scholarly journals Chelativorans multitrophicus gen. nov., sp. nov. and Chelativorans oligotrophicus sp. nov., aerobic EDTA-degrading bacteria

2010 ◽  
Vol 60 (5) ◽  
pp. 1044-1051 ◽  
Author(s):  
Nina V. Doronina ◽  
Elena N. Kaparullina ◽  
Yuri A. Trotsenko ◽  
Bernd Nörtemann ◽  
Margarete Bucheli-Witschel ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
Phenotypic Properties ◽  
Mesorhizobium Loti ◽  
Degrading Bacteria

Two previously isolated strains (DSM 9103T and LPM-4T) able to grow with EDTA (facultatively and obligately, respectively) as the source of carbon, nitrogen and energy were investigated in order to clarify their taxonomic positions. The strains were strictly aerobic, Gram-negative, asporogenous and non-motile rods that required biotin for growth. Reproduction occurred by binary fission. The strains were mesophilic and neutrophilic. Their major fatty acids were summed feature 7 (consisting of C18 : 1 ω7c, C18 : 1 ω9t and/or C18 : 1 ω12t) and C19 : 0 cyclo ω8c. The polyamine pattern revealed homospermidine as a major polyamine. Predominant polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine and diphosphatidylglycerol. Mesorhizobium-specific ornithine lipid was absent. The predominant isoprenoid quinone was Q-10. The DNA G+C values were 60.8 and 63.1 mol% (T m) for strains LPM-4T and DSM 9103T, respectively. The level of 16S rRNA gene sequence similarity between these EDTA-utilizers was 99.3 % while the DNA–DNA hybridization value was only 37 %. Both strains were phylogenetically related to members of the genera Aminobacter and Mesorhizobium (95–97 % sequence similarity). However, DNA–DNA hybridization values between the novel EDTA-degrading strains and Aminobacter aminovorans DSM 7048T and Mesorhizobium loti DSM 2626T were low (10–11 %). Based on their genomic and phenotypic properties, the new alphaproteobacterial strains are assigned to a novel genus, Chelativorans gen. nov., with the names Chelativorans multitrophicus sp. nov. (type strain DSM 9103T=VKM B-2394T) and Chelativorans oligotrophicus sp. nov. (type strain LPM-4T=VKM B-2395T=DSM 19276T).

scholarly journals Shewanella canadensis sp. nov. and Shewanella atlantica sp. nov., manganese dioxide- and hexahydro-1,3,5-trinitro-1,3,5-triazine-reducing, psychrophilic marine bacteria

2007 ◽  
Vol 57 (9) ◽  
pp. 2155-2162 ◽  
Author(s):  
Jian-Shen Zhao ◽  
Dominic Manno ◽  
Sonia Thiboutot ◽  
Guy Ampleman ◽  
Jalal Hawari
Keyword(s):  
Dna Hybridization ◽  
Genomic Dna ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties ◽  
Closely Related Species ◽  
Organic Acids And Sugars

Two strains belonging to the genus Shewanella, HAW-EB2T and HAW-EB5T, were isolated previously from marine sediment sampled from the Atlantic Ocean, near Halifax harbour in Canada, for their potential to degrade explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). In the present study, strains HAW-EB2T and HAW-EB5T were found to display high 16S rRNA gene sequence similarity (90–99.5 %) to species of Shewanella, but their gyrB sequences were significantly different from each other and from species of Shewanella (79–87.6 %). Furthermore, DNA–DNA hybridization showed that the genomic DNA of the two strains was only 22 % related and showed less than 41 % relatedness to closely related species of Shewanella. In comparison to other species of Shewanella, strains HAW-EB2T and HAW-EB5T were also unique in some phenotypic properties such as activities of β-galactosidase and tyrosine arylamidase and the ability to metabolize certain organic acids and sugars. Both strains HAW-EB2T and HAW-EB5T utilize malate, valerate, peptone and yeast extract as sole carbon and energy sources. The major membrane fatty acids of the two strains were C14 : 0, iso-C15 : 0, C16 : 0, C16 : 1 ω7, C18 : 1 ω7 and C20 : 5 ω3 and their major quinones were Q-7, Q-8 and MK-7. On the basis of these results, strain HAW-EB2T (=NCIMB 14238T =CCUG 54553T) is proposed as the type strain of Shewanella canadensis sp. nov. and strain HAW-EB5T (=NCIMB 14239T =CCUG 54554T) is proposed as the type strain of Shewanella atlantica sp. nov.

