A Novel Exopolysaccharide with Metal Adsorption Capacity Produced by a Marine Bacterium Alteromonas sp. JL2810.

Most marine bacteria can produce exopolysaccharides (EPS). However, very few structures of EPS produced by marine bacteria have been determined. The characterization of EPS structure is important for the elucidation of their biological functions and ecological roles. In this study, the structure of EPS produced by a marine bacterium, Alteromonas sp. JL2810, was characterized, and the biosorption of the EPS for heavy metals Cu2+, Ni2+, and Cr6+ was also investigated. Nuclear magnetic resonance (NMR) analysis indicated that the JL2810 EPS have a novel structure consisting of the repeating unit of [-3)-α-Rhap-(1→3)-α-Manp-(1→4)-α-3OAc-GalAp-(1→]. The biosorption of the EPS for heavy metals was affected by a medium pH; the maximum biosorption capacities for Cu2+ and Ni2+ were 140.8 ± 8.2 mg/g and 226.3 ± 3.3 mg/g at pH 5.0; however, for Cr6+ it was 215.2 ± 5.1 mg/g at pH 5.5. Infrared spectrometry analysis demonstrated that the groups of O-H, C=O, and C-O-C were the main function groups for the adsorption of JL2810 EPS with the heavy metals. The adsorption equilibrium of JL2810 EPS for Ni2+ was further analyzed, and the equilibrium data could be better represented by the Langmuir isotherm model. The novel EPS could be potentially used in industrial applications as a novel bio-resource for the removal of heavy metals.

Complete Genome Sequence of the d-Amino Acid Catabolism Bacterium Phaeobacter sp. Strain JL2886, Isolated from Deep Seawater of the South China Sea.

Phaeobacter sp. strain JL2886, isolated from deep seawater of the South China Sea, can catabolize d-amino acids. Here, we report the complete genome sequence of Phaeobacter sp. JL2886. It comprises ~4.06 Mbp, with a G+C content of 61.52%. A total of 3,913 protein-coding genes and 10 genes related to d-amino acid catabolism were obtained.

The Fate of Marine Bacterial Exopolysaccharide in Natural Marine Microbial Communities.

Most marine bacteria produce exopolysaccharides (EPS), and bacterial EPS represent an important source of dissolved organic carbon in marine ecosystems. It was proposed that bacterial EPS rich in uronic acid is resistant to mineralization by microbes and thus has a long residence time in global oceans. To confirm this hypothesis, bacterial EPS rich in galacturonic acid was isolated from Alteromonas sp. JL2810. The EPS was used to amend natural seawater to investigate the bioavailability of this EPS by native populations, in the presence and absence of ammonium and phosphate amendment. The data indicated that the bacterial EPS could not be completely consumed during the cultivation period and that the bioavailability of EPS was not only determined by its intrinsic properties, but was also determined by other factors such as the availability of inorganic nutrients. During the experiment, the humic-like component of fluorescent dissolved organic matter (FDOM) was freshly produced. Bacterial community structure analysis indicated that the class Flavobacteria of the phylum Bacteroidetes was the major contributor for the utilization of EPS. This report is the first to indicate that Flavobacteria are a major contributor to bacterial EPS degradation. The fraction of EPS that could not be completely utilized and the FDOM (e.g., humic acid-like substances) produced de novo may be refractory and may contribute to the carbon storage in the oceans.

Draft Genome Sequence of the Novel Exopolysaccharide-Producing Bacterium Altibacter lentus Strain JLT2010T, Isolated from Deep Seawater of the South China Sea.

Altibacter lentus strain JLT2010(T) is the type strain of the recently identified novel genus and species of the family Flavobacteriaceae and was first isolated from deep seawater of the South China Sea. It can produce exopolysaccharide. Here we report the first draft genome of JLT2010(T) (3,160,033 bp, with GC content of 42.12%) and major findings from its annotation. It is the first reported genome in the genus Altibacter.

Altuibacter lentus gen. nov., sp. nov., a novel member of family Flavobacteriaceae isolated from deep seawater of the South China Sea.

