scholarly journals Geomicrobium halophilum gen. nov., sp. nov., a moderately halophilic and alkaliphilic bacterium isolated from soil

2010 ◽  
Vol 60 (4) ◽  
pp. 990-995 ◽  
Author(s):  
Akinobu Echigo ◽  
Hiroaki Minegishi ◽  
Toru Mizuki ◽  
Masahiro Kamekura ◽  
Ron Usami
Keyword(s):  
Dna Hybridization ◽  
Diaminopimelic Acid ◽  
Garden Soil ◽  
Rrna Gene ◽  
Moderately Halophilic ◽  
Acid Type ◽  
Optimum Ph ◽  
Isoprenoid Quinones ◽  
Alkaliphilic Bacterium ◽  
The 16S Rrna Gene

Two moderately halophilic and alkaliphilic bacteria, designated strains BH1T and HN5, were isolated from forest soil and garden soil, respectively, in Japan. Cells of strains BH1T and HN5 were non-motile, aerobic, bean-shaped, formed irregular clusters with 2–20 cells, Gram-positive and contained A1γ, meso-diaminopimelic acid-type murein. Spore formation was not detected. Growth occurred in 5–25 % (w/v) NaCl (optimum, 10–15 %, w/v), at pH 6.0–10.0 (optimum, pH 8.5–9.0) and at 20–40 °C (optimum, 30 °C). The predominant isoprenoid quinones were menaquinone-7 and menaquinone-6. The phospholipids were diphosphatidylglycerol and phosphatidylglycerol. The major cellular fatty acids were i-C15 : 0, i-C17 : 0 and i-C18 : 0. The DNA G+C content of strains BH1T and HN5 was 45 and 46 mol%, respectively. The 16S rRNA gene sequences of the two strains were 99.9 % similar. DNA–DNA hybridization results indicated high levels of relatedness (88 and 85 % reciprocally). Similarities with recognized species were less than 90.2 %. The phylogenetic and phenotypic characteristics indicated that strains BH1T and HN5 represent a novel species in a new genus, for which the name Geomicrobium halophilum gen. nov., sp. nov. is proposed. The type strain is BH1T (=JCM 15647T=DSM 21769T).

scholarly journals Natribacillus halophilus gen. nov., sp. nov., a moderately halophilic and alkalitolerant bacterium isolated from soil

2012 ◽  
Vol 62 (2) ◽  
pp. 289-294 ◽  
Author(s):  
Akinobu Echigo ◽  
Hiroaki Minegishi ◽  
Yasuhiro Shimane ◽  
Masahiro Kamekura ◽  
Ron Usami
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Garden Soil ◽  
Rrna Gene ◽  
Moderately Halophilic ◽  
Acid Type ◽  
Optimum Ph ◽  
Sequence Similarities

A moderately halophilic and alkalitolerant bacterium, designated strain HN30T, was isolated from garden soil in Japan. Cells of strain HN30T were motile, endospore-forming, aerobic, rod-shaped and Gram-positive, and contained A1γ meso-diaminopimelic acid-type murein. Growth occurred in 7–23 % (w/v) NaCl (optimum, 10–15 %, w/v), at pH 6.5–10.0 (optimum, pH 8.0–8.5) and at 20–40 °C (optimum, 30 °C). The isoprenoid quinone was menaquinone-7. The polar lipids were phosphatidylglycerol and diphosphatidylglycerol. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and C16 : 0. The DNA G+C content of strain HN30T was 47 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HN30T was most closely related to Geomicrobium halophilum BH1T (93 % sequence similarity). 16S rRNA gene sequence similarities with other recognized species were less than 89 %. Phylogenetic and phenotypic characteristics indicated that strain HN30T represents a novel species in a new genus, for which the name Natribacillus halophilus gen. nov., sp. nov. is proposed; the type strain is HN30T ( = JCM 15649T = DSM 21771T).

scholarly journals Halalkalibacillus halophilus gen. nov., sp. nov., a novel moderately halophilic and alkaliphilic bacterium isolated from a non-saline soil sample in Japan