scholarly journals Description of Cobetia amphilecti sp. nov., Cobetia litoralis sp. nov. and Cobetia pacifica sp. nov., classification of Halomonas halodurans as a later heterotypic synonym of Cobetia marina and emended descriptions of the genus Cobetia and Cobetia marina

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 288-297 ◽  
Author(s):  
Lyudmila A. Romanenko ◽  
Naoto Tanaka ◽  
Vassilii I. Svetashev ◽  
Enevold Falsen
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Content Type ◽  
Link Type ◽  
Cobetia Marina

A group of five Gram-negative, aerobic, halotolerant, non-pigmented bacteria isolated from shallow sediment samples and invertebrate specimens collected from the Gulf of Alaska and the Sea of Japan was subjected to taxonomic study. On the basis of 16S rRNA gene sequence analysis, the novel isolates were affiliated to the genus Cobetia , sharing the highest sequence similarity of 99.3–99.9 % with Cobetia marina DSM 4741T. DNA–DNA hybridization experiments between and among the novel strains and C. marina DSM 4741T and Cobetia crustatorum JCM 15644T revealed that the five strains represent three separate genospecies, which could be differentiated in their morphological, physiological and biochemical characteristics. Halomonas halodurans NBRC 15607T was included in this study as it has recently been reported to exhibit high 16S rRNA gene sequence similarity to C. marina DSM 4741T, and it showed a high DNA relatedness value of 96 % with C. marina DSM 4741T, indicating that they belong to the same species. On the basis of phylogenetic analysis, DNA–DNA hybridization and phenotypic characterization, three novel species are proposed, named Cobetia amphilecti sp. nov. (type strain KMM 1561T  = NRIC 0815T  = CCUG 49560T), Cobetia litoralis sp. nov. (type strain KMM 3880T  = NRIC 0814T  = CCUG 49563T) and Cobetia pacifica sp. nov. (type strain KMM 3879T  = NRIC 0813T  = CCUG 49562T). It is also proposed that Halomonas halodurans is a later heterotypic synonym of Cobetia marina , and emended descriptions of the genus Cobetia and the species Cobetia marina are provided.

scholarly journals Thermaerobacter litoralis sp. nov., a strictly aerobic and thermophilic bacterium isolated from a coastal hydrothermal field

2006 ◽  
Vol 56 (7) ◽  
pp. 1531-1534 ◽  
Author(s):  
Reiji Tanaka ◽  
Satoshi Kawaichi ◽  
Hiroshi Nishimura ◽  
Yoshihiko Sako
Keyword(s):  
Dna Hybridization ◽  
Sequence Similarity ◽  
Thermophilic Bacterium ◽  
Hydrothermal Field ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
Optimum Ph ◽  
Kagoshima Prefecture ◽  
Bacterium Strain

A novel thermophilic bacterium, strain KW1T, was isolated from a coastal hydrothermal field on the Satsuma Peninsula, Kagoshima Prefecture, Japan. The variably Gram-stained cells were motile rods with flagella, did not form spores and proliferated at 52–78 °C (optimum, 70 °C), pH 5–8 (optimum, pH 7) and 0–4.5 % NaCl (optimum, 1.0 %). The novel isolate was a strictly aerobic heterotroph that utilized complex proteinaceous substrates as well as a variety of carboxylic acids and amino acids. The G+C content of the genomic DNA was 70.8 mol%. Analysis of 16S rRNA gene sequences indicated that strain KW1T is closely related to Thermaerobacter subterraneus C21T (98.4 % sequence similarity). However, the DNA–DNA hybridization value for strain KW1T and T. subterraneus ATCC BAA-137T was below 46 %. On the basis of the molecular and physiological traits of strain KW1T, it represents a novel species of the genus Thermaerobacter, for which the name Thermaerobacter litoralis sp. nov. is proposed. The type strain is KW1T (=JCM 13210T=DSM 17372T).

