genital characters among allopatric Drosophila montana populations

Drosophila montana, a species of the Drosophila virilis group, has distributed around the northern hemisphere. Phylogeographic analyses of two North American and one Eurasian population of this species offer a good background for the studies on the extent of variation in phenotypic traits between populations as well as for tracing the selection pressures likely to play a role in character divergence. In the present paper, we studied variation in the male courtship song, wing and genital characters among flies from Colorado (USA), Vancouver (Canada) and Oulanka (Finland) populations. The phenotypic divergence among populations did not coincide with the extent of their genetic divergence, suggesting that the characters are not evolving neutrally. Divergence in phenotypic traits was especially high between the Colorado and Vancouver populations, which are closer to each other in terms of their mtDNA genotypes than they are to the Oulanka population. The males of the Colorado population showed high divergence especially in song traits and the males of the Vancouver population in wing characters. Among the male song traits, two characters known to be under sexual selection and a trait important in species recognition differed clearly between populations, implying a history of directional and/or diversifying rather than balancing selection. The population divergence in wing characters is likely to have been enhanced by natural selection associated with environmental factors, whereas the male genitalia traits may have been influenced by sexual selection and/or sexual conflict.     

The multiplicity of divergence mechanisms in a single evolving population

Background

Evolutionary divergence is common within bacterial species and populations, even during a single bacterial infection. We use large-scale genomic and phenotypic analysis to identify the extent of diversification in controlled experimental populations and apply these data to differentiate between several potential mechanisms of evolutionary divergence.

Results

We defined testable differences between five proposed mechanisms and used experimental evolution studies to follow eight glucose-limited Escherichia coli chemostat populations at two growth rates. Simple phenotypic tests identified 11 phenotype combinations evolving under glucose limitation. Each evolved population exhibited 3 to 5 different combinations of the 11 phenotypic clusters. Genome sequencing of a representative of each phenotypic cluster from each population identified 193 mutations in 48 isolates. Only two of the 48 strains had evolved identically. Convergent paths to the same phenotype occurred, but two pleiotropic mutations were unique to slow-growing bacteria, permitting them greater phenotypic variance. Indeed, greater diversity arose in slower-growing, more stressed cultures. Mutation accumulation, hypermutator presence and fitness mechanisms varied between and within populations, with the evolved fitness considerably more uniform with fast growth cultures. Negative frequency-dependent fitness was shown by a subset of isolates.

Conclusions

Evolutionary diversity is unlikely to be explained by any one of the available mechanisms. For a large population as used in this study, our results suggest that multiple mechanisms contribute to the mix of phenotypes and evolved fitness types in a diversifying population. Another major conclusion is that the capacity of a population to diversify is a function of growth rate.     

Oscillatory dynamics in evolutionary games are suppressed by heterogeneous adaptation rates of players

Game dynamics in which three or more strategies are cyclically competitive, as represented by the rock-scissors-paper game, have attracted practical and theoretical interests. In evolutionary dynamics, cyclic competition results in oscillatory dynamics of densities of individual strategists. In finite-size populations, it is known that oscillations blow up until all but one strategies are eradicated if without mutation. In the present paper, we formalize replicator dynamics with players who have different adaptation rates. We show analytically and numerically that the heterogeneous adaptation rate suppresses the oscillation amplitude. In social dilemma games with cyclically competing strategies and homogeneous adaptation rates, altruistic strategies are often relatively weak and cannot survive in finite-size populations. In such situations, heterogeneous adaptation rates save coexistence of different strategies and hence promote altruism. When one strategy dominates the others without cyclic competition, fast adaptors earn more than slow adaptors. When not, mixture of fast and slow adaptors stabilizes population dynamics, and slow adaptation does not imply inefficiency for a player.     

A competition model within and across groups explaining the contrast between the societies of chimpanzees and bonobos

Two apes species, chimpanzees (Pan troglodytes) and bonobos (Pan paniscus), show a peculiar contrast in their social structure. The contrast cannot be explained simply by the differences in their ecological conditions, as has previously been suggested. This paper presents a mathematical model to interpret the contrast, through a competition game within and across groups. Two alternative strategies, dispersal and association, are applied to the model, in order to represent within-group-competition (WGC). Two more alternative strategies, Hawk and Dove, are also applied to the model, in order to represent between-group-competition (BGC). Mathematical analysis is executed for the frequencies of three mixed-strategists: dispersal-Hawk, dispersal-Dove and association. The population dominated by dispersal-Hawk and dispersal-Dove strategists, or by association strategists, is assumed to characterize the social structure of chimpanzees or bonobos, respectively. The model predicts that each social structure can be evolutionarily stable under the same ecological conditions, and will not easily recover once it has been replaced by the other. This stability is through a bi-directional influence: the influence of BGC on WGC and vice versa. The model suggests that the possibility of fatal violence within a group strengthens the robustness of each social structure.     

