Quantifying nonvertical inheritance in the evolution of Legionella pneumophila

The exchange of genetic material among bacterial strains and species is recognized as an important factor determining their evolutionary, population genetic, and epidemiological features. We present a detailed analysis of nonvertical inheritance in Legionella pneumophila, a human pathogen and facultative intracellular parasite of amoebas. We have analyzed the exchange of L. pneumophila genetic material with other bacteria at three different levels: population genetics, population genomics, and phylogenomics. At the population genetics level, we have analyzed 89 clinical and environmental isolates after sequencing six coding loci and three intergenic regions for a total of 3,923 bp. In the population genomics analysis, we have studied the roles of recombination and mutation in the common portion of the genome sequence of four L. pneumophila strains. In the phylogenomic analysis, we have studied the phylogenetic origin of 1,700 genes in the L. pneumophila pangenome. For this, we have considered 12 possible phylogenetic alternatives, derived from a reference tree obtained from 104 genes from 41 species, which have been tested under a rigorous statistical framework. The results obtained agree in assigning an important role to nonvertical inheritance in shaping the composition of the L. pneumophila genome and of the genetic variation in its populations. We have found a negative correlation between phylogenetic distance and likelihood of horizontal gene transfer. Phylogenetic proximity and increased chances resulting from sharing the ecological niche provided by the amoeba host have likely had a major influence on the rate of gene exchange in Legionella.     

FINE-SCALE GENETIC AND PHENOTYPIC STRUCTURE IN NATURAL POPULATIONS OF BACILLUS SUBTILIS AND BACILLUS LICHENIFORMIS: IMPLICATIONS FOR BACTERIAL EVOLUTION AND SPECIATION

The genetic and phenotypic structure of sympatric populations of wild bacteria traditionally identified as Bacillus subtilis and B. licheniformis was analyzed. Small soil samples were taken from a single, tiny site in the Sonoran Desert of Arizona, USA, to provide a true population analysis, in contrast to many analyses of genetic structure using bacterial strain collections of widely heterogeneous origin. Genetic analyses of isolates used multilocus enzyme electrophoresis, mismatches in restriction fragment length polymorphism, and variants from Southern hybridization with B. subtilis DNA probes. Phenotypic analyses of isolates used the API test system for detection of growth and acid production on specific carbon sources. The two species were distinct both phenotypically and genetically, despite their known potential for genetic exchange in laboratory experiments. Genic and genotypic diversity were high in both species, and only 16% of observed allozyme variants might possibly be common to both species. Hence, there is probably modest genetic exchange, if any, between the species in nature. Clear hierarchies of population-genetic structure were found for both species. Different types of genetic data yield concordant population structures for B. subtilis. For both species, two-locus and multilocus statistical analyses of linkage demonstrated modest to strong disequilibrium at the species level but truly panmictic subunits within each species. The evidence for extensive genetic recombination within these fine-scale subdivisions is unequivocal, indicating that the sexuality of these bacteria can be well expressed in nature. The relation of these results to processes of bacterial evolution and speciation is discussed.     

Bacterial population genetics

Bacterial population genetics is the study of natural bacterial genetic diversity arising from evolutionary processes. The roles of molecular mistakes, restriction–modification, plasmids and gene transfer in bacteria are also important components of population genetics. These aspects are of considerable scientific importance from a fundamental perspective, because of the short generation times of bacteria, their microscopic cell size, the large population sizes bacteria can achieve and their different mechanisms of gene transfer.     

Bacterial population genetics

Bacterial population genetics is the study of natural bacterial genetic diversity arising from evolutionary processes. The roles of molecular mistakes, restriction–modification, plasmids and gene transfer in bacteria are also important components of population genetics. These aspects are of considerable scientific importance from a fundamental perspective, because of the short generation times of bacteria, their microscopic cell size, the large population sizes bacteria can achieve and their different mechanisms of gene transfer.     

The obesity and inflammatory marker haptoglobin attracts monocytes via interaction with chemokine (C-C motif) receptor 2 (CCR2)

Background

Phylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction.

