Eco-evolutionary Dynamics Linked to Horizontal Gene Transfer in Vibrios

2018 ◽  
Vol 72 (1) ◽  
pp. 89-110 ◽  
Author(s):  
Frédérique Le Roux ◽  
Melanie Blokesch
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Evolutionary Dynamics ◽  
Heterotrophic Bacteria ◽  
Aquatic Environments ◽  
Biogeochemical Processes ◽  
Genome Plasticity ◽  
Free Living ◽  
Genomic Studies ◽  
Pathogenic Vibrios

Vibrio is a genus of ubiquitous heterotrophic bacteria found in aquatic environments. Although they are a small percentage of the bacteria in these environments, vibrios can predominate during blooms. Vibrios also play important roles in the degradation of polymeric substances, such as chitin, and in other biogeochemical processes. Vibrios can be found as free-living bacteria, attached to particles, or associated with other organisms in a mutualistic, commensal, or pathogenic relationship. This review focuses on vibrio ecology and genome plasticity, which confers an ability to adapt to new niches and is driven, at least in part, by horizontal gene transfer (HGT). The extent of HGT and its role in pathogen emergence are discussed based on genomic studies of environmental and pathogenic vibrios, mobile genetically encoded virulence factors, and mechanistic studies on the different modes of HGT.

scholarly journals panRGP: a pangenome-based method to predict genomic islands and explore their diversity

2020 ◽  
Vol 36 (Supplement_2) ◽  
pp. i651-i658 ◽  
Author(s):  
Adelme Bazin ◽  
Guillaume Gautreau ◽  
Claudine Médigue ◽  
David Vallenet ◽  
Alexandra Calteau
Keyword(s):  
Escherichia Coli ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Species Level ◽  
Genomic Islands ◽  
Genome Plasticity ◽  
Reference Dataset ◽  
Prokaryotic Genomes ◽  
Ideal Approach ◽  
Genomic Regions

Abstract Motivation Horizontal gene transfer (HGT) is a major source of variability in prokaryotic genomes. Regions of genome plasticity (RGPs) are clusters of genes located in highly variable genomic regions. Most of them arise from HGT and correspond to genomic islands (GIs). The study of those regions at the species level has become increasingly difficult with the data deluge of genomes. To date, no methods are available to identify GIs using hundreds of genomes to explore their diversity. Results We present here the panRGP method that predicts RGPs using pangenome graphs made of all available genomes for a given species. It allows the study of thousands of genomes in order to access the diversity of RGPs and to predict spots of insertions. It gave the best predictions when benchmarked along other GI detection tools against a reference dataset. In addition, we illustrated its use on metagenome assembled genomes by redefining the borders of the leuX tRNA hotspot, a well-studied spot of insertion in Escherichia coli. panRPG is a scalable and reliable tool to predict GIs and spots making it an ideal approach for large comparative studies. Availability and implementation The methods presented in the current work are available through the following software: https://github.com/labgem/PPanGGOLiN. Detailed results and scripts to compute the benchmark metrics are available at https://github.com/axbazin/panrgp_supdata.

scholarly journals Horizontal gene transfer of a unique nif island drives convergent evolution of free-living N2-fixing Bradyrhizobium

2021 ◽  
Author(s):  
Jinjin Tao ◽  
Sishuo Wang ◽  
Tianhua Liao ◽  
Haiwei Luo
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Agricultural Research ◽  
Current Knowledge ◽  
Gene Clusters ◽  
Soil Samples ◽  
Genomic Context ◽  
Free Living ◽  
Phylogenomic Analyses ◽  
Conserved Gene

SummaryThe alphaproteobacterial genus Bradyrhizobium has been best known as N2-fixing members that nodulate legumes, supported by the nif and nod gene clusters. Recent environmental surveys show that Bradyrhizobium represents one of the most abundant free-living bacterial lineages in the world’s soils. However, our understanding of Bradyrhizobium comes largely from symbiotic members, biasing the current knowledge of their ecology and evolution. Here, we report the genomes of 88 Bradyrhizobium strains derived from diverse soil samples, including both nif-carrying and non-nif-carrying free-living (nod free) members. Phylogenomic analyses of these and 252 publicly available Bradyrhizobium genomes indicate that nif-carrying free-living members independently evolved from symbiotic ancestors (carrying both nif and nod) multiple times. Intriguingly, the nif phylogeny shows that all nif-carrying free-living members comprise a cluster which branches off earlier than most symbiotic lineages. These results indicate that horizontal gene transfer (HGT) promotes nif expansion among the free-living Bradyrhizobium and that the free-living nif cluster represents a more ancestral version compared to that in symbiotic lineages. Further evidence for this rampant HGT is that the nif in free-living members consistently co-locate with several important genes involved in coping with oxygen tension which are missing from symbiotic members, and that while in free-living Bradyrhizobium nif and the co-locating genes show a highly conserved gene order, they each have distinct genomic context. Given the dominance of Bradyrhizobium in world’s soils, our findings have implications for global nitrogen cycles and agricultural research.

