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Sample records for marine sulfate-reducing bacterium

  1. DMSP: tetrahydrofolate methyltransferase from the marine sulfate-reducing bacterium strain WN

    NASA Astrophysics Data System (ADS)

    Jansen, M.; Hansen, T. A.

    2000-08-01

    Dimethylsulfoniopropionate (DMSP), an important compatible solute of many marine algae, can be metabolised by bacteria via cleavage to dimethylsulfide and acrylate or via an initial demethylation. This is the first report on the purification of an enzyme that specifically catalyses the demethylation of DMSP. The enzyme was isolated from the sulfate-reducing bacterium strain WN, which grows on DMSP and demethylates it to methylthiopropionate. DMSP:tetrahydrofolate (THF) methyltransferase from strain WN was purified 76-fold [to a specific activity of 40.5 μmol min -1 (mg protein) -1]. SDS polyacrylamide gel electrophoresis showed two bands of approximately 10 and 35 kDa; in particular the 35 kDa polypeptide became significantly enriched during the purification. Storage of the purified fraction at -20°C under nitrogen resulted in a 99% loss of activity in two days. The activity could be partially restored by addition of 200 μM cyanocobalamin, hydroxocobalamin or coenzyme B 12. ATP did not have any positive effect on activity. Reduction of the assay mixture by titanium(III)nitrilotriacetic acid slightly stimulated the activity. Gel filtration chromatography revealed a native molecular mass between 45 and 60 kDa for the DMSP:THF methyltransferase. The enzyme was most active at 35°C and pH 7.8. Glycine betaine, which can be considered an N-containing structural analogue of DMSP, did not serve as a methyl donor for DMSP:THF methyltransferase. Various sulfur-containing DMSP-analogues were tested but only methylethylsulfoniopropionate served as methyl donor. None of these compounds inhibited methyl transfer from DMSP to THF. Strain WN did not grow on any of the sulfur-containing DMSP-analogues.

  2. [Desulfovibrio hontreensis sp. nov., a Sulfate-Reducing Bacterium Isolated from Marine Biofoulings at the South Vietnam Coastal Area].

    PubMed

    Tarasov, A L; Osipov, G A; Borzenkov, I A

    2015-01-01

    A Desulfovibrio strain physiologically similar to and phylogeneticall related to "D. caledoniensis" SEBR 7250, D. portus MSL79, and D. dechloracetivorans ATCC 700912 (96.9, 95.9, and 95.8% similarity of the 16S rRNA gen sequences, respectively) was isolated from marine biofouling in the coastal zone of the South China Sae (Nha Trang, South Vietnam). The cells of strain ME were gram-negative motile vibrios (0.4-0.6 x 1.3-2 μm) with a single flagellum. The strain grew at 20 to 39 degrees C (growth optimum at 34-37 degrees C), pH 5.8 to 8.5 (pH optimum at 6.8-7.5), and salinity from 0.08 to 1.1 M Na+ (optimum at 0.2-0.3 M Na+). In the presence of sulfate, the strain grew autotrophically with hydrogen or on lactate, formate, pyruvate, fumarate, and malate. Weak growth occurred on succinate, glycerol, and fructose. In the absence of sulfate, the strain was able to ferment pyruvate, malate (weakly), but not lactate. Sulfate, sulfite, thiosulfate, elemental sulfur, and dimethyl sulfoxide were used as electron acceptors. Vitamins and yeast extract were not required for growth. The G+C content was 52.4 mol %. Predominant fatty acids were C18:0 (13.9%), C16:0 (9.6%), iso-C16:0 (9.5%), C18: 1w7 (8.8%), anteiso-C15:0 (8.1%), and iso-C 17:1 (7.2%). The fatty acid composition was close to that of D. dechloracetivorans BO and has some similarity to that of D. portus. Based on its genotypic and phenotypic characteristics, strain ME maybe considered as a new species, for which the name Desulfovibrio hontrensis sp. nov. is proposed. PMID:27169246

  3. Complete genome, catabolic sub-proteomes and key-metabolites of Desulfobacula toluolica Tol2, a marine, aromatic compound-degrading, sulfate-reducing bacterium.

    PubMed

    Wöhlbrand, Lars; Jacob, Jacob H; Kube, Michael; Mussmann, Marc; Jarling, René; Beck, Alfred; Amann, Rudolf; Wilkes, Heinz; Reinhardt, Richard; Rabus, Ralf

    2013-05-01

    Among the dominant deltaproteobacterial sulfate-reducing bacteria (SRB), members of the genus Desulfobacula are not only present in (hydrocarbon-rich) marine sediments, but occur also frequently in the anoxic water bodies encountered in marine upwelling areas. Here, we present the 5.2 Mbp genome of Desulfobacula toluolica Tol2, which is the first of an aromatic compound-degrading, marine SRB. The genome has apparently been shaped by viral attacks (e.g. CRISPRs) and its high plasticity is reflected by 163 detected genes related to transposases and integrases, a total of 494 paralogous genes and 24 group II introns. Prediction of the catabolic network of strain Tol2 was refined by differential proteome and metabolite analysis of substrate-adapted cells. Toluene and p-cresol are degraded by separate suites of specific enzymes for initial arylsuccinate formation via addition to fumarate (p-cresol-specific enzyme HbsA represents a new phylogenetic branch) as well as for subsequent modified β-oxidation of arylsuccinates to the central intermediate benzoyl-CoA. Proteogenomic evidence suggests specific electron transfer (EtfAB) and membrane proteins to channel electrons from dehydrogenation of both arylsuccinates directly to the membrane redox pool. In contrast to the known anaerobic degradation pathways in other bacteria, strain Tol2 deaminates phenylalanine non-oxidatively to cinnamate by phenylalanine ammonia-lyase and subsequently forms phenylacetate (both metabolites identified in (13) C-labelling experiments). Benzoate degradation involves CoA activation, reductive dearomatization by a class II benzoyl-CoA reductase and hydrolytic ring cleavage as found in the obligate anaerobe Geobacter metallireducens GS-15. The catabolic sub-proteomes displayed high substrate specificity, reflecting the genomically predicted complex and fine-tuned regulatory network of strain Tol2. Despite the genetic equipment for a TCA cycle, proteomic evidence supports complete oxidation of

  4. IN SITU RT-PCR WITH A SULFATE-REDUCING BACTERIUM ISOLATED FROM SEAGRASS ROOTS

    EPA Science Inventory

    Bacteria considered to be obligate anaerobes internally colonize roots of the submerged macrophyte Halodule wrightii. A sulfate reducing bacterium, Summer lac 1, was isolated on lactate from H. wrightii roots. The isolate has physiological characteristics typical of Desulfovibri...

  5. Isolation and characterization of a novel toluene-degrading, sulfate-reducing bacterium.

    PubMed Central

    Beller, H R; Spormann, A M; Sharma, P K; Cole, J R; Reinhard, M

    1996-01-01

    A novel sulfate-reducing bacterium isolated from fuel-contaminated subsurface soil, strain PRTOL1, mineralizes toluene as the sole electron donor and carbon source under strictly anaerobic conditions. The mineralization of 80% of toluene carbon to CO2 was demonstrated in experiments with [ring-U-14C]toluene; 15% of toluene carbon was converted to biomass and nonvolatile metabolic by-products, primarily the former. The observed stoichiometric ratio of moles of sulfate consumed per mole of toluene consumed was consistent with the theoretical ratio for mineralization of toluene coupled with the reduction of sulfate to hydrogen sulfide. Strain PRTOL1 also transforms o- and p-xylene to metabolic products when grown with toluene. However, xylene transformation by PRTOL1 is slow relative to toluene degradation and cannot be sustained over time. Stable isotope-labeled substrates were used in conjunction with gas chromatography-mass spectrometry to investigate the by-products of toluene and xylene metabolism. The predominant by-products from toluene, o-xylene, and p-xylene were benzylsuccinic acid, (2-methylbenzyl)succinic acid, and 4-methylbenzoic acid (or p-toluic acid), respectively. Metabolic by-products accounted for nearly all of the o-xylene consumed. Enzyme assays indicated that acetyl coenzyme A oxidation proceeded via the carbon monoxide dehydrogenase pathway. Compared with the only other reported toluene-degrading, sulfate-reducing bacterium, strain PRTOL1 is distinct in that it has a novel 16S rRNA gene sequence and was derived from a freshwater rather than marine environment. PMID:8919780

  6. Anaerobic degradation of benzene by marine sulfate-reducing bacteria

    NASA Astrophysics Data System (ADS)

    Musat, Florin; Wilkes, Heinz; Musat, Niculina; Kuypers, Marcel; Widdel, Friedrich

    2010-05-01

    Benzene, the archetypal aromatic hydrocarbon is a common constituent of crude oil and oil-refined products. As such, it can enter the biosphere through natural oil seeps or as a consequence of exploitation of fossil fuel reservoirs. Benzene is chemically very stable, due to the stabilizing aromatic electron system and to the lack of functional groups. Although the anaerobic degradation of benzene has been reported under denitrifying, sulfate-reducing and methanogenic conditions, the microorganisms involved and the initial biochemical steps of degradation remain insufficiently understood. Using marine sediment from a Mediterranean lagoon a sulfate-reducing enrichment culture with benzene as the sole organic substrate was obtained. Application of 16S rRNA gene-based methods showed that the enrichment was dominated (more than 85% of total cells) by a distinct phylotype affiliated with a clade of Deltaproteobacteria that include degraders of other aromatic hydrocarbons, such as naphthalene, ethylbenzene and m-xylene. Using benzoate as a soluble substrate in agar dilution series, several pure cultures closely related to Desulfotignum spp. and Desulfosarcina spp. were isolated. None of these strains was able to utilize benzene as a substrate and hybridizations with specific oligonucleotide probes showed that they accounted for as much as 6% of the total cells. Incubations with 13C-labeled benzene followed by Halogen in situ Hybridization - Secondary Ion Mass Spectroscopy (HISH-SIMS) analysis showed that cells of the dominant phylotype were highly enriched in 13C, while the accompanying bacteria had little or no 13C incorporation. These results demonstrate that the dominant phylotype was indeed the apparent benzene degrader. Dense-cell suspensions of the enrichment culture did not show metabolic activity toward added phenol or toluene, suggesting that benzene degradation did not proceed through anaerobic hydroxylation or methylation. Instead, benzoate was identified in

  7. Distribution of Thermophilic Marine Sulfate Reducers in North Sea Oil Field Waters and Oil Reservoirs

    PubMed Central

    Nilsen, R. K.; Beeder, J.; Thorstenson, T.; Torsvik, T.

    1996-01-01

    The distribution of thermophilic marine sulfate reducers in produced oil reservoir waters from the Gullfaks oil field in the Norwegian sector of the North Sea was investigated by using enrichment cultures and genus-specific fluorescent antibodies produced against the genera Archaeoglobus, Desulfotomaculum, and Thermodesulforhabdus. The thermophilic marine sulfate reducers in this environment could mainly be classified as species belonging to the genera Archaeoglobus and Thermodesulforhabdus. In addition, some unidentified sulfate reducers were present. Culturable thermophilic Desulfotomaculum strains were not detected. Specific strains of thermophilic sulfate reducers inhabited different parts of the oil reservoir. No correlation between the duration of seawater injection and the numbers of thermophilic sulfate reducers in the produced waters was observed. Neither was there any correlation between the concentration of hydrogen sulfide and the numbers of thermophilic sulfate reducers. The results indicate that thermophilic and hyperthermophilic sulfate reducers are indigenous to North Sea oil field reservoirs and that they belong to a deep subterranean biosphere. PMID:16535321

  8. Sulfur Isotope Enrichment during Maintenance Metabolism in the Thermophilic Sulfate-Reducing Bacterium Desulfotomaculum putei▿

    PubMed Central

    Davidson, Mark M.; Bisher, M. E.; Pratt, Lisa M.; Fong, Jon; Southam, Gordon; Pfiffner, Susan M.; Reches, Z.; Onstott, Tullis C.

    2009-01-01

    Values of Δ34S (\\documentclass[10pt]{article} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{pmc} \\usepackage[Euler]{upgreek} \\pagestyle{empty} \\oddsidemargin -1.0in \\begin{document} \\begin{equation*}={\\delta}^{34}S_{HS}-{\\delta}^{34}S_{SO_{4}}\\end{equation*}\\end{document}, where δ34SHS and \\documentclass[10pt]{article} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{pmc} \\usepackage[Euler]{upgreek} \\pagestyle{empty} \\oddsidemargin -1.0in \\begin{document} \\begin{equation*}{\\delta}^{34}S_{SO_{4}}\\end{equation*}\\end{document} indicate the differences in the isotopic compositions of the HS− and SO42− in the eluent, respectively) for many modern marine sediments are in the range of −55 to −75‰, much greater than the −2 to −46‰ ɛ34S (kinetic isotope enrichment) values commonly observed for microbial sulfate reduction in laboratory batch culture and chemostat experiments. It has been proposed that at extremely low sulfate reduction rates under hypersulfidic conditions with a nonlimited supply of sulfate, isotopic enrichment in laboratory culture experiments should increase to the levels recorded in nature. We examined the effect of extremely low sulfate reduction rates and electron donor limitation on S isotope fractionation by culturing a thermophilic, sulfate-reducing bacterium, Desulfotomaculum putei, in a biomass-recycling culture vessel, or “retentostat.” The cell-specific rate of sulfate reduction and the specific growth rate decreased progressively from the exponential phase to the maintenance phase, yielding average maintenance coefficients of 10−16 to 10−18 mol of SO4 cell−1 h−1 toward the end of the experiments. Overall S mass and isotopic balance were conserved during the experiment. The differences in the δ34S

  9. A cultured greigite-producing magnetotactic bacterium in a novel group of sulfate-reducing bacteria.

    PubMed

    Lefèvre, Christopher T; Menguy, Nicolas; Abreu, Fernanda; Lins, Ulysses; Pósfai, Mihály; Prozorov, Tanya; Pignol, David; Frankel, Richard B; Bazylinski, Dennis A

    2011-12-23

    Magnetotactic bacteria contain magnetosomes--intracellular, membrane-bounded, magnetic nanocrystals of magnetite (Fe(3)O(4)) or greigite (Fe(3)S(4))--that cause the bacteria to swim along geomagnetic field lines. We isolated a greigite-producing magnetotactic bacterium from a brackish spring in Death Valley National Park, California, USA, strain BW-1, that is able to biomineralize greigite and magnetite depending on culture conditions. A phylogenetic comparison of BW-1 and similar uncultured greigite- and/or magnetite-producing magnetotactic bacteria from freshwater to hypersaline habitats shows that these organisms represent a previously unknown group of sulfate-reducing bacteria in the Deltaproteobacteria. Genomic analysis of BW-1 reveals the presence of two different magnetosome gene clusters, suggesting that one may be responsible for greigite biomineralization and the other for magnetite. PMID:22194580

  10. Temperature and its control of isotope fractionation by a sulfate-reducing bacterium

    NASA Astrophysics Data System (ADS)

    Canfield, Donald E.; Olesen, Claus A.; Cox, Raymond P.

    2006-02-01

    A synthesis of previous results, which we dub the "standard model," provides a prediction as to how isotope fractionation during sulfate reduction should respond to physiological variables such as specific rate of sulfate reduction and environmental variables such as substrate availability and temperature. The standard model suggests that isotope fractionation should decrease with increasing specific rates of sulfate reduction (rate per cell). Furthermore, the standard model predicts that low fractionations should be found at both high and low temperatures whereas the highest fractionations should be found in the intermediate temperature range. These fractionation trends are controlled, as a function of temperature, by the balance between the transfer rates of sulfate into and out of the cell and the exchange between the sulfur pools internal to the organism. We test this standard model by conducting experiments on the growth physiology and isotope fractionation, as a function of temperature, by the sulfate-reducing bacterium Desulfovibrio desulfuricans (DSMZ 642). Our results contrast with the "standard model" by showing a positive correlation between specific rates of sulfate reduction and fractionation. Also by contrast with the standard model, we found the highest fractionations at low and high temperatures and the lowest fractionations in the intermediate temperature range. We develop a fractionation model which can be used to explain both our results as well as the results of the "standard model." Differences in fractionation with temperature relate to differences in the specific temperature response of internal enzyme kinetics as well as the exchange rates of sulfate in and out of the cell. It is expected that the kinetics of these processes will show strain-specific differences.

  11. Function of Periplasmic Hydrogenases in the Sulfate-ReducingBacterium Desulfovibrio vulgaris Hildenborough

    SciTech Connect

    Caffrey, Sean M.; Park, Hyung-Soo; Voordouw, Johanna K.; He,Zhili; Zhou, Jizhong; Voordouw, Gerrit

    2007-09-24

    The sulfate-reducing bacterium Desulfovibrio vulgarisHildenborough possesses four periplasmic hydrogenases to facilitate theoxidation of molecular hydrogen. These include an [Fe]hydrogenase, an[NiFeSe]hydrogenase, and two [NiFe]hydrogenases encoded by the hyd,hys, hyn1, and hyn2 genes, respectively. In order to understand theircellular functions, we have compared the growth rates of existing (hydand hyn1) and newly constructed (hys and hyn-1 hyd) mutants to those ofthe wild type in defined media in which lactate or hydrogen at either 5or 50 percent (vol/vol) was used as the sole electron donor for sulfatereduction. Only strains missing the [Fe]hydrogenase were significantlyaffected during growth with lactate or with 50 percent (vol/vol) hydrogenas the sole electron donor. When the cells were grown at low (5 percent[vol/vol]) hydrogen concentrations, those missing the [NiFeSe]hydrogenase suffered the greatest impairment. The growth rate datacorrelated strongly with gene expression results obtained from microarrayhybridizations and real-time PCR using mRNA extracted from cells grownunder the three conditions. Expression of the hys genes followed theorder 5 percent hydrogen>50 percent hydrogen>lactate, whereasexpression of the hyd genes followed the reverse order. These resultssuggest that growth with lactate and 50 percent hydrogen is associatedwith high intracellular hydrogen concentrations, which are best capturedby the higher activity, lower affinity [Fe]hydrogenase. In contrast,growth with 5 percent hydrogen is associated with a low intracellularhydrogen concentration, requiring the lower activity, higher affinity[NiFeSe]hydrogenase.

  12. Regulation of Nitrite Stress Response in Desulfovibrio vulgaris Hildenborough, a Model Sulfate-Reducing Bacterium

    PubMed Central

    Rajeev, Lara; Chen, Amy; Kazakov, Alexey E.; Luning, Eric G.; Zane, Grant M.; Novichkov, Pavel S.; Wall, Judy D.

    2015-01-01

    ABSTRACT Sulfate-reducing bacteria (SRB) are sensitive to low concentrations of nitrite, and nitrite has been used to control SRB-related biofouling in oil fields. Desulfovibrio vulgaris Hildenborough, a model SRB, carries a cytochrome c-type nitrite reductase (nrfHA) that confers resistance to low concentrations of nitrite. The regulation of this nitrite reductase has not been directly examined to date. In this study, we show that DVU0621 (NrfR), a sigma54-dependent two-component system response regulator, is the positive regulator for this operon. NrfR activates the expression of the nrfHA operon in response to nitrite stress. We also show that nrfR is needed for fitness at low cell densities in the presence of nitrite because inactivation of nrfR affects the rate of nitrite reduction. We also predict and validate the binding sites for NrfR upstream of the nrfHA operon using purified NrfR in gel shift assays. We discuss possible roles for NrfR in regulating nitrate reductase genes in nitrate-utilizing Desulfovibrio spp. IMPORTANCE The NrfA nitrite reductase is prevalent across several bacterial phyla and required for dissimilatory nitrite reduction. However, regulation of the nrfA gene has been studied in only a few nitrate-utilizing bacteria. Here, we show that in D. vulgaris, a bacterium that does not respire nitrate, the expression of nrfHA is induced by NrfR upon nitrite stress. This is the first report of regulation of nrfA by a sigma54-dependent two-component system. Our study increases our knowledge of nitrite stress responses and possibly of the regulation of nitrate reduction in SRB. PMID:26283774

  13. Desulfonatronum Thiodismutans sp. nov., a Novel Alkaliphilic, Sulfate-reducing Bacterium Capable of Lithoautotrophic Growth

    NASA Technical Reports Server (NTRS)

    Pikuta, Elena V.; Hoover, Richard B.; Bej, Asim K.; Marsic, Damien; Whitman, William B.; Cleland, David; Krader, Paul

    2003-01-01

    A novel alkaliphilic, sulfate-reducing bacterium, strain MLF1(sup T), was isolated from sediments of soda Mono Lake, California. Gram-negative vibrio-shaped cells were observed, which were 0.6-0.7 x 1.2-2.7 microns in size, motile by a single polar flagellum and occurred singly, in pairs or as short spirilla. Growth was observed at 15-48 C (optimum, 37 C), > 1-7 % NaCI, w/v (optimum, 3%) and pH 8.0-10.0 (optimum, 9.5). The novel isolate is strictly alkaliphilic, requires a high concentration of carbonate in the growth medium and is obligately anaerobic and catalase-negative. As electron donors, strain MLF1(sup T) uses hydrogen, formate and ethanol. Sulfate, sulfite and thiosulfate (but not sulfur or nitrate) can be used as electron acceptors. The novel isolate is a lithoheterotroph and a facultative lithoautotroph that is able to grow on hydrogen without an organic source of carbon. Strain MLF1(sup T) is resistant to kanamycin and gentamicin, but sensitive to chloramphenicol and tetracycline. The DNA G+C content is 63.0 mol% (HPLC). DNA-DNA hybridization with the most closely related species, Desulfonatronum lacustre Z-7951(sup T), exhibited 51 % homology. Also, the genome size (1.6 x 10(exp 9) Da) and T(sub m) value of the genomic DNA (71 +/- 2 C) for strain MLF1(sup T) were significantly different from the genome size (2.1 x 10(exp 9) Da) and T(sub m) value (63 +/- 2 C) for Desulfonatronum lacustre Z-7951(sup T). On the basis of physiological and molecular properties, the isolate was considered to be a novel species of the genus Desulfonatronum, for which the name Desulfonatronum thiodismutans sp. nov. is proposed (the type strain is MLF1(sup T) = ATCC BAA-395(sup T) = DSM 14708(sup T)).

  14. Anaerobic n-Alkane Metabolism by a Sulfate-Reducing Bacterium, Desulfatibacillum aliphaticivorans Strain CV2803T

    PubMed Central

    Cravo-Laureau, Cristiana; Grossi, Vincent; Raphel, Danielle; Matheron, Robert; Hirschler-Réa, Agnès

    2005-01-01

    The alkane-degrading, sulfate-reducing bacterium Desulfatibacillum aliphaticivorans strain CV2803T, recently isolated from marine sediments, was investigated for n-alkane metabolism. The total cellular fatty acids of this strain had predominantly odd numbers of carbon atoms (C odd) when the strain was grown on a C-odd alkane (pentadecane) and even numbers of carbon atoms (C even) when it was grown on a C-even alkane (hexadecane). Detailed analyses of those fatty acids by gas chromatography/mass spectrometry allowed us to identify saturated 2-, 4-, 6-, and 8-methyl- and monounsaturated 6-methyl-branched fatty acids, with chain lengths that specifically correlated with those of the alkane. Growth of D. aliphaticivorans on perdeuterated hexadecane demonstrated that those methyl-branched fatty acids were directly derived from the substrate. In addition, cultures on pentadecane and hexadecane produced (1-methyltetradecyl)succinate and (1-methylpentadecyl)succinate, respectively. These results indicate that D. aliphaticivorans strain CV2803T oxidizes n-alkanes into fatty acids anaerobically, via the addition of fumarate at C-2. Based on our observations and on literature data, a pathway for anaerobic n-alkane metabolism by D. aliphaticivorans is proposed. This involves the transformation of the initial alkylsuccinate into a 4-methyl-branched fatty acid which, in addition to catabolic reactions, can alternatively undergo chain elongation and desaturation to form storage fatty acids. PMID:16000749

  15. Identification and catalytic residues of the arsenite methyltransferase from a sulfate-reducing bacterium, Clostridium sp. BXM.

    PubMed

    Wang, Pei-Pei; Bao, Peng; Sun, Guo-Xin

    2015-01-01

    Arsenic methylation is an important process frequently occurring in anaerobic environments. Anaerobic microorganisms have been implicated as the major contributors for As methylation. However, very little information is available regarding the enzymatic mechanism of As methylation by anaerobes. In this study, one novel sulfate-reducing bacterium isolate, Clostridium sp. BXM, which was isolated from a paddy soil in our laboratory, was demonstrated to have the ability of methylating As. One putative arsenite S-Adenosyl-Methionine methyltransferase (ArsM) gene, CsarsM was cloned from Clostridium sp. BXM. Heterologous expression of CsarsM conferred As resistance and the ability of methylating As to an As-sensitive strain of Escherichia coli. Purified methyltransferase CsArsM catalyzed the formation of methylated products from arsenite, further confirming its function of As methylation. Site-directed mutagenesis studies demonstrated that three conserved cysteine residues at positions 65, 153 and 203 in CsArsM are necessary for arsenite methylation, but only Cysteine 153 and Cysteine 203 are required for the methylation of monomethylarsenic to dimethylarsenic. These results provided the characterization of arsenic methyltransferase from anaerobic sulfate-reducing bacterium. Given that sulfate-reducing bacteria are ubiquitous in various wetlands including paddy soils, enzymatic methylation mediated by these anaerobes is proposed to contribute to the arsenic biogeochemical cycling. PMID:25790486

  16. Desulfovibrio profundus sp. nov., a novel barophilic sulfate-reducing bacterium from deep sediment layers in the Japan Sea.

