scholarly journals Mesorhizobium robiniae sp. nov., isolated from root nodules of Robinia pseudoacacia

2010 ◽  
Vol 60 (11) ◽  
pp. 2552-2556 ◽  
Author(s):  
Ping Fa Zhou ◽  
Wei Min Chen ◽  
Ge Hong Wei
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Root Nodules ◽  
Phylogenetic Analyses ◽  
Robinia Pseudoacacia ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Type Strains ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

Previously, five rhizobial strains isolated from root nodules of Robinia pseudoacacia were assigned to the same genospecies on the basis of identical 16S rRNA gene sequences and phylogenetic analyses of the nodA, nodC and nifH genes, in which the five isolates formed a well-supported group that excluded other sequences found in public databases. In this study, the 16S rRNA gene sequence similarities between the isolates and Mesorhizobium mediterraneum UPM-Ca36T and Mesorhizobium temperatum SDW018T were 99.5 and 99.6 %, respectively. The five isolates were also different from defined Mesorhizobium species using ERIC fingerprint profiles and they formed a novel Mesorhizobium lineage in phylogenetic analyses of recA and atpD gene sequences. DNA–DNA relatedness values between the representative strain, CCNWYC 115T, and type strains of defined Mesorhizobium species were found to be lower than 47.5 %. These results indicated that the isolates represented a novel genomic species. Therefore, a novel species, Mesorhizobium robiniae sp. nov., is proposed, with type strain CCNWYC 115T (=ACCC 14543T =HAMBI 3082T). Strain CCNWYC 115T can form effective nodules only on its original host.

scholarly journals Polaribacter dokdonensis sp. nov., isolated from seawater

2006 ◽  
Vol 56 (6) ◽  
pp. 1251-1255 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Type Strains ◽  
The 16S Rrna Gene

A Gram-negative, non-motile, non-spore-forming, slightly halophilic bacterial strain, DSW-5T, was isolated from seawater off Dokdo, Korea, and subjected to a polyphasic taxonomic study. It grew optimally at 25–28 °C and in the presence of 2 % (w/v) NaCl. Strain DSW-5T contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C15 : 1 and iso-C15 : 0 3-OH as the major fatty acids. The major polar lipids detected were phosphatidylethanolamine, three unidentified phospholipids and an amino-group-containing lipid. The DNA G+C content was 30.0 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DSW-5T was most closely related to the genus Polaribacter. Similarity values between the 16S rRNA gene sequences of strain DSW-5T and the type strains of recognized Polaribacter species were in the range 96.2–96.8 %. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain DSW-5T (=KCTC 12392T=DSM 17204T) was classified in the genus Polaribacter as the type strain of a novel species, for which the name Polaribacter dokdonensis sp. nov. is proposed.

scholarly journals Algoriphagus terrigena sp. nov., isolated from soil

2006 ◽  
Vol 56 (4) ◽  
pp. 777-780 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Mi-Hwa Lee ◽  
So-Jung Kang ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Type Strains ◽  
The 16S Rrna Gene

A Gram-negative, non-motile, non-spore-forming bacterial strain, DS-44T, was isolated from soil from Dokdo in Korea, and its taxonomic position was investigated by using a polyphasic approach. It grew optimally at 25 °C and in the presence of 2 % (w/v) NaCl. Strain DS-44T contained MK-7 as the predominant menaquinone and iso-C15 : 0 and C16 : 1 ω7c and/or iso-C15 : 0 2-OH as the major fatty acids. The DNA G+C content was 49·0 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DS-44T belongs to the genus Algoriphagus of the phylum Bacteroidetes. Similarity values between the 16S rRNA gene sequences of strain DS-44T and those of the type strains of recognized Algoriphagus species were in the range 93·8–95·7 %, making it possible to categorize strain DS-44T as a species that is separate from previously described Algoriphagus species. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain DS-44T (=KCTC 12545T=CIP 108837T) was classified in the genus Algoriphagus as the type strain of a novel species, for which the name Algoriphagus terrigena sp. nov. is proposed.

scholarly journals Pedobacter sandarakinus sp. nov., isolated from soil

2006 ◽  
Vol 56 (6) ◽  
pp. 1273-1277 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Mi-Hwa Lee ◽  
So-Jung Kang ◽  
Soo-Yeon Park ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
The Family ◽  
Type Strains ◽  
The 16S Rrna Gene

