The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation.
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.
Qin
Qi-Long
QL
State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China.
Zhang
Xi-Ying
XY
Wang
Xu-Min
XM
Liu
Gui-Ming
GM
Chen
Xiu-Lan
XL
Xie
Bin-Bin
BB
Dang
Hong-Yue
HY
Zhou
Bai-Cheng
BC
Yu
Jun
J
Zhang
Yu-Zhong
YZ
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
D011134:Polysaccharides; D013455:Sulfur; D009584:Nitrogen
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