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International Journal of Systematic and Evolutionary Microbiology (2012), 62, 2218–2223 DOI 10.1099/ijs.0.037515-0

Pricia antarctica gen. nov., sp. nov., a member of the family , isolated from Antarctic intertidal sediment

Yong Yu, Hui-Rong Li, Yin-Xin Zeng, Kun Sun and Bo Chen

Correspondence SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, Yong Yu PR China [email protected]

A yellow-coloured, rod-shaped, Gram-reaction- and Gram-staining-negative, non-motile and aerobic bacterium, designated strain ZS1-8T, was isolated from a sample of sandy intertidal sediment collected from the Antarctic coast. Flexirubin-type pigments were absent. In phylogenetic analyses based on 16S rRNA gene sequences, strain ZS1-8T formed a distinct phyletic line and the results indicated that the novel strain should be placed in a new within the family Flavobacteriaceae. In pairwise comparisons between strain ZS1-8T and recognized species, the levels of 16S rRNA gene sequence similarity were all ,93.3 %. The strain required + + Ca2 and K ions as well as NaCl for growth. Optimal growth was observed at pH 7.5–8.0,

17–19 6C and with 2–3 % (w/v) NaCl. The major fatty acids were iso-C15 : 1 G, iso-C15 : 0,

summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1v7c), an unknown acid with an equivalent

chain-length of 13.565 and iso-C17 : 0 3-OH. The major respiratory quinone was MK-6. The predominant polar lipid was phosphatidylethanolamine. The genomic DNA G+C content was 43.9 mol%. Based on the phylogenetic, phenotypic and chemotaxonomic data, strain ZS1-8T represents a novel species in a new genus in the family Flavobacteriaceae for which the name Pricia antarctica gen. nov., sp. nov. is proposed. The type strain of the type species is ZS1-8T (5JCM 17291T5DSM 23421T).

The family Flavobacteriaceae, one of the major branches of sandy intertidal sediments in the Antarctic, a Flavo- the (Garrity & Holt, 2001), was first bacteriaceae-like bacterium, designated strain ZS1-8T, was proposed by Jooste (1985). The name of the family was isolated (Yu et al., 2010). In the present study, the taxonomic validly published by Reichenbach (1992) before the position of the novel strain was investigated using a description of the taxon was emended by Bernardet et al. polyphasic approach. The results indicate that the strain (1996, 2002). At the time of writing, the family Flavo- represents a novel species in a new genus within the family bacteriaceae comprises 94 genera representing in Flavobacteriaceae. various terrestrial, marine and freshwater environments. In March 2007, during the 23rd Chinese National Antarctic Members of 13 of the genera, namely (Bowman Research Expedition, a sample of sandy sediment was & Nichols, 2002), (Bowman et al., 1997), Gilli- collected from the intertidal zone on the coast close to the sia (Van Trappen et al., 2004), Lacinutrix (Bowman & Chinese Antarctic Zhongshan Station, which lies on the Nichols, 2005), (Nedashkovskaya et al., Larsemann Hills of Princess Elizabeth Land (69u 229 220 S 2005b), Olleya (Nichols et al., 2005), (Gosink T 76u 229 340 E). A novel bacterium, designated strain ZS1-8 , et al., 1998), (Bowman et al., 1998), Psychro- was isolated, by the dilution plating technique, on 1/10- serpens (Bowman et al., 1997), (McCammon strength marine agar (MA; Difco) after incubation in the & Bowman, 2000), Sejongia (Yi et al., 2005), Subsaxi- dark at 4 uC for up to 8 weeks (Yu et al., 2010). Costertonia bacter (Bowman & Nichols, 2005) and Subsaximicrobium aggregata JCM 13411T was obtained from the Japan (Bowman & Nichols, 2005), have been isolated from marine Collection of Microorganisms (JCM) and used as a reference and coastal zones in the Antarctic. During an investigation strain. Strains were stored at 280 uC in marine 2216 broth on the diversity of the culturable bacteria associated with (MB; Difco) supplemented with 30 % (v/v) glycerol.

