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Li C.,Third Institute of Oceanography | Li C.,Key Laboratory of Marine Genetic Resources of Fujian Province | Lai Q.,Third Institute of Oceanography | Lai Q.,Key Laboratory of Marine Genetic Resources of Fujian Province | And 6 more authors.
Systematic and Applied Microbiology | Year: 2014

A taxonomic study was carried out on strains 22II1-22F38T and 22II-S13e, which were isolated from sea water and sediment from the Atlantic Ocean, respectively. The two strains were Gram-negative, oxidase and catalase positive, oval to pear shaped, and motile by a single polar flagellum. Phylogenetic analysis based on 16S rRNA gene sequences indicated that both strains belonged to the genus Hyphomonas, with highest sequence similarity (98.2%) to the type strains H. jannaschiana DSM 5153T and H. johnsonii ATCC 43964T. The genomic ANIm values and DNA-DNA hybridization estimate values between strain 22II1-22F38T and seven type strains ranged from 82.84% to 84.10% and from 18.0% to 19.1%, respectively. Isolate 22II1-22F38T had a G+C content of 58.3% and used Q-11 as the predominant respiratory quinone. The combined phenotypic and genotypic data showed that both strains represented a novel species of the genus Hyphomonas, for which the name Hyphomonas atlanticus sp. nov. is proposed, with the type strain being 22II1-22F38T (=LMG 27916T =MCCC 1A09418T). In addition, we conclude that Hyphomonas hirschiana is a later synonym of Hyphomonas neptunium. © 2014 Elsevier GmbH.


Wang W.,Third Institute of Oceanography | Wang W.,State Key Laboratory Breeding Base of Marine Genetic Resources | Wang W.,Key Laboratory of Marine Genetic Resources of Fujian Province | Zhong R.,Third Institute of Oceanography | And 9 more authors.
Applied Microbiology and Biotechnology | Year: 2014

Indigenous oil-degrading bacteria play an important role in efficient remediation of polluted marine environments. In this study, we investigated the diversity and abundance of indigenous oil-degrading bacteria and functional genes in crude oil-contaminated seawater of the Dalian coast. The gene copy number bacterial 16S rRNA in total were determined to be about 1010 copies L-1 in contaminated seawater and 109 copies L -1 in uncontaminated seawater. Bacteria of Alcanivorax, Marinobacter, Novosphingobium, Rhodococcus, and Pseudoalteromonas were found to be predominant oil-degrading bacteria in the polluted seawater in situ. In addition, bacteria belonging to Algoriphagus, Aestuariibacter, Celeribacter, Fabibacter, Zobellia, Tenacibaculum, Citreicella, Roseivirga, Winogradskyella, Thioclava, Polaribacter, and Pelagibaca were confirmed to be the first time as an oil-degrading bacterium. The indigenous functional enzymes, including AlkB or polycyclic aromatic hydrocarbons ring-hydroxylating dioxygenases α (PAH-RHDα) coding genes from Gram-positive (GP) and Gram-negative bacteria (GN), were revealed and quite diverse. About 1010 to 1011 copies L-1 for the expression of alkB genes were recovered and showed that the two-thirds of all the AlkB sequences were closely related to widely distributed Alcanivorax and Marinobacter isolates. About 109 copies L-1 seawater for the expression of RHDαGN genes in contaminated seawater and showed that almost all RHDαGN sequences were closely related to an uncultured bacterium; however, RHDαGP genes represented only about 105 copies L-1 seawater for the expression of genes in contaminated seawater, and the naphthalene dioxygenase sequences from Rhodococcus and Mycobacterium species were most abundant. Together, their data provide evidence that there exists an active aerobic microbial community indigenous to the coastal area of the Yellow sea that is capable of degrading petroleum hydrocarbons. © 2014 Springer-Verlag.