    PubMed

    Bale, S J; Goodman, K; Rochelle, P A; Marchesi, J R; Fry, J C; Weightman, A J; Parkes, R J

    1997-04-01

    Several strains of a strictly anaerobic, vibrio-shaped or sigmoid, sulfate-reducing bacterium were isolated from deep marine sediments (depth, 80 and 500 m) obtained from the Japan Sea (Ocean Drilling Program Leg 128, site 798B). This bacterium was identified as a member of the genus Desulfovibrio on the basis of the presence of desulfoviridin and characteristic phospholipid fatty acids (iso 17:1 omega 7 and iso 15:0), the small number of growth substrates utilized (lactate, pyruvate, and hydrogen), and 16S rRNA gene sequence analysis data. Based on data for 16S rRNA sequences (1,369 bp), all of the Japan Sea strains were identical to each other and were most closely related to Desulfovibrio salexigens and less closely related to Desulfovibrio desulfuricans (levels of similarity, 91 and 89.6%, respectively). There were, however, considerable phenotypic differences (in temperatures, pressures, and salinities tolerated, growth substrates, and electron donors) between the Japan Sea isolates and the type strains of previously described desulfovibrios, as well as important differences among the Japan Sea isolates. The Japan Sea isolates were active (with sulfide production) over a wide temperature range (15 to 65 degrees C) and a wide sodium chloride concentration range (0.2 to 10%) (moderate halophile), and they were barophiles that were active at pressures up to about 40 MPa (400 atm). The optimum pressures for activity corresponded to the calculated pressures at the depths from which the organisms were isolated (for isolates obtained at depths of 80 and 500 m the optimum activities occurred at 10 and 15 MPa, respectively [100 and 150 atm, respectively]). This confirms that the organisms came from deep sediments and indicates that they are well-adapted for deep sediment conditions, which is consistent with other characteristics (utilization of hydrogen, fermentation, and utilization of ferric iron and organic sulfonates as electron acceptors). We propose that Japan

  17. Alteration of Nontronite NAU-2 by a Sulfate-Reducing Bacterium

    NASA Astrophysics Data System (ADS)

    Vali, H.; Li, Y.; Sears, S.; Yang, J.; Deng, B.; Zhang, C. L.

    2004-05-01

    Iron-rich clay minerals are abundant in the natural environment. The goal of this study is to understand the mechanisms of enhanced reduction of Fe(III) in Fe-rich clay minerals under sulfate-reducing conditions. In particular, biogenic reduction of the structural Fe(III) and release of other elements in a nontronite sample (NAu-2) are studied using a Desulfovibrio spp. strain G-11 with or without amended sulfate. The microbial production of Fe(II) from NAu-2 was about 10% of total structural Fe(III) (30 mM) when Fe(III) was available as the sole electron acceptor. The production of Fe(II), however, reached 29% of total structural Fe(III) when both Fe(III) and SO4= (50 mM) were concurrently used as the electron acceptors. Abiotic production of Fe(II) from reaction of NAu-2 with Na2S (50 mM), on the other hand, was only ca. 7.5% of total structural Fe(III). The enhanced reduction of structural Fe(III) by G-11, particularly in the presence of sulfate, is directly related to the growth rate and metabolic activities of the bacteria which results in destruction of the structure of the nontronite. Analyses by SEM, TEM, XRD, and EDS revealed significant changes in the structure and composition of NAu-2 during its alteration by bacterial sulfate reduction. G-11 could also derive nutrients from NAu-2 to support its growth in the absence of amended minerals and vitamins. Results of this study suggest that sulfate-reducing bacteria may play a more significant role in cycling of Fe, S, and other elements during alteration of Fe-rich clay minerals and other silicate minerals than previously recognized.

  18. Iron reduction and alteration of nontronite NAu-2 by a sulfate-reducing bacterium

    NASA Astrophysics Data System (ADS)

    Li, Yi-Liang; Vali, Hojatollah; Sears, S. Kelly; Yang, John; Deng, Baolin; Zhang, Chuanlun L.

    2004-08-01

    Iron-rich clay minerals are abundant in the natural environment and are an important source of iron for microbial metabolism. The objective of this study was to understand the mechanism(s) of enhanced reduction of Fe(III) in iron-rich 2:1 clay minerals under sulfate-reducing conditions. In particular, biogenic reduction of structural Fe(III) in nontronite NAu-2, an Fe-rich smectite-group mineral, was studied using a Desulfovibrio spp. strain G-11 with or without amended sulfate. The microbial production of Fe(II) from NAu-2 is about 10% of total structural Fe(III) (30 mM) when Fe(III) is available as the sole electron acceptor. The measured production of Fe(II), however, can reach 29% of the total structural Fe(III) during sulfate reduction by G-11 when sulfate (50 mM) is concurrently added with NAu-2. In contrast, abiotic production of Fe(II) from the reaction of NAu-2 with Na 2S (50 mM) is only ca. 7.5% of the total structural Fe(III). The enhanced reduction of structural Fe(III) by G-11, particularly in the presence of sulfate, is closely related to the growth rate and metabolic activities of the bacteria. Analyses by X-ray diffraction, transmission electron microscopy, and energy dispersive spectroscopy reveal significant changes in the structure and composition of NAu-2 during its alteration by bacterial sulfate reduction. G-11 can also derive nutrients from NAu-2 to support its growth in the absence of amended minerals and vitamins. Results of this study suggest that sulfate-reducing bacteria may play a more significant role than previously recognized in the cycling of Fe, S, and other elements during alteration of Fe-rich 2:1 clay minerals and other silicate minerals.

  19. Draft Genome Sequence of the Obligately Alkaliphilic Sulfate-Reducing Bacterium Desulfonatronum thiodismutans Strain MLF1

    PubMed Central

    Trubitsyn, Denis; Geurink, Corey; Pikuta, Elena; Lefèvre, Christopher T.; McShan, W. Michael; Gillaspy, Allison F.

    2014-01-01

    Desulfonatronum thiodismutans strain MLF1, an alkaliphilic bacterium capable of sulfate reduction, was isolated from Mono Lake, California. Here we report the 3.92-Mb draft genome sequence comprising 34 contigs and some results of its automated annotation. These data will improve our knowledge of mechanisms by which bacteria withstand extreme environments. PMID:25081260

  20. The genetic basis of energy conservation in the sulfate-reducing bacterium Desulfovibrio alaskensis G20

    DOE PAGESBeta

    Price, Morgan N.; Ray, Jayashree; Wetmore, Kelly M.; Kuehl, Jennifer V.; Bauer, Stefan; Deutschbauer, Adam M.; Arkin, Adam P.

    2014-10-31

    Sulfate-reducing bacteria play major roles in the global carbon and sulfur cycles, but it remains unclear how reducing sulfate yields energy. To determine the genetic basis of energy conservation, we measured the fitness of thousands of pooled mutants of Desulfovibrio alaskensis G20 during growth in 12 different combinations of electron donors and acceptors. We show that ion pumping by the ferredoxin:NADH oxidoreductase Rnf is required whenever substrate-level phosphorylation is not possible. The uncharacterized complex Hdr/flox-1 (Dde_1207:13) is sometimes important alongside Rnf and may perform an electron bifurcation to generate more reduced ferredoxin from NADH to allow further ion pumping. Similarly,more » during the oxidation of malate or fumarate, the electron-bifurcating transhydrogenase NfnAB-2 (Dde_1250:1) is important and may generate reduced ferredoxin to allow additional ion pumping by Rnf. During formate oxidation, the periplasmic [NiFeSe] hydrogenase HysAB is required, which suggests that hydrogen forms in the periplasm, diffuses to the cytoplasm, and is used to reduce ferredoxin, thus providing a substrate for Rnf. We found that during hydrogen utilization, the transmembrane electron transport complex Tmc is important and may move electrons from the periplasm into the cytoplasmic sulfite reduction pathway. Finally, mutants of many other putative electron carriers have no clear phenotype, which suggests that they are not important under our growth conditions, although we cannot rule out genetic redundancy.« less

  1. The genetic basis of energy conservation in the sulfate-reducing bacterium Desulfovibrio alaskensis G20

    SciTech Connect

    Price, Morgan N.; Ray, Jayashree; Wetmore, Kelly M.; Kuehl, Jennifer V.; Bauer, Stefan; Deutschbauer, Adam M.; Arkin, Adam P.

    2014-10-31

    Sulfate-reducing bacteria play major roles in the global carbon and sulfur cycles, but it remains unclear how reducing sulfate yields energy. To determine the genetic basis of energy conservation, we measured the fitness of thousands of pooled mutants of Desulfovibrio alaskensis G20 during growth in 12 different combinations of electron donors and acceptors. We show that ion pumping by the ferredoxin:NADH oxidoreductase Rnf is required whenever substrate-level phosphorylation is not possible. The uncharacterized complex Hdr/flox-1 (Dde_1207:13) is sometimes important alongside Rnf and may perform an electron bifurcation to generate more reduced ferredoxin from NADH to allow further ion pumping. Similarly, during the oxidation of malate or fumarate, the electron-bifurcating transhydrogenase NfnAB-2 (Dde_1250:1) is important and may generate reduced ferredoxin to allow additional ion pumping by Rnf. During formate oxidation, the periplasmic [NiFeSe] hydrogenase HysAB is required, which suggests that hydrogen forms in the periplasm, diffuses to the cytoplasm, and is used to reduce ferredoxin, thus providing a substrate for Rnf. We found that during hydrogen utilization, the transmembrane electron transport complex Tmc is important and may move electrons from the periplasm into the cytoplasmic sulfite reduction pathway. Finally, mutants of many other putative electron carriers have no clear phenotype, which suggests that they are not important under our growth conditions, although we cannot rule out genetic redundancy.

  2. Sulfur Isotope Fractionation during the Evolutionary Adaptation of a Sulfate-Reducing Bacterium

    PubMed Central

    Anderson-Trocmé, Luke; Whyte, Lyle G.; Zane, Grant M.; Wall, Judy D.; Wing, Boswell A.

    2015-01-01

    Dissimilatory sulfate reduction is a microbial catabolic pathway that preferentially processes less massive sulfur isotopes relative to their heavier counterparts. This sulfur isotope fractionation is recorded in ancient sedimentary rocks and generally is considered to reflect a phenotypic response to environmental variations rather than to evolutionary adaptation. Modern sulfate-reducing microorganisms isolated from similar environments can exhibit a wide range of sulfur isotope fractionations, suggesting that adaptive processes influence the sulfur isotope phenotype. To date, the relationship between evolutionary adaptation and isotopic phenotypes has not been explored. We addressed this by studying the covariation of fitness, sulfur isotope fractionation, and growth characteristics in Desulfovibrio vulgaris Hildenborough in a microbial evolution experiment. After 560 generations, the mean fitness of the evolved lineages relative to the starting isogenic population had increased by ∼17%. After 927 generations, the mean fitness relative to the initial ancestral population had increased by ∼20%. Growth rate in exponential phase increased during the course of the experiment, suggesting that this was a primary influence behind the fitness increases. Consistent changes were observed within different selection intervals between fractionation and fitness. Fitness changes were associated with changes in exponential growth rate but changes in fractionation were not. Instead, they appeared to be a response to changes in the parameters that govern growth rate: yield and cell-specific sulfate respiration rate. We hypothesize that cell-specific sulfate respiration rate, in particular, provides a bridge that allows physiological controls on fractionation to cross over to the adaptive realm. PMID:25662968

  3. Sulfur isotope fractionation during the evolutionary adaptation of a sulfate-reducing bacterium.

    PubMed

    Pellerin, André; Anderson-Trocmé, Luke; Whyte, Lyle G; Zane, Grant M; Wall, Judy D; Wing, Boswell A

    2015-04-01

    Dissimilatory sulfate reduction is a microbial catabolic pathway that preferentially processes less massive sulfur isotopes relative to their heavier counterparts. This sulfur isotope fractionation is recorded in ancient sedimentary rocks and generally is considered to reflect a phenotypic response to environmental variations rather than to evolutionary adaptation. Modern sulfate-reducing microorganisms isolated from similar environments can exhibit a wide range of sulfur isotope fractionations, suggesting that adaptive processes influence the sulfur isotope phenotype. To date, the relationship between evolutionary adaptation and isotopic phenotypes has not been explored. We addressed this by studying the covariation of fitness, sulfur isotope fractionation, and growth characteristics in Desulfovibrio vulgaris Hildenborough in a microbial evolution experiment. After 560 generations, the mean fitness of the evolved lineages relative to the starting isogenic population had increased by ∼ 17%. After 927 generations, the mean fitness relative to the initial ancestral population had increased by ∼ 20%. Growth rate in exponential phase increased during the course of the experiment, suggesting that this was a primary influence behind the fitness increases. Consistent changes were observed within different selection intervals between fractionation and fitness. Fitness changes were associated with changes in exponential growth rate but changes in fractionation were not. Instead, they appeared to be a response to changes in the parameters that govern growth rate: yield and cell-specific sulfate respiration rate. We hypothesize that cell-specific sulfate respiration rate, in particular, provides a bridge that allows physiological controls on fractionation to cross over to the adaptive realm. PMID:25662968

  4. The genetic basis of energy conservation in the sulfate-reducing bacterium Desulfovibrio alaskensis G20

    PubMed Central

    Price, Morgan N.; Ray, Jayashree; Wetmore, Kelly M.; Kuehl, Jennifer V.; Bauer, Stefan; Deutschbauer, Adam M.; Arkin, Adam P.

    2014-01-01

    Sulfate-reducing bacteria play major roles in the global carbon and sulfur cycles, but it remains unclear how reducing sulfate yields energy. To determine the genetic basis of energy conservation, we measured the fitness of thousands of pooled mutants of Desulfovibrio alaskensis G20 during growth in 12 different combinations of electron donors and acceptors. We show that ion pumping by the ferredoxin:NADH oxidoreductase Rnf is required whenever substrate-level phosphorylation is not possible. The uncharacterized complex Hdr/flox-1 (Dde_1207:13) is sometimes important alongside Rnf and may perform an electron bifurcation to generate more reduced ferredoxin from NADH to allow further ion pumping. Similarly, during the oxidation of malate or fumarate, the electron-bifurcating transhydrogenase NfnAB-2 (Dde_1250:1) is important and may generate reduced ferredoxin to allow additional ion pumping by Rnf. During formate oxidation, the periplasmic [NiFeSe] hydrogenase HysAB is required, which suggests that hydrogen forms in the periplasm, diffuses to the cytoplasm, and is used to reduce ferredoxin, thus providing a substrate for Rnf. During hydrogen utilization, the transmembrane electron transport complex Tmc is important and may move electrons from the periplasm into the cytoplasmic sulfite reduction pathway. Finally, mutants of many other putative electron carriers have no clear phenotype, which suggests that they are not important under our growth conditions, although we cannot rule out genetic redundancy. PMID:25400629

  5. Metabolic niche of a prominent sulfate-reducing human gut bacterium

    PubMed Central

    Rey, Federico E.; Gonzalez, Mark D.; Cheng, Jiye; Ahern, Philip P.; Gordon, Jeffrey I.

    2013-01-01

    Sulfate-reducing bacteria (SRB) colonize the guts of ∼50% of humans. We used genome-wide transposon mutagenesis and insertion-site sequencing, RNA-Seq, plus mass spectrometry to characterize genetic and environmental factors that impact the niche of Desulfovibrio piger, the most common SRB in a surveyed cohort of healthy US adults. Gnotobiotic mice were colonized with an assemblage of sequenced human gut bacterial species with or without D. piger and fed diets with different levels and types of carbohydrates and sulfur sources. Diet was a major determinant of functions expressed by this artificial nine-member community and of the genes that impact D. piger fitness; the latter includes high- and low-affinity systems for using ammonia, a limiting resource for D. piger in mice consuming a polysaccharide-rich diet. Although genes involved in hydrogen consumption and sulfate reduction are necessary for its colonization, varying dietary-free sulfate levels did not significantly alter levels of D. piger, which can obtain sulfate from the host in part via cross-feeding mediated by Bacteroides-encoded sulfatases. Chondroitin sulfate, a common dietary supplement, increased D. piger and H2S levels without compromising gut barrier integrity. A chondroitin sulfate-supplemented diet together with D. piger impacted the assemblage’s substrate utilization preferences, allowing consumption of more reduced carbon sources and increasing the abundance of the H2-producing Actinobacterium, Collinsella aerofaciens. Our findings provide genetic and metabolic details of how this H2-consuming SRB shapes the responses of a microbiota to diet ingredients and a framework for examining how individuals lacking D. piger differ from those who harbor it. PMID:23898195

  6. Anaerobic degradation of cyclohexane by sulfate-reducing bacteria from hydrocarbon-contaminated marine sediments

    PubMed Central

    Jaekel, Ulrike; Zedelius, Johannes; Wilkes, Heinz; Musat, Florin

    2015-01-01

    The fate of cyclohexane, often used as a model compound for the biodegradation of cyclic alkanes due to its abundance in crude oils, in anoxic marine sediments has been poorly investigated. In the present study, we obtained an enrichment culture of cyclohexane-degrading sulfate-reducing bacteria from hydrocarbon-contaminated intertidal marine sediments. Microscopic analyses showed an apparent dominance by oval cells of 1.5 × 0.8 μm. Analysis of a 16S rRNA gene library, followed by whole-cell hybridization with group- and sequence-specific oligonucleotide probes showed that these cells belonged to a single phylotype, and were accounting for more than 80% of the total cell number. The dominant phylotype, affiliated with the Desulfosarcina-Desulfococcus cluster of the Deltaproteobacteria, is proposed to be responsible for the degradation of cyclohexane. Quantitative growth experiments showed that cyclohexane degradation was coupled with the stoichiometric reduction of sulfate to sulfide. Substrate response tests corroborated with hybridization with a sequence-specific oligonucleotide probe suggested that the dominant phylotype apparently was able to degrade other cyclic and n-alkanes, including the gaseous alkane n-butane. Based on GC-MS analyses of culture extracts cyclohexylsuccinate was identified as a metabolite, indicating an activation of cyclohexane by addition to fumarate. Other metabolites detected were 3-cyclohexylpropionate and cyclohexanecarboxylate providing evidence that the overall degradation pathway of cyclohexane under anoxic conditions is analogous to that of n-alkanes. PMID:25806023

  7. Genome Sequence of Desulfovibrio sp. A2, a Highly Copper Resistant, Sulfate-Reducing Bacterium Isolated from Effluents of a Zinc Smelter at the Urals

    PubMed Central

    Mancini, Stefano; Abicht, Helge K.; Karnachuk, Olga V.; Solioz, Marc

    2011-01-01

    Desulfovibrio sp. A2 is an anaerobic Gram-negative sulfate-reducing bacterium with remarkable tolerance to copper. It was isolated from wastewater effluents of a zinc smelter at the Urals. Here, we report the 4.2-Mb draft genome sequence of Desulfovibrio sp. A2 and identify potential copper resistance mechanisms. PMID:22072648

  8. Draft Genome Sequence of the Sulfate-Reducing Bacterium Desulfotomaculum copahuensis Strain CINDEFI1 Isolated from the Geothermal Copahue System, Neuquén, Argentina.

    PubMed

    Willis Poratti, Graciana; Yaakop, Amira Suriaty; Chan, Chia Sing; Urbieta, M Sofía; Chan, Kok-Gan; Ee, Robson; Tan-Guan-Sheng, Adrian; Goh, Kian Mau; Donati, Edgardo R

    2016-01-01

    Desulfotomaculum copahuensis strain CINDEFI1 is a novel spore-forming sulfate-reducing bacterium isolated from the Copahue volcano area, Argentina. Here, we present its draft genome in which we found genes related with the anaerobic respiration of sulfur compounds similar to those present in the Copahue environment. PMID:27540078

  9. Draft Genome Sequence of the Sulfate-Reducing Bacterium Desulfotomaculum copahuensis Strain CINDEFI1 Isolated from the Geothermal Copahue System, Neuquén, Argentina

    PubMed Central

    Yaakop, Amira Suriaty; Chan, Chia Sing; Urbieta, M. Sofía; Ee, Robson; Tan-Guan-Sheng, Adrian; Donati, Edgardo R.

    2016-01-01

    Desulfotomaculum copahuensis strain CINDEFI1 is a novel spore-forming sulfate-reducing bacterium isolated from the Copahue volcano area, Argentina. Here, we present its draft genome in which we found genes related with the anaerobic respiration of sulfur compounds similar to those present in the Copahue environment. PMID:27540078

  10. Thermodesulfobacterium geofontis sp. nov., a hyperthermophilic, sulfate-reducing bacterium isolated from Obsidian Pool, Yellowstone National Park.

    PubMed

    Hamilton-Brehm, Scott D; Gibson, Robert A; Green, Stefan J; Hopmans, Ellen C; Schouten, Stefan; van der Meer, Marcel T J; Shields, John P; Damsté, Jaap S S; Elkins, James G

    2013-03-01

    A novel sulfate-reducing bacterium designated OPF15(T) was isolated from Obsidian Pool, Yellowstone National Park, Wyoming. The phylogeny of 16S rRNA and functional genes (dsrAB) placed the organism within the family Thermodesulfobacteriaceae. The organism displayed hyperthermophilic temperature requirements for growth with a range of 70-90 °C and an optimum of 83 °C. Optimal pH was around 6.5-7.0 and the organism required the presence of H2 or formate as an electron donor and CO2 as a carbon source. Electron acceptors supporting growth included sulfate, thiosulfate, and elemental sulfur. Lactate, acetate, pyruvate, benzoate, oleic acid, and ethanol did not serve as electron donors. Membrane lipid analysis revealed diacyl glycerols and acyl/ether glycerols which ranged from C14:0 to C20:0. Alkyl chains present in acyl/ether and diether glycerol lipids ranged from C16:0 to C18:0. Straight, iso- and anteiso-configurations were found for all lipid types. The presence of OPF15(T) was also shown to increase cellulose consumption during co-cultivation with Caldicellulosiruptor obsidiansis, a fermentative, cellulolytic extreme thermophile isolated from the same environment. On the basis of phylogenetic, phenotypic, and structural analyses, Thermodesulfobacterium geofontis sp. nov. is proposed as a new species with OPF15(T) representing the type strain. PMID:23345010

  11. Thermodesulfobacterium geofontis sp. nov., a hyperthermophilic, sulfate-reducing bacterium isolated from Obsidian Pool, Yellowstone National Park

    SciTech Connect

    Hamilton-Brehm, Scott D.; Gibson, Robert A.; Green, Stefan J.; Hopmans, Ellen C.; Schouten, Stefan; van der Meer, Marcel T. J.; Shields, John P.; Damsté, Jaap S. S.; Elkins, James G.

    2013-01-24

    A novel sulfate-reducing bacterium designated OPF15T was isolated from Obsidian Pool, Yellowstone National Park, Wyoming. The phylogeny of 16S rRNA and functional genes (dsrAB) placed the organism within the family Thermodesulfobacteriaceae. The organism displayed hyperthermophilic temperature requirements for growth with a range of 70 90 C and an optimum of 83 C. Optimal pH was around 6.5 7.0 and the organism required the presence of H2 or formate as an electron donor and CO2 as a carbon source. Electron acceptors supporting growth included sulfate, thiosulfate, and elemental sulfur. Lactate, acetate, pyruvate, benzoate, oleic acid, and ethanol did not serve as electron donors. Membrane lipid analysis revealed diacyl glycerols and acyl/ether glycerols which ranged from C14:0 to C20:0. Alkyl chains present in acyl/ether and diether glycerol lipids ranged from C16:0 to C18:0. Straight, iso- and anteiso-configurations were found for all lipid types. The presence of OPF15T was also shown to increase cellulose consumption during co-cultivation with Caldicellulosiruptor obsidiansis, a fermentative, cellulolytic extreme thermophile isolated from the same environment. On the basis of phylogenetic, phenotypic, and structural analyses, Thermodesulfobacterium geofontis sp. nov. is proposed as a new species with OPF15T representing the type strain.

  12. Desulfonatronum paiuteum sp. nov.: A New Alkaliphilic, Sulfate-Reducing Bacterium, Isolated from Soda Mono Lake, California

    NASA Technical Reports Server (NTRS)

    Pikuta, Elena; Hoover, Richard B.; Marsic, Damien; Whitman, William; Cleland, David; Krader, Paul; Six, N. Frank (Technical Monitor)

    2002-01-01

    A novel alkaliphilic, sulfate reducing bacterium strain MLF1(sup T) was isolated from sediments of soda Mono Lake, California. Gram-negative vibrion cells, motile by singular polar flagellum, with sizes 0.5 - 0.6x 1.2 - 2.0 micron occurred singly, in pairs or short spirilla. Growth was observed over the temperature range of +15 C to +48 C (optimum +37 C), NaCl concentration range is greater than 1 - 7 %, wt/vol (optimum 3 %, wt/vol) and pH range 7.8 - 10.5 (optimum pH 9.0 - 9.4). The novel isolate is strictly alkaliphilic, requires high carbonate concentration in medium, obligately anaerobic and catalase negative. As electron donors strain MLF1(sup T) uses hydrogen, formate, ethanol. Sulfate, sulfite, and thiosulfate (but not sulfur or nitrate) can be used as electron acceptors. The sole end product of growth on formate was H2S. Strain MLF1(sup T) is resistant to kanamycin and gentamycin, but sensitive to chloramphenicol and tetracycline. Na2MoO4 inhibits growth of strain MLF1(sup T). The sum of G+C in DNA is 63.1 mol% (by HPLC method). On the basis of physiological and molecular properties, the isolate was considered as novel species of genus Desulfonatronum; and the name Desulfonatronum paiuteum sp. nov., is proposed (type strain MLF1(sup T) = ATCC BAA-395(sup T) = DSMZ 14708(sup T).

  13. Halotolerant and Resistant to High pH Hydrogenase from Haloalkaliphilic Sulfate-Reducing Bacterium Desulfonatronum thiodismutans

    NASA Technical Reports Server (NTRS)

    Detkova, Ekaterina N.; Pikuta, Elena V.; Hoover, Richard B.

    2004-01-01

    Hydrogenase is the key enzyme of energetic metabolism in cells, it catalyzing the converse reaction of hydrogen oxidation and responsible for consumption and excretion of hydrogen in bacteria. Hydrogenases are proteins containing either Nickel and Iron, or the only Iron in theirs active center. Hydrogenases have been found in many microorganisms, such as Methanogenic, acetogenic, nitrogen-fixing, photosynthetic and sulfate-reducing bacteria that could utilize the hydrogen as energy source or use it as electron sink. Hydrogenases are subject for wide physiological, biochemical, physicochemical and genetic studies due to theirs abilities produce the molecular hydrogen as alternative source of pure energy. Notwithstanding on enough large quantity of works that deal with intracellular and extrasellular enzymes of halophilic bacteria, the data about hydrogenases and theirs functions of salts practically are absent. The study of hydrogenase in cell-free extracts of extremely halophilic eubacterium Acetohalobium mabaticum showed dramatic increasing activity of the enzyme at high concentrations of NaCl and KCI (close to saturated solution). Here we present the data of free-cells extracted hydrogenase from new haloalkaliphilic sulfate-reducing bacterium Desulfonatronum thiodismutans, which grow on highly miniralized carbonate-bicarbonate medium in salinity range 1 to 7 % and at pH 7.8 - 10.5. Studied enzyme was active in Concentration range from 0 to 4.3 M NaCl with optimum at 1.0 M NaCl. At 1.0 M NaCl the enzyme activity was increased on 20 %, but with changing concentration from 2.1 M to 3.4 M the activity decreased and was kept on constant level. NaHCO3 inhibited hydrogenase activity on more then 30 %. The maximum of enzyme activity was observed at pH 9.5 with limits 7.5 and 11.5 that practically equal to pH optimum of bacterial growth. Therefore the hydrogenase of Desulfanatronum thiodismutans is tolerant to high concentrations of sodium salts and it also resistant to

  14. Adaptation of Psychrophilic and Psychrotrophic Sulfate-Reducing Bacteria to Permanently Cold Marine Environments

    PubMed Central

    Isaksen, M. F.; Jorgensen, B. B.

