Antonie van Leeuwenhoek (2015) 107:1379–1386 DOI 10.1007/s10482-015-0432-4

ORIGINAL PAPER

Aureisphaera galaxeae gen. nov., sp. nov., a marine member of the family Flavobacteriaceae isolated from the hard coral Galaxea fascicularis Jaewoo Yoon • Mina Yasumoto-Hirose Hiroaki Kasai

•

Received: 19 September 2014 / Accepted: 14 March 2015 / Published online: 21 March 2015 Ó Springer International Publishing Switzerland 2015

Abstract A novel Gram-stain negative, spherical, non-motile, strictly aerobic, heterotrophic, yellow pigmented bacterium, designated strain 04OKA0037T was isolated from the hard coral Galaxea fascicularis L. collected at Akajima, Okinawa, Japan. Phylogenetic analysis based on the 16S rRNA gene sequence revealed the novel isolate is affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and that it showed highest sequence similarity (92.9 %) to Vitellibacter aestuarii JC2436T and Aureitalea marina S1-66T. The strain could be differentiated phenotypically from recognized members of the family Flavobacteriaceae. The major fatty acids of strain 04OKA003-7T were identified as iso-C15:0 and iso-

J. Yoon (&) College of Pharmacy, Keimyung University, 1095 Dalgubeoldaero, Dalseo-Gu, Daegu 704-701, Republic of Korea e-mail: [email protected] M. Yasumoto-Hirose Marine Biotechnology Institute, 3-75-1 Heita, Kamaishi, Iwate 026-0001, Japan Present Address: M. Yasumoto-Hirose Tropical Technology Plus, 12-75 Suzaki, Uruma, Okinawa 904-2234, Japan H. Kasai Marine Biosciences Kamaishi Research Laboratory, Kitasato University, 160-4 Utou, Okirai, Sanriku-cho, Ofunato, Iwate 022-0101, Japan

C17:0 3-OH as defined by the MIDI system. The DNA G?C content was determined to be 41 mol%, the major respiratory quinone was identified as menaquinone 6 (MK-6) and a polar lipid profile was present consisting of phosphatidylethanolamine, two unidentified aminolipids and an unidentified lipid. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel genus for which the name Aureisphaera galaxeae gen. nov., sp. nov. is proposed. The type strain of A. galaxeae is 04OKA003-7T (=KCTC 32993T = NBRC 110018T). Keywords Bacteroidetes
Flavobacteriaceae
Aureisphaera galaxeae gen. nov., sp. nov.
Galaxea fascicularis
16S rRNA gene
Polyphasic taxonomy

Introduction Species of the phylum Bacteroidetes (Garrity and Holt 2001; Ludwig and Klenk 2001) are widely distributed in diverse ecosystems including soil, freshwater and marine habitats (McCammon et al. 1998; Kirchman 2002; O’Sullivan et al. 2006; Zeng et al. 2013). Among them, the family Flavobacteriaceae (Reichenbach 1989; Bernardet et al. 2002) is one of the largest phylogenetic groups within the phylum including more than 120 validly named genera at the time of writing (www.bacterio.cict.fr/f/flavobacteriaceae.html). The

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species of this phylogenetic group make an important contribution to the remineralization processes in the world’s oceans (Kirchman 2002; Brettar et al. 2004). However there have been still relatively few studies of their detailed taxonomy, physiology, biochemistry and ecological niches. Coral reefs in the marine habitat represent one of the most diverse and complex ecosystems of the earth with both economic and ecological relevance (Osinga et al. 2011). In the course of our study on the diversity of culturable marine bacteria from the hard coral samples collected at Akajima, Okinawa, Japan, a bacterium, designated 04OKA003-7T, was isolated. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the novel strain belongs to the family Flavobacteriaceae within the phylum Bacteroidetes. In this study, we characterised this novel marine bacterium, 04OKA003-7T isolated from the hard coral Galaxea fascicularis L. by using polyphasic taxonomic methods, including 16S rRNA gene sequence analysis, physiological, biochemical and chemotaxonomic analyses. Based on the polyphasic taxonomic data, we suggest that the isolate represents a novel genus and a new species of the family Flavobacteriaceae within the phylum Bacteroidetes.

