scholarly journals Genetic diversity and symbiotic efficiency difference of endophytic rhizobia of Medicago sativa

2019 ◽  
Vol 65 (1) ◽  
pp. 68-83 ◽  
Author(s):  
Wenjuan Kang ◽  
Lin Xu ◽  
Zhehao Jiang ◽  
Shangli Shi
Keyword(s):  
Medicago Sativa ◽  
Common Ancestor ◽  
Fragment Length Polymorphism ◽  
Housekeeping Genes ◽  
Strain Identification ◽  
Symbiotic Efficiency ◽  
Sequence Identity ◽  
Ensifer Meliloti ◽  
The Difference ◽  
Nifh Genes

Research on rhizobium diversity has paved the way for diversification of rhizobial germplasm resources. Seventy-three endophytic bacterial isolates were collected from seven tissues of five alfalfa cultivars in three geographic locations in Gansu, China. Restriction fragment length polymorphism (RFLP) fingerprinting of 16S rRNA and analysis of concatenated sequence of three housekeeping genes (atpD, glnII, and recA) and two symbiotic genes (nodC and nifH) were used for strain identification. Results showed that the endophytic strains were genetically diverse at different taxonomic levels, and Ensifer meliloti (31) and Agrobacterium radiobacter (12) are common Medicago sativa endophytic bacteria in Gansu, China. The nifH genes (97%–98% sequence identity) of E. meliloti strains were more diverse than the nodC genes (99%–100% sequence identity), even though the strains evolved from a common ancestor. The degree of dispersion of symbiotic phenotypes of E. meliloti strains on M. sativa ‘Gannong No. 3’, ‘Gannong No. 9’, and ‘Qingshui’ was much less than that on M. sativa ‘Longzhong’ and ‘WL168HQ’. This suggested that the symbiotic efficiency of E. meliloti strains on the former three alfalfa cultivars was similar but on the latter two was discrepant. Their symbiotic efficiency differed primarily according to alfalfa cultivars and, to a lesser extent, to the tested strains, indicating the difference in the sensitivity of different alfalfa cultivars to rhizobial strains.

scholarly journals Intra- and Interspecific Comparisons of Bacterial Diversity and Community Structure Support Coevolution of Gut Microbiota and Termite Host

2005 ◽  
Vol 71 (11) ◽  
pp. 6590-6599 ◽  
Author(s):  
Yuichi Hongoh ◽  
Pinsurang Deevong ◽  
Tetsushi Inoue ◽  
Shigeharu Moriya ◽  
Savitr Trakulnaleamsai ◽  
...  
Keyword(s):  
Community Structure ◽  
Gut Microbiota ◽  
Fragment Length Polymorphism ◽  
Clonal Analysis ◽  
Polymorphism Analysis ◽  
The Novel ◽  
Termite Species ◽  
Bacterial Phyla ◽  
Sequence Identity ◽  
Interspecific Comparisons

ABSTRACT We investigated the bacterial gut microbiota from 32 colonies of wood-feeding termites, comprising four Microcerotermes species (Termitidae) and four Reticulitermes species (Rhinotermitidae), using terminal restriction fragment length polymorphism analysis and clonal analysis of 16S rRNA. The obtained molecular community profiles were compared statistically between individuals, colonies, locations, and species of termites. Both analyses revealed that the bacterial community structure was remarkably similar within each termite genus, with small but significant differences between sampling sites and/or termite species. In contrast, considerable differences were found between the two termite genera. Only one bacterial phylotype (defined with 97% sequence identity) was shared between the two termite genera, while 18% and 50% of the phylotypes were shared between two congeneric species in the genera Microcerotermes and Reticulitermes, respectively. Nevertheless, a phylogenetic analysis of 228 phylotypes from Microcerotermes spp. and 367 phylotypes from Reticulitermes spp. with other termite gut clones available in public databases demonstrated the monophyly of many phylotypes from distantly related termites. The monophyletic “termite clusters” comprised of phylotypes from more than one termite species were distributed among 15 bacterial phyla, including the novel candidate phyla TG2 and TG3. These termite clusters accounted for 95% of the 960 clones analyzed in this study. Moreover, the clusters in 12 phyla comprised phylotypes from more than one termite (sub)family, accounting for 75% of the analyzed clones. Our results suggest that the majority of gut bacteria are not allochthonous but are specific symbionts that have coevolved with termites and that their community structure is basically consistent within a genus of termites.

scholarly journals Molecular Differentiation of Mycoplasma gallisepticum Outbreaks: A Last Decade Study on Italian Farms Using GTS and MLST

