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Identification of Frateuria Aurantia Strains Isolated from Indonesian Sources

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Identification of Frateuria Aurantia Strains Isolated from Indonesian Sources Microbiol. Cult. Coll. Dec. 2003. p. 81 ― 90 Vol. 19, No. 2 Identification of Frateuria aurantia Strains Isolated from Indonesian Sources Puspita Lisdiyanti ＊, Yuzo Yamada, Tai Uchimura, and Kazuo Komagata Department of Applied Biology and Chemistry, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan In the course of the isolation of acetic acid bacteria from tropical countries, 16 water-soluble brown pigment-producing bacteria were isolated from fruits and flowers in Indonesia. Two rep- resentative isolates were clustered in the γ-Proteobacteria together with the genus Frateuria by 16S rRNA gene sequence analysis. All isolates were identified as Frateuria aurantia by DNA-DNA similarity. The strains were aerobic, Gram-negative rods and motile with a single polar flagellum. They grew at pH 3.5, produced acetic acid from ethanol and brown water-soluble pigment, oxidized lactate but not acetate, did not grow in the presence of 0.35 ％ acetic acid, and did not produce H2S. Further, they produced D-gluconate, 2-keto-D-gluconate, and 2, 5-diketo-D-gluconate from D-glucose but not 5-keto-D-gluconate. All isolates tested had Q-8 as the major ubiquinone and iso-branched acid of C15 : 0 as the major cellular fatty acid. The DNA base composition of the isolates ranged from 62 to 63 mol ％. This study is the fourth case of the isolation of F. aurantia strains so far, and showed the distribution of this species not only in Japan but also in tropical regions. Key words: Frateuria aurantia, acetic acid bacteria INTRODUCTION The second case was reported by Ameyama and Kondo The genus Frateuria was validly established by （1）with three strains isolated from rose（Rose hybri- Swings et al. in 1980（14, 15）for bacteria that are polar- da）, saffron（Crocus sativus）, and three-lady bell ly flagellated, produce brown pigment, have branched （Adenophora triphyla）, respectively. Thirdly, Yamada et cellular fatty acids , and are Q-8 equipped Gram-negative, al.（20）isolated six strains from raspberry（Rubus incorporating“Acetobacter aurantius”（Acetobacter parvifolius）. However, of the 14 above-mentioned iso- aurantium sic）described by Kondo and Ameyama（9, lates, only nine strains are preserved as F. aurantia in 10）. Frateuria aurantia is the type species and only a culture collections at present. Three strains（IFO 3245, species in this genus. The genus Frateuria is recognized 3247, and 3249）were those isolated by Kondo and as pseudo-acetic acid bacteria because the strains showed Ameyama（9, 10）and six strains（IFO 13328 to intermediate characteristics to acetic acid bacteria（1, 2, 13333）by Yamada et al.（20）. 20）. In the course of isolation of acetic acid bacteria from Up to now, three cases of the isolation of F. aurantia sources of tropical countries, 16 water-soluble brown pig- have been reported and were all conducted in Japan. ment-producing bacteria were isolated from flowers and First, Kondo and Ameyama（9, 10）reported the isola- fruits in Indonesia. tion of five strains from lily flowers（Lilium aurantum）. This study aims to identify the isolates compared with the strains of the genera in the family Acetobacteraceae. ＊ Correspondence author ― 81 ― Identification of Frateuria aurantia Strains Isolated from Indonesian Sources Lisdiyanti et al． MATERIALS AND METHODS Analysis of ubiquinones and cellular fatty acids Isolation and cultivation of acetic acid bacteria Cells cultivated on AG medium were used for the One hundred and forty-nine sources including fer- analysis of ubiquinones and cellular fatty acids. mented foods, fruits, and flowers were collected in 1999 Ubiquinones were extracted as described by Yamada et at Yogyakarta and Bogor in Indonesia. On-site isolation al.（19）and analyzed as described by Tamaoka et al. was conducted and three enrichment media at pH 3.5 （18）. Methyl esters of cellular fatty acids were prepared （EM II, EM IV, and EM V）were employed for the isola- by the direct transmethylation method with methanolic tion. EM II was composed of 2.0 ％ D-sorbitol, 0.5 ％ pep- hydrochloride and were analyzed by gas chromatography tone, 0.3 ％ yeast extract, and 100 ppm cycloheximide. as described by Komagata and Suzuki（8）. The compositions of EM IV and EM V were basically the same as that of EM II but 2.0 ％ D-sorbitol was replaced Phenotypic characterization with 2.0 ％ dulcitol for EM IV, and 0.15 ％ D-glucose and Phenotypic characterizations used in this study were 1.0 ％ methanol for EM V. When microbial growth mostly those described by Lisdiyanti et al.（12）. occurred in enrichment media, bacterial strains were iso- Oxidation of acetate and lactate was tested by the lated by the method described by Yamada et al.