The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene Cell morphology was examined by phase-contrast micro- sequence of strain ZS1-8T is FJ889677. scopy (Eclipse 80i; Nikon) and transmission electron Three supplementary figures are available with the online version of this microscopy (JEM-100CX II; JEOL). Colonial morphology paper. was observed on MA after incubation at 18 uC for 7 days.

2218 037515 G 2012 IUMS Printed in Great Britain Pricia antarctica gen. nov., sp. nov.

Table 1. Phenotypic characteristics that distinguish strain ZS1-8T from Costertonia aggregata JCM 13411T

Strains: 1, ZS1-8T;2,Costertonia aggregata JCM 13411T. All data are from this study. Both strains give a positive result for alkaline phosphatase and leucine arylamidase activities but negative for ornithine decarboxylase, lipase (C14), a-chymotrypsin, acid phosphatase, cystine arylamidase, a- galactosidase, b-glucuronidase and a-glucosidase activities. Both produce acid from aesculin and utilize D-galactose, acetic acid and citric acid but not a-cyclodextrin, D-arabitol, D-psicose, succinic acid monomethyl ester, formic acid, D-glucosaminic acid, a-hydroxybutyric acid, itaconic acid, a- ketobutyric acid, a-ketoglutaric acid, sebacic acid, succinamic acid, L-phenylalanine, thymidine or 2,3-butanediol. +, Positive; 2, negative.

Characteristic 12

Enzyme activity: Arginine dihydrolase, lysine decarboxylase, urease, trypsin, b-galactosidase, b-glucosidase, N-acetyl-b-glucosaminidase, 2 + a-mannosidase and a-fucosidase Acid production from: Glycerol, L-arabinose, D-ribose, D-xylose, D-galactose, D-glucose, D-mannitol, melezitose and D-fucose + 2 Utilization of: Dextrin, glycogen, Tweens 40 and 80, N-acetyl-D-galactosamine, N-acetyl-D-glucosamine, adonitol, L-arabinose, cellobiose, 2 + L-erythritol, D-fructose, L-fucose, gentiobiose, a-D-glucose, myo-inositol, a-lactose, lactulose, maltose, D-mannitol, D-mannose, melibiose, methyl b-D-glucoside, raffinose, L-rhamnose, D-sorbitol, sucrose, trehalose, turanose, xylitol, methyl pyruvate, acetic acid, cis-aconitic acid, D-galactonic acid lactone, D-galacturonic acid, D-gluconic acid, D-glucuronic acid, b-hydroxybutyric acid, c-hydroxybutyric acid, p-hydroxyphenylacetic acid, a-ketoglutaric acid, a-ketovaleric acid, DL-lactic acid, malonic acid, propionic acid, quinic acid, D-saccharic acid, succinic acid, bromosuccinic acid, glucuronamide, L-alaninamide, D-alanine, L-alanine, L-alanyl glycine, L-asparagine, L-aspartic acid, L-glutamic acid, glycyl L-aspartic acid, glycyl L-glutamic acid, L-histidine, hydroxy L-proline, L-leucine, L-ornithine, L-proline, L-pyroglutamic acid, D-serine, L-serine, L-threonine, c-aminobutyric acid, urocanic acid, inosine, uridine, phenylethylamine, putrescine, 2-aminoethanol, glycerol, DL-a-glycerol phosphate, glucose 1-phosphate and glucose 6-phosphate

Table 2. Phenotypic characteristics that differentiate strain ZS1-8T from closely related members of the family Flavobacteriaceae

Taxa: 1, strain ZS1-8T (data from this study); 2, Costertonia aggregata KOPRI 13342T (Kwon et al., 2006; this study); 3, Flagellimonas eckloniae DOKDO 007T (Bae et al., 2007); 4, (two species; Lee et al., 2008); 5, (six species; Arun et al., 2009; Bruns et al., 2001; Hwang et al., 2009; Yoon et al., 2005b, 2008); 6, Maribacter (10 species; Barbeyron et al., 2008; Cho et al., 2008; Nedashkovskaya et al., 2004a, 2007; Yoon et al., 2005a; Zhang et al., 2009); 7, (five species; Barbeyron et al., 2001; Nedashkovskaya et al., 2004b); 8, Pibocella ponti KMM 6031T + (Nedashkovskaya et al., 2005a). All the taxa are positive for catalase, require Na for growth and have MK-6 as their major respiratory quinone. +, Positive; 2, negative; 2/+ or +/2, variable reaction between species (where the first sign indicates the result for the type species).

