scholarly journals The genomic architecture of introgression among sibling species of bacteria

2019 ◽  
Author(s):  
Maria Izabel A Cavassim ◽  
Sara Moeskjær ◽  
Camous Moslemi ◽  
Bryden Fields ◽  
Asger Bachmann ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Rhizobium Leguminosarum ◽  
Root Nodules ◽  
Bacterial Species ◽  
Core Gene ◽  
Conjugative Plasmid ◽  
Conjugative Transfer ◽  
Recombination Rates ◽  
Transfer Genes ◽  
Selective Forces

AbstractBackgroundGene transfer between bacterial species is an important mechanism for adaptation. For example, sets of genes that confer the ability to form nitrogen-fixing root nodules on host plants have frequently moved betweenRhizobiumspecies. It is not clear, though, whether such transfer is exceptional, or if frequent inter-species introgression is typical. To address this, we sequenced the genomes of 196 isolates of theRhizobium leguminosarumspecies complex obtained from root nodules of white clover (Trifolium repens).ResultsCore gene phylogeny placed the isolates into five distinct genospecies that show high intra-genospecies recombination rates and remarkably different demographic histories. Most gene phylogenies were largely concordant with the genospecies, indicating that recent gene transfer between genospecies was rare. In contrast, very similar symbiosis gene sequences were found in two or more genospecies, suggesting recent horizontal transfer. The replication and conjugative transfer genes of the plasmids carrying the symbiosis genes showed a similar pattern, implying that introgression occurred by conjugative plasmid transfer. The only other regions that showed strong phylogenetic discordance with the genospecies classification were two small chromosomal clusters, one neighbouring a conjugative transfer system. Phage-related sequences were observed in the genomes, but appeared to have very limited impact on introgression.ConclusionsIntrogression among these closely-related species has been very limited, confined to the symbiosis plasmids and a few chromosomal islands. Both introgress through conjugative transfer, but have been subject to different types of selective forces.

scholarly journals NodC-based evaluation of the occurrence of bacteria in nodules of Pisum sativum isolated on YEM agar

2019 ◽  
Vol 70 (1) ◽  
pp. 59-67
Author(s):  
Anna Lenart-Boroń ◽  
Tadeusz Zając ◽  
Piotr Mateusz Boroń ◽  
Agnieszka Klimek-Kopyra
Keyword(s):  
Pisum Sativum ◽  
Rhizobium Leguminosarum ◽  
Reference Strain ◽  
Root Nodules ◽  
Bacterial Species ◽  
Soil Science ◽  
Associated Bacteria ◽  
Plant Cultivation ◽  
Yeast Extract Mannitol ◽  
Diverse Community

SummaryThe bacterial nodulation (nod) genes are essential in the formation process of root nodules. This study was aimed to verify the occurrence of nodule-associated bacteria in two pea varieties (“Tarchalska” and “Klif ”) inoculated withRhizobiuminoculants – Nitragine™ and a noncommercial one produced by the Polish Institute of Soil Science and Plant Cultivation (IUNG). The number of colonies isolated on yeast extract mannitol (YEM) agar from the nodules of “Klif ” inoculated with IUNG inoculants was significantly higher than the number of colonies isolated from other variants. Species identification was based on sequencing of 16S rDNA, which revealed that despite careful sterilization of nodules, sequences of other bacterial species were detected. Among them, one sequence belonged toRhizobium leguminosarum(isolated from IUNG inoculant). To assess the presence of nodulation-capableRhizobium, amplification of thenodCgene was performed, which revealed that of 29 samples, 19 were positive. The remaining isolates, including reference strain and bacteria isolated from Nitragine™, lacked this gene. The results show that pea nodules harbor a very diverse community of bacteria. The lack ofnodCgene in some strains isolated from plants inoculated with Nitragine™ and with IUNG inoculant proves that even ifR. leguminosarumare abundant, they may not be efficient in nodulation.

