scholarly journals Diverse Bacteria Affiliated with the Genera Microvirga, Phyllobacterium, and Bradyrhizobium Nodulate Lupinus micranthus Growing in Soils of Northern Tunisia

2017 ◽  
Vol 83 (6) ◽  
Author(s):  
Abdelhakim Msaddak ◽  
David Durán ◽  
Mokhtar Rejili ◽  
Mohamed Mars ◽  
Tomás Ruiz-Argüeso ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Housekeeping Genes ◽  
The Other ◽  
Vegetation Coverage ◽  
Phylogenetic Study ◽  
Bacterial Populations ◽  
Symbiotic Gene ◽  
Northern Tunisia ◽  
Content Type ◽  
Semiarid Areas

ABSTRACT The genetic diversity of bacterial populations nodulating Lupinus micranthus in five geographical sites from northern Tunisia was examined. Phylogenetic analyses of 50 isolates based on partial sequences of recA and gyrB grouped strains into seven clusters, five of which belong to the genus Bradyrhizobium (28 isolates), one to Phyllobacterium (2 isolates), and one, remarkably, to Microvirga (20 isolates). The largest Bradyrhizobium cluster (17 isolates) grouped with the B. lupini species, and the other five clusters were close to different recently defined Bradyrhizobium species. Isolates close to Microvirga were obtained from nodules of plants from four of the five sites sampled. We carried out an in-depth phylogenetic study with representatives of the seven clusters using sequences from housekeeping genes (rrs, recA, glnII, gyrB, and dnaK) and obtained consistent results. A phylogeny based on the sequence of the symbiotic gene nodC identified four groups, three formed by Bradyrhizobium isolates and one by the Microvirga and Phyllobacterium isolates. Symbiotic behaviors of the representative strains were tested, and some congruence between symbiovars and symbiotic performance was observed. These data indicate a remarkable diversity of L. micranthus root nodule symbionts in northern Tunisia, including strains from the Bradyrhizobiaceae, Methylobacteriaceae, and Phyllobacteriaceae families, in contrast with those of the rhizobial populations nodulating lupines in the Old World, including L. micranthus from other Mediterranean areas, which are nodulated mostly by Bradyrhizobium strains. IMPORTANCE Lupinus micranthus is a legume broadly distributed in the Mediterranean region and plays an important role in soil fertility and vegetation coverage by fixing nitrogen and solubilizing phosphate in semiarid areas. Direct sowing to extend the distribution of this indigenous legume can contribute to the prevention of soil erosion in pre-Saharan lands of Tunisia. However, rhizobial populations associated with L. micranthus are poorly understood. In this context, the diversity of endosymbionts of this legume was investigated. Most Lupinus species are nodulated by Bradyrhizobium strains. This work showed that about half of the isolates from northern Tunisian soils were in fact Bradyrhizobium symbionts, but the other half were found unexpectedly to be bacteria within the genera Microvirga and Phyllobacterium. These unusual endosymbionts may have a great ecological relevance. Inoculation with the appropriate selected symbiotic bacterial partners will increase L. micranthus survival with consequent advantages for the environment in semiarid areas of Tunisia.

New chromosomal lineages within Microvirga and Bradyrhizobium genera nodulate Lupinus angustifolius growing on different Tunisian soils

2019 ◽  
Vol 95 (9) ◽  
Author(s):  
M Rejili ◽  
A Msaddak ◽  
I Filali ◽  
M A Benabderrahim ◽  
M Mars ◽  
...  
Keyword(s):  
Root Nodule ◽  
Phylogenetic Analyses ◽  
Housekeeping Genes ◽  
Lupinus Angustifolius ◽  
Gene Markers ◽  
Symbiotic Gene ◽  
Northern Tunisia ◽  
Nodc Gene ◽  
Study Support ◽  
A New Species