scholarly journals Lysobacter novalis sp. nov., isolated from fallow farmland soil

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3131-3136 ◽  
Author(s):  
Hina Singh ◽  
Juan Du ◽  
Kyung-Hwa Won ◽  
Jung-Eun Yang ◽  
Shahina Akter ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Gliding Motility ◽  
Rrna Gene ◽  
The Novel ◽  
Respiratory Quinone ◽  
Gene Sequence Analysis ◽  
Farmland Soil ◽  
Major Respiratory Quinone

A novel bacterial strain, designated THG-PC7T, was isolated from fallow farmland soil in Yongin, South Korea. Cells of strain THG-PC7T were Gram-stain-negative, dark yellow, aerobic, rod-shaped and had gliding motility. Strain THG-PC7T grew optimally at 25–35 °C, at pH 7 and in the absence of NaCl. Comparative 16S rRNA gene sequence analysis identified strain THG-PC7T as belonging to the genus Lysobacter, exhibiting highest sequence similarity with Lysobacter ximonensis KCTC 22336T (98.7 %) followed by Lysobacter niastensis KACC 11588T (95.7 %). In DNA–DNA hybridization tests, DNA relatedness between strain THG-PC7T and its closest phylogenetic neighbour L. ximonensis was below 25 %. The DNA G+C content of the novel isolate was determined to be 62.5 mol%. Flexirubin-type pigments were found to be present. The major cellular fatty acids were determined to be iso-C15 : 0, iso-C16 : 0, anteiso-C15 : 0 and iso-C17 : 1ω9c. The major respiratory quinone was identified as ubiquonone-8 (Q8). The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospolipid. On the basis of results from DNA–DNA hybridization and the polyphasic data, strain THG-PC7T represents a novel species of the genus Lysobacter, for which the name Lysobacter novalis sp. nov. is proposed. The type strain is THG-PC7T( = KACC 18276T = CCTCC AB 2014319T).

scholarly journals Lysobacter niabensis sp. nov. and Lysobacter niastensis sp. nov., isolated from greenhouse soils in Korea

2007 ◽  
Vol 57 (3) ◽  
pp. 548-551 ◽  
Author(s):  
Hang-Yeon Weon ◽  
Byung-Yong Kim ◽  
Min-Kyeong Kim ◽  
Seung-Hee Yoo ◽  
Soon-Wo Kwon ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Bacterial Strains ◽  
Lysobacter Enzymogenes ◽  
Gene Sequence Analysis ◽  
Greenhouse Soils

Two bacterial strains, designated GH34-4T and GH41-7T, were isolated from greenhouse soil cultivated with cucumber. The bacteria were strictly aerobic, Gram-negative, rod-shaped and oxidase- and catalase-positive. 16S rRNA gene sequence analysis indicated that these strains belong to the genus Lysobacter within the Gammaproteobacteria. Strain GH34-4T showed highest sequence similarity to Lysobacter yangpyeongensis GH19-3T (97.5 %) and Lysobacter koreensis Dae16T (96.4 %), and strain GH41-7T showed highest sequence similarity to Lysobacter antibioticus DSM 2044T (97.5 %), Lysobacter enzymogenes DSM 2043T (97.5 %) and Lysobacter gummosus ATCC 29489T (97.4 %). Levels of DNA–DNA relatedness indicated that strains GH34-4T and GH41-7T represented species clearly different from L. yangpyeongensis, L. antibioticus, L. enzymogenes and L. gummosus. The major cellular fatty acids of strains GH34-4T and GH41-7T were iso-C16 : 0, iso-C15 : 0 and iso-C17 : 1 ω9c, and the major isoprenoid quinone was Q-8. The DNA G+C contents of GH34-4T and GH41-7T were 62.5 and 66.6 mol%, respectively. On the basis of the polyphasic taxonomic data presented, it is evident that each of these strains represents a novel species of the genus Lysobacter, for which the names Lysobacter niabensis sp. nov. (type strain GH34-4T=KACC 11587T=DSM 18244T) and Lysobacter niastensis sp. nov. (type strain GH41-7T=KACC 11588T=DSM 18481T) are proposed.