Results

Bayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia.

Conclusion

We describe an Australian origin for B. pseudomallei, characterized by a single introduction event into Southeast Asia during a recent glacial period, and variable levels of lateral gene transfer within populations. These patterns provide insights into mechanisms of genetic diversification in B. pseudomallei and its closest relatives, and provide a framework for integrating the traditionally separate fields of population genetics and phylogenetics for other bacterial species with high levels of lateral gene transfer.     

Do bacteria have sex?

Do bacteria have genes for genetic exchange? The idea that the bacterial processes that cause genetic exchange exist because of natural selection for this process is shared by almost all microbiologists and population geneticists. However, this assumption has been perpetuated by generations of biology, microbiology and genetics textbooks without ever being critically examined.     

Low species barriers in halophilic archaea and the formation of recombinant hybrids

Speciation of sexually reproducing organisms requires reproductive barriers. Prokaryotes reproduce asexually but?often exchange DNA by lateral gene transfer mechanisms and recombination [1], yet distinct lineages are still observed. Thus, barriers to gene flow such as geographic isolation, genetic incompatibility or a physiological inability to transfer DNA represent potential underlying mechanisms behind preferred exchange groups observed in prokaryotes [2-6]. In Bacteria, experimental evidence showed that sequence divergence impedes homologous recombination between bacterial species [7-11]. Here we study interspecies gene exchange in halophilic archaea that possess a parasexual mechanism of genetic exchange that is functional between species [12, 13]. In this process, cells fuse forming a diploid state containing the full genetic repertoire of both parental cells, which facilitates genetic exchange and recombination. Later, cells separate, occasionally resulting in hybrids of the parental strains [14]. We show high recombination frequencies between Haloferax volcanii and Haloferax mediterranei, two species that have an average nucleotide sequence identity of 86.6%. Whole genome sequencing of Haloferax interspecies hybrids revealed the exchange of chromosomal fragments ranging from 310Kb to 530Kb. These results show that recombination barriers may be more permissive in halophilic archaea than they are in bacteria.     

Periodic Selection, Infectious Gene Exchange and the Genetic Structure of E. COLI Populations

As a consequence of sequential replacements by clones of higher fitness (periodic selection), bacterial populations would be continually purged of genetic variability, and the fate of selectively neutral alleles in very large populations of bacteria would be similar to that in demes of sexually reproducing organisms with small genetically effective population sizes. The significance of periodic selection in reducing genetic variability in these clonally reproducing species is dependent on the amount of genetic exchange between clones (recombination). In an effort to determine the relationship between the rates of periodic selection, recombination and the genetically effective sizes of bacterial populations, a model for periodic selection and infectious gene exchange has been developed and its properties analyzed. It shows that, for a given periodic selection regime, genetically effective population size increases exponentially with the rate of recombination.—With the parameters of this model in the range anticipated for natural populations of E. coli, the purging effects of periodic selection on genetic variability are significant; individual populations or lineages of this bacterial species would have very small genetically effective population sizes.—Based on this result, some other a priori considerations and a review of the results of epidemiological and genetic variability studies, it is postulated that E. coli is composed of a relatively limited number of geographically widespread and genetically nearly isolated and monomorphic lineages. The implications of these considerations of the genetic structure of E. coli populations of the interpretation of protein variation and the neutral gene hypothesis are discussed.     

Population genomics: diversity and virulence in the Neisseria

Advances in high-throughput nucleotide sequencing and bioinformatics make the study of genomes at the population level feasible. Preliminary population genomic studies have explored the relationships among three closely related bacteria, Neisseria meningitidis, Neisseria gonorrhoeae and Neisseria lactamica, which exhibit very different phenotypes with respect to human colonisation. The data obtained have been especially valuable in the establishing of the role of horizontal genetic exchange in bacterial speciation and shaping population structure. In the meningococcus, they have been used to define invasive genetic types, search for virulence factors and potential vaccine components and investigate the effects of vaccines on population structure. These are generic approaches and their application to the Neisseria provides a foretaste for their application to the wider bacterial world.     