Bacterial therapy and mitochondrial therapy

Current methods for treatment of cellular and organ pathologies are extremely diverse and constantly evolving, going beyond the use of drugs, based on chemical interaction with biological targets to normalize the functions of the system. Because pharmacological approaches are often untenable, recent strategies in the therapy of different pathological conditions are of particular interest through introducing into the organism of some living system or its components, in particular, bacteria or isolated subcellular structures such as mitochondria. This review describes the most interesting and original examples of therapy using bacteria and mitochondria, which in perspective can dramatically change our views on the principles for the treatment of many diseases. Thus, we analyze such therapeutic effects from the perspective of the similarities between mitochondria and bacteria as the evolutionary ancestors of mitochondria.     

Characterization of five phyllosphere bacteria isolated from Rosa rugosa leaves,and their phenotypic and metabolic properties

Five gram-negative bacteria, all of which were Enterobacteriaceae, were isolated from the phyllosphere of green or senescing leaves of Rosa rugosa, and their phenotypic and physiological characteristics were examined. Partial 16S rDNA sequences led to identification of these isolates as Pantoea agglomerans, Klebsiella terrigena, Erwinia rhapontici, and two strains of Rahnella aquatilis. Interestingly, these phyllosphere bacteria had certain phenotypic and physiological convergences, while they showed their own metabolic properties toward phenolic compounds of plant origin. In particular, the two Ra. aquatilis isolates from the green leaves had a substrate-inducible gallate decarboxylase activity in the resting cells that had been cultured in 1 mM gallic acid- or protocatechuic acid-containing medium. The other three isolates from the senescing leaves did not have this enzyme activity. Simple phenolics that the Ra. aquatilis decarboxylatively produced from benzoic acid derivatives had better antimicrobial activities than those of the substrates.     

The relationship of nucleotide polymorphism, recombination rate and selection in wild tomato species

We analyzed the effects of mating system and recombination rate on single nucleotide polymorphisms using 14 single-copy nuclear loci from single populations of five species of wild tomatoes (Solanum section Lycopersicon). The taxa investigated comprise two self-compatible (SC) and three self-incompatible (SI) species. The observed reduction in nucleotide diversity in the SC populations compared to the SI populations is much stronger than expected under the neutral effects of the mating system on effective population size. Importantly, outgroup sequences available for 11 of the 14 loci yield strong positive correlations between silent nucleotide diversity and silent divergence, indicative of marked among-locus differences in mutation rates and/or selective constraints. Furthermore, using a physical estimate of local recombination rates, we find that silent nucleotide diversity (but not divergence) is positively correlated with recombination rate in two of the SI species. However, this correlation is not nearly as strong as in other well-characterized species (in particular, Drosophila). We propose that nucleotide diversity in Lycopersicon is dominated mainly by differences in neutral mutation rates and/or selective constraints among loci, demographic processes (such as population subdivision), and background selection. In addition, we hypothesize that the soil seed bank plays an important role in the maintenance of the large genetic diversity in the SI species (in particular L. peruvianum).     

EVOLUTIONARY IMPLICATIONS OF DNA DIVERGENCE IN THE DROSOPHILA OBSCURA GROUP

Using DNA–DNA hybridization, we have determined the degree of single-copy DNA (scDNA) divergence among eight species of the Drosophila obscura group. These include Old World and New World species as well as members of two subgroups. Contrary to classical systematics, members of the affinis subgroup are more closely related to American members of the obscura subgroup than are Old World species. The Old World species are not a monophyletic group. The degree of scDNA divergence among species is not necessarily correlated with morphology, chromosomal divergence, or ability to form hybrids. A unique pattern of hybrid formation was found: species separated by a ΔT_m of 6.5°C can form hybrids whereas species separated by a ΔT_m of 2.5°C cannot. As with other groups of Drosophila, the obscura group has discrete parts of the genome evolving at very different rates. The slow evolving fraction of the nuclear genome is evolving at about the same rate as mitochondrial DNA. The additional scDNA divergence accompanying the step from partial reproductive isolation (between North American pseudoobscura and the isolated Bogotà population) to full isolation is very small. The resolution of the technique was challenged by five closely related taxa with a maximum ΔT_m of 2.5°C separating them; the taxa were unambiguously resolved and the “correct” phylogeny recovered. Finally, there is some indication that scDNA in the obscura group may be evolving considerably slower than in the melanogaster subgroup.     