Materials and methods Isolation of the bacterial strain and culture conditions Strain 04OKA003-7T was isolated from the hard coral G. fascicularis L. collected at Akajima, Okinawa, Japan in March 2004. A piece of the coral (approximately 1 g) was gently rinsed in sterile artificial seawater and then homogenized with a sterilized glass rod. After leaving the homogenate for 1 h until most of the suspended material settled out, a 50 lL of the supernatant was spread onto 1/10 strength marine agar 2216 (Difco). The medium consisted of 5.51 g marine agar 2216 in filtered three-quarter strength natural seawater. The agar medium was incubated for 2 weeks at 25 °C and the yellow coloured colonies that grew were purified on a fresh marine agar 2216. The strain was routinely subcultured on marine agar 2216 at 28 °C and maintained in marine broth 2216 (Difco) supplemented with 20 % (v/v) glycerol at -70 °C.

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Morphological, physiological and biochemical analyses Cell morphology was observed by using transmission electron microscopy (TEM) and motility was measured by phase contrast microscopy (Primo Star; Zeiss). Gliding motility was determined as described by Perry (1973). For TEM, cells were mounted on Formvar-coated copper grids and negatively stained with 1 % (w/v) aqueous uranyl acetate. Grids were observed using a Hitachi H-7100 microscope operated at 75 kV at a magnification of 30,000. The temperature range (4, 10, 15, 20, 30, 37, 40 and 45 °C) and pH range (5.5–9.5) for colony growth were determined by incubating the isolate for 2 weeks on marine agar 2216. The following buffers were used for pH tests: MES (pH 5.5), ACES (pH 6.5 and 7.0), TAPSO (pH 7.6), TAPS (pH 8.5) and CHES (pH 9.0 and 9.5). The NaCl concentration for growth was determined on marine agar 2216 (Atlas 1993) containing MgCl2 0.88 %, peptone 0.5 %, Na2SO3 0.32 %, CaCl2 0.18 %, yeast extract 0.1 %, KCl 0.05 %, NaHCO3 0.02 %, ferric citrate 0.01 %, KBr 0.008 %, SrCl2 0.003 %, H3BO3 0.002 %, Na2HPO4 0.8 %, Na2SiO3 0.4 %, NaF 0.24 %, NH4NO3 0.16 and 1.5 % agar with 0–10 % (w/v) NaCl (pH 7.6 ± 0.2 at 25 °C). The total amount of NaCl in the supplemented medium ranged from 2.5 to 12.5 % (w/v). Gram-staining was performed using the BD Gram staining Kit (Becton, Dickinson and Company, USA). Spore formation was tested by staining with malachite green. Anaerobic growth was tested for up to 2 weeks on marine agar 2216 in a jar containing AnaeroPack-Anaero (Mitsubishi Gas Chemical Co, Inc.), which works as an O2 absorber and CO2 generator. Catalase activity was detected by the observation of the formation of bubbles in 3 % (v/v) H2O2 solution. Oxidase activity test was performed using commercial dropper oxidase (Becton, Dickinson and Co.). Degradation of DNA was tested using DNase agar [DNase agar (Scharlau Chemie)] (Collins and Lyne 1984), with DNase activity detected by flooding plates with 1 M HCl. The ability to hydrolyse casein, Tween 20, Tween 80 and tyrosine were determined according to Hansen and Sørheim (1991). API 20E, API 50CH and API ZYM strips (bioMe´rieux) were used to determine the physiological and biochemical characteristics. All suspension media for the API test strips were supplemented with 0.85 % (w/v) NaCl solution

