International Journal of Systematic and Evolutionary Microbiology (2015), 65, 676–680

DOI 10.1099/ijs.0.070433-0

Novosphingobium marinum sp. nov., isolated from seawater Ying-Yi Huo, Hong You, Zheng-Yang Li, Chun-Sheng Wang and Xue-Wei Xu Correspondence Xue-Wei Xu

Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China

[email protected]

A Gram-stain-negative, aerobic, short rod-shaped bacterium, strain LA53T, was isolated from a deep-sea water sample collected from the eastern Pacific Ocean. Strain LA53T grew in the presence of 0–7.0 % (w/v) NaCl and at 15-37 6C; optimum growth was observed with 1.0– 2.0 % (w/v) NaCl and at 35 6C. Chemotaxonomic analysis showed ubiquinone-10 as the predominant respiratory quinone, C18 : 1v7c and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1v7c) as major fatty acids, and diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid as major polar lipids. The genomic DNA G+C content was 57.7 mol%. Phylogenetic analyses revealed that strain LA53T belongs to the genus Novosphingobium. 16S rRNA gene sequence similarities between strain LA53T and the type strains of species of the genus Novosphingobium with validly published names ranged from 93.1 to 96.3 %. In addition, strain LA53T could be differentiated from Novosphingobium pentaromativorans DSM 17173T and Novosphingobium indicum DSM 23608T as well as the type strain of the type species of the genus, Novosphingobium capsulatum DSM 30196T, by some phenotypic characteristics, including hydrolysis of substrates, utilization of carbon sources and susceptibility to antibiotics. On the basis of phenotypic and genotypic data, strain LA53T represents a novel species within the genus Novosphingobium, for which the name Novosphingobium marinum sp. nov. is proposed. The type strain is LA53T (5CGMCC 1.12918T5JCM 30307T).

In 2001, the genus Sphingomonas was divided into four genera based on the phylogenetic, chemotaxonomic and phenotypic characteristics (Takeuchi et al., 2001). These four genera are Sphingomonas sensu stricto, Sphingobium, Sphingopyxis and Novosphingobium. At the time of writing, the genus Novosphingobium comprises 26 recognized species, the type species of which is Novosphingobium capsulatum (Takeuchi et al., 2001). Members of the genus Novosphingobium have been isolated from diverse habitats including contaminated soils (Suzuki & Hiraishi, 2007; Gupta et al., 2009; Ka¨mpfer et al., 2011; Niharika et al., 2013), freshwater sediments (Sohn et al., 2004; Liu et al., 2005; Baek et al., 2011), activated sludges or wastewater treatment plants (Fujii et al., 2003; Addison et al., 2007), and plant roots (Lin et al., 2013; Takeuchi et al., 1995). Several species have been isolated from marine environments, including Novosphingobium aromaticivorans, Novosphingobium stygium and Novosphingobium subterraneum from coastal sediments (Balkwill et al., 1997; Takeuchi et al., 2001), Novosphingobium indicum The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain LA53T is KJ708552. Two supplementary figures and a supplementary table are available with the online Supplementary Material.

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from deep-sea water (Yuan et al., 2009) and Novosphingobium malaysiense from mangrove sediment (Lee et al., 2014). Here we present the results of a polyphasic study describing a novel species of the genus Novosphingobium isolated from a deep-sea water sample. A seawater sample was collected from the eastern Pacific Ocean at a depth of 800 m (144u 599 W 7u 309 N) by using a Sea-Bird 911 plus CTD (Sea-Bird Electronics) in August 2013. The subsample was subjected to the cultural process immediately on board. Approximately 100 ml seawater was plated on natural seawater agar supplemented with 0.05 % peptone (w/v; BD) and 0.01 % yeast extract (w/v; BD). After 3 months of aerobic incubation at room temperature, a yellow colony, designated LA53T, was picked. The isolate was purified by repeated restreaking on marine agar 2216 (MA; BD) and the purity was confirmed by the uniformity of colony morphology. Strain LA53T was routinely cultured in marine broth 2216 (MB; BD) and maintained at 280 uC with 30 % (v/v) glycerol. Strain LA53T grew as aggregates in the early stage of growth, and reached late exponential growth phase after 5 days of incubation in MB at 35 uC. On MA, strain LA53T formed visible colonies after 5 days of incubation and the 070433 G 2015 IUMS Printed in Great Britain

