Chemical warfare between microbes promotes biodiversity

Antibiotic interactions that select against resistance

Multidrug combinations are increasingly important in combating the spread of antibiotic-resistance in bacterial pathogens. On a broader scale, such combinations are also important in understanding microbial ecology and evolution. Although the effects of multidrug combinations on bacterial growth have been studied extensively, relatively little is known about their impact on the differential selection between sensitive and resistant bacterial populations. Normally, the presence of a drug confers an advantage on its resistant mutants in competition with the sensitive wild-type population. Here we show, by using a direct competition assay between doxycycline-resistant and doxycycline-sensitive Escherichia coli, that this differential selection can be inverted in a hyper-antagonistic class of drug combinations. Used in such a combination, a drug can render the combined treatment selective against the drug's own resistance allele. Further, this inversion of selection seems largely insensitive to the underlying resistance mechanism and occurs, at sublethal concentrations, while maintaining inhibition of the wild type. These seemingly paradoxical results can be rationalized in terms of a simple geometric argument. Our findings demonstrate a previously unappreciated feature of the fitness landscape for the evolution of resistance and point to a trade-off between the effect of drug interactions on absolute potency and the relative competitive selection that they impose on emerging resistant populations.

Cannibalism and fratricide: mechanisms and raisons d'être

Cannibalism and fratricide refer to the killing of genetically identical cells (siblings) that was recently documented in two Gram-positive species, Bacillus subtilis and Streptococcus pneumoniae, respectively. Cannibalism occurs during the early stages of sporulation in B. subtilis, whereas fratricide occurs in S. pneumoniae during natural genetic transformation. Here, we compare and contrast these two phenomena and discuss whether these processes are fundamentally different from the more traditional 'chemical warfare' among bacteria.

Colicin biology

Colicins are proteins produced by and toxic for some strains of Escherichia coli. They are produced by strains of E. coli carrying a colicinogenic plasmid that bears the genetic determinants for colicin synthesis, immunity, and release. Insights gained into each fundamental aspect of their biology are presented: their synthesis, which is under SOS regulation; their release into the extracellular medium, which involves the colicin lysis protein; and their uptake mechanisms and modes of action. Colicins are organized into three domains, each one involved in a different step of the process of killing sensitive bacteria. The structures of some colicins are known at the atomic level and are discussed. Colicins exert their lethal action by first binding to specific receptors, which are outer membrane proteins used for the entry of specific nutrients. They are then translocated through the outer membrane and transit through the periplasm by either the Tol or the TonB system. The components of each system are known, and their implication in the functioning of the system is described. Colicins then reach their lethal target and act either by forming a voltage-dependent channel into the inner membrane or by using their endonuclease activity on DNA, rRNA, or tRNA. The mechanisms of inhibition by specific and cognate immunity proteins are presented. Finally, the use of colicins as laboratory or biotechnological tools and their mode of evolution are discussed.

Probiotic alternatives to reduce gastrointestinal infections: the poultry experience

The intestinal mucosa represents the most active defense barrier against the continuous challenge of food antigens and pathogenic microorganisms present in the intestinal lumen. Protection against harmful agents is conferred by factors such as gastric acid, peristalsis, mucus, intestinal proteolysis, and the intestinal biota. The establishment of beneficial bacterial communities and metabolites from these complex ecosystems has varying consequences for host health. This hypothesis has led to the introduction of novel therapeutic interventions based on the consumption of beneficial bacterial cultures. Mechanisms by which probiotic bacteria affect the microecology of the gastrointestinal tract are not well understood, but at least three mechanisms of action have been proposed: production/presence of antibacterial substances (e.g., bacteriocins or colicins), modulation of immune responses and specific competition for adhesion receptors to intestinal epithelium. The rapid establishment of bacterial communities has been thought to be essential for the prevention of colonization by pathogenic bacteria. Some animal models suggest that the reduction in bacterial translocation in neonatal animals could be associated with an increase in intestinal bacterial communities and bacteriocin-like inhibitory substances produced by these species. This review emphasizes the role of the intestinal microbiota in the reduction of the gastrointestinal infections and draws heavily on studies in poultry.

