scholarly journals Bacillus solimangrovi sp. nov., isolated from mangrove soil

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1622-1628 ◽  
Author(s):  
Geun-Hye Lee ◽  
Moon-Soo Rhee ◽  
Dong-Ho Chang ◽  
Kae Kyoung Kwon ◽  
Kyung Sook Bae ◽  
...  
Keyword(s):  
Cell Wall ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type ◽  
Mangrove Soil

Two novel bacterial strains, GH2-4T and GH2-5, were isolated from mangrove soil near the seashore of Weno island in Chuuk state, Micronesia, and were characterized by a polyphasic approach. The two strains were strictly aerobic, Gram-staining-positive, motile, endospore-forming rods that were catalase- and oxidase-positive. Colonies were circular, convex, stringy and transparent yellowish (GH2-4T) or opaque whitish (GH2-5). The 16S rRNA gene sequences of the two isolates were identical. The most closely related strains in terms of 16S rRNA gene sequence similarity were Bacillus kochii WCC 4582T, B. horneckiae DSM 23495T, B. azotoformans LMG 9581T, B. cohnii DSM 6307T and B. halmapalus DSM 8723T (95.6, 95.4, 95.4, 95.2 and 95.2 % similarity, respectively). The partial groEL sequence of strain GH2-4T was identical to that of strain GH2-5 and showed <85 % similarity to those of the most closely related strains. The isolates grew at pH 5–12 (optimal growth at pH 9), at 10–40 °C (optimum 30–35 °C) and at 0–9 % (w/v) NaCl (optimum 1–3 % NaCl). The cell-wall peptidoglycan of strains GH2-4T and GH2-5 contained meso-diaminopimelic acid and cell-wall hydrolysates contained ribose as a major sugar. The DNA G+C content was 36 mol%, and DNA–DNA relatedness between the isolates and five related reference strains was 20–24 %. Strain GH2-4T exhibited 81 % DNA–DNA relatedness with strain GH2-5. The major cellular fatty acids of both strains were iso-C15 : 0, iso-C16 : 0, iso-C14 : 0 and anteiso-C15 : 0 and the predominant menaquinone was MK-7. On the basis of the evidence from this polyphasic study, strains GH2-4T and GH2-5 ( = KCTC 33143 = JCM 18995 = DSM 27084) represent a novel species of the genus Bacillus , for which the name Bacillus solimangrovi sp. nov. is proposed; the type strain is GH2-4T ( = KCTC 33142T = JCM 18994T = DSM 27083T).

Rhodococcus artemisiae sp. nov., an endophytic actinobacterium isolated from the pharmaceutical plant Artemisia annua L.

2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 900-905 ◽  
Author(s):  
Guo-Zhen Zhao ◽  
Jie Li ◽  
Wen-Yong Zhu ◽  
Shou-Zheng Tian ◽  
Li-Xing Zhao ◽  
...  
Keyword(s):  
Cell Wall ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Artemisia Annua ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Endophytic Actinobacterium

A Gram-positive, non-motile actinobacterium, designated YIM 65754T, was isolated from the stem of Artemisia annua L., collected from Yunnan province, south-west China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM 65754T comprised an evolutionary lineage within the genus Rhodococcus . The isolate clustered with Rhodococcus pyridinivorans PDB9T, Rhodococcus gordoniae W 4937T and Rhodococcus rhodochrous DSM 43241T, with which it shared 98.4, 97.9 and 97.8 % 16S rRNA gene sequence similarities, respectively. However, DNA–DNA relatedness demonstrated that strain YIM 65754T was distinct from its closest phylogenetic neighbours. The cell-wall peptidoglycan contained meso-diaminopimelic acid, arabinose, galactose, mannose and glucose (cell-wall chemotype IV). The major menaquinone was MK-8(H2) and the predominant fatty acids were C16 : 0 (27.83 %), iso-C15 : 0 2-OH and/or C16 : 1ω7c (20.21 %) and 10-methyl C18 : 0 (17.50 %). The DNA G+C content was 66.2 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic evidence, the isolate represents a novel species of the genus Rhodococcus , for which the name Rhodococcus artemisiae sp. nov. is proposed; the type strain is YIM 65754T ( = CCTCC AA 209042T = DSM 45380T).

