Pseudonocardia sediminis sp. nov., isolated from marine sediment

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 745-750 ◽  
Author(s):  
Dao-Feng Zhang ◽  
Zhao Jiang ◽  
Li Li ◽  
Bing-Bing Liu ◽  
Xiao-Mei Zhang ◽  
...  
Keyword(s):  
Marine Sediment ◽  
Type Species ◽  
Major Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Substrate Mycelium ◽  
Link Type ◽  
Aerial Hyphae ◽  
The Media

A Gram-stain-positive, aerobic actinomycete, designated strain YIM M13141T, was isolated from a marine sediment sample from the South China Sea, and its taxonomic position was determined using a polyphasic approach. The strain produced branched substrate mycelium and aerial hyphae, but no diffusible pigments were produced on the media tested. At maturity, substrate mycelium was fragmented and spore chains were formed on aerial hyphae and substrate mycelium. Optimum growth occurred at 28 °C, 1–3 % (w/v) NaCl and pH 7.0. Comparative analysis of the 16S rRNA gene sequence showed that the isolate belongs to the genus Pseudonocardia , showing highest levels of similarity with respect to Pseudonocardia sichuanensis KLBMP 1115T (97.1 %), Pseudonocardia tetrahydrofuranoxydans K1T (97.1 %) and Pseudonocardia kunmingensis YIM 63158T (97.0 %). Whole-organism hydrolysates of the strain contained meso-diaminopimelic acid and the sugars galactose, glucose, mannose and arabinose. The predominant menaquinone was MK-8(H4). The polar lipids detected were diphosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, phosphatidylmethylethanolamine, phosphatidylethanolamine, two unknown phosphoglycolipids and two glycolipids. The major fatty acid was iso-C16 : 0. The G+C content of the genomic DNA was 73.1 mol%. DNA–DNA relatedness with P. tetrahydrofuranoxydans DSM 44239T was 42.8±3.5 % (mean±sd). Based on phylogenetic analysis, phenotypic and genotypic data, it is concluded that the isolate represents a novel species of the genus Pseudonocardia , for which the name Pseudonocardia sediminis sp. nov. is proposed. The type strain is YIM M13141T ( = DSM 45779T = JCM 18540T).

scholarly journals Actinophytocola sediminis sp. nov., an actinomycete isolated from a marine sediment

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2834-2840 ◽  
Author(s):  
Dao-Feng Zhang ◽  
Zhao Jiang ◽  
Xiao-Mei Zhang ◽  
Ling-Ling Yang ◽  
Xin-Peng Tian ◽  
...  
Keyword(s):  
Marine Sediment ◽  
Novel Species ◽  
Major Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Substrate Mycelium ◽  
Link Type ◽  
Aerial Hyphae ◽  
The Media

A novel actinomycete strain, designated YIM M13705T, was isolated from a marine sediment sample of the South China Sea and its characteristics were determined by a polyphasic approach. The slowly growing, Gram-stain-positive, aerobic strain produced branched substrate mycelium and aerial hyphae, and no diffusible pigment was produced on the media tested. At maturity, spore chains were formed on aerial hyphae and substrate mycelium was not fragmented. Whole-cell hydrolysates of the strain contained meso-diaminopimelic acid and galactose, glucose, ribose and rhamnose. The predominant menaquinones were MK-9(H4) and MK-10(H2). The polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylinositol and ninhydrin-positive phosphoglycolipids. The major fatty acid was iso-C16 : 0. The G+C content of the genomic DNA was 68.2  mol%. On the basis of 16S rRNA gene sequence, the strain was shown to be most closely related to species of the genus Actinophytocola . DNA–DNA hybridization relatedness values (<70 %) of the isolate with its closest neighbour Actinophytocola xinjiangensis QAIII60T supported classification of the isolate as a representative of a novel species. On the basis of phylogenetic analysis, and phenotypic and genotypic data, it is concluded that the new isolate belongs to a novel species of the genus Actinophytocola , for which the name Actinophytocola sediminis sp. nov. (type strain YIM M13705T = DSM 45939T = BCRC 16956T) is proposed.

Paenibacillus typhae sp. nov., isolated from roots of Typha angustifolia L.

