Genetic diversity in Bradyrhizobium japonicum Jordan 1982 and a proposal for Bradyrhizobium elkanii sp.nov.

1992 ◽  
Vol 38 (6) ◽  
pp. 501-505 ◽  
Author(s):  
L. D. Kuykendall ◽  
B. Saxena ◽  
T. E. Devine ◽  
S. E. Udell
Keyword(s):  
Type Strain ◽  
Homology Group ◽  
Dna Homology ◽  
Homology Groups ◽  
Hybridization Probes ◽  
Bradyrhizobium Elkanii ◽  
Group Ii ◽  
A New Species ◽  
Strain Usda ◽  
Soybean Nodulation

Fourteen randomly selected clones from cosmid libraries of Bradyrhizobium were used as hybridization probes in Southern blot analysis. Seven of the probes used were from strain USDA 83, a group II strain, and the other seven were from strain I-110, a group Ia strain. The 30 strains examined included 9 strains of Rj4-incompatible soybean bradyrhizobia. Considerable polynucleotide sequence dissimilarity between DNA homology groups was evidenced by striking differences in the number of hybridizing bands, except where the probe carried repetitive DNA. Predictable, simple restriction fragment length polymorphism differences were observed only within DNA homology groups. The previous description that 8 of 9 Rj4-incompatible strains belonged to DNA homology group II was verified. The new data, together with many previously documented differences, make it clear that the DNA homology group II organisms should be classified as a new species, for which the name Bradyrhizobium elkanii is proposed, and strain USDA 76 is designated the type strain. The ATCC number for the type strain is 49852. Key words: DNA:DNA hybridization, soybean, nodulation, bacteria, symbiosis, nitrogen fixation, host compatibility.

scholarly journals A taxonomic study of the Spirillum lipoferum group, with descriptions of a new genus, Azospirillum gen. nov. and two species, Azospirillum lipoferum (Beijerinck) comb. nov. and Azospirillum brasilense sp. nov.

1978 ◽  
Vol 24 (8) ◽  
pp. 967-980 ◽  
Author(s):  
Jeffrey J. Tarrand ◽  
Noel R. Krieg ◽  
Johanna Döbereiner
Keyword(s):  
Thermal Denaturation ◽  
New Genus ◽  
Free Medium ◽  
Dna Homology ◽  
Azospirillum Lipoferum ◽  
Dna Base Composition ◽  
Homology Groups ◽  
Group I ◽  
Dna Base ◽  
Group Ii

Sixty-one strains of the root-associated nitrogen fixer Spirillum lipoferum exhibited a similar morphology in peptone–succinate salts medium: vibrioid cells having a diameter of 1.0 μm. When grown in broth the cells had a single polar flagellum, but when grown on agar at 30 °C lateral flagella of shorter wavelength were also formed. The DNA base composition was 69–71 mol % guanine + cytosine when determined by thermal denaturation. DNA homology experiments indicated the occurrence of two distinct but related homology groups: 46 strains were in group I and 15 strains were in group II. Group II strains were distinguished by their ability to use glucose as a sole carbon source for growth in nitrogen-free medium, by their production of an acidic reaction in a peptone-based glucose medium, by their requirement for biotin, and by their formation of wider, longer, S-shaped or helical cells in semisolid nitrogen-free malate medium. The results indicate that two species exist, and on the basis of their characteristics it is proposed that they be assigned to a new genus, Azospirillum. Strains belonging to group II are named A.lipoferum (Beijerinck) comb, nov., while those belonging to group I are named A.brasilense sp. nov. Strain Sp 59b (ATCC 29707) is proposed as the neotype strain for A. lipoferum, and strain Sp 7 (ATCC 29145) is proposed as the type strain for A. brasilense.