Bacteriocin diversity and the frequency of multiple bacteriocin production in Escherichia coli

A collection of 266 faecal isolates of Escherichia coli from humans was assayed for the production of mitomycin C-inducible bacteriocins and screened using a PCR-based method for the presence of eleven colicins and seven microcins. Eight different colicins were detected and all seven microcins. Of the strains examined, 38 % produced a bacteriocin, 24 % produced a colicin and 20 % produced a microcin. Of the 102 bacteriocin-producing strains, 42 % produced one type of bacteriocin, 41 % produced two, 16 % produced three and one strain was found to produce four different bacteriocins. Strains producing more than one bacteriocin were more likely to be members of E. coli genetic group B2 and less likely to belong to genetic groups A or D. Several of the bacteriocins were found to co-occur in a strain more often than would be expected by chance: microcins H47 and M; colicin Ia and microcin V; colicins B and M; colicins E1 and M; colicins E1 and Ia. No bacteriocins released as a consequence of cell lysis were found to co-associate more often than expected by chance. Three non-mutually exclusive hypotheses are presented that might explain the high frequency of multiple bacteriocin production in E. coli strains: (1) expanded killing range, (2) expanded receptor repertoire and (3) fitness benefits in different environments.

Diversity as a product of inter-specific interactions

We demonstrate diversification rather than optimization for highly interacting organisms in a well-mixed biological system by means of a simple model of coevolution. We find the cause to be the complex network of interactions formed, allowing species that are less well adapted to an environment to succeed, instead of the 'best' species. This diversification can be considered as the construction of many coevolutionary niches by the network of interactions between species. The model predictions are discussed in relation to experimental work on dense communities of the bacteria Escherichia coli, which may coexist with their own mutants under certain conditions. We find that diversification only occurs above a certain threshold interaction strength, below which competitive exclusion occurs.

The biology of lantibiotics from the lacticin 481 group is coming of age

Lantibiotics are antimicrobial peptides from the bacteriocin family, secreted by Gram-positive bacteria. These peptides differ from other bacteriocins by the presence of (methyl)lanthionine residues, which result from enzymatic modification of precursor peptides encoded by structural genes. Several groups of lantibiotics have been distinguished, the largest of which is the lacticin 481 group. This group consists of at least 16 members, including lacticin 481, streptococcin A-FF22, mutacin II, nukacin ISK-1, and salivaricins. We present the first review devoted to this lantibiotic group, knowledge of which has increased significantly within the last few years. After updating the group composition and defining the common properties of these lantibiotics, we highlight the most recent developments. The latter concern: transcriptional regulation of the lantibiotic genes; understanding the biosynthetic machinery, in particular the ability to perform in vitro prepeptide maturation; characterization of a novel type of immunity protein; and broad application possibilities. This group differs in many aspects from the best known lantibiotic group (nisin group), but shares properties with less-studied groups such as the mersacidin, cytolysin and lactocin S groups.

Assembly of the human intestinal microbiota

Complex microbial ecosystems occupy the skin, mucosa and alimentary tract of all mammals, including humans. Recent advances have highlighted the tremendous diversity of these microbial communities and their importance to host physiology, but questions remain about the ecological processes that establish and maintain the microbiota throughout life. The prevailing view, that the gastrointestinal microbiota of adult humans is a climax community comprised of the superior competitors for a stable set of niches, does not account for all of the experimental data. We argue here that the unique history of each community and intrinsic temporal dynamics also influence the structure of human intestinal communities.

Effect of nutrient periodicity on microbial community dynamics

When microbes are subjected to temporal changes in nutrient availability, growth rate and substrate affinity can contribute to competitive fitness and thereby affect microbial community structure. This hypothesis was tested using planktonic bacterial communities exposed to nutrient additions at 1-, 3-, 7-, or 14-day intervals. Growth rates after nutrient addition were inversely proportional to the pulse interval and declined from 0.5 h(-1) to 0.15 h(-1) as the pulse interval increased from 1 to 14 days. The dynamics of community structure were monitored by 16S rRNA gene PCR-denaturing gradient gel electrophoresis. At pulse intervals of more than 1 day, the community composition continued to change over 130 days. Although replicate systems exposed to the same pulse interval were physiologically similar, their community compositions could exhibit as much dissimilarity (Dice similarity coefficients of <0.5) as did systems operated at different intervals. Bacteria were cultivated from the systems to determine if the physiological characteristics of individual members were consistent with the measured performance of the systems. The isolates fell into three bacterial divisions, Bacteroidetes, Proteobacteria, and Actinobacteria. In agreement with community results, bacteria isolated from systems pulsed every day with nutrients had higher growth rates and ectoaminopeptidase specific activities than isolates from systems pulsed every 14 days. However, the latter isolates did not survive starvation longer than those provided with nutrients every day. The present study demonstrates the dynamic nature of microbial communities exposed to even simple and regular environmental discontinuities when a substantial pool of species that can catabolize the limiting substrate is present.