Novosphingobium marinum sp. nov.

colony diameter was 0.5–1 mm after 7 days of incubation. Strain LA53T did not grow in any of the following media supplemented with 2 % (w/v) NaCl: Luria–Bertani (LB), nutrient broth (Hattori & Hattori, 1980), PY (Takeuchi et al., 2001), R2A (Reasoner & Geldreich, 1985), TSB (BD), carbon utilization basal medium (Ka¨mpfer et al., 1991), marine basal medium (Baumann & Baumann, 1981), or in acid production OF (Hugh & Leifson, 1953) and MOF (Leifson, 1963) media. All phenotypic tests in this study were carried out in MB or on MA at 35 uC. Growth at various NaCl concentrations (0, 0.5, 1.0, 2.0, 3.0, 5.0, 7.5, 10.0, 12.5 and 15.0 %, w/v) was investigated in NaCl-free MB medium (prepared according to the BD formula for MB). The pH range for growth was determined at pH 5.0–10.0 (in 0.5 pH unit intervals) in MB buffered with the following: MES (for pH 5.0–6.0), PIPES (pH 6.5– 7.0), Tricine (pH 7.5–8.5), CAPSO (pH 9.0–9.5) and CAPS (pH 10.0) at a concentration of 40 mM. The temperature range for growth was determined by incubating at 4, 10, 15, 20, 25, 30, 35, 37, 42 and 45 uC in MB. Cell morphology and motility were examined by optical microscopy (BX40; Olympus) and transmission electron microscopy (JEM1230; JEOL). Oxidase and catalase activities, nitrate reduction and hydrolysis of aesculin, casein, DNA, gelatin, starch, tyrosine, Tweens 20, 40, 60 and 80, and urea were tested according to the methods of Dong & Cai (2001). API ZYM, API 20NE and API 20E tests (bioMe´rieux) were used to determine other physiological and biochemical characteristics according to the manufacturer’s instructions, except that cells were suspended in a solution described by Sohn et al. (2004). API ZYM strips were read after 12 h, and API 20 NE and API 20 E strips after 48 h. Single carbon source assimilation tests were performed on MA with 0.05 % (w/v) yeast extract and without peptone (prepared according to the BD formula for MA). The corresponding filter-sterilized sugar (0.2 %), alcohol (0.2 %) or organic acid (0.1 %) was added into the medium. Susceptibility to antibiotics was determined using antibiotic discs containing the following (mg unless otherwise stated): amoxicillin (10), ampicillin (10), bacitracin (0.04 IU), carbenicillin (100), cefotaxime (30), chloramphenicol (30), erythromycin (15), gentamicin (10), kanamycin (30), nalidixic acid (30), nitrofurantoin (300), novobiocin (30), nystatin (100), penicillin G (10 IU), polymyxin B (300 IU), rifampicin (5), streptomycin (10), tetracycline (30), tobramycin (10) and vancomycin (30). The cellular fatty acids of strain LA53T, Novosphingobium pentaromativorans DSM 17173T and N. indicum DSM 23608T were determined under identical conditions. Strain LA53T was incubated on MA at 35 uC for 5 days, whereas the other strains were incubated for 2 days, after which cells of the third streak quadrants were collected. Cellular fatty acids were analysed according to the instructions of the Microbial Identification System (MIDI). Isoprenoid quinones were extracted from freeze-dried cells and analysed as described previously using LC-MS (Xu et al., http://ijs.sgmjournals.org

