Lateral gene transfer is of fundamental importance to the evolution of prokaryote genomes and has... more Lateral gene transfer is of fundamental importance to the evolution of prokaryote genomes and has important practical consequences, as evidenced by the rapid dissemination of antibiotic resistance and virulence determinants. Relatively little effort has so far been devoted to explicitly quantifying the rate at which accessory genes are taken up and lost, but it is possible that the combined rate of lateral gene transfer and gene loss is higher than that of point mutation. What evolutionary forces underlie the rate of lateral gene transfer are not well understood. We here use theory developed to explain the evolution of mutation rates to address this question and explore its consequences for the study of prokaryote evolution.
Efficient host exploitation by parasites is frequently likely to depend on cooperative behaviour.... more Efficient host exploitation by parasites is frequently likely to depend on cooperative behaviour. Under these conditions, mixed-strain infections are predicted to show lower virulence (host mortality) than are single-clone infections, due to competition favouring non-contributing social 'cheats' whose presence will reduce within-host growth. We tested this hypothesis using the cooperative production of iron-scavenging siderophores by the pathogenic bacterium Pseudomonas aeruginosa in an insect host. We found that infection by siderophore-producing bacteria (cooperators) results in more rapid host death than does infection by non-producers (cheats), and that mixtures of both result in intermediate levels of virulence. Within-host bacterial growth rates exhibited the same pattern. Crucially, cheats were more successful in mixed infections compared with single-clone infections, while the opposite was true of cooperators. These data demonstrate that mixed clone infections can fa...
RATIONALE: Distinguishing between individual bacterial strains below the species level is a chall... more RATIONALE: Distinguishing between individual bacterial strains below the species level is a challenge to matrixassisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) bacterial profiling. We propose a quick method for improving strain differentiation of two Staphylococcus and one Bacillus species. METHODS: An alternative procedure to the extraction protocol recommended by Bruker Daltonics was developed. Ethanol-sterilized cells of six S. aureus and six S. haemolyticus strains were digested by trypsin using 2-min microwave irradiation and were then analyzed. Twenty-eight strains belonging to two ecotypes of B. subtilis were subjected to the same procedure to extend the scope of the method. RESULTS: S. aureus and S. haemolyticus strains, only partially distinguishable by the standard sample preparation procedure, were subjected to microwave-assisted tryptic digestion. The repeatability of the procedure was checked in three experiments accomplished at weekly intervals. Clear distinction of the strains was achieved by cluster analysis. The differentiation of B. subtilis ecotypes was also improved significantly by the digestion method. The discriminatory power of the novel method was supported by an increase in the number of strain-specific peaks, as compared to the standard method. CONCLUSIONS: The method modulates the discriminatory power of MALDI-TOF MS profiling. The differentiation of a set of S. aureus, S. haemolyticus and B. subtilis strains was improved significantly after microwave-accelerated tryptic digestion of the cellular material. Figure 8. Dendrogram calculated on the basis of cluster analysis of MALDI-TOF mass spectra of 28 Bacillus subtilis strains of two ecotypes (PE10 and PE32) analyzed using microwave-assisted digestion. T. Balážová et al. wileyonlinelibrary.com/journal/rcm
The Staphylococcus intermedius group (SIG) includes zoonotic pathogens traditionally associated w... more The Staphylococcus intermedius group (SIG) includes zoonotic pathogens traditionally associated with dog bites. We describe a simple scheme for improved detection of SIG using routine laboratory methods, report its effect on isolation rates, and use sequencing to confirm that, apart from one atypical SIG strain, most isolates are Staphylococcus pseudintermedius.
