Bacterioplanes sanyensis gen. nov., sp. nov., a PHB-accumulating bacterium isolated from a pool of Spirulina platensis cultivation

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• 作者：Guanghua Wang ; Qikun Jia ; Tao Li ; Shikun Dai ; Huanlian Wu…
• 关键词：Bacterioplanes sanyensis ; 16S rRNA gene ; based phylogeny ; Chemotaxonomy
• 刊名：Archives of Microbiology
• 出版年：2014
• 出版时间：October 2014
• 年：2014
• 卷：196
• 期：10
• 页码：739-744
• 全文大小：260 KB
• 参考文献：1. Baumann L, Baumann P, Mandel M, Allen RD (1972) Taxonomy of aerobic marine eubacteria. J Bacteriol 111(1):402-29
  2. 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 52:1049-070 CrossRef
  3. Bowditch RD, Baumann L, Baumann P (1984) Description of / Oceanospirillum kriegii sp. nov. and / O. jannaschii sp. nov. and assignment of two species of / Alteromonas to this genus as / O. / commune comb. nov. and / O. vagum comb. nov. Curr Microbiol 10(4):221-29 CrossRef
  4. Choi A, Cho J (2013) / Thalassolituus marinus sp. nov., a hydrocarbon-utilizing marine bacterium. Int J Syst Evol Microbiol 63(Pt 6):2234-238 CrossRef
  5. Collins MD (1994) Isoprenoid quinones. In: Goodfellow M, Donnell AGO (eds) Chemical methods in prokaryotic systematic. Wiley, Chichester, pp 345-01
  6. Coulon F, McKew BA, Osborn AM, McGenity TJ, Timmis KN (2007) Effects of temperature and biostimulation on oil degrading microbial communities in temperate estuarine waters. Environ Microbiol 9:177-86 CrossRef
  7. Dauga C, Gillis M, Vandamme P, Ageron E, Grimont F, Kersters K, de Mahenge C, Peloux Y, Grimont PA (1993) / Balneatrix alpica gen. nov., sp. nov., a bacterium associated with pneumonia and meningitis in a spa therapy center. Res Microbiol 144(1):35-6 CrossRef
  8. Dong XZ, Cai MY (2001) Determinative manual for routine bacteriology. Scientific Press, Beijing
  9. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368-76 CrossRef
  10. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-91 CrossRef
  11. Garrity GM, Bell, J A, Lilburn T (2005) Family I. / Oceanospirillaceae fam. nov. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds) Bergey’s manual of systematic bacteriology, 2nd edn, vol 2, part B. Springer, New York, p 271
  12. Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) (1994) Methods for general and molecular bacteriology. American Society for Microbiology, Washington
  13. Golyshin PN, Werner J, Chernikova TN, Tran H, Ferrer M, Yakimov MM, Teeling H, Golyshina OV (2013) Genome sequence of / Thalassolituus oleivorans MIL-1^T (DSM 14913^T). Genome Announc 1(2):e0014113
  14. Hylemon PB, Wells JS Jr, Krieg NR, Jannasch HW (1973) The genus / Spirillum: a taxonomic study. Int J Syst Bacteriol 23:340-80 CrossRef
  15. Kamekura M (1993) Lipids of extreme halophiles. In: Vreeland RH, Hochstein LI (eds) The biology of halophilic bacteria. CRC Press, Boca Raton, pp 135-61
  16. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716-21 CrossRef
  17. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111-20 CrossRef
  18. Kloos K, Munch JC, Schloter M (2006) A new method for the detection of alkane-monooxygenase homologous genes ( / alkB) in soils based on PCR-hybridization. J Microbiol Methods 66:486-96 CrossRef
  19. Komagata K, Suzuki K (1987) Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161-07 CrossRef
  20. Kube M, Chernikova TN, Al-Ramahi Y et al (2013) Genome sequence and functional genomic analysis of the oil-degrading bacterium / Oleispira antarctica. Nat Commun 4:2156-166 CrossRef
  21. Kyrpides N, Huntemann M, Han J et al (2013) Joint Genome Institute, United States Department of Energy. http://genome.jgi.doe.gov/genome-projects/pages/projects.jsf?searchText=1010746. Accessed 5 Feb 2014
  22. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, pp 115-75
  23. McKew BA, Coulon F, Osborn AM, Timmis KN, McGenity TJ (2007) Determining the identity and roles of oil-metabolizing marine bacteria from the Thames estuary, UK. Environ Microbiol 9:165-76 CrossRef
  24. 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 39:159-67 CrossRef
  25. Pruesse E, Peplies J, Gl?ckner FO (2012) SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28:1823-829 CrossRef
  26. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic tree. Mol Biol Evol 4:406-25
  27. Sakane T, Yokota A (1994) Chemotaxonomic investigation of heterotrophic, aerobic and microaerophilic spirilla, the genera / Aquaspirillum, / Magnetospirillum, and / Oceanospirillum. Syst Appl Microbiol 17:128-34 CrossRef
  28. Satomi M, Kimura B, Hamada T, Harayama S, Fujii T (2002) Phylogenetic study of the genus / Oceanospirillum based on 16S rRNA and / gyrB genes: emended description of the genus / Oceanospirillum, description of / Pseudospirillum gen. nov., / Oceanobacter gen. nov. and / Terasakiella gen. nov. and transfer of / Oceanospirillum jannaschii and / Pseudomonas stanieri to / Marinobacterium as / Marinobacterium jannaschii comb. nov. and / Marinobacterium stanieri comb. nov. Int J Syst Evol Microbiol 52:739-47 CrossRef
  29. Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular microbiology. American Society for Microbiology, Washington, pp 611-54
  30. Swofford DL (1993) PAUP: phylogenetic analysis using parsimony. Version 3.1.1. Illinois Natural History Survey, Champaign, IL
  31. Tamura K, Peterson D, Peterson 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 28:2731-739 CrossRef
  32. Teramoto M, Suzuki M, Okazaki F, Hatmanti A, Harayama S (2009) / Oceanobacter-related bacteria are important for the degradation of petroleum aliphatic hydrocarbons in the tropical marine environment. Microbiology 155:3362-370 CrossRef
  33. Teramoto M, Ohuchi M, Hatmanti A, Darmayati Y, Widyastuti Y, Harayama S, Fukunaga Y (2011) / Oleibacter marinus gen. nov., sp. nov., a bacterium that degrades petroleum aliphatic hydrocarbons in a tropical marine environment. Int J Syst Evol Microbiol 61(2):375-80 CrossRef
  34. Tindall BJ (1990) Lipid composition of halobacterium lacusprofundi. FEMS Microbiol Lett 66:199-02 CrossRef
  35. Tindall BJ, Sikorski J, Smibert RM, Krieg NR (2007) Phenotypic characterization and the principles of comparative systematics. In: Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM, Snyder LR (eds) Methods for general and molecular microbiology. American Society for Microbiology, Washington, pp 330-93
  36. Wang GH, Wu HL, Zhang XY, Zhang H, Yang X, Tian XP, Li J, Xiang WZ, Li X (2013) / Aliidiomarina sanyensis sp. nov., a hexabromocyclododecane-assimilating bacterium from the pool of / Spirulina platensis cultivation, Sanya, China. Antonie Van Leeuwenhoek 104(3):309-14 CrossRef
  37. Williams MA, Rittenberg SC (1957) A taxonomic study of the genus / Spirillum Ehrenberg. Int Bull Bact Nom Taxon 7:49-12
  38. Yakimov MM, Giuliano L, Denaro R, Crisafi E, Chernikova TN, Abraham WR, Luensdorf H, Timmis KN, Golyshin PN (2004) / Thalassolituus oleivorans gen. nov., sp. nov., a novel marine bacterium that obligately utilizes hydrocarbons. Int J Syst Evol Microbiol 54(1):141-48 CrossRef
  39. Yakimov MM, Denaro R, Genovese M, Cappello S, D’Auria G, Chernikova TN, Timmis KN, Golyshin PN, Giluliano L (2005) Natural microbial diversity in superficial sediments of Milazzo Harbor (Sicily) and community successions during microcosm enrichment with various hydrocarbons. Environ Microbiol 7:1426-441 CrossRef
  40. Zhu C, Nomura CT, Perrotta JA, Stipanovic AJ, Nakas JP (2010) Production and characterization of poly-3-hydroxybutyrate from biodiesel–glycerol by / Burkholderia cepacia ATCC 17759. Biotechnol Prog 26(2):424-30
  
