scholarly journals Genetic and phenotypic diversity of rhizobia nodulating chickpea (Cicer arietinumL.) in soils from southern and central Ethiopia

2017 ◽  
Vol 63 (8) ◽  
pp. 690-707 ◽  
Author(s):  
Wondwosen Tena ◽  
Endalkachew Wolde-Meskel ◽  
Tulu Degefu ◽  
Fran Walley
Keyword(s):  
Phenotypic Diversity ◽  
Phylogenetic Reconstruction ◽  
Phenotypic Traits ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Sequence Analyses ◽  
Symbiotic Gene ◽  
Single Cluster ◽  
Ethiopian Soils ◽  
The 16S Rrna Gene

Forty-two chickpea-nodulating rhizobia were isolated from soil samples collected from diverse agro-ecological locations of Ethiopia and were characterized on the basis of 76 phenotypic traits. Furthermore, 18 representative strains were selected and characterized using multilocus sequence analyses of core and symbiotic gene loci. Numerical analysis of the phenotypic characteristics grouped the 42 strains into 4 distinct clusters. The analysis of the 16S rRNA gene of the 18 strains showed that they belong to the Mesorhizobium genus. On the basis of the phylogenetic tree constructed from the combined genes sequences (recA, atpD, glnII, and gyrB), the test strains were distributed into 4 genospecies (designated as genospecies I–IV). Genospecies I, II, and III could be classified with Mesorhizobium ciceri, Mesorhizobium abyssinicae, and Mesorhizobium shonense, respectively, while genospecies IV might represent an unnamed Mesorhizobium genospecies. Phylogenetic reconstruction based on the symbiosis-related (nifH and nodA) genes supported a single cluster together with a previously described symbiont of chickpea (M. ciceri and Mesorhizobium mediterraneum). Overall, our results corroborate earlier findings that Ethiopian soils harbor phylogenetically diverse Mesorhizobium species, justifying further explorative studies. The observed differences in symbiotic effectiveness indicated the potential to select effective strains for use as inoculants and to improve the productivity of chickpea in the country.

scholarly journals Paenibacillus physcomitrellae sp. nov., isolated from the moss Physcomitrella patens

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3400-3406 ◽  
Author(s):  
Xun Zhou ◽  
Guan Nan Guo ◽  
Le Qi Wang ◽  
Su Lan Bai ◽  
Chun Li Li ◽  
...  
Keyword(s):  
Physcomitrella Patens ◽  
Optimal Growth ◽  
Major Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Characteristics ◽  
Diamino Acid ◽  
Beijing China ◽  
The 16S Rrna Gene

A Gram-stain-positive, facultatively anaerobic and rod-shaped bacterium, designated strain XBT, was isolated from Physcomitrella patens growing in Beijing, China. The isolate was identified as a member of the genus Paenibacillus based on phenotypic characteristics and phylogenetic inferences. The novel strain was spore-forming, motile, catalase-negative and weakly oxidase-positive. Optimal growth of strain XBT occurred at 28°C and pH 7.0–7.5. The major polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and several unidentified components, including one phospholipid, two aminophospholipids, three glycolipids, one aminolipid and one lipid. The predominant isoprenoid quinone was MK-7. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major fatty acid components (>5 %) were anteiso-C15 : 0 (51.2 %), anteiso-C17 : 0 (20.6 %), iso-C16 : 0 (8.3 %) and C16 : 0 (6.7 %). The G+C content of the genomic DNA was 53.3 mol%. Phylogenetic analysis, based on the 16S rRNA gene sequence, showed that strain XBT fell within the evolutionary distances encompassed by the genus Paenibacillus; its closest phylogenetic neighbour was Paenibacillus yonginensis DCY84T (96.6 %). Based on phenotypic, chemotaxonomic and phylogenetic properties, strain XBT is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus physcomitrellae sp. nov., is proposed. The type strain is XBT ( = CGMCC 1.15044T = DSM 29851T).

scholarly journals Methylobacterium variabile sp. nov., a methylotrophic bacterium isolated from an aquatic environment

2005 ◽  
Vol 55 (4) ◽  
pp. 1429-1433 ◽  
Author(s):  
Virginia Gallego ◽  
Maria Teresa García ◽  
Antonio Ventosa
Keyword(s):  
Dna Hybridization ◽  
Distribution System ◽  
Bacterial Population ◽  
Sequence Similarity ◽  
Methylotrophic Bacterium ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Natural Habitats ◽  
Hybridization Data ◽  
The 16S Rrna Gene