Characteristic 1 2 3 4 5 6 7 8

Flexirubin-type pigment 222222+ 2 Gliding motility 22222+/2 ++ Growth above 25 uC 2 +++++/2 ++ Growth at 0 uC + 22222 22 Optimum temperature for growth (uC) 17–19 28–30* 26–29 29–35 20–37 21–24D 21–35 21–24 ‘Seawater’ requirementd +++22 2 22 Facultative anaerobe 2222+/22 22 Nitrate reduction 2 + 222+/2 + 2 Oxidase activity ++22+/2 +++ Hydrolysis of: Agar 22222+/2 + 2 Casein 22+ 22 2+/2 + Gelatin 2 + 2 +/22 +/2 ++ Starch 222222/++/2 + DNA G+C content (mol%) 43.9 35.8 56.3 59-67 41–51 35–39 36–43 35.5

*Data from this study. DOptimum temperature for growth of Maribacter antarcticus CL-AP4T is recorded as 10 uC. + + + + dNa alone does not support growth because additional cations that are present in seawater, such as Mg2 ,Ca2 and/or K , are also required. http://ijs.sgmjournals.org 2219 Y. Yu and others

Gram staining was determined by the Hucker staining Table 3. Cellular fatty acid contents (%) of strain ZS1-8T and method (Murray et al., 1994) and the Gram reaction was Costertonia aggregata JCM 13411T investigated by the KOH lysis method (Buck, 1982). T T Gliding motility and flexirubin-type pigment production Strains: 1, ZS1-8 ;2,Costertonia aggregata JCM 13411 . All data are from this study. 2, Not detected; ECL, equivalent chain-length. were determined as described by Bowman (2000). Oxidase activity was determined using commercial oxidase test Fatty acid 1 2 strips (bioMe´rieux). Catalase activity was detected by bubble production in 3 % (v/v) H2O2. Growth at different Straight-chain temperatures was investigated in MB for 5–30 days. The C12 : 0 2 2.1 pH range for growth was determined using MB broth at C13 : 0 2 4.2 pH 5.0–10.5 (in increments of 0.5 pH unit) and 18 uC, C15 : 0 3.6 7.0 after the pH of the medium had been adjusted by the C16 : 0 0.7 2 addition of MES, MOPS, Tris or CHES buffers (each at Branched 50 mM). Growth with various concentrations of NaCl iso-C13 : 0 2 9.5 (0–10 %, w/v, in increments of 1 %) was tested in a me- iso-C15 : 0 17.0 12.2 dium containing (l21)5gMgCl, 2 g MgSO , 0.5 g CaCl , anteiso-C15 : 0 0.6 3.8 2 4 2 2 1 g KCl, 5 g peptone and sufficient KOH to give a pH of iso-C16 : 0 1.45 + + + Unsaturated 7.5 (Smibert & Krieg, 1994). NaCl, Mg2 ,Ca2 and/or K C AT 12–13 0.7 2 requirements were tested as described by Sohn et al. (2004). 13 : 1 anteiso-C15 : 1 A 0.8 2 Growth under anaerobic conditions was determined over iso-C G 27.2 20.5 10 days in MB, using an AnaeroJar anaerobic chamber 15 : 1 C15 : 1v6c 1.3 1.1 (Oxoid). Hydrolysis of casein, starch, Tween 80 and gelatin C16 : 1v5c 0.6 2 was determined as described by Smibert & Krieg (1994), on C17 : 1v6c 0.7 1.7 MA. Utilization of carbon sources, activities of constitutive iso-C17 : 1v9c 4.1 6.3 enzymes and other physiological properties were deter- Hydroxy mined by using the GN2 plate system (Microlog) and API C13 : 0 2-OH 2 8.9 20E, API 20NE and API ZYM strips (bioMe´rieux) accord- iso-C15 : 0 3-OH 1.8 2.6 ing to the manufacturers’ instructions, except that the iso-C16 : 0 3-OH 1.3 1.8 inoculum was prepared by suspending cells in 3 % (w/v) sea iso-C17 : 0 3-OH 6.1 4.4 