scholarly journals Sphingopyxis contaminans sp. nov., isolated from a contaminated Petri dish

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2238-2243 ◽  
Author(s):  
Y. Subhash ◽  
Ch. Sasikala ◽  
Ch. V. Ramana

Strain JC216T was isolated from a contaminated Petri dish. Colonies were of pale yellow colour and cells were Gram-stain-negative, oxidase-positive and catalase-positive. Chitin, starch and gelatin were not hydrolysed. Strain JC216T contained C18 : 1ω7c/C18 : 1ω6c, C16 : 1ω7c/C16 : 1ω6c, C14 : 0 2-OH and C16 : 0 as the major (≥8 %) fatty acids with minor amounts of C12 : 0, C15 : 0 2-OH, C16 : 0 2-OH, C16  : 1 2-OH, C17 : 1ω6c, C17 : 1ω8c and C17 : 1ω9c. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and sphingoglycolipid were the major polar lipids. Minor amounts of unidentified amino lipids and unidentified lipids were also detected. The major hopanoids identified were bacterial hopane derivatives and diplopterol. Minor amounts of diploptene and an unidentified hopanoid were also present. Spermidine was the major polyamine with minor amounts of sym-homospermidine and putrescine. N-Acetylglucosamine and fructose were identified as major cell-wall sugars along with minor amounts of mannose and galactose. The genomic DNA G+C content was 55 mol%. Comparisons of the16S rRNA gene sequence indicated that strain JC216T represents a member of the genus Sphingopyxis in the family Sphingomonadaceae within the class Alphaproteobacteria . Strain JC216T had a sequence similarity of 97.28 % with Sphingopyxis wooponensis 03SU3-PT and <96.71 % with other members of the family Sphingomonadaceae . Furthermore, strain JC216T had 33±1 % relatedness (based on DNA–DNA hybridization) with S. wooponensis KCTC 23340T ( = 03SU3-PT). Distinct morphological, physiological and genotypic differences from the previously described taxa support the classification of strain JC216T as a representative of a novel species in the genus Sphingopyxis , for which the name Sphingopyxis contaminans sp. nov. is proposed. The type strain is JC216T ( = KCTC 32445T = LMG 27671T).

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 663-667 ◽  
Author(s):  
Jangho Lee ◽  
Banghyo Park ◽  
Sung-Geun Woo ◽  
Juyoun Lee ◽  
Joonhong Park

A Gram-stain-negative, fusiform-shaped, facultatively anaerobic bacterial strain, designated EBTL04T, was isolated from activated sludge using algal metabolites and taxonomically characterized through polyphasic investigation. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain EBTL04T belongs to the family Verrucomicrobiaceae , class Verrucomicrobiae , and is closely related to Prosthecobacter dejongeii DSM 12251T (98.6 % sequence similarity), Prosthecobacter fusiformis ATCC 25309T (97.9 %), Prosthecobacter debontii DSM 14044T (97.5 %), Prosthecobacter vanneervenii DSM 12252T (94.7 %) and Prosthecobacter fluviatilis KCTC 22182T (93.7 %). The G+C content of the genomic DNA of strain EBTL04T was 62.7 mol%. The menaquinone MK-6 was detected as the predominant quinone. Strain EBTL04T contained phosphatidylethanolamine, phosphatidylglycerol and phosphatidylserine as major polar lipids. A fatty acid profile with C16 : 1ω5c, iso-C14 : 0, C16 : 0, anteiso-C15 : 0 and C14 : 0 as the major components supported the classification of strain EBTL04T in the genus Prosthecobacter . Based on several phenotypic, genotypic and chemotaxonomic features, strain EBTL04T was clearly differentiated from its phylogenetic neighbours. Therefore, strain EBTL04T should be considered to represent a novel species of the genus Prosthecobacter , for which the name Prosthecobacter algae sp. nov. is proposed. The type strain is EBTL04T ( = KCTC 23681T = JCM 18053T).


