scholarly journals Bacillus tianshenii sp. nov., isolated from a marine sediment sample

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1998-2002 ◽  
Author(s):  
Zhao Jiang ◽  
Dao-Feng Zhang ◽  
Thi-Nhan Khieu ◽  
Chu Ky Son ◽  
Xiao-Mei Zhang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Sediment ◽  
Sediment Sample ◽  
Type Species ◽  
Rrna Gene ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type ◽  
Marine Sediment Sample

A novel Gram-stain-positive, motile, catalase- and oxidase-positive, aerobic, endospore-forming, peritrichous, rod-shaped bacterium, designated YIM M13235T, was isolated from a marine sediment sample collected from the South China Sea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM M13235T belonged to the genus Bacillus . The strain grew optimally at 30 °C, pH 7.0 and in the presence of 2–4 % (w/v) NaCl. meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. Strain YIM M13235T exhibited a menaquinone system with MK-7, and the major polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unknown phospholipids and one unknown glycolipid. The major fatty acids (>5 %) were iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 0, iso-C17 : 1ω10c and summed feature 4 (anteiso-C17 : 1 and/or iso-C17 : 1). The genomic DNA G+C content was 42.1 mol%. The DNA–DNA relatedness values between strain YIM M13235T and its close relatives (16S rRNA gene sequence similarities >97 %) including Bacillus halmapalus DSM 8723T, Bacillus horikoshii DSM 8719T and Bacillus zhanjiangensis JSM 099021T were 41 %, 44 % and 44 %, respectively. On the basis of genotypic, phenotypic and DNA–DNA relatedness data, it is apparent that strain YIM M13235T represents a novel species of the genus Bacillus , for which the name Bacillus tianshenii sp. nov. is proposed. The type strain is YIM M13235T ( = DSM 25879T = KCTC 33044T).

scholarly journals Frigoribacterium endophyticum sp. nov., an endophytic actinobacterium isolated from the root of Anabasis elatior (C. A. Mey.) Schischk

2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1207-1212 ◽  
Author(s):  
Hong-Fei Wang ◽  
Yong-Guang Zhang ◽  
Ji-Yue Chen ◽  
Jian-Wei Guo ◽  
Li Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type ◽  
Endophytic Actinobacterium

A novel endophytic actinobacterium, designated EGI 6500707T, was isolated from the surface-sterilized root of a halophyte Anabasis elatior (C. A. Mey.) Schischk collected from Urumqi, Xinjiang province, north-west China, and characterized using a polyphasic approach. Cells were Gram-stain-positive, non-motile, short rods and produced white colonies. Growth occurred at 10–45 °C (optimum 25–30 °C), at pH 5–10 (optimum pH 8) and in presence of 0–4 % (w/v) NaCl (optimum 0–3 %). The predominant menaquinone was MK-9. The diagnostic phospholipids were diphosphatidylglycerol and phosphatidylglycerol. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The DNA G+C content of strain EGI 6500707T was 69.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain EGI 6500707T should be placed in the genus Frigoribacterium (family Microbacteriaceae , phylum Actinobacteria ), and that the novel strain exhibited the highest 16S rRNA gene sequence similarity to Frigoribacterium faeni JCM 11265T (99.1 %) and Frigoribacterium mesophilum MSL-08T (96.5 %). DNA–DNA relatedness between strain EGI 6500707T and F. faeni JCM 11265T was 47.2 %. On the basis of phenotypic and chemotaxonomic characteristics, phylogenetic analysis and DNA–DNA relatedness data, strain EGI 6500707T represents a novel species of the genus Frigoribacterium , for which the name Frigoribacterium endophyticum sp. nov. is proposed. The type strain is EGI 6500707T ( = JCM 30093T = KCTC 29493T).

