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Laboratory of Bioresources, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
Correspondence
Linxian Ding
ding-lin-xian{at}nite.go.jp
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strains 7-1T and 7-2T are AB109890 and AB109889.
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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). However, DNA–rRNA hybridization, chemotaxonomic analysis and 16S rRNA gene sequence studies (Pot et al., 1992; Sakane & Yokota, 1994; Hamana et al., 1994; Wen et al., 1999; Ding & Yokota, 2002) have shown that the genus is taxonomically heterogeneous. Among the species of this genus, some are closely related to species of the genera Herbaspirillum, Magnetospirillum and Pseudomonas.
The genus Herbaspirillum was established by Baldani et al. (1986). The organisms of this genus show nitrogen-fixing activities (Baldani et al., 1996; Kirchhof et al., 2001). Anzai et al. (2000) reported that the phylogenetic position of [Pseudomonas] huttiensis is close to that of the genus Herbaspirillum. [Pseudomonas] lanceolata was indicated to belong to the family Comamonadaceae, and is considered a close relative of [Aquaspirillum] delicatum (Anzai et al., 2000).
In this study, we carried out the characterization and identification of two novel strains, 7-1T and 7-2T, isolated from well water, based on phenotypic characterization, chemotaxonomic analysis, 16S rRNA gene sequence analysis and DNA–DNA hybridization analysis. For these two strains, we propose the names Curvibacter gracilis gen. nov., sp. nov. and Herbaspirillum putei sp. nov., respectively. In addition, we propose to transfer [A.] delicatum, [P.] lanceolata, [Aquaspirillum] autotrophicum and [P.] huttiensis as Curvibacter delicatus comb. nov., Curvibacter lanceolatus comb. nov., Herbaspirillum autotrophicum comb. nov. and Herbaspirillum huttiense comb. nov., respectively.
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METHODS |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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) containing (per litre distilled water) 10·0 g Polypepton, 2·0 g yeast extract and 1·0 g MgSO4.7H2O, pH 7·0. Strains were incubated at 30 °C. Herbaspirillum seropedicae IAM 14977T, Herbaspirillum rubrisubalbicans IAM 14976T, Herbaspirillum frisingense IAM 14974T, [P.] huttiensis IAM 14941T and [P.] lanceolata IAM 14947T were incubated in medium B1 (IAM, 1998), composed of the following: 0·5 % polypeptone (Difco), 0·3 % yeast extract (Difco), 3 % NaCl and 1·5 % agar. The incubation temperature was 25 °C. N2-free medium was composed (per litre distilled water) of 10 g glucose, 0·1 g CaCl2.H2O, 0·1 g MgSO4.7H2O, 0·9 g K2HPO4, 0·1 g KH2PO4, 5 g CaCO3, 0·01 g FeSO4.7H2O and 0·005 g Na2MoO4.2H2O, pH 7·3.
Morphology.
Cell size and morphology were determined by optical microscopy and scanning electron microscopy of cells grown on the culture media listed above. Cells grown on solid medium were fixed in 1 % glutaraldehyde in 0·01 M phosphate buffer (pH 7·2) for 2 h at room temperature and dehydrated through a graded ethanol series and then in a Hitachi model HCP-2 critical point drying apparatus. The preparation was sputter-coated with platinum under a vacuum. Samples were observed with a scanning electron microscope (model Hitachi S4500).
Physiological and biochemical characteristics.
Oxidase activity was determined by oxidation of 1 % p-aminodimethylaniline oxalate. Catalase activity was determined by bubble formation in a 3 % (v/v) H2O2 solution. Biochemical tests were performed with API 20NE and API 50CH test strips (bioMérieux).
Phylogenetic analysis based on 16S rRNA gene sequence comparisons.
Genomic DNA extraction, PCR-mediated amplification of the 16S rRNA genes and purification of PCR products were carried out using previously described procedures (Hiraishi, 1992; Uchino et al., 1997). The universal primers 8F (5'-AGAGTTTGATCCTGGCTCAG-3') and 1510R (5'-GGCTACCTTGTTACGA-3') were used for PCR amplification. The PCR products were purified using the GFX PCR DNA and Gel Band Purification kit (Amersham Pharmacia Biotech). Primers 8F, 520F, 926F, 350R, 700R, 1100R and 1510R were used in the 16S rRNA gene sequencing reactions. The 16S rRNA gene sequences obtained from the DNA database were aligned using CLUSTAL W, version 1.74 (Thompson et al., 1994). Nucleotide substitution rates (Knuc values) were calculated. All of the sequences used were almost full-length and the sequences were derived from the type strain of each species. The phylogenetic tree was constructed using the neighbour-joining algorithm (Saitou & Nei, 1987).