Strain GR3T was isolated from drinking water during a screening programme to monitor the bacterial population present in the distribution system of Seville (Spain), and it was studied phenotypically, genotypically and phylogenetically. This pink-pigmented bacterium was identified as a Methylobacterium sp. Members of this genus are distributed in a wide variety of natural habitats, including soil, dust, air, freshwater and aquatic sediments. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain GR3T was closely related to Methylobacterium aquaticum (97·4 % sequence similarity), whereas sequence similarity values with respect to the rest of the species belonging to this genus were lower than 96 %. Furthermore, the DNA–DNA hybridization data and its phenotypic characteristics clearly indicate that the isolate represents a novel Methylobacterium species, for which the name Methylobacterium variabile sp. nov. is proposed. GR3T (=DSM 16961T=CCM 7281T=CECT 7045T) is the type strain; the DNA G+C content of this strain is 69·2 mol%.

scholarly journals Exiguobacterium indicum sp. nov., a psychrophilic bacterium from the Hamta glacier of the Himalayan mountain ranges of India

2006 ◽  
Vol 56 (12) ◽  
pp. 2765-2770 ◽  
Author(s):  
Preeti Chaturvedi ◽  
S. Shivaji
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Phenotypic Traits ◽  
Rrna Gene ◽  
Psychrophilic Bacterium ◽  
Rrna Gene Sequence ◽  
Alkaliphilic Bacterium ◽  
The 16S Rrna Gene

Strain HHS 31T, a Gram-positive, motile, rod-shaped, non-spore-forming, alkaliphilic bacterium, was isolated from the melt water of a glacier. Phenotypic and chemotaxonomic characteristics indicate that strain HHS 31T is related to species of the genus Exiguobacterium. The 16S rRNA gene sequence similarities between HHS 31T and strains of known species confirm that it is closely related to members of the genus Exiguobacterium (93–99 %) and that it exhibits >97 % similarity with Exiguobacterium acetylicum DSM 20416T (98.9 %), Exiguobacterium antarcticum DSM 14480T (98.0 %), Exiguobacterium oxidotolerans JCM 12280T (97.9 %) and Exiguobacterium undae DSM 14481T (97.4 %). Phylogenetic analysis based on the 16S rRNA gene sequence further confirms the affiliation of HHS 31T with the genus Exiguobacterium. However, the levels of DNA–DNA relatedness between HHS 31T and E. oxidotolerans JCM 12280T, E. acetylicum DSM 20416T, E. undae DSM 14481T and E. antarcticum DSM 14480T are 50, 63, 67 and 28 %, respectively. Strain HHS 31T also differs from these four closely related species in terms of a number of phenotypic traits. The phenotypic, chemotaxonomic and phylogenetic data suggest that HHS 31T merits the status of a novel species, for which the name Exiguobacterium indicum sp. nov. is proposed. The type strain is HHS 31T (=LMG 23471T=IAM 15368T).

scholarly journals Kocuria marina sp. nov., a novel actinobacterium isolated from marine sediment

2004 ◽  
Vol 54 (5) ◽  
pp. 1617-1620 ◽  
Author(s):  
Seung Bum Kim ◽  
Olga I. Nedashkovskaya ◽  
Valery V. Mikhailov ◽  
Suk Kyun Han ◽  
Kyoung-Ok Kim ◽  
...  
Keyword(s):  
Marine Sediment ◽  
Type Strain ◽  
Novel Species ◽  
Gene Tree ◽  
Growth Media ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Peter The Great ◽  
East Siberian Sea ◽  
The 16S Rrna Gene

An actinobacterial strain was isolated from marine sediment taken from the Troitsa Bay of the Gulf of Peter the Great, East Siberian Sea, and subjected to a taxonomic investigation. The isolate, designated KMM 3905T, was Gram-positive, aerobic, non-motile and coccoid. The strain tolerated up to 15 % NaCl in growth media, although its presence was not essential for growth. Chemotaxonomic and phylogenetic properties of the strain were consistent with its classification in the genus Kocuria. The strain formed an independent phylogenetic line in the 16S rRNA gene tree encompassed by members of Kocuria. Comparison of phenotypic characteristics also supported its assignment to a novel species within Kocuria. The name Kocuria marina sp. nov. (type strain KMM 3905T=KCTC 9943T) is proposed for this halotolerant actinobacterium from the marine environment.

