Contribution Of Horizontal Gene Transfer Research Articles

Unraveling the genetic diversity and evolution of Arbuscular Mycorrhizal Fungi (AMF)

The analysis of genetic differences among arbuscular mycorrhizal fungi (AMF) species has shed light on the genetic diversity and evolution of these fascinating organisms. AMF are essential constituents of land ecosystems because of their mutualistic symbiotic associations with plant roots. Their capability to amplify nutrient absorption, enhance water assimilation, and stimulate overall plant development plays a pivotal function in sustaining thriving ecosystems. By extensively examining the genomes of various AMF classifications, researchers have uncovered their evolutionary connections and gained understanding of the impact of horizontal gene transfer (HGT) on their genetic makeup. This knowledge has not only upgraded our comprehension of the evolutionary past of AMF but has also furnished valuable insights into the mechanisms that govern the symbiotic interactions between fungi and plants. In future studies on AMF genome variance, it is crucial to prioritize functional characterization, understand co-evolutionary dynamics with host plants, uncover mechanisms and implications of HGT, and integrate metagenomic approaches. By identifying the specific genes and genetic variations that contribute to AMF's ability to form mutualistic associations with plants, scientists can gain insights into the underlying mechanisms of this important ecological relationship. Furthermore, through the analysis of genetic divergence in both AMF and their host plants, researchers can elucidate the co-evolutionary dynamics that have shaped their mutualistic symbiosis. Equally, understanding the contribution of horizontal gene transfer (HGT) to AMF genetic diversity can provide insights into the evolutionary history and adaptive abilities of these fungi. Ultimately, the incorporation of metagenomic techniques into future studies on AMF genetic diversity will facilitate a broader understanding of the microorganism populations associated with these fungi. By focusing on these domains, it is possible to advance our understanding of AMF biology and unlock novel opportunities for innovative applications in agriculture and ecosystem management.

Antidepressants promote the spread of antibiotic resistance via horizontally conjugative gene transfer.

Antibiotic resistance is a global concern threatening public health. Horizontal gene transfer (HGT) between bacterial species contributes greatly to the dissemination of antibiotic resistance. Conjugation is one of the major HGT pathways responsible for the spread of antibiotic resistance genes (ARGs). Antidepressant drugs are commonly prescribed antipsychotics for major depressive disorders and are frequently detected in aquatic environments. However, little is known about how antidepressants stress bacteria and whether such effect can promote conjugation. Here, we report that commonly prescribed antidepressants, sertraline, duloxetine, fluoxetine, and bupropion, can promote the conjugative transfer of plasmid-borne multidrug resistance genes carried by environmentally and clinically relevant plasmids. Noteworthy, the transfer of plasmids across bacterial genera is significantly enhanced by antidepressants at clinically relevant concentrations. We also reveal the underlying mechanisms of enhanced conjugative transfer by employing flow cytometric analysis, genome-wide RNA sequencing and proteomic analysis. Antidepressants induce the production of reactive oxygen species and the SOS response, increase cell membrane permeability, and upregulate the expression of conjugation relevant genes. Given the contribution of HGT in the dissemination of ARGs, our findings highlight the importance of prudent prescription of antidepressants and to the potential connection between antidepressants and increasing antibiotic resistance.

Helicobacter cinaedi is a human-adapted lineage in the Helicobacter cinaedi/canicola/'magdeburgensis' complex.