A novel chemoheterotrophic, aerobic, Gram-negative, rod-shaped, yellow-pigmented, bacterial strain JLT2010(T) was isolated from deep seawater of the South China Sea. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain JLT2010(T) belongs to the family Flavobacteriaceae and is most closely related to Ulvibacter antarcticus IMCC3101(T) with 95.7 % similarity. Some phenotypic characteristics such as the absence of flexirubin-type pigments, growth at 37 °C, hydrolysis of casein differentiated strain JLT2010(T) from the genus Ulvibacter as well as other genera in the family Flavobacteriaceae. The DNA G+C content of the strain JLT2010(T) was found to be 35.7 mol% and the major respiratory quinone was found to be MK-6. On the basis of phenotypic and phylogenetic features, JLT2010(T) is classified as a novel genus and species within the family Flavobacteriaceae, for which the name Altuibacter lentus gen. nov., sp. nov. is proposed. The type strain is JLT2010(T) (=JCM 18884(T) = CGMCC 1.12167(T)).

Coralslurrinella hongkonensis gen. nov., sp. nov., a novel bacterium in the family Psychromonadaceae, isolated from the coral Platygyra carnosus.

A novel bacterial strain, JLT2006T, was isolated from the scleractinian coral Platygyra carnosus, located in Hong Kong, China. Cells of this strain were Gram-negative, rod-shaped or oval-shaped and motile by the means of polar flagella. They formed faint-yellow, round colonies on marine agar medium. Phylogenetic analyses based on the 16S rRNA gene sequence indicated that the strain JLT2006T belonged to the class Gammaproteobacteria and was most closely related to Alteromonas-like bacteria of the genera Psychromonas, Pseudoalteromonas, Moritella, Shewanella and Ferrimonas, with less than 93 % sequence similarity. The predominant fatty acids were identified as C18:1x7c/C18:1x6c (23.0 %), C16:1x7c/C16:1x6c (18.2 %) and C16:0 (16.4 %). The quinone was menaquinone-7 (100 %). The polar lipids were determined to be phosphatidylglycerol, phosphatidylethanolamine, phospholipid, glycolipid and lipid. The genomic DNA G?C content was 40.3 mol%. Based on the 16S rRNA gene sequence as well as the physiological and biochemical features that separate the strain JLT2006T from other recognized bacteria, a novel species of a new genus with the name Coralslurrinella hongkonensis gen. nov., sp. nov. is proposed. The type strain is JLT2006T (=JCM 18796T = CGMCC 1.10992T).

Euryhalocaulis caribicus gen. nov., sp. nov., a new member [corrected] of the family Hyphomonadaceae isolated from the Caribbean Sea.

A new aerobic, Gram-negative, chemo-organotrophic, euryhaline bacterium, designated strain JL2009(T), was isolated from surface water of the Caribbean Sea. The strain formed flaxen colonies on marine ager 2216 (MA; Difco) medium. Cells were dimorphic, with stalks or a polar flagellum, and reproduction occurred by means of binary fission. Growth occurred at 15-45 °C (optimum at 35 °C), 0-15 % (w/v) NaCl (optimum at 1-10 %) and pH 5-9 (optimum at pH 7-8). Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain formed a distinct evolutionary lineage within the family Hyphomonadaceae. Strain JL2009(T) was most closely related to Maricaulis parjimensis MCS 25(T) (92.2 % DNA sequence similarity), Woodsholea maritime CM2243(T) (90.9 %), and Oceanicaulis alexandrii C116-18(T) (90.9 %). The major respiratory quinone was Q-10. The dominant cellular fatty acids were summed feature 8 (C(18:1) ω7c), C(18:0) and 11-methyl C(18:1) ω7c. The polar lipid pattern indicated the presence of phospholipid, phosphatidyl glycerol and glycolipids. The G + C content of the genomic DNA was 70.5 mol%. On the basis of the chemotaxonomic and phenotypic characteristics and the phylogenetic evidence, strain JL2009(T) represents a novel genus and species in the family Hyphomonadaceae, for which the name Euryhalocaulis caribicus gen. nov., sp. nov. is proposed. The type strain of Euryhalocaulis caribicus is JL2009(T) (=CGMCC 1.12036(T) = JCM 18163(T)).

Pelagibacterium nitratireducens sp.nov., a marine Alphaproteobacterium isolated from the East China Sea.