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1037-1044 ◽  
Author(s):  
Bi He Kong ◽  
Qun Fang Liu ◽  
Min Liu ◽  
Yang Liu ◽  
Lei Liu ◽  
...  
Keyword(s):  
Type Species ◽  
Optimal Growth ◽  
Major Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Typha Angustifolia ◽  
Content Type ◽  
Link Type ◽  
Diamino Acid ◽  
Unknown Phospholipid

A Gram-stain-positive, facultatively anaerobic and rod-shaped bacterium, designated strain xj7T, was isolated from roots of Typha angustifolia L. growing in Beijing Cuihu Wetland, China. The isolate was identified as a member of the genus Paenibacillus based on phenotypic characteristics and phylogenetic inference. The novel strain was spore-forming, motile, catalase-positive and oxidase-negative. Optimal growth of strain xj7T occurred at 28–30 °C and pH 7.0–7.5. Diphosphatidylglycerol was the most abundant polar lipid and occurred along with phosphatidylglycerol, phosphatidylethanolamine, one unknown phospholipid and three unknown aminophospholipids. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. The predominant isoprenoid quinone was MK-7. The major fatty acid components were anteiso-C15 : 0 (56.1 %), iso-C16 : 0 (9.1 %), C16 : 0 (8.0 %), iso-C14 : 0 (6.3 %) and iso-C15 : 0 (5.1 %). The G+C content of genomic DNA was 47.9 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain xj7T fell within the evolutionary radiation encompassed by the genus Paenibacillus , its closest neighbours were Paenibacillus borealis KK19T (97.5 %) and Paenibacillus durus DSM 1735T (97.1 %). However, the DNA–DNA relatedness values between strain xj7T and P. borealis KK19T and between strain xj7T and P. durus DSM 1735T, were both 35 %. Based on phenotypic, chemotaxonomic and phylogenetic properties, strain xj7T is considered to represent a novel species of the genus Paenibacillus , for which the name Paenibacillus typhae sp. nov. is proposed. The type strain is xj7T ( = CGMCC 1.11012T = DSM 25190T).

scholarly journals Paracoccus sediminis sp. nov., isolated from Pacific Ocean marine sediment

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2512-2516 ◽  
Author(s):  
Jie Pan ◽  
Cong Sun ◽  
Xin-Qi Zhang ◽  
Ying-Yi Huo ◽  
Xu-Fen Zhu ◽  
...  
Keyword(s):  
Pacific Ocean ◽  
Marine Sediment ◽  
Type Species ◽  
Optimal Growth ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Pacific ◽  
The Pacific Ocean

Strain CMB17T was a short rod-shaped bacterium isolated from marine sediment of the Pacific Ocean. Cells were Gram-stain-negative and non-motile. Optimal growth occurred at 25–30 °C, pH 6.5–7 and 0.5–1 % (w/v) NaCl. The major fatty acid was C18 : 1ω7c (87.59 %), and ubiquinone-10 was detected as the only isoprenoid quinone. The DNA G+C content of the genomic DNA was 62.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CMB17T is most closely related to Paracoccus stylophorae KTW-16T (96.7 %), P. solventivorans DSM 6637T (96.4 %) and P. saliphilus YIM 90738T (96.4 %). Based on phenotypic, genotypic and phylogenetic characteristics, strain CMB17T is proposed to represent a novel species, denominated Paracoccus sediminis sp. nov. (type strain CMB17T = JCM 18467T = DSM 26170T = CGMCC 1.12681T).

Oceanobacillus chungangensis sp. nov., isolated from a sand dune

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3666-3671 ◽  
Author(s):  
Dong Chae Lee ◽  
Hyeonji Kang ◽  
Veeraya Weerawongwiwat ◽  
Beomjoon Kim ◽  
Young-Wan Choi ◽  
...  
Keyword(s):  
Type Species ◽  
Sand Dune ◽  
Major Fatty Acid ◽  
Polar Lipids ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type