Helicobacter cinaedi is an enterohepatic Helicobacter that causes bacteremia and other diseases in humans. While H. cinaedi -like strains are isolated from animals, including dog isolates belonging to a recently proposed H. canicola , little is known about the genetic differences between H. cinaedi and these animal isolates. Here, we sequenced 43 H. cinaedi- or H. canicola -like strains isolated from humans, hamsters, rats and dogs and collected 81 genome sequences of H. cinaedi , H. canicola and other enterohepatic Helicobacter strains from public databases. Genomic comparison of these strains identified four distinct clades (clades I–IV) in H. cinaedi/canicola/‘magderbugensis’ (HCCM) complex. Among these, clade I corresponds to H. cinaedi sensu stricto and represents a human-adapted lineage in the complex. We identified several genomic features unique to clade I. They include the accumulation of antimicrobial resistance-related mutations that reflects the human association of clade I and the larger genome size and the presence of a CRISPR-Cas system and multiple toxin-antitoxin and restriction-modification systems, both of which indicate the contribution of horizontal gene transfer to the evolution of clade I. In addition, nearly all clade I strains but only a few strains belonging to one minor clade contained a highly variable genomic region encoding a type VI secretion system (T6SS), which could play important roles in gut colonization by killing competitors or inhibiting their growth. We also developed a method to systematically search for H. cinaedi sequences in large metagenome data sets based on the results of genome comparison. Using this method, we successfully identified multiple HCCM complex-containing human faecal metagenome samples and obtained the sequence information covering almost the entire genome of each strain. Importantly, all were clade I strains, supporting our conclusion that H. cinaedi sensu stricto is a human-adapted lineage in the HCCM complex.

Salmonella in Swine: Prevalence, Multidrug Resistance, and Vaccination Strategies.

An estimated 1.3 million Salmonella infections and 420 deaths occur annually in the United States, with an estimated economic burden of $3.7 billion. More than 50% of US swine operations test positive for Salmonella according to the National Animal Health Monitoring System, and 20% of Salmonella from swine are multidrug resistant (resistant to ≥3 antimicrobial classes) as reported by the National Antimicrobial Resistance Monitoring System. This review on Salmonella in swine addresses the current status of these topics by discussing antimicrobial resistance and metal tolerance in Salmonella and the contribution of horizontal gene transfer. A major challenge in controlling Salmonella is that Salmonella is a foodborne pathogen in humans but is often a commensal in food animals and thereby establishes an asymptomatic reservoir state in such animals, including swine. As food animal production systems continue to expand and antimicrobial usage becomes more limited, the need for Salmonella interventions has intensified. A promising mitigation strategy is vaccination against Salmonella in swine to limit animal, environmental, and food contamination.

High-Throughput Single-Cell Technology Reveals the Contribution of Horizontal Gene Transfer to Typical Antibiotic Resistance Gene Dissemination in Wastewater Treatment Plants.

The spread of antibiotic resistance genes (ARGs) has gained much attention worldwide, while the contribution of vertical gene transfer (VGT) and horizontal gene transfer (HGT) is still elusive. Here, we improved an emerging high-throughput single-cell-based technology, emulsion, paired isolation, and concatenation polymerase chain reaction (epicPCR), by lengthening the sequence of ARG in the fused ARG-16S rRNA fragments to cover the variance of both ARG and its hosts. The improved epicPCR was applied to track the hosts of a widely detected ARG, sul1 gene, in five urban wastewater treatment plants (UWTPs) during two seasons. The sul1 host bacteria were highly diverse and mostly classified as Proteobacteria and Bacteroidetes. Clear seasonal divergence of α-diversity and interaction networks were present in the host community. The consensus phylogenetic trees of the sul1 gene and their host demonstrated incorrespondence on the whole and regularity on abundant groups, suggesting the important role of both HGT and VGT, respectively. The relative importance of these two ways was further measured; HGT (54%) generally played an equal or even more important role as VGT (46%) in UWTPs. The application of the improved epicPCR technology provides a feasible approach to quantify the relative contributions of VGT and HGT in environmental dissemination of ARGs.

Functional diversity of microbial communities in inactive seafloor sulfide deposits.