Detection of the nifH and nifD genes.
PCR for amplification of the nifH gene was carried out by using a cell lysate extracted from the organisms. A 360 bp fragment of the nifH gene was amplified using the forward primer 5'-TGCGAYCCSAARGCBGACTC-3' and the reverse primer 5'-ATSGCCATCATYTCRCCGGA-3' (Y=C or T; S=G or C; R=A or G; B=C or G or T) (Stoltzfus et al., 1997). For the nifD gene, primers nifD Fdb261 (5'-TGGGGICCIRTIAARGAYATG-3') and nifD Fdb 260 (5'-TCRTTIGCIATRTGRTGNCC-3') were used. The conditions for PCR amplification were: 1 min at 94 °C and then 30 cycles of 40 s at 94 °C, 40 s at 55 °C and 1 min at 72 °C, followed by a final step for 2 min at 72 °C. The PCR products were purified as outlined above. nifH and nifD gene sequencing of all strains was performed as described previously by Stoltzfus et al. (1997), Zehr & McReynolds (1989), Reinhold-Hurek & Hurek (1998) and Kirchhof et al. (2001).
DNA–DNA hybridization.
DNA was prepared according to the method of Meyer & Schleifer (1978). DNA–DNA hybridization analysis was carried out in microplate wells (Black Maxisorp; Nunc) using a fluorometric method (Ezaki et al., 1989). The fluorescence intensity was detected by a fluorescence multiwell plate reader (Cytofluor Series 4000; PerSeptive Biosystems). DNA–DNA hybridization was carried out at 53 °C with photobiotin-labelled DNA and microplates (Ezaki et al., 1989).
Cellular fatty acid profiles.
Cellular fatty acids were extracted according to the protocol of the MIDI system. Bacterial strains were grown on TSBA medium for 48 h at 30 °C. Analysis by gas chromatography was controlled by MIS software (Microbial ID Inc.) and the peaks were automatically integrated and identified by the Microbial Identification software package (Sasser, 1990).
Respiratory quinone analysis.
Isoprenoid quinones were extracted from freeze-dried cells with chloroform/methanol (2 : 1, v/v) and were purified by TLC by using n-hexane/diethyl ether (85 : 15, v/v) as the solvent. The ubiquinone fraction was extracted with acetone, dried under a nitrogen gas stream and then analysed by HPLC (model LC-10A apparatus; Shimadzu) with a Nacarai ODS 5C18 column (4·6x150 mm).
Determination of the DNA G+C content.
Genomic DNA was prepared according to the method of Sambrook et al. (1989). Total DNA was digested with P1 nuclease using a Yamasa GC kit (Yamasa Shoyu). The G+C content of the total DNA was measured by HPLC according to the method described by Mesbah et al. (1989).
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RESULTS AND DISCUSSION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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. On B104 agar incubated at 30 °C for 3 days, young colonies were circular, smooth, convex and yellow–brown, with a diameter of 1–2 mm. The pH range for growth was 6–7 for both strains. The optimum growth temperature range was 25–30 °C for strain 7-1T and 25–37 °C for strain 7-2T.
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) and showed 16S rRNA gene sequence similarity of 99·0 and 97·3 % to [P.] lanceolata and [A.] delicatum, respectively. Strain 7-2T fell within the radiation of the cluster comprising [P.] huttiensis, [A.] autotrophicum and species of the genus Herbaspirillum in the family Oxalobacteriaceae. [A.] autotrophicum showed 16S rRNA gene sequence similarity of 96·8–98·4 % to Herbaspirillum species. However, 16S rRNA gene sequence similarity with Oxalobacter formigenes and Paucimonas lemoignei was respectively 94·2 and 95·8 %. Strain 7-2T showed 16S rRNA gene sequence similarity of 99·0, 97·9, 98·1, 98·3, 96·6 and 96·5 % to [P.] huttiensis, H. seropedicae, H. rubrisubalbicans, H. frisingense, Herbaspirillum lusitanum and [A.] autotrophicum, respectively.
