scholarly journals Rhodococcus Yananensis Sp. Nov., Isolated From Microbial Fermentation Bed Material From a Pig Farm

2021 ◽  
Author(s):  
Yingying Jiang ◽  
Chaochao Zheng ◽  
Tianfei Yu ◽  
Jing Li ◽  
Jiamin Ai ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Microbial Fermentation ◽  
The Novel ◽  
Respiratory Quinone ◽  
Pig Farm ◽  
Bed Material

Abstract An opaque, pink-colored, gram-positive, aerobic bacteria (designated FBM22-1T), 0.5 to 1.0 μm in width and 0.5 to 1.5 μm in length, was isolated from microbial fermentation bed material from a pig farm in northwestern China. Optimal growth occurred at 30–37℃, pH 7.0, and 0.5% NaCl (w/v). Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the novel isolate belonged to the family Nocardiaceae of the class Actinomycetia. FBM22-1T is closely related to Rhodococcus zopfii NBRC 100606T and Rhodococcus rhodochrous NBRC 16069T, with 16S rRNA gene sequence similarity of 97.95% and 97.73%, respectively. The predominant respiratory quinone in FBM22-1T was ubiquinone MK-8(H2), and the cellular fatty acids consisted primarily of C16:1ω7c/16:1ω6c, C16:0, and C18:0 10-methly1. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and glycolipids. The G+C content of FBM22-1T was 68.64 mol%. Based on the phenotypic, phylogenetic, and chemotaxonomic characterization, in combination with low values of digital DNA–DNA hybridization between FBM22-1T and its closest neighbors, FBM22-1T represents a novel species of the genus Rhodococcus, for which the name Rhodococcus yananensis sp. nov. is proposed; the type strain is FBM22-1T (=KCTC 49502T = CCTCC 2020275T).

scholarly journals Flagellimonas eckloniae gen. nov., sp. nov., a mesophilic marine bacterium of the family Flavobacteriaceae, isolated from the rhizosphere of Ecklonia kurome

2007 ◽  
Vol 57 (5) ◽  
pp. 1050-1054 ◽  
Author(s):  
Seung Seob Bae ◽  
Kae Kyoung Kwon ◽  
Sung Hyun Yang ◽  
Hee-Soon Lee ◽  
Sang-Jin Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Bacterium ◽  
Optimal Growth ◽  
Rrna Gene ◽  
The Novel ◽  
Respiratory Quinone ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Major Respiratory Quinone

A marine bacterium, DOKDO 007T, was isolated from the rhizosphere of the marine alga Ecklonia kurome collected from Dokdo Island, Korea, in October 2004. The strain produced orange-coloured colonies on marine agar 2216. 16S rRNA gene sequence analysis indicated that the novel isolate belonged to the family Flavobacteriaceae and showed relatively high sequence similarities with members of the genus Muricauda (92.0–94.0 %). Phylogenetic analysis based on nearly complete 16S rRNA gene sequences revealed that the novel isolate shared a lineage with members of the genera Muricauda and Costertonia. Cells were aerobic, Gram-negative rods producing non-diffusible carotenoid pigments. In contrast to all other members of the family Flavobacteriaceae, cells of DOKDO 007T were motile by means of a polar flagellum. Optimal growth occurred in the presence of 3.5–4 % (w/v) sea salts (corresponding to 2.7–3.1 % NaCl), at pH 8 and at temperatures of 26–29 °C. The novel strain required Ca2+ ions in addition to NaCl for growth. The dominant fatty acids were iso-15 : 0, iso-15 : 1ω10c and 10-methyl-16 : 0. The major respiratory quinone was MK-6. The DNA G+C content was 56.3 mol%, an unusually high value for members of the family Flavobacteriaceae. On the basis of these polyphasic taxonomic data, strain DOKDO 007T should be classified as representing a new genus and novel species in the family Flavobacteriaceae, for which the name Flagellimonas eckloniae gen. nov., sp. nov. is proposed. The type strain is DOKDO 007T (=KCCM 42307T=JCM 13831T).

