Transfer of Bacillus halodenitrificans Denariaz et al. 1989 to the genus Virgibacillus as Virgibacillus halodenitrificans comb. nov.

Yoon, Jung‐Hoon; Oh, Tae Kwang; Park, Yong Ha

doi:10.1099/ijs.0.63196-0

Cited by 81 publications

(53 citation statements)

References 29 publications

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“…One example of such independent linage is a group comprising the genera Alkalibacillus and the genus Virgibacillus [43]. In this work, two out of the 3 clones assigned to the Virgibacillus genus showed sequence similarity to the species Virgibacillus chiguensis [44] showing a high sequence similarity (98.4-98.6 %) and the other clone was phylogenetically assigned to Virgibacillus halodenitrificans (91 % sequence similarity) [45].…”

Section: Phylogenetic Analysis Of the Bacterial Clones And Dominant Pmentioning

confidence: 55%

Phylogenetic Profiling and Diversity of Bacterial Communities in the Death Valley, an Extreme Habitat in the Atacama Desert

et al. 2015

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The Atacama Desert, one of the driest deserts in the world, represents a unique extreme environmental ecosystem to explore the bacterial diversity as it is considered to be at the dry limit for life. A 16S rRNA gene (spanning the hyper variable V3 region) library was constructed from an alkaline sample of unvegetated soil at the hyperarid margin in the Atacama Desert. A total of 244 clone sequences were used for MOTHUR analysis, which revealed 20 unique phylotypes or operational taxonomic units (OTUs). V3 region amplicons of the 16S rRNA were suitable for distinguishing the bacterial community to the genus and specie level. We found that all OTUs were affiliated with taxa representative of the Firmicutes phylum. The extremely high abundance of Firmicutes indicated that most bacteria in the soil were spore-forming survivors. In this study we detected a narrower diversity as compared to other ecological studies performed in other areas of the Atacama Desert. The reported genera were Oceanobacillus (representing the 69.5 % of the clones sequenced), Bacillus, Thalassobacillus and Virgibacillus. The present work shows physical and chemical parameters have a prominent impact on the microbial community structure. It constitutes an example of the communities adapted to live in extreme conditions caused by dryness and metal concentrations.

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Section: Phylogenetic Analysis Of the Bacterial Clones And Dominant Pmentioning

confidence: 55%

Phylogenetic Profiling and Diversity of Bacterial Communities in the Death Valley, an Extreme Habitat in the Atacama Desert

et al. 2015

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“…Cells are resistant to gentamicin (10 mg), kanamycin (30 mg), nalidixic acid (20 mg) and streptomycin (10 mg), Table 1. Differential characteristics between strain YIM kkny16 T and recognized species of the genus Virgibacillus Taxa: 1, strain YIM kkny16 T (data from the present study); 2, V. marismortui (Arahal et al, 1999(Arahal et al, , 2000Heyrman et al, 2003); 3, V. halodenitrificans (Yoon et al, 2004); 4, V. olivae (Quesada et al, 2007); 5, V. carmonensis (Heyrman et al, 2003); 6, V. proomii (Heyndrickx et al, 1999;Heyrman et al, 2003); 7, V. pantothenticus (Heyndrickx et al, 1999;Heyrman et al, 2003); 8, V. dokdonensis (Yoon et al, 2005); 9, V. necropolis (Heyrman et al, 2003); 10, V. salexigens (Garabito et al, 1997;Wainø et al, 1999;Heyrman et al, 2003); 11, V. koreensis (Lee et al, 2006); 12, V. halophilus . +, Positive; 2, negative; V, variable; W, weakly positive; pr, predominant amount; tr, trace; ND, no data available.…”

Section: Description Of Virgibacillus Kekensis Sp Novmentioning

confidence: 99%

Virgibacillus kekensis sp. nov., a moderately halophilic bacterium isolated from a salt lake in China