Competitive intransitivity promotes species coexistence

Using a spatially explicit cellular automaton model with local competition, we investigate the potential for varied levels of competitive intransitivity (i.e., nonhierarchical competition) to promote species coexistence. As predicted, on average, increased levels of intransitivity result in more sustained coexistence within simulated communities, although the outcome of competition also becomes increasingly unpredictable. Interestingly, even a moderate degree of intransitivity within a community can promote coexistence, in terms of both the length of time until the first competitive exclusion and the number of species remaining in the community after 500 simulated generations. These results suggest that modest levels of intransitivity in nature, such as those that are thought to be characteristic of plant communities, can contribute to coexistence and, therefore, community-scale biodiversity. We explore a potential connection between competitive intransitivity and neutral theory, whereby competitive intransitivity may represent an important mechanism for "ecological equivalence."

The influence of biotic interactions on soil biodiversity

Belowground communities usually support a much greater diversity of organisms than do corresponding aboveground ones, and while the factors that regulate their diversity are far less well understood, a growing number of recent studies have presented data relevant to understanding how these factors operate. This review considers how biotic factors influence community diversity within major groups of soil organisms across a broad spectrum of spatial scales, and addresses the mechanisms involved. At the most local scale, soil biodiversity may potentially be affected by interactions within trophic levels or by direct trophic interactions. Within the soil, larger bodied invertebrates can also influence diversity of smaller sized organisms by promoting dispersal and through modification of the soil habitat. At larger scales, individual plant species effects, vegetation composition, plant species diversity, mixing of plant litter types, and aboveground trophic interactions, all impact on soil biodiversity. Further, at the landscape scale, soil diversity also responds to vegetation change and succession. This review also considers how a conceptual understanding of the biotic drivers of soil biodiversity may assist our knowledge of key topics in community and ecosystem ecology, such as aboveground-belowground interactions, and the relationship between biodiversity and ecosystem functioning. It is concluded that an improved understanding of what drives the diversity of life in the soil, incorporated within appropriate conceptual frameworks, should significantly aid our understanding of the structure and functioning of terrestrial communities.

The coevolution of altruism and punishment: Role of the selfish punisher

Punishment is an important mechanism promoting the evolution of altruism among non-relatives. We investigate the coevolution of altruism and punitive behavior, considering four possible strategies: the altruist punisher (AP, a cooperator who punishes defectors), the altruist non-punisher (AN, a pure cooperator), the selfish punisher (SP, a defector who punishes defectors), and the selfish non-punisher (SN, a pure defector). The SP uses a paradoxical strategy as it punishes other defectors. We analyse the effects of SP and AN on the coevolution of altruism and punishment. We study both the score-dependent viability model (whereby the game's score affects survivorship only) and the score-dependent fertility model (whereby the score affects fertility only). In the viability model of a completely mixed population, SP first drives out SN, and hence it helps cooperators (AP and AN) to evolve. In contrast, in the fertility model of a completely mixed population, neither SP nor AN helps the evolution of cooperation. In both the viability and fertility models of a lattice-structured population, SP promotes the spread of AP. In contrast, AN discourages the evolution of AP. These results can be understood that punishment is a form of spite behavior, paying a cost to reduce the fitness of the opponents, and that different models give different magnitude of advantage to spite behavior.

Adaptations in bacterial catabolic enzyme activity and community structure in membrane-coupled bioreactors fed simple synthetic wastewater

Membrane-coupled bioreactors (MBRs) offer substantial benefits compared to conventional reactor designs for biological wastewater treatment. MBR treatment efficiency, however, has not been optimized because the effects of the MBR on process microbiology are poorly understood. In this study, the structure and function of the microbial communities growing in MBRs fed simple synthetic wastewater were investigated. In four starch-fed MBRs, the bacterial community substantially increased its alpha-glucosidase affinity (>1000-fold), while the leucine aminopeptidase and heptanoate esterase affinities increased slightly (<40-fold) or remained relatively constant. Concomitant to these physiological adaptations, shifts in the bacterial community structure in two of the starch-fed MBRs were detected by PCR-DGGE. Four of the bacterial populations detected by PCR-DGGE were isolated and exhibited specific growth rates in batch culture ranging from 0.009 to 0.22 h(-1). Our results suggest that bacterial communities growing under increasingly stringent nutrient limitation adapt their enzyme activities primarily for the nutrients provided, but that there is also a more subtle response not linked to the substrates included in the feed medium. Our research also demonstrates that MBRs can support relatively complex bacterial communities even on simple feed media.

