Ying-Yi Huo

Isolation and Complete Genome Sequence of Algibacter alginolytica sp. nov., a Novel Seaweed-Degrading Bacteroidetes Bacterium with Diverse Putative Polysaccharide Utilization Loci

ABSTRACT The members of the phylum Bacteroidetes are recognized as some of the most important specialists for the degradation of polysaccharides. However, in contrast to research on Bacteroidetes in the human gut, research on polysaccharide degradation by marine Bacteroidetes is still rare. The genus Algibacter belongs to the Flavobacteriaceae family of the Bacteroidetes, and most species in this genus are isolated from or near the habitat of algae, indicating a preference for the complex polysaccharides of algae. In this work, a novel brown-seaweed-degrading strain designated HZ22 was isolated from the surface of a brown seaweed (Laminaria japonica). On the basis of its physiological, chemotaxonomic, and genotypic characteristics, it is proposed that strain HZ22 represents a novel species in the genus Algibacter with the proposed name Algibacter alginolytica sp. nov. The genome of strain HZ22, the type strain of this species, harbors 3,371 coding sequences (CDSs) and 255 carbohydrate-active enzymes (CAZymes), including 104 glycoside hydrolases (GHs) and 18 polysaccharide lyases (PLs); this appears to be the highest proportion of CAZymes (∼7.5%) among the reported strains in the class Flavobacteria. Seventeen polysaccharide utilization loci (PUL) are predicted to be specific for marine polysaccharides, especially algal polysaccharides from red, green, and brown seaweeds. In particular, PUL N is predicted to be specific for alginate. Taking these findings together with the results of assays of crude alginate lyases, we prove that strain HZ22T can completely degrade alginate. This work reveals that strain HZ22T has good potential for the degradation of algal polysaccharides and that the structure and related mechanism of PUL in strain HZ22T are worth further research.

Paracoccus sediminis sp. nov., isolated from Pacific Ocean marine sediment.

Strain CMB17(T) was a short rod-shaped bacterium isolated from marine sediment of the Pacific Ocean. Cells were Gram-stain-negative and non-motile. Optimal growth occurred at 25-30 °C, pH 6.5-7 and 0.5-1% (w/v) NaCl. The major fatty acid was C(18 : 1)ω7c (87.59%), and ubiquinone-10 was detected as the only isoprenoid quinone. The DNA G+C content of the genomic DNA was 62.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CMB17(T) is most closely related to Paracoccus stylophorae KTW-16(T) (96.7%), P. solventivorans DSM 6637(T) (96.4%) and P. saliphilus YIM 90738(T) (96.4%). Based on phenotypic, genotypic and phylogenetic characteristics, strain CMB17(T) is proposed to represent a novel species, denominated Paracoccus sediminis sp. nov. (type strain CMB17(T) = JCM 18467(T) = DSM 26170(T) = CGMCC 1.12681(T)).

Halolamina salifodinae sp. nov. and Halolamina salina sp. nov., two extremely halophilic archaea isolated from a salt mine.

Two strictly aerobic, extremely halophilic archaea, strains WSY15-H1(T) and WSY15-H3(T), were isolated from a salt mine in Wensu county, Xinjiang province, China. Cells of the two strains were Gram-stain-negative, non-motile and pleomorphic. Colonies were pink- and red-pigmented, respectively. Strain WSY15-H1(T) grew at 20-45 °C (optimum 37-42 °C), 1.6-5.4 M NaCl (optimum 3.4-3.9 M), 0-2.0 M MgCl2 (optimum 0.1-0.5 M) and pH 6.0-9.0 (optimum 7.0), whereas strain WSY15-H3(T) grew at 20-50 °C (optimum 37 °C), 1.9-5.4 M NaCl (optimum 3.4 M), 0.02-2.5 M MgCl2 (optimum 0.5-1.0 M) and pH 6.0-7.5 (optimum 6.5). The minimal NaCl concentrations to prevent cell lysis were 9 % (w/v) for strain WSY15-H1(T) and 8 % (w/v) for strain WSY15-H3(T). The major polar lipids of the two isolates were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and phosphatidylglycerol sulfate, as well as nine glycolipids for strain WSY15-H1(T) and seven glycolipids for strain WSY15-H3(T); two of these glycolipids (GL1 and GL3) were chromatographically identical to bis-sulfated diglycosyl diether (S2-DGD-1) and sulfated diglycosyl diether (S-DGD-1), respectively. The genomic DNA G+C contents of strains WSY15-H1(T) and WSY15-H3(T) were 65.4 and 66.2 mol%. On the basis of 16S rRNA gene sequence analysis, strains WSY15-H1(T) and WSY15-H3(T) shared 97.0% similarity with each other and showed respectively 98.4 and 97.6% sequence similarity to Halolamina pelagica TBN21(T), which was the only type strain that had higher than 91% sequence similarity with the two isolates. Analysis of phylogenetic relationships and DNA-DNA relatedness indicated that strains WSY15-H1(T) and WSY15-H3(T) represent two novel lineages with closest affinity to H. pelagica TBN21(T). Based on phenotypic, chemotaxonomic and genotypic characteristics, two novel species of the genus Halolamina are proposed, Halolamina salifodinae sp. nov. (type strain WSY15-H1(T) = JCM 18548(T) = GCMCC 1.12371(T)) and Halolamina salina sp. nov. (type strain WSY15-H3(T) = JCM 18549(T) = GCMCC 1.12285(T)).