scholarly journals Sphingobacterium shayense sp. nov., isolated from forest soil

2010 ◽  
Vol 60 (10) ◽  
pp. 2377-2381 ◽  
Author(s):  
Xiang He ◽  
Ting Xiao ◽  
Haiju Kuang ◽  
Xiaojun Lan ◽  
Maripat Tudahong ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Populus Euphratica ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties

A Gram-staining-negative, yellow-coloured, strictly aerobic, non-spore-forming, rod-shaped bacterium, designated HS39T, isolated from a soil sample collected from a natural Populus euphratica forest in Xinjiang, China, was characterized using a polyphasic approach. The isolate grew optimally at 30–37 °C, at pH 6.5–8.0 and with 0–3 % NaCl. Analysis of the 16S rRNA gene sequence of strain HS39T revealed that it is a member of the genus Sphingobacterium. Sphingobacterium mizutaii ATCC 33299T was the nearest relative (94.0 % 16S rRNA gene sequence similarity). The G+C content of the genomic DNA was 40.2 mol%. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1 ω6c and/or C16 : 1 ω7c). The predominant isoprenoid quinone was MK-7. On the basis of phenotypic properties and phylogenetic inference, strain HS39T represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium shayense sp. nov. is proposed. The type strain is HS39T (=CCTCC AB 209006T =NRRL B-59203T).

scholarly journals Description of Sulfitobacter donghicola sp. nov., isolated from seawater of the East Sea in Korea, transfer of Staleya guttiformis Labrenz et al. 2000 to the genus Sulfitobacter as Sulfitobacter guttiformis comb. nov. and emended description of the genus Sulfitobacter

2007 ◽  
Vol 57 (8) ◽  
pp. 1788-1792 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Mi-Hwa Lee ◽  
Tae-Kwang Oh
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
East Sea ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Unidentified Phospholipid ◽  
Emended Description

A Gram-negative, non-motile and rod-, oval- or coccoid-shaped bacterial strain, DSW-25T, which is phylogenetically closely related to the genera Staleya and Sulfitobacter, was isolated from seawater of the East Sea, Korea, and subjected to a polyphasic taxonomic study. Strain DSW-25T grew optimally at pH 7.0–8.0 and at 25 °C. It contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. Major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. The DNA G+C content was 56.9 mol%. Strain DSW-25T exhibited 16S rRNA gene sequence similarity values of 98.4 % to the type strain of Staleya guttiformis and of 96.6–97.6 % to Sulfitobacter species. There were no distinct phenotypic, particularly chemotaxonomic, properties to differentiate Staleya guttiformis and strain DSW-25T from the genus Sulfitobacter. DNA–DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrated that strain DSW-25T differs from recognized Sulfitobacter species and Staleya guttiformis. On the basis of phenotypic, chemotaxonomic, phylogenetic and genetic data, strain DSW-25T was classified in the genus Sulfitobacter as a member of a novel species, for which the name Sulfitobacter donghicola sp. nov. is proposed. The type strain is strain DSW-25T (=KCTC 12864T =JCM 14565T). It is also proposed that Staleya guttiformis be transferred to the genus Sulfitobacter as Sulfitobacter guttiformis comb. nov.

scholarly journals Tumebacillus ginsengisoli sp. nov., isolated from soil of a ginseng field

2011 ◽  
Vol 61 (7) ◽  
pp. 1715-1719 ◽  
Author(s):  
Sang-Hoon Baek ◽  
Yingshun Cui ◽  
Sun-Chang Kim ◽  
Chang-Hao Cui ◽  
Chengri Yin ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties ◽  
Respiratory Quinone ◽  
Major Respiratory Quinone ◽  
The 16S Rrna Gene

A Gram-reaction-positive, rod-shaped, spore-forming bacterium, designated Gsoil 1105T, was isolated from soil of a ginseng field in Pocheon Province in South Korea and characterized in order to determine its taxonomic position. Comparative analysis of the 16S rRNA gene sequence showed that the isolate belongs to the order Bacillales, showing the highest level of sequence similarity with respect to Tumebacillus permanentifrigoris Eur1 9.5T (94.6 %). The phylogenetic distances from other described species with validly published names within the order Bacillales were greater than 9.0 %. Strain Gsoil 1105T had a genomic DNA G+C content of 55.6 mol% and menaquinone 7 (MK-7) as the major respiratory quinone. The major fatty acids were iso-C15 : 0 and anteiso-C15 : 0. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 1105T represents a novel species of the genus Tumebacillus, for which the name Tumebacillus ginsengisoli sp. nov. is proposed. The type strain is Gsoil 1105T ( = KCTC 13942T  = DSM 18389T).