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shows DNA–DNA binding values for strains 7-1T and 7-2T. The values of DNA–DNA hybridization between strain 7-1T and [P.] lanceolata and [A.] delicatum were respectively 42–52 and 7–9 %. DNA–DNA hybridization of strain 7-2T with [P.] huttiensis, [A.] autotrophicum, H. seropedicae, H. rubrisubalbicans and H. frisingense revealed reassociation values of 40–45, 14, 6–17, 18–21 and 14–18 %, respectively.
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Chemotaxonomic characteristics
The results of the analysis of G+C content, quinone type and fatty acid composition are shown in Tables 1, 2 and 4
. The G+C content of the DNA of strain 7-1T was 66·2 mol% and the strain contained Q-8 as an isoprenoid quinone, 16 : 0, 16 : 1 and 18 : 1 as major cellular fatty acids and 3-OH 8 : 0 as a major cellular 3-hydroxy fatty acid. The G+C content of the DNA, isoprenoid quinone composition and the major fatty acids of [A.] delicatum and [P.] lanceolata were 62·2 and 66·0 mol%, respectively, Q-8, 16 : 0, 16 : 1 and 18 : 1 and 3-OH 8 : 0. The G+C content of the DNA of strain 7-2T was 62·9 mol%. Strain 7-2T contained Q-8 as the isoprenoid quinone. The major cellular fatty acids were 16 : 0, 16 : 1, 18 : 0 and 18 : 1 and 3-OH 10 : 0 and 3-OH 12 : 0 were the major cellular 3-hydroxy fatty acids. The G+C DNA content and quinone compositions of species of the genus Herbaspirillum and [P.] huttiensis were 57·9–65 and 63·3 mol%, respectively, and Q-8 (in both cases). The major fatty acids of the species of the genus Herbaspirillum and [P.] lanceolata were 16 : 0, 16 : 1 and 18 : 1 and the major 3-hydroxy fatty acids were 3-OH 10 : 0 and 3-OH 12 : 0. The extracted fatty acid composition for strain 7-2T and related species are shown in Table 4. Tables 1 and 2 show differential characteristics among strains 7-1T, 7-2T and other closely related species.
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; Ding & Yokota, 2002). Table 5 shows the similarity among the three species and the differential characteristics from other closely related species. We propose to classify these three species in a new genus, Curvibacter gen. nov., as Curvibacter gracilis gen. nov., sp. nov., Curvibacter delicatus comb. nov. and Curvibacter lanceolatus comb. nov.
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; Anzai et al., 2000). In addition, the nifH gene was found in strain 7-2T, although it did not show N2-fixing activity. We propose to reclassify this novel species, [P.] huttiensis and [A.] autotrophicum in the genus Herbaspirillum as Herbaspirillum putei sp. nov., Herbaspirillum huttiense comb. nov. and Herbaspirillum autotrophicum comb. nov.
Description of Herbaspirillum putei sp. nov.
Herbaspirillum putei (pu.te'i. L. gen. n. putei of a well, from which the type strain was isolated).
Gram-negative, curved rods or spirilla, 0·5–0·7x2·1–3·4 µm. The optimum growth temperature is 25–37 °C. The optimum pH is 6–7. Catalase- and oxidase- positive. Contains the nifH gene. The G+C content is 66·2 mol% and the quinone system is ubiquinone Q-8. The major cellular fatty acids are 16 : 0, 16 : 1, 18 : 0 and 18 : 1. The major cellular 3-hydroxy fatty acids are 3-OH 10 : 0 and 3-OH 12 : 0.
The type strain, strain 7-2T (=IAM 15032T=ATCC BAA-806T), was isolated from well water in Osaka, Japan.
Description of Herbaspirillum huttiense comb. nov.
Herbaspirillum huttiense (hut.ti.en'se. N.L. neut. adj. huttiense pertaining to Lower Hutt, New Zealand). Note: Rule 61 of the Bacteriological Code prevents the correction of this epithet to ‘huttense’.
Basonym: Pseudomonas huttiensis Leifson 1962.