Exploitative and hierarchical antagonism in a cooperative bacterium

Social organisms that cooperate with some members of their own species, such as close relatives, may fail to cooperate with other genotypes of the same species. Such noncooperation may take the form of outright antagonism or social exploitation. Myxococcus xanthus is a highly social prokaryote that cooperatively develops into spore-bearing, multicellular fruiting bodies in response to starvation. Here we have characterized the nature of social interactions among nine developmentally proficient strains of M. xanthus isolated from spatially distant locations. Strains were competed against one another in all possible pairwise combinations during starvation-induced development. In most pairings, at least one competitor exhibited strong antagonism toward its partner and a majority of mixes showed bidirectional antagonism that decreased total spore production, even to the point of driving whole populations to extinction. Differential response to mixing was the primary determinant of competitive superiority rather than the sporulation efficiencies of unmixed populations. In some competitive pairings, the dominant partner sporulated more efficiently in mixed populations than in clonal isolation. This finding represents a novel form of exploitation in bacteria carried out by socially competent genotypes and is the first documentation of social exploitation among natural bacterial isolates. Patterns of antagonistic superiority among these strains form a highly linear dominance hierarchy. At least some competition pairs construct chimeric, rather than segregated, fruiting bodies. The cooperative prokaryote M. xanthus has diverged into a large number of distinct social types that cooperate with clone-mates but exhibit intense antagonism toward distinct social types of the same species. Most lengthy migration events in nature may thus result in strong antagonism between migratory and resident populations, and this antagonism may have large effects on local population sizes and dynamics. Intense mutual antagonism appears to be more prevalent in this prokaryotic social species than has been observed in the eukaryotic social slime mold Dictyostelium discoideum, which also exhibits multicellular development. The finding of several cases of facultative social exploitation among these natural isolates suggests that such exploitation may occur frequently in nature in many prokaryotes with cooperative traits.

Experimentally competing different natural strains of the social bacterium Myxococcus xanthus reveals that some strains exploit others, with implications for the evolution of intraspecific cooperation and the generation of bacterial diversity.

Rock-scissors-paper game in a chaotic flow: The effect of dispersion on the cyclic competition of microorganisms

Laboratory experiments and numerical simulations have shown that the outcome of cyclic competition is significantly affected by the spatial distribution of the competitors. Short-range interaction and limited dispersion allows for coexistence of competing species that cannot coexist in a well-mixed environment. In order to elucidate the mechanisms that destroy species diversity we study the intermediate situation of imperfect mixing, typical in aquatic media, in a model of cyclic competition between toxin producing, sensitive and resistant phenotypes. It is found, that chaotic mixing, by changing the character of the spatial distribution, induces coherent oscillations in the populations. The magnitude of the oscillations increases with the strength of mixing, leading to the extinction of some species beyond a critical mixing rate. When mixing is non-uniform in space, coexistence can be sustained at much stronger mixing by the formation of partially isolated regions, that prevent global extinction. The heterogeneity of mixing may enable toxin producing and sensitive strains to coexist for very long time at strong mixing.

The ecology and genetics of microbial diversity

Natural communities of microbes are often diverse, a fact that is difficult to reconcile with the action of natural selection in simple, uniform environments. We suggest that this apparent paradox may be resolved by considering the origin and fate of diversity in an explicitly ecological context. Here, we review insights into the ecological and genetic causes of diversity that stem from experiments with microbial populations evolving in the defined conditions of the laboratory environment. These studies highlight the importance of environmental structure in governing the fate of diversity and shed light on the genetic mechanisms generating diversity. We conclude by emphasizing the importance of placing detailed molecular-level studies within the context of a sound ecological and evolutionary framework.