salts solution (Sigma). Acid production from carbohydrates Summed features* was determined by using the API 50CH system, with sea salts 3 15.3 13.9 added to the API 50 CHB/E medium to give a final con- 4 0.49 2 centration of 3 % (w/v). The physiological, biochemical and Unknown morphological characteristics of strain ZS1-8T are given in ECL 11.543 2.7 2 the genus and species descriptions and in Tables 1 and 2. ECL 13.565 12.3 2 ECL 16.582 1.2 2 The identification service of the Deutsche Sammlung von Mikroorganismen und Zellkulturen, at Braunschweig, *Summed features represent two or more fatty acids that could not be Germany, determined the genomic DNA G+C content separated by GLC with the MIDI system. Summed feature 3 of the novel strain and analysed its respiratory quinones comprised iso-C15 : 0 2-OH and/or C16 : 1v7c. Summed feature 4 and polar lipids. The genomic DNA G+C content of the comprised iso-C17 : 1 I and/or anteiso-C17 : 1 B. novel strain, 43.9 mol%, was determined by HPLC, as described by Mesbah et al. (1989). Respiratory quinones were also analysed by HPLC (Wu et al., 1989), after they (27.2 %), iso-C15 : 0 (17.0 %), summed feature 3 (iso-C15 : 0 had been extracted and purified according to Collins 2-OH and/or C16 : 1v7c; 15.3 %), an unknown acid with an (1985). The major respiratory quinone detected was MK-6. equivalent chain-length of 13.565 (12.3 %) and iso-C17 : 0 Cellular polar lipids were extracted and analysed by TLC, 3-OH (6.1 %). In having three unknown fatty acids and on aluminium-backed silica gel plates (Merck), as lacking both C13 : 0 and C12 : 0, the fatty acid profile of strain described by Tindall (1990). The predominant polar lipid ZS1-8T clearly differed from that of Costertonia aggregata was phosphatidylethanolamine (see Fig. S1, available in JCM 13411T (Table 3). IJSEM Online). The extraction of genomic DNA extraction and the Cell biomass for fatty acid analysis was harvested from subsequent amplification and sequencing of the 16S rRNA cultures grown in MB at 18 uC for 7 days. Cellular fatty gene were carried out according to Yu et al. (2010). The acids were investigated (at the Shanghai Public Health almost-complete 16S rRNA gene sequence (1493 nt) of Clinical Centre, Fudan University, Shanghai, PR China) strain ZS1-8T was compared with sequences in the GenBank according to the standard protocol of the Sherlock and EMBL databases using the BLAST algorithm (Altschul Microbial Identification System (MIDI). The major fatty et al., 1990). The EzTaxon server (Chun et al., 2007) was T acids of strain ZS1-8 were identified as iso-C15 : 1 G used to identify phylogenetic neighbours and evaluate 16S

2220 International Journal of Systematic and Evolutionary Microbiology 62 Pricia antarctica gen. nov., sp. nov.

0.02 63 Muricauda jejuensis DSM 21206T (EU443206) Eudoraea adriatica AS06/20aT (AM745437) latericius KMM 426T (AF052742)

T 78 Pseudozobellia thermophila KMM 3531 (AB084261) Euzebyella saccharophila CECT 7477T (FN554868) 100 Kriegella aquimaris KMM 3665T (AB084262) Pibocella ponti KMM 6031T (AY576654) 87 Maribacter orientalis KMM 3947T (AY271624)

