IJSEM Papers in Press. Published March 11, 2015 as doi:10.1099/ijs.0.000186

International Journal of Systematic and Evolutionary Microbiology Chryseobacterium shandongense sp. nov., isolated from soil --Manuscript Draft-Manuscript Number:

IJSEM-D-14-00211R1

Full Title:

Chryseobacterium shandongense sp. nov., isolated from soil

Short Title:

Chryseobacterium shandongense sp. nov.

Article Type:

Note

Section/Category:

New taxa - Bacteroidetes

Corresponding Author:

Qing Hong College of Life Science of Nanjing Agricultural University Nanjing, CHINA

First Author:

Fan Yang

Order of Authors:

Fan Yang Hong-ming Liu Rong zhang Ding-bin chen Xiang wang Shun-peng LI Qing Hong

Manuscript Region of Origin:

CHINA

Abstract:

YF-3T was a Gram-staining-negative, non-motile, non-spore-forming, yellow-orangepigmented, rod-shaped bacterium. Its best growth conditions were at 30 °C, pH 7.0 and 1 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain YF-3T was closely related to strains Chryseobacterium hispalense AG13T and Chryseobacterium taiwanense Soil-3-27T with 98.71 % and 96.93 % sequence similarity, respectively. Strain YF-3T contained MK-6 as the main menaquinone and had a polyamine pattern with sym-homospermidine as the major component. Its major polar lipid was phosphatidylethanolamine. The dominant fatty acids of strain YF-3T were iso-C15:0, iso-C17:0 3-OH, summed feature 9 (comprising iso-C17:1 ω9c and/or C16:0 10-methyl) and summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c). The DNA G+C content of strain YF-3T was 37 mol %. The levels of DNA-DNA relatedness between strain YF-3T and the most closely related strains Chryseobacterium hispalense AG13T and Chryseobacterium taiwanense Soil-3-27T were 31.7 ± 2.1 % and 28.4 ± 5.4 %, respectively. Based on these results, a novel species named Chryseobacterium shandongense sp. nov. was proposed. The type strain is YF-3T (=CCTCC AB 2014060T=JCM 30154T).

Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation

Manuscript Including References (Word document) Click here to download Manuscript Including References (Word document): renamed_456fe.doc

1

Chryseobacterium shandongense sp. nov., isolated from soil

2

Fan Yang*, Hong-ming Liu*, Rong Zhang, Ding-bin Chen, Xiang Wang, Shun-peng Li, Qing

3

Hong**

4

Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of

5

Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.

6 7 8 9 10 11

*These authors contributed equally to this work.

12

**Author for correspondence:

13

Qing Hong

14

E-mail: [email protected]

15

Subject Category: New Taxa-(Bacteroidetes)

16

Running Title: Chryseobacterium shandongense sp. nov.

17

The 16S rRNA gene sequence has been deposited in the GenBank under accession number

18

KJ644318

19

Four supplementary figures and one supplementary table are available with the online version of

20

this paper.

21

YF-3T

22

yellow-orange-pigmented, rod-shaped bacterium. Its best growth conditions were at 30 °C,

23

pH 7.0 and 1 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence showed

24

that strain YF-3T was closely related to strains Chryseobacterium hispalense AG13T and

25

Chryseobacterium taiwanense Soil-3-27T with 98.71 % and 96.93 % sequence similarity,

26

respectively. Strain YF-3T contained MK-6 as the main menaquinone and had a polyamine

27

pattern with sym-homospermidine as the major component. Its major polar lipid was

28

phosphatidylethanolamine. The dominant fatty acids of strain YF-3T were iso-C15:0, iso-C17:0

29

3-OH, summed feature 9 (comprising iso-C17:1 ω9c and/or C16:0 10-methyl) and summed

30

feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c). The DNA G+C content of strain YF-3T was

31

37 mol %. The levels of DNA–DNA relatedness between strain YF-3T and the most closely

32

related strains Chryseobacterium hispalense AG13T and Chryseobacterium taiwanense

33

Soil-3-27T were 31.7 ± 2.1 % and 28.4 ± 5.4 %, respectively. Based on these results, a novel

34

species named Chryseobacterium shandongense sp. nov. was proposed. The type strain is

35

YF-3T (=CCTCC AB 2014060T=JCM 30154T).

was

a

Gram-staining-negative,

non-motile,

non-spore-forming,

36

37

The genus Chryseobacterium represents one of the genera with the fastest growing number of spec

38

genus ies (Herzog et al., 2008) and they could be found in a wide variety of environments. The

39

Chryseobacterium was first described by Vandamme et al. (1994). At the time of writing, it

40

contains 88 species with validly published names (http://www.bacterio.cict.fr/). During 1994-2000,

41

the genus only contained seven species: Chryseobacterium vandamme, C. balustinum, C. gleum, C.

