scholarly journals High activity of horizontal gene transfer in nodule bacteria as a strategy for interaction with legumes

2020 ◽  
Author(s):  
An. Kh. Baymiev ◽  
A. A. Vladimirova ◽  
E. S. Akimova ◽  
I. S. Koryakov ◽  
Al. Kh. Baymiev
Keyword(s):  
Genetic Diversity ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
High Activity ◽  
Horizontal Transfer ◽  
Symbiotic Genes ◽  
Nodule Bacteria ◽  
Rhizospheric Bacteria ◽  
Legume Plant

The contribution of the legume plant to the formation of the genetic diversity of nodule bacteria and its effect on the activity of horizontal transfer of symbiotic genes in rhizospheric bacteria is studied.

scholarly journals Exploring Genetic Diversity and Signatures of Horizontal Gene Transfer in Nodule Bacteria Associated with Lotus japonicus in Natural Environments

2019 ◽  
Vol 32 (9) ◽  
pp. 1110-1120 ◽  
Author(s):  
Masaru Bamba ◽  
Seishiro Aoki ◽  
Tadashi Kajita ◽  
Hiroaki Setoguchi ◽  
Yasuyuki Watano ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Lotus Japonicus ◽  
Population Expansion ◽  
Housekeeping Genes ◽  
Natural Environments ◽  
Symbiotic Genes ◽  
Nodule Bacteria ◽  
Wide Range

To investigate the genetic diversity and understand the process of horizontal gene transfer (HGT) in nodule bacteria associated with Lotus japonicus, we analyzed sequences of three housekeeping and five symbiotic genes using samples from a geographically wide range in Japan. A phylogenetic analysis of the housekeeping genes indicated that L. japonicus in natural environments was associated with diverse lineages of Mesorhizobium spp., whereas the sequences of symbiotic genes were highly similar between strains, resulting in remarkably low nucleotide diversity at both synonymous and nonsynonymous sites. Guanine-cytosine content values were lower in symbiotic genes, and relative frequencies of recombination between symbiotic genes were also lower than those between housekeeping genes. An analysis of molecular variance showed significant genetic differentiation among populations in both symbiotic and housekeeping genes. These results confirm that the Mesorhizobium genes required for symbiosis with L. japonicus behave as a genomic island (i.e., a symbiosis island) and suggest that this island has spread into diverse genomic backgrounds of Mesorhizobium via HGT events in natural environments. Furthermore, our data compilation revealed that the genetic diversity of symbiotic genes in L. japonicus-associated symbionts was among the lowest compared with reports of other species, which may be related to the recent population expansion proposed in Japanese populations of L. japonicus.

Genomic Analysis of Citrobacter Portucalensis Sb-2 Identifies a Phage Predation Driven Metalloid Resistance

2021 ◽  
Author(s):  
Yanshuang Yu ◽  
Zhenchen Xie ◽  
Jigang Yang ◽  
Jinxuan Liang ◽  
YuanPing Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Significant Role ◽  
Genome Analysis ◽  
Extreme Environments ◽  
Genomic Analysis ◽  
Resistant Bacterium ◽  
Bacterial Adaptation ◽  
Resistance Determinants

Abstract Bacterial adaptation to extreme environments is often mediated by horizontal gene transfer (HGT). At the same time, phage mediated HGT for conferring bacterial arsenite and antimonite resistance has not been documented before. In this study, a highly arsenite and antimonite resistant bacterium, C. portucalensis strain Sb-2, was isolated and subsequent genome analysis showed that putative arsenite and antimonite resistance determinants were flanked or embedded by prophages. We predict these phage-mediated resistances play a significant role in maintaining genetic diversity within the genus of Citrobacter and are responsible for endowing the corresponding resistances to C. portucalensis strain Sb-2.

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 Extensive Phenotypic Changes Associated with Large-scale Horizontal Gene Transfer

2013 ◽  
Author(s):  
Kevin Dougherty ◽  
Brian A Smith ◽  
Autum F Moore ◽  
Shannon Maitland ◽  
Chris Fanger ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Horizontal Transfer ◽  
Large Scale ◽  
Pseudomonas Stutzeri ◽  
Transfer Event ◽  
Small Plasmid ◽  
Phenotypic Changes ◽  
Evolutionary Trajectories ◽  
Evolutionary Consequences

Horizontal gene transfer often leads to phenotypic changes within recipient organisms independent of any immediate evolutionary benefits. While secondary phenotypic effects of horizontal transfer (i.e. changes in growth rates) have been demonstrated and studied across a variety of systems using relatively small plasmid and phage, little is known about how size of the acquired region affects the magnitude or number of such costs. Here we describe an amazing breadth of phenotypic changes which occur after a large-scale horizontal transfer event (~1Mb megaplasmid) within Pseudomonas stutzeri including sensitization to various stresses as well as changes in bacterial behavior. These results highlight the power of horizontal transfer to shift pleiotropic relationships and cellular networks within bacterial genomes. They also provide an important context for how secondary effects of transfer can bias evolutionary trajectories and interactions between species. Lastly, these results and system provide a foundation to investigate evolutionary consequences in real time as newly acquired regions are ameliorated and integrated into new genomic contexts.

scholarly journals Horizontal Gene Transfer of Functional Type VI Killing Genes by Natural Transformation

2017 ◽  
Author(s):  
Jacob Thomas ◽  
Samit S. Watve ◽  
William C. Ratcliff ◽  
Brian K. Hammer
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Horizontal Transfer ◽  
Direct Injection ◽  
Spatially Explicit ◽  
Type Vi Secretion System ◽  
Effector Genes ◽  
Type Vi Secretion ◽  
A Cell ◽  
Explicit Simulation