Genetic differentiation between sympatric populations of Bacillus cereus and Bacillus thuringiensis

Little is known about genetic exchanges in natural populations of bacteria of the spore-forming Bacillus cereus group, because no population genetics studies have been performed with local sympatric populations. We isolated strains of Bacillus thuringiensis and B. cereus from small samples of soil collected at the same time from two separate geographical sites, one within the forest and the other at the edge of the forest. A total of 100 B. cereus and 98 B. thuringiensis strains were isolated and characterized by electrophoresis to determine allelic composition at nine enzymatic loci. We observed genetic differentiation between populations of B. cereus and B. thuringiensis. Populations of a given Bacillus species--B. thuringiensis or B. cereus--were genetically more similar to each other than to populations of the other Bacillus species. Hemolytic activity provided further evidence of this genetic divergence, which remained evident even if putative clones were removed from the data set. Our results suggest that the rate of gene flow was higher between strains of the same species, but that exchanges between B. cereus and B. thuringiensis were nonetheless possible. Linkage disequilibrium analysis revealed sufficient recombination for B. cereus populations to be considered panmictic units. In B. thuringiensis, the balance between clonal proliferation and recombination seemed to depend on location. Overall, our data indicate that it is not important for risk assessment purposes to determine whether B. cereus and B. thuringiensis belong to a single or two species. Assessment of the biosafety of pest control based on B. thuringiensis requires evaluation of the extent of genetic exchange between strains in realistic natural conditions.     

Population fragmentation leads to spatial and temporal genetic structure in the endangered Spanish imperial eagle

The fragmentation of a population may have important consequences for population genetic diversity and structure due to the effects of genetic drift and reduced gene flow. We studied the genetic consequences of the fragmentation of the Spanish imperial eagle (Aquila adalberti) population into small patches through a temporal analysis. Thirty‐four museum individuals representing the population predating the fragmentation were analysed for a 345‐bp segment of the mitochondrial control region and a set of 10 nuclear microsatellite loci. Data from a previous study on the current population (N = 79) were re‐analysed for this subset of 10 microsatellite markers and results compared to those obtained from the historical sample. Three shared mitochondrial haplotypes were found in both populations, although fluctuations in haplotype frequencies and the occurrence of a fourth haplotype in the historical population resulted in lower current levels of haplotype and nucleotide diversity. However, microsatellite markers revealed undiminished levels of nuclear diversity. No evidence for genetic structure was observed for the historical Spanish imperial eagle population, suggesting that the current pattern of structure is the direct consequence of population fragmentation. Temporal fluctuations in mitochondrial and microsatellite allelic frequencies were found between the historical and the current population as well as for each pairwise comparison between historical and current Centro and historical and current Parque Nacional de Doñana nuclei. Our results indicate an ancestral panmictic situation for the species that management policies should aim to restore. A historical analysis like the one taken here provides the baseline upon which the relative role of recent drift in shaping current genetic patterns in endangered species can be evaluated and this knowledge is used to guide conservation actions.     

QUORUM SENSING AND GROUP SELECTION

Bacteria respond to cell density by expressing genes whose products are beneficial to the population as a whole. This response is brought about through the release into the medium of signaling molecules of the class N-acyl homoserine lactones, the concentration of which determines the level of gene expression. This form of communication between cells has been termed “quorum sensing,” and has been found to operate in the control of many functions in a variety of gram-negative bacteria. As with all signaling between individuals, if fitness costs are associated with the release of and response to the signal, the inclusive fitness of alleles responsible for the phenomenon depends upon genetic relatedness between signaler and responder. The situation is considered in explicit models for bacterial population genetics, in which the critical parameter determining the success of quorum sensing is the mean number of cells founding a population sharing a patch of resource. It is found that extensive polymorphism for the presence or absence of quorum sensing is expected for a wide range of parameter space. If local communities of bacteria contain diverse species, community stability may be the consequence of these interactions rather than polymorphism.     

Reduction of bacterial genome size and expansion resulting from obligate intracellular lifestyle and adaptation to soil habitat.

