Isolation and characterization of a novel agar-degrading marine bacterium, Gayadomonas joobiniege gen, nov, sp. nov., from the Southern Sea, Korea

Journal of Microbiology and Biotechnology

Volumn 23, Issue 11, 2013, Pages 1509-1518

  Chi, Won Jae ^a   Park, Jae Seon ^a   Kwak, Min Jung ^b   Kim, Jihyun F ^c   Chang, Yong Keun ^d   Hong, Soon Kwang ^a  

^a Myong Ji University   (South Korea)

^b University of Science and Technology (UST)   (South Korea)

^c Yonsei University   (South Korea)

^d Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

Author keywords

Agar degradation; Agarase; Alteromonadaceae; Alteromonas like Gammaproteobacteria; Gayadomonas joobiniege

Indexed keywords

AGAR; AGARASE; FATTY ACID; HYDROLASE; ISOPRENOID; MENAQUINONE; MENAQUINONE 7; QUINONE DERIVATIVE; RNA 16S; SEA WATER; UBIQUINONE; UBIQUINONE 8; UNCLASSIFIED DRUG;

ALGICOLA SAGAMIENSIS; ALTEROMONADACEAE; ANTIBIOTIC SENSITIVITY; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIUM ISOLATION; BOWMANELLA PACIFICA; CARBON UTILIZATION; CATENOVULUM AGARIVORANS; CHEMOTAXONOMY; COASTAL WATERS; CONTROLLED STUDY; DNA BASE COMPOSITION; DNA DNA HYBRIDIZATION; ENZYME ANALYSIS; ENZYME SYNTHESIS; GAMMAPROTEOBACTERIA; GAYADOMONAS JOOBINIEGE; KOREA; MARINE BACTERIUM; MICROBIAL DEGRADATION; MONOPHYLY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE HOMOLOGY;

AGAR; ALTEROMONADACEAE; BACTERIAL TYPING TECHNIQUES; BASE COMPOSITION; CLUSTER ANALYSIS; DNA, BACTERIAL; DNA, RIBOSOMAL; FATTY ACIDS; HYDROLYSIS; MICROBIAL SENSITIVITY TESTS; MICROSCOPY, ELECTRON, TRANSMISSION; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HYBRIDIZATION; PHYLOGENY; QUINONES; REPUBLIC OF KOREA; RNA, RIBOSOMAL, 16S; SEAWATER; SEQUENCE ANALYSIS, DNA;

EID: 84888139680     PISSN: 10177825     EISSN: 17388872     Source Type: Journal    
DOI: 10.4014/jmb.1308.08007     Document Type: Article

References (38)