scholarly journals Horizontal Gene Transfer Clarifies Taxonomic Confusion and Promotes the Genetic Diversity and Pathogenicity of Plesiomonas shigelloides

mSystems ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Zhiqiu Yin ◽  
Si Zhang ◽  
Yi Wei ◽  
Meng Wang ◽  
Shuangshuang Ma ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Evolutionary Dynamics ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Content Type ◽  
Pan Genome ◽  
Long Time ◽  
Taxonomic Confusion

The taxonomic position of P. shigelloides has been the subject of debate for a long time, and until now, the evolutionary dynamics and pathogenesis of P. shigelloides were unclear. In this study, pan-genome analysis indicated extensive genetic diversity and the presence of large and variable gene repertoires. Our results revealed that horizontal gene transfer was the focal driving force for the genetic diversity of the P. shigelloides pan-genome and might have contributed to the emergence of novel properties. Vibrionaceae and Aeromonadaceae were found to be the predominant donor taxa for horizontal genes, which might have caused the taxonomic confusion historically. Comparative genomic analysis revealed the potential of P. shigelloides to cause intestinal and invasive diseases. Our results could advance the understanding of the evolution and pathogenesis of P. shigelloides, particularly in elucidating the role of horizontal gene transfer and investigating virulence-related elements.

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

Genetics ◽  
2020 ◽  
Vol 216 (2) ◽  
pp. 543-558
Author(s):  
Shai Slomka ◽  
Itamar Françoise ◽  
Gil Hornung ◽  
Omer Asraf ◽  
Tammy Biniashvili ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Evolutionary Dynamics ◽  
De Novo ◽  
Growth Yield ◽  
Genomic Variation ◽  
Bacterial Populations ◽  
Flagellar Proteins ◽  
Foreign Dna

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.

scholarly journals The human pathogenic vibrios – A public health update with environmental perspectives

1989 ◽  
Vol 103 (1) ◽  
pp. 1-34 ◽  
Author(s):  
P. A. West
Keyword(s):  
Public Health ◽  
Acute Infection ◽  
Aquatic Environments ◽  
Free Living ◽  
Liver Disorders ◽  
Naturally Occurring ◽  
Pathogenic Vibrio ◽  
Ear Infections ◽  
Pathogenic Vibrios ◽  
Living Bacteria

PathogenicVibriospecies are naturally-occurring bacteria in freshwater and saline aquatic environments. Counts of free-living bacteria in water are generally less than required to induce disease. Increases in number of organisms towards an infective dose can occur as water temperatures rise seasonally followed by growth and concentration of bacteria on higher animals, such as chitinous plankton, or accumulation by shellfish and seafood. PathogenicVibriospecies must elaborate a series of virulence factors to elicit disease in humans.Activities which predispose diarrhoeal and extraintestinal infections include ingestion of seafood and shellfish and occupational or recreational exposure to natural aquatic environments, especially those above 20 °C. Travel to areas endemic for diseases due to pathogenicVibriospecies may be associated with infections. Host risk factors strongly associated with infections are lack of gastric acid and liver disorders.Involvement of pathogenicVibriospecies in cases of diarrhoea should be suspected especially if infection is associated with ingestion of seafood or shellfish, raw or undercooked, in the previous 72 h.Vibriospecies should be suspected in any acute infection associated with wounds sustained or exposed in the marine or estuarine environment. Laboratories serving coastal areas where infection due to pathogenic Vibrio species are most likely to occur should consider routine use of TCBS agar and other detection regimens for culture ofVibriospecies from faeces, blood and samples from wound and ear infections.

scholarly journals Release of Extracellular Transformable Plasmid DNA from Escherichia coli Cocultivated with Algae

2003 ◽  
Vol 69 (4) ◽  
pp. 2399-2404 ◽  
Author(s):  
Kazuaki Matsui ◽  
Nobuyoshi Ishii ◽  
Zen'ichiro Kawabata
Keyword(s):  
Escherichia Coli ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Plasmid Dna ◽  
Euglena Gracilis ◽  
Blot Hybridization ◽  
Aquatic Environments ◽  
Dot Blot ◽  
Dot Blot Hybridization ◽  
Significant Release

ABSTRACT We studied the effects of cocultivation with either Euglena gracilis (Euglenophyta), Microcystis aeruginosa (Cyanophyta), Chlamydomonas neglecta (Chlorophyta), or Carteria inversa (Chlorophyta) on the production of extracellular plasmid DNA by Escherichia coli LE392(pKZ105). Dot blot hybridization analysis showed a significant release of plasmid DNA by cocultivation with all the algae tested. Further analysis by electrotransformation confirmed the release of transformable plasmid DNA by cocultivation with either E. gracilis, M. aeruginosa, or C. inversa. These results suggest algal involvement in bacterial horizontal gene transfer by stimulating the release of transformable DNA into aquatic environments.

scholarly journals Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in Streptococcus pneumoniae

2019 ◽  
Author(s):  
Sonja Lehtinen ◽  
Claire Chewapreecha ◽  
John Lees ◽  
William P. Hanage ◽  
Marc Lipsitch ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Streptococcus Pneumoniae ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Evolutionary Dynamics ◽  
Epidemiological Data ◽  
Unified Framework ◽  
Genetic Lineages ◽  
Pneumococcal Carriage ◽  
Primary Determinant