The Rj4 allele in soybean represses nodulation by chlorosis-inducing bradyrhizobia classified as DNA homology group II by antibiotic resistance profiles

1990 ◽  
Vol 80 (1) ◽  
pp. 33-37 ◽  
Author(s):  
T. E. Devine ◽  
L. D. Kuykendall ◽  
J. J. O'Neill
Keyword(s):  
Antibiotic Resistance ◽  
Homology Group ◽  
Dna Homology ◽  
Group Ii

Genetic variability of the common nod gene in soybean bradyrhizobia isolated in Thailand and Japan

1996 ◽  
Vol 42 (12) ◽  
pp. 1209-1218 ◽  
Author(s):  
Tadashi Yokoyama ◽  
Shotaro Ando ◽  
Toshifumi Murakami ◽  
Hideo Imai
Keyword(s):  
Genetic Diversity ◽  
Bradyrhizobium Japonicum ◽  
Sequence Divergence ◽  
Gene Probe ◽  
Polymorphism Analysis ◽  
Dna Homology ◽  
Homology Groups ◽  
Phylogenetic Grouping ◽  
The Common ◽  
Bradyrhizobium Elkanii

To determine the taxonomic relationship between Thai soybean bradyrhizobia and soybean bradyrhizobia from other regions, a total of 62 Bradyrhizobium strains were isolated in Thailand. The genetic diversity of the strains was examined with reference to 46 Japanese and 15 USDA strains. The degree of sequence divergence in and around common nod gene regions of the 123 strains was estimated by restriction fragment length polymorphism analysis using the Bradyrhizobium japonicum USDA 110 common nodDYABC gene probe. The phylogenetic grouping of the strains resulted in four major clusters. Cluster 1 comprised the Japanese and USDA strains, which originated in temperate regions, whereas clusters 3 and 4 comprised the tropical Thai strains. Cluster 1 strains comprised the DNA homology groups I and Ia, and hence, were classified as B. japonicum. Cluster 2 strains were in the DNA homology group II, and hence, were classified as Bradyrhizobium elkanii. Clusters 3 and 4 strains, however, did not correspond to any known DNA homology groups. These results indicate that Thai soybean bradyrhizobia are distantly related to B. japonicum and B. elkanii.Key words: Bradyrhizobium japonicum, Bradyrhizobium elkanii, common nod gene, RFLP, genetic diversity.

scholarly journals High-quality permanent draft genome sequence of the Bradyrhizobium elkanii type strain USDA 76T, isolated from Glycine max (L.) Merr

2017 ◽  
Vol 12 (1) ◽  
Author(s):  
Wayne Reeve ◽  
Peter van Berkum ◽  
Julie Ardley ◽  
Rui Tian ◽  
Margaret Gollagher ◽  
...  
Keyword(s):  
Glycine Max ◽  
Genome Sequence ◽  
Type Strain ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
High Quality ◽  
Glycine Max L ◽  
Bradyrhizobium Elkanii ◽  
Strain Usda

scholarly journals One-relator groups and algebras related to polyhedral products

2021 ◽  
pp. 1-20
Author(s):  
Jelena Grbić ◽  
George Simmons ◽  
Marina Ilyasova ◽  
Taras Panov
Keyword(s):  
Homology Group ◽  
Homotopy Theory ◽  
Commutator Subgroup ◽  
Homology Groups ◽  
Homological Characterization ◽  
One Relator Groups ◽  
Combinatorial Condition ◽  
The Moment ◽  
Necessary And Sufficient

We link distinct concepts of geometric group theory and homotopy theory through underlying combinatorics. For a flag simplicial complex $K$ , we specify a necessary and sufficient combinatorial condition for the commutator subgroup $RC_K'$ of a right-angled Coxeter group, viewed as the fundamental group of the real moment-angle complex $\mathcal {R}_K$ , to be a one-relator group; and for the Pontryagin algebra $H_{*}(\Omega \mathcal {Z}_K)$ of the moment-angle complex to be a one-relator algebra. We also give a homological characterization of these properties. For $RC_K'$ , it is given by a condition on the homology group $H_2(\mathcal {R}_K)$ , whereas for $H_{*}(\Omega \mathcal {Z}_K)$ it is stated in terms of the bigrading of the homology groups of $\mathcal {Z}_K$ .

