Flavobacterium aquaticum sp. nov., isolated from a water sample of a rice field

International Journal of Systematic and Evolutionary Microbiology

Lee

2016

Self Cite

Two Gram-stain-negative, rod-shaped phototrophic bacteria (designated strains N1 T and C7) were isolated from lagoon sediments. Both strains were positive for catalase and oxidase activity. Casein, starch, urea and Tween 20 were hydrolysed by both strains while chitin, gelatin and Tween 80 were not. In both strains, C 16 : 0 , C 18 : 0 ,C 16 : 1 !6c/C 16 : 1 !7c and C 18 : 1 !6c/ C 18 : 1 !7c were the predominant fatty acids, with minor amounts of C 8 : 0 3-OH, anteiso-C 14 : 0 , C 17 : 0 , C 14 : 1 !5c, C 17 : 1 10-methyl and C 18 : 1 !5c. Strains N1 T and C7 contained phosphatidylglycerol and phosphatidylethanolamine as major polar lipids with minor amounts of phosphatidylcholine, unidentified lipids and an unidentified phospholipid. The mean genomic DNA G+C content was 70.6±1 mol% and the two strains were closely related (mean DNA-DNA hybridization >90 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that the two strains clustered with species of the genus Rhodobacter belonging to the family Rhodobacteraceae of the class Alphaproteobacteria. Strain N1 T has a 16S rRNA gene sequence similarity of 99.2 % with Rhodobacter capsulatus ATCC 11166 T , 99.1 % with Rhodobacter viridis JA737 T and <96.6 % with other members of the genus Rhodobacter. Strain N1 T and C7 shared 100 % 16S rRNA gene sequence similarity. DNA-DNA hybridization values between strain N1 T and the type strains of the nearest species were clearly below the 70 % threshold. On the basis of phenotypic and genotypic data, it is proposed that strain N1 T represents a novel species of the genus Rhodobacter, for which the name Rhodobacter sediminis sp. nov. is proposed. The type strain is N1 T (=KEMB 563-471 T =JCM 31175 T ), and strain C7 is an additional strain of the species.

Section: Rhodobacter Ovatus Ja234 T (Am690348)mentioning

confidence: 99%

“…Buffered medium was used for growth at different pH as described previously (Subhash et al, 2013a). Growth at different NaCl concentrations and temperatures was tested under photoheterotrophic conditions as described previously (Raj et al, 2013;Subhash et al, 2013c …”

mentioning

confidence: 99%

Rhodobacter sediminis sp. nov., isolated from lagoon sediments

International Journal of Systematic and Evolutionary Microbiology

Lee

2016

Self Cite

“…Growth at different temperatures (4,10,15,20,25,27,30,35,40,45 and 50 u C) was tested in the above-mentioned medium. The optimum temperature for growth of strain JC216 T was 30 u C. aspartic acid) was tested using basal medium that was described previously (Subhash et al, 2013b;2013c). The organic substrates were added at a concentration of 0.1 % (w/v) and the pH was adjusted to pH 7.0 using 1 M NaOH.…”

