scholarly journals Pontibacillus litoralis sp. nov., a facultatively anaerobic bacterium isolated from a sea anemone, and emended description of the genus Pontibacillus

2010 ◽  
Vol 60 (3) ◽  
pp. 560-565 ◽  
Author(s):  
Yi-Guang Chen ◽  
Yu-Qin Zhang ◽  
Lang-Bo Yi ◽  
Zhao-Yang Li ◽  
Yong-Xiao Wang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sea Anemone ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Facultatively Anaerobic ◽  
Emended Description ◽  
Anthopleura Xanthogrammica

A facultatively anaerobic, moderately halophilic, Gram-positive, endospore-forming, motile, catalase- and oxidase-positive, rod-shaped bacterium, strain JSM 072002T, was isolated from a sea anemone (Anthopleura xanthogrammica) collected from the South China Sea. Strain JSM 072002T was able to grow with 0.5–15 % (w/v) NaCl and at pH 6.0–10.0 and 15–50 °C; optimum growth was observed with 2–5 % (w/v) NaCl and at pH 7.5 and 35 °C. meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The predominant respiratory quinone was menaquinone 7 and the genomic DNA G+C content was 41.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JSM 072002T should be assigned to the genus Pontibacillus and revealed relatively low 16S rRNA gene sequence similarities (<97 %) with the type strains of the three recognized Pontibacillus species (Pontibacillus chungwhensis BH030062T, 96.8 %; Pontibacillus marinus KCTC 3917T, 96.7 %; Pontibacillus halophilus JSM 076056T, 96.0 %). The combination of phylogenetic analysis, DNA–DNA relatedness values, phenotypic characteristics and chemotaxonomic data supports the view that strain JSM 072002T represents a novel species of the genus Pontibacillus, for which the name Pontibacillus litoralis sp. nov. is proposed. The type strain is JSM 072002T (=DSM 21186T=KCTC 13237T). An emended description of the genus Pontibacillus is also presented.

scholarly journals Salininema proteolyticum gen. nov., sp. nov., a halophilic rare actinomycete isolated from wetland soil, and emended description of the family Glycomycetaceae

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3727-3733 ◽  
Author(s):  
Mahdi Moshtaghi Nikou ◽  
Mohaddaseh Ramezani ◽  
Mohammad Ali Amoozegar ◽  
Mehrnoush Rasouli ◽  
Seyed Abolhassan Shahzadeh Fazeli ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
New Genus ◽  
Diaminopimelic Acid ◽  
Wetland Soil ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Family ◽  
Emended Description

A Gram-stain-positive actinobacterial strain, Miq-4T, was isolated from soil around Meighan wetland in the centre of Iran. Strain Miq-4T was strictly aerobic, catalase- and oxidase-positive. The isolate grew in the presence of 3–15 % (w/v) NaCl, at 20–40 °C and pH 6.0–11.0. The optimum NaCl, temperature and pH for growth were 7.0 %, 30 °C and 7.0–8.5, respectively. The cell wall of strain Miq-4T contained meso-diaminopimelic acid as the diamino acid and glucose and ribose as the whole-cell sugars. The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. Strain Miq-4T synthesized cellular fatty acids of anteiso- and iso-branched types, including anteiso-C17 : 0, anteiso- C15 : 0 and iso-C16 : 0, and the major respiratory quinone was MK-9(H4). The G+C content of the genomic DNA was 68.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences and characteristic patterns of 16S rRNA gene signature nucleotides revealed that strain Miq-4T belongs to the family Glycomycetaceae and showed the closest phylogenetic similarity with Haloglycomyces albus YIM 92370T (94.1 % 16S rRNA gene sequence similarity). On the basis of phylogenetic analysis and phenotypic and chemotaxonomic characteristics, strain Miq-4T represents a novel species of a new genus in the family Glycomycetaceae, for which the name Salininema proteoliyticum gen. nov., sp. nov. is proposed. The type strain of the type species is Miq-4T ( = IBRC-M 10908T = LMG 28391T). An emended description of the family Glycomycetaceae is also proposed in order to include features of the new genus.