scholarly journals Actinoalloteichus hymeniacidonis sp. nov., an actinomycete isolated from the marine sponge Hymeniacidon perleve

2006 ◽  
Vol 56 (10) ◽  
pp. 2309-2312 ◽  
Author(s):  
Haitao Zhang ◽  
Wen Zheng ◽  
Jianyu Huang ◽  
Hongli Luo ◽  
Yan Jin ◽  
...  
Keyword(s):  
Marine Sponge ◽  
Gene Sequence ◽  
Novel Species ◽  
Taxonomic Status ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Characteristics ◽  
Actinomycete Strain ◽  
Type Strains ◽  
The 16S Rrna Gene

A polyphasic study was undertaken to establish the taxonomic status of a Gram-positive, aerobic actinomycete, strain HPA177T, isolated from a marine sponge, Hymeniacidon perleve. The organism formed branching, non-fragmenting vegetative hyphae and produced black pigment. Chemotaxonomic characteristics were consistent with its assignment to the genus Actinoalloteichus. Analysis of the 16S rRNA gene sequence showed that strain HPA177T formed a robust clade with type strains of the genus Actinoalloteichus, but was distinct from them. A number of phenotypic characteristics also readily distinguished strain HPA177T from species of the genus Actinoalloteichus with validly published names. On the basis of the above data, it is proposed that strain HPA177T represents a novel species, Actinoalloteichus hymeniacidonis sp. nov. The type strain of Actinoalloteichus hymeniacidonis is HPA177T (=CGMCC 4.2500T=JCM 13436T).

scholarly journals Winogradskyella poriferorum sp. nov., a novel member of the family Flavobacteriaceae isolated from a sponge in the Bahamas

2005 ◽  
Vol 55 (4) ◽  
pp. 1589-1592 ◽  
Author(s):  
Stanley C. K. Lau ◽  
Mandy M. Y. Tsoi ◽  
Xiancui Li ◽  
Ioulia Plakhotnikova ◽  
Sergey Dobretsov ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Gliding Motility ◽  
Molecular Evidence ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Phenotypic Characteristics ◽  
The Bahamas ◽  
The Family ◽  
Winogradskyella Poriferorum ◽  
The 16S Rrna Gene

A Gram-negative, rod-shaped bacterium (designated strain UST030701-295T) with fast gliding motility was isolated from the surface of the sponge Lissodendoryx isodictyalis in the Bahamas. Colonies of UST030701-295T were yellow in colour, 2–4 mm in diameter, convex with a smooth surface and entire margins. UST030701-295T was heterotrophic, strictly aerobic and required NaCl for growth (1·0–4·0 %). Growth was observed at pH 6·0–10·0 and at 12–44 °C. Phylogenetic analysis of the 16S rRNA gene sequence placed UST030701-295T within the genus Winogradskyella of the family Flavobacteriaceae, sharing 94·7–95·8 % similarity with the three recognized members of the genus. The G+C content of the DNA was 32·8 mol% and the predominant fatty acids were iso-C15 : 1, iso-C15 : 0, iso-C15 : 0 2-OH, iso-C15 : 0 3-OH, iso-C16 : 0 3-OH, C16 : 1 ω7 and iso-C17 : 0 3-OH (together representing 75·4 % of the total); these data supported the affiliation of UST030701-295T to the genus Winogradskyella. UST030701-295T differed from the three recognized species of Winogradskyella in 7–17 traits. Molecular evidence together with phenotypic characteristics suggests that UST030701-295T represents a novel species within the genus Winogradskyella, for which the name Winogradskyella poriferorum sp. nov. is proposed. The type strain is UST030701-295T (=NRRL B-41101T=JCM 12885T).

scholarly journals Oenococcus kitaharae sp. nov., a non-acidophilic and non-malolactic-fermenting oenococcus isolated from a composting distilled shochu residue

2006 ◽  
Vol 56 (10) ◽  
pp. 2345-2348 ◽  
Author(s):  
Akihito Endo ◽  
Sanae Okada
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Novel Species ◽  
Malolactic Fermentation ◽  
Oenococcus Oeni ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Optimum Ph ◽  
The 16S Rrna Gene

