scholarly journals Sandarakinorhabdus limnophila gen. nov., sp. nov., a novel bacteriochlorophyll a-containing, obligately aerobic bacterium isolated from freshwater lakes

2006 ◽  
Vol 56 (4) ◽  
pp. 847-854 ◽  
Author(s):  
Frederic Gich ◽  
Jörg Overmann
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Hexadecenoic Acid ◽  
Aerobic Bacterium ◽  
Freshwater Lakes ◽  
Rrna Gene Sequence ◽  
Light Harvesting Complexes

Three strains (so36, so42T and wo26) representing a novel Gram-negative, obligately aerobic, bacteriochlorophyll a-containing species of the α-4 subgroup of the Proteobacteria were isolated from freshwater lakes using a high-throughput cultivation technique. The non-motile and slender rod-shaped cells formed orange–red-pigmented colonies. The main carotenoids were nostoxanthin and keto-nostoxanthin. According to the absorption spectrum, two different photosynthetic light-harvesting complexes, an LHI complex and a B800-830-type peripheral LHII complex, were present in the cells. The predominant fatty acids of strain so42T were hexadecenoic acid (16 : 1ω7c) and octadecenoic acid (18 : 1ω7c), whereas 17 : 1ω6c and 14 : 0 iso 2-OH were present in smaller amounts. The main polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, glycolipid and sphingoglycolipids. The major respiratory lipoquinone was ubiquinone-10, whereas ubiquinone-9 was present in smaller amounts. The three strains were cytochrome oxidase-negative and catalase-positive and formed alkaline and acid phosphatases. The strains grew chemoorganoheterotrophically in mineral media supplemented with various organic acids, amino acids or complex substrates such as peptone and yeast extract. The G+C content of the genomic DNA of strain so42T was 64·3 mol%. The three novel isolates contained the same 16S rRNA gene sequence. The 16S rRNA gene sequence similarity to the closest phylogenetic relative Sandaracinobacter sibiricus was only 92·8 %. Accordingly, the three strains represent a new genus and species, for which the name Sandarakinorhabdus limnophila gen. nov., sp. nov., is proposed, with strain so42T (=DSM 17366T=CECT 7086T) as the designated type strain.

scholarly journals Salinisphaera dokdonensis sp. nov., isolated from surface seawater

2010 ◽  
Vol 60 (3) ◽  
pp. 680-685 ◽  
Author(s):  
Gi Duk Bae ◽  
Chung Yeon Hwang ◽  
Hye Min Kim ◽  
Byung Cheol Cho
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Aerobic Bacterium ◽  
Rrna Gene Sequence ◽  
The 16S Rrna Gene

A Gram-negative, strictly aerobic bacterium, designated CL-ES53T, was isolated from surface water of the East Sea in Korea. Cells of strain CL-ES53T were short rods and motile by means of monopolar flagella. Strain CL-ES53T grew with 4–21 % NaCl (optimum 10 %) and at 5–40 °C (optimum 25 °C) and pH 5.2–8.8 (optimum pH 6.3–7.2). The major isoprenoid quinone was Q-8. The major fatty acids were C18 : 1 ω7c (42.0 %), C18 : 1 ω9c (14.8 %) and C14 : 0 (9.4 %). The genomic DNA G+C content was 64.9 mol%. Analysis of the 16S rRNA gene sequence of strain CL-ES53T revealed that it was a member of the genus Salinisphaera and most closely related to Salinisphaera shabanensis E1L3A T (96.9 % sequence similarity) and Salinisphaera hydrothermalis EPR70T (93.8 %). Phylogenetic analyses based on the 16S rRNA gene sequence showed that strain CL-ES53T formed a robust cluster with S. shabanensis E1L3A T. Although the 16S rRNA gene sequence similarity between strain CL-ES53T and S. shabanensis E1L3A T was rather high (96.9 %), DNA–DNA relatedness between these strains was 12 %, suggesting that they represent genomically distinct species. Strain CL-ES53T was differentiated from S. shabanensis E1L3A T and S. hydrothermalis EPR70T on the basis of optimum temperature for growth and certain phenotypic characteristics. The phylogenetic analysis and physiological and chemotaxonomic data show that strain CL-ES53T should be classified in the genus Salinisphaera within a novel species, for which the name Salinisphaera dokdonensis sp. nov. is proposed. The type strain is CL-ES53T (=KCCM 90064T =DSM 19549T).