Zeng X.,The Third Institute of Oceanography SOA | Zeng X.,Key Laboratory of Marine Genetic Resources of Fujian Province | Zeng X.,Xiamen State Key Laboratory Breeding Base of Marine Genetic Resources | Zhang Z.,The Third Institute of Oceanography SOA | And 17 more authors.
International Journal of Systematic and Evolutionary Microbiology | Year: 2015

A novel piezophilic, thermophilic, anaerobic, fermentative bacterial strain, designated strain DY22613T, was isolated from a deep-sea hydrothermal sulfide deposit at the East Pacific Rise (GPS position: 102.66 W 3.16 S). Cells of strain DY22613T were long, motile rods (10 to 20 mm in length and 0.5 mm in width) with peritrichous flagella and were Gram-stain-negative. Growth was recorded at 44–72 6C (optimum 60–62 6C) and at hydrostatic pressures of 0.1–55 MPa (optimum 20 MPa). The pHrange for growth was frompH 5.0 to 9.0 with an optimum at pH 7.0. Growth was observed in the presence of 1 to 8% (w/v) sea salts and 0.65 to 5.2% (w/v) NaCl, with optimum salt concentrations at 3.5% for sea salts and at 2.3% for NaCl. Under optimal growth conditions, the shortest generation time observed was 27 min (60 6C, 20 MPa). Strain DY22613T was heterotrophic, able to utilize complex organic compounds, amino acids, sugars and organic acids including peptone, tryptone, beef extract, yeast extract, alanine, glutamine, methionine, phenylalanine, serine, threonine, fructose, fucose, galactose, gentiobiose, glucose, mannose, melibiose, palatinose, rhamnose, turanose, pyruvate, lactic acid, methyl ester, erythritol, galacturonic acid and glucosaminic acid. Strain DY22613T was able to reduce Fe(III) compounds, including Fe(III) oxyhydroxide (pH 7.0), amorphous iron(III) oxide (pH 9.0), goethite (a-FeOOH, pH 12.0), Fe(III) citrate and elementary sulfur. Products of fermentation were butyrate, acetate and hydrogen. Main cellular fatty acids were iso-C15:0, iso-C14:0 3-OH and C14:0. The genomic DNA G+C content of strain DY22613T was 36.7 mol%. Based on 16S rRNA gene sequence analysis, the strain forms a novel lineage within the class Clostridia and clusters with the order Haloanaerobiales (86.92% 16S rRNA gene sequence similarity). The phylogenetic data suggest that the lineage represents at least a novel genus and species, for which the name Anoxybacter fermentans gen. nov., sp. nov. is proposed. The type strain is DY22613T (5JCM 19466T5DSM 28033T5MCCC 1A06456T). ©2015 IUMS.


Jiang L.,Third Institute of Oceanography | Jiang L.,Key Laboratory of Marine Genetic Resources of Fujian Province | Jiang L.,Xiamen University | Long C.,Xiamen University | And 6 more authors.
International Journal of Hydrogen Energy | Year: 2014

A unique thermophilic fermentative hydrogen-producing strain H53214 was isolated from a deep-sea hydrothermal vent environment, and identified as Caloranaerobacter azorensis based on bacterial 16S rRNA gene analysis. The optimum culture condition for hydrogen production by the bacterium, designated C. azorensis H53214, was investigated by the response surface methodology (RSM). Eight variables including the concentration of NaCl, glucose, yeast, tryptone, FeSO4 and MgSO4, initial pH and incubation temperature were screened based on the Plackett-Burman design. The results showed that initial pH, tryptone and yeast were significant variables, which were further optimized using the steepest ascent method and Box-Behnken design. The optimal culture conditions for hydrogen production were an initial pH of 7.7, 8.3 g L-1 tryptone and 7.9 g L-1 yeast. Under these conditions, the maximum cumulative hydrogen volume, hydrogen yield and maximum H2 production rate were 1.58 L H2 L-1 medium, 1.46 mol H2 mol-1 glucose and 25.7 mmol H2 g -1 cell dry weight (CDW) h-1, respectively. By comparison analysis, strain H53214 was superior to the most thermophilic hydrogen producers because of the high hydrogen production rate. In addition, the isolation of C. azorensis H53214 indicated the deep-sea hydrothermal environment might be a potential source for fermentative hydrogen-producing thermophiles. © 2014, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.