The filamentous growth form is an important strategy for soil microbes to bridge air-filled pores... more The filamentous growth form is an important strategy for soil microbes to bridge air-filled pores in unsaturated soils. In particular, fungi perform better than bacteria in soils during drought, a property that has been ascribed to the hyphal growth form of fungi. However, it is unknown if, and to what extent, filamentous bacteria may also display similar advantages over non-filamentous bacteria in soils with low hydraulic connectivity. In addition to allowing for microbial interactions and competition across connected micro-sites, water films also facilitate the motility of non-filamentous bacteria. To examine these issues, we constructed and characterized a series of quartz sand microcosms differing in matric potential and pore size distribution and, consequently, in connection of micro-habitats via water films. Our sand microcosms were used to examine the individual and competitive responses of a filamentous bacterium (Streptomyces atratus) and a motile rod-shaped bacterium (Bacillus weihenstephanensis) to differences in pore sizes and matric potential. The Bacillus strain had an initial advantage in all sand microcosms, which could be attributed to its faster growth rate. At later stages of the incubation, Streptomyces became dominant in microcosms with low connectivity (coarse pores and dry conditions). These data, combined with information on bacterial motility (expansion potential) across a range of pore-size and moisture conditions, suggest that, like their much larger fungal counterparts, filamentous bacteria also use this growth form to facilitate growth and expansion under conditions of low hydraulic conductivity. The sand microcosm system developed and used in this study allowed for precise manipulation of hydraulic properties and pore size distribution, thereby providing a useful approach for future examinations of how these properties influence the composition, diversity and function of soil-borne microbial communities.
Microbes are incredibly abundant and diverse and are key to ecosystem functioning, yet relatively... more Microbes are incredibly abundant and diverse and are key to ecosystem functioning, yet relatively little is known about the ecological and evolutionary mechanisms that shape their distributions. Bacteriophages, viral parasites that lyse their bacterial hosts, exert intense and spatially varying selection pressures on bacteria and vice versa. We measured local adaptation of bacteria and their associated phages in a centimeter-scale soil population. We first demonstrate that a large proportion of bacteria is sensitive to locally occurring phages. We then show that sympatric phages (isolated from the same 2-gram soil samples as the bacteria) are more infective than are phages from samples some distance away. This study demonstrates the importance of biotic interactions for the small-scale spatial structuring of microbial genetic diversity in soil.
Quantifying patterns of adaptive divergence between taxa is a major goal in the comparative and e... more Quantifying patterns of adaptive divergence between taxa is a major goal in the comparative and evolutionary study of prokaryote genomes. When applied appropriately, the McDonald-Kreitman (MK) test is a powerful test of selection based on the relative frequency of non-synonymous and synonymous substitutions between species compared to non-synonymous and synonymous polymorphisms within species. The webserver ODoSE (Ortholog Direction of Selection Engine) allows the calculation of a novel extension of the MK test, the Direction of Selection (DoS) statistic, as well as the calculation of a weighted-average Neutrality Index (NI) statistic for the entire core genome, allowing for systematic analysis of the evolutionary forces shaping core genome divergence in prokaryotes. ODoSE is hosted in a Galaxy environment, which makes it easy to use and amenable to customization and is freely available at www.odose.nl. Citation: Vos M, te Beek TAH, van Driel MA, Huynen MA, Eyre-Walker A, et al. (2013) ODoSE: A Webserver for Genome-Wide Calculation of Adaptive Divergence in Prokaryotes. PLoS ONE 8(5): e62447.
Background: The 16S rRNA gene is the gold standard in molecular surveys of bacterial and archaeal... more Background: The 16S rRNA gene is the gold standard in molecular surveys of bacterial and archaeal diversity, but it has the disadvantages that it is often multiple-copy, has little resolution below the species level and cannot be readily interpreted in an evolutionary framework. We compared the 16S rRNA marker with the single-copy, protein-coding rpoB marker by amplifying and sequencing both from a single soil sample. Because the higher genetic resolution of the rpoB gene prohibits its use as a universal marker, we employed consensus-degenerate primers targeting the Proteobacteria.
