scholarly journals Rhizobium rosettiformans sp. nov., isolated from a hexachlorocyclohexane dump site, and reclassification of Blastobacter aggregatus Hirsch and Müller 1986 as Rhizobium aggregatum comb. nov.

2011 ◽  
Vol 61 (5) ◽  
pp. 1218-1225 ◽  
Author(s):  
Jaspreet Kaur ◽  
Mansi Verma ◽  
Rup Lal

A Gram-negative, rod-shaped, motile, aerobic bacterial strain, W3T, was isolated from hexachlorocyclohexane (HCH)-contaminated groundwater from Lucknow, India, and its taxonomic position was determined using a polyphasic approach. Strain W3T shared highest 16S rRNA gene sequence similarity of 97.8 % with Rhizobium selenitireducens B1T, followed by Rhizobium daejeonense L61T (97.7 %), Rhizobium radiobacter ATCC 19358T (97.5 %) and Blastobacter aggregatus IFAM 1003T (97.2 %). Strain W3T formed a monophyletic clade with Blastobacter aggregatus IFAM 1003T ( = DSM 1111T) in the cluster of species of the genus Rhizobium. Phylogenetic analyses of strain W3T using atpD and recA gene sequences confirmed the phylogenetic arrangements obtained by using 16S rRNA gene sequences. Hence, the taxonomic characterization of B. aggregatus DSM 1111T was also undertaken. Strains W3T and B. aggregatus DSM 1111T contained summed feature 8 (18 : 1ω7c and/or 18 : 1ω6c; 65.4 and 70.8 %, respectively) as the major fatty acid, characteristic of the genus Rhizobium. DNA–DNA relatedness of strain W3T with Rhizobium selenitireducens LMG 24075T, Rhizobium daejeonense DSM 17795T, Rhizobium radiobacter DSM 30147T and B. aggregatus DSM 1111T was 42, 34, 30 and 34 %, respectively. The DNA G+C contents of strain W3T and B. aggregatus DSM 1111T were 62.3 and 62.7 mol%, respectively. A nifH gene encoding dinitrogenase reductase was detected in strain W3T but not in B. aggregatus DSM 1111T. Based on the results obtained by phylogenetic and chemotaxonomic analyses, phenotypic characterization and DNA–DNA hybridization, it is concluded that strain W3T represents a novel species of the genus Rhizobium, for which the name Rhizobium rosettiformans sp. nov. is proposed (type strain W3T  = CCM 7583T  = MTCC 9454T). It is also proposed that Blastobacter aggregatus Hirsch and Müller 1986 be transferred to the genus Rhizobium as Rhizobium aggregatum comb. nov. (type strain IFAM 1003T  = DSM 1111T  = ATCC 43293T).

2007 ◽  
Vol 57 (7) ◽  
pp. 1659-1662 ◽  
Author(s):  
Hana Kim ◽  
Yoe-Jin Choo ◽  
Jaeho Song ◽  
Jung-Sook Lee ◽  
Keun Chul Lee ◽  
...  

A bacterial strain named IMCC1877T was obtained from surface seawater collected near the coast of Deokjeok island (Yellow Sea), using a standard dilution-plating method. The strain was Gram-negative, chemoheterotrophic and facultatively anaerobic, requiring NaCl, and cells were motile rods with a single polar flagellum. Colonies on marine agar were very small (average diameter 0.1 mm). Based on 16S rRNA gene sequences, the most closely related species to strain IMCC1877T was Marinobacterium stanieri (93.7 % sequence similarity to the type strain). Phylogenetic analyses based on 16S rRNA gene sequences showed that this marine isolate belonged to the order Oceanospirillales and formed an independent phyletic line within the clade forming the genus Marinobacterium. The DNA G+C content of the strain was 60.7 mol% and the predominant constituents of the cellular fatty acids were C18 : 1 ω7c (36.6 %), C16 : 1 ω7c and/or iso-C15 : 0 2-OH (26.7 %) and C16 : 0 (24.3 %). Based on the taxonomic data, only a distant relationship could be established between strain IMCC1877T and other Marinobacterium species; the strain therefore represents a novel species of the genus Marinobacterium, for which the name Marinobacterium litorale sp. nov. is proposed. The type strain is IMCC1877T (=KCTC 12756T=LMG 23872T).