2011). Genomic DNA was obtained as described by Marmur (1961). Polar lipids analysis by TLC was performed by the Identification Service of the Deutsche Sammlung von Mikoorganismen und Zellkulturen (DSMZ, Braunschweig, Germany). Total lipids were detected using molybdatophosphoric acid and specific functional groups were detected using spray reagents specific for defined functional groups according the protocol of to Tindall et al. (2007). For analysis of DNA G+C content, DNA was hydrolysed with P1 nuclease (Sigma) and the nucleotides were dephosphorylated with calf intestine alkaline phosphatase (TaKaRa). The resulting deoxyribonucleosides were separated by a UPLC system (Waters) with a UV detector at 254 nm and Acquity UPLC BEH C18 column (100 mm62.1 mm, 1.7 mm; Waters). The mobile phase contained 6 % methanol and 10 mM triethylamine phosphate (pH 5.1), and the flow rate was 0.2 ml min21. Salmon sperm DNA (Sigma) with known G+C content was used as a standard. The DNA G+C content was calculated from the ratio of deoxyguanosine (dG) and thymidine (dT) according to Mesbah & Whitman (1989). The 16S rRNA gene of strain LA53T was amplified by PCR and the resulting products were cloned into the pMD 19-T vector (TaKaRa) and sequenced (Xu et al., 2007). The sequences were compared with closely related sequences of reference organisms from the EzTaxon-e server (Kim et al., 2012). Sequences were aligned with the CLUSTAL W program (Thompson et al., 1994). Phylogenetic relationships were analysed with neighbour-joining (Saitou & Nei, 1987), maximum-parsimony (Fitch, 1971) and maximum-likelihood (Felsenstein, 1981) algorithms in the MEGA 5 software package (Tamura et al., 2011) on the basis of 1000 replicates. Evolutionary distance calculations were based on the Jukes– Cantor model (Jukes & Cantor, 1969) for the neighbourjoining and maximum-likelihood methods. Cells of strain LA53T were Gram-stain-negative, short rodshaped (0.6–1.0 mm wide and 0.8–2.0 mm long) without flagella (Fig. S1, available in the online Supplementary Material). The NaCl concentration, temperature and pH ranges for growth of strain LA53T were 0–7.0 % (w/v), 15– 37 uC and pH 6.0–8.5, respectively. Detailed phenotypic characteristics are given in the species description, and Tables 1 and S1. The almost-complete 16S rRNA gene sequence (1411 nt) of strain LA53T was obtained. Comparison of the 16S rRNA gene sequence of strain LA53T with those of species with validly published names showed that strain LA53T belonged to the genus Novosphingobium. In addition, the 16S rRNA signatures presenting at positions 52 : 359 (C : G), 134 (G), 593 (U), 987 : 1218 (G : C) and 990 : 1215 (U : A) supported this position within the genus Novosphingobium (Takeuchi et al., 2001). 16S rRNA gene sequence similarities between strain LA53T and type strains of species of the genus Novosphingobium with validly published names ranged from 93.1 to 96.3 %, and strain LA53T was most closely related to N. pentaromativorans US6-1T (96.3 % 16S rRNA gene 677

Y.-Y. Huo and others

Table 1. Characteristics differentiating strain LA53T from its closest phylogenetic relatives Strains: 1, LA53T; 2, N. pentaromativorans DSM 17173T; 3, N. indicum DSM 23608T; 4, N. capsulatum DSM 30196T. Data were obtained from this study under identical growth conditions. All strains are Gram-stain-negative, and are positive for catalase activity, nitrate reduction, Voges-Proskauer test, and hydrolysis of Tween 60 and DNA. All strains are negative for arginine dihydrolase, casein hydrolysis, citrate utilization, H2S production, indole production, lysine and ornithine carboxylases, tryptophan deaminase and urease. In all strains in the API ZYM system, acid phosphatase, alkaline phosphatase, a-glucosidase, naphthol-AS-BI-phosphohydrolase, leucine arylamidase and valine arylamidase activities are present, whereas N-acetyl-b-glucosaminidase, b-fucosidase, a-galactosidase, a-mannosidase and trypsin activities are absent. All strains are susceptible to cefotaxime, chloramphenicol, erythromycin, kanamycin and rifampicin, but not to bacitracin, nalidixic acid or nystatin. +, Positive; 2, negative. Characteristic

1

2

3

4

ONPG Hydrolysis of: Aesculin Tween 20 Tween 40 Tyrosine Utilization of: D-Fructose D-Gluconate Pyruvate D-Xylose API ZYM tests Esterase (C4) b-Galactosidase b-Glucuronidase b-Glucosidase Susceptible to: Amoxicillin Ampicillin Carbenicillin Nitrofurantoin Novobiocin Penicillin G Tetracycline Tobramycin

