title: Genomics of sponge-associated Streptomyces spp. closely related to Streptomyces albus J1074: insights into marine adaptation and secondary metabolite biosynthesis potential.
abstract: A total of 74 actinomycete isolates were cultivated from two marine sponges, Geodia barretti and Phakellia ventilabrum collected at the same spot at the bottom of the Trondheim fjord (Norway). Phylogenetic analyses of sponge-associated actinomycetes based on the 16S rRNA gene sequences demonstrated the presence of species belonging to the genera Streptomyces, Nocardiopsis, Rhodococcus, Pseudonocardia and Micromonospora. Most isolates required sea water for growth, suggesting them being adapted to the marine environment. Phylogenetic analysis of Streptomyces spp. revealed two isolates that originated from different sponges and had 99.7% identity in their 16S rRNA gene sequences, indicating that they represent very closely related strains. Sequencing, annotation, and analyses of the genomes of these Streptomyces isolates demonstrated that they are sister organisms closely related to terrestrial Streptomyces albus J1074. Unlike S. albus J1074, the two sponge streptomycetes grew and differentiated faster on the medium containing sea water. Comparative genomics revealed several genes presumably responsible for partial marine adaptation of these isolates. Genome mining targeted to secondary metabolite biosynthesis gene clusters identified several of those, which were not present in S. albus J1074, and likely to have been retained from a common ancestor, or acquired from other actinomycetes. Certain genes and gene clusters were shown to be differentially acquired or lost, supporting the hypothesis of divergent evolution of the two Streptomyces species in different sponge hosts.
authors.affiliation: Department of Biotechnology, Norwegian University of Science and Technology, Trondheim, Norway.
authors.forename: Elena
authors.initials: E
authors.lastname: Ian
authors.affiliation: N.I. Vavilov Institute of General Genetics, Department of Computational Biology, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Dmitry B
authors.initials: DB
authors.lastname: Malko
authors.affiliation: Department of Biotechnology, Norwegian University of Science and Technology, Trondheim, Norway.
authors.forename: Olga N
authors.initials: ON
authors.lastname: Sekurova
authors.affiliation: Department of Biotechnology, Norwegian University of Science and Technology, Trondheim, Norway.
authors.forename: Harald
authors.initials: H
authors.lastname: Bredholt
authors.affiliation: Institut fuer Genomforschung und Systembiologie, Centrum für Biotechnologie (CeBiTec), Universitaet Bielefeld, Bielefeld, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Rückert
authors.affiliation: A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Marina E
authors.initials: ME
authors.lastname: Borisova
authors.affiliation: Institut fuer Genomforschung und Systembiologie, Centrum für Biotechnologie (CeBiTec), Universitaet Bielefeld, Bielefeld, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Albersmeier
authors.affiliation: Institut fuer Genomforschung und Systembiologie, Centrum für Biotechnologie (CeBiTec), Universitaet Bielefeld, Bielefeld, Germany.
authors.forename: Jörn
authors.initials: J
authors.lastname: Kalinowski
authors.affiliation: A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, M.V.Lomonosov Moscow State University, Moscow, Russia.
authors.forename: Mikhail S
authors.initials: MS
authors.lastname: Gelfand
authors.affiliation: Department of Biotechnology, Norwegian University of Science and Technology, Trondheim, Norway.
authors.forename: Sergey B
authors.initials: SB
authors.lastname: Zotchev
mesh_terms: D000818:Animals; D008847:Micromonospora / Q000145:classification / Q000235:genetics; D010802:Phylogeny; D011161:Porifera / Q000382:microbiology*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D013302:Streptomyces / Q000145:classification / Q000235:genetics*
chemical_list: D012336:RNA, Ribosomal, 16S