    1996-01-01

    The potential for sulfate reduction at low temperatures was examined in two different cold marine sediments, Mariager Fjord (Denmark), which is permanently cold (3 to 6(deg)C) but surrounded by seasonally warmer environments, and the Weddell Sea (Antarctica), which is permanently below 0(deg)C. The rates of sulfate reduction were measured by the (sup35)SO(inf4)(sup2-) tracer technique at different experimental temperatures in sediment slurries. In sediment slurries from Mariager Fjord, sulfate reduction showed a mesophilic temperature response which was comparable to that of other temperate environments. In sediment slurries from Antarctica, the metabolic activity of psychrotrophic bacteria was observed with a respiration optimum at 18 to 19(deg)C during short-term incubations. However, over a 1-week incubation, the highest respiration rate was observed at 12.5(deg)C. Growth of the bacterial population at the optimal growth temperature could be an explanation for the low temperature optimum of the measured sulfate reduction. The potential for sulfate reduction was highest at temperatures well above the in situ temperature in all experiments. The results from sediment incubations were compared with those obtained from pure cultures of sulfate-reducing bacteria by using the psychrotrophic strain ltk10 and the mesophilic strain ak30. The psychrotrophic strain reduced sulfate optimally at 28(deg)C in short-term incubations, even though it could not grow at temperatures above 24(deg)C. Furthermore, this strain showed its highest growth yield between 0 and 12(deg)C. In contrast, the mesophilic strain ak30 respired and grew optimally and showed its highest growth yield at 30 to 35(deg)C. PMID:16535228

  15. Changing Microspatial Patterns of Sulfate-Reducing Microorganisms (SRM) during Cycling of Marine Stromatolite Mats

    PubMed Central

    Petrisor, Alexandru I.; Szyjka, Sandra; Kawaguchi, Tomohiro; Visscher, Pieter T.; Norman, Robert Sean; Decho, Alan W.

    2014-01-01

    Microspatial arrangements of sulfate-reducing microorganisms (SRM) in surface microbial mats (~1.5 mm) forming open marine stromatolites were investigated. Previous research revealed three different mat types associated with these stromatolites, each with a unique petrographic signature. Here we focused on comparing “non-lithifying” (Type-1) and “lithifying” (Type-2) mats. Our results revealed three major trends: (1) Molecular typing using the dsrA probe revealed a shift in the SRM community composition between Type-1 and Type-2 mats. Fluorescence in-situ hybridization (FISH) coupled to confocal scanning-laser microscopy (CSLM)-based image analyses, and 35SO4 2−-silver foil patterns showed that SRM were present in surfaces of both mat types, but in significantly (p < 0.05) higher abundances in Type-2 mats. Over 85% of SRM cells in the top 0.5 mm of Type-2 mats were contained in a dense 130 μm thick horizontal layer comprised of clusters of varying sizes; (2) Microspatial mapping revealed that locations of SRM and CaCO3 precipitation were significantly correlated (p < 0.05); (3) Extracts from Type-2 mats contained acylhomoserine-lactones (C4-, C6-, oxo-C6 C7-, C8-, C10-, C12-, C14-AHLs) involved in cell-cell communication. Similar AHLs were produced by SRM mat-isolates. These trends suggest that development of a microspatially-organized SRM community is closely-associated with the hallmark transition of stromatolite surface mats from a non-lithifying to a lithifying state. PMID:24413754

  16. The sulfate-reducing bacterium Desulfovibrio desulfuricans ND132 as a model for understanding bacterial mercury methylation

    SciTech Connect

    Gilmour, C C; Elias, Dwayne A; Kucken, A M; Brown, Steven D; Palumbo, Anthony Vito; Wall, Judy D.

    2010-01-01

    We propose the use of Desulfovibrio sp. ND132 as a model species for understanding the genetics and biochemistry of microbial Hg methylation. ND132 is a dissimilatory sulfate-reducing bacterium (DSRB) that exhibits exceptionally high rates of Hg methylation in culture, but is otherwise a characteristically typical Desulfovibrio strain. The full genome sequence of ND132 will be available soon. ND132 is very similar to other DSRB that are sequenced but do not methylate Hg, allowing comparison for potential methylation genes. Here, we describe the physiological characteristics of the strain, examine its MeHg production capability, and place the strain within the phylogeny of the Desulfovibrionales using 16S rRNA. We also examine Hg toxicity and the inducibility of MeHg production amongst the DSRB by comparing ND132 to non-methylating DSRB. The optimal growth medium for Hg methylation is pyruvate/fumarate, which supports strong respiratory growth without sulfide production. At moderate Hg concentrations (10 ng/ml), and using TiNTA as a reductant, ND132 methylates about 30% of added HgCl2 during batch culture growth on 40 mM pyruvate/fumarate. Under constant culture conditions, MeHg production is an exponential function of Hg concentration, probably reflecting Hg partitioning between aqueous and solid phases. To help understand how Hg is taken up by this organism, we examined the influence of a variety of small thiol-bearing ligands, as well as select amino acids, on methylation by D. desulfuricans ND132. All thiol bearing ligands tested affected methylation in similar ways, suggesting that Hg uptake by ND132 is not associated with uptake of a specific amino acid. To identify enzymes for the methylation activity, a genetic approach is being pursued. Conjugation from E. coli donors works well that allows the generation of a transposon library of random ND132 mutants. These mutants will be screened for affects on mercury methylation.

  17. The sulfate-reducing bacterium Desulfovibrio desulfuricans ND132 as a model for understanding bacterial mercury methylation

    SciTech Connect

    Gilmour, C C; Elias, Dwayne A; Kucken, A M; Brown, Steven D; Palumbo, Anthony Vito; Schadt, Christopher Warren; Wall, Judy D.

    2011-01-01

    We propose the use of Desulfovibrio desulfuricans ND132 as a model species for understanding the mechanism of microbial Hg methylation. Strain ND132 is an anaerobic dissimilatory sulfate-reducing bacterium (DSRB), isolated from estuarine mid-Chesapeake Bay sediments. It was chosen for study because of its exceptionally high rates of Hg methylation in culture and its metabolic similarity to the lost strain D. desulfuricans LS, the only organism for which methylation pathways have been partially defined. Strain ND132 is an incomplete oxidizer of short-chain fatty acids. It is capable of respiratory growth using fumarate as an electron acceptor, supporting growth without sulfide production. We used enriched stable Hg isotopes to show that ND132 simultaneously produces and degrades methylmercury (MeHg) during growth but does not produce elemental Hg. MeHg produced by cells is mainly excreted, and no MeHg is produced in spent medium. Mass balances for Hg and MeHg during the growth of cultures, including the distribution between filterable and particulate phases, illustrate how medium chemistry and growth phase dramatically affect Hg solubility and availability for methylation. The available information on Hg methylation among strains in the genus Desulfovibrio is summarized, and we present methylation rates for several previously untested species. About 50% of Desulfovibrio strains tested to date have the ability to produce MeHg. Importantly, the ability to produce MeHg is constitutive and does not confer Hg resistance. A 16S rRNA-based alignment of the genus Desulfovibrio allows the very preliminary assessment that there may be some evolutionary basis for the ability to produce MeHg within this genus.

  18. Draft Genome Sequence of Thermodesulfovibrio aggregans TGE-P1T, an Obligately Anaerobic, Thermophilic, Sulfate-Reducing Bacterium in the Phylum Nitrospirae

    PubMed Central

    Matsuura, Norihisa; Ohashi, Akiko; Tourlousse, Dieter M.

    2016-01-01

    We report a high-quality draft genome sequence of the type strain (TGE-P1T) of Thermodesulfovibrio aggregans, an obligately anaerobic, thermophilic, sulfate-reducing bacterium in the phylum Nitrospirae. The genome comprises 2.00 Mb in 16 contigs (3 scaffolds), has a G+C content of 34.5%, and contains 1,998 predicted protein-encoding genes. PMID:26966200

  19. Field and laboratory studies of methane oxidation in an anoxic marine sediment: Evidence for a methanogen-sulfate reducer consortium

    SciTech Connect

    Hoehler, T.M.; Alperin, M.J.; Albert, D.B.

    1994-12-01

    Field and laboratory studies of anoxic sediments from Cape Lookout Bight, North Carolina, suggest that anaerobic methane oxidation is mediated by a consortium of methanogenic and sulfate-reducing bacteria. A seasonal survey of methane oxidation and CO{sub 2} reduction rates indicates that methane production was confined to sulfate-depleted sediments at all times of year, while methane oxidation occurred in two modes. In the summer, methane oxidation was confined to sulfate-depleted sediments and occurred at rates lower than those of CO{sub 2} reduction. In the winter, net methane oxidation occurred in an interval at the base of the sulfate-containing zone. Sediment incubation experiments suggest both methanogens and sulfate reducers were responsible for the observed methane oxidation. In one incubation experiment both modes of oxidation were partially inhibited by 2-bromoethanesulfonic acid (a specific inhibitor of methanogens). This evidence, along with the apparent confinement of methane oxidation to sulfate-depleted sediments in the summer, indicates that methanogenic bacteria are involved in methane oxidation. In a second incubation experiment, net methane oxidation was induced by adding sulfate to homogenized methanogenic sediments, suggesting that sulfate reducers also a play a role in the process. We hypothesize that methanogens oxidize methane and produce hydrogen via a reversal of CO{sub 2} reduction. The hydrogen is efficiently removed and maintained at low concentrations by sulfate reducers. Pore water H{sub 2} concentrations in the sediment incubation experiments (while net methane oxidation was occurring) were low enough that methanogenic bacteria could derive sufficient energy for growth from the oxidation of methane. The methanogen-sulfate reducer consortium may also be a feasible mechanism for previously documented anaerobic methane oxidation in both freshwater and marine environments. 63 refs., 6 refs.

  20. Desulfosoma caldarium gen. nov., sp. nov., a thermophilic sulfate-reducing bacterium from a terrestrial hot spring.

    PubMed

    Baena, Sandra; Perdomo, Natalia; Carvajal, Catalina; Díaz, Carolina; Patel, Bharat K C

    2011-04-01

    A thermophilic, sulfate-reducing bacterium, designated strain USBA-053(T), was isolated from a terrestrial hot spring located at a height of 2500 m in the Colombian Andes (5° 45' 33.29″ N 73° 6' 49.89″ W), Colombia. Cells of strain USBA-053(T) were oval- to rod-shaped, Gram-negative and motile by means of a single polar flagellum. The strain grew autotrophically with H(2) as the electron donor and heterotrophically on formate, propionate, butyrate, valerate, isovalerate, lactate, pyruvate, ethanol, glycerol, serine and hexadecanoic acid in the presence of sulfate as the terminal electron acceptor. The main end products from lactate degradation, in the presence of sulfate, were acetate, CO(2) and H(2)S. Strain USBA-053(T) fermented pyruvate in the absence of sulfate and grew optimally at 57 °C (growth temperature ranged from 50 °C to 62 °C) and pH 6.8 (growth pH ranged from 5.7 to 7.7). The novel strain was slightly halophilic and grew in NaCl concentrations ranging from 5 to 30 g l(-1), with an optimum at 25 g l(-1) NaCl. Sulfate, thiosulfate and sulfite were used as electron acceptors, but not elemental sulfur, nitrate or nitrite. The G+C content of the genomic DNA was 56±1 mol%. 16S rRNA gene sequence analysis indicated that strain USBA-053(T) was a member of the class Deltaproteobacteria, with Desulfacinum hydrothermale MT-96(T) as the closest relative (93 % gene sequence similarity). On the basis of physiological characteristics and phylogenetic analysis, it is suggested that strain USBA-053(T) represents a new genus and novel species for which the name Desulfosoma caldarium gen. nov., sp. nov. is proposed. The type strain of the type species is USBA-053(T) ( = KCTC 5670(T) = DSM 22027(T)). PMID:20418410

  1. Direct analysis of sulfate reducing bacterial communities in gas hydrate-impacted marine sediments by PCR-DGGE.

    PubMed

    Bagwell, Christopher E; Formolo, Michael; Ye, Qi; Yeager, Chris M; Lyons, Timothy W; Zhang, Chuanlun L

    2009-09-01

    Molecular investigations of the sulfate reducing bacteria that target the dissimilatory sulfite-reductase subunit A gene (dsr A) are plagued by the nonspecific performance of conventional PCR primers. Here we describe the incorporation of the FailSafe PCR System to optimize environmental analysis of dsr A by PCR amplification and denaturing gradient gel electrophoresis. PCR-DGGE analysis of dsr A composition revealed that SRB diversity was greater and more variable throughout the vertical profile of a marine sediment core obtained from a gas hydrate site (GC234) in the Gulf of Mexico than in a sediment core collected from a nearby site devoid of gas hydrates (NBP). Depth profiled dsr B abundance corresponded with sulfate reduction rates at both sites, though measurements were higher at GC234. This study exemplifies the numerical and functional importance of sulfate reducing bacteria in deep-sea sedimentary environments, and incremental methodological advancements, as described herein, will continue to streamline the analysis of sulfate reducer communities in situ. PMID:19322839

  2. Draft Genome Sequence of Desulfitobacterium hafniense Strain DH, a Sulfate-Reducing Bacterium Isolated from Paddy Soils

    PubMed Central

    Zhang, Xi; Li, Guo-Xiang; Chen, Song-Can; Jia, Xiao-Yu; Wu, Kun; Cao, Chang-Li

    2016-01-01

    Desulfitobacterium hafniense strain DH is a sulfate-reducing species. Here, we report the draft genome sequence of strain DH, with a size of 5,368,588 bp, average G+C content of 47.48%, and 5,296 predicted protein-coding sequences. PMID:26868389

  3. The Effect of Temperature and Hydrogen Limited Growth on the Fractionation of Sulfur Isotopes by Thermodesulfatator indicus, a Deep-sea Hydrothermal Vent Sulfate-Reducing Bacterium

    NASA Astrophysics Data System (ADS)

    Hoek, J.; Reysenbach, A.; Habicht, K.; Canfield, D. E.

    2004-12-01

    Sulfate-reducing bacteria fractionate sulfur isotopes during dissimilatory sulfate reduction, producing sulfide depleted in 34S. Although isotope fractionation during sulfate reduction of pure cultures has been extensively studied, most of the research to date has focused on mesophilic sulfate reducers, particularly for the species Desulfovibrio desulfuricans. Results from these studies show that: 1) fractionations range from 3-46‰ with an average around 18‰ , 2) when organic electron donors are utilized, the extent of fractionation is dependent on the rate of sulfate reduction, with decreasing fractionations observed with higher specific rates, 3) fractionations are suppressed with low sulfate concentrations, and when hydrogen is used as the electron donor. High specific sulfate-reduction rates are encountered when sulfate-reducing bacteria metabolize at their optimal temperature and under non-limiting substrate conditions. Changes in both temperature and substrate availability could shift fractionations from those expressed under optimal growth conditions. Sulfate reducers may frequently experience substrate limitation and sub-optimal growth temperatures in the environment. Therefore it is important to understand how sulfate-reducing bacteria fractionate sulfur isotopes under conditions that more closely resemble the restrictions imposed by the environment. In this study the fractionation of sulfur isotopes by Thermodesulfatator indicus was explored during sulfate reduction under a wide range of temperatures and with both hydrogen-saturating and hydrogen-limited conditions. T. indicus is a thermophilic (temperature optimum = 70° C) chemolithotrophic sulfate-reducing bacterium, which was recently isolated from a deep-sea hydrothermal vent on the Central Indian Ridge. This bacterium represents the type species of a new genus and to date is the most deeply branching sulfate-reducing bacterium known. T. indicus was grown in carbonate-buffered salt-water medium

  4. Genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812T)

    SciTech Connect

    Anderson, Iain; Saunders, Elizabeth H; Lapidus, Alla L.; Nolan, Matt; Lucas, Susan; Tice, Hope; Glavina Del Rio, Tijana; Cheng, Jan-Fang; Han, Cliff; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Mavromatis, K; Pagani, Ioanna; Ivanova, N; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Jeffries, Cynthia; Chang, Yun-Juan; Brambilla, Evelyne-Marie; Rohde, Manfred; Spring, Stefan; Goker, Markus; Detter, J. Chris; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2012-01-01

    Thermodesulfatator indicus Moussard et al. 2004 is a member of the genomically so far poorly characterized family Thermodesulfobacteriaceae in the phylum Thermodesulfobacteria. Members of this phylum are of interest because they represent a distinct, deep-branching, Gram-negative lineage. T. indicus is an anaerobic, thermophilic, chemolithoautotrophic sulfate reducer isolated from a deep-sea hydrothermal vent. Here we describe the features of this organism, together with the complete genome sequence, and annotation. The 2,322,224 bp long chromosome with its 2,233 protein-coding and 58 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  5. Sulfate-reducing bacteria inhabiting natural corrosion deposits from marine steel structures.

    PubMed

    Païssé, Sandrine; Ghiglione, Jean-François; Marty, Florence; Abbas, Ben; Gueuné, Hervé; Amaya, José Maria Sanchez; Muyzer, Gerard; Quillet, Laurent

    2013-08-01

    In the present study, investigations were conducted on natural corrosion deposits to better understand the role of sulfate-reducing bacteria (SRB) in the accelerated corrosion process of carbon steel sheet piles in port environments. We describe the abundance and diversity of total and metabolically active SRB within five natural corrosion deposits located within tidal or low water zone and showing either normal or accelerated corrosion. By using molecular techniques, such as quantitative real-time polymerase chain reaction, denaturing gel gradient electrophoresis, and sequence cloning based on 16S rRNA, dsrB genes, and their transcripts, we demonstrated a clear distinction between SRB population structure inhabiting normal or accelerated low-water corrosion deposits. Although SRB were present in both normal and accelerated low-water corrosion deposits, they dominated and were exclusively active in the inner and intermediate layers of accelerated corrosion deposits. We also highlighted that some of these SRB populations are specific to the accelerated low-water corrosion deposit environment in which they probably play a dominant role in the sulfured corrosion product enrichment. PMID:23086338

  6. Crystallization and preliminary X-ray analysis of a class II release factor RF3 from a sulfate-reducing bacterium

    SciTech Connect

    Kihira, Kiyohito; Numata, Shuko; Kitamura, Masaya; Kondo, Jun; Terawaki, Shinichi; Shomura, Yasuhito; Komori, Hirofumi; Shibata, Naoki; Higuchi, Yoshiki

    2008-07-01

    Class II release factor 3 (RF3) from the sulfate-reducing bacterium D. vulgaris Miyazaki F has been overexpressed, purified and crystallized in complex with GDP. Class II release factor 3 (RF3) from the sulfate-reducing bacterium Desulfovibrio vulgaris Miyazaki F, which promotes rapid dissociation of a class I release factor, has been overexpressed, purified and crystallized in complex with GDP at 293 K using the sitting-drop vapour-diffusion method. A data set was collected to 1.8 Å resolution from a single crystal at 100 K using synchrotron radiation. The crystal belongs to space group P1, with unit-cell parameters a = 47.39, b = 82.80, c = 148.29 Å, α = 104.21, β = 89.78, γ = 89.63°. The asymmetric unit contains four molecules of the RF3–GDP complex. The Matthews coefficient was calculated to be 2.3 Å{sup 3} Da{sup −1} and the solvent content was estimated to be 46.6%.

  7. Diverse sulfate-reducing bacteria of the Desulfosarcina/Desulfococcus clade are the key alkane degraders at marine seeps

    PubMed Central

    Kleindienst, Sara; Herbst, Florian-Alexander; Stagars, Marion; von Netzer, Frederick; von Bergen, Martin; Seifert, Jana; Peplies, Jörg; Amann, Rudolf; Musat, Florin; Lueders, Tillmann; Knittel, Katrin

    2014-01-01

    Biogeochemical and microbiological data indicate that the anaerobic oxidation of non-methane hydrocarbons by sulfate-reducing bacteria (SRB) has an important role in carbon and sulfur cycling at marine seeps. Yet, little is known about the bacterial hydrocarbon degraders active in situ. Here, we provide the link between previous biogeochemical measurements and the cultivation of degraders by direct identification of SRB responsible for butane and dodecane degradation in complex on-site microbiota. Two contrasting seep sediments from Mediterranean Amon mud volcano and Guaymas Basin (Gulf of California) were incubated with 13C-labeled butane or dodecane under sulfate-reducing conditions and analyzed via complementary stable isotope probing (SIP) techniques. Using DNA- and rRNA-SIP, we identified four specialized clades of alkane oxidizers within Desulfobacteraceae to be distinctively active in oxidation of short- and long-chain alkanes. All clades belong to the Desulfosarcina/Desulfococcus (DSS) clade, substantiating the crucial role of these bacteria in anaerobic hydrocarbon degradation at marine seeps. The identification of key enzymes of anaerobic alkane degradation, subsequent β-oxidation and the reverse Wood–Ljungdahl pathway for complete substrate oxidation by protein-SIP further corroborated the importance of the DSS clade and indicated that biochemical pathways, analog to those discovered in the laboratory, are of great relevance for natural settings. The high diversity within identified subclades together with their capability to initiate alkane degradation and growth within days to weeks after substrate amendment suggest an overlooked potential of marine benthic microbiota to react to natural changes in seepage, as well as to massive hydrocarbon input, for example, as encountered during anthropogenic oil spills. PMID:24722631

  8. Diverse sulfate-reducing bacteria of the Desulfosarcina/Desulfococcus clade are the key alkane degraders at marine seeps.

    PubMed

    Kleindienst, Sara; Herbst, Florian-Alexander; Stagars, Marion; von Netzer, Frederick; von Bergen, Martin; Seifert, Jana; Peplies, Jörg; Amann, Rudolf; Musat, Florin; Lueders, Tillmann; Knittel, Katrin

    2014-10-01

    Biogeochemical and microbiological data indicate that the anaerobic oxidation of non-methane hydrocarbons by sulfate-reducing bacteria (SRB) has an important role in carbon and sulfur cycling at marine seeps. Yet, little is known about the bacterial hydrocarbon degraders active in situ. Here, we provide the link between previous biogeochemical measurements and the cultivation of degraders by direct identification of SRB responsible for butane and dodecane degradation in complex on-site microbiota. Two contrasting seep sediments from Mediterranean Amon mud volcano and Guaymas Basin (Gulf of California) were incubated with (13)C-labeled butane or dodecane under sulfate-reducing conditions and analyzed via complementary stable isotope probing (SIP) techniques. Using DNA- and rRNA-SIP, we identified four specialized clades of alkane oxidizers within Desulfobacteraceae to be distinctively active in oxidation of short- and long-chain alkanes. All clades belong to the Desulfosarcina/Desulfococcus (DSS) clade, substantiating the crucial role of these bacteria in anaerobic hydrocarbon degradation at marine seeps. The identification of key enzymes of anaerobic alkane degradation, subsequent β-oxidation and the reverse Wood-Ljungdahl pathway for complete substrate oxidation by protein-SIP further corroborated the importance of the DSS clade and indicated that biochemical pathways, analog to those discovered in the laboratory, are of great relevance for natural settings. The high diversity within identified subclades together with their capability to initiate alkane degradation and growth within days to weeks after substrate amendment suggest an overlooked potential of marine benthic microbiota to react to natural changes in seepage, as well as to massive hydrocarbon input, for example, as encountered during anthropogenic oil spills. PMID:24722631

  9. Biomolecular and Isotopic Signatures Related to Cr(VI) Reduction by a Sulfate-Reducing Bacterium Isolated from the Hanford 100H Aquifer

    NASA Astrophysics Data System (ADS)

    Han, R.; Qin, L.; Geller, J. T.; Chakraborty, R.; Christensen, J. N.; Beller, H. R.

    2011-12-01

    Chromium contamination of groundwater is widespread within the Dept. of Energy (DOE) complex. At DOE's Hanford 100H area, we have conducted Cr bioremediation (in situ reductive immobilization) studies involving injection of a lactate-containing polymer, and have observed sequential use of the dissolved electron acceptors present in groundwater (namely, oxygen, nitrate, and sulfate). Sulfate-reducing bacteria are of particular interest for chromate reduction because they can reduce Cr(VI) enzymatically (e.g., using cytochrome c3 or thioredoxin reductase) and abiotically with hydrogen sulfide, the end product of their respiration. In this poster, we use studies of a sulfate-reducing bacterium isolated from the Hanford 100H aquifer, Desulfovibrio vulgaris strain RCH1, to explore (a) isotopic signatures that might allow us to distinguish between enzymatic and sulfide-mediated Cr(VI) reduction and (b) biomolecular signatures (gene or transcript copy number of diagnostic genes) that might be used as proxies of in situ metabolic rates. In order to differentiate between the mechanisms of Cr reduction by sulfate reducers, we analyzed the isotopic fractionation during Cr(VI) reduction by strain RCH1. Cell suspension studies of strain RCH1 demonstrated that Cr(VI) reduction could occur in the presence of lactate (electron donor) alone or with both lactate and sulfate. Cr(VI) reduction in the presence of lactate and sulfate was 25-30% more rapid than enzymatic Cr reduction when only lactate was added, suggesting that biogenic hydrogen sulfide increases the specific rate of Cr(VI) reduction beyond purely enzymatic activity. Cr isotopic measurements showed different fractionation behavior for the lactate-only and lactate+sulfate systems, with fractionation (epsilon) values of 2.3 and 1.66 per mil, respectively. In order to determine whether gene or transcript copy number for diagnostic sulfate and chromate reduction genes could serve as proxies to estimate in situ metabolic

  10. Microbial reduction of structural iron in interstratified illite-smectite minerals by a sulfate-reducing bacterium

    USGS Publications Warehouse

    Liu, D.; Dong, H.; Bishop, M.E.; Zhang, Jiahua; Wang, Hongfang; Xie, S.; Wang, Shaoming; Huang, L.; Eberl, D.D.