The seafloor sulfide structures of inactive vents are known to host abundant and diverse microorganisms potentially supported by mineralogy of sulfides. However, little is known about the diversity and distribution of microbial functions. Here, we used genome-resolved metagenomics to predict microbial metabolic functions and the contribution of horizontal gene transfer to the functionality of microorganisms inhabiting several hydrothermally inactive seafloor deposits among globally distributed deep-sea vent fields. Despite of geographically distant vent fields, similar microbial community patterns were observed with the dominance of Gammaproteobacteria, Bacteroidota and previously overlooked Candidatus Patescibacteria. Metabolically flexible Gammaproteobacteria are major potential primary producers utilizing mainly sulfur, iron and hydrogen as electron donors coupled with oxygen and nitrate respiration for chemolithoautotrophic growth. In addition to heterotrophic microorganisms like free-living Bacteroidota, Ca. Patescibacteria potentially perform fermentative recycling of organic carbon. Finally, we provided evidence that many functional genes that are central to energy metabolism have been laterally transferred among members within the community and largely within the same class. Taken together, these findings shed light on microbial ecology and evolution in inactive seafloor sulfide deposits after the cessation of hydrothermal activities.

Contribution of horizontal gene transfer to the functionality of microbial biofilm on a macroalgae.

Horizontal gene transfer (HGT) is thought to be an important driving force for microbial evolution and niche adaptation and has been show in vitro to occur frequently in biofilm communities. However, the extent to which HGT takes place and what functions are being transferred in more complex and natural biofilm systems remains largely unknown. To address this issue, we investigated here HGT and enrichment of gene functions in the biofilm community of the common kelp (macroalgae) Ecklonia radiata in comparison to microbial communities inthe surrounding seawater. We found that HGTs in the macroalgal biofilms were dominated by transfers between bacterialmembers of the same class or order and frequently involved genes for nutrient transport, sugar and phlorotannin degradation as well as stress responses, all functions that would be considered beneficial for bacteria living in this particular niche. HGT did not appear to be driven by mobile gene elements, indicating rather an involvement of unspecific DNA uptake (e.g. natural transformation). There was also a low overlap between the gene functions subject to HGT and those enriched in the biofilm community in comparison to planktonic community members. This indicates that much of the functionality required for bacteria to live in an E. radiata biofilm might be derived from vertical or environmental transmissions of symbionts. This study enhances our understanding of the relative role of evolutionary and ecological processes in driving community assembly and genomic diversity of biofilm communities.

Orthology-Based Estimate of the Contribution of Horizontal Gene Transfer from Distantly Related Bacteria to the Intraspecific Diversity and Differentiation of Xylella fastidiosa.

Xylella fastidiosa is a xylem-limited bacterium phylogenetically related to the xanthomonads, with an unusually large and diversified range of plant hosts. To ascertain the origin of its peculiarities, its pan-genome was scanned to identify the genes that are not coherent with its phylogenetic position within the order Xanthomonadales. The results of the analysis revealed that a large fraction of the genes of the Xylella pan-genome have no ortholog or close paralog in the order Xanthomonadales. For a significant part of the genes, the closest homologue was found in bacteria belonging to distantly related taxonomic groups, most frequently in the Betaproteobacteria. Other species, such as Xanthomonas vasicola and Xanthomonas albilineans which were investigated for comparison, did not show a similar genetic contribution from distant branches of the prokaryotic tree of life. This finding indicates that the process of acquisition of DNA from the environment is still a relevant component of Xylella fastidiosa evolution. Although the ability of Xylella fastidiosa strains to recombine among themselves is well known, the results of the pan-genome analyses stressed the additional relevance of environmental DNA in shaping their genomes, with potential consequences on their phytopathological features.

Experimental Evolution of Bacillus subtilis Reveals the Evolutionary Dynamics of Horizontal Gene Transfer and Suggests Adaptive and Neutral Effects.