42

indologenes, C. indoltheticum, C. meningosepticum and C. scophthalmum. However, the number

43

of species increased by 45 and 33 during 2001-2010 and 2011-2014, respectively. These newly

44

found members of the genus Chryseobacterium are distributed in a variety of environments, such

45

as roots (Park et al., 2006), lake (Yochan & Kiseong, 2011), clinical samples (Vaneechoutte et al.,

46

2007), soil (Li & Zhu, 2012), sludge (Pires et al., 2010), raw milk (Hantsis-Zacharov & Halpern,

47

2007), midgut of insects (Kämpfer et al., 2010a), food products (including raw cow’s milk, fish,

48

poultry and lactic acid beverages) (Hantsis-Zacharov et al., 2008) and human clinical sources

49

(Yassin et al., 2010). In this paper, strain YF-3T was isolated from soil in Qingdao, Shandong

50

province, China (35° 35′~ 37° 09′ N 119° 30′~121° 00′ E).

51

During the isolation of strains, 10 grams of soil was added in a flask containing 100 ml trypticase

52

soy broth (TSB) and incubated at 30 °C at 150 r.p.m. for 2 days. Trypticase soy agar (TSA) plates

53

were spread with 0.1 ml diluted soil suspension and incubated at 30 °C for 2 days. A

54

yellow-orange-pigmented colony was selected, purified and then the isolate was cultivated at

55

30 °C on the same medium and preserved in 20 % (w/v) glycerol at -80 °C.

56

Strain YF-3T was cultivated on TSA plates at 30 °C for 2 days. The presence of flexirubin-type

57

pigments was investigated by noting whether a color shift occurred when the colony was flooded

58

with 20 % KOH (Fautz & Reichenbach, 1980). Gram-staining was performed by the modified

59

method of Gerhardt et al. (1994). Cell motility was determined according the procedure described

60

by Smibert & Krieg (1994). A colony of strain YF-3T was picked from the last quadrant streak

61

after it was grown on TSA at 30 °C for 24 h. Then the cell morphology and dimensions were

62

determined by transmission electron microscopy (H-7650; Hitachi) (Fig. S1 available as

63

supplementary material in IJSEM Online). Growth at different temperatures (4, 20, 25, 30, 37,

64

42 °C) and different pH values 4-10 (at 1 pH unit intervals) was assessed in TSB, the pH range

65

was buffered with citrate/phosphate buffer or Tris/hydrochloride buffer (Breznak & Costilow,

66

1994). Salt tolerance was investigated on TSB supplemented with 0-9 % (w/v) NaCl (at 1 %

67

intervals). The OD600 value of different treatments was determined after 3 days of incubation in

68

order to evaluate the growth of strain YF-3T. In addition, growth on Luria-Bertani (LB) agar, R2A

69

agar, nutrient agar (NA), cetrimide agar (CA), Simmons’ citrate (SC) agar and MacConkey agar

70

were also evaluated.

71

72

Catalase activity was determined by bubble production with 3 % (v/v) H2O2. Oxidase activity was

73

assayed using filter-paper discs (grade 388; Sartorius) impregnated with 1 % (w/v) solution of N,

74

N, N′, N′-tetramethyl-p-phenylenediamine (Sigma-Aldrich). A positive result was indicated by the

75

development of a blue-purple color after applying biomass to the filter paper. Antibiotic

76

susceptibility tests were performed with the discs (Hangzhou tianhe Microbial Reagent Co.)

77

diffusion method on TSA plates incubated at 30 °C for 2 days. Strains were considered sensitive

78

when the diameter of the inhibition zone was ≥ 10 mm (Jorgensen & Farrow, 2009). The

79

hydrolysis of DNA, cellulose, starch and casein were investigated as described by Smibert and

80

Krieg (1994). Basic biochemical, enzyme activity and carbon source tests were performed using

81

the API 20NE, the API 20E, the API ZYM systems (bioMérieux) and GN2 MicroPlate (Biolog)

82

according to the manufacturers’ instructions.