Background: Many soil-inhabiting bacteria are known to produce secondary metabolites that can sup... more Background: Many soil-inhabiting bacteria are known to produce secondary metabolites that can suppress microorganisms competing for the same resources. The production of antimicrobial compounds is expected to incur fitness costs for the producing bacteria. Such costs form the basis for models on the co-existence of antibiotic-producing and non-antibiotic producing strains. However, so far studies quantifying the costs of antibiotic production by bacteria are scarce. The current study reports on possible costs, for antibiotic production by Pseudomonas fluorescens Pf0-1, a soil bacterium that is induced to produce a broad-spectrum antibiotic when it is confronted with non-related bacterial competitors or supernatants of their cultures.
Soil habitats contain vast numbers of microorganisms and harbor a large portion of the planet's b... more Soil habitats contain vast numbers of microorganisms and harbor a large portion of the planet's biological diversity. Although high-throughput sequencing technologies continue to advance our appreciation of this remarkable phylogenetic and functional diversity, we still have only a rudimentary understanding of the forces that allow diverse microbial populations to coexist in soils. This conspicuous knowledge gap may be partially due the human perspective from which we tend to examine soilborne microorganisms. This review focusses on the highly heterogeneous soil matrix from the vantage point of individual bacteria. Methods describing micro-scale soil habitats and their inhabitants based on sieving, dissecting, and visualizing individual soil aggregates are discussed, as are microcosm-based experiments allowing the manipulation of key soil parameters. We identify how the spatial heterogeneity of soil could influence a number of ecological interactions promoting the evolution and maintenance of bacterial diversity.
Why should organisms cooperate with each other? Helping close relatives that are likely to share ... more Why should organisms cooperate with each other? Helping close relatives that are likely to share the same genes (kin selection) is one important explanation that is likely to apply across taxa. The production of metabolically costly extracellular iron-scavenging molecules (siderophores) by microorganisms is a cooperative behaviour because it benefits nearby conspecifics. We review experiments focusing on the production of the primary siderophore (pyoverdin) of the opportunistic bacterial pathogen, Pseudomonas aeruginosa, which test kin selection theories that seek to explain the evolution of cooperation. First, cooperation is indeed favoured when individuals interact with their close relatives and when there is competition between groups of cooperators and noncooperators, such that the benefit of cooperation can be realized. Second, the relative success of cheats and cooperators is a function of their frequencies within populations. Third, elevated mutation rates can confer a selective disadvantage under conditions when cooperation is beneficial, because high mutation rates reduce how closely bacteria are related to each other. Fourth, cooperative pyoverdin production is also shown to be favoured by kin selection in vivo (caterpillars), and results in more virulent infections. Finally, we briefly outline ongoing and future work using this experimental system.
A major challenge in microbial evolutionary ecology is to understand how fitness-related traits v... more A major challenge in microbial evolutionary ecology is to understand how fitness-related traits vary in natural populations of microorganisms at defined spatial scales and subsequently to identify the forces that maintain such variation. The Gram-negative soil bacterium Myxococcus xanthus is a model system for the study of gliding motility, which is driven by two complementary motility systems in this species and is central to its social lifestyle. We tested whether the ecological context of a centimetre-scale M. xanthus population allows the coexistence of diverse motility-related phenotypes. Swarming rates among 26 clones isolated at the centimetre scale were found to vary greatly in multiple laboratory environments. This variation appears to be motility-specific, as it is not explained by a correlated variation in intrinsic growth rate. In contrast to the common reference strain DK1622, most isolates swarmed faster on hard agar than on soft agar, highlighting the difficulty of inferring species characteristics from laboratory reference strains. These isolates also varied greatly in swarm morphology and in the effect of nutrient limitation on swarming rate. Our results show that diverse swarming phenotypes can coexist in a small-scale bacterial population.
Calculation of the Per-Codon d N /d S Ratio and Recombination Rate A model using a population-gen... more Calculation of the Per-Codon d N /d S Ratio and Recombination Rate A model using a population-genetics approximation to the coalescent [S1], as implemented in the program OmegaMap (available at www.danielwilson. me.uk), was used for calculating the d N /d S ratio (u) per codon in the pilA fragments of the nested-isolate set. This program uses reversible-jump MCMC to perform Bayesian inference on the dN/dS ratio, which allows it to vary over the length of the sequence. Recombination is explicitly modeled in this approach so that it does not obscure the phylogeny (and therefore the d N /d S ratio statistic).