A Gram-stain-positive, spore-forming, rod-shaped, motile, strictly aerobic bacterial strain, designated CAU 1051T, was isolated from a sand dune and its taxonomic position was investigated using a polyphasic approach. Strain CAU 1051T grew optimally at pH 5.0 and 30 °C. NaCl was not required for growth but up to 10.0 % (w/v) NaCl was tolerated. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CAU 1051T formed a distinct lineage within the genus Oceanobacillus and was most closely related to Oceanobacillus profundus CL-MP28T, Oceanobacillus caeni S-11T, and Oceanobacillus picturae LMG 19492T (96.8 %, 95.6 % and 95.3 % similarity, respectively). DNA–DNA reassociation analysis showed that strain CAU 1051T displayed 28.2±0.7 % relatedness to O. profundus KCTC 13625T. Strain CAU 1051T contained MK-7 as the only isoprenoid quinone and anteiso-C15 : 0 as the major fatty acid. The cell wall peptidoglycan of strain CAU 1051T contained meso-diaminopimelic acid. The polar lipids were composed of diphosphatidylglycerol, phosphatidylglycerol, six unidentified phospholipids, an unidentified glycolipid, and six unidentified polar lipids. The major whole-cell sugars were glucose and ribose. The DNA G+C content was 36.3 mol%. On the basis of phenotypic data and phylogenetic inference, strain CAU 1051T represents a novel species of the genus Oceanobacillus for which the name Oceanobacillus chungangensis sp. nov. is proposed. The type strain is CAU 1051T ( = KCTC 33035T = CCUG 63270T).

scholarly journals Auraticoccus cholistanensis sp. nov., an actinomycete isolated from soil of the Cholistan Desert, and emended description of the genus Auraticoccus

2020 ◽  
Vol 70 (5) ◽  
pp. 3179-3185 ◽  
Author(s):  
Mohsin Tassawar Cheema ◽  
Jing-Jing Ye ◽  
Fei-Na Li ◽  
Qin-Pei Lu ◽  
Muhammad Abbas ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Trees ◽  
Major Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Cholistan Desert ◽  
Taxonomic Approach ◽  
Phylogenomic Analyses

A Gram-stain-positive, aerobic, non-motile and non-spore-forming actinobacterium, designated as F435T, was isolated from soil sample collected from the Cholistan Desert, Pakistan. The taxonomic position of the strain was established by using a polyphasic taxonomic approach. The cells were coccoid-shaped and found in single or arrangement of pairs. The novel strain grew at 15‒37 °C (optimum, 25‒30 °C), pH 7‒11 (optimum, pH 7–8) and in the presence of 0‒8% (w/v) NaCl (optimum, 0 %). Results of blast analysis based on 16S rRNA gene sequences showed that Auraticoccus monumenti MON 2.2T was its closest relative with 97.4 % similarity followed by Desertihabitans aurantiacus CPCC 204711T (95.2 %). In phylogenetic trees, strain F435T formed a robust cluster with the only member of the genus Auraticoccus . The peptidoglycan isomer present in the cell wall was ll-diaminopimelic acid. The major fatty acid was determined to be anteiso-C15 : 0. Characteristic polar lipids of the strain were diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipids and glycolipids. The predominant menaquinone was MK-9(H4). The genomic G+C content was calculated as 73.5 mol%. The digital DNA–DNA hybridization (GGDC) and average nucleotide identity (ANI) values between strain F435T and A. monumenti MON 2.2T were 24.6 and 81.8 %, respectively. Based on the results of phenotypic, chemotaxonomic, phylogenetic and phylogenomic analyses, strain F435T represents a novel specie of the genus Auraticoccus , for which the name Auraticoccus cholistanensis sp. nov. is proposed. The type strain is F435T (=JCM 33648T=CGMCC 1.17443T). The description of the genus Auraticoccus has also been emended.

Description of Streptomonospora sediminis sp. nov. and Streptomonospora nanhaiensis sp. nov., and reclassification of Nocardiopsis arabia Hozzein & Goodfellow 2008 as Streptomonospora arabica comb. nov. and emended description of the genus Streptomonospora

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4447-4455 ◽  
Author(s):  
Dao-Feng Zhang ◽  
Hua-Qi Pan ◽  
Jie He ◽  
Xiao-Mei Zhang ◽  
Yong-Guang Zhang ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Polar Lipids ◽  
Diaminopimelic Acid ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Aerial Hyphae ◽  
Emended Description ◽  
The Media

