Frondibacter mangrovi sp. nov., a member of the family flavobacteriaceae isolated from seawater by in situ cultivation, and emended description of Frondibacter aureus

International Journal of Systematic and Evolutionary Microbiology

Volumn 67, Issue 12, 2017, Pages 5013-5018

  Yoon, Jaewoo ^a   Yasumoto Hirose, Mina ^b,d   Kasai, Hiroaki ^c  

^a Keimyung University   (South Korea)

^b MARINE BIOTECHNOLOGY INSTITUTE   (Japan)

^c KITASATO UNIVERSITY   (Japan)

^d Tropical Technology Center Ltd   (Japan)

Author keywords

16S rRNA gene; Bacteroidetes; Flavobacteriaceae; Frondibacter mangrovi sp. nov; In situ cultivation; Polyphasic taxonomy

Indexed keywords

AMINOPHOSPHOLIPID; LIPID; MENAQUINONE; PHOSPHATIDYLETHANOLAMINE; RNA 16S; SEA WATER; BACTERIAL DNA; FARNOQUINONE; FATTY ACID; PHOSPHOLIPID;

ANAEROBIC BACTERIUM; ARTICLE; BACTERIAL STRAIN; BACTERIUM CULTURE; BACTERIUM ISOLATE; BACTERIUM ISOLATION; BACTEROIDETES; DNA BASE COMPOSITION; ESTUARY; FLAVOBACTERIACEAE; FRONDIBACTER AUREUS; FRONDIBACTER MANGROVI; GENE SEQUENCE; GENOTYPE; GRAM NEGATIVE BACTERIUM; JAPAN; LIPID COMPOSITION; MANGROVE; NONHUMAN; PHENOTYPE; PHYLOGENY; PRIORITY JOURNAL; ANALOGS AND DERIVATIVES; BACTERIUM IDENTIFICATION; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; PIGMENTATION;

BACTERIAL TYPING TECHNIQUES; BASE COMPOSITION; DNA, BACTERIAL; ESTUARIES; FATTY ACIDS; FLAVOBACTERIACEAE; JAPAN; PHOSPHOLIPIDS; PHYLOGENY; PIGMENTATION; RNA, RIBOSOMAL, 16S; SEAWATER; SEQUENCE ANALYSIS, DNA; VITAMIN K 2;

EID: 85037715645     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijsem.0.002404     Document Type: Article

References (35)