Wang W.,State Oceanic Administration | Wang W.,Key Laboratory of Marine Genetic Resources of Fujian Province | Wang W.,Fujian Collaborative Innovation Center | Cai B.,State Oceanic Administration | And 6 more authors.
Frontiers in Microbiology | Year: 2014

Recent investigations of extreme environments have revealed numerous bioactive natural products. However, biosurfactant-producing strains from deep sea extreme environment are largely unknown. Here, we show that Dietzia maris As-13-3 isolated from deep sea hydrothermal field could produce di-rhamnolipid as biosurfactant. The critical micelle concentration (CMC) of the purified di-rhamnolipid was determined to be 120 mgL-1, and it lowered the surface tension of water from 74 ± 0.2 to 38 ± 0.2 mN m-1. Further, the alkane metabolic pathway-related genes and di-rhamnolipid biosynthesis-related genes were also analyzed by the sequencing genome of D. maris As-13-3 and quantitative real-time PCR (Q-PCR), respectively. Q-PCR analysis showed that all these genes were induced by n-Tetradecane, n-Hexadecane, and pristane. To the best of our knowledge, this is first report about the complete pathway of the di-rhamnolipid synthesis process in the genus Dietzia. Thus, our study provided the insights into Dietzia in respects of oil degradation and biosurfactant production, and will help to evaluate the potential of Dietzia in marine oil removal. © 2014 Wang, Cai and Shao.


Cao J.,Harbin Institute of Technology | Cao J.,State Key Laboratory Breeding Base of Marine Genetic Resources | Cao J.,Third Institute of Oceanography | Cao J.,Key Laboratory of Marine Genetic Resources of Fujian Province | And 10 more authors.
International Journal of Systematic and Evolutionary Microbiology | Year: 2014

A taxonomic study was carried out on strain GCS-AE-31T, which was isolated from a phenol-degrading consortium, enriched from coking wastewater activated sludge of the Beijing Shougang Company Limited during the screening of phenol-degrading bacteria. Cells of strain GCS-AE-31T were Gram-stain-negative, short rods, motile by gliding, oxidase- and catalase-positive. Growth was observed at salinities of 0-3% and at temperatures of 10-37 °C. On the basis of 16S rRNA gene sequence similarity, strain GCS-AE-31Twas most closely related to Pedobacter saltans LMG 10337T (96.17%), but it showed low similarity to all other species of the genus Pedobacter (89.28-92.45%). It also showed low 16S rRNA gene similarity to all other species of the family Sphingobacteriaceae (87.25-92.45 %) examined. The dominant fatty acids were iso-C15: 0, summed feature 3 (C16:1ω7c/C16:1ω6c), anteiso-C15:0and iso-C17:0 3-OH. The menaquinones were MK-7 (95.5%) and MK-6 (4.5%). The polar lipids were phosphatidylethanolamine, three aminolipids and three unknown phospholipids. Sphingolipid was present. The G+C content of the chromosomal DNA was 36.2 mol%. According to its phylogenetic position and phenotypic traits, the novel strain could not be assigned to the genus Pedobacter; it should be classified as representing a novel species of a novel genus in the family Sphingobacteriaceae, for which the name Pseudopedobacter beijingensis gen. nov., sp. nov. is proposed (type strain GCS-AE-31T = MCCC 1A01299T = CGMCC 1.12329T = LMG 27180T). The misclassified species Pedobacter saltans is transferred to the novel genus as Pseudopedobacter saltans comb. nov. (type strain LMG 10337T = MCCC 1A06472T = DSM 12145T = CCUG 39354T = CIP 105500T = JCM 21818T = NBRC 100064T). © 2014 IUMS.


Liu X.,Third Institute of Oceanography | Liu X.,State Key Laboratory Breeding Base of Marine Genetic Resources | Liu X.,Key Laboratory of Marine Genetic Resources of Fujian Province | Li G.,Third Institute of Oceanography | And 14 more authors.
Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology | Year: 2015

A new aerobic, Gram stain-negative, oxidase- and catalase- positive, ovoid or rod-shaped bacterial strain, designated HTCJW17T, was isolated from a sediment collected from the South China Sea and subjected to a polyphasic taxonomic characterization. The isolate forms small, creamy-white, opaque and circular colonies on agar plates. Growth occurs between 15 and 45 °C, 1–7 % (w/v) NaCl and pH 6–9. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HTCJW17T belongs to the family Kordiimonadaceae of the order Kordiimonadales, with highest sequence similarity to Kordiimonas gwangyangensis GW14-5T (91.1 %). The major fatty acids were identified to be summed feature 8 (C18:1ω7c/ω6c; 56.6 %), C14:0 (8.5 %), C14:0 2-OH (8.4 %), summed feature 3 (C16:1ω7c/C16:1ω6c; 6.2 %), and C16:0 (5.2 %). The polar lipids were determined to be phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, six unidentified glycolipids and two unidentified phospholipids. The respiratory quinone was identified as ubiquinone Q-10. The genomic DNA G+C content was determined to be 56.3 mol%. On the basis of genotypic, chemotaxonomic and phenotypic distinctness, we propose a novel genus, Emcibacter gen. nov., with Emcibacter nanhaiensis sp. nov. as the type species. The type strain is HTCJW17T (=CGMCC 1.12471T = LMG 27419T = MCCC 1A06723T). © 2015, Springer International Publishing Switzerland.