2

2

2

+

2 2 + 2

+ 2 2 +

2 + + +

+ + + 2

2 2 2 2

+ 2 + 2

2 2 + 2

2 + 2 +

+ 2 2 2

2 2 2 +

+ 2 2 2

+ + + +

+ + + + 2 + 2 2

2 2 2 2 + 2 + +

+ + + 2 + + + +

+ + + + + + + +

summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1v7c, 27.4 %) as the major fatty acids (Takeuchi et al., 2001). Nevertheless, the percentages of summed feature 3 and C14 : 0 2-OH in strain LA53T (27.4 % and 7.9 %, respectively) were higher than those of N. pentaromativorans DSM 17173T (10.1 % and 5.3 %, respectively) and N. indicum DSM 23608T (8.0 % and 3.8 %, respectively), whereas the amount of C18 : 1v7c in strain LA53T (40.4 %) was lower than that of N. pentaromativorans DSM 17173T (62.8 %) and N. indicum DSM 23608T (47.8 %) (Table S1). In addition, strain LA53T could be differentiated from N. pentaromativorans DSM 17173T and N. indicum DSM 23608T as well as the type strain of the type species of the genus, N. capsulatum DSM 30196T, on the basis of some phenotypic characteristics, including hydrolysis of aesculin, Tweens 20 and 40, and tyrosine; utilization of D-fructose, D-gluconate, pyruvate and D-xylose; susceptibility to amoxicillin, ampicillin, carbenicillin, nitrofurantoin, novobiocin, penicillin G, tetracycline and tobramycin; and esterase (C4), b-galactosidase, b-glucuronidase and bglucosidase activities in API ZYM tests (Table 1). On the basis of these phylogenetic, genotypic, chemotaxonomic and phenotypic data, we propose to classify strain LA53T as the type strain of a novel species of the genus Novosphingobium with the name Novosphingobium marinum sp. nov. Description of Novosphingobium marinum sp. nov. Novosphingobium marinum (ma.ri9num. L. neut. adj. marinum of the sea, marine).

Chemotaxonomic analysis showed strain LA53T had the typical characteristics of the genus Novosphingobium, such as the presence of ubiquinone-10 and sphingoglycolipid (Fig. S2), as well as containing C18 : 1v7c (40.4 %) and

Cells are Gram-stain-negative and short rod-shaped. Colonies on MA are 0.5–1 mm in diameter, circular, smooth, elevated and yellow after 7 days at 35 uC. Growth occurs in the presence of 0–7.0 % (w/v) NaCl, with optimum growth at 1.0–2.0 %. The pH and temperature ranges for growth are pH 6.0–8.5 and 15–37 uC, respectively (optimum growth at pH 7.0 and 35 uC). Positive for oxidase and catalase activities, nitrate reduction and VogesProskauer test. Tests for arginine dihydrolase, citrate utilization, H2S production, indole production, lysine and ornithine carboxylases, tryptophan deaminase and onitrophenyl-b-D-galactopyranosidase are negative. DNA and Tweens 40, 60 and 80 are hydrolysed, but aesculin, casein, gelatin, starch, Tween 20, tyrosine and urea are not. In the API ZYM system, acid phosphatase, alkaline phosphatase, esterase (C4), esterase lipase (C8), a-glucosidase, naphthol-AS-BI-phosphohydrolase, leucine arylamidase and valine arylamidase activities are present, whereas N-acetyl-b-glucosaminidase, a-chymotrypsin, cystine arylamidase, b-fucosidase, a- and b-galactosidases, b-glucosidase, b-glucuronidase, lipase (C14), a-mannosidase and trypsin activities are absent. The following substrates are not utilized for growth: adonitol, aesculin, L-arabinose, cellobiose, citrate, ethanol, formate, D-fructose, D-galactose, D-gluconate, glucose, glycerol, myo-inositol, a-lactose,

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International Journal of Systematic and Evolutionary Microbiology 65

sequence similarity) and N. indicum H25T (96.2 %). Phylogenetic analysis based on 16S rRNA gene sequences of members of the genus Novosphingobium showed that strain LA53T formed a stable cluster with N. indicum H25T and N. malaysiense MUSC 273T (Fig. 1), both of which were isolated from marine environments (Yuan et al., 2009; Lee et al., 2014).