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).

scholarly journals Actinokineospora spheciospongiae sp. nov., isolated from the marine sponge Spheciospongia vagabunda

2015 ◽  
Vol 65 (Pt_3) ◽  
pp. 879-884 ◽  
Author(s):  
Peter Kämpfer ◽  
Stefanie P. Glaeser ◽  
Hans-Jürgen Busse ◽  
Usama Ramadan Abdelmohsen ◽  
Safwat Ahmed ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

A Gram-staining-positive, aerobic organism, isolated from the Red Sea sponge Spheciospongia vagabunda was investigated to determine its taxonomic position. On the basis of results of 16S rRNA gene sequence analysis strain EG49T was most closely related to Actinokineospora cibodasensis and Actinokineospora baliensis (both 97.3 % similarity) and Actinokineospora diospyrosa and Actinokineospora auranticolor (both 97.0 % similarity). The 16S rRNA gene sequence similarity to all other species of the genus Actinokineospora was <97.0 %. The quinone system of strain EG49T contained the menaquinones MK-9(H4) (47 %), MK-9(H6) (27 %) and MK-9(H2) (15 %) in major amounts. Minor amounts of MK-7(H4) (2 %), MK-9(H0) (1 %), MK-9(H8) (3 %) and MK-10(H4) (3 %) were detected as well in addition to MK-8(H4), MK-8(H6), MK-10(H2) and MK-10(H6) (all <1 %). The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. In the polar lipid profile, diphosphatidylglycerol, phosphatidylethanolamine and hydroxyphosphatidylethanolamine were predominant. Phosphatidylinositol-mannoside, two unidentified phospholipids and two glycoglipids as well as one aminoglycolipid, one aminolipid and one unidentified lipid were found in addition. The fatty acid profile was composed of mainly iso-branched fatty acids: iso-C16 : 0, iso-C14 : 0, iso-C15 : 0 and iso-C16 : 1H. All these findings clearly supported the classification of the strain as representing a member of the genus Actinokineospora . In addition, the results of physiological and biochemical tests also allowed phenotypic differentiation of strain EG49T from the most closely related species of the genus Actinokineospora . Strain EG49T represents a novel species of the genus Actinokineospora , for which we propose the name Actinokineospora spheciospongiae sp. nov., with strain EG49T ( = DSM 45935T = CCM 8480T = LMG 27700T) as the type strain.

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).

scholarly journals Streptomyces zagrosensis sp. nov., isolated from soil

2014 ◽  
Vol 64 (Pt_10) ◽  
pp. 3434-3440 ◽  
Author(s):  
Fatemeh Mohammadipanah ◽  
Javad Hamedi ◽  
Cathrin Spröer ◽  
Manfred Rohde ◽  
María del Carmen Montero-Calasanz ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

The taxonomic position of a novel actinomycete isolated from soil in Fars Province (Iran) was determined using a polyphasic approach. Phenotypic characterization and 16S rRNA gene sequence analysis of the isolate matched those described for members of the genus Streptomyces . On ISP2 medium, strain HM 1154T produced a dark cream, branched substrate mycelium and Retinaculiaperti aerial hyphae that in some images also appeared spiral and that developed into greyish-white spore chains with a smooth surface. The isolate showed optimal growth at 28 °C and pH 6–9 with 0–4 % (w/v) NaCl. Whole-cell hydrolysates contained ll-diaminopimelic acid as diagnostic diamino acid, ribose and glucose. The main phospholipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, three unknown phospholipids and an unknown aminophospholipid; MK-9(H4) and MK-9(H2) were the predominant menaquinones. The major cellular fatty acids were the branched saturated iso-C16 : 0 and anteiso-C15 : 0. Strain HM 1154T exhibited the highest 16S rRNA gene sequence similarities to Streptomyces coerulescens DSM 40146T (99.4 %), Streptomyces varsoviensis DSM 40346T (99.3 %), Streptomyces youssoufiensis DSM 41920T (99.2 %), Streptomyces abikoensis DSM 40831T (99.2 %), Streptomyces rimosus subsp. rimosus DSM 40260T (99.1 %), Streptomyces luteireticuli DSM 40509T (99.1 %), Streptomyces thioluteus DSM 40027T (99.1 %), Streptomyces blastmyceticus DSM 40029T (99.0 %) and Streptomyces hiroshimensis DSM 40037T (99.0 %). DNA–DNA hybridization studies showed relatedness values of 11.0–35.8 % with the closest related species. Based on these results, strain HM 1154T is considered to represent a novel species within the genus Streptomyces , for which the name Streptomyces zagrosensis sp. nov. is proposed. The type strain is HM 1154T ( = DSM 42018T = UTMC 1154T = CECT 8305T).