A Gram-negative, rod-shaped, non-spore-forming aerobic bacterium, motile with a single polar flagellum, strain JLT2005(T), was isolated from surface seawater collected from the East China Sea and formed ivory white colonies on a rich organic medium. The strain was positive for catalase, oxidase, and urease. It grew in the presence of 0-12 % (w/v) NaCl (optimum 5 %), at 20-35 °C (optimum 25 °C), or at pH 6-10 (optimum pH 9). The major fatty acids (>10 %) were C(18:1)ω7c, C(19:0)ω8c cyclo, C(16:0), and C(18:0). The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, and five unidentified glycolipids. Ubiquinone-10 and Ubiquinone-11 were present as the major quinones. The DNA G+C content was 74.3 mol%. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain JLT2005(T) belongs to the genus Pelagibacterium in the family Hyphomicrobiaceae, class Alphaproteobacteria. The closest neighbors were Pelagibacterium halotolerans B2(T) (98.7 % similarity) and Pelagibacterium luteolum 1_C16_27(T) (97.1 % similarity). DNA-DNA relatedness values of strain JLT2005(T) with P. halotolerans B2(T) and with P. luteolum 1_C16_27(T) were 31.6 and 25 %. Evidence from genotypic, chemotaxonomic, and phenotypic data shows that strain JLT2005(T) represents a novel species of the genus Pelagibacterium, for which the name Pelagibacterium nitratireducens sp. nov is proposed. The type strain is JLT2005(T) (=CGMCC 1.10829(T) =JCM 17767(T)).

Roseibacterium beibuensis sp. nov., a novel member of roseobacter clade isolated from Beibu Gulf in the South China Sea.

A novel aerobic, bacteriochlorophyll-containing bacteria strain JLT1202r(T) was isolated from Beibu Gulf in the South China Sea. Cells were gram-negative, non-motile, and short-ovoid to rod-shaped with two narrower poles. Strain JLT1202r(T) formed circular, opaque, wine-red colonies, and grew optimally at 3-4 % NaCl, pH 7.5-8.0 and 28-30 °C. The strain was catalase, oxidase, ONPG, gelatin, and Voges-Proskauer test positive. In vivo absorption spectrum of bacteriochlorophyll a presented two peaks at 800 and 877 nm. The predominant cellular fatty acid was C(18:1) ω7c and significant amounts of C(16:0), C(18:0), C(10:0) 3-OH, C(16:0) 2-OH, and 11-methyl C(18:1) ω7c were present. Strain JLT1202r(T) contained Q-10 as the major respiratory quinone and the genomic DNA G+C content was 76.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences of various species with validly published names showed that strain JLT1202r(T) fell within the genus Roseibacterium, family Rhodobacteraceae, sharing the highest similarity with Roseibacterium elongatum OCh 323(T) (97.9 % similarity), followed by Dinoroseobacter shibae DFL 12(T) (95.4 % similarity). The phylogenetic distance of pufM genes between strain JLT1202r(T) and R. elongatum OCh 323(T) was 9.4 %, suggesting that strain JLT1202r(T) was distinct from the only strain of the genus Roseibacterium. Based on the variabilities of phylogenetic and phenotypic characteristics, strain JLT1202r(T) stands for a novel species of the genus Roseibacterium and the name R. beibuensis sp. nov. is proposed with JLT1202r(T) as the type strain (=JCM 18015(T) = CGMCC 1.10994(T)).

Oceaniovalibus guishaninsula gen. nov., sp. nov., a marine bacterium of the family Rhodobacteraceae.

The alphaproteobacterial strain JLT2003(T) was isolated from surface seawater off the coast of Guishan island, Taiwan. The strain was Gram negative, ovoid or coccoid, non-motile and formed pink colonies on marine agar 2216 (MA; DIFCO) medium. The dominant fatty acids were C(18:1)ω7c, cyclo C(19:0)ω8c, and C(16:0). The polar lipid profile consisted of diphosphatidylglycerol and phosphatidylglycerol. The major respiratory ubiquinone was Q-10. The DNA G+C content was 62.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain was most closely related to Pontibaca methylaminivorans GRP21(T) with 94.8% similarity. The isolate was distinguishable from members of the family Rhodobacteraceae based on phenotypic and biochemical characteristics. On the basis of the taxonomic data presented, strain JLT2003(T) is considered to represent a novel species of a new genus, for which the name Oceaniovalibus guishaninsula gen. nov., sp. nov. is proposed. The type strain of Oceaniovalibus guishaninsula is JLT2003(T) (=JCM 17765(T) = CGMCC 1.10827(T)).