Tracing evolutionary processes that lead to fixation of genomic variation in wild bacterial populations is a prime challenge in molecular evolution. In particular, the relative contribution of horizontal gene transfer (HGT) vs.de novo mutations during adaptation to a new environment is poorly understood. To gain a better understanding of the dynamics of HGT and its effect on adaptation, we subjected several populations of competent Bacillus subtilis to a serial dilution evolution on a high-salt-containing medium, either with or without foreign DNA from diverse pre-adapted or naturally salt tolerant species. Following 504 generations of evolution, all populations improved growth yield on the medium. Sequencing of evolved populations revealed extensive acquisition of foreign DNA from close Bacillus donors but not from more remote donors. HGT occurred in bursts, whereby a single bacterial cell appears to have acquired dozens of fragments at once. In the largest burst, close to 2% of the genome has been replaced by HGT. Acquired segments tend to be clustered in integration hotspots. Other than HGT, genomes also acquired spontaneous mutations. Many of these mutations occurred within, and seem to alter, the sequence of flagellar proteins. Finally, we show that, while some HGT fragments could be neutral, others are adaptive and accelerate evolution.

Comprehensive and Functional Analysis of Horizontal Gene Transfer Events in Diatoms.

Diatoms are a diverse group of mainly photosynthetic algae, responsible for 20% of worldwide oxygen production, which can rapidly respond to favorable conditions and often outcompete other phytoplankton. We investigated the contribution of horizontal gene transfer (HGT) to its ecological success. A large-scale phylogeny-based prokaryotic HGT detection procedure across nine sequenced diatoms showed that 3-5% of their proteome has a horizontal origin and a large influx occurred at the ancestor of diatoms. More than 90% of HGT genes are expressed, and species-specific HGT genes in Phaeodactylum tricornutum undergo strong purifying selection. Genes derived from HGT are implicated in several processes including environmental sensing and expand the metabolic toolbox. Cobalamin (vitamin B12) is an essential cofactor for roughly half of the diatoms and is only produced by bacteria. Five consecutive genes involved in the final synthesis of the cobalamin biosynthetic pathway, which could function as scavenging and repair genes, were detected as HGT. The full suite of these genes was detected in the cold-adapted diatom Fragilariopsis cylindrus. This might give diatoms originating from the Southern Ocean, a region typically depleted in cobalamin, a competitive advantage. Overall, we show that HGT is a prevalent mechanism that is actively used in diatoms to expand its adaptive capabilities.

Genome-wide analysis of Fusarium verticillioides reveals inter-kingdom contribution of horizontal gene transfer to the expansion of metabolism

Horizontal gene transfer (HGT) is believed to shape genomes by facilitating the rapid acquisition of adaptive traits. We hypothesized that the economically important fungus Fusarium verticillioides is an excellent candidate for investigating the potential impact of HGT on the expansion of metabolic activities given its soilborne nature and versatile lifestyle as both a symptomless endophyte as well as a maize pathogen. To test this hypothesis, we used a phylogenomic pipeline followed by manual curation to perform a genome-wide identification of inter-kingdom derived HGT events. We found strong support for 36 genes in F. verticillioides putatively acquired from bacteria. Functional enrichment assessment of these 36 candidates suggested HGT potentially influenced several biochemical activities, including lysine, glycine and nitrogen metabolism. The expression of 25 candidate HGT genes was detected among RNA-Seq datasets from normal and various stress-related growth conditions, thus indicating potential functionality. FVEG_10494, one of the HGT candidates with homologs in only a few Fusarium species, was highly and specifically up-regulated under nitric oxide (NO) challenge. Functional analysis of FVEG_10494 suggests the gene moderately enhanced NO-triggered protective responses and suppressed expression of the F. verticillioides secondary metabolism gene cluster responsible for production of fusarin C. Overall, our global analysis of HGT events in F. verticillioides identified a well-supported set of transferred genes, providing further evidence that HGT offers a mechanism by which fungi can expand their metabolic capabilities, which in turn may enhance their adaptive strategies.

Contribution of horizontal gene transfer to the emergence of VIM-4 carbapenemase producer Enterobacteriaceae in Kuwait.