83 84

For the analysis of whole-cell fatty acid, strain YF-3T and the reference strains (Chryseobacterium

85

hispalense AG13T and Chryseobacterium taiwanense Soil-3-27T) were grown on TSA at 30 °C for

86

24 h. The biomasses, harvested always from the same sector (the last quadrant streak) were freeze

87

dried, then the fatty acid methyl esters were extracted according to the standard procedure of the

88

Microbial Identification System (MIDI Corporation) (Sasser, 1990). Extracts were analyzed using

89

a Hewlett Packard model 6890 gas chromatograph equipped with a flame-ionization detector

90

(Kämpfer & Kroppenstedt, 1996) and a 5 % phenyl-methyl-silicone capillary column. The

91

extraction for the respiratory quinones was carried out from freeze-dried cell material according to

92

Collins et al. (1977) and determined by HPLC (Tamaoka et al., 1983). Polar lipids were extracted

93

from 100 mg of freeze-dried cell material using a chloroform: methanol: 0.3 % aqueous NaCl

94

mixture 1: 2: 0.8 (v/v/v) (Tindall et al., 2007). Then polar lipids were recovered into the

95

chloroform phase by adjusting the chloroform: methanol: 0.3 % aqueous NaCl mixture to a ratio

96

of 1: 1: 0.9 (v/v/v). Polar lipids were separated by two dimensional silica gel thin layer

97

chromatography. Total lipid material was detected using molybdatophosphoric acid and specific

98

functional groups were detected using spray reagents specific for defined functional groups

99

(Tindall et al., 2007) (DSMZ service, Susanne Verbarg) (Fig. S2 available as supplementary

100

material in IJSEM Online). Cells of strain YF-3T used for polyamine analysis were grown on

101

TSB, harvested at late exponential growth phase and lyophilized. Extraction of polyamines was

102

performed as described by Busse & Auling (1988) and analysis was conducted using the HPLC

103

equipment described by Stolz et al. (2007).

104 105

The genomic DNA of strain YF-3T was extracted and purified according to the method described

106

by Sambrook & Russell, 2001 and the DNA G+C content was determined by reversed-phase

107

HPLC (Tamaoka & Komagata, 1984) using Escherichia coli K-12 as a standard. DNA-DNA

108

hybridizations were performed at 50 °C, with photobiotin-labelled probes in microplate wells, as

109

described by Ezaki et al. (1989). A bioassay plate reader (HTS 7000, Perkin Elmer) was used to

110

measure the fluorescence, and reciprocal experiments were performed with each pair of strains to

111

be investigated. The 16S rRNA gene of strain YF-3T was amplified with bacterial universal

112

primers 27F and 1492R (Lane, 1991). The PCR products were purified using the AxyPrep PCR

113

Purification kit (AxyGen) and were cloned into pMD 19-T Vector. The purified plasmid DNA was

114

sequenced by an automated sequencer (Applied Biosystems, model 3730). Pairwise sequence

115

similarity

116

(http://eztaxon-e.ezbiocloud.net/; Kim et al., 2012). Phylogenetic analysis was performed by using

117

MEGA version 5.0 (Tamura et al., 2011) after multiple alignment of data by CLUSTAL_X

118

(Thompson et al., 1997). Distances were determined through distance options based on Kimura’s

119

two-parameter system (Kimura, 1980). Unrooted trees were constructed via neighbor-joining

120

(Saitou & Nei, 1987) (Fig.1), maximum-parsimony (Fitch, 1971) (Fig.S3 available as

121

supplementary material in IJSEM Online) and maximum-likelihood (Felsenstein, 1981) (Fig.S4

122

available as supplementary material in IJSEM Online) methods. Confidence values for the

123

branches of phylogenetic trees were calculated according to bootstrap analyses (based on 1000

124

resamplings) (Felsenstein, 1985).

was

calculated

with

the

known

sequences

using

the

EzTaxon

server

125

126

YF-3T was Gram-staining-negative, rod-shaped (0.5-0.7 μm in width, 2.1-2.3 μm in length),

127

non-spore-forming and non motile. The colony of strain YF-3T on TSA plate was

128

yellow-orange-pigmented, circle, convex, smooth, translucent and shiny, and the colonies were not

129

visible as single entities after prolonged incubation. The best growth conditions of YF-3T were

130

30 °C, 1 % (w/v) NaCl and pH 7.0 in TSB. Good growth also occurred on LB agar and R2A agar;

131

weak growth occurred on NA; no growth occurred on CA, SC agar or MacConkey agar. Resistant