scholarly journals Bacillus hemicentroti sp. nov., a moderate halophile isolated from a sea urchin

2011 ◽  
Vol 61 (12) ◽  
pp. 2950-2955 ◽  
Author(s):  
Yi-Guang Chen ◽  
Yu-Qin Zhang ◽  
Jian-Wu He ◽  
Hans-Peter Klenk ◽  
Jian-Qing Xiao ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sea Urchin ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Moderate Halophile

A novel Gram-staining-positive, moderately halophilic, facultatively alkaliphilic, non-motile, catalase-positive, oxidase-negative, endospore-forming, facultatively anaerobic rod, designated JSM 076093T, was isolated from a sea urchin (Hemicentrotus pulcherrimus) collected from Naozhou Island in the South China Sea. Growth occurred with 0.5–25 % (w/v) NaCl (optimum 5–8 %) and at pH 6.0–10.5 (optimum pH 8.0) and 5–40 °C (optimum 30–35 °C). meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The predominant respiratory quinone was menaquinone 7 and the polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and one unidentified phospholipid. The major cellular fatty acids (>10 % of the total) were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C14 : 0. The genomic DNA G+C content was 38.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JSM 076093T belonged to the genus Bacillus and was related most closely to Bacillus hwajinpoensis SW-72T (99.1 % 16S rRNA gene sequence similarity) and Bacillus algicola KMM 3737T (97.3 %). The combination of results from the phylogenetic analysis, DNA–DNA hybridization and phenotypic and chemotaxonomic characterization supported the conclusion that strain JSM 076093T represents a novel species of the genus Bacillus, for which the name Bacillus hemicentroti sp. nov. is proposed, with JSM 076093T ( = DSM 23007T = KCTC 13710T) as the type strain.

scholarly journals Bacillus thermolactis sp. nov., isolated from dairy farms, and emended description of Bacillus thermoamylovorans

2011 ◽  
Vol 61 (8) ◽  
pp. 1954-1961 ◽  
Author(s):  
An Coorevits ◽  
Niall A. Logan ◽  
Anna E. Dinsdale ◽  
Gillian Halket ◽  
Patsy Scheldeman ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Emended Description

A polyphasic taxonomic study was performed on 22 thermotolerant, aerobic, endospore-forming bacteria from dairy environments. Seventeen isolates were retrieved from raw milk, one from a filter cloth and four from grass, straw or milking equipment. These latter four isolates (R-6546, R-7499, R-7764 and R-7440) were identified as Bacillus thermoamylovorans based on DNA–DNA hybridizations (values above 70 % with Bacillus thermoamylovorans LMG 18084T) but showed discrepancies in characteristics with the original species description, so an emended description of this species is given. According to 16S rRNA gene sequence analysis and DNA–DNA hybridization experiments, the remaining 18 isolates (R-6488T, R-28193, R-6491, R-6492, R-7336, R-33367, R-6486, R-6770, R-31288, R-28160, R-26358, R-7632, R-26955, R-26950, R-33520, R-6484, R-26954 and R-7165) represented one single species, most closely related to Bacillus thermoamylovorans (93.9 % 16S rRNA gene sequence similarity), for which the name Bacillus thermolactis is proposed. Cells were Gram-stain-positive, facultatively anaerobic, endospore-forming rods that grew optimally at 40–50 °C. The cell wall peptidoglycan type of strain R-6488T, the proposed type strain, was A1γ based on meso-diaminopimelic acid. Major fatty acids of the strains were C16 : 0 (28.0 %), iso-C16 : 0 (12.1 %) and iso-C15 : 0 (12.0 %). MK-7 was the predominant menaquinone, and major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and some unidentified phospholipids. DNA G+C content was 35.0 mol%. Phenotypic properties allowed discrimination from other thermotolerant species of the genus Bacillus and supported the description of the novel species Bacillus thermolactis, with strain R-6488T ( = LMG 25569T  = DSM 23332T) as the proposed type strain.

scholarly journals Aeromicrobium alkaliterrae sp. nov., isolated from an alkaline soil, and emended description of the genus Aeromicrobium