The extent to which evolution is constrained by the rate at which horizontal gene transfer (HGT) allows DNA to move between genetic lineages is an open question, which we address in the context of antibiotic resistance in Streptococcus pneumoniae. We analyze microbiological, genomic and epidemiological data from the largest-to-date sequenced pneumococcal carriage study in 955 infants from a refugee camp on the Thailand-Myanmar border. Using a unified framework, we simultaneously test prior hypotheses on rates of HGT and a key evolutionary covariate (duration of carriage) as determinants of resistance frequencies. We conclude that in this setting, there is only weak evidence for the rate of HGT playing a role in the evolutionary dynamics of resistance. Instead, observed resistance frequencies are best explained as the outcome of selection acting on a pool of variants, irrespective of the rate at which resistance determinants move between genetic lineages.

scholarly journals Rapid evolution and horizontal gene transfer in the genome of a male-killing Wolbachia

2020 ◽  
Author(s):  
Tom Hill ◽  
Robert L. Unckless ◽  
Jessamyn I. Perlmutter
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Host Species ◽  
Evolutionary Dynamics ◽  
Population Genomics ◽  
Rapid Evolution ◽  
Male Killing ◽  
Show Evidence ◽  
Bacterial Endosymbionts ◽  
Unique Genes

AbstractWolbachia are widespread bacterial endosymbionts that infect a large proportion of insect species. While some strains of this bacteria do not cause observable host phenotypes, many strains of Wolbachia have some striking effects on their hosts. In some cases, these symbionts manipulate host reproduction to increase the fitness of infected, transmitting females. Here we examine the genome and population genomics of a male-killing Wolbachia strain, wInn, that infects Drosophila innubila mushroom-feeding flies. We compared wInn to other closely-related Wolbachia genomes to understand the evolutionary dynamics of specific genes. The wInn genome is similar in overall gene content to wMel, but also contains many unique genes and repetitive elements that indicate distinct gene transfers between wInn and non-Drosophila hosts. We also find that genes in the Wolbachia prophage and Octomom regions are particularly rapidly evolving, including those putatively or empirically confirmed to be involved in host pathogenicity. Of the genes that rapidly evolve, many also show evidence of recent horizontal transfer among Wolbachia symbiont genomes, suggesting frequent movement of rapidly evolving regions among individuals. These dynamics of rapid evolution and horizontal gene transfer across the genomes of several Wolbachia strains and divergent host species may be important underlying factors in Wolbachia’s global success as a symbiont.

scholarly journals Genomic Background Governs Opposing Responses to Nalidixic Acid Upon Megaplasmid Acquisition in Pseudomonas

2019 ◽  
Author(s):  
David A. Baltrus ◽  
Caitlin Smith ◽  
MacKenzie Derrick ◽  
Courtney Leligdon ◽  
Zoe Rosenthal ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Nalidixic Acid ◽  
Evolutionary Dynamics ◽  
De Novo ◽  
Horizontal Gene Transfer Event ◽  
Genetic Material ◽  
Fitness Costs ◽  
Transfer Event ◽  
Phenotypic Changes

AbstractHorizontal gene transfer is a significant driver of evolutionary dynamics across microbial populations. Although the benefits of the acquisition of new genetic material are often quite clear, experiments across systems have demonstrated that gene transfer events can cause significant phenotypic changes and entail fitness costs in a way that is dependent on the genomic and environmental context. Here we test for the generality of one previously identified cost, sensitization of cells to the antibiotic nalidixic acid after acquisition of a ∼1Mb megaplasmid, across Pseudomonas strains and species. Overall, we find that the presence of this megaplasmid sensitizes many different Pseudomonas strains to nalidixic acid, but that this same horizontal gene transfer event increases resistance of Pseudomonas putida KT2440 to nalidixic acid across assays as well as to ciprofloxacin under competitive conditions. These phenotypic results are not easily explained away as secondary consequences of overall fitness effects and appear to occur independently of another cost associated with this megaplasmid, sensitization to higher temperatures. Lastly, we draw parallels between these reported results and the phenomenon of sign epistasis for de novo mutations and explore how context dependence of effects of plasmid acquisition could impact overall evolutionary dynamics and the evolution of antimicrobial resistance.ImportanceNumerous studies have demonstrated that gene transfer events (e.g. plasmid acquisition) can entail a variety of costs that arise as byproducts of the incorporation of foreign DNA into established physiological and genetic systems. These costs can be ameliorated through evolutionary time by the occurrence of compensatory mutations, which stabilize presence of a horizontally transferred region within the genome but which also may skew future adaptive possibilities for these lineages. Here we demonstrate another possible outcome, that phenotypic changes arising as a consequence of the same horizontal gene transfer event are costly to some strains but may actually be beneficial in other genomic backgrounds under the right conditions. These results provide new a new viewpoint for considering conditions that promote plasmid maintenance and highlight the influence of genomic and environmental contexts when considering amelioration of fitness costs after HGT events.

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