2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 984-988 ◽  
Author(s):  
Y. Subhash ◽  
Ch. Sasikala ◽  
Ch. V. Ramana

Strain JC207T was isolated from a deep (265 m) sea sediment, and appeared as dark yellow colonies on agar plates with cells staining Gram-negative. Catalase, oxidase and caseinase were positive, while chitinase, gelatinase and amylase were negative. Major (>5 %) fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 1ω9c, iso-C16 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH, iso-C14 : 0 and iso-C15 : 1G. Strain JC207T contained phosphatidylethanolamine as the major polar lipid, with minor amounts of five unidentified lipids. A bacterial hopane derivative, diplopterol and adenosylhopane were the major hopanoids. Genomic DNA G+C content was 47.5 mol%. 16S rRNA gene sequence comparisons indicated that strain JC207T represented a member of the genus Salinimicrobium within the family Flavobacteriaceae of the phylum Bacteroidetes . Strain JC207T had sequence similarity with Salinimicrobium terrae YIM-C338T (98 %), Salinimicrobium xinjiangense BH206T (97.6 %) and other members of the genus Salinimicrobium (<96.8 %). However, strain JC207T showed an average of 23.6±4 and 37±4 relatedness (based on DNA–DNA hybridization) with Salinimicrobium terrae CGMCC 1.6308T ( = YIM-C338T) and Salinimicrobium xinjiangense KCTC 12883T ( = BH206T), respectively. Morphological, physiological and genotypic differences from the previously described taxa support the classification of strain JC207T as a representative of a novel species in the genus Salinimicrobium , for which the name Salinimicrobium sediminis sp. nov. is proposed. The type strain is JC207T ( = KCTC 32444T = CGMCC 1.12641T).


2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2132-2137 ◽  
Author(s):  
Y. Subhash ◽  
L. Tushar ◽  
Ch. Sasikala ◽  
Ch. V. Ramana

Two bacterial strains (JA744T and JA745) were isolated from dry soil samples collected from solar salterns at Humma, Odisha, India. Both strains were Gram-stain-negative, catalase- and oxidase-positive, motile rods. Major fatty acids in both strains included C18 : 1ω7c, C18 : 0 and C16 : 0, while minor amounts of C10 : 0 3-OH, C12 : 0, C12 : 0 3-OH, C14 : 0 and C16 : 0 were also present. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, an unidentified glycolipid, five unidentified lipids, an unidentified aminolipid and an unidentified phospholipid made up the polar lipids of both strains. Both strains had bacteriohopane derivatives (BHD1,2) and diploptene as major hopanoids. Mean genomic DNA G+C content was 75±1 mol% and the two strains were closely related (mean DNA–DNA hybridization >90 %). Phylogenetic analysis based on the 16S rRNA gene sequence showed that the two strains clustered with species of the genus Rhodobacter belonging to the family Rhodobacteraceae of the class Alphaproteobacteria . The highest sequence similarity was observed with Rhodobacter sphaeroides ATH2.4.1T (96 %) and other members of the genera Rhodobacter and Pseudorhodobacter (<96 %). However, the two strains were positioned distinctly outside the group formed by the other genera of the family Rhodobacteraceae . Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of these isolates as representatives of a novel species in a new genus, for which the name Falsirhodobacter halotolerans gen. nov., sp. nov. is proposed. The type strain of Falsirhodobacter halotolerans is JA744T ( = KCTC 32158T  = NBRC 108897T).