scholarly journals Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum

Open Biology ◽  
2015 ◽  
Vol 5 (1) ◽  
pp. 140133 ◽  
Author(s):  
Nitin Kumar ◽  
Ganesh Lad ◽  
Elisa Giuntini ◽  
Maria E. Kaye ◽  
Piyachat Udomwong ◽  
...  
Keyword(s):  
Rhizobium Leguminosarum ◽  
Bacterial Population ◽  
Population Genomics ◽  
Bacterial Species ◽  
Core Gene ◽  
Biological Species ◽  
Ecological Groups ◽  
Genetic Isolation ◽  
Taxonomic Framework ◽  
Core Genes

Biological species may remain distinct because of genetic isolation or ecological adaptation, but these two aspects do not always coincide. To establish the nature of the species boundary within a local bacterial population, we characterized a sympatric population of the bacterium Rhizobium leguminosarum by genomic sequencing of 72 isolates. Although all strains have 16S rRNA typical of R. leguminosarum , they fall into five genospecies by the criterion of average nucleotide identity (ANI). Many genes, on plasmids as well as the chromosome, support this division: recombination of core genes has been largely within genospecies. Nevertheless, variation in ecological properties, including symbiotic host range and carbon-source utilization, cuts across these genospecies, so that none of these phenotypes is diagnostic of genospecies. This phenotypic variation is conferred by mobile genes. The genospecies meet the Mayr criteria for biological species in respect of their core genes, but do not correspond to coherent ecological groups, so periodic selection may not be effective in purging variation within them. The population structure is incompatible with traditional ‘polyphasic taxonomy′ that requires bacterial species to have both phylogenetic coherence and distinctive phenotypes. More generally, genomics has revealed that many bacterial species share adaptive modules by horizontal gene transfer, and we envisage a more consistent taxonomic framework that explicitly recognizes this. Significant phenotypes should be recognized as ‘biovars' within species that are defined by core gene phylogeny.

Plasmid transfer systems in the rhizobia

2009 ◽  
Vol 55 (8) ◽  
pp. 917-927 ◽  
Author(s):  
Hao Ding ◽  
Michael F. Hynes
Keyword(s):  
Rhizobium Leguminosarum ◽  
Crop Yields ◽  
Conjugative Plasmid ◽  
Conjugative Transfer ◽  
Leguminous Plants ◽  
Agricultural Application ◽  
Leguminous Crop ◽  
Different Types ◽  
Large Plasmids ◽  
Rhizobial Inoculants

Rhizobia are agriculturally important bacteria that can form nitrogen-fixing nodules on the roots of leguminous plants. Agricultural application of rhizobial inoculants can play an important role in increasing leguminous crop yields. In temperate rhizobia, genes involved in nodulation and nitrogen fixation are usually located on one or more large plasmids (pSyms) or on symbiotic islands. In addition, other large plasmids of rhizobia carry genes that are beneficial for survival and competition of rhizobia in the rhizosphere. Conjugative transfer of these large plasmids thus plays an important role in the evolution of rhizobia. Therefore, understanding the mechanism of conjugative transfer of large rhizobial plasmids provides foundations for maintaining, monitoring, and predicting the behaviour of these plasmids during field release events. In this minireview, we summarize two types of known rhizobial conjugative plasmids, including quorum sensing regulated plasmids and RctA-repressed plasmids. We provide evidence for the existence of a third type of conjugative plasmid, including pRleVF39c in Rhizobium leguminosarum bv. viciae strain VF39SM, and we provide a comparison of the different types of conjugation genes found in members of the rhizobia that have had their genomes sequenced so far.

scholarly journals Heterospecific transcription of theEscherichia coli rpoB-3 allele in Gram-negative bacteria

