scholarly journals Sphingobium scionense sp. nov., an aromatic hydrocarbon-degrading bacterium isolated from contaminated sawmill soil

2010 ◽  
Vol 60 (2) ◽  
pp. 413-416 ◽  
Author(s):  
Quanfeng Liang ◽  
Gareth Lloyd-Jones
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Aromatic Hydrocarbon ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Degrading Bacterium

This study characterized strain WP01T, a Gram-staining-negative, rod-shaped, aerobic bacterium isolated from a polycyclic aromatic hydrocarbon-contaminated soil in New Zealand. Strain WP01T shared many characteristics of the genus Sphingobium: the predominant respiratory quinone (89 %) was ubiquinone with ten isoprene units (Q-10); the major fatty acids were C18 : 1 ω7c, C16 : 1 ω7c, C16 : 0 and C14 : 0 2-OH; spermidine was the major polyamine; the DNA G+C content was 63.8 mol%; and the Sphingobium-specific 16S rRNA signatures were conserved. A point of difference from other species of the genus Sphingobium was that strain WP01T reduced nitrate to nitrite. The polar lipid pattern consisted of the predominant compounds diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipids. 16S rRNA gene sequence analysis showed that, amongst the recognized species of the genus Sphingobium, strain WP01T was most similar to Sphingobium yanoikuyae GIFU 9882T and Sphingobium amiense YTT (>97 % 16S rRNA gene sequence similarities). The low DNA–DNA relatedness values between strain WP01T and S. yanoikuyae GIFU 9882T (46.6 %) and S. amiense DSM 16289T (25.6 %) indicated no relatedness at the species level. On the basis of these characteristics, it is concluded that strain WP01T should be considered as representing a novel species within the genus Sphingobium, for which the name Sphingobium scionense sp. nov. is proposed. The type strain is WP01T (=DSM 19371T=ICMP 13533T).

scholarly journals Diaphorobacter polyhydroxybutyrativorans sp. nov., a novel poly(3-hydroxybutyrate-co-3-hydroxyvalerate)-degrading bacterium isolated from biofilms

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 2913-2918 ◽  
Author(s):  
Tianlei Qiu ◽  
Zhengyan Zuo ◽  
Junlian Gao ◽  
Min Gao ◽  
Meilin Han ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Degrading Bacterium

A novel Gram-stain-negative, facultatively aerobic and rod-shaped strain, designated SL-205T, was isolated from the biofilms of a denitrifying reactor using poly(3-hydoxybutyrate-co-3-hydroxyvalerate) as the sole carbon source in Beijing, PR China. A polyphasic taxonomic characterization was performed on the novel isolate. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that strain SL-205T is a member of the genus Diaphorobacter. High levels of 16S rRNA gene sequence similarity were found between strain SL-205T and Diaphorobacter nitroreducens NA10BT (99.4 %) and Diaphorobacter oryzae RF3T (98.5 %), respectively. However, the DNA–DNA relatedness values between strain SL-205T and D. nitroreducens NA10BT and D. oryzae RF3T were 57 ± 1 % and 45 ± 1.5 %, respectively. The G+C content of the genomic DNA of strain SL-205T was 66.8 mol%. The major fatty acids consisted of summed feature 3 (including C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C18 : 1ω7c. Ubiquinone Q-8 was the only respiratory quinone; the polar lipid profile comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and one uncharacterized phospholipid. We conclude that strain SL-205T represents a novel species of the genus Diaphorobacter for which the name Diaphorobacter polyhydroxybutyrativorans is proposed; the type strain is SL-205T ( = ACCC 19739T = DSM 29460T).

scholarly journals Paracoccus angustae sp. nov., isolated from soil

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3469-3475 ◽  
Author(s):  
Xuelian Sun ◽  
Patrick Luo ◽  
Mingshun Li
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Carbon Sources ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Gene Similarity