Chen

Cui

Fritze

et al. 2008

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

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A Gram-positive, moderately halophilic, motile, strictly aerobic, endospore-forming, oxidase-and catalase-positive, rod-shaped bacterium, strain YIM kkny16 T , was isolated from a saline mud sample collected from the Keke salt lake in the Qaidam Basin, north-west China. This isolate grew in the presence of 0-25 % (w/v) NaCl and at pH 6.0-10.0 and 10-50 6C; optimum growth was observed with 10 % (w/v) NaCl and at pH 7.0 and 37 6C. Strain YIM kkny16 T had meso-diaminopimelic acid as the diagnostic diamino acid, MK-7 as the predominant respiratory quinone, with a significant amount of MK-6, and anteiso-C 15 : 0 , iso-C 14 : 0 and C 16 : 1 v7c alcohol as major fatty acids. Major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The DNA G+C content was 41.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain YIM kkny16 T was a member of the genus Virgibacillus, exhibiting sequence similarities of 94.9-97.3 % to the type strains of recognized Virgibacillus species. Strain YIM kkny16 T could be differentiated from recognized Virgibacillus species based on phenotypic characteristics, chemotaxonomic differences, phylogenetic analysis and DNA-DNA hybridization data. On the basis of evidence from this polyphasic study, strain YIM kkny16 T is considered to represent a novel species of the genus Virgibacillus, for which the name Virgibacillus kekensis sp. nov. is proposed. The type strain is YIM kkny16 T (5DSM 17056 T 5CGMCC 1.6298 T ).At the time of writing, the genus Virgibacillus comprises 11 recognized species, with Virgibacillus olivae (Quesada et al., 2007) and Virgibacillus halophilus (An et al., 2007) being the most recently described. Virgibacillus pantothenticus (Heyndrickx et al., 1998) is the type species. During a recent study of the microbial diversity of the Keke salt lake in the Qaidam Basin of Qinghai Province, north-west China, a moderately halophilic rod-shaped bacterium, designated strain YIM kkny16 T , was isolated from a saline mud sample. Phenotypic and chemotaxonomic characterization, together with phylogenetic analysis based on 16S rRNA gene sequences, showed that strain YIM kkny16 T was related to members of the genus Virgibacillus, but represented a novel species.Strain YIM kkny16 T was isolated from a saline mud sample by plating 1 : 10 serial dilutions of the sample on Difco marine agar 2216 (MA; pH 7.2) at 28 u C for 2 weeks. The strain was maintained both in Difco marine broth (MB) supplemented with 20 % (v/v) glycerol at 280 u C and as lyophilized cultures at 4 u C. Unless otherwise indicated, morphological and physiological studies were performed with cells grown on MA supplemented with 10 % (w/v) NaCl, and on ISP medium 2 agar (Shirling & Gottlieb, 1966), nutrient agar and trypticase soy agar (BBL) as controls. Cells for chemotaxonomic and molecular systematic studies were grown in MB supplemented with 10 % (w/v) NaCl in shake flasks (with shaking at aboutThe GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain YIM kkny1...

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“…Table 1. Differential characteristics between strain YIM kkny3 T and recognized species of the genus Virgibacillus Taxa: 1, strain YIM kkny3 T (data from the present study); 2, V. olivae (Quesada et al, 2007); 3, V. marismortui (Arahal et al, 1999(Arahal et al, , 2000Heyrman et al, 2003); 4, V. kekensis (Chen et al, 2008a); 5, V. halodenitrificans (Yoon et al, 2004); 6, V. carmonensis (Heyrman et al, 2003); 7, V. proomii (Heyndrickx et al, 1999;Heyrman et al, 2003); 8, V. pantothenticus (Heyndrickx et al, 1999;Heyrman et al, 2003); 9, V. dokdonensis (Yoon et al, 2005); 10, V. necropolis (Heyrman et al, 2003); 11, V. salexigens (Wainø et al, 1999;Heyrman et al, 2003); 12, V. koreensis (Lee et al, 2006); 13, V. halophilus ; 14, V. chiguensis (Wang et al, 2008). +, Positive; 2, negative; V, variable; W, weakly positive; ND, no data available.…”

Section: Institute Of Medicinal Biotechnology Chinese Academy Of Medmentioning

confidence: 99%

“…At the time of writing, the genus comprised 13 recognized species: Virgibacillus pantothenticus (Heyndrickx et al, 1998), V. proomii (Heyndrickx et al, 1999), V. carmonensis, V. necropolis, V. marismortui and V. salexigens (Heyrman et al, 2003), V. halodenitrificans (Yoon et al, 2004), V. dokdonensis (Yoon et al, 2005), V. koreensis (Lee et al, 2006), V. olivae (Quesada et al, 2007), V. halophilus , V. chiguensis (Wang et al, 2008) and V. kekensis (Chen et al, 2008a). During a recent study of the microbial diversity of the Qaidam Basin in Qinghai Province, north-west China (Chen et al, 2007a(Chen et al, , 2008a), a moderately halophilic bacterium, designated strain YIM kkny3 T , was isolated from a sediment sample collected from the Keke salt lake in August 2002.…”