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

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2397-2402 ◽  
Author(s):  
Zenghu Zhang ◽  
Xin Gao ◽  
Long Wang ◽  
Xiao-Hua Zhang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Ocean Drilling Program ◽  
Respiratory Quinone ◽  
Integrated Ocean Drilling Program ◽  
South Pacific Gyre

A Gram-stain-negative, strictly aerobic, non-flagellated, non-gliding, oxidase- and catalase-positive, white-pigmented and rod-shaped bacterium, designated strain XH122T, was isolated from a surface seawater sample collected from the South Pacific Gyre (45° 58′ E 163° 11′ S) during Integrated Ocean Drilling Program Expedition 329.Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XH122T belonged to the genus Leucothrix and showed highest 16S rRNA gene sequence similarity to Leucothrix mucor DSM 2157T (94.3 %). It showed lower sequence similarities ( < 90.7 %) with all other representatives of the class Gammaproteobacteria. Optimal growth occurred in the presence of 2 % (w/v) NaCl, at pH 8.0 and at 28 °C. The DNA G+C content of strain XH122T was 46.2 mol%. The major fatty acids were C16 : 0, C16 : 1ω9c and C18 : 1ω9c. The major respiratory quinone was ubiquinone-8 (Q-8). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. On the basis of data from this polyphasic study, strain XH122T is considered to represent a novel species of the genus Leucothrix, for which the name Leucothrix pacifica sp. nov. is proposed. The type strain is XH122T ( = DSM 25984T = JCM 18388T).

Parasphingopyxis lamellibrachiae gen. nov., sp. nov., isolated from a marine annelid worm

2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2224-2228 ◽  
Author(s):  
Hiromi Uchida ◽  
Koei Hamana ◽  
Masayuki Miyazaki ◽  
Takao Yoshida ◽  
Yuichi Nogi
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Properties ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Family

A Gram-stain-negative, aerobic, motile, orange-pigmented, slightly halophilic, rod-shaped bacterium, designated strain JAMH 0132T, was isolated from the trophosome of a tubeworm in Kagoshima Bay, Japan, and its taxonomic position was investigated using a polyphasic approach. The novel strain grew optimally at 28–30 °C and with about 2.0 % (w/v) NaCl. Chemotaxonomic analysis showed that Q-10 was the predominant respiratory quinone and that C18 : 1ω7c, C16 : 0 2-OH and C16 : 0 were the major fatty acids. Sphingoglycolipid, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine were the major polar lipids. The genomic DNA G+C content was 60.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JAMH 0132T belonged to the family Sphingomonadaceae , within the class Alphaproteobacteria . The novel strain appeared most closely related to Sphingopyxis baekryungensis SW-150T (95.1 % 16S rRNA gene sequence similarity) and showed less sequence similarity with representatives of the genera Blastomonas , Sphingomonas , Sphingosinicella and Novosphingobium (<94.8 %). In having no detectable polyamine, strain JAMH 0132T differed from members of all genera currently in the family Sphingomonadaceae . On the basis of its phenotypic properties and phylogenetic distinctiveness, strain JAMH 0132T represents a novel species of a new genus in the family Sphingomonadaceae for which the name Parasphingopyxis lamellibrachiae gen. nov., sp. nov. is proposed. The type strain of Parasphingopyxis lamellibrachiae gen. nov., sp. nov. is JAMH 0132T ( = JCM 15549T  = NCIMB 14486T).

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.

scholarly journals Kordiimonas gwangyangensis gen. nov., sp. nov., a marine bacterium isolated from marine sediments that forms a distinct phyletic lineage (Kordiimonadales ord. nov.) in the ‘Alphaproteobacteria’

2005 ◽  
Vol 55 (5) ◽  
pp. 2033-2037 ◽  
Author(s):  
Kae Kyoung Kwon ◽  
Hee-Soon Lee ◽  
Sung Hyun Yang ◽  
Sang-Jin Kim
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Bacterium ◽  
Enrichment Culture ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Carbon Sources ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Respiratory Quinone

A marine bacterium, designated strain GW14-5T, capable of degrading high-molecular-mass polycyclic aromatic hydrocarbons was isolated from the sediments of Gwangyang Bay, Republic of Korea, after enrichment culture for 2 years with a mixture of benzo[a]pyrene and pyrene. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate forms a phyletic lineage that is distinct from the seven known orders within the ‘Alphaproteobacteria’. 16S rRNA gene sequence similarity of strain GW14-5T to all recognized bacterial species was not greater than 92 %. The dominant fatty acids of the isolate were i-17 : 1 (46·2 %), i-15 : 0 (15·1 %) and i-17 : 0 (12·6 %). The major respiratory quinone was MK-5, and the DNA G+C content was 39·3 mol%. Cells of strain GW14-5T were Gram-negative, motile, catalase-positive, oxidase-positive and weakly halophilic. Glucose, N-acetylglucosamine and maltose were utilized as sole carbon sources. The strain was positive for β-glucosidase activity. Optimal growth of strain GW14-5T was at pH 7·0 and 37–40 °C and required the presence of 2 % (w/v) NaCl. On the basis of this evidence, strain GW14-5T represents a novel genus and species in the ‘Alphaproteobacteria’ for which the name Kordiimonas gwangyangensis gen. nov., sp. nov. is proposed. The novel order Kordiimonadales is proposed for the distinct phyletic line represented by the genus Kordiimonas. The type strain is GW14-5T (=KCCM 42021T=JCM 12864T).