1. Jooste PJ. The taxonomy and significance of Flavobacterium–Cytophaga strains from dairy sources. PhD thesis, University of the Orange Free State, South Africa; 1985.
2. Bernardet JF, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070.
3. Garrity GM, Holt JG. The road map to the manual. In: Boone DR, Castenholz RW and Garrity GM (editors). Bergey’s Manual of Systematic Bacteriology, 2nd ed, vol. 1. New York: Springer; 2001. pp. 119–166.
4. Ludwig W, Klenk HP. Overview: a phylogenetic backbone and taxonomic framework for procaryotic systematics. In: Boone DR, Castenholz RW and Garrity GM (editors). Bergey’s Manual of Systematic Bacteriology, 2nd ed, vol. 1. New York: Springer; 2001. pp. 49–66.
5. Kirchman DL. The ecology of Cytophaga-Flavobacteria in aquatic environments. FEMS Microbiol Ecol 2002;39:91–100.
6. O’Sullivan LA, Rinna J, Humphreys G, Weightman AJ, Fry JC. Culturable phylogenetic diversity of the phylum ’Bacteroidetes’ from river epilithon and coastal water and description of novel members of the family Flavobacteriaceae: Epilithonimonas tenax gen. nov., sp. nov. and Persicivirga xylanidelens gen. nov., sp. nov. Int J Syst Evol Microbiol 2006;56:169–180.
7. Zeng YX, Zhang F, He JF, Lee SH, Qiao ZY et al. Bacterioplankton community structure in the Arctic waters as revealed by pyrosequencing of 16S rRNA genes. Antonie van Leeuwenhoek 2013;103: 1309–1319.
8. Cottrell MT, Kirchman DL. Community composition of marine bacterioplankton determined by 16S rRNA gene clone libraries and fluorescence in situ hybridization. Appl Environ Microbiol 2000;66: 5116–5122.
9. Brettar I, Christen R, Höfle MG. Aquiflexum balticum gen. nov., sp. nov., a novel marine bacterium of the Cytophaga-Flavobacterium- Bacteroides group isolated from surface water of the central Baltic Sea. Int J Syst Evol Microbiol 2004;54:2335–2341.
10. Yasumoto-Hirose M, Nishijima M, Ngirchechol MK, Kanoh K, Shizuri Y et al. Isolation of marine bacteria by in situ culture on media-supplemented polyurethane foam. Mar Biotechnol 2006;8: 227–237.
11. Yoon J, Yasumoto-Hirose M, Matsuo Y, Nozawa M, Matsuda S et al. Pelagicoccus mobilis gen. nov., sp. nov., Pelagicoccus albus sp. nov. and Pelagicoccus litoralis sp. nov., three novel members of subdivision 4 within the phylum ’Verrucomicrobia’, isolated from seawater by in situ cultivation. Int J Syst Evol Microbiol 2007;57: 1377–1385.
12. Yoon J, Kasai H. Phylogenetic and taxonomic analysis of Neptunitalea chrysea gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from seawater by using an in situ cultivation technique. Antonie van Leeuwenhoek 2015;108:537–544.
13. Yoon J, Adachi K, Kasai H. Isolation and classification of a novel marine Bacteroidetes as Frondibacter aureus gen. nov., sp. nov. Antonie van Leeuwenhoek 2015;107:321–328.
14. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by highperformance liquid chromatography. Int J Syst Bacteriol 1989;39: 159–167.
15. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991;173: 697–703.
16. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBio- Cloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617.
17. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997;25:4876–4882.
18. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980;16:111–120.
19. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425.
20. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971;20:406–416.
21. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791.
22. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011;28:2731–2739.
23. Yoon J, Lee KC, Lee JS. Cribrihabitans pelagius sp. nov., a marine alphaproteobacterium isolated from seawater. Int J Syst Evol Microbiol 2016;66:3195–3200.
24. Hertel C, Schmidt G, Fischer M, Oellers K, Hammes WP. Oxygendependent regulation of the expression of the catalase gene katA of Lactobacillus sakei LTH677. Appl Environ Microbiol 1998;64:1359–1365.
25. Høvik Hansen G, Sørheim R. Improved method for phenotypical characterization of marine bacteria. J Microbiol Methods 1991;13: 231–241.
26. Power DA, Johnson JA. DifcoÔ and BBLÔ Manual: Manual of Microbiological Culture Media, 2nd ed. Sparks: Becton Dickinson and Company; 2009. pp. 359–360.
27. Lewin RA, Lounsbery DM. Isolation, cultivation and characterization of flexibacteria. J Gen Microbiol 1969;58:145–170.
28. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990.
29. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984;2:233–241.
30. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987;19:161–207.
31. Worliczek HL, Kämpfer P, Rosengarten R, Tindall BJ, Busse HJ. Polar lipid and fatty acid profiles–re-vitalizing old approaches as a modern tool for the classification of mycoplasmas? Syst Appl Microbiol 2007;30:355–370.
32. Collins MD, Jones D. A note on the separation of natural mixtures of bacterial ubiquinones using reverse-phase partition thin-layer chromatography and high performance liquid chromatography. J Appl Bacteriol 1981;51:129–134.
33. Surendra V, Bhawana P, Suresh K, Srinivas TN, Kumar PA. Imtechella halotolerans gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from estuarine water. Int J Syst Evol Microbiol 2012;62:2624–2630.
34. Quan ZX, Xiao YP, Roh SW, Nam YD, Chang HW et al. Joostella marina gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from the East Sea. Int J Syst Evol Microbiol 2008;58:1388–1392.
35. Hameed A, Shahina M, Lin SY, Lai WA, Liu YC et al. Robertkochia marina gen. nov., sp. nov., of the family Flavobacteriaceae, isolated from surface seawater, and emended descriptions of the genera Joostella and Galbibacter. Int J Syst Evol Microbiol 2014;64:533–539.