132

to tenebrimycin, streptomycin, amikacin, oxacillin, kanamycin, aztreonam and gentamicin, but

133

sensative to chloromycetin, cefotaxim, spectinomycin, minocycline, levofloxacin, cefuroxime,

134

cefoperazone, cefoxitin, norfloxacin, furadantin, ciprofloxacin, midecamycin, polymyxin B,

135

vancomycin, ofloxacin, erythromycin, clindamycin, tetracycline, benzylpenicillin, cefazolin,

136

cefepime, ampicillin, ceftriaxone, trimethoprim-sulfamethoxazole, ceftazidime, cefalotin and

137

piperacillin. The morphological, cultural, physiological and biochemical characteristics of strain

138

YF-3T are listed in the species description. The differences between strain YF-3T and reference

139

strains (Chryseobacterium hispalense AG13T and Chryseobacterium taiwanense Soil-3-27T) were

140

given in Table 1.

141 142

The predominant fatty acids of strain YF-3T ( ≥ 5 %) were iso-C15:0, iso-C17:0 3-OH, summed

143

feature 9 (comprising iso-C17:1 ω9c and/or C16:0 10-methyl) and summed feature 3 (comprising

144

C16:1 ω7c and/or C16:1 ω6c), which was consistent with those of the closest phylogenetic

145

neighbours grown under the same conditions. Smaller amounts of anteiso-C15:0 and iso-C15:0 3-OH

146

were also present. The detailed fatty acid composition of strain YF-3T is shown in Table 2 in

147

comparison

148

Chryseobacterium taiwanense Soil-3-27T). The polar lipid profile of strain YF-3T consisted of the

149

predominant compounds phosphatidylethanolamine (PE), five unknown lipids (L1-L5) and two

150

unknown aminolipids (AL1 and AL2). The main respiratory quinone was menaquinone MK-6.

with

the

reference

strains

(Chryseobacterium

hispalense

AG13T

and

151

Polyamine analysis indicated that sym-homospermidine [43.2 μmol (g dry weight)-1] was the

152

major component and that minor amounts of spermidine [3.1 μmol (g dry weight)-1] and spermine

153

[2.8 μmol (g dry weight)-1] and traces of 1,3-diaminopropane, cadaverine and putrescine [< 0.1

154

μmol (g dry weight)-1] were also present, which is consistent with the characteristics of other

155

members of the genus Chryseobacterium (Hamana & Matsuzaki, 1990; Kämpfer et al., 2003). The

156

DNA G+C content of strain YF-3T was 37 mol%.

157 158

A nearly full-length 16S rRNA gene sequence (1478bp) of strain YF-3T was determined. The

159

similarity analysis of the 16S rRNA gene sequences showed that strain YF-3T was most closely

160

related to Chryseobacterium hispalense AG13T (98.71 %) and Chryseobacterium taiwanense

161

Soil-3-27T (96.93 %). Phylogenetic analysis based on sequence similarity of 16S rRNA gene

162

indicated the relationship between strain YF-3T and the genus Chryseobacterium (Fig.1).

163

DNA–DNA hybridization was carried out to further determine the taxonomic status of YF-3T with

164

its closest relatives.

165

YF-3T and Chryseobacterium hispalense AG13T and Chryseobacterium taiwanense Soil-3-27T

166

were found to be 31.7 ± 2.1 % and 28.4 ± 5.4 %, respectively (Table. S1 available as

167

supplementary material in IJSEM Online), which were far below the value of 70 % that is

168

commonly accepted do define a new species (Wayne et al., 1987) .

In the present study, the level of DNA–DNA relatedness between strain

169 170

Therefore, on the basis of phylogenetic, phenotypic and chemotaxonomic data, strain YF-3T

171

should represent a novel species of the genus Chryseobacterium, for which the name

172

Chryseobacterium shandongense sp. nov. is proposed.

173 174

Description of Chryseobacterium shandongense sp. nov.

175

Chryseobacterium shandongense (shan.dong.en′se. N.L. neut. adj. shandongense pertaining to

176

Shandong province, the location of the soil sample from which the type strain was isolated).