ABSTRACT Thirty-one rhizobial isolates nodulating native Lupinus angustifolius (blue lupine) plants growing in Northern Tunisian soils were isolated and analysed using different chromosomal and symbiotic gene markers. Phylogenetic analyses based on recA partial sequences grouped them into at least five groups: four of them within the genus Bradyrhizobium (26 isolates) and one into the genus Microvirga (5 isolates). Representative strains were analysed by multilocus sequence analysis of three housekeeping genes rrs-recA-glnII and rrs-gyrB-dnaK for Bradyrhizobium and Microvirga isolates, respectively. Based on this analysis, eight isolates clustered with the previously described strains Bradyrhizobium lupini USDA3051 and Bradyrhizobium canariense BTA-1. However, five of the isolates clustered separately and may constitute a new species within the Bradyrhizobium genus. The remaining five isolates were closely related to the strain Microvirga sp. LmiM8 and may constitute a new Microvirga species. The analysis of the nodC gene showed that all Bradyrhizobium strains nodulating blue lupine belong to the symbiovar genistearum, whereas the Microvirga isolates are associated with the symbiovar mediterranense. The results of this study support that the L. angustifolius root nodule symbionts isolated in Northern Tunisia belong mostly to the B. canariense/B. lupini lineages. However, new clades of Bradyrhizobium and Microvirga have been identified as L. angustifolius endosymbionts.

scholarly journals Global Multilocus Sequence Type Analysis of Chlamydia trachomatis Strains from 16 Countries

2015 ◽  
Vol 53 (7) ◽  
pp. 2172-2179 ◽  
Author(s):  
Björn Herrmann ◽  
Jenny Isaksson ◽  
Martin Ryberg ◽  
Jeanette Tångrot ◽  
Isam Saleh ◽  
...  
Keyword(s):  
Chlamydia Trachomatis ◽  
Minimum Spanning Tree ◽  
Diversity Index ◽  
Phylogenetic Analyses ◽  
Housekeeping Genes ◽  
Sequence Type ◽  
Specific Gene ◽  
Whole Genome Analysis ◽  
Content Type ◽  
Global Spread

The Uppsala UniversityChlamydia trachomatismultilocus sequence type (MLST) database (http://mlstdb.bmc.uu.se) is based on five target regions (non-housekeeping genes) and theompAgene. Each target has various numbers of alleles—hctB, 89; CT058, 51; CT144, 30; CT172, 38; andpbpB, 35—derived from 13 studies. Our aims were to perform an overall analysis of allC. trachomatisMLST sequence types (STs) in the database, examine STs with global spread, and evaluate the phylogenetic capability by using the five targets. A total of 415 STs were recognized from 2,089 specimens. The addition of 49ompAgene variants created 459 profiles. ST variation and their geographical distribution were characterized using eBURST and minimum spanning tree analyses. There were 609 samples from men having sex with men (MSM), with 4 predominating STs detected in this group, comprising 63% of MSM cases. Four other STs predominated among 1,383 heterosexual cases comprising, 31% of this group. The diversity index in ocular trachoma cases was significantly lower than in sexually transmitted chlamydia infections. Predominating STs were identified in 12 availableC. trachomatiswhole genomes which were compared to 22C. trachomatisfull genomes without predominating STs. No specific gene in the 12 genomes with predominating STs could be linked to successful spread of certain STs. Phylogenetic analysis showed that MLST targets provide a tree similar to trees based on whole-genome analysis. The presented MLST scheme identifiedC. trachomatisstrains with global spread. It provides a tool for epidemiological investigations and is useful for phylogenetic analyses.

scholarly journals Bradyrhizobium ganzhouense sp. nov., an effective symbiotic bacterium isolated from Acacia melanoxylon R. Br. nodules

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1900-1905 ◽  
Author(s):  
Jun Kun Lu ◽  
Ya Jing Dou ◽  
Ya Jie Zhu ◽  
Sheng Kun Wang ◽  
Xin Hua Sui ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Restriction Analysis ◽  
Phylogenetic Analyses ◽  
Jiangxi Province ◽  
Rrna Gene ◽  
Symbiotic Gene ◽  
Content Type ◽  
Acacia Melanoxylon ◽  
Link Type