    2012-01-01

    Clay minerals are ubiquitous in soils, sediments, and sedimentary rocks and could coexist with sulfate-reducing bacteria (SRB) in anoxic environments, however, the interactions of clay minerals and SRB are not well understood. The objective of this study was to understand the reduction rate and capacity of structural Fe(III) in dioctahedral clay minerals by a mesophilic SRB, Desulfovibrio vulgaris and the potential role in catalyzing smectite illitization. Bioreduction experiments were performed in batch systems, where four different clay minerals (nontronite NAu-2, mixed-layer illite-smectite RAr-1 and ISCz-1, and illite IMt-1) were exposed to D. vulgaris in a non-growth medium with and without anthraquinone-2,6-disulfonate (AQDS) and sulfate. Our results demonstrated that D. vulgaris was able to reduce structural Fe(III) in these clay minerals, and AQDS enhanced the reduction rate and extent. In the presence of AQDS, sulfate had little effect on Fe(III) bioreduction. In the absence of AQDS, sulfate increased the reduction rate and capacity, suggesting that sulfide produced during sulfate reduction reacted with the phyllosilicate Fe(III). The extent of bioreduction of structural Fe(III) in the clay minerals was positively correlated with the percentage of smectite and mineral surface area of these minerals. X-ray diffraction, and scanning and transmission electron microscopy results confirmed formation of illite after bioreduction. These data collectively showed that D. vulgaris could promote smectite illitization through reduction of structural Fe(III) in clay minerals. ?? 2011 Blackwell Publishing Ltd.

  11. Microbial reduction of structural iron in interstratified illite-smectite minerals by a sulfate-reducing bacterium.

    PubMed

    Liu, D; Dong, H; Bishop, M E; Zhang, J; Wang, H; Xie, S; Wang, S; Huang, L; Eberl, D D

    2012-03-01

    Clay minerals are ubiquitous in soils, sediments, and sedimentary rocks and could coexist with sulfate-reducing bacteria (SRB) in anoxic environments, however, the interactions of clay minerals and SRB are not well understood. The objective of this study was to understand the reduction rate and capacity of structural Fe(III) in dioctahedral clay minerals by a mesophilic SRB, Desulfovibrio vulgaris and the potential role in catalyzing smectite illitization. Bioreduction experiments were performed in batch systems, where four different clay minerals (nontronite NAu-2, mixed-layer illite-smectite RAr-1 and ISCz-1, and illite IMt-1) were exposed to D. vulgaris in a non-growth medium with and without anthraquinone-2,6-disulfonate (AQDS) and sulfate. Our results demonstrated that D. vulgaris was able to reduce structural Fe(III) in these clay minerals, and AQDS enhanced the reduction rate and extent. In the presence of AQDS, sulfate had little effect on Fe(III) bioreduction. In the absence of AQDS, sulfate increased the reduction rate and capacity, suggesting that sulfide produced during sulfate reduction reacted with the phyllosilicate Fe(III). The extent of bioreduction of structural Fe(III) in the clay minerals was positively correlated with the percentage of smectite and mineral surface area of these minerals. X-ray diffraction, and scanning and transmission electron microscopy results confirmed formation of illite after bioreduction. These data collectively showed that D. vulgaris could promote smectite illitization through reduction of structural Fe(III) in clay minerals. PMID:22074236

  12. Anaerobic degradation of propane and butane by sulfate-reducing bacteria enriched from marine hydrocarbon cold seeps

    PubMed Central

    Jaekel, Ulrike; Musat, Niculina; Adam, Birgit; Kuypers, Marcel; Grundmann, Olav; Musat, Florin

    2013-01-01

    The short-chain, non-methane hydrocarbons propane and butane can contribute significantly to the carbon and sulfur cycles in marine environments affected by oil or natural gas seepage. In the present study, we enriched and identified novel propane and butane-degrading sulfate reducers from marine oil and gas cold seeps in the Gulf of Mexico and Hydrate Ridge. The enrichment cultures obtained were able to degrade simultaneously propane and butane, but not other gaseous alkanes. They were cold-adapted, showing highest sulfate-reduction rates between 16 and 20 °C. Analysis of 16S rRNA gene libraries, followed by whole-cell hybridizations with sequence-specific oligonucleotide probes showed that each enrichment culture was dominated by a unique phylotype affiliated with the Desulfosarcina-Desulfococcus cluster within the Deltaproteobacteria. These phylotypes formed a distinct phylogenetic cluster of propane and butane degraders, including sequences from environments associated with hydrocarbon seeps. Incubations with 13C-labeled substrates, hybridizations with sequence-specific probes and nanoSIMS analyses showed that cells of the dominant phylotypes were the first to become enriched in 13C, demonstrating that they were directly involved in hydrocarbon degradation. Furthermore, using the nanoSIMS data, carbon assimilation rates were calculated for the dominant cells in each enrichment culture. PMID:23254512

  13. Isolation and characterization of a bacteriophage lytic for Desulfovibrio salexigens, a salt-requiring, sulfate-reducing bacterium

    SciTech Connect

    Kamimura, Kazuo; Araki, Michio )

    1989-03-01

    A bacteriophage that lysed Desulfovibrio salexigens cells was isolated from marine sediments and preliminarily characterized by electron microscopy and electrophoretic analysis of structural proteins and genomic nucleic acid. The bacteriophage had an icosahedral head and a long flexible tail, and the buoyant density of the bacteriophage particles was 1.468 g/ml in cesium chloride. The particles consisted of a double-stranded DNA molecule about 33 kilobase pairs long and at least 11 structural proteins.

  14. Genome analysis of Desulfotomaculum gibsoniae strain GrollT a highly versatile Gram-positive sulfate-reducing bacterium

    PubMed Central

    Kuever, Jan; Visser, Michael; Loeffler, Claudia; Boll, Matthias; Worm, Petra; Sousa, Diana Z.; Plugge, Caroline M.; Schaap, Peter J.; Muyzer, Gerard; Pereira, Ines A.C.; Parshina, Sofiya N.; Goodwin, Lynne A.; Kyrpides, Nikos C.; Detter, Janine; Woyke, Tanja; Chain, Patrick; Davenport, Karen W.; Rohde, Manfred; Spring, Stefan; Klenk, Hans-Peter; Stams, Alfons J.M.

    2014-01-01

    Desulfotomaculum gibsoniae is a mesophilic member of the polyphyletic spore-forming genus Desulfotomaculum within the family Peptococcaceae. This bacterium was isolated from a freshwater ditch and is of interest because it can grow with a large variety of organic substrates, in particular several aromatic compounds, short-chain and medium-chain fatty acids, which are degraded completely to carbon dioxide coupled to the reduction of sulfate. It can grow autotrophically with H2 + CO2 and sulfate and slowly acetogenically with H2 + CO2, formate or methoxylated aromatic compounds in the absence of sulfate. It does not require any vitamins for growth. Here, we describe the features of D. gibsoniae strain GrollT together with the genome sequence and annotation. The chromosome has 4,855,529 bp organized in one circular contig and is the largest genome of all sequenced Desulfotomaculum spp. to date. A total of 4,666 candidate protein-encoding genes and 96 RNA genes were identified. Genes of the acetyl-CoA pathway, possibly involved in heterotrophic growth and in CO2 fixation during autotrophic growth, are present. The genome contains a large set of genes for the anaerobic transformation and degradation of aromatic compounds, which are lacking in the other sequenced Desulfotomaculum genomes. PMID:25197466

  15. Desulfocarbo indianensis gen. nov., sp. nov., a benzoate-oxidizing, sulfate-reducing bacterium isolated from water extracted from a coal bed.

    PubMed

    An, Thuy T; Picardal, Flynn W

    2014-08-01

    A novel, strictly anaerobic, sulfate-reducing bacterium, designated strain SCBM(T), was isolated from water extracted from a coal bed in Indiana, USA. The isolate was characterized by a polyphasic taxonomic approach that included phenotypic and genotypic characterizations. Cells of strain SCBM(T) were vibrio-shaped, polarly flagellated, Gram-negative, motile, oxidase-negative and weakly catalase-positive. Growth of strain SCBM(T) was observed at NaCl concentrations ranging from 0 to 300 mM. However, no growth was observed when 1 M or more NaCl was present. Growth was observed at 16-37 °C, with optimal growth at 30 °C. The optimum pH for growth was 7, although growth was observed from pH 6.5 to 8. The doubling time under optimal growth conditions (30 °C, pH 7, 2.5 mM benzoate, 14 mM sulfate) was 2.7 days. Bicarbonate, HEPES, PIPES and MES were effective buffers for growth of strain SCBM(T), but citrate inhibited growth. When sulfate was provided as the electron acceptor, strain SCBM(T) grew autotrophically with hydrogen as the electron donor and heterotrophically on benzoate, formate, acetate, pyruvate, butyrate, fumarate, succinate and palmitate. None of the substrates tested supported fermentative growth. Thiosulfate and sulfate were used as electron acceptors coupled to benzoate oxidation, but sulfite, elemental sulfur, DMSO, anthraquinone 2,6-disulfonate, nitrate, nitrite, ferric citrate, hydrous iron oxide and oxygen were not. The G+C content of genomic DNA was 62.5 mol%. The major cellular fatty acids were anteiso-C(15 : 0) and C(18 : 1)ω7c. Phylogenetic analysis based on 16S rRNA gene sequencing placed strain SCBM(T) into a distinct lineage within the class Deltaproteobacteria. The closest, cultivated phylogenetic relative of strain SCBM(T) was Desulfarculus baarsii DSM 2075(T), with only 91.7% 16S rRNA gene sequence identity. On the basis of phenotypic and genotypic analyses, strain SCBM(T) represents a novel genus and species of sulfate-reducing

  16. PHYLOGENETIC TREE OF 16S RIBOSOMAL RNA SEQUENCES FROM SULFATE-REDUCING BACTERIA IN A SANDY MARINE ENVIRONMENT

    EPA Science Inventory

    Phylogenetic divergence among sulfate-reducing bacteria in an estuarine sediment sample was investigated by PCR amplification and comparison of partial 16S rDNA sequences. wenty unique 16S RDNA sequences were found, 12 from delta subclass bacteria based on overall sequence simila...

  17. Characterization of the cytochrome system of a nitrogen-fixing strain of a sulfate-reducing bacterium: Desulfovibrio desulfuricans strain Berre-Eau.

    PubMed

    Moura, I; Fauque, G; LeGall, J; Xavier, A V; Moura, J J

    1987-02-01

    Two c-type cytochromes were purified and characterized by electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopic techniques, from the sulfate-reducer nitrogen-fixing organism, Desulfovibrio desulfuricans strain Berre-Eau (NCIB 8387). The purification procedures included several chromatographic steps on alumina, carboxymethylcellulose and gel filtration. A tetrahaem and a monohaem cytochrome were identified. The multihaem cytochrome has visible, EPR and NMR spectra with general properties similar to other low-potential bis-histidinyl axially bound haem proteins, belonging to the class of tetrahaem cytochrome c3 isolated from other Desulfovibrio species. The monohaem cytochrome c553 is ascorbate-reducible and its EPR and NMR data are characteristic of a cytochrome with methionine-histidine ligation. Their properties are compared with other homologous proteins isolated from sulfate-reducing bacteria. PMID:3030740

  18. Apparent Minimum Free Energy Requirements for Methanogenic Archaea and Sulfate-Reducing Bacteria in an Anoxic Marine Sediment

    NASA Technical Reports Server (NTRS)

    Hoehler, Tori M.; Alperin, Marc J.; Albert, Daniel B.; Martens, Christopher S.; DeVincenzi, Don (Technical Monitor)

    2000-01-01

    Among the most fundamental constraints governing the distribution of microorganisms in the environment is the availability of chemical energy at biologically useful levels. To assess the minimum free energy yield that can support microbial metabolism in situ, we examined the thermodynamics of H2-consuming processes in anoxic sediments from Cape Lookout Bight, NC, USA. Depth distributions of H2 partial pressure, along with a suite of relevant concentration data, were determined in sediment cores collected in November (at 14.5 C) and August (at 27 C) and used to calculate free energy yields for methanogenesis and sulfate reduction. At both times of year, and for both processes, free energy yields gradually decreased (became less negative) with depth before reaching an apparent asymptote. Sulfate reducing bacteria exhibited an asymptote of -19.1 +/- 1.7 kj(mol SO4(2-)(sup -1) while methanogenic archaea were apparently supported by energy yields as small as -10.6 +/- 0.7 kj(mol CH4)(sup -1).

  19. Impacts of human activities on distribution of sulfate-reducing prokaryotes and antibiotic resistance genes in marine coastal sediments of Hong Kong.

    PubMed

    Guo, Feng; Li, Bing; Yang, Ying; Deng, Yu; Qiu, Jian-Wen; Li, Xiangdong; Leung, Kenneth My; Zhang, Tong

    2016-09-01

    Sulfate-reducing prokaryotes (SRPs) and antibiotic resistance genes (ARGs) in sediments could be biomarkers for evaluating the environmental impacts of human activities, although factors governing their distribution are not clear yet. By using metagenomic approach, this study investigated the distributions of SRPs and ARGs in marine sediments collected from 12 different coastal locations of Hong Kong, which exhibited different pollution levels and were classified into two groups based on sediment parameters. Our results showed that relative abundances of major SRP genera to total prokaryotes were consistently lower in the more seriously polluted sediments (P-value < 0.05 in 13 of 20 genera), indicating that the relative abundance of SRPs is a negatively correlated biomarker for evaluating human impacts. Moreover, a unimodel distribution pattern for SRPs along with the pollution gradient was observed. Although total ARGs were enriched in sediments from the polluted sites, distribution of single major ARG types could be explained neither by individual sediment parameters nor by corresponding concentration of antibiotics. It supports the hypothesis that the persistence of ARGs in sediments may not need the selection of antibiotics. In summary, our study provided important hints of the niche differentiation of SRPs and behavior of ARGs in marine coastal sediment. PMID:27297722

  20. Extracellular Electron Transfer Is a Bottleneck in the Microbiologically Influenced Corrosion of C1018 Carbon Steel by the Biofilm of Sulfate-Reducing Bacterium Desulfovibrio vulgaris

    PubMed Central

    Li, Yingchao; Feng, Hao; Liu, Zhiyong; Li, Xiaogang; Gu, Tingyue; Yang, Ke

    2015-01-01

    Carbon steels are widely used in the oil and gas industry from downhole tubing to transport trunk lines. Microbes form biofilms, some of which cause the so-called microbiologically influenced corrosion (MIC) of carbon steels. MIC by sulfate reducing bacteria (SRB) is often a leading cause in MIC failures. Electrogenic SRB sessile cells harvest extracellular electrons from elemental iron oxidation for energy production in their metabolism. A previous study suggested that electron mediators riboflavin and flavin adenine dinucleotide (FAD) both accelerated the MIC of 304 stainless steel by the Desulfovibrio vulgaris biofilm that is a corrosive SRB biofilm. Compared with stainless steels, carbon steels are usually far more prone to SRB attacks because SRB biofilms form much denser biofilms on carbon steel surfaces with a sessile cell density that is two orders of magnitude higher. In this work, C1018 carbon steel coupons were used in tests of MIC by D. vulgaris with and without an electron mediator. Experimental weight loss and pit depth data conclusively confirmed that both riboflavin and FAD were able to accelerate D. vulgaris attack against the carbon steel considerably. It has important implications in MIC failure analysis and MIC mitigation in the oil and gas industry. PMID:26308855

  1. Extracellular Electron Transfer Is a Bottleneck in the Microbiologically Influenced Corrosion of C1018 Carbon Steel by the Biofilm of Sulfate-Reducing Bacterium Desulfovibrio vulgaris.

    PubMed

    Li, Huabing; Xu, Dake; Li, Yingchao; Feng, Hao; Liu, Zhiyong; Li, Xiaogang; Gu, Tingyue; Yang, Ke

    2015-01-01

    Carbon steels are widely used in the oil and gas industry from downhole tubing to transport trunk lines. Microbes form biofilms, some of which cause the so-called microbiologically influenced corrosion (MIC) of carbon steels. MIC by sulfate reducing bacteria (SRB) is often a leading cause in MIC failures. Electrogenic SRB sessile cells harvest extracellular electrons from elemental iron oxidation for energy production in their metabolism. A previous study suggested that electron mediators riboflavin and flavin adenine dinucleotide (FAD) both accelerated the MIC of 304 stainless steel by the Desulfovibrio vulgaris biofilm that is a corrosive SRB biofilm. Compared with stainless steels, carbon steels are usually far more prone to SRB attacks because SRB biofilms form much denser biofilms on carbon steel surfaces with a sessile cell density that is two orders of magnitude higher. In this work, C1018 carbon steel coupons were used in tests of MIC by D. vulgaris with and without an electron mediator. Experimental weight loss and pit depth data conclusively confirmed that both riboflavin and FAD were able to accelerate D. vulgaris attack against the carbon steel considerably. It has important implications in MIC failure analysis and MIC mitigation in the oil and gas industry. PMID:26308855

  2. Can microbially-generated hydrogen sulfide account for the rates of U(VI) reduction by a sulfate-reducing bacterium?

    SciTech Connect

    Boonchayaanant, Benjaporn; Gu, Baohua; Wang, Wei; Ortiz, Monica E; Criddle, Craig

    2010-01-01

    In situ remediation of uranium contaminated soil and groundwater is attractive because a diverse range of microbial and abiotic processes reduce soluble and mobile U(VI) to sparingly soluble and immobile U(IV). Often these processes are linked. Sulfate-reducing bacteria (SRB), for example, enzymatically reduce U(VI) to U(IV), but they also produce hydrogen sulfide that can itself reduce U(VI). This study evaluated the relative importance of these processes for Desulfovibrio aerotolerans, a SRB isolated from a U(VI)-contaminated site. For the conditions evaluated, the observed rate of SRB-mediated U(VI) reduction can be explained by the abiotic reaction of U(VI) with the microbially-generated H{sub 2}S. The presence of trace ferrous iron appeared to enhance the extent of hydrogen sulfide-mediated U(VI) reduction at 5 mM bicarbonate, but had no clear effect at 15 mM. During the hydrogen sulfide-mediated reduction of U(VI), a floc formed containing uranium and sulfur. U(VI) sequestered in the floc was not available for further reduction.

  3. TEM investigation of U{sup 6+} and Re{sup 7+} reduction by Desulfovibrio desulfuricans, a sulfate-reducing bacterium

    SciTech Connect

    XU,HUIFANG; BARTON,LARRY L.; CHOUDHURY,KEKA; ZHANG,PENGCHU; WANG,YIFENG

    2000-03-14

    Uranium and its fission product Tc in aerobic environment will be in the forms of UO{sub 2}{sup 2+} and TcO{sub 4}{sup {minus}}. Reduced forms of tetravalent U and Tc are sparingly soluble. As determined by transmission electron microscopy, the reduction of uranyl acetate by immobilized cells of Desulfovibrio desulfuricans results in the production of black uraninite nanocrystals precipitated outside the cell. Some nanocrystals are associated with outer membranes of the cell as revealed from cross sections of these metabolic active sulfate-reducing bacteria. The nanocrystals have an average diameter of 5 nm and have anhedral shape. The reduction of Re{sup 7+} by cells of Desulfovibrio desulfuricans is fast in media containing H{sub 2} an electron donor, and slow in media containing lactic acid. It is proposed that the cytochrome in these cells has an important role in the reduction of uranyl and Re{sup 7+} is (a chemical analogue for Tc{sup 7+}) through transferring an electron from molecular hydrogen or lactic acid to the oxyions of UO{sub 2}{sup 2+} and TcO{sub 4}{sup {minus}}.

  4. CO2 exposure at pressure impacts metabolism and stress responses in the model sulfate-reducing bacterium Desulfovibrio vulgaris strain Hildenborough

    SciTech Connect

    Wilkins, Michael J.; Hoyt, David W.; Marshall, Matthew J.; Alderson, Paul A.; Plymale, Andrew E.; Markillie, Lye Meng; Tucker, Abigail E.; Walter, Eric D.; Linggi, Bryan E.; Dohnalkova, Alice; Taylor, Ronald C.

    2014-09-01

    Geologic carbon dioxide (CO2) sequestration drives physical and geochemical changes in deep subsurface environments that impact indigenous microbial activities. The combined effects of pressurized CO2 on a model sulfate-reducing microorganism, Desulfovibrio vulgaris, have been assessed using a suite of genomic and kinetic measurements. Novel high-pressure NMR time-series measurements using 13C-lactate were used to track D. vulgaris metabolism. We identified cessation of respiration at CO2 pressures of 10 bar, 25 bar, 50 bar, and 80 bar. Concurrent experiments using N2 as the pressurizing phase had no negative effect on microbial respiration, as inferred from reduction of sulfate to sulfide. Complementary pressurized batch incubations and fluorescence microscopy measurements supported NMR observations, and indicated that non-respiring cells were mostly viable at 50 bar CO2 for at least four hours, and at 80 bar CO2 for two hours. The fraction of dead cells increased rapidly after four hours at 80 bar CO2. Transcriptomic (RNA-Seq) measurements on mRNA transcripts from CO2-incubated biomass indicated that cells up-regulated the production of certain amino acids (leucine, isoleucine) following CO2 exposure at elevated pressures, likely as part of a general stress response. Evidence for other poorly understood stress responses were also identified within RNA-Seq data, suggesting that while pressurized CO2 severely limits the growth and respiration of D. vulgaris cells, biomass retains intact cell membranes at pressures up to 80 bar CO2. Together, these data show that geologic sequestration of CO2 may have significant impacts on rates of sulfate reduction in many deep subsurface environments where this metabolism is a key respiratory process.

  5. CO2 exposure at pressure impacts metabolism and stress responses in the model sulfate-reducing bacterium Desulfovibrio vulgaris strain Hildenborough

    PubMed Central

    Wilkins, Michael J.; Hoyt, David W.; Marshall, Matthew J.; Alderson, Paul A.; Plymale, Andrew E.; Markillie, L. Meng; Tucker, Abby E.; Walter, Eric D.; Linggi, Bryan E.; Dohnalkova, Alice C.; Taylor, Ron C.

    2014-01-01

    Geologic carbon dioxide (CO2) sequestration drives physical and geochemical changes in deep subsurface environments that impact indigenous microbial activities. The combined effects of pressurized CO2 on a model sulfate-reducing microorganism, Desulfovibrio vulgaris, have been assessed using a suite of genomic and kinetic measurements. Novel high-pressure NMR time-series measurements using 13C-lactate were used to track D. vulgaris metabolism. We identified cessation of respiration at CO2 pressures of 10 bar, 25 bar, 50 bar, and 80 bar. Concurrent experiments using N2 as the pressurizing phase had no negative effect on microbial respiration, as inferred from reduction of sulfate to sulfide. Complementary pressurized batch incubations and fluorescence microscopy measurements supported NMR observations, and indicated that non-respiring cells were mostly viable at 50 bar CO2 for at least 4 h, and at 80 bar CO2 for 2 h. The fraction of dead cells increased rapidly after 4 h at 80 bar CO2. Transcriptomic (RNA-Seq) measurements on mRNA transcripts from CO2-incubated biomass indicated that cells up-regulated the production of certain amino acids (leucine, isoleucine) following CO2 exposure at elevated pressures, likely as part of a general stress response. Evidence for other poorly understood stress responses were also identified within RNA-Seq data, suggesting that while pressurized CO2 severely limits the growth and respiration of D. vulgaris cells, biomass retains intact cell membranes at pressures up to 80 bar CO2. Together, these data show that geologic sequestration of CO2 may have significant impacts on rates of sulfate reduction in many deep subsurface environments where this metabolism is a key respiratory process. PMID:25309528

  6. INFLUENCE OF THE SEAGRASS THALASSIA TESTUDINUM ON THE COMMUNITY COMPOSITION AND ACTIVITY OF SULFATE-REDUCING BACTERIA IN AN ESSENTIAL COAST MARINE HABITAT

    EPA Science Inventory

    Biogeochemical cycling of nutrients and sulfate reduction rates (SRR) were studied in relation to the community composition of sulfate-reducing bacteria SRB) in a Thalassia testudinum bed and in adjacent unvegetated areas. Sampling took place in Santa Rosa Sound, Pensacola, Flori...

  7. Study examines sulfate-reducing bacteria activity

    SciTech Connect

    McElhiney, J.E.; Hardy, J.A.; Rizk, T.Y.; Stott, J.F.D.; Eden, R.D.

    1996-12-09

    Low-sulfate seawater injection can reduce the potential of an oil reservoir turning sour because of sulfate-reducing bacteria. Sulfate-reducing bacteria (SRB) convert sulfate ions in seawater used in waterflooding into sulfide with the concomitant oxidation of a carbon source. A recent study at Capcis investigated the efficiency of SRB under various conditions of sulfate limitation. This study was conducted in a flowing bioreactor at 2,000 psia with different temperature zones (mesophilic 35 C and thermophilic 60--80 C). The study mixed microfloral populations derived from real North Sea-produced fluids, and included an active population of marine methanogenic bacteria present to provide competition for the available carbon sources. In general, results showed that SRB continue to convert sulfate to sulfide in stoichiometric quantities without regard to absolute concentrations. The paper discusses the results and recommends nanofiltration of seawater for ``sweet`` reservoirs.

  8. High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater

    PubMed Central

    Ramsay, Bradley D.; Hwang, Chiachi; Carroll, Sue L.; Lucas, Susan; Han, James; Lapidus, Alla L.; Cheng, Jan-Fang; Goodwin, Lynne A.; Pitluck, Samuel; Peters, Lin; Chertkov, Olga; Held, Brittany; Detter, John C.; Han, Cliff S.; Tapia, Roxanne; Land, Miriam L.; Hauser, Loren J.; Kyrpides, Nikos C.; Ivanova, Natalia N.; Mikhailova, Natalia; Pagani, Ioanna; Woyke, Tanja; Arkin, Adam P.; Dehal, Paramvir; Chivian, Dylan; Criddle, Craig S.; Wu, Weimin; Chakraborty, Romy

    2015-01-01

    Desulfovibrio carbinoliphilus subsp. oakridgensis FW-101-2B is an anaerobic, organic acid/alcohol-oxidizing, sulfate-reducing δ-proteobacterium. FW-101-2B was isolated from contaminated groundwater at The Field Research Center at Oak Ridge National Lab after in situ stimulation for heavy metal-reducing conditions. The genome will help elucidate the metabolic potential of sulfate-reducing bacteria during uranium reduction. PMID:25767232

  9. High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater

    DOE PAGESBeta

    Ramsay, Bradley D.; Hwang, Chiachi; Woo, Hannah L.; Carroll, Sue L.; Lucas, Susan; Han, James; Lapidus, Alla L.; Cheng, Jan-Fang; Goodwin, Lynne A.; Pitluck, Samuel; et al

    2015-03-12

    Desulfovibrio carbinoliphilus subsp. oakridgensis FW-101-2B is an anaerobic, organic acid/alcohol-oxidizing, sulfate-reducing δ-proteobacterium. FW-101-2B was isolated from contaminated groundwater at The Field Research Center at Oak Ridge National Lab after in situ stimulation for heavy metal-reducing conditions. The genome will help elucidate the metabolic potential of sulfate-reducing bacteria during uranium reduction.