Prokaryotic organisms are exposed in the course of evolution to various impacts, resulting often in drastic changes of their genome size. Depending on circumstances, the same lineage may diverge into species having substantially reduced genomes, or such whose genomes have undergone considerable enlargement. Genome reduction is a consequence of obligate intracellular lifestyle rendering numerous genes expendable. Another consequence of intracellular lifestyle is reduction of effective population size and limited possibility of gene acquirement via lateral transfer. This causes a state of relaxed selection resulting in accumulation of mildly deleterious mutations that can not be corrected by recombination with the wild type copy. Thus, gene loss is usually irreversible. Additionally, constant environment of the eukaryotic cell renders that some bacterial genes involved in DNA repair are expandable. The loss of these genes is a probable cause of mutational bias resulting in a high A+T content. While causes of genome reduction are rather indisputable, those resulting in genome expansion seem to be less obvious. Presumably, the genome enlargement is an indirect consequence of adaptation to changing environmental conditions and requires the acquisition and integration of numerous genes. It seems that the need for a great number of capabilities is common among soil bacteria irrespective of their phylogenetic relationship. However, this would not be possible if soil bacteria lacked indigenous abilities to exchange and accumulate genetic information. The latter are considerably facilitated when housekeeping genes are physically separated from adaptive loci which are useful only in certain circumstances.     

Simulating natural selection in landscape genetics

Linking landscape effects to key evolutionary processes through individual organism movement and natural selection is essential to provide a foundation for evolutionary landscape genetics. Of particular importance is determining how spatially-explicit, individual-based models differ from classic population genetics and evolutionary ecology models based on ideal panmictic populations in an allopatric setting in their predictions of population structure and frequency of fixation of adaptive alleles. We explore initial applications of a spatially-explicit, individual-based evolutionary landscape genetics program that incorporates all factors--mutation, gene flow, genetic drift and selection--that affect the frequency of an allele in a population. We incorporate natural selection by imposing differential survival rates defined by local relative fitness values on a landscape. Selection coefficients thus can vary not only for genotypes, but also in space as functions of local environmental variability. This simulator enables coupling of gene flow (governed by resistance surfaces), with natural selection (governed by selection surfaces). We validate the individual-based simulations under Wright-Fisher assumptions. We show that under isolation-by-distance processes, there are deviations in the rate of change and equilibrium values of allele frequency. The program provides a valuable tool (cdpop v1.0; http://cel.dbs.umt.edu/software/CDPOP/) for the study of evolutionary landscape genetics that allows explicit evaluation of the interactions between gene flow and selection in complex landscapes.     

A Global Population Genetic Study of Pantala flavescens

Among terrestrial arthropods, the dragonfly species Pantala flavescens is remarkable due to their nearly global distribution and extensive migratory ranges; the largest of any known insect. Capable of migrating across oceans, the potential for high rates of gene flow among geographically distant populations is significant. It has been hypothesized that P. flavescens may be a global panmictic population but no sufficient genetic evidence has been collected thus far. Through a population genetic analysis of P. flavescens samples from North America, South America, and Asia, the current study aimed to examine the extent at which gene flow is occurring on a global scale and discusses the implications of the genetic patterns we uncovered on population structure and genetic diversity of the species. This was accomplished using PCR-amplified cytochrome oxidase one (CO1) mitochondrial DNA data to reconstruct phylogenetic trees, a haplotype network, and perform molecular variance analyses. Our results suggested high rates of gene flow are occurring among all included geographic regions; providing the first significant evidence that Pantala flavescens should be considered a global panmictic population.     

Enterococcal biofilm—A nidus for antibiotic resistance transfer?