1987 ◽  
Vol 50 (2) ◽  
pp. 87-90 ◽  
Author(s):  
Zainab Al-Doori
Keyword(s):  
Rhizobium Leguminosarum ◽  
Genetic Relatedness ◽  
Azotobacter Vinelandii ◽  
Bacterial Species ◽  
Enterobacter Aerogenes ◽  
Conjugative Plasmid ◽  
Broad Host Range ◽  
Gram Negative Bacteria ◽  
Resistance Phenotype ◽  
E Coli

SummaryrpoB is the structural gene for the β-subunit ofE. coliRNA polymerase. TherpoB-3 allele confers resistance to the antibiotic rifampicin and is unusual in being dominant to the wild-type allele. We used the plasmid pZD23, a derivative of the broad host range conjugative plasmid RP4, to introduce therpoB-3 allele into a range of bacterial species. Species belonging to the same family asE. coli(Enterobacter aerogenes, Citrobacter freundii, Hafnia alvei møller, Klebsiella pneumoniae, Salmonella typhimurium) expressedrpoB-3 to give a rifampicin resistant phenotype; this demonstrated heterospecific transcription. The transfer of pZD23 to the non-Enterobacteriaceae speciesAzotobacter vinelandiiandRhizobium leguminosarumdid not result in rifampicin resistance. In the former case this was due to non-expression of therpoB-3 resistance phenotype, in the latter case the dominant resistance phenotype had been lost from pZD23. Heterospecific transcription can be used as a criterion for the investigation of genetic relatedness between bacterial species.

scholarly journals Spatio-temporal control of mutualism in legumes helps spread symbiotic nitrogen fixation

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Benoit Daubech ◽  
Philippe Remigi ◽  
Ginaini Doin de Moura ◽  
Marta Marchetti ◽  
Cécile Pouzet ◽  
...  
Keyword(s):  
N2 Fixation ◽  
Temporal Dynamics ◽  
Root Nodules ◽  
Bacterial Species ◽  
Ecological Factors ◽  
Initial Inoculum ◽  
Selective Forces ◽  
Spatio Temporal ◽  
Plant Population Size ◽  
The Relationship

Mutualism is of fundamental importance in ecosystems. Which factors help to keep the relationship mutually beneficial and evolutionarily successful is a central question. We addressed this issue for one of the most significant mutualistic interactions on Earth, which associates plants of the leguminosae family and hundreds of nitrogen (N2)-fixing bacterial species. Here we analyze the spatio-temporal dynamics of fixers and non-fixers along the symbiotic process in the Cupriavidus taiwanensis–Mimosa pudica system. N2-fixing symbionts progressively outcompete isogenic non-fixers within root nodules, where N2-fixation occurs, even when they share the same nodule. Numerical simulations, supported by experimental validation, predict that rare fixers will invade a population dominated by non-fixing bacteria during serial nodulation cycles with a probability that is function of initial inoculum, plant population size and nodulation cycle length. Our findings provide insights into the selective forces and ecological factors that may have driven the spread of the N2-fixation mutualistic trait.

scholarly journals Biofilm Formation Drives Transfer of the Conjugative Element ICEBs1inBacillus subtilis

mSphere ◽  
2018 ◽  
Vol 3 (5) ◽  
Author(s):  
Frédéric Lécuyer ◽  
Jean-Sébastien Bourassa ◽  
Martin Gélinas ◽  
Vincent Charron-Lamoureux ◽  
Vincent Burrus ◽  
...  
Keyword(s):  
Extracellular Matrix ◽  
Antibiotic Resistance ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Biofilm Formation ◽  
Bacterial Species ◽  
High Rate ◽  
Conjugative Transfer ◽  
Bacterial Strains ◽  
Content Type