Bacillus pocheonensis sp. nov., a moderately halotolerant, aerobic bacterium isolated from soil of a ginseng field

2007 ◽  
Vol 57 (11) ◽  
pp. 2532-2537 ◽  
Author(s):  
Leonid N. Ten ◽  
Sang-Hun Baek ◽  
Wan-Taek Im ◽  
Liudmila L. Larina ◽  
Jung-Sook Lee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Aerobic Bacterium ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties

A Gram-positive, non-motile, endospore-forming bacterial strain, designated Gsoil 420T, was isolated from soil of a ginseng field in Pocheon Province, South Korea, and was characterized, using a polyphasic approach, in order to determine its taxonomic position. The novel isolate consisted of strictly aerobic, rod-shaped cells and was able to grow in medium supplemented with up to 12 % NaCl at 25 °C and pH 6.5–7.0. Comparative 16S rRNA gene sequence analysis showed that strain Gsoil 420T fell within the radiation of the cluster comprising Bacillus species and formed a coherent cluster with Bacillus niacini (16S rRNA gene sequence similarity, 98.6 %), Bacillus bataviensis (98.6 %), Bacillus soli (98.3 %), Bacillus drentensis (98.0 %), Bacillus novalis (98.0 %), Bacillus vireti (97.9 %), Bacillus foraminis (97.6 %), Bacillus fumarioli (97.4 %) and Bacillus jeotgali (97.0 %). The levels of 16S rRNA gene sequence similarity with respect to other Bacillus species with validly published names were less than 96.8 %. Strain Gsoil 420T had a genomic DNA G+C content of 44.9 mol% and the predominant respiratory quinone was MK-7. The major fatty acids were anteiso-C15 : 0 (33.9 %), iso-C15 : 0 (24.5 %) and iso-C14 : 0 (19.9 %). These chemotaxonomic results supported the affiliation of strain Gsoil 420T to the genus Bacillus. However, low DNA–DNA relatedness values and distinguishing phenotypic characteristics allowed genotypic and phenotypic differentiation of strain Gsoil 420T from recognized Bacillus species. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 420T represents a novel species of the genus Bacillus, for which the name Bacillus pocheonensis sp. nov. is proposed. The type strain is Gsoil 420T (=KCTC 13943T=DSM 18135T).

scholarly journals Sphingobium scionense sp. nov., an aromatic hydrocarbon-degrading bacterium isolated from contaminated sawmill soil

2010 ◽  
Vol 60 (2) ◽  
pp. 413-416 ◽  
Author(s):  
Quanfeng Liang ◽  
Gareth Lloyd-Jones
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Aromatic Hydrocarbon ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Degrading Bacterium

This study characterized strain WP01T, a Gram-staining-negative, rod-shaped, aerobic bacterium isolated from a polycyclic aromatic hydrocarbon-contaminated soil in New Zealand. Strain WP01T shared many characteristics of the genus Sphingobium: the predominant respiratory quinone (89 %) was ubiquinone with ten isoprene units (Q-10); the major fatty acids were C18 : 1 ω7c, C16 : 1 ω7c, C16 : 0 and C14 : 0 2-OH; spermidine was the major polyamine; the DNA G+C content was 63.8 mol%; and the Sphingobium-specific 16S rRNA signatures were conserved. A point of difference from other species of the genus Sphingobium was that strain WP01T reduced nitrate to nitrite. The polar lipid pattern consisted of the predominant compounds diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipids. 16S rRNA gene sequence analysis showed that, amongst the recognized species of the genus Sphingobium, strain WP01T was most similar to Sphingobium yanoikuyae GIFU 9882T and Sphingobium amiense YTT (>97 % 16S rRNA gene sequence similarities). The low DNA–DNA relatedness values between strain WP01T and S. yanoikuyae GIFU 9882T (46.6 %) and S. amiense DSM 16289T (25.6 %) indicated no relatedness at the species level. On the basis of these characteristics, it is concluded that strain WP01T should be considered as representing a novel species within the genus Sphingobium, for which the name Sphingobium scionense sp. nov. is proposed. The type strain is WP01T (=DSM 19371T=ICMP 13533T).

