Novel rhodococci and other mycolate actinomycetes from the deep sea

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology

Volumn 74, Issue 1-3, 1998, Pages 27-40

  Colquhoun, Joy A ^a   Mexson, Joanne ^a   Goodfellow, Michael ^b   Ward, Alan C ^b   Horikoshi, Koki ^c   Bull, Alan T ^a  

^a UNIVERSITY OF KENT   (United Kingdom)

^b NEWCASTLE UNIVERSITY   (United Kingdom)

^c JAPAN AGENCY FOR MARINE EARTH SCIENCE AND TECHNOLOGY   (Japan)

Author keywords

Deep sea; Mycolata; Polyphasic taxonomy; Pyrolysis mass spectrometry; Rhodococcus

Indexed keywords

BACTERIAL DNA; MYCOLIC ACID; RNA 16S;

DEEP-SEA BENTHOS; NEW SPECIES;

ACTINOBACTERIA; AQUATIC FAUNA; ARTICLE; BIODIVERSITY; CORYNEBACTERIUM; GENE SEQUENCE; MASS SPECTROMETRY; MICROBIAL GENETICS; MOLECULAR BIOLOGY; MYCOBACTERIUM; NONHUMAN; PACIFIC OCEAN; PRIORITY JOURNAL; RHODOCOCCUS; SEDIMENT; TAXONOMY; THERMOACTINOMYCES;

ACTINOMYCETALES; BACTERIAL TYPING TECHNIQUES; BASE COMPOSITION; DNA, RIBOSOMAL; GEOLOGIC SEDIMENTS; MARINE BIOLOGY; MASS SPECTROMETRY; MICROMONOSPORACEAE; MYCOBACTERIUM; MYCOLIC ACIDS; PACIFIC OCEAN; RHODOCOCCUS; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

EID: 0032453682     PISSN: 00036072     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1001743625912     Document Type: Article

References (35)