（23）. method of Leifson（11）. Ketogenesis from glycerol and The isolation medium contained 2.0 ％ D-glucose, 0.8 ％ mannitol were examined by the method of Shimwell et al. yeast extract, 0.5 ％ peptone, 0.5 ％ ethanol, 0.3 ％ CaCO3, （16）and Asai et al.（2）. Production of H2S was detect- and 1.5 ％ agar. Isolates were maintained on agar slants ed by lead acetate paper strips on a medium containing of AG medium consisting of 0.1 ％ D-glucose, 1.5 ％ glyc- 5.0 ％ D-glucose, 0.5 ％ peptone, 0.5 ％ yeast extract, erol, 0.5 ％ peptone, 0.5 ％ yeast extract, 0.2 ％ malt 0.1 ％ L-cysteine, and 0.05 ％ Na2SO4（pH 7.0）as extract, 0.7 ％ CaCO3, and 1.5 ％ agar as described by described by Swings et al.（14）and on Triple Sugar Katsura et al.（7）. Iron agar medium（TSI）（Eiken, Tokyo, Japan）. Growth on methanol was examined by using yeast Reference strains used extract omitted medium C as described by Yamashita et F. aurantia IFO 3245T and IFO 13328, Acetobacter aceti al.（24）. IFO 14818T, Acidomonas methanolica NRIC 0498T, Asaia bogorensis NRIC 0311T, Gluconacetobacter liquefaciens RESULTS IFO 12238T, Gluconobacter oxydans IFO 14819T, Kozakia Isolation of acetic acid bacteria and identification baliensis NRIC 0488T, Escherichia coli NRIC 1999, and at the genus level Pseudomonas aeruginosa NRIC 0201T were used as ref- Of 149 samples collected in 1999 in Indonesia, only 24 erence strains. samples showed bacterial growth on enrichment media. As a result, 62 isolates of acetic acid bacteria were select- 16S rRNA gene sequencing and phylogenetic analysis ed for subsequent study because they were all Gram-neg- The amplification, sequencing, and analytical method ative, rod-shaped bacteria, produced clear zones on the of 16S rRNA genes were those described by Lisdiyanti et isolation medium, and grew on AG medium at pH 3.5. Of al.（12）. the 62 isolates, 16 were regarded as Frateuria strains because they produced water-soluble brown pigment, oxi- Determination of DNA base composition and dized ethanol, did not grow in the presence of 0.35 ％ DNA-DNA hybridization acetic acid, and had Q-8 as the major ubiquinone. The DNAs were extracted by the method of Saito and remaining 11 isolates were presumed to be Gluconobacter Miura（13）. DNA base composition was determined as and 35 isolates to be Asaia. The 16 Frateuria strains were described by Tamaoka and Komagata（17）. DNA-DNA subjected to the subsequent study. The designation of hybridization was carried out as described by Ezaki et al. isolates is shown in Table 1. （5）. ― 82 ― Microbiol. Cult. Coll. Dec. 2003 Vol. 19, No. 2 Table 1. List of isolates and their sources Isolate Time of isolation Sources EM used Place of isolation B71D-1, B71D-3, B71D-4 February, 1999 fruit Mangifera foetida EM IV Bogor B72D-1, B72M-1, B72M-2, February, 1999 fruit Baccaurea racemosa EM IV and V Bogor B72M-3, B72M-4, B72M-5 B73M-1, B73M-3A, B73M-3B February, 1999 fruit Artocarpus champeden EM V Bogor B79M-1 February, 1999 fruit kemaris EM V Bogor Y3S-1A, Y3S-1B, Y3S-3 February, 1999 flower coconut flower EM II Yogyakarta Abbreviation: EM., Enrichment medium. Fig. 1. Phylogenetic relationship of Frateuria strains deduced from 16S rRNA gene sequences The scale bar represents 1 nucleotide substitution per 100 nucleotides. Numerals indicate the bootstrap value derived from 1000 replications. Phylogenetic analysis from 62 to 63 mol ％. They showed high values（76 to Two isolates（B79M-1 and Y3S-3）were determined 100 ％）of DNA-DNA similarity to the type strain of F. for their 16S rRNA gene sequences. The phylogenetic aurantia IFO 3245T and F. aurantia IFO 13328. They tree of the isolates is shown in Fig. 1. The two represen- showed low values（10 to 36 ％）of DNA-DNA similar- tative isolates were located in the γ-Proteobacteria togeth- ity to other reference strains. Thus, all strains studied er with F. aurantia IFO 3245T（AJ010481）and were were identified as F. aurantia. Table 2 shows DNA base closely related to the genera Fulvimonas and compositions and values of DNA-DNA similarity of the Rhodanobacter. Sequence similarity of the isolates was 16 isolates and the reference strains. 99.8 ％ to F. aurantia IFO 3245T（AJ010481）. The acces- sion number of 16S rRNA gene sequences in DDBJ was Ubiquinone systems and fatty acid compositions AB120123 for B79M-1 and AB120124 for Y3S-3. The 16 isolates had Q-8 as the major ubiquinone that accounted for 97.5 to 100 ％, and iso-branched acid of C15:0 DNA base composition and DNA-DNA similarity as the major cellular fatty acid that accounted for 40.6 to All isolates had the DNA base composition ranging 51.0 ％ of the total acids（Table 3）. ― 83 ― Identification of Frateuria aurantia Strains Isolated from Indonesian Sources Lisdiyanti et al． Table 2. DNA base compositions and values of DNA-DNA similarity Strain or isolate G＋C content DNA-DNA similarity（％）with strain: （mol ％） IFO 3245T IFO 13328 B79M-1 Y3S-3 F.
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