2011 ◽  
Vol 61 (5) ◽  
pp. 1182-1188 ◽  
Author(s):  
Ki-Hoon Oh ◽  
Yong-Taek Jung ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon

A Gram-negative-staining, non-motile and rod-shaped bacterial strain, HD-28T, was isolated from a tidal flat of the Yellow Sea, Korea. Strain HD-28T grew optimally at pH 7.0–8.0 and 30 °C in the presence of 2–3 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain HD-28T was most closely related to species of the genus Ruegeria and exhibited 95.5–96.9 % 16S rRNA gene sequence similarity to the type strains of Ruegeria species. A neighbour-joining phylogenetic tree based on gyrB gene sequences also showed that strain HD-28T fell within the cluster comprising recognized species of the genus Ruegeria, showing 77.5–83.9 % sequence similarity. Strain HD-28T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The major polar lipids detected in strain HD-28T were phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid and two unidentified lipids. The DNA G+C content was 57.9 mol%. Differential phenotypic properties, together with phylogenetic distinctiveness, demonstrated that strain HD-28T could be distinguished from recognized species of the genus Ruegeria. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain HD-28T is considered to represent a novel species of the genus Ruegeria, for which the name Ruegeria faecimaris sp. nov. is proposed. The type strain is HD-28T ( = KCTC 23044T = CCUG 58878T).


2006 ◽  
Vol 56 (11) ◽  
pp. 2523-2527 ◽  
Author(s):  
Sabri M. Naser ◽  
Marc Vancanneyt ◽  
Cindy Snauwaert ◽  
Gino Vrancken ◽  
Bart Hoste ◽  
...  

The taxonomic position of six Lactobacillus amylophilus strains isolated from swine waste-corn fermentations was reinvestigated. All strains were included in a multilocus sequence analysis (MLSA) study for species identification of Lactobacillus using the genes encoding the phenylalanyl-tRNA synthase alpha subunit (pheS) and RNA polymerase alpha subunit (rpoA). Partial pheS and rpoA gene sequences showed that strains LMG 11400 and NRRL B-4435 represent a separate lineage that is distantly related to the type strain of L. amylophilus, LMG 6900T, and to three other strains of the species. The MLSA data showed that the two strains LMG 11400 and NRRL B-4435 constituted a distinct cluster, sharing 100 % pheS and rpoA gene sequence similarity. The other reference strains clustered together with the type strain of L. amylophilus, LMG 6900T, and were clearly differentiated from strains LMG 11400 and NRRL B-4435 (80 and 89 % pheS and rpoA gene sequence similarity, respectively). The 16S rRNA gene sequences of the latter two strains are 100 % identical, with the nearest phylogenetic neighbour L. amylophilus LMG 6900T showing only 97.2 % 16S rRNA gene sequence similarity. Further polyphasic taxonomic study based on whole-cell protein fingerprinting, DNA–DNA hybridization and biochemical features demonstrated that the two strains represent a single, novel Lactobacillus species, for which the name Lactobacillus amylotrophicus sp. nov. is proposed. The type strain is LMG 11400T (=NRRL B-4436T=DSM 20534T).


2005 ◽  
Vol 55 (2) ◽  
pp. 913-917 ◽  
Author(s):  
F. L. Thompson ◽  
C. C. Thompson ◽  
S. Naser ◽  
B. Hoste ◽  
K. Vandemeulebroecke ◽  
...  