2005 ◽  
Vol 55 (5) ◽  
pp. 2171-2175 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Choong-Hwan Lee ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Alkaline Soil ◽  
Rrna Gene Sequence ◽  
Emended Description ◽  
A Cell

A Gram-positive, aerobic, non-motile bacterial strain, KSL-107T, was isolated from an alkaline soil from Korea and subjected to a polyphasic taxonomic study. Strain KSL-107T grew optimally at 25 °C and pH 7·0–7·5. Strain KSL-107T had a cell-wall peptidoglycan based on ll-2,6-diaminopimelic acid. It contained MK-9(H4) as the predominant menaquinone and C16 : 0, C16 : 0 2-OH and 10-methyl C18 : 0 as the major fatty acids. The DNA G+C content was 71·5 mol%. Comparative 16S rRNA gene sequence analyses showed that strain KSL-107T was phylogenetically affiliated to the genus Aeromicrobium of the family Nocardioidaceae. Similarity values between the 16S rRNA gene sequence of strain KSL-107T and those of type strains of Aeromicrobium species were in the range 97·9–98·2 %. The isolate could be distinguished from other Aeromicrobium species by levels of DNA–DNA relatedness and differences in some phenotypic characteristics. On the basis of the data presented, it is suggested that strain KSL-107T (=KCTC 19073T=DSM 16824T) represents a novel Aeromicrobium species, for which the name Aeromicrobium alkaliterrae sp. nov. is proposed. An emended description of the genus Aeromicrobium is also proposed.

scholarly journals Croceifilum oryzae gen. nov., sp. nov., isolated from rice paddy soil

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4061-4065 ◽  
Author(s):  
Kouta Hatayama ◽  
Teruaki Kuno
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Paddy Soil ◽  
Rice Paddy ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Rice Paddy Soil

A mesophilic, aerobic, Gram-stain-positive, filamentous bacterial strain, designated ZYf1a3T, was isolated from rice paddy soil in Japan. This strain grew on a solid medium with formation of substrate mycelium; endospores were produced singly along the mycelium. Formation of aerial mycelium was not observed on any of the media tested. This strain produced a characteristic saffron yellow soluble pigment. Cloned 16S rRNA gene sequences of strain ZYf1a3T yielded three different copies (similarity between the three sequences: 99.8–99.9 %). One of these sequences had one base deletion. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain ZYf1a3T belongs to an independent phylogenetic lineage of the family Thermoactinomycetaceae. The cell wall of strain ZYf1a3T contained meso-diaminopimelic acid, alanine and glutamic acid, but no characteristic sugars. It contained menaquinone 7 as the sole menaquinone. The major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0.The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidyl-N-methylethanolamine and unidentified aminophospholipids. The DNA G+C content was 42.5 mol%. From phylogenetic analysis based on 16S rRNA gene sequences and phenotypic characteristics, this strain is considered to represent a novel species in a new genus, for which the name Croceifilum oryzae gen. nov., sp. nov. is proposed. The type strain of Croceifilum oryzae is ZYf1a3T ( = JCM 30426T = CCUG 66446T = DSM 46876T).

Albimonas pacifica sp. nov., isolated from seawater of the Pacific, and emended description of the genus Albimonas

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3597-3601 ◽  
Author(s):  
Guo-Wei Li ◽  
Xi-Ying Zhang ◽  
Chun-Sheng Wang ◽  
Yan-Jiao Zhang ◽  
Xue-Wei Xu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Pacific ◽  
Emended Description