As a monophyletic group, the myxobacteria are known to produce a broad spectrum of secondary meta... more As a monophyletic group, the myxobacteria are known to produce a broad spectrum of secondary metabolites. However, the degree of metabolic diversity that can be found within a single species remains unexplored. The model species Myxococcus xanthus produces several metabolites also present in other myxobacterial species, but only one compound unique to M. xanthus has been found to date. Here, we compare the metabolite profiles of 98 M. xanthus strains that originate from 78 locations worldwide and include 20 centimeter-scale isolates from one location. This screen reveals a strikingly high level of intraspecific diversity in the M. xanthus secondary metabolome. The identification of 37 nonubiquitous candidate compounds greatly exceeds the small number of secondary metabolites previously known to derive from this species. These results suggest that M. xanthus may be a promising source of future natural products and that thorough intraspecific screens of other species could reveal many new compounds of interest.
Myxococcus xanthus is a gram-negative soil bacterium best known for its remarkable life history o... more Myxococcus xanthus is a gram-negative soil bacterium best known for its remarkable life history of social swarming, social predation, and multicellular fruiting body formation. Very little is known about genetic diversity within this species or how social strategies might vary among neighboring strains at small spatial scales. To investigate the small-scale population structure of M. xanthus, 78 clones were isolated from a patch of soil (16 by 16 cm) in Tübingen, Germany. Among these isolates, 21 genotypes could be distinguished from a concatemer of three gene fragments: csgA (developmental C signal), fibA (extracellular matrix-associated zinc metalloprotease), and pilA (the pilin subunit of type IV pili). Accumulation curves showed that most of the diversity present at this scale was sampled. The pilA gene contains both conserved and highly variable regions, and two frequency-distribution tests provide evidence for balancing selection on this gene. The functional domains in the csgA gene were found to be conserved. Three instances of lateral gene transfer could be inferred from a comparison of individual gene phylogenies, but no evidence was found for linkage equilibrium, supporting the view that M. xanthus evolution is largely clonal. This study shows that M. xanthus is surrounded by a variety of distinct conspecifics in its natural soil habitat at a spatial scale at which encounters among genotypes are likely.
Cooperation is integral to much of biological life but can be threatened by selfish evolutionary ... more Cooperation is integral to much of biological life but can be threatened by selfish evolutionary strategies. Diverse cooperative traits have evolved among microbes, but particularly sophisticated forms of sociality have arisen in the myxobacteria, including group motility and multicellular fruiting body development. Myxobacterial cooperation has succeeded against socially destructive cheaters and can readily re-evolve from some socially defective genotypes. However, social harmony does not extend far. Spatially structured natural populations of the model species Myxococcus xanthus have fragmented into a large number of socially incompatible genotypes that exclude, exploit, and/or antagonize one another, including genetically similar neighbors. Here, we briefly review basic social evolution concepts as they pertain to microbes, discuss potential benefits of myxobacterial social traits, highlight recent empirical studies of social evolution in M. xanthus, and consider their implications for how myxobacterial cooperation and conflict evolve in the wild. 599 Annu. Rev. Microbiol. 2009.63:599-623. Downloaded from arjournals.annualreviews.org by Dr Michiel Vos on 10/02/09. For personal use only.
The Staphylococcus intermedius group (SIG) includes zoonotic pathogens traditionally associated w... more The Staphylococcus intermedius group (SIG) includes zoonotic pathogens traditionally associated with dog bites. We describe a simple scheme for improved detection of SIG using routine laboratory methods, report its effect on isolation rates, and use sequencing to confirm that, apart from one atypical SIG strain, most isolates are Staphylococcus pseudintermedius.