Author(s):  
Hye Jeong Kang ◽  
Min-Kyeong Kim ◽  
Su Gwon Roh ◽  
Seung Bum Kim

A Gram-stain-negative, oxidase-positive, catalase-positive, aerobic, orange-pigmented, rod-shaped and non-motile bacterium designated strain MMS17-SY002T was isolated from island soil. The isolate grew at 20–37 °C (optimum, 30 °C), at pH 6.0–9.5 (optimum, pH 7) and in the presence of 0.5–4.0 % (w/v) NaCl (optimum, 2.0 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MMS17-SY002T was mostly related to the genus Muriicola of the family Flavobacteriaceae and had highest sequence similarity of 96.82 % to Muriicola marianensis A6B8T and Muriicola jejuensis EM44T, but formed a distinct phylogenetic line within the genus. Chemotaxonomic analyses showed that menaquinone 6 was the predominant isoprenoid quinone, the major fatty acids were iso-C15 : 1 G and iso-C15 : 0, and the diagnostic polar lipid was phosphatidylethanolamine. The genomic DNA G+C content was 42.4 mol%. Strain MMS17-SY002T could be distinguished from related species by the combination of trypsin, α-chymotrypsin, acid phosphatase, naphthol-AS-BI-phosphohydrolase, α-galactosidase, β-galactosidase and β-glucosidase activities. The orthologous average nucleotide identity between the genomes of strain MMS17-SY002T and M. jejuensis and that between the strain and M. marianensis A6B8T were 73.26 and 73.33%, respectively, thus confirming the separation of the strain from related species at species level. Based on the phenotypic, phylogenetic, chemotaxonomic and genomic characterization, MMS17-SY002T should be recognized as a novel species of the genus Muriicola , for which the name Muriicola soli sp. nov. is proposed. The type strain is MMS17-SY002T (=KCTC 62790T=JCM 32370T).


2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2163-2168 ◽  
Author(s):  
Yong-Taek Jung ◽  
Ji-Hoon Kim ◽  
So-Jung Kang ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon

A Gram-staining-negative, non-flagellated, non-gliding and pleomorphic bacterial strain, designated DPG-25T, was isolated from seawater in a seaweed farm in the South Sea in Korea and its taxonomic position was investigated by using a polyphasic approach. Strain DPG-25T grew optimally at 25 °C, at pH 7.0–7.5 and in the presence of 2 % (w/v) NaCl. Flexirubin-type pigments were not produced. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DPG-25T formed a cluster with the type strains of Actibacter sediminis , Aestuariicola saemankumensis and Lutimonas vermicola . Strain DPG-25T exhibited 16S rRNA gene sequence similarity values of 95.3, 93.1 and 93.6 % to the type strains of Actibacter sediminis , Aestuariicola saemankumensis and L. vermicola , respectively. Strain DPG-25T contained MK-6 as the predominant menaquinone and iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids detected in strain DPG-25T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content was 39.9 mol%. Differential phenotypic properties and the phylogenetic distinctiveness of strain DPG-25T demonstrated that this strain is distinguishable from Actibacter sediminis , Aestuariicola saemankumensis and L. vermicola . On the basis of the data presented here, strain DPG-25T represents a novel species in a novel genus of the family Flavobacteriaceae , for which the name Namhaeicola litoreus gen. nov., sp. nov. is proposed. The type strain of Namhaeicola litoreus is DPG-25T ( = KCTC 23702T  = CCUG 61485T).


Author(s):  
Zhaobin Huang ◽  
Xiaomei Wei ◽  
Qiliang Lai ◽  
Shiyong Chen ◽  
Jianjun Yuan

Two marine bacterial strains, designated S2-4-21T and MT2-5-19, were isolated from two tidal flat sediments of cordgrass Spartina alterniflora and adjacent oyster culture field in Quanzhou bay, China, respectively. Both strains were Gram-staining-negative, rod-shaped, non-flagellated, non-motile, aerobic, had NaCl requirements, and contained carotenoid and flexirubin pigments. The 16S rRNA gene sequence similarity (99.8%), average nucleotide identity value (99.4%) and average amino acid identity (99.3%) between strain S2-4-21T and strain MT2-5-19 strongly supported that they belonged to a single species. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S2-4-21T and strain MT2-5-19 formed a monophyletic branch affiliated to the family Flavobacteriaceae , sharing similarities of 94.6% with Euzebyella marina CY01T and E. saccharophila 7SM30T, and of 94.1 and 92.8% with E. algicola MEBiC 12267T and Pseudozobellia thermophile DSM 19858T, respectively. Phylogenomic analysis based on the whole genome sequences supported that the two strains formed a distinct monophyletic clade within Flavobacteriaceae members, which was phylogenetically different from the clades of Euzebyella and Pseudozobellia . The major respiratory quinone was menaquinone MK-6. The major fatty acids (>10%) consisted of C15 : 0 iso, C16 : 0, summed feature 9 (C17 : 1 iso ω9c/C16 : 0 10-methyl) and C17 : 0 iso 3-OH. The polar lipid profiles of strain S2-4-21T and strain MT2-5-19 are identical, including phosphatidylethanolamine, four unidentified aminolipids, and four unidentified lipids. The genomic size was 4.9–5.0 Mb with genomic DNA G+C content of 41.5 mol%. Based on the above characteristics, strains S2-4-21T and MT2-5-19 represented a novel species of a novel genus in the family Flavobacteriaceae . Thus, Pareuzebyella sediminis gen. nov. sp. nov. is proposed with type strain S2-4-21T (=MCCC 1K03818T=KCTC 72152T), and another strain MT2-5-19 (=KCTC 72539=MCCC 1K03874).


