Abstract
BackgroundZunongwangia 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.ResultsThe 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.ConclusionHere, 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.
Highlights
Zunongwangia profunda SM-A87, which was isolated from deep-sea sediment, is an aerobic, gramnegative bacterium that represents a new genus of Flavobacteriaceae
Most of the deep-sea floor environment is characterized by darkness, high hydrostatic pressure and low temperatures, more than half of the world's prokaryotes live in sub-seafloor sediments [2,3,4], which play a major role in marine biogeochemical cycling [5]
Studies of both cultivated and uncultivated marine Bacteroidetes have shown that Bacteroidetes are able to efficiently consume biopolymers such as protein and chitin [15,16], which make up a significant fraction of the high-molecular-weight dissolved organic matter (HMW DOM) pool in the ocean [17]
Summary
Zunongwangia profunda SM-A87, which was isolated from deep-sea sediment, is an aerobic, gramnegative bacterium that represents a new genus of Flavobacteriaceae This is the first sequenced genome of a deep-sea bacterium from the phylum Bacteroidetes. Bacteroidetes (formerly Cytophaga-FlavobacteriumBacteroides (CFB)) are a widespread and diverse group of bacteria that can be found throughout the sea, from surface water to deep-sea sediment. Studies of both cultivated and uncultivated marine Bacteroidetes have shown that Bacteroidetes are able to efficiently consume biopolymers such as protein and chitin [15,16], which make up a significant fraction of the high-molecular-weight dissolved organic matter (HMW DOM) pool in the ocean [17].
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