Lateral gene transfer is of fundamental importance to the evolution of prokaryote genomes and has... more Lateral gene transfer is of fundamental importance to the evolution of prokaryote genomes and has important practical consequences, as evidenced by the rapid dissemination of antibiotic resistance and virulence determinants. Relatively little effort has so far been devoted to explicitly quantifying the rate at which accessory genes are taken up and lost, but it is possible that the combined rate of lateral gene transfer and gene loss is higher than that of point mutation. What evolutionary forces underlie the rate of lateral gene transfer are not well understood. We here use theory developed to explain the evolution of mutation rates to address this question and explore its consequences for the study of prokaryote evolution.
Efficient host exploitation by parasites is frequently likely to depend on cooperative behaviour.... more Efficient host exploitation by parasites is frequently likely to depend on cooperative behaviour. Under these conditions, mixed-strain infections are predicted to show lower virulence (host mortality) than are single-clone infections, due to competition favouring non-contributing social 'cheats' whose presence will reduce within-host growth. We tested this hypothesis using the cooperative production of iron-scavenging siderophores by the pathogenic bacterium Pseudomonas aeruginosa in an insect host. We found that infection by siderophore-producing bacteria (cooperators) results in more rapid host death than does infection by non-producers (cheats), and that mixtures of both result in intermediate levels of virulence. Within-host bacterial growth rates exhibited the same pattern. Crucially, cheats were more successful in mixed infections compared with single-clone infections, while the opposite was true of cooperators. These data demonstrate that mixed clone infections can fa...
RATIONALE: Distinguishing between individual bacterial strains below the species level is a chall... more RATIONALE: Distinguishing between individual bacterial strains below the species level is a challenge to matrixassisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) bacterial profiling. We propose a quick method for improving strain differentiation of two Staphylococcus and one Bacillus species. METHODS: An alternative procedure to the extraction protocol recommended by Bruker Daltonics was developed. Ethanol-sterilized cells of six S. aureus and six S. haemolyticus strains were digested by trypsin using 2-min microwave irradiation and were then analyzed. Twenty-eight strains belonging to two ecotypes of B. subtilis were subjected to the same procedure to extend the scope of the method. RESULTS: S. aureus and S. haemolyticus strains, only partially distinguishable by the standard sample preparation procedure, were subjected to microwave-assisted tryptic digestion. The repeatability of the procedure was checked in three experiments accomplished at weekly intervals. Clear distinction of the strains was achieved by cluster analysis. The differentiation of B. subtilis ecotypes was also improved significantly by the digestion method. The discriminatory power of the novel method was supported by an increase in the number of strain-specific peaks, as compared to the standard method. CONCLUSIONS: The method modulates the discriminatory power of MALDI-TOF MS profiling. The differentiation of a set of S. aureus, S. haemolyticus and B. subtilis strains was improved significantly after microwave-accelerated tryptic digestion of the cellular material. Figure 8. Dendrogram calculated on the basis of cluster analysis of MALDI-TOF mass spectra of 28 Bacillus subtilis strains of two ecotypes (PE10 and PE32) analyzed using microwave-assisted digestion. T. Balážová et al. wileyonlinelibrary.com/journal/rcm
The Staphylococcus intermedius group (SIG) includes zoonotic pathogens traditionally associated w... more The Staphylococcus intermedius group (SIG) includes zoonotic pathogens traditionally associated with dog bites. We describe a simple scheme for improved detection of SIG using routine laboratory methods, report its effect on isolation rates, and use sequencing to confirm that, apart from one atypical SIG strain, most isolates are Staphylococcus pseudintermedius.