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

2010 ◽  
Vol 60 (2) ◽  
pp. 364-368 ◽  
Author(s):  
Ying-Shun Cui ◽  
Jung-Sook Lee ◽  
Sung-Taik Lee ◽  
Wan-Taek Im
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Rrna Gene Sequence ◽  
Biochemical Tests

A Gram-positive, non-spore-forming, aerobic bacterium, designated Gsoil 001T, was isolated from the soil of a ginseng field in Pocheon province, South Korea. On the basis of 16S rRNA gene sequence analysis, strain Gsoil 001T was shown to belong to the genus Kribbella. The closest phylogenetic relatives were Kribbella koreensis LM 161T (99.0 % 16S rRNA gene sequence similarity), Kribbella flavida KACC 20248T (98.8 %) and Kribbella alba (98.8%). Lower similarity (98.4–96.9 %) was found with the other recognized species of the genus Kribbella. The major quinone was MK-9(H4), the major fatty acids were anteiso-C15 : 0 and iso-C16 : 0 and the major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol and phosphatidylinositol. The cell-wall peptidoglycan contained ll-2,6-diaminopimelic acid. These chemotaxonomic data and the high genomic DNA G+C content (66.3 mol%) supported the affiliation of strain Gsoil 001T to the genus Kribbella. The results of physiological and biochemical tests differentiated strain Gsoil 001T genotypically and phenotypically from the Kribbella species with validly published names. Therefore, this isolate represents a novel species, for which the name Kribbella ginsengisoli sp. nov. is proposed, with the type strain Gsoil 001T (=KCTC 19134T =DSM 17941T).

scholarly journals Kangiella Shandongensis Sp. Nov., A Novel Species Isolated From Saltern In Yantai, China

2021 ◽  
Author(s):  
Li-Yang Peng ◽  
Rui Yin ◽  
Shu-Kun Gao ◽  
Hui-Ning Jiang ◽  
Xiao-Xiao Liu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Amino Acid Identity ◽  
16S Rrna Gene Sequence ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Rrna Gene Sequence

Abstract A Gram-stain-negative, wheat, rod-shaped, motile, non-spore forming, and aerobic bacterium, designated as strain PIT, was isolated from saline silt samples collected in saltern in Yantai, Shandong, China, and subjected to a polyphasic taxonomic study. The 16S rRNA gene sequence analysis revealed a clear affiliation of strain PIT with the genus Kangiella. Strain PIT showed the closest phylogenetic relationship with Kangiella taiwanensis KT1T with the highest 16S rRNA gene sequence similarity of 98.3%. The genome size of the strain PIT was 2809662 bp consisting of 2653 genes which include 39 tRNAs genes, 2 sRNA genes and 4 rRNA genes. The major cellular fatty acids of strain PIT were identified as iso-C15:0, iso-C11:0, iso-C11:0 3-OH and Summed Feature 9 (iso-C17:1ω9c), and the major respiratory isoprenoid quinone was Q8. The major polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylmonomethylethanolamine (PME) and phosphatidylinositol (PI). The G+C content of the genomic DNA was 45.8 mol%. The Average Amino Acid identity (AAI) value between strain PIT and Kangiella sediminilitoris was 83.9%. The Average Nucleotide Identity (ANI) values between strain PIT and Kangiella sediminilitoris, Kangiella aquimarina and Kangiella taiwanensis were 76.9%, 71.0% and 74.6%, respectively. The digital DNA-DNA Hybridization (dDDH) values between strain PIT and Kangiella sediminilitoris, Kangiella aquimarina and Kangiella taiwanensis were 19.8%, 19.1% and 18.7%, respectively. The results of 16S rRNA gene phylogeny, phenotypic characterizations, chemotaxonomic characterization and genome features indicate that strain PIT represents a novel specie of the genus Kangiella, for which the name Kangiella shandongensis sp. nov. is proposed. The type strain is PIT (KCTC 82509T = MCCC 1K04352T).

scholarly journals Silanimonas lenta gen. nov., sp. nov., a slightly thermophilic and alkaliphilic gammaproteobacterium isolated from a hot spring

2005 ◽  
Vol 55 (1) ◽  
pp. 385-389 ◽  
Author(s):  
Eun Mi Lee ◽  
Che Ok Jeon ◽  
Inpyo Choi ◽  
Kyu-Seob Chang ◽  
Chang-Jin Kim
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Hot Spring ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Rrna Gene Sequence ◽  
Moderately Thermophilic