Enterococci, which are on the WHO list of priority pathogens, are commonly encountered in hospital acquired infection and are becoming increasing significant due to the development of strains resistant to multiple antibiotics. Enterococci are also important microorganisms in the environment, and their presence is frequently used as an indicator of faecal pollution. Their success is related to their ability to survive within a broad range of habitats and the ease by which they acquire mobile genetic elements, including plasmids, from other bacteria. The enterococci are frequently present within a bacterial biofilm, which provides stability and protection to the bacterial population along with an opportunity for a variety of bacterial interactions. Enterococci can accept extrachromosomal DNA both from within its own species and from other bacterial species, and this is enhanced by the proximity of the donor and recipient strains. It is this exchange of genetic material that makes the role of biofilms such an important aspect of the success of enterococci. There remain many questions regarding the most suitable model systems to study enterococci in biofilms and regarding the transfer of genetic material including antibiotic resistance in these biofilms. This review focuses on some important aspects of biofilm in the context of horizontal gene transfer (HGT) in enterococci.     

Dynamics of Horizontal Gene Transfer and the Ecological Risk Assessment of Genetically Engineered Organisms

The extensive published discussion of potential ecological impacts of introduced genetic sequences and genetically engineered organisms has lacked a quantified delineation of the critical questions for the estimation of risk. Ultimately, the ecological risk assessment of introduced gene sequences is the application of evolution, population genetics, and ecology to risk estimation and decision making. This paper provides a framework for the estimation of risk due to introduced sequences in bacteria, and the principles should also hold for many diploid species. Horizontal genetic exchange poses new challenges for ecological risk assessment. Plasmid transfer can occur without any impacts, although the sequence can become ubiquitous in the population. Conversely, the introduction of a plasmid can change the dynamics of the host population, potentially altering the population minimum and maximum characteristics of its dynamics. Because of genetic exchange, new genetic information is unlikely to be constrained among one type of prokaryote. An example of the use of the model is given using genetic exchange data from a series of published soil microcosm experiments. The model demonstrates the increase in plasmid frequency when using experimentally derived conjugation frequencies. Application of these results to ongoing discussion of the risks of genetically engineered organisms is presented. Particular attention is paid to the transfer of genetic material and the resultant changes in host population dynamics.     

Analyses of Nuclear ldhA Gene and mtDNA Control Region Sequences of Atlantic Northern Bluefin Tuna Populations

There has been considerable debate about whether the Atlantic northern bluefin tuna exist as a single panmictic unit. We have addressed this issue by examining both mitochondrial DNA control region nucleotide sequences and nuclear gene ldhA allele frequencies in replicate size or year class samples of northern bluefin tuna from the Mediterranean Sea and the northwestern Atlantic Ocean. Pairwise comparisons of multiple year class samples from the 2 regions provided no evidence for population subdivision. Similarly, analyses of molecular variance of both mitochondrial and ldhA data revealed no significant differences among or between samples from the 2 regions. These results demonstrate the importance of analyzing multiple year classes and large sample sizes to obtain accurate estimates when using allele frequencies to characterize a population. It is important to note that the absence of genetic evidence for population substructure does not unilaterally constitute evidence of a single panmictic population, as genetic differentiation can be prevented by large population sizes and by migration.     

Population genetic structure and history of a generalist parasite infecting multiple sympatric host species

Host specificity is predicted to shape patterns of parasite gene flow between host species; specialist parasites should have low gene flow between host species, while generalists are predicted to have high gene flow between species. However, even for generalist parasites external forces, including ecological differences between host species may sometimes intervene to limit gene flow and create genetic structure. To investigate the potential for cryptic parasite genetic structure to arise under such circumstances, we examined the population genetic structure and history of the generalist nematode, Trichostrongylus axei, infecting six sympatric wild ungulate species in North America. Using genotypes for 186 T. axei larvae at two mitochondrial genes, cox1 and nad4, we found that T. axei was completely panmictic across host species, with 0% of genetic variation structured between host species and 97% within individual hosts. In addition, T. axei showed no evidence of recent genetic bottlenecks, had high nucleotide diversities (above 2%), and an effective population size estimated to be in the tens of millions. Our result that T. axei maintains high rates of gene flow between multiple sympatric host species adds to a growing body of information on trichostrongylid population genetic structure in different ecological contexts. Furthermore, the high rates of gene flow, coupled with high levels of genetic diversity and large effective population size which we observed in T. axei, point to a potentially broad capacity for rapid evolutionary change in this parasite.