Two actinomycete strains isolated from marine sediment samples, designated YIM M11335T (from the Indian Ocean) and 12A09T (from the South China Sea), were obtained and examined by a polyphasic approach. The two Gram-staining-positive, aerobic strains produced branched substrate mycelia and aerial hyphae that were not fragmented, and no diffusible pigment was produced on the media tested. At maturity, spore chains and single spores were formed on aerial hyphae and substrate mycelium, respectively. Whole-organism hydrolysates of both strains contained meso-diaminopimelic acid and the diagnostic sugars glucose and galactose. Their predominant menaquinones were MK-10(H4), MK-10(H6), MK-11(H4), MK-11(H6) and MK-11(H8) for strain YIM 11335T and MK-10(H4), MK-10(H6), MK-11(H4), MK-11(H6) and MK-11(H8) for strain 12A09T. The polar lipids detected in the two strains were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol mannoside, phosphatidylinositol, phosphatidylcholine, an unknown phosphoglycolipid and several unknown glycolipids, phospholipids and polar lipids. The major fatty acids (>10 %) were iso-C16 : 0 and C16 : 0 for strain YIM 11335T and iso-C16 : 0 for strain 12A09T. The G+C contents of the genomic DNA of strains YIM 11335T and 12A09T were 70.7 % and 74.4 %, respectively. DNA–DNA hybridization relatedness values of these two isolates with the type strains Nocardiopsis arabia DSM 45083T and Streptomonospora halophila YIM 91355T supported the hypothesis they are representatives of two different species. Based on phylogenetic analysis, phenotypic and genotypic data, it is concluded that the two isolates belong to the genus Streptomonospora of the family Nocardiopsaceae and that the type strain of N. arabia should be reclassified as a representative of Streptomonospora arabica comb. nov. The names proposed for the two novel species are Streptomonospora sediminis sp. nov. (type strain YIM M11335T = DSM 45723T = CCTCC AB 2012051T) and Streptomonospora nanhaiensis sp. nov. (type strain 12A09T = KCTC 29145T = CCTCC AB 2013140T), respectively. An emended description of the genus Streptomonospora is also proposed in the light of the new data.

Actinoplanes atraurantiacus sp. nov., isolated from soil

2012 ◽  
Vol 62 (Pt_10) ◽  
pp. 2533-2537 ◽  
Author(s):  
Yabo Zhang ◽  
Jianli Zhang ◽  
Lei Fan ◽  
Huancheng Pang ◽  
Yuhua Xin ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Methyl Esters ◽  
Major Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Positive Staining ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type

A Gram-positive-staining bacterium, designated Y16T, was isolated from a soil sample from Yunnan Province, China. The isolate grew optimally at 25–30 °C, grew at pH 6.0–9.0 and could grow with 3 % NaCl. Strain Y16T had cell-wall peptidoglycan based on meso-diaminopimelic acid. The predominant menaquinones were MK-9(H4) and MK-9(H2). The major fatty acid methyl esters were anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0 and C16 : 0. These chemotaxonomic characteristics suggested that the organism belonged to the genus Actinoplanes . Strain Y16T shared 98.7, 98.3 and 97.9 % 16S rRNA gene sequence similarity with Actinoplanes deccanensis IFO 13994T, A. abujensis A4029T and A. brasiliensis DSM 43805T, respectively. The DNA G+C content of the isolate was 70.8 mol%. DNA–DNA relatedness between the novel isolate and the type strains of A. deccanensis , A. abujensis and A. brasiliensis was 35.2, 32.0 and 22.3 %, respectively. In addition, the pattern of phenotypic properties distinguished strain Y16T from its closest phylogenetic neighbours. It is therefore concluded that strain Y16T ( = CGMCC 4.6857T = JCM 17700T) represents a novel species of the genus Actinoplanes , for which the name Actinoplanes atraurantiacus sp. nov. is proposed.

Micromonospora sediminicola sp. nov., isolated from marine sediment

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 570-575 ◽  
Author(s):  
Khomsan Supong ◽  
Chanwit Suriyachadkun ◽  
Somboon Tanasupawat ◽  
Khanit Suwanborirux ◽  
Pattama Pittayakhajonwut ◽  
...  
Keyword(s):  
Marine Sediment ◽  
Type Species ◽  
Andaman Sea ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Marine Sediment Sample ◽  
Actinomycete Strain

An actinomycete strain, designated strain SH2-13T, was isolated from a marine sediment sample collected from the Andaman Sea of Thailand. Applying a polyphasic approach, the isolate was identified as a member of the genus Micromonospora using morphological and chemotaxonomic characteristics, including the presence of meso-diaminopimelic acid in the peptidoglycan. Whole-cell sugars were arabinose, galactose, glucose, rhamnose, ribose and xylose. Diagnostic polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides and phosphoglycolipids. The major menaquinones were MK-10(H2), MK-10(H4) and MK-10(H6). 16S rRNA gene sequence analysis revealed similarity to Micromonospora marina JSM1-1T (99.1 %), Micromonospora coxensis 2-30-b(28)T (99.1 %), Micromonospora aurantiaca DSM 43813T (98.8 %) and Micromonospora chalcea DSM 43026T (98.7 %). However, a combination of DNA–DNA hybridization results and phenotypic properties indicated that strain SH2-13T ( = NBRC 107934T = BCC 45601T) should be classified as the type strain of a novel species, with the proposed name Micromonospora sediminicola sp. nov.