  10. Pangenome Evolution in the Marine Bacterium Alteromonas

    PubMed Central

    López-Pérez, Mario; Rodriguez-Valera, Francisco

    2016-01-01

    We have examined a collection of the free-living marine bacterium Alteromonas genomes with cores diverging in average nucleotide identities ranging from 99.98% to 73.35%, i.e., from microbes that can be considered members of a natural clone (like in a clinical epidemiological outbreak) to borderline genus level. The genomes were largely syntenic allowing a precise delimitation of the core and flexible regions in each. The core was 1.4 Mb (ca. 30% of the typical strain genome size). Recombination rates along the core were high among strains belonging to the same species (37.7–83.7% of all nucleotide polymorphisms) but they decreased sharply between species (18.9–5.1%). Regarding the flexible genome, its main expansion occurred within the boundaries of the species, i.e., strains of the same species already have a large and diverse flexible genome. Flexible regions occupy mostly fixed genomic locations. Four large genomic islands are involved in the synthesis of strain-specific glycosydic receptors that we have called glycotypes. These genomic regions are exchanged by homologous recombination within and between species and there is evidence for their import from distant taxonomic units (other genera within the family). In addition, several hotspots for integration of gene cassettes by illegitimate recombination are distributed throughout the genome. They code for features that give each clone specific properties to interact with their ecological niche and must flow fast throughout the whole genus as they are found, with nearly identical sequences, in different species. Models for the generation of this genomic diversity involving phage predation are discussed. PMID:27189983

  11. Pangenome Evolution in the Marine Bacterium Alteromonas.

    PubMed

    López-Pérez, Mario; Rodriguez-Valera, Francisco

    2016-01-01

    We have examined a collection of the free-living marine bacterium Alteromonas genomes with cores diverging in average nucleotide identities ranging from 99.98% to 73.35%, i.e., from microbes that can be considered members of a natural clone (like in a clinical epidemiological outbreak) to borderline genus level. The genomes were largely syntenic allowing a precise delimitation of the core and flexible regions in each. The core was 1.4 Mb (ca. 30% of the typical strain genome size). Recombination rates along the core were high among strains belonging to the same species (37.7-83.7% of all nucleotide polymorphisms) but they decreased sharply between species (18.9-5.1%). Regarding the flexible genome, its main expansion occurred within the boundaries of the species, i.e., strains of the same species already have a large and diverse flexible genome. Flexible regions occupy mostly fixed genomic locations. Four large genomic islands are involved in the synthesis of strain-specific glycosydic receptors that we have called glycotypes. These genomic regions are exchanged by homologous recombination within and between species and there is evidence for their import from distant taxonomic units (other genera within the family). In addition, several hotspots for integration of gene cassettes by illegitimate recombination are distributed throughout the genome. They code for features that give each clone specific properties to interact with their ecological niche and must flow fast throughout the whole genus as they are found, with nearly identical sequences, in different species. Models for the generation of this genomic diversity involving phage predation are discussed. PMID:27189983

  12. CHARACTERIZATION OF A NEW THERMOPHILIC SULFATE-REDUCING BACTERIUM THERMODESULFOVIBRIO YELLOWSTONII GEN. NOV. AND SP. NOV.: ITS PHYLOGENETIC RELATIONSHIP TO THERMODESULFOBACTERIUM COMMUNE AND THEIR ORIGINS DEEP WITHIN THE BACTERIAL DOMAIN

    EPA Science Inventory

    A thermophilic sulfate-reducing vibrio isolated from thermal vent water in Yellowstone Lake, Wyoming USA, is described. he Gram-negative, curve rod-shaped cells averaged 0.3 um wide and 1.5 um long. hey were motile by means of a single polar flagellum. rowth was observed between ...

  13. Draft Genome Sequence of a Novel Desulfobacteraceae Member from a Sulfate-Reducing Bioreactor Metagenome

    PubMed Central

    Pinto, Ameet J.; Figueroa, Linda A.; Sharp, Jonathan O.

    2016-01-01

    Sulfate-reducing bacteria are important players in the global sulfur cycle and of considerable commercial interest. The draft genome sequence of a sulfate-reducing bacterium of the family Desulfobacteraceae, assembled from a sulfate-reducing bioreactor metagenome, indicates that heavy-metal– and acid-resistance traits of this organism may be of importance for its application in acid mine drainage mitigation. PMID:26769931

  14. Draft Genome Sequence of a Novel Desulfobacteraceae Member from a Sulfate-Reducing Bioreactor Metagenome.

    PubMed

    Almstrand, Robert; Pinto, Ameet J; Figueroa, Linda A; Sharp, Jonathan O

    2016-01-01

    Sulfate-reducing bacteria are important players in the global sulfur cycle and of considerable commercial interest. The draft genome sequence of a sulfate-reducing bacterium of the family Desulfobacteraceae, assembled from a sulfate-reducing bioreactor metagenome, indicates that heavy-metal- and acid-resistance traits of this organism may be of importance for its application in acid mine drainage mitigation. PMID:26769931

  15. Characterization of a new thermophilic sulfate-reducing bacterium Thermodesulfovibrio yellowstonii, gen. nov. and sp. nov.: its phylogenetic relationship to Thermodesulfobacterium commune and their origins deep within the bacterial domain

    NASA Technical Reports Server (NTRS)

    Henry, E. A.; Devereux, R.; Maki, J. S.; Gilmour, C. C.; Woese, C. R.; Mandelco, L.; Schauder, R.; Remsen, C. C.; Mitchell, R.

    1994-01-01

    A thermophilic sulfate-reducing vibrio isolated from thermal vent water in Yellowstone Lake, Wyoming, USA is described. The gram-negative, curved rod-shaped cells averaged 0.3 micrometer wide and 1.5 micrometers long. They were motile by means of a single polar flagellum. Growth was observed between 40 degrees and 70 degrees C with optimal growth at 65 degrees C. Cultures remained viable for one year at 27 degrees C although spore-formation was not observed. Sulfate, thiosulfate and sulfite were used as electron acceptors. Sulfur, fumarate and nitrate were not reduced. In the presence of sulfate, growth was observed only with lactate, pyruvate, hydrogen plus acetate, or formate plus acetate. Pyruvate was the only compound observed to support fermentative growth. Pyruvate and lactate were oxidized to acetate. Desulfofuscidin and c-type cytochromes were present. The G + C content was 29.5 mol%. The divergence in the 16 S ribosomal RNA sequences between the new isolate and Thermodesulfobacterium commune suggests that these two thermophilic sulfate-reducing bacteria represent different genera. These two bacteria depict a lineage that branches deeply within the Bacteria domain and which is clearly distinct from previously defined phylogenetic lines of sulfate-reducing bacteria. Strain YP87 is described as the type strain of the new genus and species Thermodesulfovibrio yellowstonii.

  16. Microcalorimetric Measurements of Glucose Metabolism by Marine Bacterium Vibrio alginolyticus

    PubMed Central

    Gordon, Andrew S.; Millero, Frank J.; Gerchakov, Sol M.

    1982-01-01

    Microcalorimetric measurements of heat production from glucose by Vibrio alginolyticus were made to assess the viability of calorimetry as a technique for studying the metabolism of marine bacteria at organic nutrient concentrations found in marine waters. The results show that the metabolism of glucose by this bacterium can be measured by calorimetry at submicromolar concentrations. A linear correlation between glucose concentration and total heat production was observed over a concentration range of 8 mM to 0.35 μM. It is suggested that these data indicate a constant efficiency of metabolism for this bacterium over the wide range of glucose concentrations studied. PMID:16346131

  17. Analysis of membrane-protein complexes of the marine sulfate reducer Desulfobacula toluolica Tol2 by 1D blue native-PAGE complexome profiling and 2D blue native-/SDS-PAGE.

    PubMed

    Wöhlbrand, Lars; Ruppersberg, Hanna S; Feenders, Christoph; Blasius, Bernd; Braun, Hans-Peter; Rabus, Ralf

    2016-03-01

    Sulfate-reducing bacteria (SRB) obtain energy from cytoplasmic reduction of sulfate to sulfide involving APS-reductase (AprAB) and dissimilatory sulfite reductase (DsrAB). These enzymes are predicted to obtain electrons from membrane redox complexes, i.e. the quinone-interacting membrane-bound oxidoreductase (QmoABC) and DsrMKJOP complexes. In addition to these conserved complexes, the genomes of SRB encode a large number of other (predicted) membrane redox complexes, the function and actual formation of which is unknown. This study reports the establishment of 1D Blue Native-PAGE complexome profiling and 2D BN-/SDS-PAGE for analysis of the membrane protein complexome of the marine sulfate reducer Desulfobacula toluolica Tol2. Analysis of normalized score profiles of >800 proteins in combination with hierarchical clustering and identification of 2D BN-/SDS-PAGE separated spots demonstrated separation of membrane complexes in their native form, e.g. ATP synthase. In addition to the QmoABC and DsrMKJOP complexes, other complexes were detected that constitute the basic membrane complexome of D. toluolica Tol2, e.g. transport proteins (e.g. sodium/sulfate symporters) or redox complexes involved in Na(+) -based bioenergetics (RnfABCDEG). Notably, size estimation indicates dimer and quadruple formation of the DsrMKJOP complex in vivo. Furthermore, cluster analysis suggests interaction of this complex with a rhodanese-like protein (Tol2_C05230) possibly representing a periplasmic electron transfer partner for DsrMKJOP. PMID:26792001

  18. Diversity of Sulfur Isotope Fractionations by Sulfate-Reducing Prokaryotes†

    PubMed Central

    Detmers, Jan; Brüchert, Volker; Habicht, Kirsten S.; Kuever, Jan

    2001-01-01

    Batch culture experiments were performed with 32 different sulfate-reducing prokaryotes to explore the diversity in sulfur isotope fractionation during dissimilatory sulfate reduction by pure cultures. The selected strains reflect the phylogenetic and physiologic diversity of presently known sulfate reducers and cover a broad range of natural marine and freshwater habitats. Experimental conditions were designed to achieve optimum growth conditions with respect to electron donors, salinity, temperature, and pH. Under these optimized conditions, experimental fractionation factors ranged from 2.0 to 42.0‰. Salinity, incubation temperature, pH, and phylogeny had no systematic effect on the sulfur isotope fractionation. There was no correlation between isotope fractionation and sulfate reduction rate. The type of dissimilatory bisulfite reductase also had no effect on fractionation. Sulfate reducers that oxidized the carbon source completely to CO2 showed greater fractionations than sulfate reducers that released acetate as the final product of carbon oxidation. Different metabolic pathways and variable regulation of sulfate transport across the cell membrane all potentially affect isotope fractionation. Previous models that explained fractionation only in terms of sulfate reduction rates appear to be oversimplified. The species-specific physiology of each sulfate reducer thus needs to be taken into account to understand the regulation of sulfur isotope fractionation during dissimilatory sulfate reduction. PMID:11157259

  19. NATURAL RELATIONSHIPS AMONG SULFATE-REDUCING EUBACTERIA

    EPA Science Inventory

    Phylogenetic relationships among 20 nonsporeforming and two endospore-forming species of sulfate-reducing eubacteria were inferred from comparative 16S rRNA seguencing. ll genera of mesophilic sulfate-reducing eubacteria except the new genus Desulfomicrobium and the gliding Desul...

  20. Depth-related coupling relation between methane-oxidizing bacteria (MOBs) and sulfate-reducing bacteria (SRBs) in a marine sediment core from the Dongsha region, the South China Sea.

    PubMed

    Xu, Xiao-Ming; Fu, Shao-Ying; Zhu, Qing; Xiao, Xi; Yuan, Jian-Ping; Peng, Juan; Wu, Chou-Fei; Wang, Jiang-Hai

    2014-12-01

    The vertical distributions of methane-oxidizing bacteria (MOBs) and sulfate-reducing bacteria (SRBs) in the marine sediment core of DH-CL14 from the Dongsha region, the South China Sea, were investigated. To enumerate MOBs and SRBs, their specific genes of pmoA and apsA were quantified by a culture-independent molecular biological technique, real-time polymerase chain reaction (RT-PCR). The result shows that the pmoA gene copies per gram of sediments reached the maximum of 1,118,679 at the depth of 140-160 cm. Overall considering the detection precision, sample amount, measurement cost, and sensitivity to the seepage of methane from the oil/gas reservoirs or gas hydrates, we suggest that the depth of 140-160 cm may be the optimal sampling position for the marine microbial exploration of oils, gases, and gas hydrates in the Dongsha region. The data of the pmoA and apsA gene copies exhibit an evident coupling relation between MOBs and SRBs as illustrated in their vertical distributions in this sediment core, which may well be interpreted by a high sulfate concentration inhibiting methane production and further leading to the reduction of MOBs. In comparison with the numbers of the pmoA and apsA copies at the same sediment depth, we find out that there were two methane-oxidizing mechanisms of aerobic and anaerobic oxidation in this sediment core, i.e., the aerobic oxidation with free oxygen dominantly occurred above the depth of 210-230 cm, while the anaerobic oxidation with the other electron acceptors such as sulfates and manganese-iron oxides happened below the depth of 210-230 cm. PMID:25064353

  1. Marine transducing bacteriophage attacking a luminous bacterium.

    PubMed

    Keynan, A; Nealson, K; Sideropoulos, H; Hastings, J W

    1974-08-01

    The isolation and partial characterization of a marine bacteriophage attacking a strain of luminous bacteria is described, including some physical, biological, and genetic properties. It is a DNA phage of density of 1.52 with a long flexible tail and an apparently icosohedral head. With respect to stability in suspension, it has a rather specific requirement for the sodium ion in high concentration; it is further stabilized by the addition of calcium and magnesium ions. These same ions are likewise all required for both good plating efficiency and plaque uniformity. Although it goes through a typical lytic growth cycle (about 45 min), with a burst size of 100, and no stable lysogens have been isolated, it is nevertheless a transducing phage specifically for the tryptophan region, transducing several, but not all, independently isolated Trp(-) auxotrophs to protrophy. No other auxotrophs of a variety of amino acids were transduced by this phage to prototrophy. Phage infection does not change the normal expression of the luminescent system, and light remains at near normal levels until cell lysis occurs. PMID:16789143

  2. Real-Time PCR Quantification and Diversity Analysis of the Functional Genes aprA and dsrA of Sulfate-Reducing Prokaryotes in Marine Sediments of the Peru Continental Margin and the Black Sea

    PubMed Central

    Blazejak, Anna; Schippers, Axel

    2011-01-01

    Sulfate-reducing prokaryotes (SRP) are ubiquitous and quantitatively important members in many ecosystems, especially in marine sediments. However their abundance and diversity in subsurface marine sediments is poorly understood. In this study, the abundance and diversity of the functional genes for the enzymes adenosine 5′-phosphosulfate reductase (aprA) and dissimilatory sulfite reductase (dsrA) of SRP in marine sediments of the Peru continental margin and the Black Sea were analyzed, including samples from the deep biosphere (ODP site 1227). For aprA quantification a Q-PCR assay was designed and evaluated. Depth profiles of the aprA and dsrA copy numbers were almost equal for all sites. Gene copy numbers decreased concomitantly with depth from around 108/g sediment close to the sediment surface to less than 105/g sediment at 5 mbsf. The 16S rRNA gene copy numbers of total bacteria were much higher than those of the functional genes at all sediment depths and used to calculate the proportion of SRP to the total Bacteria. The aprA and dsrA copy numbers comprised in average 0.5–1% of the 16S rRNA gene copy numbers of total bacteria in the sediments up to a depth of ca. 40 mbsf. In the zone without detectable sulfate in the pore water from about 40–121 mbsf (Peru margin ODP site 1227), only dsrA (but not aprA) was detected with copy numbers of less than 104/g sediment, comprising ca. 14% of the 16S rRNA gene copy numbers of total bacteria. In this zone, sulfate might be provided for SRP by anaerobic sulfide oxidation. Clone libraries of aprA showed that all isolated sequences originate from SRP showing a close relationship to aprA of characterized species or form a new cluster with only distant relation to aprA of isolated SRP. For dsrA a high diversity was detected, even up to 121 m sediment depth in the deep biosphere. PMID:22203820

  3. The terminal oxidase in the marine bacterium Pseudomonas nautica 617.

    PubMed

    Simpson, H; Denis, M; Malatesta, F

    1997-06-01

    The molecular properties of a novel membrane quinol oxidase from the marine bacterium Pseudomonas nautica 617 are presented. The protein contains 2b hemes/mole which may be distinguished by EPR spectroscopy but not by optical spectroscopy and electrochemistry. Respiration, though being cyanide insensitive, is not inhibited by carbon monoxide and oxygen reduction is carried out only half-way with production of hydrogen peroxide. The terminal oxidase represents, therefore, a unique example in the large family of terminal oxidases known up to date. PMID:9337488

  4. Desulfoluna spongiiphila sp. nov., a dehalogenating bacterium in the Desulfobacteraceae from the marine sponge Aplysina aerophoba.

    PubMed

    Ahn, Young-Beom; Kerkhof, Lee J; Häggblom, Max M

    2009-09-01

    A reductively dehalogenating, strictly anaerobic, sulfate-reducing bacterium, designated strain AA1T, was isolated from the marine sponge Aplysina aerophoba collected in the Mediterranean Sea and was characterized phenotypically and phylogenetically. Cells of strain AA1T were Gram-negative, short, curved rods. Growth of strain AA1T was observed between 20 and 37 degrees C (optimally at 28 degrees C) at pH 7-8. NaCl was required for growth; optimum growth occurred in the presence of 25 g NaCl l(-1). Growth occurred with lactate, propionate, pyruvate, succinate, benzoate, glucose and sodium citrate as electron donors and carbon sources and either sulfate or 2-bromophenol as electron acceptors, but not with acetate or butyrate. Strain AA1T was able to dehalogenate several different bromophenols, and 2- and 3-iodophenol, but not monochlorinated or fluorinated phenols. Lactate, pyruvate, fumarate and malate were not utilized without an electron acceptor. The G+C content of the genomic DNA was 58.5 mol%. The predominant cellular fatty acids were C14:0, iso-C14:0, C14:0 3-OH, anteiso-C15:0, C16:0, C16:1omega7c and C18:1omega7c. Phylogenetic analysis based on 16S rRNA gene sequence comparisons placed the novel strain within the class Deltaproteobacteria. Strain AA1T was related most closely to the type strains of Desulfoluna butyratoxydans (96% 16S rRNA gene sequence similarity), Desulfofrigus oceanense (95%) and Desulfofrigus fragile (95%). Based on its phenotypic, physiological and phylogenetic characteristics, strain AA1T is considered to represent a novel species of the genus Desulfoluna, for which the name Desulfoluna spongiiphila sp. nov. is proposed. The type strain is AA1T (=DSM 17682T=ATCC BAA-1256T). PMID:19605712

  5. Penetration of sulfate reducers through a porous North Sea oil reservoir

    SciTech Connect

    Beeder, J.; Nilsen, R.K.; Thorstenson, T.; Torsvik, T.

    1996-09-01

    During offshore oil production, seawater is often injected into the reservoir to maintain pressure. Sulfate reducers have been reported from water samples in Norwegian oil fields. However in order to demonstrate penetration, a suitable indicator microorganism is required. This paper reports the isolation of one such indicator bacterium from injection water followed by isolation of the same bacterium from water from oil field production system. 28 refs., 1 fig., 2 tabs.

  6. Nitrate reduction in sulfate-reducing bacteria.

    PubMed

    Marietou, Angeliki

    2016-08-01

    Sulfate-reducing bacteria (SRBs) gain their energy by coupling the oxidation of organic substrate to the reduction of sulfate to sulfide. Several SRBs are able to use alternative terminal electron acceptors to sulfate such as nitrate. Nitrate-reducing SRBs have been isolated from a diverse range of environments. In order to be able to understand the significance of nitrate reduction in SRBs, we need to examine the ecology and physiology of the nitrate-reducing SRB isolates. PMID:27364687

  7. Anaerobic 1-Alkene Metabolism by the Alkane- and Alkene-Degrading Sulfate Reducer Desulfatibacillum aliphaticivorans Strain CV2803T▿

    PubMed Central

    Grossi, Vincent; Cravo-Laureau, Cristiana; Méou, Alain; Raphel, Danielle; Garzino, Frédéric; Hirschler-Réa, Agnès

    2007-01-01

    The alkane- and alkene-degrading, marine sulfate-reducing bacterium Desulfatibacillum aliphaticivorans strain CV2803T, known to oxidize n-alkanes anaerobically by fumarate addition at C-2, was investigated for its 1-alkene metabolism. The total cellular fatty acids of this strain were predominantly C-(even number) (C-even) when it was grown on C-even 1-alkenes and predominantly C-(odd number) (C-odd) when it was grown on C-odd 1-alkenes. Detailed analyses of those fatty acids by gas chromatography-mass spectrometry after 6- to 10-week incubations allowed the identification of saturated 2- and 4-ethyl-, 2- and 4-methyl-, and monounsaturated 4-methyl-branched fatty acids with chain lengths that correlated with those of the 1-alkene. The growth of D. aliphaticivorans on (per)deuterated 1-alkenes provided direct evidence of the anaerobic transformation of these alkenes into the corresponding 1-alcohols and into linear as well as 10- and 4-methyl-branched fatty acids. Experiments performed with [13C]bicarbonate indicated that the initial activation of 1-alkene by the addition of inorganic carbon does not occur. These results demonstrate that D. aliphaticivorans metabolizes 1-alkene by the oxidation of the double bond at C-1 and by the subterminal addition of organic carbon at both ends of the molecule [C-2 and C-(ω-1)]. The detection of ethyl-branched fatty acids from unlabeled 1-alkenes further suggests that carbon addition also occurs at C-3. Alkylsuccinates were not observed as potential initial intermediates in alkene metabolism. Based on our observations, the first pathways for anaerobic 1-alkene metabolism in an anaerobic bacterium are proposed. Those pathways indicate that diverse initial reactions of 1-alkene activation can occur simultaneously in the same strain of sulfate-reducing bacterium. PMID:17965214

  8. Anaerobic 1-alkene metabolism by the alkane- and alkene-degrading sulfate reducer Desulfatibacillum aliphaticivorans strain CV2803T.

    PubMed

    Grossi, Vincent; Cravo-Laureau, Cristiana; Méou, Alain; Raphel, Danielle; Garzino, Frédéric; Hirschler-Réa, Agnès

    2007-12-01

    The alkane- and alkene-degrading, marine sulfate-reducing bacterium Desulfatibacillum aliphaticivorans strain CV2803(T), known to oxidize n-alkanes anaerobically by fumarate addition at C-2, was investigated for its 1-alkene metabolism. The total cellular fatty acids of this strain were predominantly C-(even number) (C-even) when it was grown on C-even 1-alkenes and predominantly C-(odd number) (C-odd) when it was grown on C-odd 1-alkenes. Detailed analyses of those fatty acids by gas chromatography-mass spectrometry after 6- to 10-week incubations allowed the identification of saturated 2- and 4-ethyl-, 2- and 4-methyl-, and monounsaturated 4-methyl-branched fatty acids with chain lengths that correlated with those of the 1-alkene. The growth of D. aliphaticivorans on (per)deuterated 1-alkenes provided direct evidence of the anaerobic transformation of these alkenes into the corresponding 1-alcohols and into linear as well as 10- and 4-methyl-branched fatty acids. Experiments performed with [(13)C]bicarbonate indicated that the initial activation of 1-alkene by the addition of inorganic carbon does not occur. These results demonstrate that D. aliphaticivorans metabolizes 1-alkene by the oxidation of the double bond at C-1 and by the subterminal addition of organic carbon at both ends of the molecule [C-2 and C-(omega-1)]. The detection of ethyl-branched fatty acids from unlabeled 1-alkenes further suggests that carbon addition also occurs at C-3. Alkylsuccinates were not observed as potential initial intermediates in alkene metabolism. Based on our observations, the first pathways for anaerobic 1-alkene metabolism in an anaerobic bacterium are proposed. Those pathways indicate that diverse initial reactions of 1-alkene activation can occur simultaneously in the same strain of sulfate-reducing bacterium. PMID:17965214

  9. The first genomic and proteomic characterization of a deep-sea sulfate reducer: insights into the piezophilic lifestyle of Desulfovibrio piezophilus.

    PubMed

    Pradel, Nathalie; Ji, Boyang; Gimenez, Grégory; Talla, Emmanuel; Lenoble, Patricia; Garel, Marc; Tamburini, Christian; Fourquet, Patrick; Lebrun, Régine; Bertin, Philippe; Denis, Yann; Pophillat, Matthieu; Barbe, Valérie; Ollivier, Bernard; Dolla, Alain

    2013-01-01

    Desulfovibrio piezophilus strain C1TLV30(T) is a piezophilic anaerobe that was isolated from wood falls in the Mediterranean deep-sea. D. piezophilus represents a unique model for studying the adaptation of sulfate-reducing bacteria to hydrostatic pressure. Here, we report the 3.6 Mbp genome sequence of this piezophilic bacterium. An analysis of the genome revealed the presence of seven genomic islands as well as gene clusters that are most likely linked to life at a high hydrostatic pressure. Comparative genomics and differential proteomics identified the transport of solutes and amino acids as well as amino acid metabolism as major cellular processes for the adaptation of this bacterium to hydrostatic pressure. In addition, the proteome profiles showed that the abundance of key enzymes that are involved in sulfate reduction was dependent on hydrostatic pressure. A comparative analysis of orthologs from the non-piezophilic marine bacterium D. salexigens and D. piezophilus identified aspartic acid, glutamic acid, lysine, asparagine, serine and tyrosine as the amino acids preferentially replaced by arginine, histidine, alanine and threonine in the piezophilic strain. This work reveals the adaptation strategies developed by a sulfate reducer to a deep-sea lifestyle. PMID:23383081

  10. Denitrification characteristics of a marine origin psychrophilic aerobic denitrifying bacterium.

    PubMed

    Zheng, Haiyan; Liu, Ying; Sun, Guangdong; Gao, Xiyan; Zhang, Qingling; Liu, Zhipei

    2011-01-01

    A psychrophilic aerobic denitrifying bacterium, strain S1-1, was isolated from a biological aerated filter conducted for treatment of recirculating water in a marine aquaculture system. Strain S1-1 was preliminarily identified as Psychrobacter sp. based on the analysis of its 16S rRNA gene sequence, which showed 100% sequence similarity to that of Psychrobacter sp. TSBY-70. Strain S1-1 grew well either in high nitrate or high nitrite conditions with a removal of 100% nitrate or 63.50% nitrite, and the total nitrogen removal rates could reach to 46.48% and 31.89%, respectively. The results indicated that nitrate was mainly reduced in its logarithmic growth phase with a very low level accumulation of nitrite, suggesting that the aerobic denitrification process of strain S1-1 occurred mainly in this phase. The GC-MS results showed that N2O was formed as the major intermediate during the aerobic denitrifying process of strain S1-1. Finally, factors affecting the growth of strain S1-1 and its aerobic denitrifying ability were also investigated. Results showed that the optimum aerobic denitrification conditions for strain S1-1 were sodium succinate as carbon source, C/N ratio15, salinity 10 g/L NaCl, incubation temperature 20 degrees C and initial pH 6.5. PMID:22432315

  11. Methanogenic archaea and sulfate reducing bacteria co-cultured on acetate: teamwork or coexistence?

    PubMed Central

    Ozuolmez, Derya; Na, Hyunsoo; Lever, Mark A.; Kjeldsen, Kasper U.; Jørgensen, Bo B.; Plugge, Caroline M.