Three slow-growing rhizobial strains, designated RITF806T, RITF807 and RITF211, isolated from root nodules of Acacia melanoxylon grown in Ganzhou city, Jiangxi Province, China, had been previously defined, based on amplified 16S rRNA gene restriction analysis, as a novel group within the genus Bradyrhizobium . To clarify their taxonomic position, these strains were further analysed and compared with reference strains of related bacteria using a polyphasic approach. According to 16S rRNA gene sequence analysis, the isolates formed a group that was closely related to ‘Bradyrhizobium rifense’ CTAW71, with a similarity value of 99.9 %. In phylogenetic analyses of the housekeeping and symbiotic gene sequences, the three strains formed a distinct lineage within the genus Bradyrhizobium , which was consistent with the results of DNA–DNA hybridization. In analyses of cellular fatty acids and phenotypic features, some differences were found between the novel group and related species of the genus Bradyrhizobium , indicating that these three strains constituted a novel group distinct from any recognized species of the genus Bradyrhizobium . Based on the data obtained in this study, we conclude that our strains represent a novel species of the genus Bradyrhizobium , for which the name Bradyrhizobium ganzhouense sp. nov. is proposed, with RITF806T ( = CCBAU 101088T = JCM 19881T) as the type strain. The DNA G+C content of strain RITF806T is 64.6 mol% (T m).

scholarly journals Genotypic and Chemotypic Diversity of Neotyphodium Endophytes in Tall Fescue from Greece

2012 ◽  
Vol 78 (16) ◽  
pp. 5501-5510 ◽  
Author(s):  
Johanna E. Takach ◽  
Shipra Mittal ◽  
Ginger A. Swoboda ◽  
Sherrita K. Bright ◽  
Michael A. Trammell ◽  
...  
Keyword(s):  
Tall Fescue ◽  
Festuca Arundinacea ◽  
Phylogenetic Analyses ◽  
Housekeeping Genes ◽  
Gene Clusters ◽  
Content Type ◽  
Chemotype Diversity ◽  
Group 2 ◽  
Specific Association ◽  
Insight Into

ABSTRACTEpichloid endophytes provide protection from a variety of biotic and abiotic stresses for cool-season grasses, including tall fescue. A collection of 85 tall fescue lines from 15 locations in Greece, including both Continental and Mediterranean germplasm, was screened for the presence of native endophytes. A total of 37 endophyte-infected lines from 10 locations were identified, and the endophytes were classified into five distinct groups (G1 to G5) based on physical characteristics such as colony morphology, growth rate, and conidial morphology. These classifications were supported by phylogenetic analyses of housekeeping genestefAandtubB, and the endophytes were further categorized asNeotyphodium coenophialumisolates (G1, G4, and G5) orNeotyphodiumsp. FaTG-2 (Festuca arundinaceataxonomic group 2 isolates (G2 and G3). Analyses of the tall fescuematKchloroplast genes indicated a population-wide, host-specific association betweenN. coenophialumand Continental tall fescue and between FaTG-2 and Mediterranean tall fescue that was also reflected by differences in colonization of host tillers by the native endophytes. Genotypic analyses of alkaloid gene loci combined with chemotypic (chemical phenotype) profiles provided insight into the genetic basis of chemotype diversity. Variation in alkaloid gene content, specifically the presence and absence of genes, and copy number of gene clusters explained the alkaloid diversity observed in the endophyte-infected tall fescue, with one exception. The results from this study provide insight into endophyte germplasm diversity present in living tall fescue populations.

Ingroup relationships of Lagerpetidae (Avemetatarsalia: Dinosauromorpha): a further phylogenetic investigation on the understanding of dinosaur relatives

Zootaxa ◽  
2018 ◽  
Vol 4392 (1) ◽  
pp. 149 ◽  
Author(s):  
RODRIGO TEMP MÜLLER ◽  
MAX CARDOSO LANGER ◽  
SÉRGIO DIAS-DA-SILVA
Keyword(s):  
Phylogenetic Analyses ◽  
Sister Group ◽  
The Other ◽  
Sister Taxon ◽  
Phylogenetic Study ◽  
Sister Group Relationship ◽  
Independent Data ◽  
New Findings ◽  
Alternative Topology ◽  
Western Portion