2007 ◽  
Vol 57 (5) ◽  
pp. 1081-1085 ◽  
Author(s):  
Akinobu Echigo ◽  
Tadamasa Fukushima ◽  
Toru Mizuki ◽  
Masahiro Kamekura ◽  
Ron Usami
Keyword(s):  
Diaminopimelic Acid ◽  
Garden Soil ◽  
Phylogenetic Distance ◽  
Phenotypic Characteristics ◽  
Moderately Halophilic ◽  
Acid Type ◽  
Optimum Ph ◽  
Novel Genus And Species ◽  
Total Dna ◽  
Alkaliphilic Bacterium

A moderately halophilic and alkaliphilic bacterium, designated strain BH2T, was isolated from non-saline garden soil in Saitama, Japan. Cells of strain BH2T were motile, aerobic, rod-shaped and Gram-positive and contained A1γ, meso-diaminopimelic acid-type murein. Growth occurred in 5.0–25 % (w/v) NaCl (optimum, 10–15 %, w/v), at pH 5.5–10.0 (optimum, pH 8.5–9.0) and at 20–40 °C. The predominant isoprenoid quinone was menaquinone-7. The major cellular fatty acids were ai-C15 : 0, i-C16 : 0, ai-C17 : 0 and i-C15 : 0. The G+C content of the total DNA of strain BH2T was 35.1±0.4 mol% (±sd; n=5). The phylogenetic distance from species with validly published names was less than 94.1 %. The phylogenetic and phenotypic characteristics indicated that strain BH2T represents a novel genus and species, for which the name Halalkalibacillus halophilus gen. nov., sp. nov. is proposed. The type strain is BH2T (=JCM 14192T=DSM 18494T).

scholarly journals Asanoa iriomotensis sp. nov., isolated from mangrove soil

2005 ◽  
Vol 55 (2) ◽  
pp. 725-727 ◽  
Author(s):  
Tomohiko Tamura ◽  
Takeshi Sakane
Keyword(s):  
Dna Hybridization ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Monophyletic Cluster ◽  
Mangrove Soil ◽  
Acid Type ◽  
The Family ◽  
Agar Surface ◽  
The 16S Rrna Gene ◽  
Fatty Acid Type

During a study of the distribution of actinomycetes in a mangrove zone, a strain forming spore chains borne on the tip of short sporophores arising directly from the agar surface was isolated from soil. The isolate contained glutamic acid, glycine, alanine and meso-diaminopimelic acid as cell-wall amino acids, menaquinone MK-10(H6, H8), fatty acid type 2d and xylose in the whole-cell hydrolysate. The 16S rRNA gene sequence of the isolate formed a monophyletic cluster with the members of the genus Asanoa in the family Micromonosporaceae. On the basis of morphological and chemotaxonomic characteristics, phylogenetic analysis and DNA–DNA hybridization, a novel species of the genus Asanoa is proposed for strain TT 97-02T (=NBRC 100142T=DSM 44745T), Asanoa iriomotensis sp. nov.

scholarly journals Tumebacillus luteolus sp. nov., isolated from soil

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4107-4112 ◽  
Author(s):  
Jihee Her ◽  
Sathiyaraj Srinivasan ◽  
Sang-Seob Lee
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Agar Medium ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Optimum Ph ◽  
The 16S Rrna Gene

Two strains of Gram-stain-positive, aerobic, spore-forming and rod-shaped bacteria, designated U13T and U14, were isolated from soil of the Ukraine. Comparative analysis of the 16S rRNA gene sequences indicated that these strains belong to the genus Tumebacillus, with the highest 16S rRNA gene sequence similarity with Tumebacillus ginsengisoli Gsoil 1105T (95.48 % and 95.49 %, respectively). Strains U13T and U14 had iso-C15 : 0 and summed features 1 and 4 as the main fatty acids, and were able to grow at pH ranging from pH 5.0 to 9.0 (optimum pH 6.0–7.0), temperatures ranging from 25 to 42 °C (optimum 28–37 °C) and with 0–1 % (w/v) NaCl (optimum 0 %, w/v) on R2A agar medium. Chemotaxonomic data revealed that the cell-wall peptidoglycan type of the two strains was type A1γ (meso-diaminopimelic acid). On the basis of the evidence from this study, strains U13T and U14 represent a novel species of the genus Tumebacillus, for which the name Tumebacillus luteolus sp. nov. is proposed. The type strain is U13T ( = KEMB 7305-100T = JCM 19866T) and a second strain is U14 ( = KEMB 7305-101 = JCM 19867).