A Gram-negative, non-motile, rod-shaped bacterial strain, designated DS-27T, was isolated from a soil sample, and its taxonomic position was investigated by using a polyphasic approach. The organism grew optimally at 30 °C and in the presence of 0–0.5 % (w/v) NaCl. Strain DS-27T contained MK-7 as the predominant menaquinone and iso-C15 : 0, C16 : 1 ω7c and/or iso-C15 : 0 2-OH and iso-C17 : 0 3-OH as the major fatty acids. The DNA G+C content was 39.7 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DS-27T is most closely related to the genus Pedobacter of the family Sphingobacteriaceae. Similarity values between the 16S rRNA gene sequences of strain DS-27T and the type strains of recognized Pedobacter species ranged from 90.6 to 95.5 %. Differential phenotypic properties, together with the phylogenetic distinctiveness, were sufficient to categorize strain DS-27T as representing a species that is separate from recognized Pedobacter species. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain DS-27T (=KCTC 12559T=CIP 108922T) was classified in the genus Pedobacter as a member of a novel species, for which the name Pedobacter sandarakinus sp. nov. is proposed.

scholarly journals Isoptericola dokdonensis sp. nov., isolated from soil

2006 ◽  
Vol 56 (12) ◽  
pp. 2893-2897 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Peter Schumann ◽  
So-Jung Kang ◽  
Seo-Youn Jung ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Bacterium Strain ◽  
Type Strains ◽  
The 16S Rrna Gene

A Gram-positive, non-motile, rod- or coccoid-shaped Isoptericola-like bacterium, strain DS-3T, was isolated from a soil sample from Dokdo, Korea, and its taxonomic position was investigated by a polyphasic approach. The organism grew optimally at 30 °C and pH 7.0–8.0. Strain DS-3T had the peptidoglycan type based on l-lys–d-Asp, and galactose, glucose, rhamnose and ribose as the whole-cell sugars. It contained MK-9(H4) as the predominant menaquinone and anteiso-C15 : 0 and iso-C15 : 0 as the major fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two unidentified glycolipids. The DNA G+C content was 74.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-3T was most closely related to members of the genus Isoptericola. Similarity values between the 16S rRNA gene sequences of strain DS-3T and the type strains of Isoptericola species ranged from 98.0 to 98.4 %. DNA–DNA relatedness values (11–23 %) and differential phenotypic properties demonstrated that strain DS-3T was distinguishable from recognized Isoptericola species. On the basis of phenotypic properties and phylogenetic and genetic distinctiveness, strain DS-3T represents a novel species in the genus Isoptericola, for which the name Isoptericola dokdonensis sp. nov. is proposed. The type strain is DS-3T (=KCTC 19128T=CIP 108921T).

scholarly journals Paracoccus laeviglucosivorans sp. nov., an l-glucose-utilizing bacterium isolated from soil

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 3878-3884 ◽  
Author(s):  
Akira Nakamura
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
Physiological Data ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Dna Relatedness ◽  
Type Strains ◽  
The 16S Rrna Gene

Strain 43PT was isolated as an l-glucose-utilizing bacterium from soil in Japan. Cells of the strain were Gram-stain-negative, aerobic and non-motile cocci. The 16S rRNA gene sequence of the strain showed high similarity to that of Paracoccus limosus (98.5 %). Phylogenetic analyses based on 16S rRNA gene sequences revealed that this strain belongs to the genus Paracoccus. Strain 43PT contained Q-10 as the sole isoprenoid quinone. The major cellular fatty acids were C18 : 1ω7c or C18 : 1ω6c and C16 : 0, and C18 : 0, C18 : 1ω9c, C10 : 0 3-OH and summed feature 2 were detected as minor components. The DNA G+C content of strain 43PT was 64.1 mol%. Strain 43PT contained the major polar lipids phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unknown aminolipid and two unknown glycolipids. The DNA–DNA relatedness between strain 43PT and the six related type strains of the genus Paracoccus, including P. limosus, was below 23 %. Based on the chemotaxonomic and physiological data and the values of DNA–DNA relatedness, especially the ability to assimilate l-glucose, this strain should be classified as a representative of a novel species of the genus Paracoccus, for which the name Paracoccus laeviglucosivorans sp. nov. (type strain 43PT = JCM 30587T = DSM 100094T) is proposed.