Thalassomonas eurytherma sp. nov., a marine proteobacterium.

Two Gram-staining-negative, aerobic, rod-shaped bacterial strains, designated Za6a-12(T) and Za6a-17, were isolated from seawater of the East China Sea. Cells of Za6a-12(T) and Za6a-17 were approximately 1.5-2.0 µm×0.5-0.7 µm and motile by a single polar flagellum. Strains grew optimally at pH 7.5-8.0, 28 °C, and in the presence of 2.5-3.0% (w/v) NaCl. Chemotaxonomic analysis showed that the predominant respiratory quinone of strains Za6a-12(T) and Za6a-17 was ubiquinone-8 (>97%), and the major fatty acids were C(14 : 0), C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH, C(16 : 0) and C(17 : 1)ω8c. Their DNA G+C contents were 42.7 mol% and 42.8 mol%, respectively. 16S rRNA gene sequence analysis revealed that the isolates belonged to the genus Thalassomonas and showed the highest sequence similarity to Thalassomonas loyana CBMAI 722(T) (95.9%). Strains Za6a-12(T) and Za6a-17 could be differentiated from T. loyana CBMAI 722(T) according to their phenotypic and chemotaxonomic features, DNA G+C contents and fatty acid composition. On the basis of these features, we propose strains Za6a-12(T) and Za6a-17 to be representatives of a novel species of the genus Thalassomonas with the name Thalassomonas eurytherma sp. nov. suggested. Strain Za6a-12(T) ( = CGMCC 1.12115(T) = JCM 18482(T)) is the type strain of this novel species.

Novosphingobium marinum sp. nov., isolated from seawater.

A Gram-stain-negative, aerobic, short rod-shaped bacterium, strain LA53(T), was isolated from a deep-sea water sample collected from the eastern Pacific Ocean. Strain LA53(T) grew in the presence of 0-7.0 % (w/v) NaCl and at 15-37 °C; optimum growth was observed with 1.0-2.0 % (w/v) NaCl and at 35 °C. Chemotaxonomic analysis showed ubiquinone-10 as the predominant respiratory quinone, C18 : 1ω7c and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c) as major fatty acids, and diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid as major polar lipids. The genomic DNA G+C content was 57.7 mol%. Phylogenetic analyses revealed that strain LA53(T) belongs to the genus Novosphingobium. 16S rRNA gene sequence similarities between strain LA53(T) and the type strains of species of the genus Novosphingobium with validly published names ranged from 93.1 to 96.3 %. In addition, strain LA53(T) could be differentiated from Novosphingobium pentaromativorans DSM 17173(T) and Novosphingobium indicum DSM 23608(T) as well as the type strain of the type species of the genus, Novosphingobium capsulatum DSM 30196(T), by some phenotypic characteristics, including hydrolysis of substrates, utilization of carbon sources and susceptibility to antibiotics. On the basis of phenotypic and genotypic data, strain LA53(T) represents a novel species within the genus Novosphingobium, for which the name Novosphingobium marinum sp. nov. is proposed. The type strain is LA53(T) ( = CGMCC 1.12918(T) = JCM 30307(T)).

Halomonas zincidurans sp. nov., a heavy-metal-tolerant bacterium isolated from the deep-sea environment

A Gram-stain-negative, aerobic, rod-like, motile by peritrichous flagella and moderately halophilic bacterium, designated strain B6(T), was isolated a deep-sea sediment collected from the South Atlantic Ocean. The isolate grew with 0.5-15 % (w/v) NaCl, at 4-37 °C and pH 5.0-8.5 and showed a high tolerance to zinc, manganese, cobalt and copper ions. The major fatty acids were C16 : 0, C19 : 0 cyclo ω8c, C12 : 0 3-OH and C12 : 0. The predominant ubiquinone was Q-9. The genomic DNA G+C content was 61.1 mol%. Phylogenetic analysis based on 16S rRNA gene comparisons indicated that strain B6(T) belonged to the genus Halomonas, and the closest relative was Halomonas xinjiangensis TRM 0175(T) (96.1 %). Based upon the phenotypic, chemotaxonomic and genetic data, strain B6(T) represents a novel species from the genus Halomonas, for which the name Halomonas zincidurans sp. nov. is proposed. The type strain is B6(T) ( = CGMCC 1.12450(T) = JCM 18472(T)).