T 62 Maribacter dokdonensis DSW-8 (AY960749) 79 Maribacter sedimenticola KMM 3903T (AY271623) 56 Pricia antarctica ZS1-8T (FJ889677) KOPRI 13342T (DQ167246) Costertonia aggregata Fig. 1. A maximum-likelihood phylogenetic tree 54 DOKDO 007T (DQ191180) 100 Flagellimonas eckloniae based on 16S rRNA gene sequences, show- T 93 Croceitalea eckloniae KCCM 42309T (DQ191183) ing the relationship between strain ZS1-8 and B1T (AF218782) the most closely related members of the family

T Flavobacteriaceae. Bootstrap values ¢50 % 100 Dsij (AF208293) (based on 1000 resampled datasets) are given ATCC 14397T (M62799) Zobellia uliginosa at branch points. Bar, 0.02 substitution per biformata KCTC 12146T (AY424900) nucleotide position.

rRNA gene sequence similarities from pairwise compar- and Pibocella by many characteristics, such as the pre- isons. Sequences were aligned using version 1.8 of CLUSTAL_X sence/absence of flexirubin-type pigment, gliding motility (Thompson et al., 1997) and edited manually using version and oxidase activity and the temperature range for growth 5.0.9 of BioEdit (Hall, 1999). A phylogenetic tree was (Table 2). then constructed using the maximum-likelihood algorithm Based on the phenotypic and phylogenetic data presented within version 3.69 of the PHYLIP software package (Felsenstein, here, strain ZS1-8T represents a novel species of a new 2009). By implementing Kimura’s two-parameter model in genus for which the name Pricia antarctica gen. nov., sp. version 4 of the MEGA software suite (Tamura et al., 2007), a nov. is proposed. neighbour-joining tree was also constructed. Overall, 1391 unambiguously aligned positions were compared. In terms Description of Pricia gen. nov. of their 16S rRNA gene sequences, the closest relatives of strain ZS1-8T appeared to be Maribacter dokdonensis Pricia [Pri9ci.a. N.L. fem. n., arbitrary name derived from DSW-8T (93.3 % sequence similarity), Maribacter orientalis the acronym for the Polar Research Institute of China KMM 3947T (93.2 %) and Zobellia uliginosa ATCC 14397T (PRIC), where the type species was first isolated and (93.1 %). In pairwise comparisons with strain ZS1-8T, all examined]. other species belonging to the family Flavobacteriaceae Cells are rod-shaped, non-motile and Gram-staining- and showed 16S rRNA gene sequence similarities of ,93.0 %. An Gram-reaction-negative. Do not form endospores. Require + unrooted tree constructed using the maximum-likelihood Na ions for growth. Produce non-diffusible yellow T method showed the phylogenetic position of strain ZS1-8 pigments but no flexirubin-type pigments. The major within the family Flavobacteriaceae (Fig. 1). Although the respiratory quinone is MK-6 and the predominant polar topology of the corresponding neighbour-joining tree lipid is phosphatidylethanolamine. The major cellular fatty T (Fig. S2) was somewhat different, strain ZS1-8 shared a acids are iso-C G, iso-C , summed feature 3 (iso- T 15 : 1 15 : 0 phyletic line with Costertonia aggregata KOPRI 13342 C15 : 0 2-OH and/or C16 : 1v7c), an unknown acid with an (92.3 %) in both trees. At the time of writing, Costertonia equivalent-length of 13.565 and iso-C17 : 0 3-OH. Oxidase- aggregata is the only recognized species in the genus and catalase-positive. Analysis of 16S rRNA gene sequences T Costertonia. The small clade holding strain ZS1-8 and indicates that the genus Pricia should be considered a Costertonia aggregata KOPRI 13342T lies within a larger member of the family Flavobacteriaceae, phylum clade containing the genera Croceitalea, Flagellimonas and Bacteroidetes. The type species is Pricia antarctica. Muricauda. The carbohydrate utilization pattern and fatty acid profile of strain ZS1-8T were sufficient to distinguish T Description of Pricia antarctica sp. nov. the novel strain from Costertonia aggregata KOPRI 13342 (Tables 1 and 3). Furthermore, the novel strain could be Pricia antarctica (an.tarc9ti.ca. L. fem. adj. antarctica easily distinguished from species of the genera Costertonia, southern and, by extension, pertaining to Antarctic, the Croceitalea, Flagellimonas, Muricauda, Maribacter, Zobellia geographical origin of the type strain). http://ijs.sgmjournals.org 2221 Y. Yu and others