scholarly journals Caenispirillum bisanense gen. nov., sp. nov., isolated from sludge of a dye works

2007 ◽  
Vol 57 (6) ◽  
pp. 1217-1221 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Sooyeon Park ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Analyses ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
The 16S Rrna Gene

Two Gram-negative, non-spore-forming, motile and helical-shaped bacterial strains, K92T and K93, were isolated from sludge from a dye works in Korea, and their taxonomic positions were investigated by means of a polyphasic approach. Strains K92T and K93 grew optimally at 37 °C and pH 7.0–8.0 in the presence of 0.5 % (w/v) NaCl. They contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and two unidentified amino-group-containing lipids that were ninhydrin-positive. Their DNA G+C contents were 70.0 mol%. The 16S rRNA gene sequences of K92T and K93 showed no differences, and the two strains had a mean DNA–DNA relatedness of 93 %. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains K92T and K93 formed a distinct evolutionary lineage within the Alphaproteobacteria. The 16S rRNA gene sequences of strains K92T and K93 exhibited similarity values of less than 91.5 % with respect to the 16S rRNA gene sequences of other members of the Alphaproteobacteria. The two strains were distinguishable from phylogenetically related genera through differences in several phenotypic properties. On the basis of the phenotypic, phylogenetic and genetic data, strains K92T and K93 represent a novel genus and species, for which the name Caenispirillum bisanense gen. nov., sp. nov. is proposed. The type strain of Caenispirillum bisanense is K92T (=KCTC 12839T=JCM 14346T).

scholarly journals Ribosomal protein gene-based phylogeny for finer differentiation and classification of phytoplasmas

2007 ◽  
Vol 57 (9) ◽  
pp. 2037-2051 ◽  
Author(s):  
M. Martini ◽  
I.-M. Lee ◽  
K. D. Bottner ◽  
Y. Zhao ◽  
S. Botti ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Tree ◽  
Ribosomal Protein ◽  
Phylogenetic Analyses ◽  
Rflp Analysis ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Gram Positive ◽  
The 16S Rrna Gene

Extensive phylogenetic analyses were performed based on sequences of the 16S rRNA gene and two ribosomal protein (rp) genes, rplV (rpl22) and rpsC (rps3), from 46 phytoplasma strains representing 12 phytoplasma 16Sr groups, 16 other mollicutes and 28 Gram-positive walled bacteria. The phylogenetic tree inferred from rp genes had a similar overall topology to that inferred from the 16S rRNA gene. However, the rp gene-based tree gave a more defined phylogenetic interrelationship among mollicutes and Gram-positive walled bacteria. Both phylogenies indicated that mollicutes formed a monophyletic group. Phytoplasmas clustered with Acholeplasma species and formed one clade paraphyletic with a clade consisting of the remaining mollicutes. The closest relatives of mollicutes were low-G+C-content Gram-positive bacteria. Comparative phylogenetic analyses using the 16S rRNA gene and rp genes were performed to evaluate their efficacy in resolving distinct phytoplasma strains. A phylogenetic tree was constructed based on analysis of rp gene sequences from 87 phytoplasma strains belonging to 12 16Sr phytoplasma groups. The phylogenetic relationships among phytoplasmas were generally in agreement with those obtained on the basis of the 16S rRNA gene in the present and previous works. However, the rp gene-based phylogeny allowed for finer resolution of distinct lineages within the phytoplasma 16Sr groups. RFLP analysis of rp gene sequences permitted finer differentiation of phytoplasma strains in a given 16Sr group. In this study, we also designed several semi-universal and 16Sr group-specific rp gene-based primers that allow for the amplification of 11 16Sr group phytoplasmas.

scholarly journals EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences

2007 ◽  
Vol 57 (10) ◽  
pp. 2259-2261 ◽  
Author(s):  
Jongsik Chun ◽  
Jae-Hak Lee ◽  
Yoonyoung Jung ◽  
Myungjin Kim ◽  
Seil Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Multiple Sequence ◽  
Web Based ◽  
Routine Identification ◽  
Type Strains