Vaccines ◽  
2020 ◽  
Vol 8 (4) ◽  
pp. 665
Author(s):  
Andrea Matucci ◽  
Elisabetta Stefani ◽  
Michele Gastaldelli ◽  
Ilenia Rossi ◽  
Gelinda De Grandi ◽  
...  
Keyword(s):  
Multilocus Sequence Typing ◽  
Evolutionary Dynamics ◽  
Housekeeping Genes ◽  
Mycoplasma Gallisepticum ◽  
Economic Losses ◽  
Strain Identification ◽  
Molecular Differentiation ◽  
Typing Methods ◽  
Infection Monitoring ◽  
Monitoring Activity

Mycoplasma gallisepticum (MG) infects many avian species and leads to significant economic losses in the poultry industry. Transmission of this pathogen occurs both horizontally and vertically, and strategies to avoid the spread of MG rely on vaccination and the application of biosecurity measures to maintain breeder groups as pathogen-free. Two live attenuated MG vaccine strains are licensed in Italy: 6/85 and ts-11. After their introduction, the implementation of adequate genotyping tools became necessary to distinguish between field and vaccine strains and to guarantee proper infection monitoring activity. In this study, 40 Italian MG isolates collected between 2010–2019 from both vaccinated and unvaccinated farms were genotyped using gene-targeted sequencing (GTS) of the cythadesin gene mgc2 and multilocus sequence typing (MLST) based on six housekeeping genes. The discriminatory power of GTS typing ensures 6/85-like strain identification, but the technique does not allow the identification ts-11 strains; conversely, MLST differentiates both vaccine strains, describing more detailed interrelation structures. Our study describes MG genetic scenario within a mixed farming context. In conclusion, the use of adequate typing methods is essential to understand the evolutionary dynamics of MG strains in a particular area and to conduct epidemiological investigations in the avian population.

scholarly journals EFFETS DES SOUCHES DE RHIZOBIUM MELILOTI ET DES COUPES SUCCESSIVES DE LA LUZERNE (MEDICAGO SATIVA) SUR LA FIXATION SYMBIOTIQUE D’AZOTE

1977 ◽  
Vol 57 (2) ◽  
pp. 433-439 ◽  
Author(s):  
L. M. BORDELEAU ◽  
H. ANTOUN ◽  
R. A. LACHANCE
Keyword(s):  
Nitrogen Fixation ◽  
Medicago Sativa ◽  
Statistical Study ◽  
Symbiotic Nitrogen Fixation ◽  
Rhizobium Meliloti ◽  
Dry Weight ◽  
Indirect Measurement ◽  
Controlled Environment ◽  
Symbiotic Efficiency ◽  
Plant Yield

Symbiotic nitrogen fixation with 49 isolates of Rhizobium meliloti was studied under controlled environment with alfalfa cv. Saranac. It was shown that plant yield in dry weight can be used as an indirect measurement of nitrogen fixation, and as a criterion for selecting efficient strains of R. meliloti. Statistical study on yields of three cuttings has established that the second cutting gives the most necessary information to correctly evaluate the symbiotic efficiency of the isolates. Six very efficient strains were selected.

scholarly journals Infectivity of Lactobacillus rhamnosus and Lactobacillus paracasei isolates in a rat model of experimental endocarditis

2007 ◽  
Vol 56 (8) ◽  
pp. 1017-1024 ◽  
Author(s):  
Vanessa Vankerckhoven ◽  
Philippe Moreillon ◽  
Stéphane Piu ◽  
Marlyse Giddey ◽  
Geert Huys ◽  
...  
Keyword(s):  
Rat Model ◽  
Fragment Length Polymorphism ◽  
Lactobacillus Rhamnosus ◽  
Lactobacillus Paracasei ◽  
Clinical Isolates ◽  
Adhesion Properties ◽  
Platelet Microbicidal Protein ◽  
The Difference ◽  
Probiotic Lactobacilli ◽  
Potential Pathogenicity

The potential pathogenicity of selected (potentially) probiotic and clinical isolates of Lactobacillus rhamnosus and Lactobacillus paracasei was investigated in a rat model of experimental endocarditis. In addition, adhesion properties of the lactobacilli for fibrinogen, fibronectin, collagen and laminin, as well as the killing activity of the platelet-microbicidal proteins fibrinopeptide A (FP-A) and connective tissue activating peptide 3 (CTAP-3), were assessed. The 90 % infective dose (ID90) of the L. rhamnosus endocarditis isolates varied between 106 and 107 c.f.u., whereas four of the six (potentially) probiotic L. rhamnosus isolates showed an ID90 that was at least 10-fold higher (108 c.f.u.) (P<0.001). In contrast, the two other probiotic L. rhamnosus isolates exhibited an ID90 (106 and 107 c.f.u.) comparable to the ID90 of the clinical isolates of this species investigated (P>0.05). Importantly, these two probiotic isolates shared the same fluorescent amplified fragment length polymorphism cluster type as the clinical isolate showing the lowest ID90 (106 c.f.u.). L. paracasei tended to have a lower infectivity than L. rhamnosus (ID90 of 107 to ≥108 c.f.u.). All isolates had comparable bacterial counts in cardiac vegetations (P>0.05). Except for one L. paracasei strain adhering to all substrates, all tested lactobacilli adhered only weakly or not at all. The platelet peptide FP-A did not show any microbicidal activity against the tested lactobacilli, whereas CTAP-3 killed the majority of the isolates. In general, these results indicate that probiotic lactobacilli display a lower infectivity in experimental endocarditis compared with true endocarditis pathogens. However, the difference in infectivity between L. rhamnosus endocarditis and (potentially) probiotic isolates could not be explained by differences in adherence or platelet microbicidal protein susceptibility. Other disease-promoting factors may exist in these organisms and warrant further investigation.