The description is identical to the description given for [P.] huttiensis by Leifson (1962). In addition, this bacterium is catalase- and oxidase-positive. The G+C content of the DNA is 63·3 mol% and its quinone system is ubiquinone Q-8. The major cellular fatty acids are 16 : 0, 16 : 1, 18 : 0 and 18 : 1. The major 3-hydroxy fatty acids are 3-OH 10 : 0 and 3-OH 12 : 0. The sample used for classification was isolated from distilled water. The type strain is IAM 14941T (=ATCC 14670T).
Description of Herbaspirillum autotrophicum comb. nov.
Herbaspirillum autotrophicum (au.to.tro'phi.cum. Gr. pron. autos self; Gr. adj. trophikos nursing, tending or feeding; N.L. neut. adj. autotrophicum self-nursing or self-feeding).
Basonym: Aquaspirillum autotrophicum Aragno and Schlegel 1978.
The description is identical to the description given for [A.] autotrophicum by Aragno & Schlegel (1978). In addition, the major cellular fatty acids are 16 : 0, 16 : 1 and 18 : 1. The major 3-hydroxy fatty acids are 3-OH 12 : 0 and 3-OH 14 : 0. The type strain is IAM 14942T (=DSM 732T).
Description of Curvibacter gen. nov.
Curvibacter (Cur.vi.bac'ter. L. adj. curvus curved or crooked; N.L. masc. n. bacter rod; N.L. masc. n. Curvibacter curved rod).
Gram-negative, vibrioid or slightly curved, rod-shaped cells, 0·3–0·9x1·1–1·8 µm, with an anticlockwise helix; may or may not have flagella. Catalase-, oxidase- and phosphatase-positive. The temperature range necessary for growth is 9–40 °C and the pH range for growth is 5·5–8·5. No growth occurs in the presence of 3 % NaCl. The G+C content of the DNA is 62·2–66·0 mol% and the quinone type is Q-8. The major cellular fatty acids are 16 : 0, 16 : 1 and 18 : 1 and the major 3-hydroxy fatty acid is 3-OH 8 : 0. The type species is Curvibacter gracilis.
Description of Curvibacter gracilis sp. nov.
Curvibacter gracilis (gra'ci.lis. L. masc. adj. gracilis slender or thin).
Displays the following properties in addition to those given in the genus description. Slightly curved rod, 0·4–0·5x1·1–2·8 µm. The optimum growth temperature is 30 °C. The optimum pH for growth is 6–7. The G+C content of the DNA is 66·0 mol% and the quinone type is ubiquinone Q-8.
The type strain, strain 7-1T (=IAM 15033T=ATCC BAA-807 T), was isolated from well water in Osaka, Japan.
Description of Curvibacter lanceolatus comb. nov.
Curvibacter lanceolatus (lan.ce.o.la'tus. L. masc. adj. lanceolatus lancet-shaped).
Basonym: Pseudomonas lanceolata Leifson 1962.
The description is identical to the description given for [P.] lanceolata by Leifson (1962). In addition, this bacterium is catalase- and oxidase-positive. The G+C content of the DNA is 66·2 mol% and the quinone type is ubiquinone 8. The major cellular fatty acids are 16 : 0, 16 : 1 and 18 : 1. The major 3-hydroxy fatty acid is 3-OH 8 : 0. The type strain is IAM 14947T (=ATCC 14669T).
Description of Curvibacter delicatus comb. nov.
Curvibacter delicatus (de.li.ca'tus. L. masc. adj. delicatus delicate).
Basonym: Aquaspirillum delicatum (Leifson 1962) Hylemon et al. 1973.
The description is identical to the description given for [A.] delicatum by Hylemon et al. (1973). The type strain is IAM 14955T (=ATCC 14667T).
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ACKNOWLEDGEMENTS |
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REFERENCES |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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Aragno, M. & Schlegel, H. G. (1978). Aquaspirillum autotrophicum, a new species of hydrogen-oxidizing, facultatively autotrophic bacteria. Int J Syst Bacteriol 28, 112–116.
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Baldani, J. I., Pot, B., Kirchhof, G. & 8 other authors (1996). Emended description of Herbaspirillum; inclusion of [Pseudomonas] rubrisubalbicans, a mild plant pathogen, as Herbaspirillum rubrisubalbicans comb. nov.; and classification of a group of clinical isolates (EF group 1) as Herbaspirillum species 3. Int J Syst Bacteriol 46, 802–810.
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