Antonie van Leeuwenhoek (2015) 107:1379–1386

(final concentration). API 20E, API 50CH and API ZYM test strips were read after 72 h incubation at 28 °C. Flexirubin-type pigments were investigated by using the bathochromic shift test with a 20 % (w/v) KOH solution (Bernardet et al. 2002). Determination of DNA G?C content, 16S rRNA gene sequencing and phylogenetic analyses Genomic DNA was prepared according to the method of Marmur (1961) from cells grown on marine agar 2216 and the DNA base composition was determined by using the HPLC method of Mesbah et al. (1989). Reciprocal genomic DNA G?C content was calculated in triplicate. An approximately 1500 bp long fragment of the 16S rRNA gene was amplified from the extracted DNA by using bacterial universal primers specific to the 16S rRNA gene: 27F and 1492R (Escherichia coli numbering system; Weisburg et al. 1991). To ascertain the phylogenetic position of the novel isolate, the 16S rRNA gene sequence of strain 04OKA003-7T was compared with sequences obtained from GenBank (National Center for Biotechnology Information, http://www.ncbi.nlm.nih.gov). Multiple alignments of the sequences were performed using CLUSTAL_X (version 1.83; Thompson et al. 1997). Alignment gaps and ambiguous bases were not taken into consideration when 1338 bases of the 16S rRNA gene were compared. Evolutionary distances (distance options according to Kimura’s two-parameter model; Kimura 1983) were calculated and clustering was performed with the neighbor-joining method (Saitou and Nei 1987), maximum-parsimony (Fitch 1971) and maximum-likelihood (Felsenstein 1985) methods using MEGA5 software (Tamura et al. 2011). Bootstrap analysis was used to evaluate the tree topology of the neighbor-joining data by performing 1000 resamplings (Felsenstein 1985). The topology of the phylogenetic tree was evaluated by the bootstrap resampling method of Felsenstein (1985) with 1000 replicates.

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to standard protocols provided by the MIDI/Hewlett packard microbial identification system Sherlock version 3.10/TSBA 50 (Sasser 1990). Polar lipids were extracted according to the procedures described by Minnikin et al. (1984). They were identified by two-dimensional TLC followed by spraying with appropriate detection reagents (Minnikin et al. 1984; Komagata and Suzuki 1987). Phospholipids were detected with the Zinzadze reagent of Dittmer and Lester (1964). Whole lipid profiles were detected by spraying with molybdatophosphoric acid (5 g molybdatophosphoric acid hydrate in 100 ml ethanol) followed by heating at 150 °C (Worliczek et al. 2007). Determination of the respiratory quinone system was carried out as described previously (Collins and Jones 1981).

Results and discussion Morphological, physiological and biochemical characteristics Cells of strain 04OKA003-7T grown on marine agar 2216 were observed to be coccoid and mostly 0.4–0.5 lm in diameter, devoid of flagella or cell appendages (Fig. 1) and produced a yellow pigment. Gliding motility was not observed by light microscopy. Flexirubin-type pigments were not produced.

Chemotaxonomic analysis Gas chromatography analysis of the cellular fatty acid methyl esters was performed using a culture grown on marine agar 2216 at 28 °C for 3 days and fatty acid methyl esters were extracted and prepared according

Fig. 1 Transmission electron micrograph of a negatively stained cell of strain 04OKA003-7T. Bar 500 nm

123

123 Coccus

Cell shape

Urea

-

? ? -

Lactose

Maltose

41 ± 1.4

DNA G?C content (mol%)

41.3

PE, UL

48.7

PE, UL

-

-

-

-

-

-

ND

-

?

-

?

-

?

6

10–41

-

8

Rod

Yellowish-orange

3

38.9

PE, UL

-

-

-

-

?

-

-

-

?

-

?

?

-

12

10–37

?

0.7–5.0

Rod

Strong yellow

4

48.1

PE, UL

?

?

-

?

-

-

-

?

?

?

?

-

-

4

15–30

-

0.5–6

Rod

Yellow

5

43

ND

?

?

ND

-

ND

ND

-

-

?

?

?

?

-

6

15–37

-

3.0–5.0

Rod

Yellow

6

33.5–39.1

PE, UAL, UGL, UL

±

±

±

±

±

±

-

-

?

-

-

-

-

10

4–40

±

2.0–4.5

Rod

Yellow–orange

7

PE phosphatidylethanolamine, UAL unidentified aminolipid, UL unidentified lipid, ? positive, - negative, V variable, ND no data

Strains: 1 04OKA003-7T (Aureisphaera galaxeae gen. nov., sp. nov.; present study), 2 Vitellibacter vladivostokensis NBRC 16718T (Nedashkovskaya et al. 2003; Park et al. 2014), 3 Vitellibacter aestuarii JC2436T (Kim et al. 2010; Park et al. 2014), 4 Vitellibacter soesokkakensis RSSK-12T (Park et al. 2014), 5 Aureitalea marina S1-66T (Park et al. 2012, 2013), 6 Gilvibacter sediminis Mok-1-36T (Khan et al. 2007), 7 Aequorivita spp. (Park et al. 2009; Liu et al. 2013)

PE, 2UAL, UL

Polar lipids

Sucrose

-

?