Novosphingobium marinum sp. nov. 76

Novosphingobium chloroacetimidivorans BUT-14T (KF676669) Novosphingobium soli CC-TPE-1T (FJ425737) 59 Novosphingobium naphthalenivorans TUT562T (AB177883) 78 Novosphingobium resinovorum NCIMB 8767T (EF029110) 7 8 Novosphingobium barchaimii LL02T (JN695619) 80 Novosphingobium lindaniclasticum LE124T (ATHL01000125) 7 79 Novosphingobium panipatense SM16T (EF424402) 8 89 Novosphingobium mathurense SM117T (EF424403) 87 8 Novosphingobium pentaromativorans US6-1T (AGFM01000099) 7

0.01

9 90

7

6 76

Novosphingobium sediminicola HU1-AH51T (FJ177534) Novosphingobium rosa NBRC 15208T (D13945) Novosphingobium aquaticum FNE08-86T (JN399173)

60 6 60

6

Novosphingobium marinum LA53T (KJ708552) Novosphingobium indicum H25T (EF549586) Novosphingobium malaysiense MUSC 273T (KC907395)

Novosphingobium tardaugens NBRC 16725T (BASZ01000029) 64

8

89

Novosphingobium nitrogenifigens DSM 19370T (AEWJ01000057) Novosphingobium acidiphilum DSM 19966T (AUBA01000045) Novosphingobium hassiacum W-51T (AJ416411) Novosphingobium stygium NBRC 16085T (AB025013) Novosphingobium fuchskuhlense FNE08-7T (JN399172) Novosphingobium arabidopsis CC-ALB-2T (KC479803)

Novosphingobium lentum MT1T (AJ303009) Novosphingobium taihuense T3-B9T (AY500142) Novosphingobium capsulatum GIFU 11526T (D16147) 94 Novosphingobium subterraneum NBRC 16086T (AB025014) 9 Novosphingobium aromaticivorans DSM 12444T (CP000248) 10

Novosphingobium aquiterrae E-II-3T (FJ772064) 100 Novosphingobium kunmingense 18-11HKT (JQ246446) Sphingomonas paucimobilis ATCC 29837T (U37337)

Fig. 1. Neighbour-joining tree based on 16S rRNA gene sequences, showing the phylogenetic relationships of the novel isolate and other members of the genus Novosphingobium. Sphingomonas paucimobilis ATCC 29837T (GenBank accession no. U37337) was used as an outgroup. Bootstrap values are based on 1000 replicates; only values .50 % are shown. Filled circles indicate nodes recovered in both maximum-parsimony and maximum-likelihood trees. Open circles indicate nodes recovered in maximum-parsimony or maximum-likelihood trees. Bar, 0.01 substitutions per nucleotide position.

malonate, maltose, pyruvate, raffinose, L-rhamnose, Dribose, D-salicin, D-sorbitol, L-sorbose, starch, sucrose, succinate, trehalose or D-xylose. Susceptible to amoxicillin, ampicillin, carbenicillin, cefotaxime, chloramphenicol, erythromycin, gentamicin, kanamycin, nitrofurantoin, penicillin G, rifampicin and vancomycin, but not to bacitracin, nalidixic acid, novobiocin, nystatin, polymyxin B, streptomycin, tetracycline and tobramycin. The predominant quinone is ubiquinone-10. The major polar lipids are diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid. The major fatty acids (.10 %) are C18 : 1v7c and iso-C15 : 0 2-OH and/or C16 : 1v7c (summed feature 3).

DY125-14-E-02), the National Natural Science Foundation of China (41276173), the Zhejiang Provincial Natural Science Foundation of China (LQ13D060002) and the Scientific Research Fund of the Second Institute of Oceanography, SOA (JT1305).

The type strain, LA53T (5CGMCC 1.12918T5JCM 30307T), was isolated from a seawater sample of the Eastern Pacific Ocean. The DNA G+C content of the type strain is 57.7 mol% (by HPLC).

Balkwill, D. L., Drake, G. R., Reeves, R. H., Fredrickson, J. K., White, D. C., Ringelberg, D. B., Chandler, D. P., Romine, M. F., Kennedy, D. W. & Spadoni, C. M. (1997). Taxonomic study of aromatic-

Acknowledgements We are highly indebted to Dr Aharon Oren of the Hebrew University of Jerusalem for critical reading of the manuscript. This work was supported by grants from China Ocean Mineral Resources R & D Association (COMRA) Special Foundation (DY125-15-R-03 and http://ijs.sgmjournals.org

References Addison, S. L., Foote, S. M., Reid, N. M. & Lloyd-Jones, G. (2007).