A Gram-stain-negative, coccus-shaped, aerobic bacterium, strain E6T, was isolated from soil. 16S rRNA gene sequence analysis revealed a cluster containing strain E6T and Paracoccus sediminis CMB17T (the highest 16S rRNA gene similarity of 97.2 %). The other strains investigated showed 16S rRNA gene sequence similarities of less than 97 % to strain E6T. The DNA–DNA relatedness between strain E6T and P. sediminis DSM 26170T was 59.2 %. Strain E6T also shows some differences compared with other Paracoccus strains such as motility and inability to utilize lactate and propionate as sole carbon sources. The major fatty acids of strain E6T were C18 : 1ω7c and C18 : 0 and ubiquinone-10 was the only respiratory quinone. Strain E6T had diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, an unknown aminolipid and an unknown glycolipid as major polar lipids. The genomic DNA G+C content was 68.1 mol%. On the basis of phenotypic and genotypic characteristics, strain E6T is concluded to represent a novel species of the genus Paracoccus, for which the name Paracoccus angustae sp. nov. is proposed. The type strain is E6T ( = KCTC 42473T = CCTCC AB 2015056T).

scholarly journals Effusibacillus dendaii sp. nov. isolated from farm soil

2021 ◽  
Author(s):  
Tomoyuki Konishi ◽  
Tomohiko Tamura ◽  
Toru Tobita ◽  
Saori Sakai ◽  
Namio Matsuda ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Genome Analyses

Abstract Gram-positive, rod-shaped, spore-forming, thermophilic, acidophilic bacterium, designated strain skT53T, was isolated from farm soil in Tokyo, Japan. The strain grew aerobically at 37–55°C (optimum 50°C) and pH 4.0–6.0 (optimum 5.0). Phylogenetic analysis of the 16S rRNA gene sequence showed that the isolate was most closely related to the type strain of Effusibacillus consociatus (94.3% similarity). The G + C content of the genomic DNA was 48.22 mol%. MK-7 was the predominant respiratory quinone. The major fatty acids were anteiso-C15:0, iso-C15:0, iso-C16:0 and C18:3ω6c. The results of phenotypic and chemotaxonomic, 16S rRNA gene sequence similarity, and whole genome analyses support strain skT53T as representing a novel species of Effusibacillus dendaii sp. nov. is proposed. The type strain is strain skT53T (= NBRC 114101T = TBRC 11241T).

scholarly journals Lysobacter ruishenii sp. nov., a chlorothalonil-degrading bacterium isolated from a long-term chlorothalonil-contaminated soil

2011 ◽  
Vol 61 (3) ◽  
pp. 674-679 ◽  
Author(s):  
Guang-Li Wang ◽  
Li Wang ◽  
Hong-Hong Chen ◽  
Bin Shen ◽  
Shun-Peng Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Contaminated Soil ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Degrading Bacterium

An aerobic, Gram-negative bacterial strain, designated CTN-1T, capable of degrading chlorothalonil was isolated from a long-term chlorothalonil-contaminated soil in China, and was subjected to a polyphasic taxonomic investigation. Strain CTN-1T grew at 15–37 °C (optimum 28–30 °C) and at pH 6.0–9.0 (optimum pH 7.0–7.5). The G+C content of the total DNA was 67.1 mol%. Based on 16S rRNA gene sequence analysis, strain CTN-1T was related most closely to Lysobacter daejeonensis DSM 17634T (97.1 % similarity), L. soli DCY21T (95.7 %), L. concretionis Ko07T (95.5 %), L. gummosus LMG 8763T (95.3 %) and L. niastensis DSM 18481T (95.2 %). The novel strain showed less than 95.0 % 16S rRNA gene sequence similarity to the type strains of other Lysobacter species. The major cellular fatty acids of strain CNT-1T were iso-C16 : 0 (23.0 %), iso-C15 : 0 (21.4 %) and iso-C17 : 1 ω9c (15.3 %). The major isoprenoid quinone was Q-8 (99 %), and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. These chemotaxonomic data supported the affiliation of strain CTN-1T to the genus Lysobacter. Levels of DNA–DNA relatedness between strain CTN-1T and L. daejeonensis DSM 17634T were 34.6–36.1 %. Phylogenetic analysis based on 16S rRNA gene sequences, DNA–DNA hybridization data and biochemical and physiological characteristics strongly supported the genotypic and phenotypic differentiation of strain CTN-1T from recognized species of the genus Lysobacter. Strain CTN-1T is therefore considered to represent a novel species of the genus Lysobacter, for which the name Lysobacter ruishenii sp. nov. is proposed. The type strain is CTN-1T (=DSM 22393T =CGMCC 1.10136T).

