Gramella planctonica sp. nov., a zeaxanthin-producing bacterium isolated from surface seawater, and emended descriptions of Gramella aestuarii and Gramella echinicola

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology

Volumn 105, Issue 4, 2014, Pages 771-779

  Shahina, Mariyam ^a   Hameed, Asif ^a   Lin, Shih Yao ^a   Lee, Ren Jye ^a   Lee, Maw Rong ^a   Young, Chiu Chung ^a  

^a NATIONAL CHUNG HSING UNIVERSITY   (Taiwan)

Author keywords

Carotenoid; Ecophysiological; Filamentous; Flavobacteriaceae; Organic matter

Indexed keywords

AMINOLIPID; BACTERIAL DNA; CYTOSINE; FARNOQUINONE; GUANINE; LIPID; PHOSPHATIDYLETHANOLAMINE; POLYAMINE; QUINONE DERIVATIVE; RNA 16S; SEA WATER; SPERMIDINE; SURFACE WATER; UNCLASSIFIED DRUG; ZEAXANTHIN;

16S RRNA GENE; AEROBIC BACTERIUM; ARTICLE; BACTERIAL CELL; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM ISOLATION; COASTAL WATERS; CONTROLLED STUDY; GENE SEQUENCE; GRAM NEGATIVE BACTERIUM; GRAMELLA AESTUARII; GRAMELLA ECHINICOLA; GRAMELLA PLANCTONICA; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN CONTENT; SEQUENCE HOMOLOGY; TAIWAN;

BACTERIA (MICROORGANISMS); FLAVOBACTERIACEAE; GRAMELLA; GRAMELLA ECHINICOLA;

BACTERIAL TYPING TECHNIQUES; BASE COMPOSITION; CLUSTER ANALYSIS; DNA, BACTERIAL; DNA, RIBOSOMAL; FATTY ACIDS; FLAVOBACTERIACEAE; LOCOMOTION; MOLECULAR SEQUENCE DATA; PHOSPHOLIPIDS; PHYLOGENY; QUINONES; RNA, RIBOSOMAL, 16S; SEAWATER; SEQUENCE ANALYSIS, DNA; TAIWAN; XANTHOPHYLLS;

EID: 84896493038     PISSN: 00036072     EISSN: 15729699     Source Type: Journal    
DOI: 10.1007/s10482-014-0133-4     Document Type: Article