Novosphingobium nitrogenifigens sp. nov., a polyhydroxyalkanoateaccumulating diazotroph isolated from a New Zealand pulp and paper wastewater. Int J Syst Evol Microbiol 57, 2467–2471. Baek, S.-H., Lim, J. H., Jin, L., Lee, H.-G. & Lee, S.-T. (2011).

Novosphingobium sediminicola sp. nov. isolated from freshwater sediment. Int J Syst Evol Microbiol 61, 2464–2468.

degrading bacteria from deep-terrestrial-subsurface sediments and description of Sphingomonas aromaticivorans sp. nov., Sphingomonas subterranea sp. nov., and Sphingomonas stygia sp. nov. Int J Syst Bacteriol 47, 191–201. Baumann, P. & Baumann, L. (1981). The marine Gram-negative

eubacteria: genera Photobacterium, Beneckea, Alteromonas, Pseudomonas, and Alcaligenes. In The Prokaryotes, pp. 1302–1331. Edited by M. P. Starr, H. Stolp, H. G. Tru¨per, A. Balows & H. G. Schlegel. Berlin: Springer. 679

Y.-Y. Huo and others Dong, X.-Z. & Cai, M.-Y. (editors) (2001). Determinative Manual for

Routine Bacteriology. Beijing: Scientific Press (English translation).

Niharika, N., Moskalikova, H., Kaur, J., Sedlackova, M., Hampl, A., Damborsky, J., Prokop, Z. & Lal, R. (2013). Novosphingobium

Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368–376.

barchaimii sp. nov., isolated from hexachlorocyclohexane-contaminated soil. Int J Syst Evol Microbiol 63, 667–672.

Fitch, W. M. (1971). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20, 406–416.

Reasoner, D. J. & Geldreich, E. E. (1985). A new medium for the

Fujii, K., Satomi, M., Morita, N., Motomura, T., Tanaka, T. & Kikuchi, S. (2003). Novosphingobium tardaugens sp. nov., an oestradiol-

enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 49, 1–7. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new

degrading bacterium isolated from activated sludge of a sewage treatment plant in Tokyo. Int J Syst Evol Microbiol 53, 47–52.

method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406– 425.

Gupta, S. K., Lal, D. & Lal, R. (2009). Novosphingobium panipatense sp.

Sohn, J. H., Kwon, K. K., Kang, J.-H., Jung, H.-B. & Kim, S.-J. (2004).

nov. and Novosphingobium mathurense sp. nov., from oil-contaminated soil. Int J Syst Evol Microbiol 59, 156–161. Hattori, R. & Hattori, T. (1980). Sensitivity to salts and organic

compounds of soil bacteria isolated on diluted media. J Gen Appl Microbiol 26, 1–14. Hugh, R. & Leifson, E. (1953). The taxonomic significance of

fermentative versus oxidative metabolism of carbohydrates by various gram negative bacteria. J Bacteriol 66, 24–26. Jukes, T. H. & Cantor, C. R. (1969). Evolution of protein molecules.

In Mammalian Protein Metabolism, vol. 3, pp. 21–132. Edited by H. N. Munro. New York: Academic Press. Ka¨mpfer, P., Steiof, M. & Dott, W. (1991). Microbiological

characterization of a fuel-oil contaminated site including numerical identification of heterotrophic water and soil bacteria. Microb Ecol 21, 227–251. Ka¨mpfer, P., Young, C.-C., Busse, H.-J., Lin, S.-Y., Rekha, P. D., Arun, A. B., Chen, W.-M., Shen, F.-T. & Wu, Y.-H. (2011). Novosphingobium

soli sp. nov., isolated from soil. Int J Syst Evol Microbiol 61, 259–263. Kim, O.-S., Cho, Y.-J., Lee, K., Yoon, S.-H., Kim, M., Na, H., Park, S.-C., Jeon, Y. S., Lee, J.-H. & other authors (2012). Introducing EzTaxon-

