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Applied and Environmental Microbiology, August 2005, p. 4840-4849, Vol. 71, No. 8
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.8.4840-4849.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Metagenomic Analysis Reveals Diverse Polyketide Synthase Gene Clusters in Microorganisms Associated with the Marine Sponge Discodermia dissoluta{dagger}

Andreas Schirmer,1* Rishali Gadkari,1 Christopher D. Reeves,1 Fadia Ibrahim,1,{ddagger} Edward F. DeLong,2,§ and C. Richard Hutchinson1

Kosan Biosciences, Inc., Hayward, California 94545,1 Monterey Bay Aquarium Research Institute, Moss Landing, California 950292

Received 28 August 2004/ Accepted 9 March 2005

Sponge-associated bacteria are thought to produce many novel bioactive compounds, including polyketides. PCR amplification of ketosynthase domains of type I modular polyketide synthases (PKS) from the microbial community of the marine sponge Discodermia dissoluta revealed great diversity and a novel group of sponge-specific PKS ketosynthase domains. Metagenomic libraries totaling more than four gigabases of bacterial genomes associated with this sponge were screened for type I modular PKS gene clusters. More than 90% of the clones in total sponge DNA libraries represented bacterial DNA inserts, and 0.7% harbored PKS genes. The majority of the PKS hybridizing clones carried small PKS clusters of one to three modules, although some clones encoded large multimodular PKSs (more than five modules). The most abundant large modular PKS appeared to be encoded by a bacterial symbiont that made up <1% of the sponge community. Sequencing of this PKS revealed 14 modules that, if expressed and active, is predicted to produce a multimethyl-branched fatty acid reminiscent of mycobacterial lipid components. Metagenomic libraries made from fractions enriched for unicellular or filamentous bacteria differed significantly, with the latter containing numerous nonribosomal peptide synthetase (NRPS) and mixed NRPS-PKS gene clusters. The filamentous bacterial community of D. dissoluta consists mainly of Entotheonella spp., an unculturable sponge-specific taxon previously implicated in the biosynthesis of bioactive peptides.

* Corresponding author. Mailing address: Kosan Biosciences, Inc., 3832 Bay Center Place, Hayward, CA 94545. Phone: (510) 731-5284. Fax: (510) 732-8401. E-mail: schirmer{at}kosan.com.

{dagger} Supplemental material for this article may be found at http://aem.asm.org/.

{ddagger} Present address: University of Nebraska, E249 Beadle Center, 19th & Vine St., Lincoln, NE 68588.

§ Present address: Massachusetts Institute of Technology, Department of Civil and Environmental Engineering & Division of Biological Engineering, 48-427 MIT, 15 Vassar St., Cambridge, MA 02139.

Applied and Environmental Microbiology, August 2005, p. 4840-4849, Vol. 71, No. 8
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.8.4840-4849.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



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