A moderately thermophilic aerobic bacterium, strain 25-4T, was isolated from a hot spring at Baekdoo Mountain in Korea. The cells were Gram-negative, motile rods each having a polar flagellum. Analysis of the 16S rRNA gene sequence indicated that the strain represented a new lineage within the family ‘Xanthomonadaceae’ of the ‘Gammaproteobacteria’, being most closely related to the genera Thermomonas, Xanthomonas, Luteimonas, Pseudoxanthomonas, Stenotrophomonas and Xylella and having 16S rRNA gene sequence similarities to the most related species of the genera of between 92·9 and 94·4 %. The strain contained Q-8 as the major isoprenoid quinone and had a fatty acid profile with predominant iso-branched fatty acids. Growth occurred at pH 6·0–10, with an optimum at pH 9·0, and at 25–53 °C, with an optimum at 47 °C. The G+C content of the genomic DNA was 50·7 mol%. On the basis of phylogenetic analyses and its phenotypic characteristics, strain 25-4T belongs to a new genus, Silanimonas gen. nov., within the ‘Gammaproteobacteria’. The sole species of this genus is Silanimonas lenta sp. nov. (type strain, 25-4T=DSM 16282T=KCTC 12236T).

scholarly journals Thermus amyloliquefaciens sp. nov., isolated from a hot spring sediment sample

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2491-2495 ◽  
Author(s):  
Tian-Tian Yu ◽  
Hong Ming ◽  
Ji-Cheng Yao ◽  
En-Min Zhou ◽  
Dong-Jin Park ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Hot Spring ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Rrna Gene Sequence

A Gram-stain-negative, aerobic bacterium, designated strain YIM 77409T, was isolated from the Niujie hot spring in the Eryuan county of Dali, Yunnan province, south-west China. Cells of the strain were rod-shaped and colonies were yellow and circular. The strain grew at pH 6.0–8.0 (optimum, pH 7.0) and 50–70°C (optimum, 60–65°C). The predominant menaquinone was MK-8 and the DNA G+C content was 66.4 mol%. Major fatty acids (>10 %) were iso-C15 : 0 and iso-C17 : 0.The polar lipids consisted of one aminophospholipid, one phospholipid and two glycolipids. 16S rRNA gene sequence analysis showed that strain YIM 77409T formed a cluster with Thermus scotoductus DSM 8553T, Thermus antranikianii DSM 12462T, Thermus caliditerrae YIM 77925T and Thermus tengchongensis YIM 77924T, with highest 16S rRNA gene sequence similarity to T. scotoductus DSM 8553T (97.57 %). However, DNA–DNA hybridization indicated that strain YIM 77409T should be viewed as a representative of a novel species, as there was only 30.6 ± 1.6 % reassociation with T. scotoductus DSM 8553T. On the basis of the morphological and chemotaxonomic characteristics, as well as the genotypic data, it is proposed that strain YIM 77409T represents a novel species of the genus Thermus, with the name Thermus amyloliquefaciens sp. nov. The type strain is YIM 77409T ( = DSM 25898T = KCTC 32024T).

scholarly journals Planococcus donghaensis sp. nov., a starch-degrading bacterium isolated from the East Sea, South Korea

2007 ◽  
Vol 57 (11) ◽  
pp. 2645-2650 ◽  
Author(s):  
Jeong-Hwa Choi ◽  
Wan-Taek Im ◽  
Qing-Mei Liu ◽  
Jae-Soo Yoo ◽  
Jae-Ho Shin ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
South Korea ◽  
Gene Sequence ◽  
East Sea ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Rrna Gene Sequence ◽  
The 16S Rrna Gene