e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62, 716– 721. Lee, L.-H., Azman, A.-S., Zainal, N., Eng, S.-K., Fang, C.-M., Hong, K. & Chan, K.-G. (2014). Novosphingobium malaysiense sp. nov. isolated

from mangrove sediment. Int J Syst Evol Microbiol 64, 1194–1201. Leifson, E. (1963). Determination of carbohydrate metabolism of

marine bacteria. J Bacteriol 85, 1183–1184. Lin, S.-Y., Hameed, A., Liu, Y.-C., Hsu, Y.-H., Lai, W.-A., Huang, H.-I. & Young, C.-C. (2013). Novosphingobium arabidopsis sp. nov., a DDT-

resistant bacterium isolated from the rhizosphere of Arabidopsis thaliana. Int J Syst Evol Microbiol 64, 594–598. Liu, Z.-P., Wang, B.-J., Liu, Y.-H. & Liu, S.-J. (2005). Novosphingobium

Novosphingobium pentaromativorans sp. nov., a high-molecular-mass polycyclic aromatic hydrocarbon-degrading bacterium isolated from estuarine sediment. Int J Syst Evol Microbiol 54, 1483–1487. Suzuki, S. & Hiraishi, A. (2007). Novosphingobium naphthalenivorans

sp. nov., a naphthalene-degrading bacterium isolated from polychlorinated-dioxin-contaminated environments. J Gen Appl Microbiol 53, 221–228. Takeuchi, M., Sakane, T., Yanagi, M., Yamasato, K., Hamana, K. & Yokota, A. (1995). Taxonomic study of bacteria isolated from plants:

proposal of Sphingomonas rosa sp. nov., Sphingomonas pruni sp. nov., Sphingomonas asaccharolytica sp. nov., and Sphingomonas mali sp. nov. Int J Syst Bacteriol 45, 334–341. Takeuchi, M., Hamana, K. & Hiraishi, A. (2001). Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int J Syst Evol Microbiol 51, 1405–1417. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. & Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using

maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28, 2731–2739. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673–4680.

Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994).

Tindall, B. J., Sikorski, J., Smibert, R. A. & Kreig, N. R. (2007).

Phenotypic characterization and the principles of comparative systematics. In Methods for General and Molecular Microbiology, 3rd edn, pp. 330–393. Edited by C. A. Reddy, T. J. Beveridge, J. A. Breznak, G. Marzluf, T. M. Schmidt & L. R. Synder. Washington, DC: American Society for Microbiology. Xu, X.-W., Wu, Y.-H., Zhou, Z., Wang, C.-S., Zhou, Y.-G., Zhang, H.-B., Wang, Y. & Wu, M. (2007). Halomonas saccharevitans sp. nov.,

Halomonas arcis sp. nov. and Halomonas subterranea sp. nov., halophilic bacteria isolated from hypersaline environments of China. Int J Syst Evol Microbiol 57, 1619–1624.

taihuense sp. nov., a novel aromatic-compound-degrading bacterium isolated from Taihu Lake, China. Int J Syst Evol Microbiol 55, 1229– 1232.

Xu, X.-W., Huo, Y.-Y., Bai, X.-D., Wang, C.-S., Oren, A., Li, S.-Y. & Wu, M. (2011). Kordiimonas lacus sp. nov., isolated from a ballast water

Marmur, J. (1961). A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 3, 208–218.

tank, and emended description of the genus Kordiimonas. Int J Syst Evol Microbiol 61, 422–426.

Mesbah, M. & Whitman, W. B. (1989). Measurement of deoxyguano-

Yuan, J., Lai, Q., Zheng, T. & Shao, Z. (2009). Novosphingobium

sine/thymidine ratios in complex mixtures by high-performance liquid chromatography for determination of the mole percentage guanine + cytosine of DNA. J Chromatogr A 479, 297–306.

indicum sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from a deep-sea environment. Int J Syst Evol Microbiol 59, 2084–2088.

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International Journal of Systematic and Evolutionary Microbiology 65

Novosphingobium marinum sp. nov., isolated from seawater.

A Gram-stain-negative, aerobic, short rod-shaped bacterium, strain LA53(T), was isolated from a deep-sea water sample collected from the eastern Pacif...
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