Diversity and fruiting patterns of ectomycorrhizal and saprobic fungi in an old-growth Mediterranean forest dominated by Quercus ilex L

We collected and mapped epigeous fruitbodies of both ectomycorrhizal (ECM) and saprobic fungi in an old-growth Quercus ilex L. Mediterranean forest within a permanent transect of 6400 m2 over three consecutive fruiting seasons. Out of 5382 fruitbodies, a total of 234 species were found, including 166 and 68 ECM and saprobic taxa, respectively. Both communities were mainly composed of rare species. Two genera, Russula and Cortinarius, accounted for 34.4% of ECM fruitbodies and 50% of species diversity. The three most abundant ECM species were Laccaria laccata (Scop.: Fr.) Berk. & Broome, Inocybe tigrina R. Heim, and Lactarius chrysorrheus Fr. The fruiting ECM community encompassed a few Mediterranean species and numerous broad host range temperate species. We also analysed the fruiting patterns in relation to forest structure, host composition, and natural canopy gaps. The results showed (i) a significant correlation of species richness to tree density, (ii) a richness decrease as the number of vegetation layers increases, and (iii) a preferential fruiting of some species near Q. ilex or Arbutus unedo L. Another noteworthy feature was that richness and production were greatly enhanced in canopy gaps. Selective fruiting was also observed among species. These results highlight the importance of forest structure and large woody debris for fungal conservation.Key words: ECM community, saprophytic fungi, holm oak, macromycete fruiting patterns, canopy gaps, fungal conservation.

Spatial variation in Streptomyces genetic composition and diversity in a prairie soil

Understanding how microbial genotypes are arrayed in space is crucial for identifying local factors that may influence the spatial distribution of genetic diversity. In this study we investigated variation in 16S rDNA sequences and rep-PCR fingerprints of Streptomyces stains isolated from prairie soil among three locations and four soil depths. Substantial variation in Streptomyces OTU (operational taxonomic unit) and BOX-PCR fingerprint diversity was found among locations within a limited spatial area (1 m2). Further, phylogenetic lineages at each location were distinct. However, there was little variation in genetic diversity among isolates from different soil depths and similar phylogenetic lineages were found at each depth. Some clones were found at a localized scale while other clones had a relatively widespread distribution. There was poor correspondence between 16S rDNA groupings and rep-PCR fingerprint groupings. The finding of distinct phylogenetic lineages and the variation in spatial distribution of clones suggests that selection pressures may vary over the soil landscape.

Bacteriocins, spite and virulence

There has been much interest in using social evolution theory to predict the damage to a host from parasite infection, termed parasite virulence. Most of this work has focused on how high kinship between the parasites infecting a host can select for more prudent exploitation of the host, leading to a negative relationship between virulence and parasite kinship. However, it has also been shown that if parasites can cooperate to overcome the host, then high parasite kinship within hosts can select for greater cooperation and higher growth rates, hence leading to a positive relationship between virulence and parasite kinship. We examine the impact of a spiteful behaviour, chemical (bacteriocin) warfare between microbes, on the evolution of virulence, and find a new relationship: virulence is maximized when the frequency of kin among parasites' social partners is low or high, and is minimized at intermediate values. This emphasizes how biological details can fundamentally alter the qualitative nature of theoretical predictions made by models of parasite virulence.

Interference competition and parasite virulence

Within-host competition between parasites, a consequence of infection by multiple strains, is predicted to favour rapid host exploitation and greater damage to hosts (virulence). However, the inclusion of biological variables can drastically change this relationship. For example, if competing parasite strains produce toxins that kill each other (interference competition), their growth rates and virulence may be reduced relative to single-strain infections. Bacteriocins are antimicrobial toxins produced by bacteria that target closely related strains and species, and to which the producing strain is immune. We investigated competition between bacteriocin-producing, insect-killing bacteria (Photorhabdus and Xenorhabdus) and how this competition affected virulence in caterpillars. Where one strain could kill the other, and not vice versa, the non-killing strain was competitively excluded, and insect mortality was the same as that of the killing strain alone. However, when caterpillars were multiply infected by strains that could kill each other, we did not observe competitive exclusion and their virulence was less than single-strain infections. The ubiquity and diversity of bacteriocins among pathogenic bacteria suggest mixed infections will be, on average, less virulent than single infections.