A new species of trypanosome, Trypanosoma desterrensis sp. n., isolated from South American bats

Parasitology ◽  
2003 ◽  
Vol 127 (3) ◽  
pp. 265-271 ◽  
Author(s):  
E. C. GRISARD ◽  
N. R. STURM ◽  
D. A. CAMPBELL
Keyword(s):  
New Species ◽  
Dna Sequence ◽  
Sequence Data ◽  
Rrna Gene ◽  
South American ◽  
Sequence Variability ◽  
Dna Sequence Data ◽  
Hybridization Probes ◽  
5S Rrna Gene ◽  
A New Species

Trypanosomes isolated from South American bats include the human pathogen Trypanosoma cruzi. Other Trypanosoma spp. that have been found exclusively in bats are not well characterized at the DNA sequence level and we have therefore used the SL RNA gene to differentiate and characterize kinetoplastids isolated from bats in South America. A Trypanosoma sp. isolated from bats in southern Brazil was compared with the geographically diverse isolates T. cruzi marinkellei, T. vespertilionis, and T. dionisii. Analysis of the SL RNA gene repeats revealed size and sequence variability among these bat trypanosomes. We have developed hybridization probes to separate these bat isolates and have analysed the DNA sequence data to estimate their relatedness. A new species, Trypanosoma desterrensis sp. n., is proposed, for which a 5S rRNA gene was also found within the SL RNA repeat.

scholarly journals Proposal for the creation of a new genus Musicola gen. nov., reclassification of Dickeya paradisiaca (Samson et al. 2005) as Musicola paradisiaca comb. nov. and description of a new species Musicola keenii sp. nov.

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Nicole Hugouvieux-Cotte-Pattat ◽  
Cécile Jacot des-Combes ◽  
Jérôme Briolay ◽  
Leighton Pritchard
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Type Species ◽  
Plant Pathogens ◽  
Phenotypic Analysis ◽  
Content Type ◽  
Link Type ◽  
Type Strains ◽  
A New Species ◽  
Laboratory Collection

The Pectobacteriaceae family of important plant pathogens includes the genus Dickeya . There are currently 12 described species of Dickeya , although some are poorly characterized at the genomic level. Only two genomes of Dickeya paradisiaca , the type strain CFBP 4178T and strain Ech703, have previously been sequenced. Members of this species are mostly of tropical or subtropical origin. During an investigation of strains present in our laboratory collection we sequenced the atypical strain A3967, registered as CFBP 722, isolated from Solanum lycopersicum (tomato) in the South of France in 1965. The genome of strain A3967 shares digital DNA–DNA hybridization and average nucleotide identity (ANI) values of 68 and 96 %, respectively, with the D. paradisiaca type strain CFBP 4178T. However, ANI analysis showed that D. paradisiaca strains are significantly dissimilar to the other Dickeya species, such that less than one third of their genomes align to any other Dickeya genome. On phenotypic, phylogenetic and genomic grounds, we propose a reassignment of D. paradisiaca to the genus level, for which we propose the name Musicola gen. nov., with Musicola paradisiaca as the type species and CFBP 4178T (NCPPB 2511T) as the type strain. Phenotypic analysis showed differences between strain A3967T and CFBP 4178T, such as for the assimilation of melibiose, raffinose and myo-inositol. These results support the description of two novel species, namely Musicola paradisiaca comb. nov. and Musicola keenii sp. nov., with CFBP 4178T (NCPPB 2511T=LMG 2542T) and A3967T (CFBP 8732T=LMG 31880T) as the type strains, respectively.