Section: Sphingopyxis Marina Fr1087 T (Dq781320) Sphingopyxis Litorismentioning

confidence: 99%

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

International Journal of Systematic and Evolutionary Microbiology

Sasikala

Ramana

2014

Self Cite

Strain JC216 T 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 JC216 T contained C 18 : 1 v7c/C 18 : 1 v6c, C 16 : 1 v7c/ C 16 : 1 v6c, C 14 : 0 2-OH and C 16 : 0 as the major (¢8 %) fatty acids with minor amounts of C 12 : 0 , C 15 : 0 2-OH, C 16 : 0 2-OH, C 16 : 1 2-OH, C 17 : 1 v6c, C 17 : 1 v8c and C 17 : 1 v9c. 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 JC216 T represents a member of the genus Sphingopyxis in the family Sphingomonadaceae within the class Alphaproteobacteria. Strain JC216 T had a sequence similarity of 97.28 % with Sphingopyxis wooponensis 03SU3-P T and ,96.71 % with other members of the family Sphingomonadaceae. Furthermore, strain JC216 T had 33±1 % relatedness (based on DNA-DNA hybridization) with S. wooponensis KCTC 23340 T (503SU3-P T ). Distinct morphological, physiological and genotypic differences from the previously described taxa support the classification of strain JC216 T 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 JC216 T (5KCTC 32445 T 5LMG 27671 T ).The genus Sphingopyxis was first described by Takeuchi et al. (2001). At the time of writing a total of 20 validly published species names were described. Among the 20 species, only one accepted from India (Sphingopyxis indica DS15 T ) was described (Jindal et al., 2013), which was isolated from a high dose point hexachlorocycohexane (HCH) dumpsite. Members of the genus Sphingopyxis are Gram-stain-negative, non-spore-forming, yellow to brown pigmented and contain sphingoglycolipids (Yoon et al., 2005). In this study, we isolated a strain (JC216 T ) which had clear distinguishing characteristics from the type strains of species of the genus Sphingopyxis.Strain JC216 T was isolated in March 2013, from a contaminated Petri dish from our laboratory (GPS position; 17 u 279 20.6199 N 78 u 199 0099 E) while growing a strain of the genus Pontibacter on agar medium (Subhash et al., 2013a) containing (g l 21 ): KH 2 PO 4 (0.2), NaCl (1), NH 4 Cl (0.25), KCl (0.5), CaCl 2 . 2H 2 0 (0.15), MgCl 2 . 6H 2 O (0.62), Na 2 SO 4 (2.84), HEPES (2.83), yeast extract (3.0), peptone (3), Casamino acids (0.5), D-glucose (0.5) and sodi...

“…S3 T was isolated from lagoon sediments (pH 7.5) collected from North Carolina, USA. Sediment samples (1 g) were serially diluted up to a 10 À9 dilution and 100 µl was spread on a 1.5 % agar (w/v) medium (pH 7.5) which contained (g l À1 ): KH 2 PO 4 (0.2), NH 4 Cl (0.25), KCl (0.5), CaCl 2 .2H 2 0 (0.15), NaCl (1.0), MgCl 2 .6H 2 O (0.62), Na 2 SO 4 (2.84), HEPES {2-[4-(2-hydroxyethyl)1-piperazinyl ethane sulphonic acid]} (2.83), yeast extract (3.0), peptone (3.0), casamino acid (0.5), dextrose (0.5) and sodium pyruvate (3.0, Subhash et al, 2013a). Cultures were purified by repeated streaking on agar plates and preserved using lyophilization.…”

mentioning

confidence: 99%

“…Purified cultures were grown in conical flasks (500 ml) with shaking (160 r.p.m.) in liquid medium (pH 7.5) as described previously (Subhash et al, 2013a). For routine culturing and for physiological tests, strain S3 T was grown at pH 7.5 and 30 C.…”

mentioning

confidence: 99%

Description of Comamonas sediminis sp. nov., isolated from lagoon sediments

International Journal of Systematic and Evolutionary Microbiology

Bang

You

et al. 2016

Self Cite

Strain S3 T was isolated from lagoon sediments, and appeared as transparent colonies on agar plates, with cells staining Gram-negative. Catalase and oxidase were positive. S3 T hydrolyzed starch, casein and tween-20, while urea, chitin, gelatin and tween-80 were not hydrolysed. C 18 : 1 !6c/C 18 : 1 !7c, C 16 : 1 !6c/C 16 : 1 !7c,C 17 : 0 cyclo and C 16 : 0 were the predominant fatty acids with minor amounts of C 10 : 0 3-OH, C 12 : 0 , C 14 : 0 and C 16 : 0 2-OH. S3 T contained diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), and phosphatidylethanolamine (PE) as major polar lipids with minor amounts of unidentified phospholipid (PL) and unidentified lipids (L1-2). Genomic DNA G+C content was 68.3 mol%. 16S rRNA gene sequence comparisons indicated that S3 T represents a member of the genus Comamonas in family Comamonadaceae of the class Betaproteobacteria. S3 T has a sequence similarity of 98.96 % with Comamonas koreensis YH12 T , 97.93 % with Comamonas guangdongensis CY01 T and <96.97 % with other members of the genus Comamonas. DNA-DNA hybridization values between S3 T and the type strains of the most closely related species were clearly below the 70 % threshold. On the basis of phenotypic, genotypic and phylogenetic analysis, it is proposed that S3 T represents a novel species of the genus Comamonas, for which the name Comamonas sediminis sp. nov. is proposed. The type strain is S3 T (=KEMB 563-466 T =JCM 31169 T ).