Six new Vibrio-like isolates originating from different species of bleached and healthy corals around Magnetic Island (Australia) were investigated using a polyphasic approach. Phylogenetic analyses based on 16S rRNA, recA and rpoA gene sequences split the isolates in two new groups. Strains LMG 22223T, LMG 22224, LMG 22225, LMG 22226 and LMG 22227 were phylogenetic neighbours of Photobacterium leiognathi LMG 4228T (95·6 % 16S rRNA gene sequence similarity), whereas strain LMG 22228T was related to Enterovibrio norvegicus LMG 19839T (95·5 % 16S rRNA gene sequence similarity). The two new groups can be distinguished from closely related species on the basis of several phenotypic features, including fermentation of d-mannitol, melibiose and sucrose, and utilization of different compounds as carbon sources, arginine dihydrolase activity, nitrate reduction, resistance to the vibriostatic agent O/129 and the presence of fatty acids 15 : 0 iso and 17 : 0 iso. The names Photobacterium rosenbergii sp. nov. (type strain LMG 22223T=CBMAI 622T=CC1T) and Enterovibrio coralii sp. nov. (type strain LMG 22228T=CBMAI 623T=CC17T) are proposed to accommodate these new isolates. The G+C contents of the DNA of the two type strains are respectively 47·6 and 48·2 mol%.


Author(s):  
Huibin Lu ◽  
Zhipeng Cai ◽  
Tongchu Deng ◽  
Youfeng Qian ◽  
Meiying Xu

Two Gram-stain-negative, catalase-positive, oxidase-negative, rod-shaped, non-flagellated, non-spore-forming and non-motile strains (YJ13CT and H41T) were isolated from a mariculture fishpond in PR China. Comparisons based on 16S rRNA gene sequences indicated that YJ13CT and H41T shared 16S rRNA gene sequences similarities between 92.6 and 99.2 % with species of the genus Algoriphagus . YJ13CT only shared 93.8 % 16S rRNA gene sequence similarity with H41T. The reconstructed phylogenetic and phylogenomic trees indicated that YJ13CT and H41T clustered closely with species of the genus Algoriphagus . The calculated pairwise orthologous average nucleotide identity with usearch (OrthoANIu) values between strains YJ13CT and H41T and other related strains were all less than 79.5 %. The OrthoANIu value between YJ13CT and H41T was only 69.9 %. MK-7 was the predominant respiratory quinone of YJ13CT and H41T and their major cellular fatty acids contained iso-C15 : 0, C16 : 1 ω7c and C17 : 1 ω9c. The polar lipids profiles of YJ13CT and H41T consisted of phosphatidylethanolamine and several kinds of unidentified lipids. Combining the above descriptions, strains YJ13CT and H41T represent two distinct novel species of the genus Algoriphagus , for which the names Algoriphagus pacificus sp. nov. (type strain YJ13CT=GDMCC 1.2178T=KCTC 82450T) and Algoriphagus oliviformis sp. nov. (type strain H41T=GDMCC 1.2179T=KCTC 82451T) are proposed.


Author(s):  
Juan Zhou ◽  
Yuyuan Huang ◽  
Jing Yang ◽  
Xin-He Lai ◽  
Dong Jin ◽  
...  

Four aerobic, Gram-stain-positive, rod-shaped bacteria (HY60T, HY54, HY82T and HY89) were isolated from bat faeces of Hipposideros and Rousettus species collected in PR China. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the four novel strains formed two separate but adjacent subclades close to Microbacterium agarici CGMCC 1.12260T (97.6–97.7 % similarity), Microbacterium humi JCM 18706T (97.3–97.5 %) and Microbacterium lindanitolerans JCM 30493T (97.3–97.4 %). The 16S rRNA gene sequence similarity was 98.3 % between strains HY60T and HY82T, and identical within strain pairs HY60T/HY54 and HY82T/HY89. The DNA G+C contents of strains HY60T and HY82T were 61.9 and 63.3 mol%, respectively. The digital DNA–DNA hybridization and average nucleotide identity values between each novel strain and their closest relatives were all below the 70 % and 95–96 % thresholds for species delimitation, respectively. All four novel strains contained anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 0 as the main fatty acids, MK-11 and MK-12 as the major respiratory quinones, and diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid as the predominant polar lipids. The cell-wall peptidoglycan was of B type and contained alanine, glutamate, glycine and ornithine. The acyl type of the muramic acid was glycolyl. The whole-cell sugars were rhamnose and ribose. Based on the foregoing polyphasic analyses, it was concluded that the four uncharacterized strains represented two novel species of the genus Microbacterium , for which the names Microbacterium chengjingii sp. nov. [type strain HY60T (=CGMCC 1.17468T=GDMCC 1.1951T=KACC 22102T)] and Microbacterium fandaimingii sp. nov. [type strain HY82T (=CGMCC 1.17469T=GDMCC 1.1949T=KACC 22101T)] are proposed, respectively.