Wang W.,State Key Laboratory Breeding Base of Marine Genetic Resources | Wang W.,State Oceanic Administration | Wang W.,Key Laboratory of Marine Genetic Resources of Fujian Province | Shao Z.,State Key Laboratory Breeding Base of Marine Genetic Resources | And 2 more authors.
Frontiers in Microbiology | Year: 2013

Alkanes are major constituents of crude oil. They are also present at low concentrations in diverse non-contaminated because many living organisms produce them as chemo-attractants or as protecting agents against water loss. Alkane degradation is a widespread phenomenon in nature. The numerous microorganisms, both prokaryotic and eukaryotic, capable of utilizing alkanes as a carbon and energy source, have been isolated and characterized. This review summarizes the current knowledge of how bacteria metabolize alkanes aerobically, with a particular emphasis on the oxidation of long-chain alkanes, including factors that are responsible for chemotaxis to alkanes, transport across cell membrane of alkanes, the regulation of alkane degradation gene and initial oxidation. © 2013 Wang and Shao.


Huang Z.,State Key Laboratory Breeding Base of Marine Genetic Resources | Huang Z.,Third Institute of Oceanography | Huang Z.,Key Laboratory of Marine Genetic Resources of Fujian Province | Dong C.,State Key Laboratory Breeding Base of Marine Genetic Resources | And 5 more authors.
International Journal of Systematic and Evolutionary Microbiology | Year: 2016

A novel Gram-stain-negative bacterium, named strain NSCS20N07DT, was isolated from surface seawater of the South China Sea. Cells of this strain contained poly-b-hydroxybutyrate granules. Growth was observed at 15-35 °C with optimum of 30 °C, at a salinity range of 1-6% (w/v) NaCl with optimum of 3% and at pH 5-8 with optimum of pH 5. The full-length 16S rRNA gene sequence of strain NSCS20N07DT showed highest similarity to Photobacterium iliopiscarium ATCC 51760T of 96.0 %, followed by Photobacterium kishitanii pjapo.1.1T, Photobacterium phosphoreum ATCC 11040T and Photobacterium aquimaris LC2-065T of 96.0, 95.8 and 95.7 %, respectively. Phylogenetic analysis showed that strain NSCS20N07DT formed a separate clade distinct from species of the genus Photobacterium and other genera within the family Vibrionaceae, indicating that strain NSCS20N07DT represented a novel genus affiliated with this family. The genome size of strain NSCS20N07DT was 2.5 Mb, which was much smaller than those of related species in the family Vibrionaceae. The predominant fatty acids were C16:0, C17:0 cyclo, C19:0 cyclo ω8c, C18:0 and summed feature 2 (C14:0 3-OH/iso-C16:1 I). The respiratory quinone was Q-8. The polar lipids were identified as phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and four unidentified lipids. The DNA G+C content was 30.7 mol%. Combined, these results suggest that strain NSCS20N07DT represents a novel species of a new genus, for which the name Paraphotobacterium marinum gen. nov., sp. nov. is proposed. The type strain of Paraphotobacterium marinum is NSCS20N07DT (=KCTC 52126T=MCCC 1A01886T=CIP 111031T). © 2016 IUMS.


Zhou M.,State Oceanic Administration | Zhou M.,Key Laboratory of Marine Genetic Resources of Fujian Province | Liu Q.,State Oceanic Administration | Liu Q.,Key Laboratory of Marine Genetic Resources of Fujian Province | And 6 more authors.
Marine Genomics | Year: 2016

Thermococcus sp. strain EP1 is a novel anaerobic hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent on the East Pacific Rise. It grows optimally at 80 °C and can produce industrial enzymes at high temperature. We report here the draft genome of EP1, which contains 1,819,157 bp with a G + C content of 39.3%. The sequence will provide the genetic basis for better understanding of adaptation to hydrothermal environment and the development of novel thermostable enzymes for industrial application. © 2015 Elsevier B.V.

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