Glucose

-

? -

Cellobiose

-

-

?

Galactose

Acid production from

-

?

-

?

Starch

Hydrolysis of Gelatin

-

?

-

Nitrate reduction

Oxidase

?

-

-

Production of flexirubin-type pigments

6 ?

5.5

Highest NaCl tolerance (%, w/v)

4–43

V

3.0–10

Rod

Yellow–orange

2

-

20–30

Temperature range for growth (°C)

Catalase

-

Length

Gliding motility

0.4–0.5

Yellow

Pigmentation

Cell size (um)

1

Characterisitic

Table 1 Differential characteristics of strain 04OKA003-7T and other closely related taxa

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Antonie van Leeuwenhoek (2015) 107:1379–1386

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Fig. 2 Neighbor-joining tree of 16S rRNA gene sequence similarity, showing the phylogenetic position of strain 04OKA003-7T and representatives of the family Flavobacteriaceae. The sequence of Flammeovirga aprica NBRC 15941T

(AB247553) was used as an outgroup. The sequence determined in this study is shown in bold. Bootstrap values from neighborjoining, maximum-parsimony and maximum-likelihood analyses are shown (NJ/MP/ML). Bar 2 % sequence divergence

The strain also showed distinct phenotypic, physiological and biochemical features that discriminated it from the closest described members in the family Flavobacteriaceae as shown in Table 1.

Chemotaxonomic characteristics

Phylogenetic analysis The almost complete 16S rRNA gene sequence was determined for strain 04OKA003-7T (GenBank/ EMBL/DDBJ accession number AB983370). Comparative phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 04OKA003-7T belongs to the family Flavobacteriaceae in the phylum Bacteroidetes (Fig. 2). Analysis of the 16S rRNA gene sequence also indicated that that strain 04OKA003-7T showed the highest sequence similarity (92.9 %) to Vitellibacter aestuarii JC2436T and Aureitalea marina S1-66T, followed by Gilvibacter sediminis Mok-1-36T (92.7 %) and Aequorivita viscosa 8-1bT (92.6 %). Sequence similarity was less than 92.0 % with all other members of the family Flavobacteriaceae with validly published names (Fig. 2). Thus, on the basis of phylogenetic data presented, we believe that strain 04OKA003-7T should be considered as representative of a novel genus and species of the family Flavobacteriaceae within the phylum Bacteroidetes.

As shown in Table 2, the predominant cellular fatty acids of strain 04OKA003-7T were identified as isoC15:0 and iso-C17:0 3-OH as defined by the MIDI system (Version 3.10/TSBA 50). On the basis of the fatty acid composition, strain 04OKA003-7T could be differentiated from the phylogenetically closest taxa such as Vitellibacter vladivostokensis NBRC 16718T, V. aestuarii JC2436T, Vitellibacter soesokkakensis RSSK-12T, A. marina S1-66T and G. sediminis Mok1-36T as shown in Table 2. The polar lipids of strain 04OKA003-7T were determined to be composed of phosphatidylethanolamine, two unidentified aminolipids and an unidentified lipid. From these results, it is strongly suggested that strain 04OKA003-7T represents an independent genus of the family Flavobacteriaceae within the phylum Bacteroidetes. Polyphasic taxonomic conclusion From the distinct phylogenetic position and combinations of genotypic and phenotypic characteristics, strain 04OKA003-7T cannot be assigned to any previously recognized bacterial genus and thus can be described as representing a novel species within a

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Table 2 Comparison of cellular fatty acids for strain 04OKA003-7T and other closely related taxa Fatty acid