177 178

Cells are Gram-staining-negative, non-motile, non-spore-forming, rod-shaped, approximately

179

0.5-0.7 μm in width, 2.1-2.3 μm in length. Best growth occurs on TSA; good growth occurs on

180

LB agar and R2A agar; weak growth occurs on NA; no growth occurs on CA, SC agar or

181

MacConkey agar. Colonies grown 24 h on TSA are about 3 mm in diameter, circular with a shiny

182

surface and entire edges, yellow-orange-pigmented (flexirubin-type, non-diffusible), translucent

183

and mucoid. Growth conditions are 25-37 °C (optimum 30 °C), at pH 5.0-8.0 (optimum 7.0),

184

with 0-5 % (w/v) NaCl (optimum 1 %). Positive for hydrolysis of DNA, starch, casein and for

185

oxidase and catalase activities. Negative for reduction of nitrate and cellulose hydrolysis. In the

186

API 20E and 20NE kits, positive for citrate utilization, acetoin production, indole production,

187

aesculin hydrolysis and gelatin hydrolysis, but negative for arginine dihydrolase, urease, lysine

188

decarboxylase, ornithine decarboxylase, H2S production and tryptophane deaminase. Acid is

189

produced from D-mannose, but not from mannitol, inositol, sorbitol, melibiose, amygdalin,

190

arabinose, N-acetyl-glucosamine or potassium gluconate. In GN2 Microplates, utilization of

191

dextrin, glycogen, Tween 40, Tween 80, adonitol, i-erythritol, D-fructose, L-fucose, gentiobiose,

192

α-D-glucose, α-D-lactose, lactulose, maltose, D-psicose, D-raffinose, L-rhamnose, sucrose,

193

turanose, xylitol, mono-methyl-succinate, acetic acid, cis-aconitic acid, D-galactonic acid,

194

lactone, D-galacturonic acid, D-glucosaminic acid, α-hydroxy butyric acid, β-hydroxy butyric

195

acid, p-hydroxy phenylacetic acid, α-keto butyric acid, D,L-lactic acid, malonic acid, propionic

196

acid, quinic acid, succinic acid, L-alaninamide, L-alanine, L-asparagine, L-aspartic acid,

197

L-glutamic acid, glycyl-L-aspartic acid, glycyl-L-glutamic acid, L-proline, L-pyroglutamic acid,

198

inosine,

199

glucose-6-phosphate and N-acetyl-D-glucosamine are positive, but not α-cyclodextrin,

200

N-acetyl-D-galactosamine, L-arabinose, D-arabitol, D-cellobiose, D-galactose, m-inositol,

201

β-methyl-D-glucoside, D-trehalose, methyl pyruvate, citric acid, formic acid, D-gluconic acid,

202

D-glucuronic acid, γ-hydroxy butyric acid, itaconic acid, α-keto glutaric acid, α-keto valeric acid,

203

D-saccharic acid, sebacic acid, succinamic acid, glucuronamide, D-alanine, L-alanyl-glycine,

204

L-phenylalanine, D-serine, L-threonine, D,L-carnitine, γ-amino butyric acid, phenyethylamine,

205

putrescine or 2-aminoethanol. In API ZYM tests, alkaline phosphatase, esterase (C4), esterase

206

lipase (C8), lipase (C14), leucine aminopeptidase, valine aminopeptidase, acid phosphatase,

207

naphtol-AS-Bl-phosphoamidase,

208

aminopeptidase (weak), trypsin (weak), α-chymotrypsin (weak) activities are present, but

209

α-galactosidase, β-galactosidase, β-glucuronidase, α-mannosidase, α-fucosidase activities are

210

absent. Menaquinone-6 is the main respiratory quinone. The predominant fatty acids (≥ 5 %) are

211

iso-C15:0, iso-C17:0 3-OH, summed feature 9 (comprising iso-C17:1 ω9c and/or C16:0 10-methyl)

212

and summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c).

213

phosphatidylethanolamine, five unidentified lipids and two unidentified aminolipids.

214

Sym-homospermidine is the predominant polyamine but minor amounts of spermidine and

215

spermine are also present. The DNA G+C content of strain YF-3T is 37 mol %.

216

thymidine,

2,3-butanediol,

D,L-α-glycerol,

α-glucosidase,

phosphate,

glucose-1-phosphate,

N-acetyl-β-glucosaminidase,

cystine

Polar lipids consist of

217

The type strain is YF-3T (=CCTCC AB 2014060T =JCM 30154T), isolated from farmland soil

218

collected from Qingdao city, Shandong province, China.

219 220

Acknowledgements

221

This work was supported by The National High Technology Research and Development Program of

222

China (2012AA101403), Chinese National Natural Science Fund (31370155, J1210056) and The

223

Project for Science and Technology of Jiangsu Province (BE2012749).