Autecological properties of 3-chlorobenzoate-degrading bacteria and their population dynamics when introduced into sediments

Ecologically significant properties of wild-type and genetically engineered bacteria capable of degrading 3-chlorobenzoate (3-CB) were compared in the laboratory, and isolates were introduced into streambed sediments in microcosms to observe their population dynamics. 3-CB metabolism, growth on algal extract, temperature optima, and ingestion by protozoa were ecological properties considered relevant to the persistence of these bacteria if introduced into nature. Cell-specific Vmax for 3-CB metabolism and cell-specific mineralization rates each spanned approximately 2 orders of magnitude, but isolates did not rank consistently. The Ks for 3-CB metabolism for Alcaligenes sp. BR60 was approximately 40-fold lower than the mean value for the other isolates, which differed only approximately 4-fold among themselves. All isolates grew on an algal extract nearly as well as on tryptone-yeast extract, implying potential for survival on natural metabolic substrates in situ. Most isolates had temperature optima that were 3-15 degrees C higher than maximum stream water temperature (22 degrees C). Ciliates preferentially ingested P. acidovorans M3GY, and either P. putida RC-4(pSI30) or its parent strain were least preferred, but microflagellates did not exhibit consistent preferences. Fluorescent antibodies were prepared against isolates to permit detection of target cells in natural communities. In three different microcosm experiments the cell densities of introduced isolates declined over a period of days. In one experiment, 3-CB additions (100 mg/L) led to increases of P. alcaligenes C-0 and P. acidovorans M3GY cell densities within 1 day, although P. putida RC-4(pSI30) took 4 days. In a second experiment, the persistence of P. putida RC-4(pSI30) and its parent strain P. putida RC-4 were compared and rates of initial population decline were not statistically different. 3-CB addition stimulated the growth of other organisms while densities of the P. putida strains further declined. In a third experiment exposure to 100 mg 3-CB/L slowed the rate of decline of P. acidovorans M3GY densities compared to a 10 mg/L concentration or unamended control. Competition with the native flora was a significant factor affecting the persistence of introduced 3-CB degraders.     

The effects of pesticides on the diversity of culturable soil bacteria

The numbers of culturable soil bacteria in plots that had received either no pesticides or the full combination (aldicarb, chlorfenvinphos, benomyl, glyphosate, plus chlorotoluron or triadimefon) over a 20 year period were compared. Differences were very small although there were consistently higher numbers on the treated plot, possibly reflecting the greater crop yields which had been reported previously. There was no significant difference in numbers of bacterial colonies with homology to a nif gene probe in soils from the two plots. Genetic fingerprinting of Pseudomonas fluorescens isolates from the plots, using ERIC-PCR, showed that the dominant strains in the two populations were not the same although there was no obvious difference in the degree of diversity. Substrate utilization by microbial populations from the two plots was compared using Biolog plates. The population from the pesticide-treated plot showed a higher rate of substrate utilization which could reflect a slightly higher inoculum of heterotrophic bacteria, but could also indicate greater metabolic diversity in the population.     

Mismatch induced speciation in Salmonella: model and data

In bacteria, DNA sequence mismatches act as a barrier to recombination between distantly related organisms and can potentially promote the cohesion of species. We have performed computer simulations which show that the homology dependence of recombination can cause de novo speciation in a neutrally evolving population once a critical population size has been exceeded. Our model can explain the patterns of divergence and genetic exchange observed in the genus Salmonella, without invoking either natural selection or geographical population subdivision. If this model was validated, based on extensive sequence data, it would imply that the named subspecies of Salmonella enterica correspond to good biological species, making species boundaries objective. However, multilocus sequence typing data, analysed using several conventional tools, provide a misleading impression of relationships within S. enterica subspecies enterica and do not provide the resolution to establish whether new species are presently being formed.