Carbapenem-resistant Enterobacteriaceae encountered in countries of the Arabian Peninsula usually produce OXA-48-like and New Delhi metallo-beta-lactamases (NDM) carbapenemases. However, a temporary increase in VIM-4-producing, clonally unrelated Enterobacteriaceae strains was described earlier in a Kuwaiti hospital. We investigated the genetic support of blaVIM-4 in six Klebsiella pneumoniae strains, one Escherichia coli, and one Enterobacter cloacae strain and compared it to that of VIM-4-producing isolates from other countries of the region. Five K. pneumoniae strains and the E. coli strain from Kuwait carried an ~165 kb IncA/C-type plasmid indistinguishable by restriction fragment length polymorphism. The complete sequence of one of them (pKKp4-VIM) was established. pKKp4-VIM exhibited extensive similarities to episomes pKP-Gr642 carrying blaVIM-19 encountered in Greece and to the partially sequenced pCC416 harboring blaVIM-4 detected in Italy. In other countries of the region, the only similar plasmid was the one detected in the isolate from the UAE. In all Kuwaiti strains, irrespective of the species and their VIM plasmids, the blaVIM-4 gene was located within the same integron structure (In416), different from those of other countries of the region. Our data show that the spread of this IncA/C plasmid and particularly that of the In416 integron caused a considerable, albeit temporary, increase in the rate of mostly clonally unrelated VIM-producing Enterobacteriaceae strains of multiple species. Monitoring of such events is of high importance as the interference with the spread of mobile genetic elements may represent a formidable challenge to infection control.

The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights

BackgroundPseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms to study the biological mechanisms involved in the adaptation to cold conditions. A remarkable feature shared by these bacteria is their ability to produce secondary metabolites with a strong antimicrobial and antitumor activity. Despite their biotechnological relevance, representatives of this genus are still lacking (with few exceptions) an extensive genomic characterization, including features involved in the evolution of secondary metabolites production. Indeed, biotechnological applications would greatly benefit from such analysis.ResultsHere, we analyzed the genomes of 38 strains belonging to different Pseudoalteromonas species and isolated from diverse ecological niches, including extreme ones (i.e. Antarctica). These sequences were used to reconstruct the largest Pseudoalteromonas pangenome computed so far, including also the two main groups of Pseudoalteromonas strains (pigmented and not pigmented strains). The downstream analyses were conducted to describe the genomic diversity, both at genus and group levels. This allowed highlighting a remarkable genomic heterogeneity, even for closely related strains. We drafted all the main evolutionary steps that led to the current structure and gene content of Pseudoalteromonas representatives. These, most likely, included an extensive genome reduction and a strong contribution of Horizontal Gene Transfer (HGT), which affected biotechnologically relevant gene sets and occurred in a strain-specific fashion. Furthermore, this study also identified the genomic determinants related to some of the most interesting features of the Pseudoalteromonas representatives, such as the production of secondary metabolites, the adaptation to cold temperatures and the resistance to abiotic compounds.ConclusionsThis study poses the bases for a comprehensive understanding of the evolutionary trajectories followed in time by this peculiar bacterial genus and for a focused exploitation of their biotechnological potential.

Antibiotics and Antibiotic Resistance in Agroecosystems: State of the Science.

We propose a simple causal model depicting relationships involved in dissemination of antibiotics and antibiotic resistance in agroecosystems and potential effects on human health, functioning of natural ecosystems, and agricultural productivity. Available evidence for each causal link is briefly summarized, and key knowledge gaps are highlighted. A lack of quantitative estimates of human exposure to environmental bacteria, in general, and antibiotic-resistant bacteria, specifically, is a significant data gap hindering the assessment of effects on human health. The contribution of horizontal gene transfer to resistance in the environment and conditions that might foster the horizontal transfer of antibiotic resistance genes into human pathogens also need further research. Existing research has focused heavily on human health effects, with relatively little known about the effects of antibiotics and antibiotic resistance on natural and agricultural ecosystems. The proposed causal model is used to elucidate gaps in knowledge that must be addressed by the research community and may provide a useful starting point for the design and analysis of future research efforts.

Insights into the CRISPR/Cas system of Gardnerella vaginalis.