The filamentous growth form is an important strategy for soil microbes to bridge air-filled pores... more The filamentous growth form is an important strategy for soil microbes to bridge air-filled pores in unsaturated soils. In particular, fungi perform better than bacteria in soils during drought, a property that has been ascribed to the hyphal growth form of fungi. However, it is unknown if, and to what extent, filamentous bacteria may also display similar advantages over non-filamentous bacteria in soils with low hydraulic connectivity. In addition to allowing for microbial interactions and competition across connected micro-sites, water films also facilitate the motility of non-filamentous bacteria. To examine these issues, we constructed and characterized a series of quartz sand microcosms differing in matric potential and pore size distribution and, consequently, in connection of micro-habitats via water films. Our sand microcosms were used to examine the individual and competitive responses of a filamentous bacterium (Streptomyces atratus) and a motile rod-shaped bacterium (Bacillus weihenstephanensis) to differences in pore sizes and matric potential. The Bacillus strain had an initial advantage in all sand microcosms, which could be attributed to its faster growth rate. At later stages of the incubation, Streptomyces became dominant in microcosms with low connectivity (coarse pores and dry conditions). These data, combined with information on bacterial motility (expansion potential) across a range of pore-size and moisture conditions, suggest that, like their much larger fungal counterparts, filamentous bacteria also use this growth form to facilitate growth and expansion under conditions of low hydraulic conductivity. The sand microcosm system developed and used in this study allowed for precise manipulation of hydraulic properties and pore size distribution, thereby providing a useful approach for future examinations of how these properties influence the composition, diversity and function of soil-borne microbial communities.
Microbes are incredibly abundant and diverse and are key to ecosystem functioning, yet relatively... more Microbes are incredibly abundant and diverse and are key to ecosystem functioning, yet relatively little is known about the ecological and evolutionary mechanisms that shape their distributions. Bacteriophages, viral parasites that lyse their bacterial hosts, exert intense and spatially varying selection pressures on bacteria and vice versa. We measured local adaptation of bacteria and their associated phages in a centimeter-scale soil population. We first demonstrate that a large proportion of bacteria is sensitive to locally occurring phages. We then show that sympatric phages (isolated from the same 2-gram soil samples as the bacteria) are more infective than are phages from samples some distance away. This study demonstrates the importance of biotic interactions for the small-scale spatial structuring of microbial genetic diversity in soil.
Quantifying patterns of adaptive divergence between taxa is a major goal in the comparative and e... more Quantifying patterns of adaptive divergence between taxa is a major goal in the comparative and evolutionary study of prokaryote genomes. When applied appropriately, the McDonald-Kreitman (MK) test is a powerful test of selection based on the relative frequency of non-synonymous and synonymous substitutions between species compared to non-synonymous and synonymous polymorphisms within species. The webserver ODoSE (Ortholog Direction of Selection Engine) allows the calculation of a novel extension of the MK test, the Direction of Selection (DoS) statistic, as well as the calculation of a weighted-average Neutrality Index (NI) statistic for the entire core genome, allowing for systematic analysis of the evolutionary forces shaping core genome divergence in prokaryotes. ODoSE is hosted in a Galaxy environment, which makes it easy to use and amenable to customization and is freely available at www.odose.nl. Citation: Vos M, te Beek TAH, van Driel MA, Huynen MA, Eyre-Walker A, et al. (2013) ODoSE: A Webserver for Genome-Wide Calculation of Adaptive Divergence in Prokaryotes. PLoS ONE 8(5): e62447.
Background: The 16S rRNA gene is the gold standard in molecular surveys of bacterial and archaeal... more Background: The 16S rRNA gene is the gold standard in molecular surveys of bacterial and archaeal diversity, but it has the disadvantages that it is often multiple-copy, has little resolution below the species level and cannot be readily interpreted in an evolutionary framework. We compared the 16S rRNA marker with the single-copy, protein-coding rpoB marker by amplifying and sequencing both from a single soil sample. Because the higher genetic resolution of the rpoB gene prohibits its use as a universal marker, we employed consensus-degenerate primers targeting the Proteobacteria.