scholarly journals Domibacillus tundrae sp. nov., isolated from active layer soil of tussock tundra in Alaska, and emended description of the genus Domibacillus

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3407-3412 ◽  
Author(s):  
Hye Ryeon Gyeong ◽  
Kiwoon Baek ◽  
Chung Yeon Hwang ◽  
Key Hun Park ◽  
Hye Min Kim ◽  
...  
Keyword(s):  
Active Layer ◽  
Optimal Growth ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Acid Type ◽  
Tussock Tundra ◽  
Emended Description ◽  
Isoprenoid Quinones ◽  
A Minor

A novel Gram-stain-positive, spore-forming, aerobic, motile and rod-shaped bacterium designated strain PAMC 80007T was isolated from an active layer soil sample of Council, Alaska. Optimal growth of strain PAMC 80007T was observed at 30 °C, pH 7.0 and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain PAMC 80007T belonged to the genus Domibacillus. This strain was closely related to Domibacillus enclensis (98.3 %), Domibacillus robiginosus (98.3 %) and Domibacillus indicus (97.2 %). Genomic DNA G+C content was 43.5 mol% and genomic relatedness analyses based on the average nucleotide identity and the genome-to-genome distance showed that strain PAMC 80007T is clearly distinguished from the closely related species of the genus Domibacillus. The major fatty acids (>5 %) were iso-C15 : 0 (24.7 %), C16 : 1ω11c (16.8 %), anteiso-C15 : 0 (16.5 %), C16 : 0 (15.6 %) and anteiso-C17 : 0 (8.7 %). The major respiratory isoprenoid quinones were menaquinone-6 (MK-6) and menaquinone-7 (MK-7), and the polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid, phospholipid and two unidentified lipids. meso-Diaminopimelic acid (type A1γ) was present in the cell-wall peptidoglycan, and the major whole-cell sugar was ribose with a minor quantity of glucose. Results from a polyphasic study suggested that strain PAMC 80007T represents a novel species of the genus Domibacillus for which the name Domibacillus tundrae sp. nov. is proposed. The type strain is PAMC 80007T ( = JCM 30371T = KCTC 33549T = DSM 29572T). An emended description of the genus Domibacillus is also provided.

Micromonospora humida sp. nov., exhibiting antimicrobial potential, isolated from riverside soil

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Jun Sik Ra ◽  
Min Ji Kim ◽  
Dong Hyeon Lee ◽  
Ji Won Jeong ◽  
Seung Bum Kim
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Clusters ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Biosynthetic Gene Clusters ◽  
Content Type ◽  
Link Type ◽  
Type Strains ◽  
The 16S Rrna Gene

An actinobacterial strain designated MMS20-R1-14T was isolated from a riverside soil sample. Colonies on agar plates were orange to strong orange brown in colour, which later became black. The cells grew at 10–40 °C (optimum, 37 °C), pH 5.0–11.0 (pH 8.0) and in the presence of 0–4 % NaCl (1 %). The 16S rRNA gene sequence of strain MMS20-R1-14T showed highest similarities to Micromonospora wenchangensis CCTCC AA 2012002T (99.51 %) and Micromonospora rifamycinica AM105T (99.37 %). The orthoANI values between strain MMS20-R1-14T and the two type strains were 95.72 and 90.99 %, and the digital DNA–DNA hybridization values were 63.6 and 40.8 %, respectively, thus confirming the distinction of strain MMS20-R1-14T from its mostly related species. The DNA G+C content of strain MMS20-R1-14T was 72.9 mol%. The strain contained meso-diaminopimelic acid as the major cell-wall amino acid, and the characteristic whole-cell sugars were arabinose, xylose, glucose, ribose and rhamnose. The main cellular fatty acids were C18 : 1  ω9c, iso-C15 : 0 and iso-C16 : 0, the diagnostic polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and the predominant menaquinones were MK-10(H4) and MK-10(H6), all of which were consistent with those of Micromonospora . Strain MMS20-R1-14T showed antimicrobial activity against a range of bacterial and yeast species. The genome of the strain was found to contain 33 potential biosynthetic gene clusters for secondary metabolites, thus showing a high potential as a producer of bioactive compounds. On the basis of these phenotypic, genotypic and chemotaxonomic data, strain MMS20-R1-14T merits recognition as representing a novel species of the genus Micromonospora , for which the name Micromonospora humida sp. nov. (type strain=MMS20 R1-14T=KCTC 49541T=JCM 34494T) is proposed.