Microbulbifer chitinilyticus sp. nov. and Microbulbifer okinawensis sp. nov., chitin-degrading bacteria isolated from mangrove forests

2011 ◽  
Vol 61 (9) ◽  
pp. 2215-2220 ◽  
Author(s):  
Atsushi Baba ◽  
Masayuki Miyazaki ◽  
Takahiko Nagahama ◽  
Yuichi Nogi
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Threshold Level ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Mangrove Forests ◽  
The Novel ◽  
Separate Species ◽  
Gene Sequence Analysis ◽  
Degrading Bacteria

Three chitin-degrading strains representing two novel species were isolated from mangrove forests in Okinawa, Japan. The isolates, ABABA23T, ABABA211 and ABABA212T, were Gram-negative, non-spore-forming, strictly aerobic chemo-organotrophs. The novel strains produced Q-8 as the major isoprenoid quinone component. The predominant fatty acids were iso-C15 : 0 and C16 : 0. On the basis of 16S rRNA gene sequence analysis, the isolates were closely affiliated with members of the genus Microbulbifer. The DNA G+C contents of strains ABABA23T and ABABA212T were 57.8 and 60.2 mol%, respectively. DNA–DNA relatedness values between these two strains and Microbulbifer reference strains were significantly lower than 70 %, the generally accepted threshold level below which strains are considered to belong to separate species. Based on differences in taxonomic characteristics, the three isolates represent two novel species of the genus Microbulbifer, for which the names Microbulbifer chitinilyticus sp. nov. (type strain, ABABA212T = JCM 16148T = NCIMB 14577T) and Microbulbifer okinawensis sp. nov. (type strain, ABABA23T = JCM 16147T = NCIMB 14576T; reference strain, ABABA211) are proposed.

Taibaiella koreensis sp. nov., isolated from soil of a ginseng field

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 1018-1023 ◽  
Author(s):  
Heung-Min Son ◽  
MooChang Kook ◽  
Ju-Han Kim ◽  
Tae-Hoo Yi
Keyword(s):  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
Biochemical Tests ◽  
Phenotypic Data ◽  
Link Type ◽  
Gram Staining ◽  
The Republic

A Gram-staining-negative, strictly aerobic, motile (by gliding), non-spore-forming and rod-shaped bacterial strain, designated THG-DT86T, was isolated from soil of a ginseng field of Pocheon province in the Republic of Korea and its taxonomic position was investigated by a polyphasic approach. Growth occurred at 10–35 °C, at pH 6.5–8.5 and with 0–1.5 % (w/v) NaCl on trypticase soy agar. Flexirubin-type pigments were found to be present. On the basis of 16S rRNA gene sequence similarity, strain THG-DT86T was shown to belong to the genus Taibaiella and was related to Taibaiella smilacinae PTJT-5T (95.3 %). The G+C content of the genomic DNA was 50.1 mol%. The only isoprenoid quinone detected in strain THG-DT86T was menaquinone-7 (MK-7) and the only polyamine was homospermidine. The predominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 0, iso-C15 : 1 G and iso-C17 : 0, and the major polar lipids were phosphatidylethanolamine, an unidentified aminophosphoglycolipid and an unidentified aminophospholipid. Phenotypic data and phylogenetic inference supported the affiliation of strain THG-DT86T to the genus Taibaiella , and a number of biochemical tests differentiated strain THG-DT86T from the recognized species of the genus Taibaiella . Therefore, the novel isolate represents a novel species, for which the name Taibaiella koreensis sp. nov. is proposed, with THG-DT86T as the type strain ( = KACC 17171T = JCM 18823T).

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