Paenibacillus catalpae sp. nov., isolated from the rhizosphere soil of Catalpa speciosa

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1776-1781 ◽  
Author(s):  
Jian Zhang ◽  
Zi-Ting Wang ◽  
Hui-Min Yu ◽  
Yuchao Ma
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Rhizosphere Soil ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type

A bacterial strain, designated D75T, was isolated from the rhizosphere soil of Catalpa speciosa. Phylogenetic analysis based on the complete 16S rRNA gene sequence revealed that strain D75T was a member of the genus Paenibacillus . High levels of 16S rRNA gene sequence similarity were found between strain D75T and Paenibacillus glycanilyticus DS-1T (99.2 %), Paenibacillus xinjiangensis B538T (97.5 %) and Paenibacillus castaneae Ch-32T (97.2 %). The chemotaxonomic properties of strain D75T were consistent with those of the genus Paenibacillus : the cell-wall peptidoglycan type was based on meso-diaminopimelic acid (A1γ), the predominant menaquinone was MK-7, and the major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and C16 : 0. However, levels of DNA–DNA relatedness between strain D75T and P. glycanilyticus NBRC 16618T, P. xinjiangensis DSM 16970T and P. castaneae DSM 19417T were 35, 20 and 18 %, respectively. On the basis of phenotypic and chemotaxonomic analyses, phylogenetic data and DNA–DNA relatedness values, strain D75T is considered to represent a novel species of the genus Paenibacillus , for which the name Paenibacillus catalpae sp. nov. is proposed. The type strain is D75T ( = DSM 24714T = CGMCC 1.10784T).

scholarly journals Lysinibacillus varians sp. nov., an endospore-forming bacterium with a filament-to-rod cell cycle

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3644-3649 ◽  
Author(s):  
Chunjie Zhu ◽  
Guoping Sun ◽  
Xingjuan Chen ◽  
Jun Guo ◽  
Meiying Xu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Single Cells ◽  
Rrna Gene ◽  
Phylogenetic Distance ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type

Six Gram-stain-positive, motile, filamentous and/or rod-shaped, spherical spore-forming bacteria (strains GY32T, L31, F01, F03, F06 and F07) showing polybrominated diphenyl ether transformation were investigated to determine their taxonomic status. After spore germination, these organisms could grow more than one hundred microns long as intact single cells and then divide into rod cells and form endospores in 33 h. The cell-wall peptidoglycan of these strains was type A4α, the predominant menaquinone was MK-7 and the major fatty acids were iso-C16 : 0, iso-C15 : 0 and C16 : 1ω7C. Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were detected in the polar lipid profile. Analysis of the 16S rRNA gene sequences indicated that these strains should be placed in the genus Lysinibacillus and they were most closely related to Lysinibacillus sphaericus DSM 28T (99 % 16S rRNA gene sequence similarity). The gyrB sequence similarity and DNA–DNA relatedness between strain GY32T and L. sphaericus JCM 2502T were 81 % and 52 %, respectively. The G+C content of the genomic DNA of strain GY32T was 43.2 mol%. In addition, strain GY32T showed differences in nitrate reduction, starch and gelatin hydrolysis, carbon resource utilization and cell morphology. The phylogenetic distance from its closest relative measured by DNA–DNA relatedness and DNA G+C content, and its phenotypic properties demonstrated that strain GY32T represents a novel species of the genus Lysinibacillus , for which the name Lysinibacillus varians sp. nov. is proposed. The type strain is GY32T ( = NBRC 109424T = CGMCC 1.12212T = CCTCC M 2011307T).