Streptomyces graminilatus sp. nov., isolated from bamboo litter

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 528-532 ◽  
Author(s):  
Hyo-Jin Lee ◽  
Kyung-Sook Whang
Keyword(s):  
Dna Hybridization ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph ◽  
Sequence Similarities

A Gram-stain-positive, novel actinobacterium, designated strain JL-6T, was isolated from the litter of a bamboo (Sasa borealis) forest in Damyang, Korea. Strain JL-6T had white‐grey, smooth, cylindrical spores that were borne in straight, long spore-chains. The novel strain grew aerobically at 15–28 °C (optimum, 28 °C), pH 4.0–8.0 (optimum, pH 5.5) and with 0–1.5 % (w/v) NaCl. The cell-wall peptidoglycan contained ll-diaminopimelic acid, glutamic acid, alanine and glycine. The predominant menaquinones were MK-9(H6) and MK-9(H8). Whole-cell hydrolysates mainly contained glucose and ribose. Phosphatidylinositol and phosphatidylcholine were the diagnostic phospholipids. The G+C content of the genomic DNA was 72.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JL-6T belonged to the genus Streptomyces with sequence similarities ranging from 97.3 % to 98.3 %. However, DNA–DNA hybridization between JL-6T and the closest related strain, Streptomyces turgidiscabies , ATCC 700248T and other closely related species in the genus Streptomyces showed <50 % relatedness. Based on these observations, strain JL-6T is proposed to represent a novel species of the genus Streptomyces , for which the name Streptomyces graminilatus sp. nov. is proposed. The type strain is JL-6T ( = KACC 16470T = NBRC 108882T).

scholarly journals Virgibacillus alimentarius sp. nov., isolated from a traditional Korean food

2011 ◽  
Vol 61 (12) ◽  
pp. 2851-2855 ◽  
Author(s):  
Jandi Kim ◽  
Mi-Ja Jung ◽  
Seong Woon Roh ◽  
Young-Do Nam ◽  
Kee-Sun Shin ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Marine Agar ◽  
Acid Type ◽  
Gene Sequence Analysis ◽  
Optimum Ph ◽  
Korean Food

A novel, Gram-positive, rod-shaped, motile, endospore-forming, halophilic bacterial strain, J18T, was isolated from a traditional salt-fermented seafood made of gizzard shad in Korea. Colonies were convex, cream-coloured and 1.0–2.0 mm in diameter after incubation for 3 days on marine agar. Growth occurred at pH 7.0–11.0 (optimum, pH 10.0), at 4–40 °C (optimum, 37 °C) and in the presence of 0–30 % NaCl (optimum, 9–10 %). On the basis of 16S rRNA gene sequence analysis, strain J18T was related most closely to Virgibacillus byunsanensis ISL-24T (96.3 % similarity), Virgibacillus carmonensis LMG 20964T (96.2 %), Virgibacillus halodenitrificans DSM 10037T (96.0 %), Virgibacillus arcticus Hal 1T (95.5 %) and Virgibacillus necropolis LMG 19488T (95.5 %). The major fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. The DNA G+C content of strain J18T was 37.0 mol%. The cell-wall peptidoglycan was of the meso-diaminopimelic acid type. The major quinone was menaquinone 7 (MK-7). Based on phenotypic, chemotaxonomic and phylogenetic data, strain J18T is considered to represent a novel species of the genus Virgibacillus, for which the name Virgibacillus alimentarius sp. nov. is proposed. The type strain is J18T ( = KACC 14624T  = JCM 16994T).