1

2

3

4

5

6

7

anteiso-C13:0

tr

–

–

–

–

–

–

iso-C14:0

2.7

tr

tr

tr

–

1

–

C14:0 iso-C15:1

tr –

– –

– –

– –

– 20.3

– 15

– –

iso-C15:1 G

7.7

1.6

4.7

–

–

–

4.1–6.4

iso-C15:0

29.9

40.1

36.7

34.2

26.4

19

7.7–34.4

anteiso-C15:0

1.4

4.5

5.4

2.9

3.8

1

5–20.7

C15:0

–

–

–

–

4.6

–

tr–3.6

iso-C14:0 3-OH

tr

–

–

–

–

–

–

iso-C16:1

–

–

–

–

–

4

–

iso-C16:1 G

tr

–

–

–

–

–

–

iso-C16:0

1.6

1.7

1.7

2.8

5.3

7

tr–5.3

C16:0

1.9

2.9

1.4

2

tr

2

tr–3.9

iso-C15:0 3-OH

7

–

3.9

4.3

3.3

–

1.5–5.4

C15:0 2-OH

tr

–

1

tr

–

1

tr–2.3

C15:0 3-OH

tr

–

–

–

–

5

–

iso-C17:0

tr

2.4

tr

1.2

–

–

–

anteiso-C17:0

tr

–

–

–

–

–

–

iso-C17:1 x9c C17:0

– tr

6.8 –

6.7 –

6.6 –

– –

– –

8.7–13.7 –

iso-C16:0 3-OH

4.2

tr

1.4

2.3

2.9

9

1.1–9.2

C16:0 3-OH

1.2

–

–

–

–

–

–

C18:1 x9c

tr

–

–

–

–

–

–

C18:0

tr

–

–

–

–

–

2.8

iso-C17:0 3-OH

31.1

25.3

20.8

29.4

14.2

16

2–18.3

C17:0 2-OH

1.1

1

tr

1.1

–

tr

tr–5.3

C17:0 3-OH

tr

tr

tr

1.1

–

–

–

Summed feature 2a

tr

–

–

–

–

–

–

Summed feature 3b

5.9

5.6

10.9

5.8

7.8

7

3.5–7.3

Strains: 1 04OKA003-7T (Aureisphaera galaxeae gen. nov., sp. nov.; present study), 2 Vitellibacter vladivostokensis NBRC 16718T (Park et al. 2014), 3 Vitellibacter aestuarii JC2436T (Park et al. 2014), 4 Vitellibacter soesokkakensis RSSK-12T (Park et al. 2014), 5 Aureitalea marina S1-66T (Park et al. 2012), 6 Gilvibacter sediminis Mok-1-36T (Khan et al. 2007), 7 Aequorivita spp. (Park et al. 2009; Liu et al. 2013) tr trace (less than 1.0 %), – not detected. The data were typically obtained by GLC using the MIDI system a

Summed feature 2 consists of C14:0 3-OH and/or iso-C16:1 I

b

Summed feature 3 consists of C16:1 x6c and/or C16:1 x7c

new genus, Aureisphaera galaxeae gen. nov., sp. nov.

Description of Aureisphaera gen. nov. Aureisphaera (Au.re.i.sphae’ra. L. adj. aureus golden; L. fem. n.sphaera sphere; N.L. fem. n. Aureisphaera golden sphere).

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A member of the family Flavobacteriaceae, phylum Bacteroidetes, according to 16S rRNA gene sequence analyses. Cells are Gram-stain negative, motile, spherical and strictly aerobic. Endospores are not formed. Catalase- and oxidase-negative. Flexirubin-type pigments are absent. The major respiratory quinone is menaquinone 6 (MK-6). The predominant cellular fatty acids are iso-C15:0 and iso-C17:0 3-OH as identified by the MIDI system. The DNA G?C

Antonie van Leeuwenhoek (2015) 107:1379–1386

content of the type strain of the type species is 41 ± 1.4 mol%. The type species is Aureisphaera galaxeae.