A Gram-stain-negative, aerobic, catalase- and oxidase-positive, non-flagellated, rod-shaped bacterium, designated strain P-50-3T, was isolated from seawater of the Pacific. The strain grew at 10–40 °C (optimum at 30 °C) and with 0–12 % (w/v, optimum 2 %) NaCl. It reduced nitrate to nitrite but did not hydrolyse gelatin, starch or Tween 80. Analysis of 16S rRNA gene sequences showed that strain P-50-3T clustered tightly with the genus Albimonas and shared the highest 16S rRNA gene sequence similarity (94.3 %) with the type strain of Albimonas donghaensis . The major respiratory quinone was Q-10 and the major cellular fatty acids were C18 : 1ω7c, C18 : 0, 11-methyl C18 : 1ω7c and C16 : 0. Polar lipids included phosphatidylglycerol (PG), phosphatidylcholine (PC), two unidentified aminolipids and an unidentified lipid. The genomic DNA G+C content of strain P-50-3T was 69.0 mol%. On the basis of the data obtained in this polyphasic study, strain P-50-3T represents a novel species within the genus Albimonas , for which the name Albimonas pacifica sp. nov. is proposed. The type strain of Albimonas pacifica is P-50-3T ( = KACC 16527T = CGMCC 1.11030T). An emended description of the genus Albimonas Lim et al. 2008 is also proposed.

Mariniflexile jejuense sp. nov., isolated from the junction between seawater and a freshwater spring, and emended description of the genus Mariniflexile

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1329-1334 ◽  
Author(s):  
Yong-Taek Jung ◽  
Jung-Hoon Yoon
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Emended Description ◽  
Freshwater Spring

A Gram-negative, non-spore-forming, non-flagellated, motile-by-gliding rod, designated SSK2-3T, was isolated from the junction between seawater and a freshwater spring at Jeju island, South Korea. Strain SSK2-3T grew optimally at 25–30 °C, at pH 7.0–7.5 and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SSK2-3T clustered with type strains of species of the genus Mariniflexile , with which it exhibited 97.2–97.8 % 16S rRNA gene sequence similarity. Sequence similarity between the isolate and the other strains used in the phylogenetic analysis was <95.6 %. Strain SSK2-3T contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C15 : 1 G and C15 : 0 as the major fatty acids. The major polar lipids of strain SSK2-3T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain SSK2-3T was 32.4 mol%. DNA–DNA relatedness between the isolate and Mariniflexile gromovii KCTC 12570T, Mariniflexile fucanivorans DSM 18792T and Mariniflexile aquimaris HWR-17T was 19, 15 and 20 %, respectively. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain SSK2-3T is separate from other members of the genus Mariniflexile . On the basis of the data presented, strain SSK2-3T is considered to represent a novel species of the genus Mariniflexile , for which the name Mariniflexile jejuense sp. nov. is proposed. The type strain is SSK2-3T ( = KCTC 23958T  = CCUG 62414T). An emended description of the genus Mariniflexile is given.

scholarly journals Formosa spongicola sp. nov., isolated from the marine sponge Hymeniacidon flavia

2011 ◽  
Vol 61 (2) ◽  
pp. 330-333 ◽  
Author(s):  
Byoung-Jun Yoon ◽  
Duck-Chul Oh
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Sponge ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Respiratory Quinone ◽  
The Family ◽  
Major Respiratory Quinone

A Gram-negative, yellow-pigmented, rod-shaped, strictly aerobic, non-flagellated, oxidase- and catalase-positive, marine bacterium, designated A2T, was isolated from a marine sponge, Hymeniacidon flavia, collected from the coast of Jeju Island, South Korea. Phylogenetic analysis based on nearly complete 16S rRNA gene sequences revealed that strain A2T was a member of the family Flavobacteriaceae. Its closest relatives were Formosa agariphila KMM 3901T and Formosa algae KMM 3553T (96.99 and 96.98 % 16S rRNA gene sequence similarity, respectively). DNA–DNA relatedness between strain A2T and F. agariphila KMM 3901T and F. algae KMM 3553T was 14.1 and 26.8 %, respectively. The dominant fatty acids (>5 %) of strain A2T were iso-C15 : 0 (33.9 %), iso-C17 : 0 3-OH (20.8 %), iso-C15 : 1 G (10.5 %) and iso-C15 : 0 3-OH (6.1 %). The DNA G+C content of strain A2T was 36.0 mol% and the major respiratory quinone was MK-6. On the basis of phenotypic and phylogenetic analysis, strain A2T represents a novel species of the genus Formosa, for which the name Formosa spongicola sp. nov. is proposed. The type strain is A2T (=KCTC 22662T =DSM 22637T).