224

References

225

Breznak, J. A. & Costilow, R. N. (1994). Physicochemical factors in growth. In Methods for

226

general and molecular bacteriology, pp. 137–154. Edited by P. Gerhardt, R. G. E. Murray, W. A.

227

Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.

228

Busse, H. J. & Auling, G. (1988). Polyamine pattern as a chemotaxonomic marker within the

229

Proteobacteria. Syst Appl Microbiol 11, 1–8.

230

Collins, M. D., Pirouz, T., Goodfellow, M. & Minnikin, D. E. (1977). Distribution of

231

menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100, 221–230.

232

Ezaki, T., Hashimoto, Y. & Yabuuchi, E. (1989). Fluorometric deoxyribonucleic

233

acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane

234

filter hybridization in which radioisotopes are used to determine genetic relatedness among

235

bacterial strains. Int J Syst Bacteriol 39, 224–229.

236

Fautz, E. & Reichenbach, H. (1980). A simple test for flexirubin-type pigments. FEMS

237

Microbiol Lett 8, 87–91.

238

Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach.

239

J Mol Evol 17, 368–376.

240

Felsenstein, J. (1985). Confidence limits on phylogenies: an approachusing thebootstrap.

241

Evolution 39, 783–791.

242

Fitch, W. M. (1971). Toward defining the course of evolution: minimum change for a specific tree

243

topology. Syst Zool 20, 406–416.

244

Gerhardt, P., Murray, R. G. E., Wood, W. A. & Krieg, N. R. (1994). Methods for General and

245

Molecular Bacteriology. Washington, DC: American Society for Microbiology.

246

Hamana, K. & Matsuzaki, S. (1990). Occurrence of homospermidine as a major polyamine in

247

the authentic genus Flavobacterium. Can J Microbiol 36, 228–231.

248

Hantsis-Zacharov, E. & Halpern, M. (2007). Chryseobacterium haifense sp. nov., a

249

psychrotolerant bacterium isolated from raw milk. Int J Syst Evol Microbiol 57, 2344–2348.

250

Hantsis-Zacharov, E., Shakéd, T., Senderovich, Y. & Halpern, M. (2008). Chryseobacterium

251

oranimense sp. nov., a psychrotolerant, proteolytic and lipolytic bacterium isolated from raw

252

cow’s milk. Int J Syst Evol Microbiol 58, 2635–2639.

253

Jorgensen, J. H. & Ferraro, M. J. (2009). Antimicrobial susceptibilitytesting: a review of

254

general principles and contemporary practices. Clin Infect Dis 49, 1749–1755.

255

Kämpfer, P., Chandel, K., Prasad, G. B. K. S., Shouche, Y. S. & Veer, V. (2010a).

256

Chryseobacterium culicis sp. nov., isolated from the midgut of the mosquito Culex

257

quinquefasciatus. Int J Syst Evol Microbiol 60, 2387–2391.

258

Kämpfer, P., Dreyer, U., Neef, A., Dott, W. & Busse, H.-J. (2003). Chryseobacterium defluvii sp.

259

nov., isolated from wastewater. Int J Syst Evol Microbiol 53, 93–97.

260

Kämpfer, P. & Kroppenstedt, R. M. (1996). Numerical analysis of fatty acid patterns of

261

coryneform bacteria and related taxa. Can J Microbiol 42, 989–1005.

262

Kim, O.-S., Cho, Y.-J., Lee, K., Yoon, S.-H., Kim, M., Na, H., Park, S.-C., Jeon, Y.-S., Lee,

263

J.-H. & other authors (2012). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence

264

database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62, 716–721.

265

Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions

266

through comparative studies of nucleotide sequences. J Mol Evol 16, 111–120.

267

Lane, D. J. (1991). 16S/23S rRNA Sequencing. Nucleic Acid Techniques in Bacterial Systematics,

268

pp. 115–175. Edited by E. Stackebrandt & M. Goodfellow. New York, NY: John Wiley and Sons.

269

Li, Z. & Zhu, H. (2012). Chryseobacterium vietnamense sp. nov., isolated from forest soil. Int J

270

Syst Evol Microbiol 62, 827–831.

271

Park, M. S., Jung, S. R., Lee, K. H., Lee, M. S., Do, J. O., Kim, S. B. & Bae, K. S. (2006).

272

Chryseobacterium soldanellicola sp. nov. and Chryseobacterium taeanense sp. nov., isolated from

273

roots of sand-dune plants. Int J Syst Evol Microbiol 56, 433–438.

