Species-specific secondary metabolite production in marine actinomycetes of the genus Salinispora

Abstract

Here we report associations between secondary metabolite production and phylogenetically distinct but closely related marine actinomycete species belonging to the genus Salinispora. The pattern emerged in a study that included global collection sites, and it indicates that secondary metabolite production can be a species-specific, phenotypic trait associated with broadly distributed bacterial populations. Associations between actinomycete phylotype and chemotype revealed an effective, diversity-based approach to natural product discovery that contradicts the conventional wisdom that secondary metabolite production is strain specific. The structural diversity of the metabolites observed, coupled with gene probing and phylogenetic analyses, implicates lateral gene transfer as a source of the biosynthetic genes responsible for compound production. These results conform to a model of selection-driven pathway fixation occurring subsequent to gene acquisition and provide a rare example in which demonstrable physiological traits have been correlated to the fine-scale phylogenetic architecture of an environmental bacterial community.

FIG. 1.

Neighbor-joining distance tree created from 46 nearly complete (1,449 nucleotides) Salinispora 16S rRNA gene sequences. The three major Salinispora phylotypes, consisting of the two formally described species S. tropica and S. arenicola and the proposed species “S. pacifica,” are clearly delineated. Species names are followed by strain number, source (BA, Bahamas; RS, Red Sea; GU, Guam; PA, Palau; USVI, U.S. Virgin Islands; SC, Sea of Cortez), year of collection (89 = 1989, etc.), and accession number (for representative sequences). *, produces compound 6; **, produces cyclomarin A (compound 7). P. propionicus and B. aggregatus were used as outgroups.

FIG. 2.

Secondary metabolites produced by Salinispora strains. Compound names and the producing species or phylotype are listed under the structures. Compounds 1, 2, 5, 6, 8, and 9 are new secondary metabolites recently discovered from Salinispora strains, while compounds 3, 4, and 7 were previously reported for other actinomycetes (see references , , and , respectively).

FIG. 3.

AHBA synthase gene (rifK) PCR amplification. Presence of the AHBA synthase (rifK) gene in the three major Salinispora phylotypes was assessed using PCR primers specific for a 440-bp region of the gene. M, 100-bp marker; lanes 1 to 6, S. arenicola (strains CNH-643, CNR-562, CNP-161, CNR-107, CNP-193, and CNS-051); lanes 7 and 8, S. tropica (strains CNB-440 and CNB-476); lanes 9 and 10, “S. pacifica” (strains CNH-732 and CNQ-768). Loading dye is seen as a dark band.

FIG. 4.

Neighbor-joining distance tree created from translated AHBA synthase gene sequences (88 amino acids) obtained from six S. arenicola strains and NCBI BLAST homologues. Bootstrap results based on 1,000 resamplings are presented for values greater than 60% at the respective nodes. The tree was rooted using a related aminotransferase gene from R. ferrireducens.