Section: Institute Of Medicinal Biotechnology Chinese Academy Of Medmentioning

confidence: 99%

Virgibacillus sediminis sp. nov., a moderately halophilic bacterium isolated from a salt lake in China

Chen

Cui

Fritze

et al. 2009

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

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Virgibacillus sediminis sp. nov., a moderately halophilic bacterium isolated from a salt lake in China A Gram-positive, moderately halophilic, alkalitolerant, strictly aerobic, oxidase-and catalasepositive, rod-shaped bacterium, strain YIM kkny3 T , was isolated from a sediment sample collected from a salt lake in the Qaidam Basin of north-west China. Cells were motile by means of peritrichous flagella and formed ellipsoidal endospores lying in subterminal swollen sporangia. Growth occurred with 1-20 % (w/v) total salts (optimum, 5-10 %) and at pH 6.0-10.5 (optimum, pH 7.5-8.0) and 10-55 6C (optimum, 35-40 6C). It was unable to grow with NaCl as the only salt. meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The strain contained menaquinone 7 (MK-7) as the predominant respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid as polar lipids. The major cellular fatty acids were anteiso-C 15 : 0 and anteiso-C 17 : 0 . The DNA G+C content was 40.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM kkny3 T belonged to the genus Virgibacillus, and was most closely related to the type strains of Virgibacillus olivae (97.1 % similarity), Virgibacillus marismortui (97.0 %) and Virgibacillus kekensis (96.8 %). Levels of DNA-DNA relatedness between strain YIM kkny3 T and the type strains of V. olivae, V. marismortui and V. kekensis were 12.4, 10.6 and 15.7 %, respectively. The combination of phylogenetic analysis, genotypic data, phenotypic characteristics and chemotaxonomic differences indicated that strain YIM kkny3 T represents a novel species of the genus Virgibacillus, for which the name Virgibacillus sediminis sp. nov. is proposed. The type strain is YIM kkny3 T (5CCTCC AA 207023 T 5DSM 19797 T 5KCTC 13193 T ).The genus Virgibacillus was proposed by Heyndrickx et al. (1998). At the time of writing, the genus comprised 13 recognized species: Virgibacillus pantothenticus et al., 2007a, 2008a, b, c, d), a moderately halophilic bacterium, designated strain YIM kkny3 T , was isolated from a sediment sample collected from the Keke salt lake in August 2002. The lake is located at 36 u 189-36 u 559 N 99 u 029-99 u 129 E; the lake water was at 18 u C, had a pH of 6.5-7.5 and had a salinity of 298 g l 21 . Based on the results of the present polyphasic taxonomic study, strain YIM kkny3 T is considered to represent a novel species of the genus Virgibacillus.Strain YIM kkny3 T was isolated from a saline sediment sample by plating 1 : 10 serial dilutions of the sample onThe GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain YIM kkny3 T is AY121430.Maximum-parsimony and minimum-evolution phylogenetic trees based on 16S rRNA gene sequences showing the position of strain YIM kkny3 T among its closest neighbours, and a table giving the whole-cell fatty acid profiles of strain YIM kkny3 T and recognized species of the genus Virgibacillus are available with the online version of this ...

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Transfer of Bacillus halodenitrificans Denariaz et al. 1989 to the genus Virgibacillus as Virgibacillus halodenitrificans comb. nov.

Cited by 81 publications

References 29 publications

Phylogenetic Profiling and Diversity of Bacterial Communities in the Death Valley, an Extreme Habitat in the Atacama Desert

Phylogenetic Profiling and Diversity of Bacterial Communities in the Death Valley, an Extreme Habitat in the Atacama Desert

Virgibacillus kekensis sp. nov., a moderately halophilic bacterium isolated from a salt lake in China

Virgibacillus sediminis sp. nov., a moderately halophilic bacterium isolated from a salt lake in China

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