Study of the diversity of culturable actinomycetes in the North Pacific and Caribbean coasts of Costa Rica

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology

Volumn 96, Issue 1, 2009, Pages 71-78

  Solano, Godofredo ^a,b   Rojas Jiménez, Keilor ^b   Jaspars, Marcel ^a   Tamayo Castillo, Giselle ^b,c  

^a UNIVERSITY OF ABERDEEN   (United Kingdom)

^b INSTITUTO NACIONAL DE BIODIVERSIDAD   (Costa Rica)

^c UNIVERSIDAD DE COSTA RICA   (Costa Rica)

Author keywords

Actinomycetes; Cabo Blanco; Cahuita; Gandoca Manzanillo; Las Baulas; Microbial Ecology

Indexed keywords

RIBOSOME RNA;

ACTINOBACTERIA; ARTICLE; BACTERIUM CULTURE; BACTERIUM ISOLATE; CONTROLLED STUDY; COSTA RICA; GENE SEQUENCE; GENETIC VARIABILITY; MICROBIAL DIVERSITY; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; SEASHORE; SPECIES DISTRIBUTION; STREPTOMYCES;

ACTINOBACTERIA; ATLANTIC OCEAN; BIODIVERSITY; CLUSTER ANALYSIS; COSTA RICA; DNA, BACTERIAL; DNA, RIBOSOMAL; GEOLOGIC SEDIMENTS; PACIFIC OCEAN; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID;

ACTINOBACTERIA (CLASS); STREPTOMYCES;

EID: 67349177769     PISSN: 00036072     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10482-009-9337-4     Document Type: Article

References (40)

1. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389-3402. doi: 10.1093/ nar/25.17.3389
2. Atlas RM (1993) Handbook of microbial media L.C. Parks (ed) CRC Press, London
3. Bredholdt H, Galatenko O, Engelhardt K, Fjærvik E, Terekhova L, Zotchev S (2007) Rare actinomycete bacteria from the shallow water sediments of the Trondheim fjord, Norway: Isolation, diversity and biological activity. Environ Microbiol 11:2756-2764. doi: 10.1111/ j.1462-2920.2007.01387.x
4. Brenes CL, Coen JE, Chelton DB, Enfields BB, Leon S, Ballestero D (2002) Wind driven upwelling in the Gulf of Nicoya, Costa Rica. Int J Remote Sens 5:1127-1133
5. Bull AT, Stach JEM (2007) Marine actinobacteria: New opportunities for natural product search and discovery. Trends Microbiol 11:491-499. doi: 10.1016/j.tim.2007.10.004
6. Bull AT, Ward AC, Goodfellow M (2000) Search and discovery strategies for biotechnology: The paradigm shift. Microbiol Mol Biol Rev 64:573-606. doi: 10.1128/MMBR.64.3.573-606.2000
7. Bull AT, Stach JEM, Ward AC, Goodfellow M (2005) Marine actinobacteria: perspectives, challenges, future directions. Antonie Van Leeuwenhoek 87:65-79. doi: 10.1007/s10482-004-6562-8
8. Chao A (1984) Non-parametric estimation of the number of classes in a population. Scand J Stat 11:265-270
9. Chao A, Lee SM (1992) Estimating the number of classes via sample coverage. J Am Stat Assoc 87:210-217. doi: 10.2307/2290471
10. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM (2009) The ribosomal database project: Improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37:141-145. doi: 10.1093/nar/gkn879
11. Cortes J (2002) The coral reefs of Costa Rica's Caribbean Coast. Instituto Nacional de Biodiversidad, Heredia, Costa Rica, p 140
12. Donadio S, Monciardini P, Alduina R, Mazza P, Chiocchini C, Cavaletti L, Sosio M, Puglia AM (2002) Microbial technologies for the discovery of novel bioactive metabolites. J Biotechnol 99:187-198. doi: 10.1016/ S0168-1656(02)00209-2
13. Fenical W (1993) Chemical studies of marine bacteria: Developing a new resource. Chem Rev 93:1673-1683. doi: 10.1021/cr00021a001
14. Godon RE, Mihm JM (1962) Identification of Nocardia caviae (Erikson) nov. comb. Ann N Y Acad Sci 98:628-636. doi: 10.1111/ j.1749-6632.1962.tb30585.x
15. 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
16. Jensen PR, Dwight R, Fenical W (1991) Distribution of actinomycetes in near-shore tropical marine sediments. Appl Environ Microbiol 57:1102-1108
17. Jensen PR, Gontang E, Mafnas C, Mincer TJ, Fenical W (2005a) Culturable marine actinomycete diversity from tropical Pacific Ocean sediments. Environ Microbiol 7:1039-1048. doi: 10.1111/j.1462-2920.2005.00785.x
18. Jensen PR, Mincer TJ, Williams PG, Fenical W (2005b) Marine actinomycete diversity and natural product discovery. Antonie Van Leeuwenhoek 87:43-48. doi: 10.1007/s10482-004-6540-1
19. Kumar S, Dudley J, Nei M, Tamura K (2008) MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 9:299-306. doi: 10.1093/bib/bbn017
20. Lam KS (2006) Discovery of novel metabolites from marine actinomycetes. Curr Opin Microbiol 9:245-251. doi: 10.1016/j.mib.2006.03.004
21. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stachebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, NY
22. Lazzarini A, Cavaletti L, Toppo G, Marinelli F (2000) Rare genera of actinomycetes as potential producers of new antibiotics. Antonie Van Leeuwenhoek 78:399-405. doi: 10.1023/A:1010287600557
23. Lozupone C, Knight R (2005) UniFrac: A new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71:8228-8235. doi: 10.1128/AEM.71.12.8228-8235.2005
24. Lozupone C, Hamady M, Knight R (2006) UniFrac - an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 7:371. doi: 10.1186/1471-2105-7-371
25. Magarvey NA, Keller JM, Bernan V, Dworkin M, Sherman DH (2004) Isolation and characterization of novel marine-derived Actinomycete taxa rich in bioactive metabolites. Appl Environ Microbiol 70:7520-7529. doi: 10.1128/ AEM.70.12.7520-7529.2004
26. Maldonado LA, Fenical W, Jensen PR, Kauffman CA, Mincer TJ, Ward AC (2005a) Salinispora arenicola gen nov., and Salinispora tropica sp. nov., obligate marine actinomycetes belonging to the family Micromonosporaceae. Int J Syst Evol Microbiol 55:1759-1766. doi: 10.1099/ ijs.0.63625-0
27. Maldonado LA, Stach JE, Pathom-aree W, Ward AC, Bull AT, Goodfellow M (2005b) Diversity of cultivable Actinobacteria in geographically widespread marine sediments. Antonie Van Leeuwenhoek 87:11-18. doi: 10.1007/s10482-004-6525-0
28. Martin A (2002) Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl Environ Microbiol 68:3673-3682. doi: 10.1128/AEM.68.8.3673-3682.2002
29. Mincer TJ, Jensen PR, Kauffman CA, Fenical W (2002) Widespread and persistent populations of a major new marine actinomycete taxon in ocean sediments. Appl Environ Microbiol 68:5005-5011. doi: 10.1128/ AEM.68.10.5005-5011.2002
30. Rich DV, Rich TH (1983) The Central American dispersal route: Biotic history and peleogeography. Costa Rican Natural History. Ed. Daniel H. Janzen. The University of Chicago Press, In, pp 12-34
31. Saitou N, Nei M (1984) The neighbour-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
32. Salazar A, Lizano O, Alfaro E (2004) Composición de sedimentos en las zonas costeras de Costa Rica utilizando Florescencia de Rayos-X (FRX). Rev Biol Trop 52:61-75
33. Schloss PD, Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71:1501-1506. doi: 10.1128/ AEM.71.3.1501-1506.2005
34. Schloss PD, Handelsman J (2006) Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community membership and structures. Appl Environ Microbiol 72:6773-6779. doi: 10.1128/ AEM.00474-06
35. Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313-340
36. Stach JEM, Maldonado LA, Ward AC, Goodfellow M, Bull AT (2003) New primers specific for Actinobacteria: Application to marine and terrestrial environments. Environ Microbiol 5:828-841. doi: 10.1046/ j.1462-2920.2003.00483.x
37. Stackebrandt E, Goebel BM (1994) Taxonomic note: A place for DNA-DNA reassociation and 16S rDNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846-849
38. Stackenbrandt E, Rainey FA, Ward-Rainey NL (1997) Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 47:479-491
39. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261-5267. doi: 10.1128/AEM.00062-07
40. Williams ST, Lanning S, Wellington EMH (1983) Ecology of actinomycetes. In: Goodfellow M, Mordarski M, Williams ST (eds) The biology of actinomycetes. Academic Press, London, UK, pp 481-528