BackgroundGardnerella vaginalis is identified as the predominant colonist of the vaginal tracts of women diagnosed with bacterial vaginosis (BV). G. vaginalis can be isolated from healthy women, and an asymptomatic BV state is also recognised. The association of G. vaginalis with different clinical phenotypes could be explained by different cytotoxicity of the strains, presumably based on disparate gene content. The contribution of horizontal gene transfer to shaping the genomes of G. vaginalis is acknowledged. The CRISPR loci of the recently discovered CRISPR/Cas microbial defence system provide a historical view of the exposure of prokaryotes to a variety of foreign genetic elements.ResultsThe CRISPR/Cas loci were analysed using available sequence data from three G. vaginalis complete genomes and 18 G. vaginalis draft genomes in the NCBI database, as well as PCR amplicons of the genomic DNA of 17 clinical isolates. The cas genes in the CRISPR/Cas loci of G. vaginalis belong to the E. coli subtype. Approximately 20% of the spacers had matches in the GenBank database. Sequence analysis of the CRISPR arrays revealed that nearly half of the spacers matched G. vaginalis chromosomal sequences. The spacers that matched G. vaginalis chromosomal sequences were determined to not be self-targeting and were presumably neither constituents of mobile-element-associated genes nor derived from plasmids/viruses. The protospacers targeted by these spacers displayed conserved protospacer-adjacent motifs.ConclusionsThe CRISPR/Cas system has been identified in about one half of the analysed G. vaginalis strains. Our analysis of CRISPR sequences did not reveal a potential link between their presence and the virulence of the G. vaginalis strains. Based on the origins of the spacers found in the G. vaginalis CRISPR arrays, we hypothesise that the transfer of genetic material among G. vaginalis strains could be regulated by the CRISPR/Cas mechanism. The present study is the first attempt to determine and analyse the CRISPR loci of bacteria isolated from the human vaginal tract.

Scientific Opinion on application EFSA-GMO-RX-MON1445 for renewal of the authorisation for continued marketing of cottonseed oil, food additives, feed materials and feed additives produced from cotton MON 1445 that were notified as existing products under

This scientific opinion evaluates the risk assessment for the authorisation for continued marketing of genetically modified herbicide tolerant cotton MON 1445 for food and feed produced from it. Cotton MON 1445 contains single copies of functional CP4 epsps and nptII expression cassettes and an aadA gene as non-functional element. Stability of the inserted DNA was confirmed over several generations. Bioinformatic analyses and levels of recombinant proteins did not reveal safety issues. No biologically relevant differences were identified in the compositional, phenotypic and agronomic characteristics of cotton MON 1445 in comparison to its conventional counterpart and its composition fell within the range of non-GM cotton varieties, except for CP4 EPSPS and NPTII proteins. No toxicity and allergenicity issues were identified regarding the newly expressed protens. Products from cotton MON 1445 do not contain viable plant parts. Insert structure in cotton MON 1445 may facilitate the stabilisation of the nptII gene in plasmids of environmental bacteria through double homologous recombination. However, considering the expected low frequency of gene transfer from cotton MON 1445 to bacteria compared to that between bacteria, and the very low exposure to DNA from cotton MON 1445, the EFSA GMO Panel concludes that the contribution of horizontal gene transfer to the environmental prevalence of nptII genes is negligible. Potential interactions of cotton MON 1445 with non-target organisms and the abiotic environment were not considered to be an issue because of low exposure levels. A post-market environmental monitoring plan is not required. The EFSA GMO Panel concludes that the information available for cotton MON 1445 addresses the questions raised by the Member States and that MON 1445-derived products are as safe as products derived from the conventional counterpart in the context of their intended uses.

Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes

Gene duplication followed by neo- or sub-functionalization deeply impacts the evolution of protein families and is regarded as the main source of adaptive functional novelty in eukaryotes. While there is ample evidence of adaptive gene duplication in prokaryotes, it is not clear whether duplication outweighs the contribution of horizontal gene transfer in the expansion of protein families. We analyzed closely related prokaryote strains or species with small genomes (Helicobacter, Neisseria, Streptococcus, Sulfolobus), average-sized genomes (Bacillus, Enterobacteriaceae), and large genomes (Pseudomonas, Bradyrhizobiaceae) to untangle the effects of duplication and horizontal transfer. After removing the effects of transposable elements and phages, we show that the vast majority of expansions of protein families are due to transfer, even among large genomes. Transferred genes—xenologs—persist longer in prokaryotic lineages possibly due to a higher/longer adaptive role. On the other hand, duplicated genes—paralogs—are expressed more, and, when persistent, they evolve slower. This suggests that gene transfer and gene duplication have very different roles in shaping the evolution of biological systems: transfer allows the acquisition of new functions and duplication leads to higher gene dosage. Accordingly, we show that paralogs share most protein–protein interactions and genetic regulators, whereas xenologs share very few of them. Prokaryotes invented most of life's biochemical diversity. Therefore, the study of the evolution of biology systems should explicitly account for the predominant role of horizontal gene transfer in the diversification of protein families.

The contribution of mobile genetic elements to the evolution and ecology of Vibrios

An increase in the frequency of seafood-borne gastroenteritis in humans and Vibrio-related disease of fish and invertebrates has generated interest in the ecology of disease-causing Vibrios and the mechanisms driving their evolution. Genome sequencing studies have indicated a substantial contribution of horizontal gene transfer (HGT) to the evolution of Vibrios. Of particular interest is the contribution of HGT to the evolution of Vibrios pathogens and the adaptation of disease-causing Vibrios for survival in diverse environments. In this review, we discuss the diversity and distribution of mobile genetic elements (MGEs) isolated from Vibrios and the contribution of these elements to the expansion of the ecological and pathogenic niches of the host strain. Much of the research on Vibrio MGEs has focused on understanding phages and plasmids and we will primarily discuss the evolution of these elements and also briefly highlight the other diverse elements characterized from Vibrios, which includes genomic islands and conjugative elements.

Horizontal gene transfer in evolution: facts and challenges

The contribution of horizontal gene transfer to evolution has been controversial since it was suggested to be a force driving evolution in the microbial world. In this paper, I review the current standpoint on horizontal gene transfer in evolutionary thinking and discuss how important horizontal gene transfer is in evolution in the broad sense, and particularly in prokaryotic evolution. I review recent literature, asking, first, which processes are involved in the evolutionary success of transferred genes and, secondly, about the extent of horizontal gene transfer towards different evolutionary times. Moreover, I discuss the feasibility of reconstructing ancient phylogenetic relationships in the face of horizontal gene transfer. Finally, I discuss how horizontal gene transfer fits in the current neo-Darwinian evolutionary paradigm and conclude there is a need for a new evolutionary paradigm that includes horizontal gene transfer as well as other mechanisms in the explanation of evolution.

Order and Disorder during Escherichia coli Divergence

Escherichia coli is a single species with numerous recognized roles, from lab workhorse to beneficial intestinal commensal or deadly pathogen. The extant strains have disparate lifestyles as a result of differential niche expansion since their divergence 25–40 million years ago, ten times longer than the estimated divergence between chimpanzees and humans [1,2]. Not only do these roles vary by strain (variant) of the species, but the recognition of a strain’s role in one context does not exclude radically different behaviour in another, due to differential gene expression [3]. These are organisms adapting on evolutionary and lifetime scales to myriad environments and pressures. How do these strains differ from one another and what sustains their identification as a single species? To address these questions, Touchon et al. have completely sequenced and annotated six strains of E. coli while reannotating previously sequenced strains, as discussed in this issue of PLoS Genetics [4]. Comparative genomics analyses of 20 E. coli strains and one out-group provided insights into the contributions of horizontal gene transfer (HGT) and mutation on evolution in this species. In addition, the strains were tested in a mouse model to compare their virulence.