A survey of mathematical models of competition with an inhibitor

Mathematical models of the effect of inhibitors on microbial competition are surveyed. The term inhibitor is used in a broad sense and includes toxins, contaminants, allelopathic agents, etc. This includes both detoxification where the inhibitor is viewed as a pollutant and control where the inhibitor is viewed as an aid to controlling a bioreactor. The inhibitor may be supplied externally or may be created as an anti-competitor toxin. This includes plasmid-bearing, plasmid-free competition. The literature is spread across journals in different disciplines and with different notation. The survey attempts to present the mathematical models and the results of the corresponding analysis within a common framework and notation. Detailed mathematical proofs are not given but the methods of proof are indicated, references cited, and the results presented in tables. Open problems are indicated where there is a gap in the theory.

Statistical approaches for estimating actinobacterial diversity in marine sediments

Bacterial diversity in a deep-sea sediment was investigated by constructing actinobacterium-specific 16S ribosomal DNA (rDNA) clone libraries from sediment sections taken 5 to 12, 15 to 18, and 43 to 46 cm below the sea floor at a depth of 3,814 m. Clones were placed into operational taxonomic unit (OTU) groups with >/= 99% 16S rDNA sequence similarity; the cutoff value for an OTU was derived by comparing 16S rRNA homology with DNA-DNA reassociation values for members of the class Actinobacteria. Diversity statistics were used to determine how the level of dominance, species richness, and genetic diversity varied with sediment depth. The reciprocal of Simpson's index (1/D) indicated that the pattern of diversity shifted toward dominance from uniformity with increasing sediment depth. Nonparametric estimation of the species richness in the 5- to 12-, 15- to 18-, and 43- to 46-cm sediment sections revealed a trend of decreasing species number with depth, 1,406, 308, and 212 OTUs, respectively. Application of the LIBSHUFF program indicated that the 5- to 12-cm clone library was composed of OTUs significantly (P = 0.001) different from those of the 15- to 18- and 43- to 46-cm libraries. F(ST) and phylogenetic grouping of taxa (P tests) were both significant (P < 0.00001 and P < 0.001, respectively), indicating that genetic diversity decreased with sediment depth and that each sediment community harbored unique phylogenetic lineages. It was also shown that even nonconservative OTU definitions result in severe underestimation of species richness; unique phylogenetic clades detected in one OTU group suggest that OTUs do not correspond to real ecological groups sensu Palys (T. Palys, L. K. Nakamura, and F. M. Cohan, Int. J. Syst. Bacteriol. 47:1145-1156, 1997). Mechanisms responsible for diversity and their implications are discussed.

Spatial variation in frequency and intensity of antibiotic interactions among Streptomycetes from prairie soil

Antibiotic interactions are believed to be significant to microbial fitness in soil, yet little is known of the frequency, intensity, and diversity of antibiotic inhibition and resistance among indigenous microbes. To begin to address these issues, we studied the abilities of streptomycete isolates from prairie soil to inhibit growth and display resistance to antibiotics produced by a test collection of 10 streptomycete isolates. Wide variations in antibiotic inhibition and resistance for prairie isolates among three locations and four soil depths within a 1-m2 plot were revealed. Fewer than 10% of 153 prairie isolates inhibited all 10 test isolates, while more than 40% of the isolates did not inhibit any of the test isolates. No field isolate was resistant to all of the test isolates, nor was any isolate susceptible to all of the test isolates. No correlation between inhibition and resistance phenotypes was found, suggesting that inhibition and resistance are under independent selection. The significant spatial variation in the frequency and intensity of antibiotic inhibition implies that the fitness benefits of antibiotic production are not the same among locations in soil. In contrast, the consistency of resistance over space indicates that its significance to fitness across locations is stable or the costs of maintaining resistance in the absence of selection are small or nonexistent. The spatial clustering of antibiotic inhibitory activity suggests a variable matrix of selection pressures and microbial responses across the soil landscape.

Strategies of microbial cheater control

The potential benefits of cooperation in microorganisms can be undermined by genetic conflict within social groups, which can take the form of 'cheating'. For cooperation to succeed as an evolutionary strategy, the negative effects of such conflict must somehow be either prevented or mitigated. To generate an interpretive framework for future research in microbial behavioural ecology, here we outline a wide range of hypothetical mechanisms by which cheaters might be constrained.