Thalassolituus marinus sp. nov., a hydrocarbon-utilizing marine bacterium

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2234-2238 ◽  
Author(s):  
Ahyoung Choi ◽  
Jang-Cheon Cho
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type

Gram-negative strains, motile by a single polar flagellum, non-pigmented and with a curved rod-shaped morphology, designated IMCC1826T and IMCC1883, were isolated from a surface seawater sample from the Yellow Sea. The two strains shared 99.9 % 16S rRNA gene sequence similarity and showed 92 % DNA–DNA relatedness, suggesting that they belonged to the same genomic species. Phylogenetic analysis based on 16S rRNA gene sequences showed that the two isolates were related most closely to the type strain of Thalassolituus oleivorans with a sequence similarity of 96.4 % and formed a robust phyletic lineage with T. oleivorans . DNA–DNA relatedness between the two strains and T. oleivorans DSM 14913T was 8.7–11.6 %. A putative alkane hydroxylase (alkB) gene was detected in strain IMCC1826T by PCR, but the amino acid sequence of the gene was distantly related to that of the AlkB homologue of T. oleivorans DSM 14913T. As expected from the presence of the alkB gene, the new strains utilized n-tetradecane and n-hexadecane as a carbon source. The DNA G+C content was 54.6–56.0 mol% and the main isoprenoid quinone detected was Q-9. Polar lipids of strain IMCC1826T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and amino-group-containing lipids. On the basis of taxonomic data obtained in this study, strains IMCC1826T and IMCC1883 represent a novel species of the genus Thalassolituus , for which the name Thalassolituus marinus sp. nov. is proposed, with IMCC1826T ( = KCTC 23084T = NBRC 107590T) as the type strain.

scholarly journals Description of Kribbella italica sp. nov., isolated from a Roman catacomb

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 491-496 ◽  
Author(s):  
Gareth J. Everest ◽  
Sarah M. Curtis ◽  
Filomena De Leo ◽  
Clara Urzì ◽  
Paul R. Meyers
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Species ◽  
Rrna Gene ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type ◽  
Type Strains ◽  
The 16S Rrna Gene

A novel actinobacterium, strain BC637T, was isolated from a biodeteriogenic biofilm sample collected in 2009 in the Saint Callixstus Roman catacomb. The strain was found to belong to the genus Kribbella by analysis of the 16S rRNA gene. Phylogenetic analysis using the 16S rRNA gene and the gyrB, rpoB, relA, recA and atpD concatenated gene sequences showed that strain BC637T was most closely related to the type strains of Kribbella lupini and Kribbella endophytica . DNA–DNA hybridization experiments confirmed that strain BC637T is a genomic species that is distinct from its closest phylogenetic relatives, K. endophytica DSM 23718T (63 % DNA relatedness) and K. lupini LU14T (63 % DNA relatedness). Physiological comparisons showed that strain BC637T is phenotypically distinct from the type strains of K. endophytica and K. lupini . Thus, strain BC637T represents the type strain of a novel species, for which the name Kribella italica sp. nov. is proposed ( = DSM 28967T = NRRL B-59155T).

scholarly journals Acinetobacter gandensis sp. nov. isolated from horse and cattle

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4007-4015 ◽  
Author(s):  
Annemieke Smet ◽  
Piet Cools ◽  
Lenka Krizova ◽  
Martina Maixnerova ◽  
Ondrej Sedo ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Rrna Gene ◽  
Content Type ◽  
Dna Relatedness ◽  
Maldi Tof Ms ◽  
Link Type ◽  
Maldi Tof ◽  
Tof Ms

We previously reported the presence of an OXA-23 carbapenemase in an undescribed species of the genus Acinetobacter isolated from horse dung at the Faculty of Veterinary Medicine, Ghent University, Belgium. Here we include six strains to corroborate the delineation of this taxon by phenotypic characterization, DNA–DNA hybridization, 16S rRNA gene and rpoB sequence analysis, % G+C determination, MALDI-TOF MS and fatty acid analysis. The nearly complete 16S rRNA gene sequence of strain UG 60467T showed the highest similarities with those of the type strains of Acinetobacter bouvetii (98.4 %), Acinetobacter haemolyticus (97.7 %), and Acinetobacter schindleri (97.2 %). The partial rpoB sequence of strain UG 60467T showed the highest similarities with ‘Acinetobacter bohemicus’ ANC 3994 (88.6 %), A. bouvetii NIPH 2281 (88.6 %) and A. schindleri CIP 107287T (87.3 %). Whole-cell MALDI-TOF MS analyses supported the distinctness of the group at the protein level. The predominant fatty acids of strain UG 60467T were C12 : 0 3-OH, C12 : 0, C16 : 0, C18 : 1ω9c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). Strains UG 60467T and UG 60716 showed a DNA–DNA relatedness of 84 % with each other and a DNA–DNA relatedness with A. schindleri LMG 19576T of 17 % and 20 %, respectively. The DNA G+C content of strain UG 60467T was 39.6 mol%. The name Acinetobacter gandensis sp. nov. is proposed for the novel taxon. The type strain is UG 60467T ( = ANC 4275T = LMG 27960T = DSM 28097T).

