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Algimonas Porphyrae Gen. Nov., Sp. Nov., a Member of the Family Hyphomonadaceae, Isolated from a Red Alga Porphyra Yezoensis

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Algimonas Porphyrae Gen. Nov., Sp. Nov., a Member of the Family Hyphomonadaceae, Isolated from a Red Alga Porphyra Yezoensis See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/221715854 Algimonas porphyrae gen. nov., sp. nov., a member of the family Hyphomonadaceae, isolated from a red alga Porphyra yezoensis. Article in International Journal of Systematic and Evolutionary Microbiology · March 2012 DOI: 10.1099/ijs.0.040485-0 · Source: PubMed CITATIONS READS 20 67 7 authors, including: Youhei Fukui Mahiko Abe National Institute for Agro-Environmental Sciences in Japan National Fisheries University 29 PUBLICATIONS 414 CITATIONS 25 PUBLICATIONS 348 CITATIONS SEE PROFILE SEE PROFILE Hiroaki Saito Yutaka Yano Ishikawa Prefectural University Fisheries Research Agency 73 PUBLICATIONS 2,148 CITATIONS 44 PUBLICATIONS 1,442 CITATIONS SEE PROFILE SEE PROFILE All content following this page was uploaded by Yutaka Yano on 22 July 2015. The user has requested enhancement of the downloaded file. IJSEM Papers in Press. Published March 16, 2012 as doi:10.1099/ijs.0.040485-0 1 Algimonas porphyrae gen. nov., sp. nov., a member of the family Hyphomonadaceae, 2 isolated from a red alga Porphyra yezoensis. 3 4 Youhei Fukui1, Mahiko Abe2, Masahiro Kobayashi3, Hiroaki Saito1, Hiroshi Oikawa4, 5 Yutaka Yano 5, and Masataka Satomi1*. 6 7 1 National Research Institute of Fisheries Science, Fisheries Research Agency, 8 Yokohama, 236-8648, Japan 9 2 National Fisheries University, Shimonoseki, 759-6595, Japan 10 3 Seikai National Fisheries Research Institute, Nagasaki, 851-2213, Japan 11 4National Research Institute of Fisheries and Environment of Inland Sea, Fisheries 12 Research Agency, Hiroshima, 739-0452, Japan 13 5National Salmon Resources Center, Fisheries Research Agency, Sapporo, 062-0922, 14 Japan 15 *Author for correspondence: Masataka Satomi. Tel. & Fax: +81-45-788-7669 16 e-mail: [email protected]. 17 National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4, 18 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan 19 Subjective category: Proteobacteria 20 Running title: Algimonas porphyrae gen. nov., sp. nov. 21 22 The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of 23 strains 0C-2-2T, 0C-17, and LNM-3 are AB689189, AB689190, and AB689191, 24 respectively. 25 Summary 26 Three Gram-negative, stalked, motile bacteria, designated 0C-2-2T, 0C-17, and LNM-3, 27 were isolated from a red alga Porphyra yezoensis. 16S rRNA gene sequence analysis 28 revealed that the three novel strains belonged in the family Hyphomonadaceae, and are 29 closely related to Litorimonas taeanensis G5T (96.5 % 16S rRNA gene sequence 30 similarity) and Hellea balneolensis 26III/A02/215T (94.3 % similarity). The DNA G+C 31 contents of the new isolates (58.5-60.2 mol%) were clearly distinguished from L. 32 taeanensis G5 T (47.1 mol%) and H. balneolensis DSM 19091T (47.9 mol%). The G+C 33 content of L. taeanensis G5 T obtained in this study was distinct from a previous report 34 (63.6 mol%). DNA-DNA hybridization experiments showed that the new strains 35 constituted a single species. Eleven phenotypic features of the three isolates differed 36 from those of both related genera. The predominant respiratory quinone was 37 ubiquinone-10 and the major fatty acid was C18:1ω7c. On the basis of polyphasic 38 taxonomic analysis, the novel strains represent a novel genus and species for which the 39 name Algimonas porphyrae gen. nov., sp. nov. is proposed, with the type strain 0C-2-2T 40 (= LMG 26424T = NBRC 108216T). 41 42 43 44 45 46 47 48 49 The families Caulobacteraceae and Rhodobacteraceae have been classified into the 50 order Caulobacterales and Rhodobacterales within the class Alphaproteobacteria, 51 respectively (Garrity et al., 2005). However, the family Rhodobacteraceae was 52 integrated into the order Caulobacterales on the basis of 16S rRNA gene sequences, and 53 the family Hyphomonadaceae was newly founded in the order Caulobacterales (Lee et 54 al., 2005). The family Hyphomonadaceae included four genera of Hyphomonas, 55 Hirschia, Maricaulis, and Oceanicaulis (Lee et al., 2005) which were previously 56 classified as the family Rhodobacteraceae (Strömpl et al., 2003; Garrity et al., 2005). 57 Subsequently, additional genera, including Hellea, Henriciella, Litorimonas, Ponticaulis, 58 Robiginitomaculum, and Woodsholea have been classified as members of the family 59 Hyphomonadaceae (http://www.bacterio.cict.fr). Most bacteria of the family 60 Hyphomonadaceae are characterized by having a single or two stalks. These type strains 61 have been isolated from marine habitats such as seawater (Lee et al., 2007; Alain et al., 62 2008), brackish water (Schlesner et al., 1990), hydrothermal vent (Weiner et al., 2000), 63 beach sand (Jung et al., 2011), shellfish beds (Weiner et al., 1985), and dinoflagellates 64 (Strömpl et al., 2003). In this study, three strains designed as 0C-2-2T, 0C-17, and 65 LNM-3, were isolated from a red alga Porphyra yezoensis. We describe the 66 phylogenetic, genetic, phenotypic, and chemotaxonomic characters of the three novel 67 strains. 