Background: Many soil-inhabiting bacteria are known to produce secondary metabolites that can sup... more Background: Many soil-inhabiting bacteria are known to produce secondary metabolites that can suppress microorganisms competing for the same resources. The production of antimicrobial compounds is expected to incur fitness costs for the producing bacteria. Such costs form the basis for models on the co-existence of antibiotic-producing and non-antibiotic producing strains. However, so far studies quantifying the costs of antibiotic production by bacteria are scarce. The current study reports on possible costs, for antibiotic production by Pseudomonas fluorescens Pf0-1, a soil bacterium that is induced to produce a broad-spectrum antibiotic when it is confronted with non-related bacterial competitors or supernatants of their cultures.
Soil habitats contain vast numbers of microorganisms and harbor a large portion of the planet's b... more Soil habitats contain vast numbers of microorganisms and harbor a large portion of the planet's biological diversity. Although high-throughput sequencing technologies continue to advance our appreciation of this remarkable phylogenetic and functional diversity, we still have only a rudimentary understanding of the forces that allow diverse microbial populations to coexist in soils. This conspicuous knowledge gap may be partially due the human perspective from which we tend to examine soilborne microorganisms. This review focusses on the highly heterogeneous soil matrix from the vantage point of individual bacteria. Methods describing micro-scale soil habitats and their inhabitants based on sieving, dissecting, and visualizing individual soil aggregates are discussed, as are microcosm-based experiments allowing the manipulation of key soil parameters. We identify how the spatial heterogeneity of soil could influence a number of ecological interactions promoting the evolution and maintenance of bacterial diversity.
Why should organisms cooperate with each other? Helping close relatives that are likely to share ... more Why should organisms cooperate with each other? Helping close relatives that are likely to share the same genes (kin selection) is one important explanation that is likely to apply across taxa. The production of metabolically costly extracellular iron-scavenging molecules (siderophores) by microorganisms is a cooperative behaviour because it benefits nearby conspecifics. We review experiments focusing on the production of the primary siderophore (pyoverdin) of the opportunistic bacterial pathogen, Pseudomonas aeruginosa, which test kin selection theories that seek to explain the evolution of cooperation. First, cooperation is indeed favoured when individuals interact with their close relatives and when there is competition between groups of cooperators and noncooperators, such that the benefit of cooperation can be realized. Second, the relative success of cheats and cooperators is a function of their frequencies within populations. Third, elevated mutation rates can confer a selective disadvantage under conditions when cooperation is beneficial, because high mutation rates reduce how closely bacteria are related to each other. Fourth, cooperative pyoverdin production is also shown to be favoured by kin selection in vivo (caterpillars), and results in more virulent infections. Finally, we briefly outline ongoing and future work using this experimental system.
A major challenge in microbial evolutionary ecology is to understand how fitness-related traits v... more A major challenge in microbial evolutionary ecology is to understand how fitness-related traits vary in natural populations of microorganisms at defined spatial scales and subsequently to identify the forces that maintain such variation. The Gram-negative soil bacterium Myxococcus xanthus is a model system for the study of gliding motility, which is driven by two complementary motility systems in this species and is central to its social lifestyle. We tested whether the ecological context of a centimetre-scale M. xanthus population allows the coexistence of diverse motility-related phenotypes. Swarming rates among 26 clones isolated at the centimetre scale were found to vary greatly in multiple laboratory environments. This variation appears to be motility-specific, as it is not explained by a correlated variation in intrinsic growth rate. In contrast to the common reference strain DK1622, most isolates swarmed faster on hard agar than on soft agar, highlighting the difficulty of inferring species characteristics from laboratory reference strains. These isolates also varied greatly in swarm morphology and in the effect of nutrient limitation on swarming rate. Our results show that diverse swarming phenotypes can coexist in a small-scale bacterial population.
Calculation of the Per-Codon d N /d S Ratio and Recombination Rate A model using a population-gen... more Calculation of the Per-Codon d N /d S Ratio and Recombination Rate A model using a population-genetics approximation to the coalescent [S1], as implemented in the program OmegaMap (available at www.danielwilson. me.uk), was used for calculating the d N /d S ratio (u) per codon in the pilA fragments of the nested-isolate set. This program uses reversible-jump MCMC to perform Bayesian inference on the dN/dS ratio, which allows it to vary over the length of the sequence. Recombination is explicitly modeled in this approach so that it does not obscure the phylogeny (and therefore the d N /d S ratio statistic).