scholarly journals Exiguobacterium enclense sp. nov., isolated from sediment

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1611-1616 ◽  
Author(s):  
Syed G. Dastager ◽  
Rahul Mawlankar ◽  
Vidya V. Sonalkar ◽  
Meghana N. Thorat ◽  
Poonam Mual ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Phenotypic Traits ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Marine Sediment Sample

A Gram-stain-positive bacterium, designated strain NIO-1109T, was isolated from a marine sediment sample from Chorao Island, Goa, India. Phenotypic and chemotaxonomic characteristics and data from phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NIO-1109T was related to the genus Exiguobacterium . Strain NIO-1109T exhibited >98.0 % 16S rRNA gene sequence similarity with respect to Exiguobacterium indicum HHS 31T (99.5 %) and Exiguobacterium acetylicum NCIMB 9889T (99.1 %); the type strains of other species showed <98 % similarity. Levels of DNA–DNA relatedness between strain NIO-1109T and E. acetylicum DSM 20416T and E. indicum LMG 23471T were less than 70 % (33.0±2.0 and 37±3.2 %, respectively). Strain NIO-1109T also differed from these two closely related species in a number of phenotypic traits. Based on phenotypic, chemotaxonomic and phylogenetic data, strain NIO-1109T is considered to represent a novel species of the genus Exiguobacterium , for which the name Exiguobacterium enclense sp. nov. is proposed. The type strain is NIO-1109T ( = NCIM 5457T = DSM 25128T = CCTCC AB 2011124T).

Marininema halotolerans sp. nov., a novel thermoactinomycete isolated from a sediment sample, and emended description of the genus Marininema Li et al. 2012

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4562-4567 ◽  
Author(s):  
Xiao-Mei Zhang ◽  
Jie He ◽  
Dao-Feng Zhang ◽  
Wei Chen ◽  
Zhao Jiang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sediment Sample ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type

A novel Gram-stain-positive bacterium, designated strain YIM M11385T, was isolated from a marine sediment sample collected from the South Bay, Little Andaman Island, India with a salinity of 35 p.p.m., pH 8.5. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM M11385T belongs to the genus Marininema , supported by a bootstrap value of 100 %. The taxonomic position of this organism was further established by using a polyphasic approach. Strain YIM M11385T grew optimally at 28 °C, pH 7.0 and in the presence of 0–5 % (w/v) NaCl. The 16S rRNA gene sequence similarity between strain YIM M11385T and Marininema mesophilum SCSIO 10219T was 98.3 %. Strain YIM M11385T exhibited a quinone system with only MK-7, the polar lipid profile included diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as major components, and the major fatty acids were anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The level of DNA–DNA relatedness between strain YIM M11385T and M. mesophilum SCSIO 10219T was 59.36 %. On the basis of genotypic and phenotypic data, it is apparent that strain YIM M11385T represents a novel species of the genus Marininema , for which the name Marininema halotolerans sp. nov. is proposed. The type strain is YIM M11385T ( = CCTCC AB 2012052T = DSM 45789T). In addition, we propose that the description of the genus Marininema should be further emended based on the results of the present study.

scholarly journals Streptomyces gramineus sp. nov., an antibiotic-producing actinobacterium isolated from bamboo (Sasa borealis) rhizosphere soil