Structural insights of a hormone sensitive lipase homologue Est22.

Hormone sensitive lipase (HSL) catalyzes the hydrolysis of triacylglycerols into fatty acids and glycerol, thus playing key roles in energy homeostasis. However, the application of HSL serving as a pharmaceutical target and an industrial biocatalyst is largely hampered due to the lack of high-resolution structural information. Here we report biochemical properties and crystal structures of a novel HSL homologue esterase Est22 from a deep-sea metagenomic library. Est22 prefers short acyl chain esters and has a very high activity with substrate p-nitrophenyl butyrate. The crystal structures of wild type and mutated Est22 with its product p-nitrophenol are solved with resolutions ranging from 1.4 Å to 2.43 Å. The Est22 exhibits a α/β-hydrolase fold consisting with a catalytic domain and a substrate-recognizing cap domain. Residues Ser188, Asp287, and His317 comprise the catalytic triad in the catalytic domain. The p-nitrophenol molecule occupies the substrate binding pocket and forms hydrogen bonds with adjacent residues Gly108, Gly109, and Gly189. Est22 exhibits a dimeric form in solution, whereas mutants D287A and H317A change to polymeric form, which totally abolished its enzymatic activities. Our study provides insights into the catalytic mechanism of HSL family esterase and facilitates the understanding for further industrial and biotechnological applications of esterases.

Ecological functions of uncultured microorganisms in the cobalt-rich ferromanganese crust of a seamount in the central Pacific are elucidated by fosmid sequencing

Cobalt-rich ferromanganese is an important seafloor mineral and is abundantly present in the seamount crusts. Such crusts form potential hotspots for biogeochemical activity and microbial diversity, yet our understanding of their microbial communities is lacking. In this study, a cultivation-independent approach was used to recover genomic information and derive ecological functions of the microbes in a sediment sample collected from the cobalt-rich ferromanganese crust of a seamount region in the central Pacific. A total of 78 distinct clones were obtained by fosmid library screening with a 16S rRNA based PCR method. Proteobacteria and MGI Thaumarchaeota dominated the bacterial and archaeal 16S rRNA gene sequence results in the microbial community. Nine fosmid clones were sequenced and annotated. Numerous genes encoding proteins involved in metabolic functions and heavy metal resistance were identified, suggesting alternative metabolic pathways and stress responses that are essential for microbial survival in the cobalt-rich ferromanganese crust. In addition, genes that participate in the synthesis of organic acids and exoploymers were discovered. Reconstruction of the metabolic pathways revealed that the nitrogen cycle is an important biogeochemical process in the cobalt-rich ferromanganese crust. In addition, horizontal gene transfer (HGT) events have been observed, and most of them came from bacteria, with some occurring in archaea and plants. Clone W4-93a, belonging to MGI Thaumarchaeota, contained a region of gene synteny. Comparative analyses suggested that a high frequency of HGT events as well as genomic divergence play important roles in the microbial adaption to the deep-sea environment.

Devosia pacifica sp. nov., isolated from deep-sea sediment.

A novel bacterial strain, NH131(T), was isolated from deep-sea sediment of South China Sea. Cells were strictly aerobic, Gram-stain negative, short rod-shaped and motile with a single lateral flagellum. Strain NH131(T) grew optimally at pH 6.5-7.0 and 25-30 °C. 16S rRNA gene sequence analysis revealed that strain NH131(T) belonged to the genus Devosia, sharing the highest sequence similarity with the type strain, Devosia geojensis BD-c194(T) (96.2%). The predominant fatty acids were C(18 : 1)ω7c, 11-methyl C(18 : 1)ω7c, C(18 : 0) and C(16 : 0). Ubiquinone 10 was the predominant ubiquinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phospholipid, three glycolipids and two unknown lipids. The DNA G+C content of strain NH131(T) was 63.0 mol%. On the basis of the results of polyphasic identification, it is suggested that strain NH131(T) represents a novel species of the genus Devosia for which the name Devosia pacifica sp. nov. is proposed. The type strain is NH131(T) ( = JCM 19305(T) = KCTC 32437(T)).

Complete genome sequence of a benzo[a]pyrene-degrading bacterium Altererythrobacter epoxidivorans CGMCC 1.7731T

Altererythrobacter epoxidivorans CGMCC 1.7731(T) is a Gram-negative bacterium isolated from marine sediments. It is able to utilize benzo[a]pyrene as sole carbon and energy source. Here, we describe the complete genome sequence and annotation of A. epoxidivorans CGMCC 1.7731(T). The genome has a size of 2,786,256 bp (61.50 mol% G+C content), which consists of 2773 coding genes, 43 tRNA genes and 3 rRNA genes. According to the genome information, strain A. epoxidivorans CGMCC 1.7731(T) encodes 22 genes related to degradation of benzo[a]pyrene. These genes may have potential in bioremediation of PAH-polluted environments.