DNA Homology Group and the Identity of Bradyrhizobial Strains Producing Rhizobitoxine‐Induced Foliar Chlorosis on Soybean

Crop Science ◽  
1988 ◽  
Vol 28 (6) ◽  
pp. 938-941 ◽  
Author(s):  
T. E. Devine ◽  
J. J. O'Neill ◽  
L. D. Kuykendall
Keyword(s):  
Homology Group ◽  
Dna Homology

Deinococcus aetherius sp. nov., isolated from the stratosphere

2010 ◽  
Vol 60 (4) ◽  
pp. 776-779 ◽  
Author(s):  
Yinjie Yang ◽  
Takashi Itoh ◽  
Shin-ichi Yokobori ◽  
Haruo Shimada ◽  
Shiho Itahashi ◽  
...  
Keyword(s):  
Gamma Rays ◽  
Nitrate Reduction ◽  
Type Strain ◽  
Bacterial Population ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Polar Lipid Profile ◽  
Closely Related Species ◽  
Type Strains ◽  
A New Species

A pink-red pigmented, non-motile, coccoid bacterial strain, ST0316T, was isolated from dust samples collected from the stratosphere in Japan. Phylogenetic analysis based on 16S rRNA gene sequences showed that it belonged to the genus Deinococcus. DNA G+C content (69.8 mol%), desiccation tolerance, and resistance to gamma-rays [D10 (dose required to reduce the bacterial population by 10-fold) >8 kGy] and UV radiation (D10 1000 J m−2) supported the affiliation of strain ST0316T to the genus Deinococcus. The major peptidoglycan amino acids were d-glutamic acid, glycine, d-alanine, l-alanine and ornithine. Predominant fatty acids were C16 : 1 ω7c, C16 : 0, C17 : 0 and iso-C17 : 0. Strain ST0316T diverged from recognized species of the genus Deinococcus, showing less than 93.0 % similarity values to its closest relatives Deinococcus apachensis, D. aerius, D. geothermalis and D. murrayi. Strain ST0316T also differed from the type strains of closely related species in its polar lipid profile, nitrate reduction and carbon-source assimilation tests. Therefore, we propose a new species of the genus Deinococcus, Deinococcus aetherius sp. nov. (type strain, ST0316T =JCM 11751T =DSM 21230T).

scholarly journals Bradyrhizobium elkanii rtxC Gene Is Required for Expression of Symbiotic Phenotypes in the Final Step of Rhizobitoxine Biosynthesis

2004 ◽  
Vol 70 (1) ◽  
pp. 535-541 ◽  
Author(s):  
Shin Okazaki ◽  
Masayuki Sugawara ◽  
Kiwamu Minamisawa
Keyword(s):  
Glycine Max ◽  
Type Strain ◽  
Wild Type Strain ◽  
Null Mutant ◽  
Wild Type ◽  
In Planta ◽  
Distinct Effect ◽  
Nodulation Competitiveness ◽  
Macroptilium Atropurpureum ◽  
Bradyrhizobium Elkanii

ABSTRACT We disrupted the rtxC gene on the chromosome of Bradyrhizobium elkanii USDA94 by insertion of a nonpolar aph cartridge. The rtxC mutant, designated ΔrtxC, produced serinol and dihydrorhizobitoxine but no rhizobitoxine, both in culture and in planta. The introduction of cosmids harboring the rtxC gene into the ΔrtxC mutant complemented rhizobitoxine production, suggesting that rtxC is involved in the final step of rhizobitoxine biosynthesis in B. elkanii USDA94. Glycine max cv. Lee inoculated with ΔrtxC or with a null mutant, Δrtx::Ω1, showed no foliar chlorosis, whereas the wild-type strain USDA94 caused severe foliar chlorosis. The two mutants showed significantly less nodulation competitiveness than the wild-type strain on Macroptilium atropurpureum. These results indicate that dihydrorhizobitoxine, the immediate precursor of the oxidative form of rhizobitoxine, has no distinct effect on nodulation phenotype in these legumes. Thus, desaturation of dihydrorhizobitoxine by rtxC-encoded protein is essential for the bacterium to show rhizobitoxine phenotypes in planta. In addition, complementation analysis of rtxC by cosmids differing in rtxC transcription levels suggested that rhizobitoxine production correlates with the amount of rtxC transcript.

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