Pontibacter rubellus sp. nov., and Pontibacter situs sp. nov. bacteria isolated from soil

2021 ◽  
Author(s):  
Soohyun Maeng ◽  
Yuna Park ◽  
Tuvshinzaya Damdintogtokh ◽  
Hyejin Oh ◽  
Minji Bang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Bacterial Species ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Major Polar Lipid ◽  
Respiratory Quinone ◽  
Distinct Lineage

Abstract Gram-stain-negative, aerobic, non-flagellated strains 172403-2T and BT310T were isolated from the soil collected in Pyeongchang city and Uijeongbu city, Korea. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strains 172403-2T and BT310T formed a distinct lineage within the family Hymenobacteraceae (order Chitinophagales, class Chitinophagia) and were most closely related to members of the genus Pontibacter, Pontibacter chitinilyticus 17gy-14T (95.7%), and Pontibacter populi HLY7-15T (97.1% 16S rRNA gene sequence similarity) respectively. The optimal growth of strains 172403-2T and BT310T occurred at pH 7.0, in the absence of NaCl, and 25°C and 30°C, respectively. The predominant cellular fatty acids were iso-C15:0 and summed feature 4 (iso-C17:1 I / anteiso-C17:1 B). The major respiratory quinone of the two strains was MK-7. The major polar lipid of the two strains was phosphatidylethanolamine. Biochemical, chemotaxonomic and phylogenetic analyses indicated that strains 172403-2T and BT310T represent novel bacterial species within the genus Pontibacter, for which the names Pontibacter rubellus and Pontibacter situs are proposed. The type strains of Pontibacter rubellus and Pontibacter situs are 172403-2T and BT310T, respectively.

scholarly journals Oceanisphaera sediminis sp. nov., isolated from marine sediment

2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1552-1557 ◽  
Author(s):  
Na-Ri Shin ◽  
Tae Woong Whon ◽  
Seong Woon Roh ◽  
Min-Soo Kim ◽  
Young-Ok Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Sediment ◽  
Dna Hybridization ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type

Two strains, designated TW92T and TW93, were isolated from marine sediment collected from the south coast of Korea. Cells of both strains were Gram-staining-negative, coccus-shaped, aerobic, motile and catalase- and oxidase-positive. Strain TW92T grew optimally in the presence of 2 % (w/v) NaCl (range 1–5 %) while strain TW93 grew optimally in the presence of 1 % (w/v) NaCl (range 0–12 %), and both strains had an optimal growth temperature of 30 °C (range 4–37 °C). Strains TW92T and TW93 had the same optimum pH (pH 7), but differed in their ability to grow at pH 10. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strains TW92T and TW93 were most closely related to Oceanisphaera donghaensis BL1T, with 98.8 % and 98.7 % similarity, respectively. Pairwise similarity between the 16S rRNA gene sequences of strains TW92T and TW93 was 99.9 %. The major fatty acids of both strains were summed features 3 (comprising C16 : 1ω7c/iso-C15 2-OH), C16 : 0 and C18 : 1ω7c. Both strains possessed the ubiquinone Q-8 as the predominant respiratory quinone and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol as the polar lipids. The genomic DNA G+C contents of strains TW92T and TW93 were 58.5 and 59.6 mol%, respectively. Genomic relatedness values based on DNA–DNA hybridization of strains TW92T and TW93 with related species were below 47 % and 31 %, respectively. DNA–DNA hybridization values between strains TW92T and TW93 were above 85 %. On the basis of a taxonomic study using polyphasic analysis, it is proposed that the two isolates represent a novel species, Oceanisphaera sediminis sp. nov., with strain TW92T ( = KACC 15117T = JCM 17329T) as the type strain and strain TW93 ( = KACC 15118 = JCM 17330) as an additional strain.

scholarly journals Roseovarius nanhaiticus sp. nov., a member of the Roseobacter clade isolated from marine sediment

2010 ◽  
Vol 60 (6) ◽  
pp. 1289-1295 ◽  
Author(s):  
Baojiang Wang ◽  
Fengqin Sun ◽  
Qiliang Lai ◽  
Yaping Du ◽  
Xiupian Liu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Sandy Sediment ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Gram Staining