scholarly journals Bacillus aquiflavi sp. nov., isolated from yellow water of strongly flavored Chinese baijiu

2020 ◽  
Vol 70 (5) ◽  
pp. 3406-3412 ◽  
Author(s):  
Jiuyan Xie ◽  
Kun Cheng ◽  
Dong Zhao ◽  
Guanrong Yang ◽  
Zongwei Qiao ◽  
...  
Keyword(s):  
Type Species ◽  
Major Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Optimum Growth ◽  
Content Type ◽  
Link Type ◽  
Pr China ◽  
Type Strains

A Gram-stain-positive, strictly aerobic and rod-shaped bacterium, designated as 3 H-10T, was isolated from a yellow water sample collected from the manufacturing process of strong flavor Chinese baijiu in Yibin region of Sichuan province (PR China). Oval endospores were formed at the subtermini of cells with swollen sporangia. The isolate was able to grow at temperatures of 20–45 °C (optimum growth at 37 °C), at pH 6.0–10.0 (optimum growth at pH 8.0) and in the presence of 0–2 % (w/v) NaCl (optimum growth with 0 % NaCl). Ribose was the major cell-wall sugar, and meso-diaminopimelic acid (meso-DAP) was the diagnostic amino acid. The main polar lipids of 3 H-10T included diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylethanolamine (PE). MK-7 was predominant menaquinone and iso-C15 : 0 (60.7 %) was the major fatty acid. Comparisons of 16S rRNA gene sequence indicated that 3 H-10T was most closely related to Bacillus mesophilus SA4T (96.30 %), Bacillus ginsengihumi Gsoil 114T (96.27 %) and Bacillus shackletonii LMG 18435T (96.27 %). The average nucleotide identity (ANI) values between strain 3 H-10T and the three type strains mentioned above were 69.56, 70.19 and 70.67 %, respectively. The genomic DNA G+C content was 35.4 mol%. On the basis of its phenotypic, chemotaxonomic and phylogenetic properties, strain 3 H-10T represents a novel species of the genus Bacillus , for which the name Bacillus aquiflavi sp. nov. is proposed. The type strain is Bacillus aquiflavi 3 H-10T (=CICC 24755T=JCM 33703T).

Paenibacillus tianjinensis sp. nov., isolated from corridor air

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Hongxiang Liu ◽  
Lijing Lu ◽  
Sijin Wang ◽  
Meng Yu ◽  
Xiaoyun Cao ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Major Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type ◽  
Pr China ◽  
Type Strains

A Gram-stain-positive, facultatively anaerobic, non-motile, endospore-forming and rod-shaped bacterium, occurring singly or in pairs, designated TB2019T, was isolated from environmental monitoring samples of corridor air collected at the Tianjin Institute for Drug Control, Tianjin Province (PR China). The isolate was able to grow at 15–40 °C (optimum growth at 37 °C), pH 6.0–8.0 (pH 7.0) and in the presence of 0–2% (w/v) NaCl (0% NaCl). Comparison of 16S rRNA gene sequences indicated that TB2019T was most closely related to Paenibacillus typhae CGMCC 1.11012T (98.63%), Paenibacillus albidus Q4-3T (98.19%), Paenibacillus borealis DSM 13188T (97.55%), Paenibacillus helianthi P26ET (97.33%) and Paenibacillus odorifer DSM 15391T (97.19%). The digital DNA–DNA hybridization and the average nucleotide identity values between TB2019T and the five type strains mentioned above ranged from 20.7 to 25.0% and 75.2 to 81.3%, respectively, and the genomic DNA G+C content was 49.52 mol%. The diagnostic cell-wall sugar was ribose, and the diagnostic amino acid was meso-diaminopimelic acid. The polar lipids of TB2019T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified aminophospholipids and one unidentified phospholipid. MK-7 was the predominant menaquinone, and anteiso-C15:0 (30.6%) was the major fatty acid. Based on the polyphasic taxonomic data, strain TB2019T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus tianjinensis sp. nov. is proposed. The type strain is TB2019T (=CICC 25065T=JCM 34610T).

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