    2015-01-01

    Acetate is a major product of fermentation processes and an important substrate for sulfate reducing bacteria and methanogenic archaea. Most studies on acetate catabolism by sulfate reducers and methanogens have used pure cultures. Less is known about acetate conversion by mixed pure cultures and the interactions between both groups. We tested interspecies hydrogen transfer and coexistence between marine methanogens and sulfate reducers using mixed pure cultures of two types of microorganisms. First, Desulfovibrio vulgaris subsp. vulgaris (DSM 1744), a hydrogenotrophic sulfate reducer, was cocultured together with the obligate aceticlastic methanogen Methanosaeta concilii using acetate as carbon and energy source. Next, Methanococcus maripaludis S2, an obligate H2- and formate-utilizing methanogen, was used as a partner organism to M. concilii in the presence of acetate. Finally, we performed a coexistence experiment between M. concilii and an acetotrophic sulfate reducer Desulfobacter latus AcSR2. Our results showed that D. vulgaris was able to reduce sulfate and grow from hydrogen leaked by M. concilii. In the other coculture, M. maripaludis was sustained by hydrogen leaked by M. concilii as revealed by qPCR. The growth of the two aceticlastic microbes indicated co-existence rather than competition. Altogether, our results indicate that H2 leaking from M. concilii could be used by efficient H2-scavengers. This metabolic trait, revealed from coculture studies, brings new insight to the metabolic flexibility of methanogens and sulfate reducers residing in marine environments in response to changing environmental conditions and community compositions. Using dedicated physiological studies we were able to unravel the occurrence of less obvious interactions between marine methanogens and sulfate-reducing bacteria. PMID:26074892

  12. Commensal symbiosis between agglutinated polychaetes and sulfate-reducing bacteria.

    PubMed

    Guido, A; Mastandrea, A; Rosso, A; Sanfilippo, R; Tosti, F; Riding, R; Russo, F

    2014-05-01

    Pendant bioconstructions occur within submerged caves in the Plemmirio Marine Protected Area in SE Sicily, Italy. These rigid structures, here termed biostalactites, were synsedimentarily lithified by clotted-peloidal microbial carbonate that has a high bacterial lipid biomarker content with abundant compounds derived from sulfate-reducing bacteria. The main framework builders are polychaete serpulid worms, mainly Protula with subordinate Semivermilia and Josephella. These polychaetes have lamellar and/or fibrillar wall structure. In contrast, small agglutinated terebellid tubes, which are a minor component of the biostalactites, are discontinuous and irregular with a peloidal micritic microfabric. The peloids, formed by bacterial sulfate reduction, appear to have been utilized by terebellids to construct tubes in an environment where other particulate sediment is scarce. We suggest that the bacteria obtained food from the worms in the form of fecal material and/or from the decaying tissue of surrounding organisms and that the worms obtained peloidal micrite with which to construct their tubes, either as grains and/or as tube encompassing biofilm. Peloidal worm tubes have rarely been reported in the recent but closely resemble examples in the geological record that extend back at least to the early Carboniferous. This suggests a long-lived commensal relationship between some polychaete worms and heterotrophic, especially sulfate-reducing, bacteria. PMID:24636469

  13. Sulfate-reducing bacteria: Microbiology and physiology

    NASA Technical Reports Server (NTRS)

    Peck, H. D.

    1985-01-01

    The sulfate reducing bacteria, the first nonphotosynthetic anaerobic bacteria demonstrated to contain c type cytochromes, perform electron transfer coupled to phosphorylation. A new bioenergetic scheme for the formation of a proton gradient for growth of Desulfovibrio on organic substrates and sulfate involving vectors electron transfer and consistent with the cellular localization of enzymes and electron transfer components was proposed. Hydrogen is produced in the cytoplasm from organic substrates and, as a permease molecule diffuses rapidly across the cytoplasmic membrane, it is oxidized to protons and electrons by the periplasmic hydrogenase. The electrons only are transferred across the cytoplasmic membrane to the cytoplasm where they are used to reduce sulfate to sulfide. The protons are used for transport or to drive a reversible ATPOSE. The net effect is the transfer of protons across the cytoplasmic membrane with the intervention of a proton pump. This type of H2 cycling is relevant to the bioenergetics of other types of anaerobic microorganisms.

  14. Seasonal composition and activity of sulfate-reducing prokaryotic communities in seagrass bed sediments

    EPA Science Inventory

    Sulfate-reducing prokaryotes (SRP) play a key role in the carbon and nutrient cycles of coastal marine, vegetated ecosystems, but the interactions of SRP communities with aquatic plants remain little studied. The abundance, activity, and community composition of SRP was studied i...

  15. Monitoring sulfide and sulfate-reducing bacteria

    SciTech Connect

    Tanner, R.S.

    1995-12-31

    Simple yet precise and accurate methods for monitoring sulfate-reducing bacteria (SRB) and sulfide remain useful for the study of bacterial souring and corrosion. Test kits are available to measure sulfide in field samples. A more precise methylene blue sulfide assay for both field and laboratory studies is described here. Improved media, compared to that in API RP-38, for enumeration of SRB have been formulated. One of these, API-RST, contained cysteine (1.1 mM) as a reducing agent, which may be a confounding source of sulfide. While cysteine was required for rapid enumeration of SRB from environmental samples, the concentration of cysteine in medium could be reduced to 0.4 mM. It was also determined that elevated levels of yeast extract (>1 g/liter) could interfere with enumeration of SRB from environmental samples. The API-RST medium was modified to a RST-11 medium. Other changes in medium composition, in addition to reduction of cysteine, included reduction of the concentration of phosphate from 3.4 mM to 2.2 mM, reduction of the concentration of ferrous iron from 0.8 mM to 0.5 mM and preparation of a stock mineral solution to ease medium preparation. SRB from environmental samples could be enumerated in a week in this medium.

  16. Ammonificins C and D, Hydroxyethylamine Chromene Derivatives from a Cultured Marine Hydrothermal Vent Bacterium, Thermovibrio ammonificans

    PubMed Central

    Andrianasolo, Eric H.; Haramaty, Liti; Rosario-Passapera, Richard; Vetriani, Costantino; Falkowski, Paul; White, Eileen; Lutz, Richard

    2012-01-01

    Chemical and biological investigation of the cultured marine hydrothermal vent bacterium, Thermovibrio ammonifican led to the isolation of two hydroxyethylamine chromene derivatives, ammonificins C and D. Their structures were elucidated using combination of NMR and mass spectrometry. Absolute stereochemistry was ascertained by comparison of experimental and calculated CD spectra. Biological evaluation and assessment were determined using the patented ApopScreen cell-based screen for apoptosis-induction. Ammonificins C and D induce apoptosis in micromolar concentrations. To our knowledge, this finding is the first report of chemical compounds that induce apoptosis from the cultured deep-sea marine organism, hydrothermal vent bacterium, Thermovibrio ammonificans. PMID:23170085

  17. Korormicin, a novel antibiotic specifically active against marine gram-negative bacteria, produced by a marine bacterium.

    PubMed

    Yoshikawa, K; Takadera, T; Adachi, K; Nishijima, M; Sano, H

    1997-11-01

    A novel antibiotic named korormicin was isolated from the marine bacterium, Pseudoalteromonas sp. F-420. This strain was isolated from the surface of a macro alga Halimeda sp. collected from Palau (the Republic of Belau). The planar structure of korormicin was determined by the result of 2D NMR studies and mass spectral data. Korormicin had specific inhibitory activity against marine Gram-negative bacteria, but was inactive against terrestrial microorganisms. PMID:9592569

  18. Sulfate-reducing bacteria and their activities in cyanobacterial mats of solar lake (Sinai, Egypt).

    PubMed

    Teske, A; Ramsing, N B; Habicht, K; Fukui, M; Küver, J; Jørgensen, B B; Cohen, Y

    1998-08-01

    The sulfate-reducing bacteria within the surface layer of the hypersaline cyanobacterial mat of Solar Lake (Sinai, Egypt) were investigated with combined microbiological, molecular, and biogeochemical approaches. The diurnally oxic surface layer contained between 10(6) and 10(7) cultivable sulfate-reducing bacteria ml-1 and showed sulfate reduction rates between 1,000 and 2, 200 nmol ml-1 day-1, both in the same range as and sometimes higher than those in anaerobic deeper mat layers. In the oxic surface layer and in the mat layers below, filamentous sulfate-reducing Desulfonema bacteria were found in variable densities of 10(4) to 10(6) cells ml-1. A Desulfonema-related, diurnally migrating bacterium was detected with PCR and denaturing gradient gel electrophoresis within and below the oxic surface layer. Facultative aerobic respiration, filamentous morphology, motility, diurnal migration, and aggregate formation were the most conspicuous adaptations of Solar Lake sulfate-reducing bacteria to the mat matrix and to diurnal oxygen stress. A comparison of sulfate reduction rates within the mat and previously published photosynthesis rates showed that CO2 from sulfate reduction in the upper 5 mm accounted for 7 to 8% of the total photosynthetic CO2 demand of the mat. PMID:9687455

  19. PSEUDOMONAS NATRIEGENS, A MARINE BACTERIUM WITH A GENERATION TIME OF LESS THAN 10 MINUTES

    PubMed Central

    Eagon, R. G.

    1962-01-01

    Eagon, R. G. (University of Georgia, Athens). Pseudomonas natriegens, a marine bacterium with a generation time of less than 10 minutes. J. Bacteriol. 83:736–737. 1962.—Pseudomonas natriegens, a marine microorganism, was demonstrated to have a generation time of 9.8 min. This is the shortest generation time reported to date. Optimal growth occurred at 37 C in brain heart infusion broth supplemented with 1.5% sea salt. PMID:13888946

  20. Five New Amicoumacins Isolated from a Marine-Derived Bacterium Bacillus subtilis

    PubMed Central

    Li, Yongxin; Xu, Ying; Liu, Lingli; Han, Zhuang; Lai, Pok Yui; Guo, Xiangrong; Zhang, Xixiang; Lin, Wenhan; Qian, Pei-Yuan

    2012-01-01

    Four novel amicoumacins, namely lipoamicoumacins A–D (1–4), and one new bacilosarcin analog (5) were isolated from culture broth of a marine-derived bacterium Bacillus subtilis, together with six known amicoumacins. Their structures were elucidated on the basis of extensive spectroscopic (2D NNR, IR, CD and MS) analysis and in comparison with data in literature. PMID:22412803

  1. Enzymatic iron and uranium reduction by sulfate-reducing bacteria

    USGS Publications Warehouse

    Lovley, D.R.; Roden, E.E.; Phillips, E.J.P.; Woodward, J.C.

    1993-01-01

    The potential for sulfate-reducing bacteria (SRB) to enzymatically reduce Fe(III) and U(VI) was investigated. Five species of Desulfovibrio as well as Desulfobacterium autotrophicum and Desulfobulbus propionicus reduced Fe(III) chelated with nitrilotriacetic acid as well as insoluble Fe(III) oxide. Fe(III) oxide reduction resulted in the accumulation of magnetite and siderite. Desulfobacter postgatei reduced the chelated Fe(III) but not Fe(III) oxide. Desulfobacter curvatus, Desulfomonile tiedjei, and Desulfotomaculum acetoxidans did not reduce Fe(III). Only Desulfovibrio species reduced U(VI). U(VI) reduction resulted in the precipitation of uraninite. None of the SRB that reduced Fe(III) or U(VI) appeared to conserve enough energy to support growth from this reaction. However, Desulfovibrio desulfuricans metabolized H2 down to lower concentrations with Fe(III) or U(VI) as the electron acceptor than with sulfate, suggesting that these metals may be preferred electron acceptors at the low H2 concentrations present in most marine sediments. Molybdate did not inhibit Fe(III) reduction by D. desulfuricans. This indicates that the inability of molybdate to inhibit Fe(III) reduction in marine sediments does not rule out the possibility that SRB are important catalysts for Fe(III) reduction. The results demonstrate that although SRB were previously considered to reduce Fe(III) and U(VI) indirectly through the production of sulfide, they may also directly reduce Fe(III) and U(VI) through enzymatic mechanisms. These findings, as well as our recent discovery that the So-reducing microorganism Desulfuromonas acetoxidans can reduce Fe(III), demonstrate that there are close links between the microbial sulfur, iron, and uranium cycles in anaerobic marine sediments. ?? 1993.

  2. Novel Epibiotic Thiothrix Bacterium on a Marine Amphipod

    PubMed Central

    Gillan, David C.; Dubilier, Nicole

    2004-01-01

    Comparative analysis of the 16S rRNA gene and fluorescent in situ hybridization (FISH) was used to identify epibiotic filamentous bacteria living on the marine amphipod crustacean Urothoe poseidonis. The epibionts belong to the gamma proteobacteria and represent a novel marine phylotype within the genus Thiothrix. FISH and denaturing gradient gel electrophoresis revealed that the Thiothrix filaments are present on the majority of the amphipods examined. PMID:15184190

  3. Impact of elevated nitrate on sulfate-reducing bacteria: A comparative study of Desulfovibrio vulgaris

    SciTech Connect

    He, Q.; He, Z.; Joyner, D.C.; Joachimiak, M.; Price, M.N.; Yang, Z.K.; Yen, H.-C. B.; Hemme, C. L.; Chen, W.; Fields, M.; Stahl, D. A.; Keasling, J. D.; Keller, M.; Arkin, A. P.; Hazen, T. C.; Wall, J. D.; Zhou, J.

    2010-07-15

    Sulfate-reducing bacteria have been extensively studied for their potential in heavy-metal bioremediation. However, the occurrence of elevated nitrate in contaminated environments has been shown to inhibit sulfate reduction activity. Although the inhibition has been suggested to result from the competition with nitrate-reducing bacteria, the possibility of direct inhibition of sulfate reducers by elevated nitrate needs to be explored. Using Desulfovibrio vulgaris as a model sulfate-reducing bacterium, functional genomics analysis reveals that osmotic stress contributed to growth inhibition by nitrate as shown by the upregulation of the glycine/betaine transporter genes and the relief of nitrate inhibition by osmoprotectants. The observation that significant growth inhibition was effected by 70 mM NaNO{sub 3} but not by 70 mM NaCl suggests the presence of inhibitory mechanisms in addition to osmotic stress. The differential expression of genes characteristic of nitrite stress responses, such as the hybrid cluster protein gene, under nitrate stress condition further indicates that nitrate stress response by D. vulgaris was linked to components of both osmotic and nitrite stress responses. The involvement of the oxidative stress response pathway, however, might be the result of a more general stress response. Given the low similarities between the response profiles to nitrate and other stresses, less-defined stress response pathways could also be important in nitrate stress, which might involve the shift in energy metabolism. The involvement of nitrite stress response upon exposure to nitrate may provide detoxification mechanisms for nitrite, which is inhibitory to sulfate-reducing bacteria, produced by microbial nitrate reduction as a metabolic intermediate and may enhance the survival of sulfate-reducing bacteria in environments with elevated nitrate level.

  4. Denitrification by a marine bacterium Pseudomonas nautica strain 617.

    PubMed

    Bonin, P; Gilewicz, M; Bertrand, J C

    1987-01-01

    A bacterial strain was isolated from a marine sediment highly contaminated by hydrocarbons. From taxonomic tests, it was identified as Pseudomonas nautica. This marine strain was able to grow on nitrate, nitrite and nitrous oxide as an electron acceptor. The terminal product from the denitrification was dinitrogen. Thus, P. nautica was a denitrifier. The kinetics of each step of denitrification was examined in resting cell suspensions. The relative rates of nitrate and nitrite reduction and of nitrite reduction and nitrous oxide production explain, respectively, the presence of accumulated nitrite and that of compound intermediate between nitrite and nitrous oxide. PMID:3620203

  5. Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin

    NASA Technical Reports Server (NTRS)

    Dhillon, Ashita; Teske, Andreas; Dillon, Jesse; Stahl, David A.; Sogin, Mitchell L.

    2003-01-01

    The Guaymas Basin (Gulf of California) is a hydrothermal vent site where thermal alteration of deposited planktonic and terrestrial organic matter forms petroliferous material which supports diverse sulfate-reducing bacteria. We explored the phylogenetic and functional diversity of the sulfate-reducing bacteria by characterizing PCR-amplified dissimilatory sulfite reductase (dsrAB) and 16S rRNA genes from the upper 4 cm of the Guaymas sediment. The dsrAB sequences revealed that there was a major clade closely related to the acetate-oxidizing delta-proteobacterial genus Desulfobacter and a clade of novel, deeply branching dsr sequences related to environmental dsr sequences from marine sediments in Aarhus Bay and Kysing Fjord (Denmark). Other dsr clones were affiliated with gram-positive thermophilic sulfate reducers (genus Desulfotomaculum) and the delta-proteobacterial species Desulforhabdus amnigena and Thermodesulforhabdus norvegica. Phylogenetic analysis of 16S rRNAs from the same environmental samples resulted in identification of four clones affiliated with Desulfobacterium niacini, a member of the acetate-oxidizing, nutritionally versatile genus Desulfobacterium, and one clone related to Desulfobacula toluolica and Desulfotignum balticum. Other bacterial 16S rRNA bacterial phylotypes were represented by non-sulfate reducers and uncultured lineages with unknown physiology, like OP9, OP8, as well as a group with no clear affiliation. In summary, analyses of both 16S rRNA and dsrAB clone libraries resulted in identification of members of the Desulfobacteriales in the Guaymas sediments. In addition, the dsrAB sequencing approach revealed a novel group of sulfate-reducing prokaryotes that could not be identified by 16S rRNA sequencing.

  6. Cadherin Domains in the Polysaccharide-Degrading Marine Bacterium Saccharophagus degradans 2-40 Are Carbohydrate-Binding Modules▿

    PubMed Central

    Fraiberg, Milana; Borovok, Ilya; Bayer, Edward A.; Weiner, Ronald M.; Lamed, Raphael

    2011-01-01

    The complex polysaccharide-degrading marine bacterium Saccharophagus degradans strain 2-40 produces putative proteins that contain numerous cadherin and cadherin-like domains involved in intercellular contact interactions. The current study reveals that both domain types exhibit reversible calcium-dependent binding to different complex polysaccharides which serve as growth substrates for the bacterium. PMID:21036994

  7. Chitin Degradation Proteins Produced by the Marine Bacterium Vibrio harveyi Growing on Different Forms of Chitin

    PubMed Central

    Svitil, A. L.; Chadhain, S.; Moore, J. A.; Kirchman, D. L.

    1997-01-01

    Relatively little is known about the number, diversity, and function of chitinases produced by bacteria, even though chitin is one of the most abundant polymers in nature. Because of the importance of chitin, especially in marine environments, we examined chitin-degrading proteins in the marine bacterium Vibrio harveyi. This bacterium had a higher growth rate and more chitinase activity when grown on (beta)-chitin (isolated from squid pen) than on (alpha)-chitin (isolated from snow crab), probably because of the more open structure of (beta)-chitin. When exposed to different types of chitin, V. harveyi excreted several chitin-degrading proteins into the culture media. Some chitinases were present with all of the tested chitins, while others were unique to a particular chitin. We cloned and identified six separate chitinase genes from V. harveyi. These chitinases appear to be unique based on DNA restriction patterns, immunological data, and enzyme activity. This marine bacterium and probably others appear to synthesize separate chitinases for efficient utilization of different forms of chitin and chitin by-products. PMID:16535505

  8. The mannitol utilization system of the marine bacterium Zobellia galactanivorans.

    PubMed

    Groisillier, Agnès; Labourel, Aurore; Michel, Gurvan; Tonon, Thierry

    2015-03-01

    Mannitol is a polyol that occurs in a wide range of living organisms, where it fulfills different physiological roles. In particular, mannitol can account for as much as 20 to 30% of the dry weight of brown algae and is likely to be an important source of carbon for marine heterotrophic bacteria. Zobellia galactanivorans (Flavobacteriia) is a model for the study of pathways involved in the degradation of seaweed carbohydrates. Annotation of its genome revealed the presence of genes potentially involved in mannitol catabolism, and we describe here the biochemical characterization of a recombinant mannitol-2-dehydrogenase (M2DH) and a fructokinase (FK). Among the observations, the M2DH of Z. galactanivorans was active as a monomer, did not require metal ions for catalysis, and featured a narrow substrate specificity. The FK characterized was active on fructose and mannose in the presence of a monocation, preferentially K(+). Furthermore, the genes coding for these two proteins were adjacent in the genome and were located directly downstream of three loci likely to encode an ATP binding cassette (ABC) transporter complex, suggesting organization into an operon. Gene expression analysis supported this hypothesis and showed the induction of these five genes after culture of Z. galactanivorans in the presence of mannitol as the sole source of carbon. This operon for mannitol catabolism was identified in only 6 genomes of Flavobacteriaceae among the 76 publicly available at the time of the analysis. It is not conserved in all Bacteroidetes; some species contain a predicted mannitol permease instead of a putative ABC transporter complex upstream of M2DH and FK ortholog genes. PMID:25548051

  9. Characterization of a marine origin aerobic nitrifying-denitrifying bacterium.

    PubMed

    Zheng, Hai-Yan; Liu, Ying; Gao, Xi-Yan; Ai, Guo-Min; Miao, Li-Li; Liu, Zhi-Pei

    2012-07-01

    The bacterial strain F6 was isolated from a biological aerated filter that is used for purifying recirculating water in a marine aquaculture system and was identified as Marinobacter sp. based on the analysis of its 16S rRNA gene sequence. Strain F6 showed efficient aerobic denitrifying ability. One hundred percent of nitrates and 73.10% of nitrites were removed, and the total nitrogen (TN) removal rates reached 50.08% and 33.03% under a high nitrate and nitrite concentration in the medium, respectively. N(2)O and (15)N(2), as revealed by GC-MS and GC-IRMS, were the products of aerobic denitrification. Factors affecting the growth and aerobic denitrifying performance of strain F6 were investigated. The results showed that the optimum aerobic denitrification conditions for strain F6 were the presence of sodium succinate as a carbon source, a C/N ratio of 15, salinity ranging from 32-35 g/L of NaCl, incubation temperature of 30°C, an initial pH of 7.5, and rotation speed of 150 rpm [dissolved oxygen (DO) 6.75 mg/L]. In addition, strain F6 was confirmed to be a heterotrophic nitrifier through its NO(2)(-) generation and 25.96% TN removal when NH(4)(+) was used as the sole N source. Therefore, strain F6, the first reported member of genus Marinobacter with aerobic heterotrophic nitrifying-denitrifying ability, is an excellent candidate for facilitating simultaneous nitrification and denitrification (SND) in industry and aquaculture wastewater. PMID:22578593

  10. The Mannitol Utilization System of the Marine Bacterium Zobellia galactanivorans

    PubMed Central

    Groisillier, Agnès; Labourel, Aurore; Michel, Gurvan

    2014-01-01

    Mannitol is a polyol that occurs in a wide range of living organisms, where it fulfills different physiological roles. In particular, mannitol can account for as much as 20 to 30% of the dry weight of brown algae and is likely to be an important source of carbon for marine heterotrophic bacteria. Zobellia galactanivorans (Flavobacteriia) is a model for the study of pathways involved in the degradation of seaweed carbohydrates. Annotation of its genome revealed the presence of genes potentially involved in mannitol catabolism, and we describe here the biochemical characterization of a recombinant mannitol-2-dehydrogenase (M2DH) and a fructokinase (FK). Among the observations, the M2DH of Z. galactanivorans was active as a monomer, did not require metal ions for catalysis, and featured a narrow substrate specificity. The FK characterized was active on fructose and mannose in the presence of a monocation, preferentially K+. Furthermore, the genes coding for these two proteins were adjacent in the genome and were located directly downstream of three loci likely to encode an ATP binding cassette (ABC) transporter complex, suggesting organization into an operon. Gene expression analysis supported this hypothesis and showed the induction of these five genes after culture of Z. galactanivorans in the presence of mannitol as the sole source of carbon. This operon for mannitol catabolism was identified in only 6 genomes of Flavobacteriaceae among the 76 publicly available at the time of the analysis. It is not conserved in all Bacteroidetes; some species contain a predicted mannitol permease instead of a putative ABC transporter complex upstream of M2DH and FK ortholog genes. PMID:25548051

  11. Development of a gene cloning system for the hydrogen-producing marine photosynthetic bacterium Rhodopseudomonas sp.

    PubMed Central

    Matsunaga, T; Matsunaga, N; Tsubaki, K; Tanaka, T

    1986-01-01

    Seventy-six strains of marine photosynthetic bacteria were analyzed by agarose gel electrophoresis for plasmid DNA content. Among these strains, 12 carried two to four different plasmids with sizes ranging from 3.1 to 11.0 megadaltons. The marine photosynthetic bacterium Rhodopseudomonas sp. NKPB002106 had two plasmids, pRD06S and pRD06L. The smaller plasmid, pRD06S, had a molecular weight of 3.8 megadaltons and was cut at a single site by restriction endonucleases SalI, SmaI, PstI, XhoI, and BglII. Moreover, the marine photosynthetic bacterium Rhodopseudomonas sp. NKPB002106 containing plasmid pRD06 had a satisfactory growth rate (doubling time, 7.5 h), a hydrogen-producing rate of 0.96 mumol/mg (dry weight) of cells per h, and nitrogen fixation capability. Plasmid pRD06S, however, had neither drug resistance nor heavy-metal resistance, and its copy number was less than 10. Therefore, a recombinant plasmid consisting of pRD06S and Escherichia coli cloning vector pUC13 was constructed and cloned in E. coli. The recombinant plasmid was transformed into Rhodopseudomonas sp. NKPB002106. As a result, Rhodopseudomonas sp. NKPB002106 developed ampicillin resistance. Thus, a shuttle vector for gene transfer was constructed for marine photosynthetic bacteria. PMID:3020006

  12. Methods for Engineering Sulfate Reducing Bacteria of the Genus Desulfovibrio

    SciTech Connect

    Chhabra, Swapnil R; Keller, Kimberly L.; Wall, Judy D.