An aerobic, Gram-staining-negative, rod or ovoid-shaped bacterial isolate, strain NH52JT, was isolated from a sandy sediment sample from the South China Sea. Strain NH52JT exhibited tumbling motility, formed beige or faint pink colonies, gave a positive reaction in tests for catalase and oxidase and required NaCl for growth. Optimal growth was observed at pH 7.8–9.3, at 30 °C and in the presence of 2.0–4.0 % (w/v) NaCl. The novel strain did not synthesize bacteriochlorophyll a, and the DNA G+C content was 62 %. The major fatty acids were C18 : 1 ω7c, C16 : 0 and C18 : 1 ω7c 11-methyl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NH52JT was affiliated to the genus Roseovarius of the class Alphaproteobacteria. Roseovarius pacificus and Roseovarius aestuarii were the most closely related recognized species to strain NH52JT with 16S rRNA gene sequence similarity values of 95.0 and 95.7 %, respectively. Sequence similarity values between strain NH52JT and other phylogenetically related species were all below 95.0 %. Based on the phenotypic, chemotaxonomic and phylogenetic data presented, strain NH52JT is considered to represent a novel species of the genus Roseovarius, for which the name Roseovarius nanhaiticus sp. nov. is proposed. The type strain is NH52JT (=LMG 24840T=CCTCC AB 208317T=MCCC 1A03543T).

scholarly journals Characterization of the Aerobic Anoxygenic Phototrophic Bacterium Sphingomonas sp. AAP5

2021 ◽  
Vol 9 (4) ◽  
pp. 768
Author(s):  
Karel Kopejtka ◽  
Yonghui Zeng ◽  
David Kaftan ◽  
Vadim Selyanin ◽  
Zdenko Gardian ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Orthologous Gene ◽  
Gene Clusters ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Close Phylogenetic Relationship

An aerobic, yellow-pigmented, bacteriochlorophyll a-producing strain, designated AAP5 (=DSM 111157=CCUG 74776), was isolated from the alpine lake Gossenköllesee located in the Tyrolean Alps, Austria. Here, we report its description and polyphasic characterization. Phylogenetic analysis of the 16S rRNA gene showed that strain AAP5 belongs to the bacterial genus Sphingomonas and has the highest pairwise 16S rRNA gene sequence similarity with Sphingomonas glacialis (98.3%), Sphingomonas psychrolutea (96.8%), and Sphingomonas melonis (96.5%). Its genomic DNA G + C content is 65.9%. Further, in silico DNA-DNA hybridization and calculation of the average nucleotide identity speaks for the close phylogenetic relationship of AAP5 and Sphingomonas glacialis. The high percentage (76.2%) of shared orthologous gene clusters between strain AAP5 and Sphingomonas paucimobilis NCTC 11030T, the type species of the genus, supports the classification of the two strains into the same genus. Strain AAP5 was found to contain C18:1ω7c (64.6%) as a predominant fatty acid (>10%) and the polar lipid profile contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, six unidentified glycolipids, one unidentified phospholipid, and two unidentified lipids. The main respiratory quinone was ubiquinone-10. Strain AAP5 is a facultative photoheterotroph containing type-2 photosynthetic reaction centers and, in addition, contains a xathorhodopsin gene. No CO2-fixation pathways were found.

scholarly journals Marinobacter gudaonensis sp. nov., isolated from an oil-polluted saline soil in a Chinese oilfield

2007 ◽  
Vol 57 (2) ◽  
pp. 250-254 ◽  
Author(s):  
Jun Gu ◽  
Hua Cai ◽  
Su-Lin Yu ◽  
Ri Qu ◽  
Bin Yin ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Saline Soil ◽  
Sequence Similarity ◽  
Eastern China ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Shengli Oilfield ◽  
Major Respiratory Quinone ◽  
Reference Strains

Two novel strains, SL014B61AT and SL014B11A, were isolated from an oil-polluted saline soil from Gudao in the coastal Shengli Oilfield, eastern China. Cells of strains SL014B61AT and SL014B11A were motile, Gram-negative and rod-shaped. Growth occurred at NaCl concentrations of between 0 and 15 % and at temperatures of between 10 and 45 °C. Strain SL014B61AT had Q9 as the major respiratory quinone and C16 : 0 (21.2 %), C18 : 1ω9c (20.3 %), C16 : 1ω7c (7.3 %) and C16 : 1ω9c (6.4 %) as predominant fatty acids. The G+C content of the DNA was 57.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SL014B61AT belonged to the genus Marinobacter in the class Gammaproteobacteria. Strain SL014B61AT showed the highest 16S rRNA gene sequence similarity with Marinobacter bryozoorum (97.9 %) and showed 97.8 % sequence similarity to Marinobacter lipolyticus. DNA–DNA relatedness to the reference strains Marinobacter bryozoorum and Marinobacter lipolyticus was 35.5 % and 33.8 %, respectively. On the basis of these data, it is proposed that strains SL014B61AT and SL014B11A represent a novel species, Marinobacter gudaonensis sp. nov. The type strain is strain SL014B61AT (=DSM 18066T=LMG 23509T=CGMCC 1.6294T).

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