Oceanitalea nanhaiensis gen. nov., sp. nov., an actinobacterium isolated from seawater.

A Gram-positive, motile, short-rod-shaped bacterium, designated strain JLT1488(T), was isolated from the South China Sea and investigated in a taxonomic study using a polyphasic approach. The peptidoglycan type determined for strain JLT1488(T) was A4α with lysine as the diagnostic cell-wall diamino acid and an interpeptide bridge of L-Lys-L-Glu. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, an unknown glycolipid and an unknown phospholipid. The only detected menaquinone was MK-8(H(4)), and the major fatty acids were summed feature 8 (C(18 : 1)ω7c/C(18 : 1)ω6c) , C(16 : 0) and summed feature 3 (C(16 : 1)ω7c/C(16 : 1)ω6c); significant amounts of C(12 : 0) 3-OH, C(10 : 0) and C(19 : 0) cyclo ω8c were also present. The G+C content of the genomic DNA was 62.3 mol%. Comparison of the 16S rRNA gene sequence of strain JLT1488(T) with those of related type strains demonstrated that it represented a novel lineage within the family Bogoriellaceae, suborder Micrococcineae, being closely related to species of the genera Georgenia, Bogoriella and Cellulomonas (94.6-96.8 % sequence similarity). These results demonstrate that strain JLT1488(T) is a member of a new genus, for which the name Oceanitalea nanhaiensis gen. nov., sp. nov. is proposed. The type strain of the type species is JLT1488(T) ( = JCM 17755(T) = CGMCC 1.10826(T)).

Paracoccus oceanense sp. nov., isolated from the West Pacific.

A Gram-negative, short ovoid- to coccus-shaped, aerobic, motile, non-spore-forming bacterium (designated strain JLT1679(T)) was isolated from West Pacific. Cells have subpolar flagella, dividing by binary fission. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain belongs to branch of the evolutionary radiation occupied by the genus Paracoccus, family Rhodobacteraceae, order Rhodobacterales, class Alphaproteobacteria. The closest neighbours were Paracoccus stylophorae KTW-16(T) (97.1% similarity), Paracoccus caeni strain MJ17(T) (96.5% similarity), Paracoccus homiensis DD-R11(T) (96.0% similarity) and Paracoccus alcaliphilus JCM 7364(T) (95.8% similarity). The predominant cellular fatty acids of strain JLT1679(T) were summed feature 8 (18:1ω6c) (38.8%), C(18:0) (27.7%), C(16:0) (22.5%), and significant amounts of C(18:1) ω9c (5.1%), C(14:0) (3.8%) and C(18:1) ω7c 11-methyl (2.1%), were present. The predominant respiratory ubiquinone of strain JLT1679(T) was Q-10 and the DNA G + C content of strain JLT1679(T) was 59.5 mol%. The polar lipid profile consisted of a mixture of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. The isolate was distinguishable from members of the genus Paracoccus on the basis of phenotypic and biochemical characteristics. It is evident from the genotypic, chemotaxonomic and phenotypic data that strain JLT1679(T) represents a novel species of the genus Paracoccus, for which the name Paracoccus oceanense sp. nov. is proposed. The type strain is JLT1679(T) (= JCM 17768(T) = CGMCC 1.10831(T)).

Paracoccus beibuensis sp. nov., isolated from the South China Sea.