Despite representing a key-taxon in dinosauromorph phylogeny, Lagerpertidae is one of the most obscure and enigmatic branches from the stem that leads to the dinosaurs. Recent new findings have greatly increased our knowledge about lagerpetids, but no phylogenetic analysis has so far included all known members of this group. Here, we present the most inclusive phylogenetic study so far conducted for Lagerpetidae. Phylogenetic analyses were performed based on three independent data matrixes. In two of them, Lagerpeton chanarensis Romer, 1971 is the sister taxon to all other known Lagerpetidae, whereas Ixalerpeton polesinensis Cabreira et al., 2016 is in a sister group relationship with a clade that includes PVSJ 883 and Dromomeron. Conversely, the other analysis supports an alternative topology, where I. polesinensis is the sister taxon to either L. chanarensis or all other Lagerpetidae. Although coeval and geographically close, I. polesinensis and PVSJ 883 do not form a clade exclusive of other lagerpetids. As previously suggested D. gigas Martínez, Apaldetti, Correa & Abelín, 2016 is the sister taxon of D. romeri Irmis et al., 2007. The phylogenetic analyses also indicate that the earliest lagerpetids are restricted to southwestern Pangea, whereas later forms spread across the entire western portion of the supercontinent. Finally, quantification of the codified characters of our analysis reveals that Lagerpetidae is one of the poorest known among the Triassic dinosauromorph groups in terms of their anatomy, so that new discoveries of more complete specimens are awaited to establish a more robust phylogeny. 

scholarly journals Replicon-Dependent Differentiation of Symbiosis-Related Genes in Sinorhizobium Strains Nodulating Glycine max

2013 ◽  
Vol 80 (4) ◽  
pp. 1245-1255 ◽  
Author(s):  
Hui Juan Guo ◽  
En Tao Wang ◽  
Xing Xing Zhang ◽  
Qin Qin Li ◽  
Yan Ming Zhang ◽  
...  
Keyword(s):  
Glycine Max ◽  
Genetic Differentiation ◽  
Phylogenetic Analyses ◽  
Housekeeping Genes ◽  
Distinct Species ◽  
Average Nucleotide Identity ◽  
Test Species ◽  
Content Type ◽  
Intraspecies Diversity ◽  
Different Levels

ABSTRACTIn order to investigate the genetic differentiation ofSinorhizobiumstrains nodulatingGlycine maxand related microevolutionary mechanisms, three housekeeping genes (SMc00019,truA, andthrA) and 16 symbiosis-related genes on the chromosome (7 genes), pSymA (6 genes), and pSymB (3 genes) were analyzed. Five distinct species were identified among the test strains by calculating the average nucleotide identity (ANI) ofSMc00019-truA-thrA:Sinorhizobium fredii,Sinorhizobium sojae,Sinorhizobiumsp. I,Sinorhizobiumsp. II, andSinorhizobiumsp. III. These species assignments were also supported by population genetics and phylogenetic analyses of housekeeping genes and symbiosis-related genes on the chromosome and pSymB. Different levels of genetic differentiation were observed among these species or different replicons.S. sojaewas the most divergent from the other test species and was characterized by its low intraspecies diversity and limited geographic distribution. Intergenic recombination dominated the evolution of 19 genes from different replicons. Intraspecies recombination happened frequently in housekeeping genes and symbiosis-related genes on the chromosome and pSymB, whereas pSymA genes showed a clear pattern of lateral-transfer events between different species. Moreover, pSymA genes were characterized by a lower level of polymorphism and recombination than those on the chromosome and pSymB. Taken together, genes from different replicons of rhizobia might be involved in the establishment of symbiosis with legumes, but these symbiosis-related genes might have evolved differently according to their corresponding replicons.

scholarly journals Disentangling the Taxonomy of Rickettsiales and Description of Two Novel Symbionts (“Candidatus Bealeia paramacronuclearis” and “Candidatus Fokinia cryptica”) Sharing the Cytoplasm of the Ciliate Protist Paramecium biaurelia