1. Akagawa-Matsushita M, Matsuo M, Koga Y, Yamasato K. 1992. Alteromonas atlantica sp. nov. and Alteromonas carrageenovora sp. nov., bacteria that decompose algal polysaccharides. Int. J. Syst. Evol. Bacteriol. 42: 621-627.
2. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang A, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein data base. Nucleic Acids Res. 25: 3389-3402.
3. Chen H-M, Zheng L, Yan X-J. 2005. The preparation and bioactivity research of agaro-oligosaccharides. Food Technol. Biotechnol. 43: 29-36.
4. Chen LP, Xu HY, Fu SZ, Fan HX, Liu YH, Liu SJ, et al. 2009. Glaciecola lipolytica sp. nov., isolated from seawater near Tianjin city, China. Int. J. Syst. Evol. Bacteriol. 59: 73-76.
5. Chi W-J, Lim J-H, Park DY, Kim M-C, Kim C-J, Chang Y-K, et al. 2013. Isolation and characterization of a novel agar degrading bacterium, Alteromonas macleodii subsp. GNUM08120, from red macroalgae. Korean J. Microbiol. Biotechnol. 41: 8-16.
6. Chi W-J, Chang Y-K, Hong S-K. 2012. Agar degradation by microorganisms and agar-degrading enzymes. Appl. Microbiol. Biotechnol. 94: 917-930.
7. Chimetto LA, Cleenwerck L, Moreira APB, Brocchi M, Willems A, Vos PD, et al. 2011. Vibrio variabilis sp. nov. and Vibrio marinus sp. nov., isolated from Palythoa caribaeorum. Int. J. Syst. Evol. Bacteriol. 61: 3009-3015.
8. Chiu HH, Shieh WY, Lin SY, Tseng CM, Chiang PW, Wagner-Dobler I. 2007. Alteromonas tagae sp. nov. and Alteromonas simiduii sp. nov., mercury-resistant bacteria isolated from a Taiwanense estuary. Int. J. Syst. Evol. Microbiol. 57: 1209-1216.
9. Chun JS, Lee JH, Jung YY, Kim MJ, Kim SI, Kim BK, et al. 2007. Extaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int. J. Syst. Evol. Microbiol. 57: 2259-2261.
10. Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P. 2006. Toward automatic reconstruction of a highly resolved tree of life. Science 311: 1283-1287.
11. Enoki T, Okuda S, Kudo Y, Takashima F, Sagawa H, Kato I. 2010. Oligosaccharides from agar inhibit pro-inflammatory mediator release by inducing heme oxygenase 1. Biosci. Biotechnol. Biochem. 74: 766-770.
12. Felsenstein J. 1993. PHYLIP (phylogeny inference package), version 3.5c. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
13. Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/ NT. Nucleic Acids Symp. Ser. 41: 95-98.
14. Invanova EP, Mikhailov VV. 2001. A new family, Alteromonadaceae fam. nov., including marine proteobacteria of the genera Alteromonas, Pseudoalteromonas, Idiomarina, and Colwellia. Mikrobiologiya 70: 15023 (in Russian).
15. Ivanova EP, Bowman JP, Lysenko AM, Zhukova NV, Gorshkova NM, Sergeev AF, et al. 2005. Alteromonas addita sp. nov. Int. J. Syst. Evol. Microbiol. 55: 1065-1068.
16. Ivanova EP, Flavier S, Christen R. 2004. Phylogenetic relationships among marine Alteromonas-like proteobacteria: emended description of the family Altermonadaceae and proposal of Pseudolateromonadaceae fam. nov., Colwelliaceae fam. nov., Shewanellaceae fam. nov., Moritellaceae fam. nov., Ferrimonadaceae fam. nov., Idiomarinaceae fam. nov. and Psychromonadaceae fam. nov. Int. J. Syst. Evol. Microbiol. 54: 1773-1778.
17. Jean WD, Chen JS, Lin YT, Shieh WY. 2006. Bowmanella denitrificans gen. nov., sp. nov., a denitrifying bacterium isolated from seawater from An-Ping Harbour, Taiwan. Int. J. Syst. Evol. Microbiol. 56: 2463-2467.
18. Jean WD, Shieh WY, Liu TY. 2006. Thalassomonas agarivorans sp. nov., a marine agarolytic bacterium isolated from shallow coastal water of An-Ping Harbour, Taiwan, and emended description of the genus Thalassomonas. Int. J. Syst. Evol. Microbiol. 56: 1245-1250.
19. Ji J, Wang L-C, Wu H, Luan H-M. 2011. Bio-function summary of marine oligosaccharides. Int. J. Biol. 3: 74-86.
20. Kim J, Hong S-K. 2012. Isolation and characterization of an agarase-producing bacterial strain, Alteromonas sp. GNUM-1, from the west sea, Korea. J. Microbiol. Biotechnol. 22: 1621-1628.
21. Kimura M. 1983. The Neutral Theory of Molecular Evolution. Cambridge Univesity Press, UK.
22. Kobayashi T, Imada C, Hiraishi A, Tsujibo H, Miyamoto K, Inamori Y, et al. 2003. Pseudoalteromonas sagamiensis sp. nov., a marine bacterium that produces protease inhibitors. Int. J. Syst. Evol. Microbiol. 53: 1807-1811.
23. Komagata K, Suzuki K. 1987. Lipid and cell-wall analysis in bacterial systematic. Methods Microbiol. 19: 161-207.
24. Kwak MJ, Song JY, Kim BK, Chi W-J, Kwon S-K, Choi S, et al. 2012. Genome sequence of the agar-degrading marine bacterium Alteromonadaceae sp. G7. J. Bacteriol. 194: 6961-6962.
25. Lai Q, Yuan JY, Wang B, Sun F, Qiao N, Zheng T, et al. 2009. Bowmanella pacifica sp. nov., isolated from a py renedegrading consortium. Int. J. Syst. Evol. Microbiol. 59: 1579-1582.
26. Martinez-Checa F, Bejar W, Llamas I, del Moral A, Quesda E. 2005. Alteromonas hispanica sp. nov., a polyunsaturatedfatty-acid-producing, halophilic bacterium isolated from Fuente de Piedra, southern Spain. Int. J. Syst. Evol. Microbiol. 55: 2385-2390.
27. Miller GL. 1959. Use of dinitrosalicylic acid reagent for determination of reducing sugar. Anal. Chem. 31: 426-428.
28. Miller L, Berger T. 1985. Bacterial identification by gas chromatography of whole cell fatty acids. Hewlett-Packard Application note 228-241. Hewlett-Packard Co., Avondale, PA.
29. Richter M, Rosselló-Móra R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. USA 106: 19126-19131.
30. Romanenko LA, Zhukova NV, Lysenko AM, Mikhailov VV, Stackebrandt E. 2003. Assignment of 'Alteromonas marinoglutinosa' NCIMB 1770 to Pseudoalteromonas mariniglutinosa sp. nov., nom. rev., comb. nov. Int. J. Syst. Evol. Microbiol. 53: 1105-1109.
31. Romanenko LA, Zhukova NV, Rohde M, Lysenko AM, Mikhailov VV, Stackebrandt E. 2003. Glaciecola mesophila sp. nov., a novel marine agar-digesting bacterium. Int. J. Syst. Evol. Microbiol. 53: 647-651.
32. Sasser M. 1990. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. MIDI Inc., Newark, DE.
33. Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24: 1596-1599.
34. Tanaka H, Romanenko LA, Frolova GM, Mikhailov VV. 2010. Aestuariibacter litoralis sp. nov., isolated from a sandy sediment of the Sea of Japan. Int. J. Syst. Evol. Microbiol. 60: 317-320.
35. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
36. Van Trappen S, Tan TL, Yang J, Mergaert J, Swings J. 2004. Glaciecola polaris sp. nov., a novel budding and prosthecate bacterium from the Artic Ocean, and emended description of the genus Glaciecola. Int. J. Syst. Evol. Microbiol. 54: 1765-1771.
37. Yan S, Yu M, Wang Y, Shen C, Zhang XH. 2011. Catenovulum agarivorans gen. nov. sp. nov., a peritrichously flagellated, catenated, agar-hydrolyzing γ-Proteobacterium isolated from Yellow Sea. Int. J. Syst. Evol. Microbiol. 61: 2866-2873.
38. Yi H, Bae KS, Chun J. 2004. Aestuariibacter salexigens gen. nov., sp. nov. and Aestuariibacter halophilus sp. nov., isolated from tidal flat sediment, and emended description of Altermonas macleodii. Int. J. Syst. Evol. Microbiol. 54: 571-576.