2007 ◽  
Vol 57 (9) ◽  
pp. 2073-2078 ◽  
Author(s):  
Jennifer C. Ast ◽  
Ilse Cleenwerck ◽  
Katrien Engelbeen ◽  
Henryk Urbanczyk ◽  
Fabiano L. Thompson ◽  
...  

Six representatives of a luminous bacterium commonly found in association with deep, cold-dwelling marine fishes were isolated from the light organs and skin of different fish species. These bacteria were Gram-negative, catalase-positive, and weakly oxidase-positive or oxidase-negative. Morphologically, cells of these strains were coccoid or coccoid-rods, occurring singly or in pairs, and motile by means of polar flagellation. After growth on seawater-based agar medium at 22 °C for 18 h, colonies were small, round and white, with an intense cerulean blue luminescence. Analysis of 16S rRNA gene sequence similarity placed these bacteria in the genus Photobacterium. Phylogenetic analysis based on seven housekeeping gene sequences (16S rRNA gene, gapA, gyrB, pyrH, recA, rpoA and rpoD), seven gene sequences of the lux operon (luxC, luxD, luxA, luxB, luxF, luxE and luxG) and four gene sequences of the rib operon (ribE, ribB, ribH and ribA), resolved the six strains as members of the genus Photobacterium and as a clade distinct from other species of Photobacterium. These strains were most closely related to Photobacterium phosphoreum and Photobacterium iliopiscarium. DNA–DNA hybridization values between the designated type strain, Photobacterium kishitanii pjapo.1.1T, and P. phosphoreum LMG 4233T, P. iliopiscarium LMG 19543T and Photobacterium indicum LMG 22857T were 51, 43 and 19 %, respectively. In AFLP analysis, the six strains clustered together, forming a group distinct from other analysed species. The fatty acid C17 : 0 cyclo was present in these bacteria, but not in P. phosphoreum, P. iliopiscarium or P. indicum. A combination of biochemical tests (arginine dihydrolase and lysine decarboxylase) differentiates these strains from P. phosphoreum and P. indicum. The DNA G+C content of P. kishitanii pjapo.1.1T is 40.2 %, and the genome size is approximately 4.2 Mbp, in the form of two circular chromosomes. These strains represent a novel species, for which the name Photobacterium kishitanii sp. nov. is proposed. The type strain, pjapo.1.1T (=ATCC BAA-1194T=LMG 23890T), is a luminous symbiont isolated from the light organ of the deep-water fish Physiculus japonicus.


2005 ◽  
Vol 55 (5) ◽  
pp. 2051-2055 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Soo-Young Lee ◽  
Choong-Hwan Lee ◽  
Tae-Kwang Oh

Two Gram-negative, non-spore-forming, slightly halophilic gliding bacterial strains, DSW-8T and DSW-9, were isolated from sea water off a Korean island, Dokdo, of the East Sea, Korea, and their taxonomic position was investigated by a polyphasic study. The two strains grew optimally at 30 °C and in the presence of 2–3 % (w/v) NaCl. Strains DSW-8T and DSW-9 were characterized chemotaxonomically as containing MK-6 as the predominant menaquinone and iso-C17 : 0 3-OH, iso-C15 : 0 and iso-C15 : 1 as the major fatty acids. Major polar lipids were phosphatidylethanolamine, two unidentified phospholipids, an unidentified glycolipid and an amino group-containing lipid that was ninhydrin-positive. Their DNA G+C contents were 36·1 and 35·9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains DSW-8T and DSW-9 fell within the genus Maribacter of the family Flavobacteriaceae. Strains DSW-8T and DSW-9 exhibited no difference in their 16S rRNA gene sequences and possessed a mean DNA–DNA relatedness level of 89 %. Strains DSW-8T and DSW-9 exhibited 16S rRNA gene sequence similarity levels of 96·9–98·0 % to the type strains of the four recognized Maribacter species, but their low level of DNA–DNA relatedness with these species demonstrated that they constitute a distinct Maribacter species. On the basis of phenotypic and phylogenetic data and genetic distinctiveness, strains DSW-8T (=KCTC 12393T=DSM 17201T) and DSW-9 were classified in the genus Maribacter as members of a novel species, for which the name Maribacter dokdonensis sp. nov. is proposed.