scholarly journals Sediminicola luteus gen. nov., sp. nov., a novel member of the family Flavobacteriaceae

2006 ◽  
Vol 56 (4) ◽  
pp. 841-845 ◽  
Author(s):  
Shams Tabrez Khan ◽  
Yasuyoshi Nakagawa ◽  
Shigeaki Harayama
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Golden Yellow ◽  
The Family

The taxonomic position of four Gram-negative, rod-shaped, golden-yellow-coloured bacteria isolated from marine sediments was determined. Analysis of the almost complete 16S rRNA gene sequences indicated that these isolates belong to the family Flavobacteriaceae. An unclassified bacterium, NBRC 15975, was found to be the closest relative, showing 16S rRNA gene sequence similarity of 93 %; other related genera shared only 87·9–90·5 % similarity. In contrast, the four isolates shared high levels of 16S rRNA gene sequence similarity (99·3–99·7 %) and high DNA–DNA reassociation values (93–104 %). The isolates could be differentiated phenotypically from other genera by the abilities to reduce nitrate and to degrade gelatin, casein and starch. The only respiratory quinone was MK-6, and the major fatty acids were iso-C15 : 0, iso-C15 : 1, anteiso-C15 : 0, iso-C17 : 1 ω9c and iso-C17 : 0 3-OH. The DNA G+C content was 38–40 mol%. Differentiating phenotypic characteristics and large phylogenetic distances between the isolates and previously published genera indicated that the isolates constitute a novel genus, for which the name Sediminicola gen. nov. is proposed. The type species is Sediminicola luteus sp. nov. (type strain CNI-3T=NBRC 100966T=LMG 23246T).

scholarly journals Sandarakinorhabdus limnophila gen. nov., sp. nov., a novel bacteriochlorophyll a-containing, obligately aerobic bacterium isolated from freshwater lakes

2006 ◽  
Vol 56 (4) ◽  
pp. 847-854 ◽  
Author(s):  
Frederic Gich ◽  
Jörg Overmann
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Hexadecenoic Acid ◽  
Aerobic Bacterium ◽  
Freshwater Lakes ◽  
Rrna Gene Sequence ◽  
Light Harvesting Complexes

Three strains (so36, so42T and wo26) representing a novel Gram-negative, obligately aerobic, bacteriochlorophyll a-containing species of the α-4 subgroup of the Proteobacteria were isolated from freshwater lakes using a high-throughput cultivation technique. The non-motile and slender rod-shaped cells formed orange–red-pigmented colonies. The main carotenoids were nostoxanthin and keto-nostoxanthin. According to the absorption spectrum, two different photosynthetic light-harvesting complexes, an LHI complex and a B800-830-type peripheral LHII complex, were present in the cells. The predominant fatty acids of strain so42T were hexadecenoic acid (16 : 1ω7c) and octadecenoic acid (18 : 1ω7c), whereas 17 : 1ω6c and 14 : 0 iso 2-OH were present in smaller amounts. The main polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, glycolipid and sphingoglycolipids. The major respiratory lipoquinone was ubiquinone-10, whereas ubiquinone-9 was present in smaller amounts. The three strains were cytochrome oxidase-negative and catalase-positive and formed alkaline and acid phosphatases. The strains grew chemoorganoheterotrophically in mineral media supplemented with various organic acids, amino acids or complex substrates such as peptone and yeast extract. The G+C content of the genomic DNA of strain so42T was 64·3 mol%. The three novel isolates contained the same 16S rRNA gene sequence. The 16S rRNA gene sequence similarity to the closest phylogenetic relative Sandaracinobacter sibiricus was only 92·8 %. Accordingly, the three strains represent a new genus and species, for which the name Sandarakinorhabdus limnophila gen. nov., sp. nov., is proposed, with strain so42T (=DSM 17366T=CECT 7086T) as the designated type strain.