A novel Gram-positive, aerobic bacterium, strain JH1T, was isolated from deep-sea sediment of the East Sea, South Korea, and identified by methods of polyphasic taxonomy. The strain was oxidase-positive, motile and coccus-shaped. The genomic DNA G+C content of strain JH1T was 47 mol%. The major fatty acid of strain JH1T was anteiso-C15 : 0 and the predominant menaquinones were MK-7 and MK-8. Similarity of the 16S rRNA gene sequence (1452 nt) of strain JH1T to those of species of the genera Planococcus and Planomicrobium was 96.0–98.2 %. The signature nucleotides in the 16S rRNA gene sequence were compared with those of previously studied type strains of species in the genera Planococcus and Planomicrobium, and suggested that strain JH1T belongs to the genus Planococcus. In addition, phylogenetic analysis showed that strain JH1T was located within the cluster comprising Planococcus antarcticus and Planococcus kocurii. DNA–DNA hybridization showed that it had 9.3 % genomic relatedness with Planococcus antarcticus DSM 14505T and 22.9 % with Planococcus kocurii DSM 20747T. On the basis of the phenotypic, phylogenetic and genomic data, a novel species of the genus Planococcus, Planococcus donghaensis sp. nov., is proposed, with type strain JH1T (=KCTC 13050T=LMG 23779T).

scholarly journals Marinobacterium coralli sp. nov., isolated from mucus of coral (Mussismilia hispida)

2011 ◽  
Vol 61 (1) ◽  
pp. 60-64 ◽  
Author(s):  
Luciane A. Chimetto ◽  
Ilse Cleenwerck ◽  
Marcelo Brocchi ◽  
Anne Willems ◽  
Paul De Vos ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Related Species ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Rrna Gene Sequence ◽  
Type Strains ◽  
Sequence Similarities

A Gram-negative, aerobic bacterium, designated R-40509T, was isolated from mucus of the reef builder coral (Mussismilia hispida) located in the São Sebastião Channel, São Paulo, Brazil. The strain was oxidase-positive and catalase-negative, and required Na+ for growth. Its phylogenetic position was in the genus Marinobacterium and the closest related species were Marinobacterium sediminicola, Marinobacterium maritimum and Marinobacterium stanieri; the isolate exhibited 16S rRNA gene sequence similarities of 97.5–98.0 % with the type strains of these species. 16S rRNA gene sequence similarities with other type strains of the genus Marinobacterium were below 96 %. DNA–DNA hybridizations between strain R-40509T and the type strains of the phylogenetically closest species of the genus Marinobacterium revealed less than 70 % DNA–DNA relatedness, supporting the novel species status of the strain. Phenotypic characterization revealed that the strain was able to grow at 15–42 °C and in medium containing up to 9 % NaCl. The isolate could be differentiated from phenotypically related species by several features, including its ability to utilize d-alanine, l-alanine, bromosuccinic acid, β-hydroxybutyric acid and α-ketovaleric acid, but not acetate or l-arabinose. It produced acetoin (Voges–Proskauer), but did not have esterase lipase (C8) or catalase activities. It possessed C18 : 1 ω7c (35 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c; 25 %) and C16 : 0 (22 %) as major cellular fatty acids. The DNA G+C content was 58.5 mol%. The name Marinobacterium coralli sp. nov. is proposed to accommodate this novel isolate; the type strain is R-40509T (=LMG 25435T =CAIM 1449T).

scholarly journals Fangia hongkongensis gen. nov., sp. nov., a novel gammaproteobacterium of the order Thiotrichales isolated from coastal seawater of Hong Kong

2007 ◽  
Vol 57 (11) ◽  
pp. 2665-2669 ◽  
Author(s):  
Ken W. K. Lau ◽  
Jianping Ren ◽  
Ming-Chiu Fung ◽  
Patrick C. Y. Woo ◽  
Kwok-Yung Yuen ◽  
...  
Keyword(s):  
Hong Kong ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Physiological Data ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Rrna Gene Sequence ◽  
Francisella Novicida

A Gram-negative, coccobacillus-shaped, aerobic bacterium, designated strain UST040201-002T, was isolated in February 2004 from seawater at the outlet of a sandfilter in Port Shelter, Hong Kong SAR, China. This strain possessed ubiquinone-8; its 16S rRNA gene sequence shared only 91 % similarity with the sequence from Caedibacter taeniospiralis and 89–90 % similarity with sequences from Francisella tularensis, Francisella novicida, Francisella philomiragia and Wolbachia persica. 16S rRNA gene sequence analysis showed that the strain formed a distinct clade with C. taeniospiralis. This subcluster formed a tight coherent group with members of the family Francisellaceae and W. persica. Combined phylogenetic and physiological data suggest that strain UST040201-002T represents a novel genus and species within the order Τhiotrichales. The name Fangia hongkongensis gen. nov., sp. nov. is proposed; the type strain is UST040201-002T (=JCM 14605T=NRRL B-41860T).

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