    2011-03-15

    Sulfate reducing bacteria are physiologically important given their nearly ubiquitous presence and have important applications in the areas of bioremediation and bioenergy. This chapter provides details on the steps used for homologous-recombination mediated chromosomal manipulation of Desulfovibrio vulgaris Hildenborough, a well-studied sulfate reducer. More specifically, we focus on the implementation of a 'parts' based approach for suicide vector assembly, important aspects of anaerobic culturing, choices for antibiotic selection, electroporation-based DNA transformation, as well as tools for screening and verifying genetically modified constructs. These methods, which in principle may be extended to other sulfate-reducing bacteria, are applicable for functional genomics investigations, as well as metabolic engineering manipulations.

  13. The structure of ferricytochrome c552 from the psychrophilic marine bacterium Colwellia psychrerythraea 34H

    PubMed Central

    Harvilla, Paul B.; Wolcott, Holly N.

    2014-01-01

    Approximately 40% of all proteins are metalloproteins, and approximately 80% of Earth’s ecosystems are at temperatures ≤ 5 °C, including 90% of the global ocean. Thus, an essential aspect of marine metallobiochemistry is an understanding of the structure, dynamics, and mechanisms of cold adaptation of metalloproteins from marine microorganisms. Here, the molecular structure of the electron-transfer protein cytochrome c552 from the psychrophilic marine bacterium Colwellia psychrerythraea 34H has been determined by X-ray crystallography (PDB: 4O1W). The structure is highly superimposable with that of the homologous cytochrome from the mesophile Marinobacter hydrocarbonoclasticus. Based on structural analysis and comparison of psychrophilic, psychrotolerant, and mesophilic sequences, a methionine-based ligand-substitution mechanism for psychrophilic protein stabilization is proposed. PMID:24727932

  14. The structure of ferricytochrome c552 from the psychrophilic marine bacterium Colwellia psychrerythraea 34H.

    PubMed

    Harvilla, Paul B; Wolcott, Holly N; Magyar, John S

    2014-06-01

    Approximately 40% of all proteins are metalloproteins, and approximately 80% of Earth's ecosystems are at temperatures ≤5 °C, including 90% of the global ocean. Thus, an essential aspect of marine metallobiochemistry is an understanding of the structure, dynamics, and mechanisms of cold adaptation of metalloproteins from marine microorganisms. Here, the molecular structure of the electron-transfer protein cytochrome c552 from the psychrophilic marine bacterium Colwellia psychrerythraea 34H has been determined by X-ray crystallography (PDB: ). The structure is highly superimposable with that of the homologous cytochrome from the mesophile Marinobacter hydrocarbonoclasticus. Based on structural analysis and comparison of psychrophilic, psychrotolerant, and mesophilic sequences, a methionine-based ligand-substitution mechanism for psychrophilic protein stabilization is proposed. PMID:24727932

  15. Complete Genome Sequence of a Marine Bacterium, Pseudomonas pseudoalcaligenes Strain S1, with High Mercury Resistance and Bioaccumulation Capacity.

    PubMed

    Liu, Bing; Bian, Chao; Huang, Huiwei; Yin, Zhiwei; Shi, Qiong; Deng, Xu

    2016-01-01

    Pseudomonas pseudoalcaligenes S1, a marine bacterium, exhibited strong resistance to a high concentration of Hg(2+) and remarkable Hg(2+) bioaccumulation capacity. Here, we report the 6.9-Mb genome sequence of P. pseudoalcaligenes S1, which may help clarify its phylogenetic status and provide further understanding of the mechanisms of mercury bioremediation in a marine environment. PMID:27198018

  16. Isolation and biological characteristics of aerobic marine magnetotactic bacterium YSC-1

    NASA Astrophysics Data System (ADS)

    Gao, Jun; Pan, Hongmiao; Yue, Haidong; Song, Tao; Zhao, Yong; Chen, Guanjun; Wu, Longfei; Xiao, Tian

    2006-12-01

    Magnetotactic bacteria have become a hot spot of research in microbiology attracting intensive interest of researchers in multiple disciplinary fields. However, the studies were limited in few fastidious bacteria. The objective of this study aims at isolating new marine magnetic bacteria and better comprehension of magnetotactic bacteria. In this study, an aerobic magnetotactic bacterium YSC-1 was isolated from sediments in the Yellow Sea Cold Water Mass (YSCWM). In TEM, magnetic cells have one or several circular magnetosomes in diameter of 100nm, and consist of Fe and Co shown on energy dispersive X-ray spectrum. The biological and physiological characteristics of this bacterium were also described. The colour of YSC-1 colony is white in small rod. The gram stain is negative. Results showed that Strain YSC-1 differs from microaerophile magnetotactic bacteria MS-1 and WD-1 in biology.

  17. N-Acyl Dehydrotyrosines, Tyrosinase Inhibitors from the Marine Bacterium Thalassotalea sp. PP2-459.

    PubMed

    Deering, Robert W; Chen, Jianwei; Sun, Jiadong; Ma, Hang; Dubert, Javier; Barja, Juan L; Seeram, Navindra P; Wang, Hong; Rowley, David C

    2016-02-26

    Thalassotalic acids A-C and thalassotalamides A and B are new N-acyl dehydrotyrosine derivatives produced by Thalassotalea sp. PP2-459, a Gram-negative bacterium isolated from a marine bivalve aquaculture facility. The structures were elucidated via a combination of spectroscopic analyses emphasizing two-dimensional NMR and high-resolution mass spectrometric data. Thalassotalic acid A (1) displays in vitro inhibition of the enzyme tyrosinase with an IC50 value (130 μM) that compares favorably to the commercially used control compounds kojic acid (46 μM) and arbutin (100 μM). These are the first natural products reported from a bacterium belonging to the genus Thalassotalea. PMID:26824128

  18. Isolation of Sulfate-Reducing Bacteria from Human Thoracoabdominal Pus

    PubMed Central

    Loubinoux, Julien; Jaulhac, Benoit; Piemont, Yves; Monteil, Henri; Le Faou, Alain E.

    2003-01-01

    To evaluate the prevalence of sulfate-reducing bacteria in septic processes, we searched for these bacteria by culture in 100 consecutive abdominal and pleural pus specimens. Twelve isolates were obtained from abdominal samples and were identified by a multiplex PCR as Desulfovibrio piger (formerly Desulfomonas pigra) (seven strains), Desulfovibrio fairfieldensis (four strains), and Desulfovibrio desulfuricans (one strain). PMID:12624073

  19. Remediation of Acid Mine Drainage with Sulfate Reducing Bacteria

    ERIC Educational Resources Information Center

    Hauri, James F.; Schaider, Laurel A.

    2009-01-01

    Sulfate reducing bacteria have been shown to be effective at treating acid mine drainage through sulfide production and subsequent precipitation of metal sulfides. In this laboratory experiment for undergraduate environmental chemistry courses, students design and implement a set of bioreactors to remediate acid mine drainage and explain observed…

  20. Bisucaberin B, a linear hydroxamate class siderophore from the marine bacterium Tenacibaculum mesophilum.

    PubMed

    Fujita, Masaki J; Nakano, Koji; Sakai, Ryuichi

    2013-01-01

    A siderophore, named bisucaberin B, was isolated from Tenacibaculum mesophilum bacteria separated from a marine sponge collected in the Republic of Palau. Using spectroscopic and chemical methods, the structure of bisucaberin B (1) was clearly determined to be a linear dimeric hydroxamate class siderophore. Although compound 1 is an open form of the known macrocyclic dimer bisucaberin (2), and was previously described as a bacterial degradation product of desferrioxamine B (4), the present report is the first description of the de novo biosynthesis of 1. To the best of our knowledge, compound 1 is the first chemically characterized siderophore isolated from a bacterium belonging to the phylum Bacteroidetes. PMID:23549298

  1. An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3

    PubMed Central

    2014-01-01

    When the genome of Ruegeria pomeroyi DSS-3 was published in 2004, it represented the first sequence from a heterotrophic marine bacterium. Over the last ten years, the strain has become a valuable model for understanding the cycling of sulfur and carbon in the ocean. To ensure that this genome remains useful, we have updated 69 genes to incorporate functional annotations based on new experimental data, and improved the identification of 120 protein-coding regions based on proteomic and transcriptomic data. We review the progress made in understanding the biology of R. pomeroyi DSS-3 and list the changes made to the genome. PMID:25780504

  2. Desulfotomaculum spp. and related gram-positive sulfate-reducing bacteria in deep subsurface environments

    PubMed Central

    Aüllo, Thomas; Ranchou-Peyruse, Anthony; Ollivier, Bernard; Magot, Michel

    2013-01-01

    Gram-positive spore-forming sulfate reducers and particularly members of the genus Desulfotomaculum are commonly found in the subsurface biosphere by culture based and molecular approaches. Due to their metabolic versatility and their ability to persist as endospores. Desulfotomaculum spp. are well-adapted for colonizing environments through a slow sedimentation process. Because of their ability to grow autotrophically (H2/CO2) and produce sulfide or acetate, these microorganisms may play key roles in deep lithoautotrophic microbial communities. Available data about Desulfotomaculum spp. and related species from studies carried out from deep freshwater lakes, marine sediments, oligotrophic and organic rich deep geological settings are discussed in this review. PMID:24348471

  3. Complete Genome Sequence of the Complex Carbohydrate-Degrading Marine Bacterium, Saccharophagus degradans Strain 2-40T

    PubMed Central

    Weiner, Ronald M.; Taylor, Larry E.; Henrissat, Bernard; Hauser, Loren; Land, Miriam; Coutinho, Pedro M.; Rancurel, Corinne; Saunders, Elizabeth H.; Longmire, Atkinson G.; Zhang, Haitao; Bayer, Edward A.; Gilbert, Harry J.; Larimer, Frank; Zhulin, Igor B.; Ekborg, Nathan A.; Lamed, Raphael; Richardson, Paul M.; Borovok, Ilya; Hutcheson, Steven

    2008-01-01

    The marine bacterium Saccharophagus degradans strain 2-40 (Sde 2-40) is emerging as a vanguard of a recently discovered group of marine and estuarine bacteria that recycles complex polysaccharides. We report its complete genome sequence, analysis of which identifies an unusually large number of enzymes that degrade >10 complex polysaccharides. Not only is this an extraordinary range of catabolic capability, many of the enzymes exhibit unusual architecture including novel combinations of catalytic and substrate-binding modules. We hypothesize that many of these features are adaptations that facilitate depolymerization of complex polysaccharides in the marine environment. This is the first sequenced genome of a marine bacterium that can degrade plant cell walls, an important component of the carbon cycle that is not well-characterized in the marine environment. PMID:18516288

  4. Microfabrication of patterns of adherent marine bacterium Phaeobacter inhibens using soft lithography and scanning probe lithography.

    PubMed

    Zhao, Chuan; Burchardt, Malte; Brinkhoff, Thorsten; Beardsley, Christine; Simon, Meinhard; Wittstock, Gunther

    2010-06-01

    Two lithographic approaches have been explored for the microfabrication of cellular patterns based on the attachment of marine bacterium Phaeobacter inhibens strain T5. Strain T5 produces a new antibiotic that makes this bacterium potentially interesting for the pharmaceutical market and as a probiotic organism in aquacultures and in controlling biofouling. The microcontact printing (microCP) method is based on the micropatterning of self-assembled monolayers (SAMs) terminated with adhesive end groups such as CH(3) and COOH and nonadhesive groups (e.g., short oligomers of ethylene glycol (OEG)) to form micropatterned substrates for the adhesion of strain T5. The scanning probe lithographic method is based on the surface modification of OEG SAM by using a microelectrode, the probe of a scanning electrochemical microscope (SECM). Oxidizing agents (e.g., Br(2)) were electrogenerated in situ at the microelectrodes from Br(-) in aqueous solution to remove OEG SAMs locally, which allows the subsequent adsorption of bacteria. Various micropatterns of bacteria could be formed in situ on the substrate without a prefabricated template. The fabricated cellular patterns may be applied to a variety of marine biological studies that require the analysis of biofilm formation, cell-cell and cell-surface interactions, and cell-based biosensors and bioelectronics. PMID:20397716

  5. Enrichment and physiological characterization of a novel Nitrospira-like bacterium obtained from a marine sponge.

    PubMed

    Off, Sandra; Alawi, Mashal; Spieck, Eva

    2010-07-01

    Members of the nitrite-oxidizing genus Nitrospira are most likely responsible for the second step of nitrification, the conversion of nitrite (NO(2)(-)) to nitrate (NO(3)(-)), within various sponges. We succeeded in obtaining an enrichment culture of Nitrospira derived from the mesohyl of the marine sponge Aplysina aerophoba using a traditional cultivation approach. Electron microscopy gave first evidence of the shape and ultrastructure of this novel marine Nitrospira-like bacterium (culture Aa01). We characterized these bacteria physiologically with regard to optimal incubation conditions, especially the temperature and substrate range in comparison to other Nitrospira cultures. Best growth was obtained at temperatures between 28 degrees C and 30 degrees C in mineral medium with 70% North Sea water and a substrate concentration of 0.5 mM nitrite under microaerophilic conditions. The Nitrospira culture Aa01 is very sensitive against nitrite, because concentrations higher than 1.5 mM resulted in a complete inhibition of growth. Sequence analyses of the 16S rRNA gene revealed that the novel Nitrospira-like bacterium is separated from the sponge-specific subcluster and falls together with an environmental clone from Mediterranean sediments (98.6% similarity). The next taxonomically described species Nitrospira marina is only distantly related, with 94.6% sequence similarity, and therefore the culture Aa01 represents a novel species of nitrite-oxidizing bacteria. PMID:20511427

  6. Data supporting functional diversity of the marine bacterium Cobetia amphilecti KMM 296.

    PubMed

    Balabanova, Larissa; Nedashkovskaya, Olga; Podvolotskaya, Anna; Slepchenko, Lubov; Golotin, Vasily; Belik, Alexey; Shevchenko, Ludmila; Son, Oksana; Rasskazov, Valery

    2016-09-01

    Data is presented in support of functionality of hyper-diverse protein families encoded by the Cobetia amphilecti KMM 296 (formerly Cobetia marina KMM 296) genome ("The genome of the marine bacterium Cobetia marina KMM 296 isolated from the mussel Crenomytilus grayanus (Dunker, 1853)" [1]) providing its nutritional versatility, adaptability and biocontrol that could be the basis of the marine bacterium evolutionary and application potential. Presented data include the information of growth and biofilm-forming properties of the food-associated isolates of Pseudomonas, Bacillus, Listeria, Salmonella and Staphylococcus under the conditions of their co-culturing with C. amphilecti KMM 296 to confirm its high inter-species communication and anti-microbial activity. Also included are the experiments on the crude petroleum consumption by C. amphilecti KMM 296 as the sole source of carbon in the presence of sulfate or nitrate to ensure its bioremediation capacity. The multifunctional C. amphilecti KMM 296 genome is a promising source for the beneficial psychrophilic enzymes and essential secondary metabolites. PMID:27508225

  7. Isolation and Characterization of Strain MMB-1 (CECT 4803), a Novel Melanogenic Marine Bacterium.

    PubMed

    Solano, F; Garcia, E; Perez, D; Sanchez-Amat, A

    1997-09-01

    A novel marine melanogenic bacterium, strain MMB-1, was isolated from the Mediterranean Sea. The taxonomic characterization of this strain indicated that it belongs to the genus Alteromonas. Under in vivo conditions, L-tyrosine was the specific monophenolic precursor for melanin synthesis. This bacterium contained all types of activities associated with polyphenol oxidases (PPOs), cresolase (EC 1.18.14.1), catecholase (EC 1.10.3.1), and laccase (EC 1.10.3.2). These activities were due to the presence of two different PPOs. The first one showed all the enzymatic activities, but it was not involved in melanogenesis in vivo, since amelanogenic mutant strains obtained by nitrosoguanidine treatment contained levels of this PPO similar to that of the wild-type MMB-1 strain. The second PPO showed cresolase and catecholase activities but no laccase, and it was involved in melanogenesis, since this enzyme was lost in amelanogenic mutant strains. This PPO was strongly activated by sodium dodecyl sulfate below the critical micelle concentration, and it is a tyrosinase-like enzyme showing a lag period in its tyrosine hydroxylase activity that could be avoided by small amounts of L-dopa. This is the first report of a bacterium that contains two PPOs and also the first report of a pluripotent PPO showing all types of oxidase activities. The bacterium and the pluripotent PPO may be useful models for exploring the roles of PPOs in cellular physiology, aside from melanin formation. On the other hand, the high oxidizing capacity of the PPO for a wide range of substrates could make possible its application in phenolic biotransformations, food processing, or the cosmetic industry, where fungal and plant PPOs are being used. PMID:16535688

  8. Isolation and Characterization of Strain MMB-1 (CECT 4803), a Novel Melanogenic Marine Bacterium

    PubMed Central

    Solano, F.; Garcia, E.; Perez, De; Sanchez-Amat, A.

    1997-01-01

    A novel marine melanogenic bacterium, strain MMB-1, was isolated from the Mediterranean Sea. The taxonomic characterization of this strain indicated that it belongs to the genus Alteromonas. Under in vivo conditions, L-tyrosine was the specific monophenolic precursor for melanin synthesis. This bacterium contained all types of activities associated with polyphenol oxidases (PPOs), cresolase (EC 1.18.14.1), catecholase (EC 1.10.3.1), and laccase (EC 1.10.3.2). These activities were due to the presence of two different PPOs. The first one showed all the enzymatic activities, but it was not involved in melanogenesis in vivo, since amelanogenic mutant strains obtained by nitrosoguanidine treatment contained levels of this PPO similar to that of the wild-type MMB-1 strain. The second PPO showed cresolase and catecholase activities but no laccase, and it was involved in melanogenesis, since this enzyme was lost in amelanogenic mutant strains. This PPO was strongly activated by sodium dodecyl sulfate below the critical micelle concentration, and it is a tyrosinase-like enzyme showing a lag period in its tyrosine hydroxylase activity that could be avoided by small amounts of L-dopa. This is the first report of a bacterium that contains two PPOs and also the first report of a pluripotent PPO showing all types of oxidase activities. The bacterium and the pluripotent PPO may be useful models for exploring the roles of PPOs in cellular physiology, aside from melanin formation. On the other hand, the high oxidizing capacity of the PPO for a wide range of substrates could make possible its application in phenolic biotransformations, food processing, or the cosmetic industry, where fungal and plant PPOs are being used. PMID:16535688

  9. [Achievement of Sulfate-Reducing Anaerobic Ammonium Oxidation Reactor Started with Nitrate-Reducting Anaerobic Ammonium Oxidation].

    PubMed

    Liu, Zheng-chuan; Yuan, Lin-jiang; Zhou, Guo-biao; Li, Jing

    2015-09-01

    The transformation of nitrite-reducing anaerobic ammonium oxidation to sulfate-reducing anaerobic ammonium oxidation in an UASB was performed and the changes in microbial community were studied. The result showed that the sulfate reducing anaerobic ammonium oxidation process was successfully accomplished after 177 days' operation. The removal rate of ammonium nitrogen and sulfate were up to 58. 9% and 15. 7%, the removing load of ammonium nitrogen and sulfate were 74. 3 mg.(L.d)-1 and 77. 5 mg.(L.d)-1 while concentration of ammonium nitrogen and sulfate of influent were 130 mg.(L.d)-1 and 500 mg.(L.d)-1, respectively. The lost nitrogen and sulphur was around 2 in molar ratio. The pH value of the effluent was lower than that of the influent. Instead of Candidatus brocadia in nitrite reducing anaerobic ammonium oxidation granular sludge, Bacillus benzoevorans became the dominant species in sulfate reducing anaerobic ammonium oxidation sludge. The dominant bacterium in the two kinds of anaerobic ammonium oxidation process is different. Our results imply that the two anaerobic ammonium oxidation processes are carried out by different kind of bacterium. PMID:26717697

  10. Stable isotopic studies of n-alkane metabolism by a sulfate-reducing bacterial enrichment culture.

    PubMed

    Davidova, Irene A; Gieg, Lisa M; Nanny, Mark; Kropp, Kevin G; Suflita, Joseph M

    2005-12-01

    Gas chromatography-mass spectrometry and nuclear magnetic resonance spectroscopy were used to study the metabolism of deuterated n-alkanes (C6 to C12) and 1-13C-labeled n-hexane by a highly enriched sulfate-reducing bacterial culture. All substrates were activated via fumarate addition to form the corresponding alkylsuccinic acid derivatives as transient metabolites. Formation of d14-hexylsuccinic acid in cell extracts from exogenously added, fully deuterated n-hexane confirmed that this reaction was the initial step in anaerobic alkane metabolism. Analysis of resting cell suspensions amended with 1-13C-labeled n-hexane confirmed that addition of the fumarate occurred at the C-2 carbon of the parent substrate. Subsequent metabolism of hexylsuccinic acid resulted in the formation of 4-methyloctanoic acid, and 3-hydroxy-4-methyloctanoic acid was tentatively identified. We also found that 13C nuclei from 1-13C-labeled n-hexane became incorporated into the succinyl portion of the initial metabolite in a manner that indicated that 13C-labeled fumarate was formed and recycled during alkane metabolism. Collectively, the findings obtained with a sulfate-reducing culture using isotopically labeled alkanes augment and support the previously proposed pathway (H. Wilkes, R. Rabus, T. Fischer, A. Armstroff, A. Behrends, and F. Widdel, Arch. Microbiol. 177:235-243, 2002) for metabolism of deuterated n-hexane by a denitrifying bacterium. PMID:16332800

  11. Oxidation of polycyclic aromatic hydrocarbons under sulfate-reducing conditions

    USGS Publications Warehouse

    Coates, J.D.; Anderson, R.T.; Lovley, D.R.

    1996-01-01

    [14C]naphthalene and phenanthrene were oxidized to 14CO2 without a detectable lag under strict anaerobic conditions in sediments from San Diego Bay, San Diego, Calif., that were heavily contaminated with polycyclic aromatic hydrocarbons (PAHs) but not in less contaminated sediments. Sulfate reduction was necessary for PAH oxidation. These results suggest that the self-purification capacity of PAH-contaminated sulfate-reducing environments may be greater than previously recognized.

  12. Remediation of acid mine drainage with sulfate reducing bacteria

    SciTech Connect

    Hauri, J.F.; Schaider, L.A.

    2009-02-15

    Sulfate reducing bacteria have been shown to be effective at treating acid mine drainage through sulfide production and subsequent precipitation of metal sulfides. In this laboratory experiment for undergraduate environmental chemistry courses, students design and implement a set of bioreactors to remediate acid mine drainage and explain observed changes in dissolved metal concentrations and pH. Using synthetic acid mine drainage and combinations of inputs, students monitor their bioreactors for decreases in dissolved copper and iron concentrations.

  13. Bioremediation of coal contaminated soil under sulfate-reducing condition.

    PubMed

    Kuwano, Y; Shimizu, Y

    2006-01-01

    The objective of this study was to investigate the biodegradation of coal-derived hydrocarbons, especially high molecular weight (HMW) components, under anaerobic conditions. For this purpose biodegradation experiments were performed, using specifically designed soil column bioreactors. For the experiment, coal-contaminated soil was prepared, which contains high molecular weight hydrocarbons at high concentration (approx. 55.5 mgC g-drysoil(-1)). The experiment was carried out in two different conditions: sulfate reducing (SR) condition (SO4(2-) = 10 mmol l(-1) in the liquid medium) and control condition (SO4(2-)<0.5 mmol l(-1)). Although no degradation was observed under the control condition, the resin fraction decreased to half (from 6,541 to 3,386 mgC g-soil(-1)) under SR condition, with the concomitant increase of two PAHs (phenanthrene and fluoranthene, 9 and 2.5 times, respectively). From these results, we could conclude that high molecular hydrocarbons were biodegradable and transformed to low molecular weight PAHs under the sulfate-reducing condition. Since these PAHs are known to be biologically degraded under aerobic condition, a serial combination of anaerobic (sulfate reducing) and then aerobic bioremediations could be effective and useful for the soil pollution by petroleum and/or coal derived hydrocarbons. PMID:16457179

  14. Inhibiting mild steel corrosion from sulfate-reducing and iron-oxidizing bacteria using gramicidin-S-producing biofilms.

    PubMed

    Zuo, Rongjun; Wood, Thomas K

    2004-11-01

    A gramicidin-S-producing Bacillus brevis 18-3 biofilm was shown to reduce corrosion rates of mild steel by inhibiting both the sulfate-reducing bacterium Desulfosporosinus orientis and the iron-oxidizing bacterium Leptothrix discophora SP-6. When L. discophora SP-6 was introduced along with D. orientis to a non-antimicrobial-producing biofilm control, Paenibacillus polymyxa ATCC 10401, a corrosive synergy was created and mild steel coupons underwent more severe corrosion than when only D. orientis was present, showing a 2.3-fold increase via electrochemical impedance spectroscopy (EIS) and a 1.8-fold difference via mass-loss measurements. However, when a gramicidin-S-producing, protective B. brevis 18-3 biofilm was established on mild steel, the metal coupons were protected against the simultaneous attack of D. orientis and L. discophora SP-6. EIS data showed that the protective B. brevis 18-3 biofilm decreased the corrosion rate about 20-fold compared with the non-gramicidin-producing P. polymyxa ATCC 10401 biofilm control. The mass loss for the protected mild steel coupons was also significantly lower than that for the unprotected ones (4-fold decrease). Scanning electron microscope images corroborated the corrosion inhibition by the gramicidin-S-producing B. brevis biofilm on mild steel by showing that the metal surface remained untarnished, i.e., the polishing grooves were still visible after exposure to the simultaneous attack of the sulfate-reducing bacterium and the iron-oxidizing bacterium. PMID:15278311

  15. Modification of Lignins by Growing Cells of the Sulfate-Reducing Anaerobe Desulfovibrio desulfuricans†

    PubMed Central

    Ziomek, E.; Williams, R. E.