Description of Aureisphaera galaxeae sp. nov. Aureisphaera galaxeae (ga.la’xe.ae. N.L. gen. n. galaxeae of the hard coral G. fascicularis from which the organism was isolated). In addition to the properties given in the genus description, cells are strictly aerobic cocci that are 0.4–0.5 lm in diameter. Cells lack flagella and are non-motile. Gliding motility is not observed. Colonies grown on marine agar 2216 are circular and yellow pigmented after 5 days of incubation at 28 °C. Temperature range for growth is 20–30 °C; the optimal temperature is around 28 °C but no growth occurs at 4 or 45 °C. The pH range for growth is 7–9 (optimum, pH 7), while no growth is observed below 6 or above 10. NaCl is required for growth and can be tolerated at a concentration of up to 5.5 % (w/v) but no growth occurs above 6.5 % (w/v) NaCl. Nitrate is not reduced. Gelatin and urea are hydrolysed but agar, casein, DNA, starch, tyrosine, Tween 20 and Tween 80 are not. The reactions for o-nitrophenyl-b-D-galactopyranoside (ONPG), Voges–Proskauer test, citrate utilization, hydrogen sulfide production, indole production, arginine dihydrolase, lysine decarboxylase and ornithine decarboxylase activities are negative (API 20E). Acid production tests using API 50CH strips give the following reactions: acid is produced from methyl-b-D-xylopyranoside, glucose, amygdalin, arbutin, esculin ferric citrate, cellobiose, maltose and lactose but not from D-arabinose, galactose, fructose, mannose, melibiose, D-turanose, salicin, L-arabitol, 5-keto-gluconate, sucrose, trehalose, starch, glycogen, gentiobiose, L-fucose, ribose, sorbose, rhamnose, sorbitol, methyl-a-D-mannopyranoside, L-arabinose, D-xylose, L-xylose, methyl-a-D-glucopyranoside, Nacetyl-glucosamine, melezitose, D-lyxose, D-tagatose, D-fucose, inulin, raffinose, glycerol, erythritol, adonitol, dulcitol, inositol, mannitol, xylitol, D-arabitol, gluconate and 2-keto-gluconate. In the API ZYM strip, alkaline phosphatase, leucine arylamidase, valine arylamidase, acid phosphatase and naphthol-AS-BIphosphohydrolase are present but trypsin, b-galactosidase, a-glucosidase, b-glucosidase, N-acetyl-bglucosaminidase, esterase (C4), esterase lipase (C8),

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a-galactosidase, lipase (C4), cystine arylamidase, achymotrypsin, b-glucuronidase, a-mannosidase and a-fucosidase are absent. The major fatty acids are isoC15:0 and iso-C17:0 3-OH. The major polar lipids are phosphatidylethanolamine, two unidentified aminolipids and an unidentified lipid. The G?C of the genomic DNA of the type strain is 41 mol%. The type strain is 04OKA003-7T (=KCTC 32993T = NBRC 110018T), which was isolated isolated from from the hard coral G. fascicularis L. collected at Akajima, Okinawa, Japan. The GenBank/EMBL/ DDBJ accession number of the 16S rRNA gene sequence of strain 04OKA003-7T is AB983370. Acknowledgments The present research has been conducted by the Educational-Industrial Collaboration Research Grant of SAMICK THK in 2015.

References Atlas RM (1993) In: Parks LC (ed) Handbook of microbiological media. CRC, Boca Raton Bernardet JF, Nakagawa Y, Holmes B (2002) Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52:1049–1070 Brettar I, Christen R, Ho¨fle MG (2004) Aquiflexum balticum gen. nov., sp. nov., a novel marine bacterium of the Cytophaga-Flavobacterium-Bacteroides group isolated from surface water of the central Baltic Sea. Int J Syst Evol Microbiol 54:2335–2341 Collins MD, Jones D (1981) A note on the separation of natural mixtures of bacterial ubiquinones using reverse-phase partition thin-layer chromatography and high performance liquid chromatography. J Appl Bacteriol 51:129–134 Collins CH, Lyne PM (1984) Microbiological methods, 5th edn. Butterworth, London Dittmer JC, Lester RL (1964) A simple, specific spray for the detection of phospholipids on thin-layer chromoatograms. J Lipid Res 15:126–127 Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 Fitch WM (1971) Towards defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416 Garrity GM, Holt JG (2001) The road map to the manual. In: Boone DR, Castenholz RW, Garrity GM (eds) Bergey’s manual of systematic bacteriology, vol 1, 2nd edn. Springer, New York, pp 119–166 Hansen GH, Sørheim R (1991) Improved method for phenotypical characterization of marine bacteria. J Microbiol Methods 13:231–241 Khan ST, Nakagawa Y, Harayama S (2007) Sediminibacter furfurosus gen. nov., sp. nov. and Gilvibacter sediminis gen. nov., sp. nov., novel members of the family Flavobacteriaceae. Int J Syst Evol Microbiol 57:265–269