Author(s):  
Soon Dong Lee ◽  
In Seop Kim ◽  
Hanna Choe ◽  
Ji-Sun Kim

A Gram-negative, facultatively anaerobic bacterium, designated SAP-6T, was isolated from sap extracted from Acer pictum in Mt. Halla in Jeju, Republic of Korea and its precise taxonomic status was determined by a polyphasic approach. Cells were non-sporulating, motile, short rods and showed growth at 4–37 °C, pH 6.0–8.0 and 0–4% NaCl. Phylogenomic analysis based on 92 core gene sequences showed that strain SAP-6T belonged to the family Pectobacteriaceae and formed a distinct clade between members of the genera Sodalis and Biostraticola with gene support index of 89. The closest phylogenetic neighbours were Biostraticola tofi DSM 19580T (97.3% 16S rRNA gene sequence similarity) and Sodalis praecaptivus HS1T (96.8%), with the average amino acid identity values of 75.3% and 74.0%, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. The major isoprenoid quinones were Q-7 and Q-8. The predominant fatty acids were C16:0, C17:0 cyclo and summed feature 3. The DNA G+C content was 57.0%. On the basis of data presented here, strain SAP-6T (=KCTC 52622T=DSM 104038T) represents a novel species of a new genus in the family Pectobacteriaceae , for which the name Acerihabitans arboris gen. nov., sp. nov. is proposed.


Author(s):  
Renju Liu ◽  
Qiliang Lai ◽  
Li Gu ◽  
Peisheng Yan ◽  
Zongze Shao

A novel Gram-stain-negative, aerobic, gliding, rod-shaped and carotenoid-pigmented bacterium, designated A20-9T, was isolated from a microbial consortium of polyethylene terephthalate enriched from a deep-sea sediment sample from the Western Pacific. Growth was observed at salinities of 1–8 %, at pH 6.5–8 and at temperatures of 10–40 °C. The results of phylogenetic analyses based on the genome indicated that A20-9T formed a monophyletic branch affiliated to the family Schleiferiaceae , and the 16S rRNA gene sequences exhibited the maximum sequence similarity of 93.8 % with Owenweeksia hongkongensis DSM 17368T, followed by similarities of 90.4, 90.1 and 88.8 % with Phaeocystidibacter luteus MCCC 1F01079T, Vicingus serpentipes DSM 103558T and Salibacter halophilus MCCC 1K02288T, respectively. Its complete genome size was 4 035 598 bp, the genomic DNA G+C content was 43.2 mol%. Whole genome comparisons indicated that A20-9T and O. hongkongensis DSM 17368T shared 67.8 % average nucleotide identity, 62.7 % average amino acid identity value, 46.6% of conserved proteins and 17.8 % digital DNA–DNA hybridization identity. A20-9T contained MK-7 as the major respiratory quinone. Its major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phospatidylcholine; and the major fatty acids were iso-C15 : 0 (37.5 %), iso-C16 : 0 3-OH (12.4 %), and summed feature 3 (C16 : 1ω7c /C16 : 1ω6c, 11.6 %). Combining the genotypic and phenotypic data, A20-9T could be distinguished from the members of other genera within the family Schleiferiaceae and represents a novel genus, for which the name Croceimicrobium hydrocarbonivorans gen. nov., sp. nov. is proposed. The type strain is A20-9T (=MCCC 1A17358T =KCTC 72878T).