Properties are as described above for the genus with the description of the genus Maribacter. Int J Syst Evol Microbiol 58, 790– following additions. Cells are 0.6–0.9 mm in length and 0.3– 797. 0.9 mm in diameter. Growth occurs at 0–25 uC(optimum Bernardet, J.-F., Segers, P., Vancanneyt, M., Berthe, F., Kersters, K. & 17–19 uC), at pH 6.0–9.5 (optimum pH 7.5–8.0) and with Vandamme, P. (1996). Cutting a Gordian knot: emended classification 0.5–6 % (w/v) NaCl (optimum 2–3 %). After 7 days’ incuba- and description of the genus , emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis u tion at 18 C, colonies on MA are yellow, convex, circular nom. nov. (basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J and smooth, have entire edges and measure 0.5–1.0 mm in Syst Bacteriol 46, 128–148. diameter. Positive for alkaline phosphatase, leucine arylamidase Bernardet, J.-F., Nakagawa, Y., Holmes, B. for the Subcommittee and cytochrome oxidase activities but negative result for indole on the of Flavobacterium and Cytophaga-like bacteria of production, the Voges–Proskauer reaction, nitrate reduction the International Committee on Systematics of Prokaryotes and the production of H2S. Also negative result in tests for (2002). Proposed minimal standards for describing new taxa of the arginine dihydrolase, lysine decarboxylase, ornithine decarbox- family Flavobacteriaceae and emended description of the family. Int J ylase, lipase (C14), a-chymotrypsin, acid phosphatase, trypsin, Syst Evol Microbiol 52, 1049–1070. cystine arylamidase, a-galactosidase, b-galactosidase, b-glucur- Bowman, J. P. (2000). Description of algicola sp. nov., onidase, a-glucosidase, N-acetyl-b-glucosaminidase, a-manno- isolated from the surfaces of Antarctic algae, and reclassification of sidase and a-fucosidase activities. Positive result, in API 50CH Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 50, 1861– tests, for acid production from glycerol, L-arabinose, D-ribose, 1868. D-xylose, D-galactose, D-glucose, D-mannitol, aesculin, melezi- Bowman, J. P. & Nichols, D. S. (2002). Aequorivita gen. nov., a tose and D-fucose. In GN2 plates, D-galactose, acetic acid and member of the family Flavobacteriaceae isolated from terrestrial and citric acid are utilized as sole carbon sources. marine Antarctic habitats. Int J Syst Evol Microbiol 52, 1533–1541. The type strain, ZS1-8T (5JCM 17291T5DSM 23421T), Bowman, J. P. & Nichols, D. S. (2005). Novel members of the family was isolated from sandy intertidal sediment on the coast Flavobacteriaceae from Antarctic maritime habitats including Subsaxi- near the Chinese Antarctic Zhongshan Station in eastern microbium wynnwilliamsii gen. nov., sp. nov., Subsaximicrobium sa- + xinquilinus sp. nov., broadyi gen. nov., sp. nov., Lacinutrix Antarctica. The genomic DNA G C content of the type copepodicola gen. nov., sp. nov., and novel species of the genera , strain (as determined by HPLC) is 43.9 mol%. Gelidibacter and Gillisia. Int J Syst Evol Microbiol 55, 1471–1486. Bowman, J. P., McCammon, S. A., Brown, J. L., Nichols, P. D. & McMeekin, T. A. (1997). burtonensis gen. nov., sp. nov., Acknowledgements and Gelidibacter algens gen. nov., sp. nov., psychrophilic bacteria This work was supported by the National Natural Science Foundation isolated from Antarctic lacustrine and sea ice habitats. 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