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Applied and Environmental Microbiology, November 2005, p. 7019-7028, Vol. 71, No. 11
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.11.7019-7028.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Culture-Dependent and Culture-Independent Diversity within the Obligate Marine Actinomycete Genus Salinispora

Tracy J. Mincer, William Fenical, and Paul R. Jensen^*

Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0204

Received 16 April 2005/ Accepted 4 July 2005

Salinispora is the first obligate marine genus within the order Actinomycetales and a productive source of biologically active secondary metabolites. Despite a worldwide, tropical or subtropical distribution in marine sediments, only two Salinispora species have thus far been cultivated, suggesting limited species-level diversity. To further explore Salinispora diversity and distributions, the phylogenetic diversity of more than 350 strains isolated from sediments collected around the Bahamas was examined, including strains cultured using new enrichment methods. A culture-independent method, using a Salinispora-specific seminested PCR technique, was used to detect Salinispora from environmental DNA and estimate diversity. Overall, the 16S rRNA gene sequence diversity of cultured strains agreed well with that detected in the environmental clone libraries. Despite extensive effort, no new species level diversity was detected, and 97% of the 105 strains examined by restriction fragment length polymorphism belonged to one phylotype (S. arenicola). New intraspecific diversity was detected in the libraries, including an abundant new phylotype that has yet to be cultured, and a new depth record of 1,100 m was established for the genus. PCR-introduced error, primarily from Taq polymerase, significantly increased clone library sequence diversity and, if not masked from the analyses, would have led to an overestimation of total diversity. An environmental DNA extraction method specific for vegetative cells provided evidence for active actinomycete growth in marine sediments while indicating that a majority of sediment samples contained predominantly Salinispora spores at concentrations that could not be detected in environmental clone libraries. Challenges involved with the direct sequence-based detection of spore-forming microorganisms in environmental samples are discussed.

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* Corresponding author. Mailing address: Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093-0204. Phone: (858) 534-7322. Fax: (858) 558-3703. E-mail:pjensen{at}ucsd.edu.

Present address: Massachusetts Institute of Technology, 15 Vassar St., Cambridge, MA 02139.

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Applied and Environmental Microbiology, November 2005, p. 7019-7028, Vol. 71, No. 11
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.11.7019-7028.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

This article has been cited by other articles:

• Gontang, E. A., Fenical, W., Jensen, P. R. (2007). Phylogenetic Diversity of Gram-Positive Bacteria Cultured from Marine Sediments. Appl. Environ. Microbiol. 73: 3272-3282 [Abstract] [Full Text]  
• Jensen, P. R., Williams, P. G., Oh, D.-C., Zeigler, L., Fenical, W. (2007). Species-Specific Secondary Metabolite Production in Marine Actinomycetes of the Genus Salinispora. Appl. Environ. Microbiol. 73: 1146-1152 [Abstract] [Full Text]