2016 ◽  
Vol 82 (24) ◽  
pp. 7236-7247 ◽  
Author(s):  
Franziska Szokoli ◽  
Michele Castelli ◽  
Elena Sabaneyeva ◽  
Martina Schrallhammer ◽  
Sascha Krenek ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Small Subunit ◽  
Sensu Stricto ◽  
The Other ◽  
Rrna Genes ◽  
Small Subunit Rrna ◽  
Taxonomic Assignment ◽  
Content Type ◽  
The Family ◽  
Critical Revision

ABSTRACTIn the past 10 years, the number of endosymbionts described within the bacterial orderRickettsialeshas constantly grown. Since 2006, 18 novelRickettsialesgenera inhabiting protists, such as ciliates and amoebae, have been described. In this work, we characterize two novel bacterial endosymbionts fromParameciumcollected near Bloomington, IN. Both endosymbiotic species inhabit the cytoplasm of the same host. The Gram-negative bacterium “CandidatusBealeia paramacronuclearis” occurs in clumps and is frequently associated with the host macronucleus. With its electron-dense cytoplasm and a distinct halo surrounding the cell, it is easily distinguishable from the second smaller symbiont, “CandidatusFokinia cryptica,” whose cytoplasm is electron lucid, lacks a halo, and is always surrounded by a symbiontophorous vacuole. For molecular characterization, the small-subunit rRNA genes were sequenced and used for taxonomic assignment as well as the design of species-specific oligonucleotide probes. Phylogenetic analyses revealed that “CandidatusBealeia paramacronuclearis” clusters with the so-called “basal”Rickettsiales, and “CandidatusFokinia cryptica” belongs to “CandidatusMidichloriaceae.” We obtained tree topologies showing a separation ofRickettsialesinto at least two groups: one represented by the familiesRickettsiaceae,Anaplasmataceae, and “CandidatusMidichloriaceae” (RAM clade), and the other represented by “basalRickettsiales,” including “CandidatusBealeia paramacronuclearis.” Therefore, and in accordance with recent publications, we propose to limit the orderRickettsialesto the RAM clade and to raise “basalRickettsiales” to an independent order,Holosporalesord. nov., insideAlphaproteobacteria, which presently includes four family-level clades. Additionally, we define the family “CandidatusHepatincolaceae” and redefine the familyHolosporaceae.IMPORTANCEIn this paper, we provide the characterization of two novel bacterial symbionts inhabiting the sameParameciumhost (Ciliophora, Alveolata). Both symbionts belong to “traditional”Rickettsiales, one representing a new species of the genus “CandidatusFokinia” (“CandidatusMidichloriaceae”), and the other representing a new genus of a “basal”Rickettsiales. According to newly characterized sequences and to a critical revision of recent literature, we propose a taxonomic reorganization of “traditional”Rickettsialesthat we split into two orders:Rickettsiales sensu strictoandHolosporalesord. nov. This work represents a critical revision, including new records of a group of symbionts frequently occurring in protists and whose biodiversity is still largely underestimated.

scholarly journals Bradyrhizobium ingae sp. nov., isolated from effective nodules of Inga laurina grown in Cerrado soil

2014 ◽  
Vol 64 (Pt_10) ◽  
pp. 3395-3401 ◽  
Author(s):  
Krisle da Silva ◽  
Sofie E. De Meyer ◽  
Luc F. M. Rouws ◽  
Eliane N. C. Farias ◽  
Marco A. O. dos Santos ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Content Type ◽  
Slow Growth Rate ◽  
Link Type ◽  
Commercial Inoculant