RAPD marker and substrate utilization pattern applied to study microbial community diversity in the soil affected by agricultural chemicals

Present analyses of random amplified polymorphic DNA (RAPD) and Biolog GN substrate utilization pattern are combined to further study the diversity of microbial communities in four soils affected by agricultural chemicals. The results showed that the four soil microbial communities were apparently distinguishable in the diversity at RAPD level in terms of the richness and modified richness in the summer, which supports our previous report using the same soils in winter. A significant difference for the average well color development (AWCD) at 72 h incubation was found among the soils in winter using Biolog GN substrate utilization pattern, but this difference was not found among the soils in summer. However, Shannon-Weaver indices for microbial communities in the summer soils polluted by agricultural chemicals were significantly higher than those in winter at metabolic level; in contrast, no significant difference existed between the two seasons for microbial communities in the soil without chemical pollution. Present results suggest that the combined approach using RAPD and substrate utilization pattern could be used to effectively quantify microbial community diversity and its changes among the seasons in the soils affected by agricultural chemicals, simultaneously at molecular and physiological levels.

Killer-sensitive coexistence in metapopulations of micro-organisms

Many micro-organisms are known to produce efficient toxic substances against conspecifics and closely related species. The widespread coexistence of killer (toxin producer) and sensitive (non-producer) strains is a puzzle calling for a theoretical explanation. Based on stochastic cellular automaton simulations and the corresponding semi-analytical configuration-field approximation models, we suggest that metapopulation dynamics offers a plausible rationale for the maintenance of polymorphism in killer-sensitive systems. A slight trade-off between toxin production and population growth rate is sufficient to maintain the regional coexistence of toxic and sensitive strains, if toxic killing is a local phenomenon restricted to small habitat patches and local populations regularly go extinct and are renewed via recolonizations from neighbouring patches. Pattern formation on the regional scale does not play a decisive part in this mechanism, but the local manner of interactions is essential.

A phylogenetic approach to assessing the targets of microbial warfare

Bacteriocins are the most abundant and diverse defense systems in bacteria. As a result of the specific mechanisms of bacteriocin recognition and translocation into the target cell it is assumed that these toxins mediate intra-specific or population-level interactions. However, no published studies specifically address this question. We present here a survey of bacteriocin production in a collection of enteric bacteria isolated from wild mammals in Australia. A subset of the bacteriocin-producing strains was assayed for the ability to kill a broad range of enteric bacteria from the same bacterial collection. A novel method of estimating killing breadth was developed and used to compare the surveyed bacteriocins in terms of the phylogenetic range over which they kill. The most striking result is that although bacteriocin-producers kill members of their own species most frequently, some kill phylogenetically distant taxa more frequently than they kill closer relatives. This study calls into question the role these toxins play in natural populations. A significant number of bacteriocins are highly effective in killing inter-specific strains and thus bacteriocins may serve to mediate bacterial community interactions.

Pathogen self-defense: mechanisms to counteract microbial antagonism,

Natural and agricultural ecosystems harbor a wide variety of microorganisms that play an integral role in plant health, crop productivity, and preservation of multiple ecosystem functions. Interactions within and among microbial communities are numerous and range from synergistic and mutualistic to antagonistic and parasitic. Antagonistic and parasitic interactions have been exploited in the area of biological control of plant pathogenic microorganisms. To date, biocontrol is typically viewed from the perspective of how antagonists affect pathogens. This review examines the other face of this interaction: how plant pathogens respond to antagonists and how this can affect the efficacy of biocontrol. Just as microbial antagonists utilize a diverse arsenal of mechanisms to dominate interactions with pathogens, pathogens have surprisingly diverse responses to counteract antagonism. These responses include detoxification, repression of biosynthetic genes involved in biocontrol, active efflux of antibiotics, and antibiotic resistance. Understanding pathogen self-defense mechanisms for coping with antagonist assault provides a novel approach to improving the durability of biologically based disease control strategies and has implications for the deployment of transgenes (microorganisms or plants).

Bacteriocins: evolution, ecology, and application

Microbes produce an extraordinary array of microbial defense systems. These include classical antibiotics, metabolic by-products, lytic agents, numerous types of protein exotoxins, and bacteriocins. The abundance and diversity of this potent arsenal of weapons are clear. Less clear are their evolutionary origins and the role they play in mediating microbial interactions. The goal of this review is to explore what we know about the evolution and ecology of the most abundant and diverse family of microbial defense systems: the bacteriocins. We summarize current knowledge of how such extraordinary protein diversity arose and is maintained in microbial populations and what role these toxins play in mediating microbial population-level and community-level dynamics. In the latter half of this review we focus on the potential role bacteriocins may play in addressing human health concerns and the current role they serve in food preservation.