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1386 Kim BS, Kim OS, Moon EY, Chun J (2010) Vitellibacter aestuarii sp. nov., isolated from tidal-flat sediment, and an emended description of the genus Vitellibacter. Int J Syst Evol Microbiol 60:1989–1992 Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge Kirchman DL (2002) The ecology of Cytophaga-Flavobacteria in aquatic environments. FEMS Microbiol Ecol 39:91–100 Komagata K, Suzuki K (1987) Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–207 Liu JJ, Zhang XQ, Pan J, Sun C, Zhang Y, Li CQ, Zhu XF, Wu M (2013) Aequorivita viscosa sp. nov., isolated from an intertidal zone, and emended descriptions of Aequorivita antarctica and Aequorivita capsosiphonis. Int J Syst Evol Microbiol 63:3192–3196 Ludwig W, Klenk HP (2001) Overview: a phylogenetic backbone and taxonomic framework for procaryotic systematics. In: Boone DR, Castenholz RW, Garrity GM (eds) Bergey’s manual of systematic bacteriology, vol 1, 2nd edn. Springer, New York, pp 49–66 Marmur J (1961) A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 3:208–218 McCammon SA, Innes BH, Bowman JP, Franzmann PD, Dobson SJ, Holloway PE, Skerratt JH, Nichols PD, Rankin LM (1998) Flavobacterium hibernum sp. nov., a lactose utilizing bacterium from a freshwater Antarctic lake. Int J Syst Bacteriol 48:1405–1412 Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G?C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167 Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinines and polar lipids. J Microbiol Methods 2:233–241 Nedashkovskaya OI, Suzuki M, Vysotskii MV, Mikhailov VV (2003) Vitellibacter vladivostokensis gen. nov., sp. nov., a new member of the phylum Cytophaga–Flavobacterium– Bacteroides. Int J Syst Evol Microbiol 53:1281–1286 O’Sullivan LA, Rinna J, Humphreys G, Weightman AJ, Fry JC (2006) Culturable phylogenetic diversity of the phylum ‘Bacteroidetes’ from river epilithon and coastal water and description of novel members of the family Flavobacteriaceae: Epilithonimonas tenax gen. nov., sp. nov. and Persicivirga xylanidelens gen. nov., sp. nov. Int J Syst Evol Microbiol 56:169–180 Osinga R, Schutter M, Griffioen B, Wijffels RH, Verreth JA, Shafir S, Henard S, Taruffi M, Gili C, Lavorano S (2011) The biology and economics of coral growth. Mar Biotechnol (NY) 13:658–671 Park SC, Baik KS, Kim MS, Kim SS, Kim SR, Oh MJ, Kim D, Bang BH, Seong CN (2009) Aequorivita capsosiphonis sp.

123

Antonie van Leeuwenhoek (2015) 107:1379–1386 nov., isolated from the green alga Capsosiphon fulvescens, and emended description of the genus Aequorivita. Int J Syst Evol Microbiol 59:724–728 Park S, Yoshizawa S, Inomata K, Kogure K, Yokota A (2012) Aureitalea marina gen. nov., sp. nov., a member of the family Flavobacteriaceae, isolated from seawater. Int J Syst Evol Microbiol 62:912–916 Park S, Lee JS, Lee KC, Yoon JH (2013) Jejudonia soesokkakensis gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from the junction between the ocean and a freshwater spring, and emended description of the genus Aureitalea Park et al. 2012. Antonie Van Leeuwenhoek 104:139–147 Park S, Lee KC, Bae KS, Yoon JH (2014) Vitellibacter soesokkakensis sp. nov., isolated from the junction between the ocean and a freshwater spring and emended description of the genus Vitellibacter. Int J Syst Evol Microbiol 64: 588–593 Perry LB (1973) Gliding motility in some non-spreading flexibacteria. J Appl Microbiol 36:227–232 Reichenbach H (1989) Genus I. Cytophaga Winogradsky 1929, 577, AL emend. In: Staley JT, Bryant MP, Pfennig N, Holt JC (eds) Bergey’s manual of systematic bacteriology, vol 3. Williams, Wilkins, Baltimore, pp 2015–2050 Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425 Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. MIDI, Inc. Newark Tamura K, Peterson D, Petersen 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 Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882 Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703 Worliczek HL, Ka¨mpfer P, Rosengarten R, Tindall BJ, Busse HJ (2007) Polar lipid and fatty acid profiles-re-vitalizing old approaches as a modern tool for the classification of mycoplasmas? Syst Appl Microbiol 30:355–370 Zeng YX, Zhang F, He JF, Lee SH, Qiao ZY, Yu Y, Li HR (2013) Bacterioplankton community structure in the Arctic waters as revealed by pyrosequencing of 16S rRNA genes. Antonie Van Leeuwenhoek 103:1309–1319