Six strains of lactic acid bacteria were isolated in Japan from a composting distilled shochu residue. The six isolates grew poorly on MRS agar and slowly in MRS broth. The 16S rRNA gene sequences did not show high levels of similarity to those of the recognized species of lactic acid bacteria, and formed a subcluster within the cluster comprising obligately heterofermentative lactic acid bacteria closely related to Oenococcus oeni. The levels of DNA–DNA relatedness revealed that the isolates belonged to the same taxon and were genetically separate from O. oeni. Furthermore, various phenotypic characteristics such as the optimum pH for growth, malolactic fermentation and resistance to 10 % ethanol revealed that the isolates are distinguishable from O. oeni. On the basis of their phylogenetic and phenotypic characteristics, the isolates represent a novel species, for which the name Oenococcus kitaharae sp. nov. is proposed. The type strain is NRIC 0645T (=JCM 13282T=DSM 17330T).

scholarly journals Proof that Burkholderia Strains Form Effective Symbioses with Legumes: a Study of Novel Mimosa-Nodulating Strains from South America

2005 ◽  
Vol 71 (11) ◽  
pp. 7461-7471 ◽  
Author(s):  
Wen-Ming Chen ◽  
Sergio M. de Faria ◽  
Rosângela Straliotto ◽  
Rosa M. Pitard ◽  
Jean L. Simões-Araùjo ◽  
...  
Keyword(s):  
Fluorescent Protein ◽  
Restriction Analysis ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Consensus Sequences ◽  
Mimosa Pigra ◽  
Green Fluorescent ◽  
Gene Restriction ◽  
Single Cluster ◽  
The 16S Rrna Gene

ABSTRACT Twenty Mimosa-nodulating bacterial strains from Brazil and Venezuela, together with eight reference Mimosa-nodulating rhizobial strains and two other β-rhizobial strains, were examined by amplified rRNA gene restriction analysis. They fell into 16 patterns and formed a single cluster together with the known β-rhizobia, Burkholderia caribensis, Burkholderia phymatum, and Burkholderia tuberum. The 16S rRNA gene sequences of 15 of the 20 strains were determined, and all were shown to belong to the genus Burkholderia; four distinct clusters could be discerned, with strains isolated from the same host species usually clustering very closely. Five of the strains (MAP3-5, Br3407, Br3454, Br3461, and Br3469) were selected for further studies of the symbiosis-related genes nodA, the NodD-dependent regulatory consensus sequences (nod box), and nifH. The nodA and nifH sequences were very close to each other and to those of B. phymatum STM815, B. caribensis TJ182, and Cupriavidus taiwanensis LMG19424 but were relatively distant from those of B. tuberum STM678. In addition to nodulating their original hosts, all five strains could also nodulate other Mimosa spp., and all produced nodules on Mimosa pudica that had nitrogenase (acetylene reduction) activities and structures typical of effective N2-fixing symbioses. Finally, both wild-type and green fluorescent protein-expressing transconjugant strains of Br3461 and MAP3-5 produced N2-fixing nodules on their original hosts, Mimosa bimucronata (Br3461) and Mimosa pigra (MAP3-5), and hence this confirms strongly that Burkholderia strains can form effective symbioses with legumes.

scholarly journals Streptomyces sparsus sp. nov., isolated from a saline and alkaline soil

2011 ◽  
Vol 61 (7) ◽  
pp. 1601-1605 ◽  
Author(s):  
Yi Jiang ◽  
Yan-Ru Cao ◽  
Jutta Wiese ◽  
Shu-Kun Tang ◽  
Li-Hua Xu ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Alkaline Soil ◽  
Rrna Gene Sequence ◽  
Phenotypic Characteristics ◽  
Aerial Hyphae ◽  
Actinomycete Strain ◽  
The 16S Rrna Gene

A salt- and alkali-tolerant actinomycete strain, YIM 90018T, was isolated from a saline and alkaline soil sample collected from Qinghai, China. Aerial hyphae of strain YIM 90018T were only produced on YIM 82 agar. Vegetative hyphae were well developed and did not fragment. Straight or flexuous (rectiflexibiles) spore chains were produced. The isolate grew well with 25 % (w/v) MgCl2 . 6H2O and at pH 10. All of these characters indicated that strain YIM 90018T belonged to the genus Streptomyces. On the basis of phylogenetic analysis of the 16S rRNA gene sequence, DNA–DNA hybridization and phenotypic characteristics, strain YIM 90018T could be differentiated from all recognized species of the genus Streptomyces. A novel species, Streptomyces sparsus sp. nov., is proposed, with strain YIM 90018T ( = CCTCC AA204019T = DSM 41858T) as the type strain.

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