2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 856-859 ◽  
Author(s):  
Hyo-Jin Lee ◽  
Song-Ih Han ◽  
Kyung-Sook Whang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Xanthomonas Campestris ◽  
Rhizosphere Soil ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type

Two actinobacterial strains, JR-43T and JR-4, were isolated from bamboo (Sasa borealis) rhizosphere soil. The isolates produced grey aerial mycelium and a yellow soluble pigment on ISP 4. Microscopic observation revealed that strains JR-43T and JR-4 produced rectiflexibiles spore chains with spiny surfaces. Both isolates had antibacterial activity against plant-pathogenic bacteria, such as Xanthomonas campestris LMG 568T and Xanthomonas axonopodis pv. vesicatoria LMG 905. The isolates contained iso-C14 : 0, iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0 as the major fatty acids and MK-9(H6) and MK-9(H8) as the major isoprenoid quinones. Phylogenetic analysis of the 16S rRNA gene sequences of strains JR-43T and JR-4 showed that they grouped within Streptomyces cluster II and had highest sequence similarity to Streptomyces seoulensis NBRC 16668T and Streptomyces recifensis NBRC 12813T (both 98.2 % 16S rRNA gene sequence similarity). DNA–DNA relatedness between strain JR-43T and S. seoulensis NBRC 16668T and S. recifensis NBRC 12813T ranged from 31.42 to 42.92 %. Based on DNA–DNA relatedness and morphological and phenotypic data, strains JR-43T and JR-4 could be distinguished from the type strains of phylogenetically related species. They are therefore considered to represent a novel species of the genus Streptomyces , for which the name Streptomyces gramineus sp. nov. is proposed. The type strain is JR-43T ( = KACC 15079T  = NBRC 107863T). Strain JR-43 ( = KACC 15078  = NBRC 107864) is a reference strain.

scholarly journals Paracoccus panacisoli sp. nov., isolated from a forest soil cultivated with Vietnamese ginseng

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1491-1497 ◽  
Author(s):  
Ngoc-Lan Nguyen ◽  
Yeon-Ju Kim ◽  
Van-An Hoang ◽  
Bao-Tram Tran ◽  
Huong-Son Pham ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Forest Soil ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type

A novel bacterial strain, designated DCY94T, was isolated from forest soil cultivated with ginseng in Vietnam. The strain was Gram-reaction-negative, facultatively anaerobic, non-motile, rod-shaped and catalase- and oxidase-positive. 16S rRNA gene sequence analysis demonstrated that strain DCY94T was closely related to Paracoccus sphaerophysae Zy-3T (97.5 % 16S rRNA gene sequence similarity) and Paracoccus caeni MJ17T (96.9 %). The fatty acid profile of strain DCY94T contained a predominant amount of summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 88.4 %) and moderate to small quantities of C8 : 0 3-OH (1.0 %), C10 : 0 3-OH (2.8 %) and C18 : 0 (5.2 %). Phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and one unidentified glycolipid were major polar lipids; one unidentified aminolipid, one unidentified aminophospholipid, one unidentified phospholipid and four unidentified polar lipids were minor components. The polyamine pattern comprised the major compounds putrescine and spermidine and minor amounts of sym-homospermidine and spermine. The ubiquinone of the strain was Q-10 and the G+C content of its genomic DNA was 68.3 mol%. All these results support the placement of strain DCY94T within the genus Paracoccus . Levels of DNA–DNA relatedness between strain DCY94T and P. sphaerophysae HAMBI 3106T and P. caeni KCTC 22480T were 52 and 50 %, respectively. The results of phylogenetic analysis, phenotypic tests, chemotaxonomic characterization and DNA–DNA relatedness studies distinguished strain DCY94T from the closest recognized species of the genus Paracoccus , suggesting that this strain represents a novel species, for which the name Paracoccus panacisoli sp. nov. is proposed. The type strain is DCY94T ( = KCTC 42086T = JCM 30337T).

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