68 69 Thalli of P. yezoensis were cultured in a sterile modified half-strength SWM-III medium 70 (Ogata, 1970) at 17 °C. The samples of the culture medium and the thalli were 71 incubated on Marine agar 2216 (MA; Difco) at 20 °C for 2 weeks. Strains 0C-2-2T and 72 0C-17 were isolated from each culture medium in separate lots. Strain LNM-3 was 73 isolated from a thallus surface. Litorimonas taeanensis G5T and Hellea balneolensis 74 DSM 19091T were used as reference strains in all following tests. MA and Marine broth 75 2216 (MB; Difco) were used for the routine culture of all strains. Novel strains were 76 maintained at 20 °C. L. taeanensis G5T and H. balneolensis DSM 19091T were 77 maintained at 25 °C. All strains were stored at -80 °C in 20 % (v/v) glycerol. 78 79 DNA was prepared by the method of Johnson (1981). The 16S rRNA genes of the three 80 strains were amplified using universal primers of 27F and 1492R (Weisburg et al., 81 1991). The almost-complete 16S rRNA gene sequences of strains 0C-2-2T (1331 bp), 82 0C-17 (1349 bp), and LNM-3 (1331 bp) were determined using six sequencing primers 83 27F, 519F, 1190F, 530R, 760R, and 1492R (Satomi et al., 1997) using an automated 84 DNA sequencer (model 3100; Applied Biosystems). The sequences close to the novel 85 strains were obtained from the BLAST-N algorithm (Altschul et al., 1990) in the 86 GenBank, EMBL, and DDBJ databases. The 16S rRNA gene sequences of novel strains 87 and the related strains were aligned using Clustal X programs (Thompson et al., 1997) 88 and the sequence similarities were calculated except for alignment gaps and ambiguous 89 bases, using MEGA version 4 (Tamura et al., 2007). Phylogenetic trees were 90 constructed according to three methods of neighbour-joining, maximum-likelihood, and 91 maximum-parsimony analyses. Neighbour-joining tree was constructed with a bootstrap 92 through 1000 replications based on Kimura’s 2 parameter model (Kimura, 1980) using 93 MEGA version 4 (Tamura et al., 2007). Maximum-likelihood and maximum-parsimony 94 trees were constructed using PHYLIP version 3.69 (Felsenstein, 2009). The similarities 95 of 16S rRNA gene sequences among the three strains were 100 %. The 16S rRNA gene 96 sequence of strain 0C-2-2T had the similarities of 96.5 % and 94.3 % with L. taeanensis 97 G5T and H. balneolensis 26III/A02/215T, respectively. The phylogenetic tree based on 98 neighbour-joining analysis showed that the three strains belonged in the family 99 Hyphomonadaceae, and formed an independent group with a high bootstrap value of 100 100 % (Fig. 1). The clustering formation was also recovered in the maximum-likelihood 101 and the maximum-parsimony analyses. 102 103 DNA G+C content was determined using a HPLC with a reversed-phase column 104 (COSMOSIL 5C18-MS-II, Nacalai Tesque) according to the method of Tamaoka & 105 Komagata (1984). DNA of Tetragenococcus halophilus industrial strain (Bio’c) was 106 used as a control in the experiment. DNA-DNA hybridization was performed by a 107 microplate hybridization method (Ezaki et al., 1989). Each DNA of strain 0C-2-2T, L. 108 taeanensis G5T, and H. balneolensis DSM 19091T was labeled with a photobiotin. The 109 DNA G+C contents and the DNA-DNA relatedness among the three strains, L. 110 taeanensis G5T, and H. balneolensis DSM 19091T are shown in Table 1. The G+C 111 contents of the three isolates ranged from 58.5 to 60.2 mol%. The values of L. 112 taeanensis G5T and H. balneolensis DSM 19091T were 47.1 and 47.9 mol%, 113 respectively. The value of H. balneolensis DSM 19091Twas similar to 46.8 mol% 114 (original value, Alain et al., 2008), but the value of L. taeanensis G5T measured in this 115 study was distinct from 63.6 mol% (original value, Jung et al., 2011). The content of T. 116 halophilus industrial strain was 36.1 mol%, which was similar to a previous value by 117 Justé et al. (2012), and our method yield accurate measurements in a previous study 118 (Fukui et al., 2012). Furthermore, we examined a partial sequence of the 16S rRNA gene of 119 L. taeanensis G5T, and confirmed that the sequence had 100 % similarity with that in database. 120 There were significant differences of > 10 mol% in the G+C contents between the three 121 strains (58.5-60.2 mol%) and the closest phylogenic neighbours (47.1-47.9 mol%), 122 which indicates the three strains belong to a different genus (Stackebrandt & Liesack, 123 1993). DNA-DNA hybridization relatedness among strains 0C-2-2T, 0C-17, and LNM-3 124 were 99.0-101.6 %, suggested that the three isolates belonged to the same species 125 (Wayne et al., 1987).
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