• 作者单位：Guanghua Wang (1)
  Qikun Jia (1) (2)
  Tao Li (1)
  Shikun Dai (1)
  Huanlian Wu (1)
  Hui He (1)
  Jiewei Fan (1)
  Wenzhou Xiang (1)
  Xiang Li (1)
  
  1. CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB-CAS), Guangdong Key Laboratory of Marine Materia Medica (LMMM-GD), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
  2. University of Chinese Academy of Sciences, Beijing, 100049, China
  
• ISSN：1432-072X

文摘

A Gram-negative, poly-3-hydroxybutyrate-accumulating rod bacterium, strain GYP-2T, was isolated from a pool of marine Spirulina platensis cultivation, Sanya, China. Growth was observed at 10-5?°C and pH 6-0 in the presence of 1-0?% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the new isolate belonged to Gammaproteobacteria and displayed 93.8-5.3?% 16S rRNA gene sequences similarities to members of the genera Thalassolituus, Oleibacter, and Oceanobacter, but house-keeping gene gyrB (encode DNA gyrase beta subunit) demonstrated that the new isolate was distantly related to Thalassolituus, Oleibacter, and Oceanobacter species (only 77-3?% gene gyrB sequences similarities).The G+C content of genomic DNA was 55?mol%. The major respiratory quinone was Q-9, while that for Oceanobacter kriegii LMG 6238T was Q-8. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. On the basis of its physiological, chemotaxonomic, and molecular properties, strain GYP-2T is suggested to represent a novel species of a new genus in Gammaproteobacteria, for which the name Bacterioplanes sanyensis gen. nov., sp. nov. is proposed. The type strain is GYP-2T (=CGMCC 1.12392T=KCTC 32220T).