AbstractHorizontal gene transfer can have profound effects on bacterial evolution by allowing individuals to rapidly acquire adaptive traits that shape their strategies for competition. One strategy for intermicrobial antagonism often used by Proteobacteria is the genetically-encoded contact-dependent Type VI secretion system (T6SS); a weapon used to kill heteroclonal neighbors by direct injection of toxic effectors. Here, we experimentally demonstrate thatVibrio choleraecan acquire new T6SS effector genes via horizontal transfer and utilize them to kill neighboring cells. Replacement of one or more parental alleles with novel effectors allows the recombinant strain to dramatically outcompete its parent. Through spatially-explicit simulation modeling, we show that the HGT is risky: transformation brings a cell into conflict with its former clonemates, but can be adaptive when superior T6SS alleles are acquired. More generally, we find that these costs and benefits are not symmetric, and that high rates of HGT can act as hedge against competitors with unpredictable T6SS efficacy. We conclude that antagonism and horizontal transfer drive successive rounds of weapons-optimization and selective sweeps, dynamically shaping the composition of microbial communities.

scholarly journals Horizontal Gene Transfer and the Evolution of Microvirid Coliphage Genomes

2006 ◽  
Vol 188 (3) ◽  
pp. 1134-1142 ◽  
Author(s):  
D. R. Rokyta ◽  
C. L. Burch ◽  
S. B. Caudle ◽  
H. A. Wichman
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Horizontal Transfer ◽  
Sparse Sampling ◽  
Apparent Difference ◽  
Genomic Evolution ◽  
Single Family ◽  
Bacterial Host ◽  
Double Stranded Dna ◽  
The Family

ABSTRACT Bacteriophage genomic evolution has been largely characterized by rampant, promiscuous horizontal gene transfer involving both homologous and nonhomologous source DNA. This pattern has emerged through study of the tailed double-stranded DNA (dsDNA) phages and is based upon a sparse sampling of the enormous diversity of these phages. The single-stranded DNA phages of the family Microviridae, including φX174, appear to evolve through qualitatively different mechanisms, possibly as result of their strictly lytic lifestyle and small genome size. However, this apparent difference could reflect merely a dearth of relevant data. We sought to characterize the forces that contributed to the molecular evolution of the Microviridae and to examine the genetic structure of this single family of bacteriophage by sequencing the genomes of microvirid phage isolated on a single bacterial host. Microvirids comprised 3.5% of the detectable phage in our environmental samples, and sequencing yielded 42 new microvirid genomes. Phylogenetic analysis of the genes contained in these and five previously described microvirid phages identified three distinct clades and revealed at least two horizontal transfer events between clades. All members of one clade have a block of five putative genes that are not present in any member of the other two clades. Our data indicate that horizontal transfer does contribute to the evolution of the microvirids but is both quantitatively and qualitatively different from what has been observed for the dsDNA phages.

scholarly journals Involvement of β-Carbonic Anhydrase Genes in Bacterial Genomic Islands and Their Horizontal Transfer to Protists

2018 ◽  
Vol 84 (15) ◽  
Author(s):  
Reza Zolfaghari Emameh ◽  
Harlan R. Barker ◽  
Vesa P. Hytönen ◽  
Seppo Parkkila
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Carbonic Anhydrase ◽  
Horizontal Transfer ◽  
Bacterial Species ◽  
Critical Role ◽  
Genomic Islands ◽  
Ph Homeostasis ◽  
Gene Sequences ◽  
Biochemical Pathways

ABSTRACT Genomic islands (GIs) are a type of mobile genetic element (MGE) that are present in bacterial chromosomes. They consist of a cluster of genes that produce proteins that contribute to a variety of functions, including, but not limited to, the regulation of cell metabolism, antimicrobial resistance, pathogenicity, virulence, and resistance to heavy metals. The genes carried in MGEs can be used as a trait reservoir in times of adversity. Transfer of genes using MGEs, occurring outside reproduction, is called horizontal gene transfer (HGT). Previous data have shown that numerous HGT events have occurred through endosymbiosis between prokaryotes and eukaryotes. β-Carbonic anhydrase (β-CA) enzymes play a critical role in the biochemical pathways of many prokaryotes and eukaryotes. We previously suggested the horizontal transfer of β-CA genes from plasmids of some prokaryotic endosymbionts to their protozoan hosts. In this study, we set out to identify β-CA genes that might have been transferred between prokaryotic and protist species through HGT in GIs. Therefore, we investigated prokaryotic chromosomes containing β-CA-encoding GIs and utilized multiple bioinformatics tools to reveal the distinct movements of β-CA genes among a wide variety of organisms. Our results identify the presence of β-CA genes in GIs of several medically and industrially relevant bacterial species, and phylogenetic analyses reveal multiple cases of likely horizontal transfer of β-CA genes from GIs of ancestral prokaryotes to protists. IMPORTANCE The evolutionary process is mediated by mobile genetic elements (MGEs), such as genomic islands (GIs). A gene or set of genes in the GIs is exchanged between and within various species through horizontal gene transfer (HGT). Based on the crucial role that GIs can play in bacterial survival and proliferation, they were introduced as environment- and pathogen-associated factors. Carbonic anhydrases (CAs) are involved in many critical biochemical pathways, such as the regulation of pH homeostasis and electrolyte transfer. Among the six evolutionary families of CAs, β-CA gene sequences are present in many bacterial species, which can be horizontally transferred to protists during evolution. This study shows the involvement of bacterial β-CA gene sequences in the GIs and suggests their horizontal transfer to protists during evolution.

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