Root-nodule bacteria were isolated from Inga laurina (Sw.) Willd. growing in the Cerrado Amazon region, State of Roraima, Brazil. The 16S rRNA gene sequences of six strains (BR 10250T, BR 10248, BR 10249, BR 10251, BR 10252 and BR 10253) showed low similarities with currently described species of the genus Bradyrhizobium . Phylogenetic analyses of sequences of five housekeeping genes (dnaK, glnII, gyrB, recA and rpoB) revealed Bradyrhizobium iriomotense EK05T to be the closest type strain (97.4 % sequence similarity or less). Chemotaxonomic data, including fatty acid profiles [with the major components C16 : 0 and summed feature 8 (C18 : 1ω6c/C18 : 1ω7c)], the slow growth rate and carbon compound utilization patterns supported the assignment of our strains to the genus Bradyrhizobium . Results from DNA–DNA hybridizations and physiological traits differentiated our strains from the closest related species of the genus Bradyrhizobium with validly published names. Sequences of symbiosis-related genes for nodulation (nodC) and nitrogen fixation (nifH) grouped together with those of B. iriomotense EK05T and Bradyrhizobium sp. strains BR 6610 (used as a commercial inoculant for Inga marginata in Brazil) and TUXTLAS-10 (previously observed in Central America). Based on these data, the six strains represent a novel species, for which the name Bradyrhizobium ingae sp. nov. is proposed. The type strain is BR 10250T ( = HAMBI 3600T).

Multilocus sequence analysis and 16S rRNA gene sequencing reveal that Yersinia frederiksenii genospecies 2 is Yersinia massiliensis

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 3124-3129 ◽  
Author(s):  
Roberto A. Souza ◽  
Priscilla F. M. Imori ◽  
Juliana P. Falcão
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequencing ◽  
The Other ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

Since Yersinia frederiksenii was first described in 1980, it has been recognized genotypically as a heterogeneous species, comprising three phenotypically indistinguishable genospecies. In this study, the sequence of the 16S rRNA gene and the concatenated sequences of six housekeeping genes (glnA, gyrB, hsp60, recA, rpoB and sodA) of all the currently known species of the genus Yersinia were used to determine the phylogenetic position of Y. frederiksenii genospecies 2 in the genus Yersinia . The phylogenetic analyses grouped the Y. frederiksenii genospecies 2 strains in a monophyletic group together with representative strains of Yersinia massiliensis . Moreover, the Y. frederiksenii genospecies 2 strains were also grouped apart from the other species of the genus Yersinia and far from the other two genospecies of Y. frederiksenii . All of the observations made in this study support the conclusion that Y. frederiksenii genospecies 2 should be reclassified as Y. massiliensis .

scholarly journals Bifidobacterium tibiigranuli sp. nov. isolated from homemade water kefir

2020 ◽  
Vol 70 (3) ◽  
pp. 1562-1570 ◽  
Author(s):  
Viktor P. L. Eckel ◽  
Lisa-Marie Ziegler ◽  
Rudi F. Vogel ◽  
Matthias Ehrmann
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Marker Gene ◽  
Housekeeping Genes ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
The Family

Two Bifidobacterium strains, TMW 2.2057T and TMW 2.1764 were isolated from two different homemade water kefirs from Germany. Both strains were oxidase- and catalase-negative and Gram-staining-positive. Cells were non-motile, irregular rods that were aerotolerant anaerobes. On basis of fructose 6-phosphate phosphoketolase activity, they were assigned to the family Bifidobacteriaceae. Comparative analysis of 16S rRNA and concatenated housekeeping genes (clpC, dnaB, dnaG, dnaJ, hsp60 and rpoB) demonstrated that both strains represented a member of the genus Bifidobacterium , with Bifidobacterium subtile DSM 20096T as the closest phylogenetic relative (98.35 % identity). Both strains can be distinguished using randomly amplified polymorphic DNA fingerprinting. Analysis of concatenated marker gene sequences as well as average nucleotide identity by blast (ANIb) and in silico DNA–DNA hybridization (isDDH) calculations of their genome sequences confirmed Bifidobacterium subtile DSM 20096T as the closest relative (87.91 and 35.80 % respectively). All phylogenetic analyses allow differentiation of strains TMW 2.2057T and TMW 2.1764 from all hitherto described species of the genus Bifidobacterium with validly published names. We therefore propose a novel species with the name Bifidobacterium tibiigranuli, for which TMW 2.2057T (=DSM 108414T=LMG 31086T) is the type strain.

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