Abstract
Genomic islands have been shown to harbor functional traits that differentiate ecologically distinct populations of environmental bacteria. A comparative analysis of the complete genome sequences of the marine Actinobacteria Salinispora tropica and Salinispora arenicola reveals that 75% of the species-specific genes are located in 21 genomic islands. These islands are enriched in genes associated with secondary metabolite biosynthesis providing evidence that secondary metabolism is linked to functional adaptation. Secondary metabolism accounts for 8.8% and 10.9% of the genes in the S. tropica and S. arenicola genomes, respectively, and represents the major functional category of annotated genes that differentiates the two species. Genomic islands harbor all 25 of the species-specific biosynthetic pathways, the majority of which occur in S. arenicola and may contribute to the cosmopolitan distribution of this species. Genome evolution is dominated by gene duplication and acquisition, which in the case of secondary metabolism provide immediate opportunities for the production of new bioactive products. Evidence that secondary metabolic pathways are exchanged horizontally, coupled with earlier evidence for fixation among globally distributed populations, supports a functional role and suggests that the acquisition of natural product biosynthetic gene clusters represents a previously unrecognized force driving bacterial diversification. Species-specific differences observed in clustered regularly interspaced short palindromic repeat sequences suggest that S. arenicola may possess a higher level of phage immunity, whereas a highly duplicated family of polymorphic membrane proteins provides evidence for a new mechanism of marine adaptation in Gram-positive bacteria.
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Acknowledgements
This paper is dedicated to Professor William Fenical for his pioneering work on the secondary metabolites of marine actinomycetes. PRJ and BSM were funded by the California Sea Grant Program (R/NMP-98), NOAA Grant NAO80AR4170669 and the JGI Community Sequencing Program. Additional funding was from NIH Grant CA127622 to BSM and a post-doctoral fellowship from the DAAD to MN. EEA thanks the Gordon and Betty Moore Foundation for funding through CAMERA. We acknowledge Dr Jonathan Badger for assistance with APIS and Professor Terry Gaasterland for computational assistance. Genome sequences have been deposited in GenBank under accession numbers CP000667 (S. tropica) and CP000850 (S. arenicola).
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Penn, K., Jenkins, C., Nett, M. et al. Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria. ISME J 3, 1193–1203 (2009). https://doi.org/10.1038/ismej.2009.58
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DOI: https://doi.org/10.1038/ismej.2009.58
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