scholarly journals Salinisphaera dokdonensis sp. nov., isolated from surface seawater

2010 ◽  
Vol 60 (3) ◽  
pp. 680-685 ◽  
Author(s):  
Gi Duk Bae ◽  
Chung Yeon Hwang ◽  
Hye Min Kim ◽  
Byung Cheol Cho
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Aerobic Bacterium ◽  
Rrna Gene Sequence ◽  
The 16S Rrna Gene

A Gram-negative, strictly aerobic bacterium, designated CL-ES53T, was isolated from surface water of the East Sea in Korea. Cells of strain CL-ES53T were short rods and motile by means of monopolar flagella. Strain CL-ES53T grew with 4–21 % NaCl (optimum 10 %) and at 5–40 °C (optimum 25 °C) and pH 5.2–8.8 (optimum pH 6.3–7.2). The major isoprenoid quinone was Q-8. The major fatty acids were C18 : 1 ω7c (42.0 %), C18 : 1 ω9c (14.8 %) and C14 : 0 (9.4 %). The genomic DNA G+C content was 64.9 mol%. Analysis of the 16S rRNA gene sequence of strain CL-ES53T revealed that it was a member of the genus Salinisphaera and most closely related to Salinisphaera shabanensis E1L3A T (96.9 % sequence similarity) and Salinisphaera hydrothermalis EPR70T (93.8 %). Phylogenetic analyses based on the 16S rRNA gene sequence showed that strain CL-ES53T formed a robust cluster with S. shabanensis E1L3A T. Although the 16S rRNA gene sequence similarity between strain CL-ES53T and S. shabanensis E1L3A T was rather high (96.9 %), DNA–DNA relatedness between these strains was 12 %, suggesting that they represent genomically distinct species. Strain CL-ES53T was differentiated from S. shabanensis E1L3A T and S. hydrothermalis EPR70T on the basis of optimum temperature for growth and certain phenotypic characteristics. The phylogenetic analysis and physiological and chemotaxonomic data show that strain CL-ES53T should be classified in the genus Salinisphaera within a novel species, for which the name Salinisphaera dokdonensis sp. nov. is proposed. The type strain is CL-ES53T (=KCCM 90064T =DSM 19549T).

scholarly journals Gracilibacillus ureilyticus sp. nov., a halotolerant bacterium from a saline–alkaline soil

2010 ◽  
Vol 60 (6) ◽  
pp. 1383-1386 ◽  
Author(s):  
Ying-Yi Huo ◽  
Xue-Wei Xu ◽  
Heng-Lin Cui ◽  
Min Wu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Alkaline Soil ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone

A Gram-stain-positive, halotolerant, neutrophilic, rod-shaped bacterium, strain MF38T, was isolated from a saline–alkaline soil in China and subjected to a polyphasic taxonomic characterization. The isolate grew in the presence of 0–15 % (w/v) NaCl and at pH 6.5–8.5; optimum growth was observed with 3.0 % (w/v) NaCl and at pH 7.0. Chemotaxonomic analysis showed menaquinone MK-7 as the predominant respiratory quinone and anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0, C17 : 0 and C16 : 0 as major fatty acids. The genomic DNA G+C content was 35.3 mol%. 16S rRNA gene sequence similarities of strain MF38T with type strains of described Gracilibacillus species ranged from 95.3 to 97.7 %. Strain MF38T exhibited the closest phylogenetic affinity to the type strain of Gracilibacillus dipsosauri, with 97.7 % 16S rRNA gene sequence similarity. The DNA–DNA reassociation between strain MF38T and G. dipsosauri DSM 11125T was 45 %. On the basis of phenotypic and genotypic data, strain MF38T represents a novel species of the genus Gracilibacillus, for which the name Gracilibacillus ureilyticus sp. nov. (type strain MF38T =CGMCC 1.7727T =JCM 15711T) is proposed.