Author(s):  
Yu-Wen Wang ◽  
Wen-Ting Ren ◽  
Yuan-You Xu ◽  
Xin-Qi Zhang

An aerobic, Gram-stain-negative, non-sporulating, flagellated and spindle-like bacterium, designated HY14T, was isolated from a pickle-processing factory wastewater sample. The isolate chemoheterotrophically grew at 4–42 °C (optimum, 35 °C) and pH 5.5–9.0 (optimum, pH 6.0–6.5). Salt was required for growth (0.5–12 % NaCl, w/v). A deep brown and water-soluble uncharacterized pigment was produced when grown in certain media. The predominant fatty acids (>5 %) included C16 : 0, C18 : 1  ω7c, 11-methyl C18 : 1  ω7c and C19 : 0 cyclo ω8c. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids, two unidentified phospholipids, two unidentified glycolipids and five unknown lipids. The major isoprenoid quinone was ubiquinone-10. Pairwise alignment based on 16S rRNA gene sequences indicated that strain HY14T had the highest sequence similarity to genera Maritimibacter (95.61–96.05 %) and Boseongicola (95.82 %). Phylogenetic analysis based on core genome illustrated that strain HY14T formed a monophyletic lineage with members of the genus Maritimibacter in the clade of the Roseobacter group in the family Rhodobacteraeceae. The core-gene average amino acid identity used to define bacterial genera by a threshold of 60–80 % was calculated to be 68.56–76.5 % between HY14T and closely related taxa. Several genomic characteristics, such as carrying two RuBisCO-mediated pathways and different osmoprotectant transport pathways, exhibited the genotypic discrepancies of strain HY14T. Based on the polyphasic taxonomic characterization, strain HY14T is considered to represent a novel species of a novel genus belonging to the family Rhodobacteraeceae, for which the name Muriiphilus fusiformis gen. nov., sp. nov. is proposed. The type strain is HY14T (=CGMCC 1.15973T=KCTC 52499T). Maritimibacter lacisalsi (Zhong et al. 2015) is considered to diverge from Maritimibacter alkaliphilus at the genus level, and should be reassigned as a novel genus, for which the name Muriicola lacisalsi gen. nov., comb. nov. is proposed.


Author(s):  
Md. Amdadul Huq ◽  
Muhammad Zubair Siddiqi ◽  
Sri Renukadevi Balusamy ◽  
M. Mizanur Rahman ◽  
Md Ashrafudoulla ◽  
...  

A Gram-stain-negative, aerobic and rod-shaped novel bacterial strain, designated MAH-26T, was isolated from rhizospheric soil of a pine tree. The colonies were orange coloured, smooth, spherical and 0.7–1.8 mm in diameter when grown on Reasoner's 2A (R2A) agar for 2 days. Strain MAH-26T was able to grow at 10–40 °C, at pH 6.0–9.0 and with 0–1.0 % NaCl. Cell growth occurred on nutrient agar, R2A agar, tryptone soya agar and Luria–Bertani agar. The strain gave positive results in oxidase and catalase tests. Strain MAH-26T was closely related to Flavihumibacter sediminis CJ663T and Parasegetibacter terrae SGM2-10T with a low 16S rRNA gene sequence similarity (92.8 and 92.9 %, respectively) and phylogenetic analysis indicated that the strain formed a distinct phylogenetic lineage from the members of the closely related genera of the family Chitinophagaceae . Strain MAH-26T has a draft genome size of 6 857 405 bp, annotated with 5173 protein-coding genes, 50 tRNA and two rRNA genes. The genomic DNA G+C content was 41.5 mol%. The predominant isoprenoid quinone was menaquinone 7. The major fatty acids were identified as iso-C15:0, iso-C15:1 G and iso-C17:0 3OH. On the basis of phylogenetic inference and phenotypic, chemotaxonomic and molecular properties, strain MAH-26T represents a novel species of a novel genus of the family Chitinophagaceae , for which the name Pinibacter aurantiacus gen. nov., sp. nov. is proposed. The type strain of Pinibacter aurantiacus is MAH-26T (=KACC 19749T=CGMCC 1.13701T).


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