scholarly journals Streptomonospora halotolerans sp. nov., an actinomycete isolated from soil

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3183-3189 ◽  
Author(s):  
Junwei Zhao ◽  
Lifeng Guo ◽  
Chongxi Liu ◽  
Pengyu Sun ◽  
Jiansong Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Northern China ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Diamino Acid ◽  
Type Strains ◽  
The 16S Rrna Gene

A novel actinomycete, designated strain NEAU-Jh2-17T, was isolated from muddy soil collected from a riverbank in Jilin Province, northern China, and characterized using a polyphasic approach. The 16S rRNA gene sequence of strain NEAU-Jh2-17T showed highest similarity to those of Streptomonospora nanhaiensis 12A09T (99.26 %), Nocardiopsis rosea YIM 90094T (97.31 %), Streptomonospora halophila YIM 91355T (97.24 %) and Streptomonospora arabica S186T (97.02 %). Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain NEAU-Jh2-17T fell within a cluster consisting of the type strains of species of the genus Streptomonospora and formed a stable clade with S. nanhaiensis 12A09T in trees generated with two algorithms. Key morphological and chemotaxonomic properties also confirmed the affiliation of strain NEAU-Jh2-17T to the genus Streptomonospora. The cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid and whole-cell hydrolysates contained glucose, ribose and galactose. The polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), phosphatidylinositol (PI), phosphatidylinositol mannoside (PIM), two unknown phospholipids (PLs) and two unknown glycolipids (GLs). The predominant menaquinones were MK-10(H2), MK-10(H8), MK-10(H6) and MK-10(H4). Major fatty acids were C18 : 0 10-methyl, anteiso-C17 : 0, C16 : 0 10-methyl, iso-C15 : 0, C17 : 0 10-methyl and C18 : 0. The DNA G+C content was 71.82 mol%. However, a combination of DNA–DNA hybridization results and some phenotypic characteristics demonstrated that strain NEAU-Jh2-17T could be distinguished from its closely related relatives. Therefore, strain NEAU-Jh2-17T is considered to represent a novel species of the genus Streptomonospora, for which the name Streptomonospora halotolerans sp. nov. is proposed. The type strain is NEAU-Jh2-17T ( = CGMCC 4.7218T = JCM 30347T).

scholarly journals Micromonospora zhanjiangensis sp. nov., isolated from mangrove forest soil

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4880-4885 ◽  
Author(s):  
Li Zhang ◽  
Lei Li ◽  
Zixin Deng ◽  
Kui Hong
Keyword(s):  
Dna Hybridization ◽  
Mangrove Forest ◽  
Gene Sequence ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
Hybridization Data ◽  
Reference Strains ◽  
Physiological And Biochemical ◽  
The 16S Rrna Gene

A novel actinomycete, designated strain 2902at01T was isolated from soil collected at a mangrove forest in Zhanjiang, Guangdong province, China. The strain was identified using a polyphasic classification method. The 16S rRNA gene sequence of strain 2902at01T showed the highest similarity to Micromonospora equina Y22T (98.3 %) and Micromonospora pattaloongensis TJ2-2T (98.1 %). Phylogenetic analysis based on the gyrB gene sequence also clearly showed that the strain was different from any previously discovered species of the genus Micromonospora. The characteristic whole-cell sugars were ribose and xylose. The cell-wall hydrolysates contained alanine, asparagine, glycine and meso-diaminopimelic acid. MK-10(H6) and MK-10(H8) were the major menaquinones of the novel strain. The predominant fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0. The characteristic polar lipids of strain 2902at01T were phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and diphosphatidylglycerol. The DNA G+C content was 70.2 mol%. DNA–DNA hybridization data combined with other physiological and biochemical features could distinguish strain 2902at01T from the reference strains M. equina Y22T and M. pattaloongensis TJ2-2 T. On the basis of these phenotypic and genotypic data, strain 2902at01T represents a novel species of the genus Micromonospora, for which the name Micromonospora zhanjiangensis sp. nov. is proposed. The type strain is 2902at01T ( = CCTCC AA2014018T = DSM 45902T).

Sign in / Sign up

Export Citation Format

Share Document