274

Peter, H., Ilka, W., Dorothee, W., Peter, K. & André, L. (2008). Chryseobacterium ureilyticum

275

sp. nov., Chryseobacterium gambrini sp. nov., Chryseobacterium pallidum sp. nov. and

276

Chryseobacterium molle sp. nov., isolated from beer-bottling plants. Int J Syst Evol Microbiol 58,

277

26–33.

278

Pires, C., Carvalho, M. F., De Marco, P., Magan, N. & Castro, P. M. L. (2010).

279

Chryseobacterium palustre sp. nov. and Chryseobacterium humi sp. nov., isolated from

280

industrially contaminated sediments. Int J Syst Evol Microbiol 60, 402–407.

281

Sambrook, J. & Russell, D. W. (2001). Molecular cloning: a laboratory manual. Cold Spring

282

Harbor, NY: Cold Spring Harbor Laboratory Press.

283

Sasser, M. (1990). Identification of bacteria by gas chromatographyn of cellular fatty acids. MIDI

284

Technical Note 101. Newark, DE: MIDI.

285

Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing

286

phylogenetic trees. Mol Biol Evol 4, 406–425.

287

Smibert, R. M. & Krieg, N. R. (1994). Phenotypic characterization. In Methods for General and

288

Molecular Bacteriology, pp. 607–654. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R.

289

Krieg. Washington, DC: American Society for Microbiology.

290

Stolz, A., Busse, H.-J. & Kämpfer, P. (2007). Pseudomonas knackmussii sp. nov. Int J Syst Evol

291

Microbiol 57, 572–576.

292

Tamaoka, J., Katayama-Fujimura, Y. & Kuraishi, H. (1983). Analysis of bacterial

293

menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 54, 31–36.

294

Tamaoka, J. & Komagata, K. (1984). Determination of DNA base composition by reversed-

295

phased high-performance liquid chromatography. FEMS Microbiol Lett 25, 125–128.

296

Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. & Kumar, S. (2011). MEGA5:

297

molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and

298

maximum parsimony methods. Mol Biol Evo 28, 2731–2739.

299

Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. (1997). The

300

CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by

301

quality analysis tools. Nucleic Acids Res 25, 4876–4882.

302

Tindall, B. J., Sikorski, J., Smibert, R. M. & Kreig, N. R. (2007). Phenotypic characterization

303

and the principles of comparative systematics. In Methods for General and Molecular

304

Microbiology, 3rd edn, pp. 330–393.

305

Vandamme, P., Bernardet, J.-F., Segers, P., Kersters, K. & Holmes, B. (1994). New

306

perspectives in the classification of the Flavobacteria: description of Chryseobacterium gen. nov.,

307

Bergeyella gen. nov., and Empedobacter nom. rev. Int J Syst Bacteriol 44, 827–831.

308

Vaneechoutte, M., Kämpfer, P., De Baere, T., Avesani, V., Janssens, M. & Wauters, G. (2007).

309

Description of Chryseobacterium hominis sp. nov. to accommodate clinical isolates biochemically

310

similar to CDC groups II-h and II-c. Int J Syst Evol Microbiol 57, 2623–2628.

311

Wayne, L. G., Brenner, D. J., Colwell, R. R., Grimont, P. A. D., Kandler, O., Krichevsky, M.

312

I., Moore, L. H., Moore, W. E. C., Murray, R. G. E. & other authors (1987). International

313

Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of

314

approaches to bacterial systematics. Int J Syst Bacteriol 37, 463–464.

315

Yassin, A. F., Hupfer, H., Siering, C. & Busse, H.-J. (2010). Chryseobacterium treverense sp.

316

nov., isolated from a human clinical source. Int J Syst Evol Microbiol 60, 1993–1998.

317

Yochan J. & Kiseong J. (2011). Chryseobacterium yonginense sp. nov., isolated from a

318

mesotrophic artificial lake. Int J Syst Evol Microbiol 61, 1413–1417.

319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334

335

Fig. 1. Neighbour-joining phylogenetic tree according to 16S rRNA gene sequences indicating the

336

relationship of strain YF-3T to closely related species of the genus Chryseobacterium. Asterisks

337

indicate branches that were also recovered using maximum-parsimony and maximum-likelihood

338

algorithms. Bootstrap values more than 70 % (based on 1000 replications) are shown at branch

339

points. The 16S rRNA gene sequences of Ornithobacterium rhinotracheale LMG 9086T was used

340

as outgroups. Bar, 0.01 substitutions per nucleotide position.