scholarly journals Devosia psychrophila sp. nov. and Devosia glacialis sp. nov., from alpine glacier cryoconite, and an emended description of the genus Devosia

2012 ◽  
Vol 62 (Pt_3) ◽  
pp. 710-715 ◽  
Author(s):  
De-Chao Zhang ◽  
Mersiha Redzic ◽  
Hong-Can Liu ◽  
Yu-Guang Zhou ◽  
Franz Schinner ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Alpine Glacier ◽  
Emended Description

Two psychrophilic strains, Cr7-05T and Cr4-44T, isolated from alpine glacier cryoconite, were characterized by using a polyphasic approach. Both strains were psychrophilic, showing good growth over a temperature range of 1–20 °C. The chemotaxonomic characteristics of these isolates included the presence of C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the major cellular fatty acids, Q-10 as the predominant ubiquinone and diphosphatidylglycerol, phosphatidylglycerol and unknown glycolipids as major polar lipids. The DNA G+C contents of strains Cr7-05T and Cr4-44T were 61.4 and 63.6 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates belong to the genus Devosia. The 16S rRNA gene sequence similarity between the two strains was 98.6 %, but DNA–DNA hybridization indicated 54 % relatedness. Strains Cr7-05T and Cr4-44T exhibited 16S rRNA gene sequence similarity of 94.7–97.2 and 94.9–96.9 %, respectively, to the type strains of recognized Devosia species. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data, strains Cr7-05T and Cr4-44T represent two novel species within the genus Devosia, for which the names Devosia psychrophila sp. nov. (type strain Cr7-05T  = DSM 22950T  = CGMCC 1.10210T  = CIP 110130T) and Devosia glacialis sp. nov. (type strain Cr4-44T  = CGMCC 1.10691T  = LMG 26051T) are proposed. An emended description of the genus Devosia is also provided.

scholarly journals Paucisalibacillus globulus gen. nov., sp. nov., a Gram-positive bacterium isolated from potting soil

2006 ◽  
Vol 56 (8) ◽  
pp. 1841-1845 ◽  
Author(s):  
Inês Nunes ◽  
Igor Tiago ◽  
Ana Luísa Pires ◽  
Milton S. da Costa ◽  
António Veríssimo
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Positive Bacterium ◽  
Gram Positive ◽  
Respiratory Quinone ◽  
Bootstrap Analysis

A Gram-positive bacterium, designated B22T, was isolated from potting soil produced in Portugal. This organism is a catalase-positive, oxidase-negative, motile, spore-forming, aerobic rod that grows optimally at 37 °C and pH 8.0–8.5. Optimal growth occurs in media containing 1 % (w/v) NaCl, although the organism can grow in 0–8 % NaCl. The cell wall peptidoglycan is of the A4α type with a cross-linkage containing d-Asp. The major respiratory quinone is menaquinone 7 and the major fatty acids are anteiso-15 : 0, anteiso-17 : 0 and iso-15 : 0. The DNA G+C content is 37.9 mol%. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain B22T formed a new branch within the family Bacillaceae. The novel isolate is phylogenetically closely related to members of genera of moderately halophilic bacilli and formed a coherent cluster with species of the genera Salinibacillus, Virgibacillus, Oceanobacillus and Lentibacillus, supported by bootstrap analysis at a confidence level of 71 %. Strain B22T exhibited 16S rRNA gene pairwise sequence similarity values of 94.7–94.3 % with members of the genus Salinibacillus, 95.1–92.8 % with members of the genus Virgibacillus, 94.7–93.2 % with members of the genus Oceanobacillus and 93.1–92.3 % with members of the genus Lentibacillus. On the basis of phylogenetic analysis and physiological and biochemical characteristics, it is proposed that strain B22T represents a novel species in a new genus, Paucisalibacillus globulus gen. nov., sp. nov. Strain B22T (=LMG 23148T=CIP 108857T) is the type strain of Paucisalibacillus globulus.

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