References (40)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
2. Bauer M, Kube M, Teeling H, Richter M, Lombardot T, Allers E, Würdemann CA, Quast C, Kuhl H, Knaust F, Woebken D, Bischof K, Mussmann M, Choudhuri JV, Meyer F, Reinhardt R, Amann RI, Glöckner FO (2006) Whole genome analysis of the marine Bacteroidetes 'Gramella forsetii' reveals adaptations to degradation of polymeric organic matter. Environ Microbiol 8:2201-2213 (Pubitemid 44730250)
3. Bernardet JF (2011) Family I. Flavobacteriaceae Reichenbach 1992. In: Krieg NR, Ludwig W, Whitman WB, Hedlund BP, Paster BJ, Staley JT, Ward N, Brown D, Parte A (eds) Bergey's manual of systematic bacteriology, vol 4. Springer, New York, pp 106-111
4. 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 52:1049-1070 (Pubitemid 34591240)
5. Cho S, Chae S, Cho M, Kim T, Choi S, Han J, Kim Y, Joung Y, Joh K, Nedashkovskaya OI, Kim SB (2011) Gramella gaetbulicola sp. nov., a member of the family Flavobacteriaceae isolated from foreshore soil. Int J Syst Evol Microbiol 61:2654-2658
6. Collins MD (1985) Analysis of isoprenoid quinones. Methods Microbiol 18:329-366
7. Embley TM, Wait R (1994) Structural lipids of eubacteria. In: Goodfellow M, O'Donnell AG (eds) Chemical methods in prokaryotic systematics. Wiley, Chichester, pp 121-161
8. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368-376
9. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791
10. Fitch WM (1971) Towards defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406-416
11. GCG (1995) Wisconsin Package Version 8.1 Program Manual. Madison, WI: Computer Group
12. T. J Agric Food Chem 59:4119-4124
13. Hameed A, Shahina M, Lin S-Y, Sridhar KR, Young L-S, Lee M-R, Chen W-M, Chou J-H, Young C-C (2012) Siansivirga zeaxanthinifaciens gen. nov., sp. nov., a novel zeaxanthin-producing member of the family Flavobacteriaceae isolated from coastal seawater of Taiwan. FEMS Microbiol Lett 333:37-45
14. Hameed A, Shahina M, Lin S-Y, Cho JC, Lai W-A, Young C-C (2013a) Kordia aquimaris sp. nov., a zeaxanthin-producing member of the family Flavobacteriaceae isolated from surface seawater, and emended description of the genus Kordia. Int J Syst Evol Microbiol 63:4790-4796
15. Hameed A, Shahina M, Lin S-Y, Lai W-A, Hsu Y-H, Liu Y-C, Young C-C (2013b) Aquibacter zeaxanthinifaciens gen. nov., sp. nov., a zeaxanthin-producing bacterium of the family Flavobacteriaceae isolated from surface seawater, and emended descriptions of the genera Aestuariibaculum and Gaetbulibacter. Int J Syst Evol Microbiol 64:138-145
16. Heiner CR, Hunkapiller KL, Chen SM, Glass JI, Chen EY (1998) Sequencing multimegabase-template DNA with BigDye terminator chemistry. Genome Res 8:557-561
17. Jeong SH, Jin HM, Jeon CO (2013) Gramella aestuarii sp. nov., isolated from a tidal flat, and emended description of Gramella echinicola. Int J Syst Evol Microbiol 63:2872-2878
18. Joung Y, Kim H, Jang T, Ahn TS, Joh K (2011) Gramella jeungdoensis sp. nov., isolated from a solar saltern in Korea. J Microbiol 49:1022-1026
19. Kämpfer P, Kroppenstedt RM (1996) Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 42:989-1005 (Pubitemid 26380214)
20. Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M, Na H, Park S-C, Jeon YS, Lee J-H, 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 62:716-721
21. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111-120
22. Lau SC, Tsoi MM, Li X, Plakhotnikova I, Dobretsov S, Wong PK, Qian PY (2005) Gramella portivictoriae sp. nov., a novel member of the family Flavobacteriaceae isolated from marine sediment. Int J Syst Evol Microbiol 55:2497-2500 (Pubitemid 41646433)
23. Liu K, Li S, Jiao N, Tang K (2013) Gramella flava sp. nov., a novel member of the family Flavobacteriaceae isolated from the Southeastern Pacific. Int J Syst Evol Microbiol 64:165-168
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 39:159-167
25. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233-241 (Pubitemid 14058168)
26. Montero-Calasanz MD, Göker M, Rohde M, Spröer C, Schumann P, Busse H-J, Schmid M, Tindall BJ, Klenk H-P, Camacho M (2013) Chryseobacterium hispalense sp. nov., a plant growth-promoting bacterium isolated from a rainwater pond in an olive plant nursery and emendation of the species Chryseobacterium defluvii, Chryseobacterium indologenes, Chryseobacterium wanjuense and Chryseobacterium gregarium. Int J Syst Evol Microbiol 63:4386-4395
27. Murray RGE, Doetsch RN, Robinow CF (1994) Determinative and cytological light microscopy. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society of Microbiology, Washington DC, pp 21-41
28. Nedashkovskaya OI, Kim SB, Lysenko AM, Frolova GM, Mikhailov VV, Bae KS, Lee DH, Kim IS (2005) Gramella echinicola gen. nov., sp. nov., a novel halophilic bacterium of the family Flavobacteriaceae isolated from the sea urchin Strongylocentrotus intermedius. Int J Syst Evol Microbiol 55:391-394 (Pubitemid 40185518)
29. Nedashkovskaya OI, Kim SB, Bae KS (2010) Gramella marina sp. nov., isolated from the sea urchin Strongylocentrotus intermedius. Int J Syst Evol Microbiol 60:2799-2802
30. Reichenbach H (1992) The order cytophagales. In: Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH (eds) The prokaryotes. A handbook on the biology of bacteria: ecophysiology, isolation, identification, applications. Springer, New York, pp 3631-3675
31. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
32. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 20:16
33. Scherer P, Kneifel H (1983) Distribution of polyamines in methanogenic bacteria. J Bacteriol 154:1315-1322 (Pubitemid 13099046)
34. Shahina M, Hameed A, Lin S-Y, Hsu Y-H, Liu Y-C, Cheng I-C, Lee M-R, Lai W-A, Lee R-J, Young C-C (2013)
35. Sphingomicrobium astaxanthinifaciens sp. nov., an asta-xanthin-producing glycolipid-rich bacterium isolated from surface seawater and emended description of the genus Sphingomicrobium. Int J Syst Evol Microbiol 63:3415-3422
36. Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society of Microbiology, Washington DC, pp 607-654
37. 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 28:2731-2739
38. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876-4882 (Pubitemid 28022245)
39. Tindall BJ, Rosselló-Móra R, Busse H-J, Ludwig W, Kämpfer P (2010) Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60:249-266
40. Watts D, MacBeath JR (2001) Automated fluorescent DNA sequencing on the ABI PRISM 310 Genetic Analyzer. Methods Mol Biol 167:153-170