Regulation of antibiotic production in root-colonizing Peudomonas spp. and relevance for biological control of plant disease

Certain strains of fluorescent pseudomonads are important biological components of agricultural soils that are suppressive to diseases caused by pathogenic fungi on crop plants. The biocontrol abilities of such strains depend essentially on aggressive root colonization, induction of systemic resistance in the plant, and the production of diffusible or volatile antifungal antibiotics. Evidence that these compounds are produced in situ is based on their chemical extraction from the rhizosphere and on the expression of antibiotic biosynthetic genes in the producer strains colonizing plant roots. Well-characterized antibiotics with biocontrol properties include phenazines, 2,4-diacetylphloroglucinol, pyoluteorin, pyrrolnitrin, lipopeptides, and hydrogen cyanide. In vitro, optimal production of these compounds occurs at high cell densities and during conditions of restricted growth, involving (i) a number of transcriptional regulators, which are mostly pathway-specific, and (ii) the GacS/GacA two-component system, which globally exerts a positive effect on the production of extracellular metabolites at a posttranscriptional level. Small untranslated RNAs have important roles in the GacS/GacA signal transduction pathway. One challenge in future biocontrol research involves development of new strategies to overcome the broad toxicity and lack of antifungal specificity displayed by most biocontrol antibiotics studied so far.

Long-term experimental evolution in Escherichia coli. XI. Rejection of non-transitive interactions as cause of declining rate of adaptation

BACKGROUND

Experimental populations of Escherichia coli have evolved for 20,000 generations in a uniform environment. Their rate of improvement, as measured in competitions with the ancestor in that environment, has declined substantially over this period. This deceleration has been interpreted as the bacteria approaching a peak or plateau in a fitness landscape. Alternatively, this deceleration might be caused by non-transitive competitive interactions, in particular such that the measured advantage of later genotypes relative to earlier ones would be greater if they competed directly.

RESULTS

To distinguish these two hypotheses, we performed a large set of competitions using one of the evolved lines. Twenty-one samples obtained at 1,000-generation intervals each competed against five genetically marked clones isolated at 5,000-generation intervals, with three-fold replication. The pattern of relative fitness values for these 315 pairwise competitions was compared with expectations under transitive and non-transitive models, the latter structured to produce the observed deceleration in fitness relative to the ancestor. In general, the relative fitness of later and earlier generations measured by direct competition agrees well with the fitness inferred from separately competing each against the ancestor. These data thus support the transitive model.

CONCLUSION

Non-transitive competitive interactions were not a major feature of evolution in this population. Instead, the pronounced deceleration in its rate of fitness improvement indicates that the population early on incorporated most of those mutations that provided the greatest gains, and subsequently relied on beneficial mutations that were fewer in number, smaller in effect, or both.

Local dispersal promotes biodiversity in a real-life game of rock-paper-scissors

One of the central aims of ecology is to identify mechanisms that maintain biodiversity. Numerous theoretical models have shown that competing species can coexist if ecological processes such as dispersal, movement, and interaction occur over small spatial scales. In particular, this may be the case for non-transitive communities, that is, those without strict competitive hierarchies. The classic non-transitive system involves a community of three competing species satisfying a relationship similar to the children's game rock-paper-scissors, where rock crushes scissors, scissors cuts paper, and paper covers rock. Such relationships have been demonstrated in several natural systems. Some models predict that local interaction and dispersal are sufficient to ensure coexistence of all three species in such a community, whereas diversity is lost when ecological processes occur over larger scales. Here, we test these predictions empirically using a non-transitive model community containing three populations of Escherichia coli. We find that diversity is rapidly lost in our experimental community when dispersal and interaction occur over relatively large spatial scales, whereas all populations coexist when ecological processes are localized.

Bacteriocin diversity: ecological and evolutionary perspectives

The bacteriocin family is the most abundant and diverse group of bacterial defense systems. Bacteriocins range from the well-studied narrow spectrum, high molecular weight colicins produced by Escherichia coli and the short polypeptide lantibiotics of lactic acid bacteria to the relatively unknown halocins produced almost universally by the haolobacteria. The abundance and diversity of this potent arsenal of weapons is clear. Less clear is their evolutionary origins and the role they play in mediating microbial interactions. The goal of this review is to explore what we know about the evolution and ecology of the best-characterized family of bacteriocins, the colicins. We summarize current knowledge of how such extraordinary protein diversity arose and is maintained in microbial populations and what role these toxins play in mediating microbial population-level and community-level dynamics.