scholarly journals Distribution and Phylogeny of Microsymbionts Associated with Cowpea (Vigna unguiculata) Nodulation in Three Agroecological Regions of Mozambique

2017 ◽  
Vol 84 (2) ◽  
Author(s):  
Ifeoma N. Chidebe ◽  
Sanjay K. Jaiswal ◽  
Felix D. Dakora
Keyword(s):  
Sequence Analysis ◽  
Root Nodules ◽  
Single Gene ◽  
Housekeeping Genes ◽  
Sub Saharan Africa ◽  
Bacterial Isolates ◽  
Rhizobium Tropici ◽  
Symbiotic Efficiency ◽  
Content Type ◽  
N Nutrition

ABSTRACTCowpea derives most of its N nutrition from biological nitrogen fixation (BNF) via symbiotic bacteroids in root nodules. In Sub-Saharan Africa, the diversity and biogeographic distribution of bacterial microsymbionts nodulating cowpea and other indigenous legumes are not well understood, though needed for increased legume production. The aim of this study was to describe the distribution and phylogenies of rhizobia at different agroecological regions of Mozambique using PCR of the BOX element (BOX-PCR), restriction fragment length polymorphism of the internal transcribed spacer (ITS-RFLP), and sequence analysis of ribosomal, symbiotic, and housekeeping genes. A total of 122 microsymbionts isolated from two cowpea varieties (IT-1263 and IT-18) grouped into 17 clades within the BOX-PCR dendrogram. The PCR-ITS analysis yielded 17 ITS types for the bacterial isolates, while ITS-RFLP analysis placed all test isolates in six distinct clusters (I to VI). BLASTnsequence analysis of 16S rRNA and four housekeeping genes (glnII,gyrB,recA, andrpoB) showed their alignment withRhizobiumandBradyrhizobiumspecies. The results revealed a group of highly diverse and adapted cowpea-nodulating microsymbionts which includedBradyrhizobium pachyrhizi,Bradyrhizobium arachidis,Bradyrhizobium yuanmingense, and a novelBradyrhizobiumsp., as well asRhizobium tropici,Rhizobium pusense, andNeorhizobium galegaein Mozambican soils. Discordances observed in single-gene phylogenies could be attributed to horizontal gene transfer and/or subsequent recombinations of the genes. Natural deletion of 60 bp of thegyrBregion was observed in isolate TUTVU7; however, this deletion effect on DNA gyrase function still needs to be confirmed. The inconsistency ofnifHwith core gene phylogenies suggested differences in the evolutionary history of both chromosomal and symbiotic genes.IMPORTANCEA diverse group of bothBradyrhizobiumandRhizobiumspecies responsible for cowpea nodulation in Mozambique was found in this study. Future studies could prove useful in evaluating these bacterial isolates for symbiotic efficiency and strain competitiveness in Mozambican soils.

scholarly journals Crystal structure of an alleged mannosylphosphate transferase Ktr6p at 3.06 Å

2014 ◽  
Vol 70 (a1) ◽  
pp. C1671-C1671
Author(s):  
Dmitry Rodionov ◽  
Daniella Marks ◽  
Pedro Romero ◽  
Albert Berghuis
Keyword(s):  
Room Temperature ◽  
Sequence Similarity ◽  
Transferase Activity ◽  
Molecular Replacement ◽  
Sequence Identity ◽  
Mannose Binding ◽  
The Difference ◽  
Resolution Dataset ◽  
Close Homolog