16S rRNA gene sequences have been widely used for the identification of prokaryotes. However, the flood of sequences of non-type strains and the lack of a peer-reviewed database for 16S rRNA gene sequences of type strains have made routine identification of isolates difficult and labour-intensive. In the present study, we generated a database containing 16S rRNA gene sequences of all prokaryotic type strains. In addition, a web-based tool, named EzTaxon, for analysis of 16S rRNA gene sequences was constructed to achieve identification of isolates based on pairwise nucleotide similarity values and phylogenetic inference methods. The system developed provides users with a similarity-based search, multiple sequence alignment and various phylogenetic analyses. All of these functions together with the 16S rRNA gene sequence database of type strains can be successfully used for automated and reliable identification of prokaryotic isolates. The EzTaxon server is freely accessible over the Internet at http://www.eztaxon.org/

scholarly journals Herbaspirillum rhizosphaerae sp. nov., isolated from rhizosphere soil of Allium victorialis var. platyphyllum

2007 ◽  
Vol 57 (10) ◽  
pp. 2284-2288 ◽  
Author(s):  
Seo-Youn Jung ◽  
Mi-Hwa Lee ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rhizosphere Soil ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Dna Relatedness ◽  
Type Strains

Two Gram-negative, milky-white-pigmented, motile, slightly curved rod-shaped bacterial isolates, UMS-37T and UMS-40, were isolated from rhizosphere soil of wild edible greens cultivated on Ulleung island, Korea, and their taxonomic positions were investigated by a polyphasic approach. They grew optimally at 25–30 °C and contained Q-8 as the predominant ubiquinone. The major cellular fatty acids (>10 % of total fatty acids) were C16 : 0, cyclo C17 : 0 and C16 : 1 ω7c and/oriso-C15 : 0 2-OH. The DNA G+C contents of the two isolates were 59.8 and 60.0 mol%. Isolates UMS-37T and UMS-40 exhibited no difference in their 16S rRNA gene sequences and possessed a mean DNA–DNA relatedness level of 94 %; they exhibited 16S rRNA gene sequence similarity levels of 96.8–98.2 % to the type strains of recognized Herbaspirillum species. Phylogenetic analyses based on 16S rRNA gene sequences showed that isolates UMS-37T and UMS-40 formed a distinct phylogenetic lineage within the genus Herbaspirillum. DNA–DNA relatedness levels between isolates UMS-37T and UMS-40 and the type strains of some phylogenetically related Herbaspirillum species were in the range 3–56 %. On the basis of differences in phenotypic properties and phylogenetic distinctiveness and genomic data, isolates UMS-37T and UMS-40 were classified in the genus Herbaspirillum within a novel species, for which the name Herbaspirillum rhizosphaerae sp. nov. is proposed, with the type strain UMS-37T (=KCTC 12558T =CIP 108917T).

scholarly journals Nocardioides kongjuensis sp. nov., an N-acylhomoserine lactone-degrading bacterium

2006 ◽  
Vol 56 (8) ◽  
pp. 1783-1787 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Jung-Kee Lee ◽  
Seo-Youn Jung ◽  
Jung-Ae Kim ◽  
Ha-Kun Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Analyses ◽  
Homoserine Lactone ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Acylhomoserine Lactone ◽  
Degrading Bacterium ◽  
Type Strains ◽  
The 16S Rrna Gene

A Gram-positive, rod- or coccoid-shaped and N-hexanoyl-l-homoserine lactone-degrading bacterial strain, A2-4T, was isolated from a soil in Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain A2-4T grew optimally at pH 7.0–8.0 and 30 °C without NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain A2-4T is most closely related to members of the genus Nocardioides. Strain A2-4T possessed chemotaxonomic properties indicative of members of the genus Nocardioides; the cell-wall peptidoglycan type was based on ll-diaminopimelic acid, MK-8(H4) was the predominant menaquinone and iso-C16 : 0 was the predominant fatty acid. The DNA G+C content was 72.1 mol%. The 16S rRNA gene sequence of strain A2-4T was 98.3–99.1 % similar to those of the type strains of Nocardioides simplex, Nocardioides aromaticivorans and Nocardioides nitrophenolicus and 93.8–96.3 % similar to those of the type strains of other Nocardioides species. Strain A2-4T could be distinguished from the three phylogenetic relatives, N. nitrophenolicus, N. aromaticivorans and N. simplex, by DNA–DNA relatedness (25–42 %) and by differences in some phenotypic characteristics. On the basis of the phenotypic, phylogenetic and genetic data, the strain represents a novel species of the genus Nocardioides, for which the name Nocardioides kongjuensis sp. nov. is proposed. The type strain is A2-4T (=KCTC 19054T=JCM 12609T).

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