2004 ◽  
Vol 54 (6) ◽  
pp. 2163-2167 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Tae-Kwang Oh ◽  
Yong-Ha Park

A Gram-variable, endospore-forming moderately halophilic rod, strain SF-121, was isolated from a marine solar saltern of the Yellow Sea in Korea. The result of 16S rRNA gene sequence analysis showed that strain SF-121 has highest sequence similarity (99·7 %) with the type strain of Bacillus halodenitrificans. Phylogenetic analyses based on 16S rRNA gene sequences revealed that B. halodenitrificans DSM 10037T and strain SF-121 are more closely related to the genus Virgibacillus than to the genus Bacillus. Strain SF-121 and B. halodenitrificans DSM 10037T exhibited 16S rRNA gene similarity levels of 95·3–97·5 % with the type strains of Virgibacillus species and 94·0 % with the type strain of Bacillus subtilis. DNA–DNA relatedness and phenotypic data indicated that B. halodenitrificans DSM 10037T and strain SF-121 are members of the same species. B. halodenitrificans DSM 10037T and strain SF-121 exhibited DNA–DNA relatedness values of 9–11 % with the type strains of Virgibacillus carmonensis and Virgibacillus marismortui. On the basis of the phenotypic, chemotaxonomic, phylogenetic and genetic data, B. halodenitrificans should be reclassified in the genus Virgibacillus as Virgibacillus halodenitrificans comb. nov.


2011 ◽  
Vol 61 (6) ◽  
pp. 1315-1321 ◽  
Author(s):  
J. Killer ◽  
J. Kopečný ◽  
J. Mrázek ◽  
I. Koppová ◽  
J. Havlík ◽  
...  

Our previous study, based primarily on PCR-denaturing gradient gel electrophoresis and 16S rRNA gene sequencing, focused on the isolation of four bifidobacterial groups from the digestive tract of three bumblebee species. In that study, we proposed that these isolated groups potentially represented novel species of the family Bifidobacteriaceae. One of the four, Bifidobacterium bombi, has been described recently. Strains representing two of the other groups have been classified as members of the genus Bifidobacterium on the basis of positive results for fructose-6-phosphate phosphoketolase activity and analysis of partial 16S rRNA and heat-shock protein 60 (hsp60) gene sequences. Analysis of 16S rRNA gene sequence similarities revealed that the isolates of the first group were affiliated to Bifidobacterium asteroides YIT 11866T, B. indicum JCM 1302T and B. coryneforme ATCC 25911T (96.2, 96.0 and 95.9 % sequence similarity, respectively), together with other bifidobacteria showing lower sequence similarity. Additional representatives of the second group were found to be affiliated to Bifidobacterium minimum YIT 4097T and B. coryneforme ATCC 25911T (96.0 and 96.3 % sequence similarity) and also to other bifidobacteria with lower sequence similarity. These results indicate that the isolates of the two groups belong to novel species within the genus Bifidobacterium. This observation was further substantiated by the results of partial sequencing of hsp60. On the basis of phylogenetic and phenotypic analyses and analysis of 16S rRNA and partial hsp60 gene sequences, we propose two novel species, Bifidobacterium actinocoloniiforme sp. nov. (type strain LISLUCIII-P2T  = DSM 22766T  = CCM 7728T) and Bifidobacterium bohemicum sp. nov. (type strain JEMLUCVIII-4T  = DSM 22767T  = CCM 7729T).


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