ABSTRACTHorizontal gene transfer by integrative and conjugative elements (ICEs) is a very important mechanism for spreading antibiotic resistance in various bacterial species. In environmental and clinical settings, most bacteria form biofilms as a way to protect themselves against extracellular stress. However, much remains to be known about ICE transfer in biofilms. Using ICEBs1fromBacillus subtilis, we show that the natural conjugation efficiency of this ICE is greatly affected by the ability of the donor and recipient to form a biofilm. ICEBs1transfer considerably increases in biofilm, even at low donor/recipient ratios. Also, while there is a clear temporal correlation between biofilm formation and ICEBs1transfer, biofilms do not alter the level of ICEBs1excision in donor cells. Conjugative transfer appears to be favored by the biophysical context of biofilms. Indeed, extracellular matrix production, particularly from the recipient cells, is essential for biofilms to promote ICEBs1transfer. Our study provides basic new knowledge on the high rate of conjugative transfer of ICEs in biofilms, a widely preponderant bacterial lifestyle in the environment, which could have a major impact on our understanding of horizontal gene transfer in natural and clinical environments.IMPORTANCETransfer of mobile genetic elements from one bacterium to another is the principal cause of the spread of antibiotic resistance. However, the dissemination of these elements in environmental contexts is poorly understood. In clinical and environmental settings, bacteria are often found living in multicellular communities encased in a matrix, a structure known as a biofilm. In this study, we examined how forming a biofilm influences the transmission of an integrative and conjugative element (ICE). Using the model Gram-positive bacteriumB. subtilis, we observed that biofilm formation highly favors ICE transfer. This increase in conjugative transfer is due to the production of extracellular matrix, which creates an ideal biophysical context. Our study provides important insights into the role of the biofilm structure in driving conjugative transfer, which is of major importance since biofilm is a widely preponderant bacterial lifestyle for clinically relevant bacterial strains.

scholarly journals An Evolutionary Link between Natural Transformation and CRISPR Adaptive Immunity

mBio ◽  
2012 ◽  
Vol 3 (5) ◽  
Author(s):  
Peter Jorth ◽  
Marvin Whiteley
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Bacterial Diversity ◽  
Natural Transformation ◽  
Bacterial Species ◽  
Comparative Genomic ◽  
Content Type ◽  
Immune Systems ◽  
Adaptive Immune ◽  
Adaptive Immune Systems

ABSTRACTNatural transformation by competent bacteria is a primary means of horizontal gene transfer; however, evidence that competence drives bacterial diversity and evolution has remained elusive. To test this theory, we used a retrospective comparative genomic approach to analyze the evolutionary history ofAggregatibacter actinomycetemcomitans, a bacterial species with both competent and noncompetent sister strains. Through comparative genomic analyses, we reveal that competence is evolutionarily linked to genomic diversity and speciation. Competence loss occurs frequently during evolution and is followed by the loss of clustered regularly interspaced short palindromic repeats (CRISPRs), bacterial adaptive immune systems that protect against parasitic DNA. Relative to noncompetent strains, competent bacteria have larger genomes containing multiple rearrangements. In contrast, noncompetent bacterial genomes are extremely stable but paradoxically susceptible to infective DNA elements, which contribute to noncompetent strain genetic diversity. Moreover, incomplete noncompetent strain CRISPR immune systems are enriched for self-targeting elements, which suggests that the CRISPRs have been co-opted for bacterial gene regulation, similar to eukaryotic microRNAs derived from the antiviral RNA interference pathway.IMPORTANCEThe human microbiome is rich with thousands of diverse bacterial species. One mechanism driving this diversity is horizontal gene transfer by natural transformation, whereby naturally competent bacteria take up environmental DNA and incorporate new genes into their genomes. Competence is theorized to accelerate evolution; however, attempts to test this theory have proved difficult. Through genetic analyses of the human periodontal pathogenAggregatibacter actinomycetemcomitans, we have discovered an evolutionary connection between competence systems promoting gene acquisition and CRISPRs (clustered regularly interspaced short palindromic repeats), adaptive immune systems that protect bacteria against genetic parasites. We show that competentA. actinomycetemcomitansstrains have numerous redundant CRISPR immune systems, while noncompetent bacteria have lost their CRISPR immune systems because of inactivating mutations. Together, the evolutionary data linking the evolution of competence and CRISPRs reveals unique mechanisms promoting genetic heterogeneity and the rise of new bacterial species, providing insight into complex mechanisms underlying bacterial diversity in the human body.