scholarly journals Paenibacillus humicus sp. nov., isolated from poultry litter compost

2007 ◽  
Vol 57 (10) ◽  
pp. 2267-2271 ◽  
Author(s):  
Ivone Vaz-Moreira ◽  
Cátia Faria ◽  
M. Fernanda Nobre ◽  
Peter Schumann ◽  
Olga C. Nunes ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Poultry Litter ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Respiratory Quinone

Two bacterial strains, PC-142 and PC-147T, isolated from poultry litter compost, were characterized with respect to their phenetic and phylogenetic characteristics. The isolates were endospore-forming rods that were reddish in colour after Gram staining. They were catalase- and oxidase-positive, were able to degrade starch and gelatin and grew at 15–40 °C and pH 5.5–10.0. The predominant fatty acids were anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0, the major respiratory quinone was menaquinone MK-7, the cell-wall peptidoglycan was of the A1γ type and the G+C content of the DNA was 58 mol%. The 16S rRNA gene sequence analysis and phenetic characterization indicated that these organisms belong to the genus Paenibacillus, with Paenibacillus pasadenensis SAFN-007T as the closest phylogenetic neighbour (97.5 %). Strains PC-142, PC-147T and P. pasadenensis SAFN-007T represent a novel lineage within the genus Paenibacillus, characterized by a high DNA G+C content (58–63 mol%). The low levels of 16S rRNA gene sequence similarity with respect to other taxa with validly published names and the identification of distinctive phenetic features in the two isolates indicate that strains PC-142 and PC-147T represent a novel species of the genus Paenibacillus, for which the name Paenibacillus humicus sp. nov. is proposed. The type strain is PC-147T (=DSM 18784T =NBRC 102415T =LMG 23886T).

scholarly journals Gulbenkiania mobilis gen. nov., sp. nov., isolated from treated municipal wastewater

2007 ◽  
Vol 57 (5) ◽  
pp. 1108-1112 ◽  
Author(s):  
Ivone Vaz-Moreira ◽  
M. Fernanda Nobre ◽  
Olga C. Nunes ◽  
Célia M. Manaia
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Municipal Wastewater ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Treated Municipal Wastewater

A bacterial strain (E4FC31T) isolated from treated municipal wastewater was characterized phenotypically and phylogenetically. Cells were Gram-negative, curved rods with a polar flagellum. The isolate was catalase-, oxidase- and arginine dihydrolase-positive, and able to grow between 15 and 45 °C and between pH 5.5 and 9.0. The predominant fatty acids were C16 : 1/iso-C15 : 0 2-OH and C16 : 0, the major respiratory quinone was ubiquinone 8 and the G+C content of the genomic DNA was 63 mol%. 16S rRNA gene sequence analysis indicated that strain E4FC31T belonged to the class Betaproteobacteria and was a member of the family Neisseriaceae. Its closest phylogenetic neighbours were Aquitalea magnusonii and Chromobacterium violaceum (<94 % 16S rRNA gene sequence similarity). Phylogenetic analysis and phenotypic characteristics of strain E4FC31T suggest that it represents a novel species of a new genus, for which the name Gulbenkiania mobilis gen. nov., sp. nov. is proposed. The type strain of Gulbenkiania mobilis is E4FC31T (=DSM 18507T=LMG 23770T).

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