title: Genome Analysis of Planctomycetes Inhabiting Blades of the Red Alga Porphyra umbilicalis.
abstract: Porphyra is a macrophytic red alga of the Bangiales that is important ecologically and economically. We describe the genomes of three bacteria in the phylum Planctomycetes (designated P1, P2 and P3) that were isolated from blades of Porphyra umbilicalis (P.um.1). These three Operational Taxonomic Units (OTUs) belong to distinct genera; P2 belongs to the genus Rhodopirellula, while P1 and P3 represent undescribed genera within the Planctomycetes. Comparative analyses of the P1, P2 and P3 genomes show large expansions of distinct gene families, which can be widespread throughout the Planctomycetes (e.g., protein kinases, sensors/response regulators) and may relate to specific habitat (e.g., sulfatase gene expansions in marine Planctomycetes) or phylogenetic position. Notably, there are major differences among the Planctomycetes in the numbers and sub-functional diversity of enzymes (e.g., sulfatases, glycoside hydrolases, polysaccharide lyases) that allow these bacteria to access a range of sulfated polysaccharides in macroalgal cell walls. These differences suggest that the microbes have varied capacities for feeding on fixed carbon in the cell walls of P.um.1 and other macrophytic algae, although the activities among the various bacteria might be functionally complementary in situ. Additionally, phylogenetic analyses indicate augmentation of gene functions through expansions arising from gene duplications and horizontal gene transfers; examples include genes involved in cell wall degradation (e.g., κ-carrageenase, alginate lyase, fucosidase) and stress responses (e.g., efflux pump, amino acid transporter). Finally P1 and P2 contain various genes encoding selenoproteins, many of which are enzymes that ameliorate the impact of environmental stresses that occur in the intertidal habitat.
authors.affiliation: Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America.
authors.forename: Jay W
authors.initials: JW
authors.lastname: Kim
authors.affiliation: School of Marine Sciences, University of Maine, Orono, Maine, United States of America.
authors.forename: Susan H
authors.initials: SH
authors.lastname: Brawley
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America.
authors.forename: Simon
authors.initials: S
authors.lastname: Prochnik
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America.
authors.forename: Mansi
authors.initials: M
authors.lastname: Chovatia
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America.|HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America.
authors.forename: Jane
authors.initials: J
authors.lastname: Grimwood
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America.|HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America.
authors.forename: Jerry
authors.initials: J
authors.lastname: Jenkins
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America.
authors.forename: Kurt
authors.initials: K
authors.lastname: LaButti
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America.
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Mavromatis
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America.
authors.forename: Matt
authors.initials: M
authors.lastname: Nolan
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America.
authors.forename: Matthew
authors.initials: M
authors.lastname: Zane
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America.|HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Schmutz
authors.affiliation: Department of Biology, East Carolina University, Greenville, North Carolina, United States of America.
authors.forename: John W
authors.initials: JW
authors.lastname: Stiller
authors.affiliation: Department of Plant Biology, Carnegie Institution for Science, Stanford, California, United States of America.
authors.forename: Arthur R
authors.initials: AR
authors.lastname: Grossman
mesh_terms: D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D010802:Phylogeny; D061328:Planctomycetales / Q000235:genetics*; D044664:Porphyra / Q000235:genetics / Q000382:microbiology*; D013429:Sulfatases / Q000235:genetics
chemical_list: D013429:Sulfatases