Alpinimonas psychrophila gen. nov., sp. nov., an actinobacterium of the family Microbacteriaceae isolated from alpine glacier cryoconite

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2724-2730 ◽  
Author(s):  
Peter Schumann ◽  
De-Chao Zhang ◽  
Mersiha Redzic ◽  
Rosa Margesin
Keyword(s):  
Cell Wall ◽  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Rrna Gene ◽  
Content Type ◽  
Alpine Glacier ◽  
Dna Relatedness ◽  
Link Type ◽  
The Family

A Gram-type positive, Gram-reaction variable, non-motile, psychrophilic actinobacterium, designated Cr8-25T, was isolated from alpine glacier cryoconite and was able to grow well over a temperature range of 1–15 °C. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Cr8-25T belonged to the family Microbacteriaceae and showed highest 16S rRNA gene sequence similarity with Klugiella xanthotipulae 44C3T (97.0 %). However, strain Cr8-25T could be differentiated from the type strain of K. xanthotipulae on the level of genomospecies by a DNA–DNA relatedness value of only 37.2 %. Strain Cr8-25T contained a cell-wall peptidoglycan that was cross-linked according to the B-type, which is based on 2,4-diaminobutyric acid. The cell wall contained the sugars galactose, fucose and rhamnose. The predominant cellular fatty acids of strain Cr8-25T were C15 : 0 anteiso (64.6 %) and iso-C16 : 0 (22.5 %) and the major menaquinones were MK-11 and MK-10. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and unknown glycolipids. The G+C content of the genomic DNA was 58.8 mol%. On the basis of the phenotypic characteristics, phylogenetic and chemotaxonomic analyses and DNA–DNA relatedness data, strain Cr8-25T represents a novel species of a new genus in the family Microbacteriaceae , for which the name Alpinimonas psychrophila gen. nov., sp. nov. is proposed. The type strain is Cr8-25T ( = DSM 23737T = LMG 26215T).

scholarly journals Nocardia sungurluensis sp. nov., isolated from soil

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1629-1634 ◽  
Author(s):  
Mustafa Camas ◽  
Aysel Veyisoglu ◽  
Nevzat Sahin
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Gene Tree ◽  
Diaminopimelic Acid ◽  
Morphological Properties ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

A novel Gram-reaction-positive, rod-shaped, non-motile and mycolic acid-containing strain, CR3272T, isolated from soil, was studied using a polyphasic approach. The organism showed a combination of chemotaxonomic and morphological properties typical of the genus Nocardia . The cell wall contained meso-diaminopimelic acid (type IV) and whole-cell sugars were galactose, glucose, arabinose and xylose. The predominant menaquinone was MK-8(H4cyc). The major phospholipids were diphosphatidylglycerol and phosphatidylinositol mannosides. Major fatty acids were C16 : 0, C18 : 1 cis9, C18 : 0 10-methyl (TBSA) and C16 : 1 cis9. The novel strain formed distinct phyletic line in the Nocardia 16S rRNA gene tree and was closely associated with Nocardia goodfellowii A2012T (98.6 % 16S rRNA gene sequence similarity), Nocardia alba YIM 30243T (98.5 %) and Nocardia caishijiensis F829T (97.9 %). However, DNA–DNA relatedness values and phenotypic data demonstrated that strain CR3272T was clearly distinguished from all closely related species of the genus Nocardia . It is concluded that the organism be classified as representing a novel species of the genus Nocardia , for which the name Nocardia sungurluensis is proposed. The type strain is CR3272T ( = DSM 45714T = KCTC 29094T).

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).

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