scholarly journals Transposase-Mediated Excision, Conjugative Transfer, and Diversity of ICE6013 Elements in Staphylococcus aureus

2017 ◽  
Vol 199 (8) ◽  
Author(s):  
Emily A. Sansevere ◽  
Xiao Luo ◽  
Joo Youn Park ◽  
Sunghyun Yoon ◽  
Keun Seok Seo ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Sequence Analysis ◽  
Integration Site ◽  
Consensus Sequence ◽  
Open Reading Frames ◽  
Conjugative Plasmid ◽  
Site Preference ◽  
Conjugative Transfer ◽  
Content Type ◽  
Integrative Conjugative Elements

ABSTRACT ICE6013 represents one of two families of integrative conjugative elements (ICEs) identified in the pan-genome of the human and animal pathogen Staphylococcus aureus. Here we investigated the excision and conjugation functions of ICE6013 and further characterized the diversity of this element. ICE6013 excision was not significantly affected by growth, temperature, pH, or UV exposure and did not depend on recA. The IS30-like DDE transposase (Tpase; encoded by orf1 and orf2) of ICE6013 must be uninterrupted for excision to occur, whereas disrupting three of the other open reading frames (ORFs) on the element significantly affects the level of excision. We demonstrate that ICE6013 conjugatively transfers to different S. aureus backgrounds at frequencies approaching that of the conjugative plasmid pGO1. We found that excision is required for conjugation, that not all S. aureus backgrounds are successful recipients, and that transconjugants acquire the ability to transfer ICE6013. Sequencing of chromosomal integration sites in serially passaged transconjugants revealed a significant integration site preference for a 15-bp AT-rich palindromic consensus sequence, which surrounds the 3-bp target site that is duplicated upon integration. A sequence analysis of ICE6013 from different host strains of S. aureus and from eight other species of staphylococci identified seven divergent subfamilies of ICE6013 that include sequences previously classified as a transposon, a plasmid, and various ICEs. In summary, these results indicate that the IS30-like Tpase functions as the ICE6013 recombinase and that ICE6013 represents a diverse family of mobile genetic elements that mediate conjugation in staphylococci. IMPORTANCE Integrative conjugative elements (ICEs) encode the abilities to integrate into and excise from bacterial chromosomes and plasmids and mediate conjugation between bacteria. As agents of horizontal gene transfer, ICEs may affect bacterial evolution. ICE6013 represents one of two known families of ICEs in the pathogen Staphylococcus aureus, but its core functions of excision and conjugation are not well studied. Here, we show that ICE6013 depends on its IS30-like DDE transposase for excision, which is unique among ICEs, and we demonstrate the conjugative transfer and integration site preference of ICE6013. A sequence analysis revealed that ICE6013 has diverged into seven subfamilies that are dispersed among staphylococci.

scholarly journals Acquisition of Beta-Lactamase by Neisseria meningitidis through Possible Horizontal Gene Transfer

2018 ◽  
Vol 62 (9) ◽  
Author(s):  
Eva Hong ◽  
Ala-Eddine Deghmane ◽  
Muhamed-Kheir Taha
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Genome Sequencing ◽  
Meningococcal Disease ◽  
Bacterial Species ◽  
Whole Genome ◽  
Beta Lactamase ◽  
Content Type ◽  
Beta Lactamases ◽  
Lactamase Gene

ABSTRACT We report the detection in France of a beta-lactamase-producing invasive meningococcal isolate. Whole-genome sequencing of the isolate revealed a ROB-1-type beta-lactamase gene that is frequently encountered in Haemophilus influenzae, suggesting horizontal transfer between isolates of these bacterial species. Beta-lactamases are exceptional in meningococci, with no reports for more than 2 decades. This report is worrying, as the expansion of such isolates may jeopardize the effective treatment against invasive meningococcal disease.

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