As a monophyletic group, the myxobacteria are known to produce a broad spectrum of secondary meta... more As a monophyletic group, the myxobacteria are known to produce a broad spectrum of secondary metabolites. However, the degree of metabolic diversity that can be found within a single species remains unexplored. The model species Myxococcus xanthus produces several metabolites also present in other myxobacterial species, but only one compound unique to M. xanthus has been found to date. Here, we compare the metabolite profiles of 98 M. xanthus strains that originate from 78 locations worldwide and include 20 centimeter-scale isolates from one location. This screen reveals a strikingly high level of intraspecific diversity in the M. xanthus secondary metabolome. The identification of 37 nonubiquitous candidate compounds greatly exceeds the small number of secondary metabolites previously known to derive from this species. These results suggest that M. xanthus may be a promising source of future natural products and that thorough intraspecific screens of other species could reveal many new compounds of interest.
Myxococcus xanthus is a gram-negative soil bacterium best known for its remarkable life history o... more Myxococcus xanthus is a gram-negative soil bacterium best known for its remarkable life history of social swarming, social predation, and multicellular fruiting body formation. Very little is known about genetic diversity within this species or how social strategies might vary among neighboring strains at small spatial scales. To investigate the small-scale population structure of M. xanthus, 78 clones were isolated from a patch of soil (16 by 16 cm) in Tübingen, Germany. Among these isolates, 21 genotypes could be distinguished from a concatemer of three gene fragments: csgA (developmental C signal), fibA (extracellular matrix-associated zinc metalloprotease), and pilA (the pilin subunit of type IV pili). Accumulation curves showed that most of the diversity present at this scale was sampled. The pilA gene contains both conserved and highly variable regions, and two frequency-distribution tests provide evidence for balancing selection on this gene. The functional domains in the csgA gene were found to be conserved. Three instances of lateral gene transfer could be inferred from a comparison of individual gene phylogenies, but no evidence was found for linkage equilibrium, supporting the view that M. xanthus evolution is largely clonal. This study shows that M. xanthus is surrounded by a variety of distinct conspecifics in its natural soil habitat at a spatial scale at which encounters among genotypes are likely.
Cooperation is integral to much of biological life but can be threatened by selfish evolutionary ... more Cooperation is integral to much of biological life but can be threatened by selfish evolutionary strategies. Diverse cooperative traits have evolved among microbes, but particularly sophisticated forms of sociality have arisen in the myxobacteria, including group motility and multicellular fruiting body development. Myxobacterial cooperation has succeeded against socially destructive cheaters and can readily re-evolve from some socially defective genotypes. However, social harmony does not extend far. Spatially structured natural populations of the model species Myxococcus xanthus have fragmented into a large number of socially incompatible genotypes that exclude, exploit, and/or antagonize one another, including genetically similar neighbors. Here, we briefly review basic social evolution concepts as they pertain to microbes, discuss potential benefits of myxobacterial social traits, highlight recent empirical studies of social evolution in M. xanthus, and consider their implications for how myxobacterial cooperation and conflict evolve in the wild. 599 Annu. Rev. Microbiol. 2009.63:599-623. Downloaded from arjournals.annualreviews.org by Dr Michiel Vos on 10/02/09. For personal use only.
The Staphylococcus intermedius group (SIG) includes zoonotic pathogens traditionally associated w... more The Staphylococcus intermedius group (SIG) includes zoonotic pathogens traditionally associated with dog bites. We describe a simple scheme for improved detection of SIG using routine laboratory methods, report its effect on isolation rates, and use sequencing to confirm that, apart from one atypical SIG strain, most isolates are Staphylococcus pseudintermedius.
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