Ktr6p is an alleged mannosylphosphate transferase from yeast Golgi. It has been implicated in decorating both O-linked and N-lined glycans with mannosylphosphate in vivo. However, based on sequence similarity, Ktr6p belongs to GT15 family of α-1,2-mannosyltransferases. To address this disagreement, the soluble portion of Ktr6p was expressed in P. pastoris and purified by liquid chromatography. The purified protein, GDP-mannose and various acceptors were used in a number of direct and indirect activity assays, however, neither manosyltransferase nor mannosylphosphate transferase activity was detected. Ktr6p was crystallized in a number of PEG- containing conditions, but the crystals resisted all attempts at cryoprotection. Three crystals were used to collect a 3.06 Å resolution dataset on a home source at room temperature. The crystals belong to P 21 21 21 spacegroup with 2 molecules per asymmetric unit. The structure was solved by molecular replacement using a structure of Kre2p, a close homolog from GT15 family (40% sequence identity). The structure was refined to R/Rfree 16.1%/21.2% The overall structure of Ktr6p is very similar to the structure of Kre2p having less than 2 Å overall backbone RMSD. However even at 3 Å resolution the difference in the active site is striking. The guanine moiety binding pocked is occluded by a well-ordered loop making GDP-mannose binding impossible in this conformation. Several aminoacid substitutions in the Mn2+ coordinating environment suggest that Ktr6 does not depend on manganese for its postulated activity. These observations indicate that Ktr6p functions quite differently from Kre2p.

scholarly journals The asgardarchaeal-unique contribution to protein families of the eukaryotic common ancestor was 0.3%

2021 ◽  
Author(s):  
Michael Knopp ◽  
Simon Stockhorst ◽  
Mark van der Giezen ◽  
Sriram G. Garg ◽  
Sven B. Gould
Keyword(s):  
Cell Biology ◽  
Common Ancestor ◽  
Unique Contribution ◽  
Clustering Methods ◽  
Protein Families ◽  
Archaeal Lineage ◽  
Specific Proteins ◽  
The Difference ◽  
Coding Capacity ◽  
Eukaryotic Genomes

Significance StatementEver since the first report of a new archaeal lineage, the asgardarchaea, their metagenome analyses have encouraged continued speculations on a type of cell biology ranging between that of prokaryotes and eukaryotes. While it appears a tempting notion, recent microscopic images of an asgardarchaeon suggest otherwise. We inspected the origin of eukaryotic protein families with respect to their distribution across bacteria and archaea. This reveals that the protein families shared exclusively between asgardarchaea and eukaryotes amounts to only 0.3% of the protein families conserved across all eukaryotes. Asgardarchaeal diversity is likely unrivaled across archaea, but their cell biology remains prokaryotic in nature and lends support for the importance of endosymbiosis in evolving eukaryotic traits.SummaryThe difference between pro- and eukaryotic biology is evident in their genomes, cell biology, and evolution of complex and macroscopic body plans. The lack of intermediates between the two types of cells places the endosymbiotic acquisition of the mitochondrion through an archaeal host at the event horizon of eukaryote origin. The identification of eukaryote specific proteins in a new archaeal phylum, the asgardarchaea, has fueled speculations about their cellular complexity, suggesting they could be eukaryote-like. Here we analyzed the coding capacity of 150 eukaryotes, 1000 bacteria, and 226 archaea, including the only cultured member of the asgardarchaea, Candidatus Prometheoarchaeon syntrophicum MK-D1. Established clustering methods that recover endosymbiotic contributions to eukaryotic genomes, recover an asgardarchaeal-unique contribution of a mere 0.3% to protein families present in the last eukaryotic common ancestor, while simultaneously suggesting that asgardarchaeal diversity rivals that of all other archaea combined. Furthermore, we show that the number of homologs shared exclusively between asgardarchaea and eukaryotes is only 27 on average. Genomic and in particular cellular complexity remains a eukaryote-specific feature and, we conclude, is best understood as the archaeal host’s solution to housing an endosymbiont and not as a preparation for obtaining one.

scholarly journals Molecular Genetic Basis of Ribotyping

2008 ◽  
Vol 21 (2) ◽  
pp. 262-273 ◽  
Author(s):  
Valérie Bouchet ◽  
Heather Huot ◽  
Richard Goldstein
Keyword(s):  
Genetic Basis ◽  
Fragment Length Polymorphism ◽  
A Priori ◽  
Molecular Genetic ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Sequence Variability ◽  
Gene Sequences ◽  
Molecular Genetic Basis ◽  
Pcr Ribotyping

SUMMARY Nearly 2,000 ribotyping-based studies exist, ranging from epidemiology to phylogeny and taxonomy. None precisely reveals the molecular genetic basis, with many incorrectly attributing detected polymorphisms to rRNA gene sequences. Based on in silico genomics, we demonstrate that ribotype polymorphisms result from sequence variability in neutral housekeeping genes flanking rRNA operons, with rRNA gene sequences serving solely as conserved, flank-linked tags. We also reveal that from such an informatics perspective, it is readily feasible a priori to design an interpretable ribotyping scheme for a genomically sequenced microbial species, and we discuss limitations to the basic restriction fragment length polymorphism-based method as well as alternate PCR ribotyping-based schemes.

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