341 342 343 344 345 346 347 348 349 350 351 352 353 354 355

356

Table 1. Differential biochemical characteristics of strain YF-3T and closely related species of the

357

genus Chryseobacterium.

358

Strains: 1, Chryseobacterium shandongense sp. nov. YF-3T; 2, Chryseobacterium hispalense

359

AG13T; 3, Chryseobacterium taiwanense BCRC 17412T. All data are from this study.

360

+, Positive; w, weakly positive; -, negative.

361 Characteristic API 20 NE strip: reduction of nitrate L-malic acid β-glucosidase Utilization of (GN 2 plate): L-serine Histidine Dextrin D-Fructose L-Fucose D-Galactose Gentiobiose α-D-Glucose Maltose D-Mannose L-Rhamnose D-Sorbitol D-Glucuronic Acid Inosine L-proline Glycyl-L-AsparticAcid Turanose Enzymatic activities(API ZYM strip): esterase (C4) esterase lipase (C8) lipase (C14) trypsin α-chymotrypsin N-acetyl-β-glucosaminidase cystine aminopeptidase

1

2

3

+

+ + -

-

+ + + + + + + + + + + + +

+ + + + + + + + + + + +

+ + -

+ + + w w + w

+ -

+ -

362

Table 2. Fatty acid compositions of strain YF-3T and closely related species of the genus

363

Chryseobacterium.

364

Strains: 1, Chryseobacterium shandongense sp. nov. YF-3T; 2, Chryseobacterium hispalense

365

AG13T; 3, Chryseobacterium taiwanense BCRC 17412T.

366

percentages of total fatty acids. Fatty acids amounting to less than 1 % of the total fatty acids in all

367

strains are not shown. TR, Trace (less than 1 %); -, not detected/not reported.

C16:0 iso-C15:0 iso-C17:0 anteiso-C15:0 iso-C15:0 3-OH iso-C17:0 3-OH C16:0 3-OH C18:1ω9c C20:1ω9c summed feature 3 summed feature 9

All data are from this study. Values are

1

2

3

1.44 47.06 TR 2.85 2.74 15.06 1.33 1.04 1.71 5.57 13.76

1.31 42.48 TR 1.93 2.68 13.59 1.02 TR 10.54 19.25

1.96 44.17 1.17 TR 4.31 17.92 TR 9.47 16.16

368 369

Summed feature 3 contains C16:1 ω7c and/or C16:1 ω6c. Summed feature 9 contains iso-C17:1 ω9c

370

and/or C16:0 10-methyl.

371 372 373 374

Figure1 Click here to download Figure: Fig.1new.pdf

C. gwangjuense THG-A18T (JN196134)

85*

C. geocarposphaerae 91A-561T (HG738132)

*

C. defluvii B2T (AJ309324) C. yeoncheonense DCY67T (JX141782)

99*

*

C. aahli T68T (JX287893)

*

C. massiliae 90B (AF531766) C. gambrini 5-1St1aT (AM232810)

*

C. daecheongense CPW 406T (AJ457206)

*

C. wanjuense R2A10-2T (DQ256729) C. taiwanense BCRC 17412T (DQ318789)

*

C. gregarium P 461/12T (AM773820) *

*

C. hagamense RHA2-9T (DQ673672) C. camelliae THG C4-1T (JX843771)

71*

98*

Chryseobacterium shandongense YF-3T (KJ644318) C. hispalense AG13T (EU336941)

96* *

C. taeanense PHA3-4T (AY883416) C. taichungense CC-TWGS1-8T (AJ843132) C. vietnamense GIMN1.005T (HM212415)

100

86*

C. gleum ATCC 35910T (ACKQ01000057) C. arthrosphaerae CC-VM-7T (FN398101) C. indologenes LMG 8337T (AM232) C. nakagawai NCTC 13529T (JX100822)

98*

C. lactis NCTC 11390T (JX100821) C.viscerum 687B-08T (FR871426) Ornithobacterium rhinotracheale LMG 9086T (L19156)

0.01

Supplementary Material table S1 and Fig S1-4 Click here to download Supplementary Material Files: supplementary materials Table 1 and FigS1-4.pdf

Chryseobacterium shandongense sp. nov., isolated from soil.

YF-3T is a Gram-stain-negative, non-motile, non-spore-forming, yellow-orange, rod-shaped bacterium. Optimal growth conditions were at 30 °C, pH 7.0 an...
1MB Sizes 2 Downloads 17 Views