1. Bruun AF (1957) Deep sea and abyssal depths. Mem. Geol. Soc. Am. 67: 641-672.
2. Colquhoun JA, Heald SC, Kato C, Li L, Tamaoka J, Horikoshi K & Bull AT (1998) Taxonomy and biotransformation activities of some deep-sea actinomyctes. Extremophiles 2: 269-277.
3. Colwell RR (1970) Polyphasic taxonomy of bacteria. In: Iizuka H, Hasegawa T (Eds) Culture Collections of Microorganisms (pp 421-436). University of Tokyo Press, Tokyo.
4. Cross T (1981) The monosporic actinomycetes. In: Starr MP, Stolp H, Trüper HG, Balows A & Schlegel HG (Eds) The Prokaryotes, Vol II, (pp 2091-2102). Springer-Verlag, Berlin.
5. Duckworth, A, Grant, S, Grant, W, Jones, B and Meijer, D. (1998) Dietzia natronolimnaios sp.nov. A new member of the genus Dietzia isolated from an East African soda lake. International Congress, Extremophiles'98, Yokohama. Abstract 54-P23, p. 388. Japan Marine Science and Technology Center, Tokyo.
6. Ezaki T, Hashimoto Y & Yabuuchi E (1989) Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int. J. Syst. Bacteriol. 39: 224-229.
7. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
8. Feng DF & Doolittle RF (1987) Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J Mol. Evolution. 25: 351-360
9. Fox G, Wisotskey JD & Jurtshuk P (1992) How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int. J. Syst. Bacteriol. 42: 166-170.
10. Goodacre R & Kell DB (1996) Pyrolysis mass spectrometry and its applications in biotechnology. Curr. Opinion Biotechnol. 7: 20-28.
11. Goodfellow M & Haynes JA (1984) Actinomycetes in marine sediments. In: Ortiz-Ortiz L, Bojalil LF, Yakoleff V (Eds) Biological, Biochemical and Biomedial Aspects of Actinomycetes, (pp 453-472). Academic Press, Orlando.
12. Goodfellow M, Manfio GP & Chun J (1997) Towards a practical species concept for cultivable bacteria. In: Claridge MF, Dawah HA & Wilson MR (Eds) Species: The Units of Biodiversity (pp 25-59). Chapman & Hall, London.
13. Goodfellow M, Alderson G & Chun J (1998) Rhodococcus systematics: problems and developments. Antonie van Leeuwenhoek, 74: 3-20
14. Gordon RE & Mihm JM (1962) Identification of Nocardia caviae (Erikson) nov.comb. Ann. NY Acad. Sci. 98: 628-636.
15. Hamamoto T & Horikoshi K (1993) Deep-sea microbiology research within the Deepstar program. J. Mar. Biotechnol. 1: 119-124.
16. Helmke E & Weyland H (1984) Rhodococcus marinonascens sp.nov., an actinomycete from the sea. Int. J. Syst. Bacteriol. 34: 127-138.
17. Higgins DG, Bleasby AJ & Fuchs R (1991) CLUSTAL V: improved software for multiple sequence alignment. CABIOS 8: 189-191.
18. Kato C, Li L, Tamaoka J & Horikoshi K (1997) Molecular analyses of the sediment of the 11 000-m deep Mariana Trench. Extremophiles 1: 117-123.
19. Küster E & Williams ST (1964) Selection of media for isolation of streptomycetes. Nature 202: 928-929.
20. Litchfield CD (1976) Marine Microbiology. Dowden, Hutchison & Ross, Stroudburg, USA.
21. Magee JT (1994) Analytical fingerprinting methods. In: Goodfellow M, O'Donnell AG (Eds) Chemical Methods in Prokaryotic Systematics (pp 523-553). John Wiley & Sons, Chichester, UK.
22. Minnikin DE (1988) Isolation and purification of mycobacterial cell wall lipids. In: Hancock IC, Poxton IR (Eds) Bacterial Cell Surface Techniques, (pp 125-135). John Wiley & Sons, Winchester, UK.
23. Nesterenko OA, Kasumova SA & Kvasnikov EI (1978) Microorganisms of the Nocardia genus and the 'rhodochrous' group in soils of the Ukranian SSR. Mikrobiol. 47: 866-870.
24. Pitcher DG, Saunders NA & Owen RJ (1989) Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett. Appl. Microbiol. 8: 151-156.
25. Rainey FA, Burghardt J, Kroppenstedt RM, Klatte S & Stackebrandt E (1995) Phylogenetic analysis of the genera Rhodococcus and Nocardia and evidence for the evolutionary origin of the genus Nocardia from within the radiation of Rhodococcus species. Microbiology 141: 523-528.
26. Rowbotham TJ & Cross T (1977) Ecology of Rhodococcus coprophilus and associated actinomycetes in freshwater and agricultural habitats. J. Gen.Microbiol. 100: 231-240.
27. Saitou N & Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
28. Sanger F, Coulson AR, Hong GF, Hill DF & Peterson GB (1982) Nucleotide sequence of bacteriophage lambda DNA. J.Mol. Biol. 162: 729-773.
29. Sanglier JJ, Whitehead D, Saddler GS, Ferguson EV & Goodfellow M (1992) Pyrolysis mass spectrometry as a method for the classification and selection of actinomycetes. Gene 115: 235-242.
30. Sneath PHA & Sokal RR (1973) Numerical Taxonomy: the Principles and Practice of Numerical Classification. W. H. Freeman, San Francisco.
31. Takami H, Inoue A, Fuji F, & Horikoshi K (1997) Microbial flora in the deepest sea mud of the Mariana Trench. FEMS Microbiol. Lett. 152: 279-285.
32. Takizawa M, Colwell RR & Hill RT (1993) Isolation and diversity of actinomycetes in the Chesapeake Bay. Appl. Env. Microbiol. 59: 997-1002.
33. Tamaoka J & Komagata K (1984) Determination of DNA base composition by reverse phase high performance liquid chromatography. FEMS Microbiol. Lett. 25: 125-128.
34. Wellington EMH & Williams ST (1978) Preservation of actinomycete inoculum in frozen glycerol. Microbios Lett. 6: 151-157.
35. Weyland H (1969) Actinomycetes in North Sea and Atlantic Ocean sediments. Nature (London) 223: 858