title: The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation.
abstract: BACKGROUND
  Zunongwangia profunda SM-A87, which was isolated from deep-sea sediment, is an aerobic, gram-negative bacterium that represents a new genus of Flavobacteriaceae. This is the first sequenced genome of a deep-sea bacterium from the phylum Bacteroidetes.
  
  
  RESULTS
  The Z. profunda SM-A87 genome has a single 5 128 187-bp circular chromosome with no extrachromosomal elements and harbors 4 653 predicted protein-coding genes. SM-A87 produces a large amount of capsular polysaccharides and possesses two polysaccharide biosynthesis gene clusters. It has a total of 130 peptidases, 61 of which have signal peptides. In addition to extracellular peptidases, SM-A87 also has various extracellular enzymes for carbohydrate, lipid and DNA degradation. These extracellular enzymes suggest that the bacterium is able to hydrolyze organic materials in the sediment, especially carbohydrates and proteinaceous organic nitrogen. There are two clustered regularly interspaced short palindromic repeats in the genome, but their spacers do not match any sequences in the public sequence databases. SM-A87 is a moderate halophile. Our protein isoelectric point analysis indicates that extracellular proteins have lower predicted isoelectric points than intracellular proteins. SM-A87 accumulates organic osmolytes in the cell, so its extracelluar proteins are more halophilic than its intracellular proteins.
  
  
  CONCLUSIONS
  Here, we present the first complete genome of a deep-sea sedimentary bacterium from the phylum Bacteroidetes. The genome analysis shows that SM-A87 has some common features of deep-sea bacteria, as well as an important capacity to hydrolyze sedimentary organic nitrogen.
authors.affiliation: State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China.
authors.forename: Qi-Long
authors.initials: QL
authors.lastname: Qin
authors.forename: Xi-Ying
authors.initials: XY
authors.lastname: Zhang
authors.forename: Xu-Min
authors.initials: XM
authors.lastname: Wang
authors.forename: Gui-Ming
authors.initials: GM
authors.lastname: Liu
authors.forename: Xiu-Lan
authors.initials: XL
authors.lastname: Chen
authors.forename: Bin-Bin
authors.initials: BB
authors.lastname: Xie
authors.forename: Hong-Yue
authors.initials: HY
authors.lastname: Dang
authors.forename: Bai-Cheng
authors.initials: BC
authors.lastname: Zhou
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
authors.forename: Yu-Zhong
authors.initials: YZ
authors.lastname: Zhang
mesh_terms: D003080:Cold Temperature; D041965:Flavobacteriaceae / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D016680:Genome, Bacterial; D019015:Geologic Sediments / Q000382:microbiology*; D006868:Hydrolysis; D009584:Nitrogen / Q000378:metabolism*; D011134:Polysaccharides / Q000378:metabolism; D054712:Salinity; D012623:Seawater / Q000382:microbiology*; D013455:Sulfur / Q000378:metabolism
chemical_list: D011134:Polysaccharides; D013455:Sulfur; D009584:Nitrogen
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