A Gram-negative, non-motile, short rod-shaped or spherical bacterial strain that accumulates poly-ß-hydroxybutyrate (PHB) granules was isolated from the Beibu Gulf in the South China Sea. Cells have no polar or subpolar flagella, dividing by binary fission. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Paracoccus, family Rhodobacteraceae, order Rhodobacterales, class Alphaproteobacteria. The closest neighbours were Paracoccus aestuarii strain B7(T) (97.2% similarity), Paracoccus zeaxanthinifaciens ATCC 21588(T) (97.1% similarity) and Paracoccus homiensis DD-R11(T) (96.8%). The predominant fatty acids were C(18:1) ω7c (82.1%), and significant amounts of C(18:0) (5.6%), C(10:0) 3-OH (2.3%) and C(16:0) (1.5%) were present. The predominant respiratory ubiquinone of strain JLT1284(T) was Q-10 and the DNA G+C content of strain JLT1284(T) was 67.0 mol%. The isolate was also distinguishable from members of the genus Paracoccus on the basis of phenotypic and biochemical characteristics. It is evident from the genotypic, chemotaxonomic and phenotypic data, therefore, that strain JLT1284(T) represents a novel species of the genus Paracoccus, for which the name Paracoccus beibuensis sp. nov. is proposed. The type strain is JLT1284(T)=LMG 24871(T)=CGMCC 1.7295(T)).

[Identification and characterization of a purple sulfur bacterium from mangrove with rhodopin as predominant carotenoid].

OBJECTIVE: To exploit resources of purple sulfur bacteria in China and further investigate its response mechanism to ecological environment of mangrove. METHODS: Repeated agar shake dilution method, microscope techniques, UV-Vis absorption spectra, thin layer chromatography, HPLC and MS were used. RESULTS: We isolated a purple sulfur bacterium, designated as strain YL28, from a intertidal sediment sample collected from inshore mangrove near Luoyang Bridge of Quanzhou city, Fujian Province of China. Cells were ovoid to rod shaped, 0.5 microm - 1 microm x 2 microm - 3 microm. Color of cell suspensions was reddish-brown. It possessed vesicular intracytoplasmic membrane structures, contained rhodopin and phytylated bacteriochlorophyll a as well as the other two novel bacteriochlorophyll a intermediates. The optimum growth was at 2% - 3.5% NaCl, pH 5.7 - 6.7 and 20 degrees C - 35 degrees C. Photoautotrophically growth anaerobically in the light with sulphide, sulphur, thiosulfate, sulfite as electron donor. Globules of S(0) distributed inside the cells. Photoheterotrophic growth with various organic substrates, especially citrate, glucose, sucrose, fructose and propanol in the presence of sulfide. Nitrogen sources: ammonium salts, N2, urea, glutamate, nitrate and nitrite. Vitamins were not required. Qualitative assessment of IC50 values of chloromycetin, cefazolin, benzene, hydroxy biphenyl, enrofloxacin, acetamiprid, mercuric chloride and cadmium chloride were 70, 100, 20, 20, 3, 170, 5 mg/L and 25 mg/L, respectively. CONCLUSION: Based on phenotype characteristics and 16S rRNA gene sequence similarity of 99% to M. gracile, strain YL28 was identified as novel isolate of M. gracile despite its different physiological characteristics with respect to the species of M. gracile. The organism is possessed of slightly acid tolerance, higher amount of carotenoid of rhodopin and tolerance towards certain antibiotics, pesticide as well as heavy metals.

[Characterization of the ectC gene and its expression product in Halomonas sp. Nj223 from Antarctica deep-sea sediment].

A moderately halophilic bacterium Halomonas sp. NJ223 was isolated from Antarctica deep-sea sediment. This bacterium accumulates ectoine as the main compatible solute in response to severe osmotic stress. Ecoine synthase catalyzes circulation of gamma-N-acetyl-alpha, gamma-diaminobutyric acid (ADABA) to ectoine in the last step of the three enzymatic steps. The gene of ectoine synthase from this strain was amplified by PCR and the DNA sequence of a 393-bp segment was sequenced. The amino acid sequences of this enzyme present high homology to the known sequence. The significance of this gene was proved by the expression in Escherichia coli. Thus, the amplified fragment was cloned into the expression vector pET-his. The insert position, the size and the reading frame were identified by PCR, restriction digestion and the sequence analysis of the recombinant plasmids. SDS-PAGE shows that the relative molecular mass of the expression product was 15 kDa as predicted, which indicated that the recombinant plasmids could express the gene of ectoine synthase. The biosynthetic pathway of ectoine was partially elucidated by renaturation and enzyme activity detection of purified ectoine synthase in vitro. Determination of effect of pH and temperature on enzyme activity shows that the optimal reaction condition of pH was 8.0 and temperature was 25 degrees C.