    1989-01-01

    The anaerobic sulfate-reducing bacterium Desulfovibrio desulfuricans was grown on medium supplemented with either Kraft lignin or lignosulfonate. Only lignosulfonate contributed to the growth of D. desulfuricans cells, by replacing sulfate, a natural electron acceptor for this microorganism. Kraft lignin added to the culture medium could not substitute for lactate or sulfate, both necessary culture medium components. However, it was found to enhance the viability of D. desulfuricans cells. When changes occurring in lignin during growth of Desulfovibrio cultures were monitored, it was found that both lignin preparations could be partially depolymerized. Spectrophotometric and elemental analysis of biologically treated lignins suggested that both the polyphenolic backbone and lignin functional groups were affected by D. desulfuricans. After treatment, a twofold increase in the sulfur content of Kraft lignin and a minor decrease (14%) in the sulfur content of lignosulfonate were observed. After biological treatment, Kraft lignin and lignosulfonate both bound larger quantities of heavy metals. PMID:16348007

  16. Fabivirga thermotolerans gen. nov., sp. nov., a novel marine bacterium isolated from culture broth of a marine cyanobacterium.

    PubMed

    Tang, M; Chen, C; Li, J; Xiang, W; Wu, H; Wu, J; Dai, S; Wu, H; Li, T; Wang, G

    2016-02-01

    A Gram-stain-negative, red, non-spore-forming, strictly aerobic bacterium, designated strain A4T, was isolated from culture broth of a marine cyanobacterium. Cells were flexible rods with gliding motility. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain A4T formed a coherent cluster with members of the genera Roseivirga and Fabibacter, and represents a distinct lineage in the family Flammeovirgaceae. Thermotolerance and a distinctive cellular fatty acid profile could readily distinguish this isolate from any bacteria of the genera Roseivirga and Fabibacter with a validly published name. On the basis of the phenotypic, chemotaxonomic and phylogenetic characteristics, strain A4T is suggested to represent a novel species in a novel genus, for which the name Fabivirga thermotolerans gen. nov., sp. nov. is proposed. The type strain is A4T ( = KCTC 42507T = CGMCC 1.15111T). PMID:26652750

  17. Comparison of sulfate-reducing and conventional Anammox upflow anaerobic sludge blanket reactors.

    PubMed

    Rikmann, Ergo; Zekker, Ivar; Tomingas, Martin; Vabamäe, Priit; Kroon, Kristel; Saluste, Alar; Tenno, Taavo; Menert, Anne; Loorits, Liis; Rubin, Sergio S C dC; Tenno, Toomas

    2014-10-01

    Autotrophic NH4(+) removal has been extensively researched, but few studies have investigated alternative electron acceptors (for example, SO4(2-)) in NH4(+) oxidation. In this study, sulfate-reducing anaerobic ammonium oxidation (SRAO) and conventional Anammox were started up in upflow anaerobic sludge blanket reactors (UASBRs) at 36 (±0.5)°C and 20 (±0.5)°C respectively, using reject water as a source of NH4(+). SO4(2-) or NO2(-), respectively, were applied as electron acceptors. It was assumed that higher temperature could promote the SRAO, partly compensating its thermodynamic disadvantage comparing with the conventional Anammox to achieve comparable total nitrogen (TN) removal rate. Average volumetric NH4(+)-N removal rate in the sulfate-reducing UASBR1 was however 5-6 times less (0.03 kg-N/(m(3) day)) than in the UASBR2 performing conventional nitrite-dependent autotrophic nitrogen removal (0.17 kg-N/(m(3) day)). However, the stoichiometric ratio of NH4(+) removal in UASBR1 was significantly higher than could be expected from the extent of SO4(2-) reduction, possibly due to interactions between the N- and S-compounds and organic matter of the reject water. Injections of N2H4 and NH2OH accelerated the SRAO. Similar effect was observed in batch tests with anthraquinone-2,6-disulfonate (AQDS). For detection of key microorganisms PCR-DGGE was used. From both UASBRs, uncultured bacterium clone ATB-KS-1929 belonging to the order Verrucomicrobiales, Anammox bacteria (uncultured Planctomycete clone Pla_PO55-9) and aerobic ammonium-oxidizing bacteria (uncultured sludge bacterium clone ASB08 "Nitrosomonas") were detected. Nevertheless the SRAO process was shown to be less effective for the treatment of reject water, compared to the conventional Anammox. PMID:24863179

  18. Complete Genome Sequence of the Complex Carbohydrate-Degrading Marine Bacterium, Saccharophagus degradans strain 2-40

    SciTech Connect

    Weiner, Ronald M; TaylorII, Larry E; Henrissat, Bernard; Hauser, Loren John; Land, Miriam L; Coutinho, Pedro M; Rancurel, Corinne; Saunders, Elizabeth H; Longmire, Atkinson G; Zhang, Haitao; Bayer, Ed; Gilbert, Harry J; Larimer, Frank W; Zhulin, Igor B; Ekborg, Nathan A.; Lamed, Raphael; Richardson, P M; Borovok, Ilya; Hutcheson, Steven

    2008-05-01

    The marine bacterium Saccharophagus degradans strain 2-40 (Sde 2-40) is emerging as a vanguard of a recently discovered group of marine and estuarine bacteria that recycles complex polysaccharides (CP). We report its complete genome sequence, analysis of which identifies an unusually large number of enzymes that degrade >10 CP. Not only is this an extraordinary range of catabolic capability, but many of the enzymes contain domains and features - some unusual, others unique - that are believed to facilitate depolymerization of CP. This is the first sequenced genome of a marine bacterium that can degrade plant cell walls, an important component of the carbon cycle that is not well characterized in the marine environment.

  19. Discovery of a novel iota carrageenan sulfatase isolated from the marine bacterium Pseudoalteromonas carrageenovora

    NASA Astrophysics Data System (ADS)

    Genicot, Sabine; Groisillier, Agnès; Rogniaux, Hélène; Meslet-Cladière, Laurence; Barbeyron, Tristan; Helbert, William

    2014-08-01

    Carrageenans are sulfated polysaccharides extracted from the cell wall of some marine red algae. These polysaccharides are widely used as gelling, stabilizing, and viscosifying agents in the food and pharmaceutical industries. Since the rheological properties of these polysaccharides depend on their sulfate content, we screened several isolated marine bacteria for carrageenan specific sulfatase activity, in the aim of developing enzymatic bioconversion of carrageenans. As a result of the screening, an iota-carrageenan sulfatase was detected in the cell-free lysate of the marine bacterium Pseudoalteromonas carrageenovora strain PscT. It was purified through Phenyl Sepharose and Diethylaminoethyl Sepharose chromatography. The pure enzyme, Psc ?-CgsA, was characterized. It had a molecular weight of 115.9 kDaltons and exhibited an optimal activity/stability at pH ~8.3 and at 40°C ± 5°C. It was inactivated by phenylmethylsulfonyl fluoride but not by ethylene diamine tetraacetic acid. Psc ?-CgsA specifically catalyzes the hydrolysis of the 4-S sulfate of iota-carrageenan. The purified enzyme could transform iota-carrageenan into hybrid iota-/alpha- or pure alpha-carrageenan under controlled conditions. The gene encoding Psc ?-CgsA, a protein of 1038 amino acids, was cloned into Escherichia coli, and the sequence analysis revealed that Psc ?-CgsA has more than 90% sequence identity with a putative uncharacterized protein Q3IKL4 from the marine strain Pseudoalteromonas haloplanktis TAC 125, but besides this did not share any homology to characterized sulfatases. Phylogenetic studies show that P. carrageenovora sulfatase thus represents the first characterized member of a new sulfatase family, with a C-terminal domain having strong similarity with the superfamily of amidohydrolases, highlighting the still unexplored diversity of marine polysaccharide modifying enzymes.

  20. Discovery of a novel iota carrageenan sulfatase isolated from the marine bacterium Pseudoalteromonas carrageenovora

    PubMed Central

    Genicot, Sabine M.; Groisillier, Agnès; Rogniaux, Hélène; Meslet-Cladière, Laurence; Barbeyron, Tristan; Helbert, William

    2014-01-01

    Carrageenans are sulfated polysaccharides extracted from the cell wall of some marine red algae. These polysaccharides are widely used as gelling, stabilizing, and viscosifying agents in the food and pharmaceutical industries. Since the rheological properties of these polysaccharides depend on their sulfate content, we screened several isolated marine bacteria for carrageenan specific sulfatase activity, in the aim of developing enzymatic bioconversion of carrageenans. As a result of the screening, an iota-carrageenan sulfatase was detected in the cell-free lysate of the marine bacterium Pseudoalteromonas carrageenovora strain PscT. It was purified through Phenyl Sepharose and Diethylaminoethyl Sepharose chromatography. The pure enzyme, Psc ι-CgsA, was characterized. It had a molecular weight of 115.9 kDaltons and exhibited an optimal activity/stability at pH ~8.3 and at 40 ± 5°C. It was inactivated by phenylmethylsulfonyl fluoride but not by ethylene diamine tetraacetic acid. Psc ι-CgsA specifically catalyzes the hydrolysis of the 4-S sulfate of iota-carrageenan. The purified enzyme could transform iota-carrageenan into hybrid iota-/alpha- or pure alpha-carrageenan under controlled conditions. The gene encoding Psc ι-CgsA, a protein of 1038 amino acids, was cloned into Escherichia coli, and the sequence analysis revealed that Psc ι-CgsA has more than 90% sequence identity with a putative uncharacterized protein Q3IKL4 from the marine strain Pseudoalteromonas haloplanktis TAC 125, but besides this did not share any homology to characterized sulfatases. Phylogenetic studies show that P. carrageenovora sulfatase thus represents the first characterized member of a new sulfatase family, with a C-terminal domain having strong similarity with the superfamily of amidohydrolases, highlighting the still unexplored diversity of marine polysaccharide modifying enzymes. PMID:25207269

  1. Evidence for quorum sensing and differential metabolite production by a marine bacterium in response to DMSP

    PubMed Central

    Johnson, Winifred M; Kido Soule, Melissa C; Kujawinski, Elizabeth B

    2016-01-01

    Microbes, the foundation of the marine foodweb, do not function in isolation, but rather rely on molecular level interactions among species to thrive. Although certain types of interactions between autotrophic and heterotrophic microorganisms have been well documented, the role of specific organic molecules in regulating inter-species relationships and supporting growth are only beginning to be understood. Here, we examine one such interaction by characterizing the metabolic response of a heterotrophic marine bacterium, Ruegeria pomeroyi DSS-3, to growth on dimethylsulfoniopropionate (DMSP), an abundant organosulfur metabolite produced by phytoplankton. When cultivated on DMSP, R. pomeroyi synthesized a quorum-sensing molecule, N-(3-oxotetradecanoyl)-l-homoserine lactone, at significantly higher levels than during growth on propionate. Concomitant with the production of a quorum-sensing molecule, we observed differential production of intra- and extracellular metabolites including glutamine, vitamin B2 and biosynthetic intermediates of cyclic amino acids. Our metabolomics data indicate that R. pomeroyi changes regulation of its biochemical pathways in a manner that is adaptive for a cooperative lifestyle in the presence of DMSP, in anticipation of phytoplankton-derived nutrients and higher microbial density. This behavior is likely to occur on sinking marine particles, indicating that this response may impact the fate of organic matter. PMID:26882264

  2. Thymidine uptake, thymidine incorporation, and thymidine kinase activity in marine bacterium isolates

    SciTech Connect

    Jeffrey, W.H.; Paul, J.H. )

    1990-05-01

    One assumption made in bacterial production estimates from ({sup 3}H)thymidine incorporation is that all heterotrophic bacteria can incorporate exogenous thymidine into DNA. Heterotrophic marine bacterium isolates from Tampa Bay, Fla., Chesapeake Bay, Md., and a coral surface microlayer were examined for thymidine uptake (transport), thymidine incorporation, the presence of thymidine kinase genes, and thymidine kinase enzyme activity. Of the 41 isolates tested, 37 were capable of thymidine incorporation into DNA. The four organisms that could not incorporate thymidine also transported the thymidine poorly and lacked thymidine kinase activity. Attempts to detect thymidine kinase genes in the marine isolates by molecular probing with gene probes made from Escherichia coli and herpes simplex virus thymidine kinase genes proved unsuccessful. To determine if the inability to incorporate thymidine was due to the lack of thymidine kinase, one organism, Vibro sp. strain DI9, was transformed with a plasmid (pGQ3) that contained an E. coli thymidine kinase gene. Although enzyme assays indicated high levels of thymidine kinase activity in transformants, these cells still failed to incorporate exogenous thymidine into DNA or to transport thymidine into cells. These results indicate that the inability of certain marine bacteria to incorporate thymidine may not be solely due to the lack of thymidine kinase activity but may also be due to the absence of thymidine transport systems.

  3. Evidence for quorum sensing and differential metabolite production by a marine bacterium in response to DMSP.

    PubMed

    Johnson, Winifred M; Kido Soule, Melissa C; Kujawinski, Elizabeth B

    2016-09-01

    Microbes, the foundation of the marine foodweb, do not function in isolation, but rather rely on molecular level interactions among species to thrive. Although certain types of interactions between autotrophic and heterotrophic microorganisms have been well documented, the role of specific organic molecules in regulating inter-species relationships and supporting growth are only beginning to be understood. Here, we examine one such interaction by characterizing the metabolic response of a heterotrophic marine bacterium, Ruegeria pomeroyi DSS-3, to growth on dimethylsulfoniopropionate (DMSP), an abundant organosulfur metabolite produced by phytoplankton. When cultivated on DMSP, R. pomeroyi synthesized a quorum-sensing molecule, N-(3-oxotetradecanoyl)-l-homoserine lactone, at significantly higher levels than during growth on propionate. Concomitant with the production of a quorum-sensing molecule, we observed differential production of intra- and extracellular metabolites including glutamine, vitamin B2 and biosynthetic intermediates of cyclic amino acids. Our metabolomics data indicate that R. pomeroyi changes regulation of its biochemical pathways in a manner that is adaptive for a cooperative lifestyle in the presence of DMSP, in anticipation of phytoplankton-derived nutrients and higher microbial density. This behavior is likely to occur on sinking marine particles, indicating that this response may impact the fate of organic matter. PMID:26882264

  4. NH4+ transport system of a psychrophilic marine bacterium, Vibrio sp. strain ABE-1.

    PubMed

    Chou, M; Matsunaga, T; Takada, Y; Fukunaga, N

    1999-05-01

    NH4(+) transport system of a psychrophilic marine bacterium Vibrio sp. strain ABE-1 (Vibrio ABE-1) was examined by measuring the uptake of [14C]methylammonium ion (14CH3NH3+) into the intact cells. 14CH3NH3+ uptake was detected in cells grown in medium containing glutamate as the sole nitrogen source, but not in those grown in medium containing NH4Cl instead of glutamate. Vibrio ABE-1 did not utilize CH3NH3+ as a carbon or nitrogen source. NH4Cl and nonradiolabeled CH3NH3+ completely inhibited 14CH3NH3+ uptake. These results indicate that 14CH3NH3+ uptake in this bacterium is mediated via an NH4+ transport system and not by a specific carrier for CH3NH3+. The respiratory substrate succinate was required to drive 14CH3NH3+ uptake and the uptake was completely inhibited by KCN, indicating that the uptake was energy dependent. The electrochemical potentials of H+ and/or Na+ across membranes were suggested to be the driving forces for the transport system because the ionophores carbonylcyanide m-chlorophenylhydrazone and monensin strongly inhibited uptake activities at pH 6.5 and 8.5, respectively. Furthermore, KCl activated 14CH3NH3+ uptake. The 14CH3NH3+ uptake activity of Vibrio ABE-1 was markedly high at temperatures between 0 degrees and 15 degrees C, and the apparent Km value for CH3NH3+ of the uptake did not change significantly over the temperature range from 0 degrees to 25 degrees C. Thus, the NH4+ transport system of this bacterium was highly active at low temperatures. PMID:10356994

  5. Draft Genome Sequence of Bacillus plakortidis P203T (DSM 19153), an Alkali- and Salt-Tolerant Marine Bacterium

    PubMed Central

    Wang, Jie-ping; Liu, Guo-hong; Ge, Ci-bin; Xiao, Rong-feng; Zheng, Xue-fang; Shi, Huai

    2016-01-01

    Bacillus plakortidis P203T is a Gram-positive, spore-forming, and alkali- and salt-tolerant marine bacterium. Here, we report the 3.97-Mb draft genome sequence of B. plakortidis P203T, which will promote its fundamental research and provide useful information for genomic taxonomy and phylogenomics of Bacillus-like bacteria. PMID:26847896

  6. Draft Genome of Shewanella frigidimarina Ag06-30, a Marine Bacterium Isolated from Potter Peninsula, King George Island, Antarctica

    PubMed Central

    Parmeciano Di Noto, Gisela; Vázquez, Susana C.; MacCormack, Walter P.; Iriarte, Andrés

    2016-01-01

    We present the draft genome of Shewanella frigidimarina Ag06-30, a marine bacterium from King George Island, Antarctica, which encodes the carbapenemase SFP-1. The assembly contains 4,799,218 bp (G+C content 41.24%). This strain harbors several mobile genetic elements that provide insight into lateral gene transfer and bacterial plasticity and evolution. PMID:27151790

  7. Draft Genome of Shewanella frigidimarina Ag06-30, a Marine Bacterium Isolated from Potter Peninsula, King George Island, Antarctica.

    PubMed

    Parmeciano Di Noto, Gisela; Vázquez, Susana C; MacCormack, Walter P; Iriarte, Andrés; Quiroga, Cecilia

    2016-01-01

    We present the draft genome of Shewanella frigidimarina Ag06-30, a marine bacterium from King George Island, Antarctica, which encodes the carbapenemase SFP-1. The assembly contains 4,799,218 bp (G+C content 41.24%). This strain harbors several mobile genetic elements that provide insight into lateral gene transfer and bacterial plasticity and evolution. PMID:27151790

  8. Marine bacterium strain screening and pyrethroid insecticide-degrading efficiency analysis

    NASA Astrophysics Data System (ADS)

    Sun, Aili; Liu, Jinghua; Shi, Xizhi; Li, Dexiang; Chen, Jiong; Tang, Daojun

    2014-09-01

    A pyrethroid insecticide-degrading bacterium, strain HS-24, was isolated from an offshore seawater environment. The strain, which can degrade cypermethrin (CYP) and deltamethrin (DEL), was identified as Methylophaga sp. The optimal culture and degradation conditions for CYP and DEL by strain HS-24 is pH 7 at 28°C. Under optimum culture conditions, strain HS-24 exhibited a broad degradation concentration range of 100, 200, 400, 600, and 800 mg/L for CYP and DEL. The metabolic intermediates were analyzed by NMR, which provided strong evidence that CYP and DEL removal occurred mainly because of a biological process. The toxicity of the degradation products of strain HS-24 was studied simultaneously by measuring the light output of the luminescence bacterium. This demonstrated that the biodegradation ability of strain HS-24 significantly decreased the toxicity of CYP- and DEL-contaminated aquaculture seawater. Finally, the findings of this paper indicate that strain HS-24 is thus revealed as a biological agent for the remediation of marine aquatic environments.

  9. Marinobacter hydrocarbonoclasticus NY-4, a novel denitrifying, moderately halophilic marine bacterium.

    PubMed

    Li, Rongpeng; Zi, Xiaoli; Wang, Xinfeng; Zhang, Xia; Gao, Haofeng; Hu, Nan

    2013-01-01

    The isolation and characterization of a novel halophilic denitrifying marine bacterium is described. The halophilic bacterium, designated as NY-4, was isolated from soil in Yancheng City, China, and identified as Marinobacter hydrocarbonoclasticus by 16S rRNA gene sequence phylogenetic analysis. This organism can grow in NaCl concentrations ranging from 20 to 120 g/L. Optimum growth occurs at 80 g/L NaCl and pH 8.0. The organism can grow on a broad range of carbon sources and demonstrated efficient denitrifying ability (94.2% of nitrate removal and 80.9% of total nitrogen removal in 48 h). During denitrification by NY-4, no NO2 (-)-N was accumulated, N2 was the only gaseous product and no harmful N2O was produced. Because of its rapid denitrification ability, broad carbon use range and ability to grow under high salinity and pH conditions, NY-4 holds promise for the treatment of saline waste waters. PMID:25538872

  10. Characterization of acetonitrile-tolerant marine bacterium Exiguobacterium sp. SBH81 and its tolerance mechanism.

    PubMed

    Kongpol, Ajiraporn; Kato, Junichi; Tajima, Takahisa; Vangnai, Alisa S

    2012-01-01

    A Gram-positive marine bacterium, Exiguobacterium sp. SBH81, was isolated as a hydrophilic organic-solvent tolerant bacterium, and exhibited high tolerance to various types of toxic hydrophilic organic solvents, including acetonitrile, at relatively high concentrations (up to 6% [v/v]) under the growing conditions. Investigation of its tolerance mechanisms illustrated that it does not rely on solvent inactivation processes or modification of cell surface characteristics, but rather, increase of the cell size lowers solvent partitioning into cells and the extrusion of solvents through the efflux system. A test using efflux pump inhibitors suggested that secondary transporters, i.e. resistance nodulation cell division (RND) and the multidrug and toxic compound extrusion (MATE) family, are involved in acetonitrile tolerance in this strain. In addition, its acetonitrile tolerance ability could be stably and significantly enhanced by repetitive growth in the presence of toxic acetonitrile. The marked acetonitrile tolerance of Exiguobacterium sp. SBH81 indicates its potential use as a host for biotechnological fermentation processes as well as bioremediation. PMID:21971080

  11. Photobacterium damselae subsp. damselae, a bacterium pathogenic for marine animals and humans.

    PubMed

    Rivas, Amable J; Lemos, Manuel L; Osorio, Carlos R

    2013-01-01

    Photobacterium damselae subsp. damselae (formerly Vibrio damsela) is a pathogen of a variety of marine animals including fish, crustaceans, molluscs, and cetaceans. In humans, it can cause opportunistic infections that may evolve into necrotizing fasciitis with fatal outcome. Although the genetic basis of virulence in this bacterium is not completely elucidated, recent findings demonstrate that the phospholipase-D Dly (damselysin) and the pore-forming toxins HlyApl and HlyAch play a main role in virulence for homeotherms and poikilotherms. The acquisition of the virulence plasmid pPHDD1 that encodes Dly and HlyApl has likely constituted a main driving force in the evolution of a highly hemolytic lineage within the subspecies. Interestingly, strains that naturally lack pPHDD1 show a strong pathogenic potential for a variety of fish species, indicating the existence of yet uncharacterized virulence factors. Future and deep analysis of the complete genome sequence of Photobacterium damselae subsp. damselae will surely provide a clearer picture of the virulence factors employed by this bacterium to cause disease in such a varied range of hosts. PMID:24093021

  12. The nucleotide sequence of Beneckea harveyi 5S rRNA. [bioluminescent marine bacterium

    NASA Technical Reports Server (NTRS)

    Luehrsen, K. R.; Fox, G. E.

    1981-01-01

    The primary sequence of the 5S ribosomal RNA isolated from the free-living bioluminescent marine bacterium Beneckea harveyi is reported and discussed in regard to indications of phylogenetic relationships with the bacteria Escherichia coli and Photobacterium phosphoreum. Sequences were determined for oligonucleotide products generated by digestion with ribonuclease T1, pancreatic ribonuclease and ribonuclease T2. The presence of heterogeneity is indicated for two sites. The B. harveyi sequence can be arranged into the same four helix secondary structures as E. coli and other prokaryotic 5S rRNAs. Examination of the 5S-RNS sequences of the three bacteria indicates that B. harveyi and P. phosphoreum are specifically related and share a common ancestor which diverged from an ancestor of E. coli at a somewhat earlier time, consistent with previous studies.

  13. Acetylcholinesterase-Inhibiting Activity of Pyrrole Derivatives from a Novel Marine Gliding Bacterium, Rapidithrix thailandica

    PubMed Central

    Sangnoi, Yutthapong; Sakulkeo, Oraphan; Yuenyongsawad, Supreeya; Kanjana-opas, Akkharawit; Ingkaninan, Kornkanok; Plubrukarn, Anuchit; Suwanborirux, Khanit

    2008-01-01

    Acetylcholinesterase-inhibiting activity of marinoquinoline A (1), a new pyrroloquinoline from a novel species of a marine gliding bacterium Rapidithrix thailandica, was assessed (IC50 4.9 μM). Two related pyrrole derivatives, 3-(2′-aminophenyl)-pyrrole (3) and 2,2-dimethyl-pyrrolo-1,2-dihydroquinoline (4), were also isolated from two other strains of R. thailandica. The isolation of 3 from a natural source is reported here for the first time. Compound 4 was proposed to be an isolation artifact derived from 3. The two isolated compounds were virtually inactive in the acetylcholinesterase-inhibitory assay (enzyme inhibition < 30% at 0.1 g L−1). PMID:19172195

  14. Bioinformatics comparison of sulfate-reducing metabolism nucleotide sequences

    NASA Astrophysics Data System (ADS)

    Tremberger, G.; Dehipawala, Sunil; Nguyen, A.; Cheung, E.; Sullivan, R.; Holden, T.; Lieberman, D.; Cheung, T.

    2015-09-01

    The sulfate-reducing bacteria can be traced back to 3.5 billion years ago. The thermodynamics details of the sulfur cycle have been well documented. A recent sulfate-reducing bacteria report (Robator, Jungbluth, et al , 2015 Jan, Front. Microbiol) with Genbank nucleotide data has been analyzed in terms of the sulfite reductase (dsrAB) via fractal dimension and entropy values. Comparison to oil field sulfate-reducing sequences was included. The AUCG translational mass fractal dimension versus ATCG transcriptional mass fractal dimension for the low temperature dsrB and dsrA sequences reported in Reference Thirteen shows correlation R-sq ~ 0.79 , with a probably of about 3% in simulation. A recent report of using Cystathionine gamma-lyase sequence to produce CdS quantum dot in a biological method, where the sulfur is reduced just like in the H2S production process, was included for comparison. The AUCG mass fractal dimension versus ATCG mass fractal dimension for the Cystathionine gamma-lyase sequences was found to have R-sq of 0.72, similar to the low temperature dissimilatory sulfite reductase dsr group with 3% probability, in contrary to the oil field group having R-sq ~ 0.94, a high probable outcome in the simulation. The other two simulation histograms, namely, fractal dimension versus entropy R-sq outcome values, and di-nucleotide entropy versus mono-nucleotide entropy R-sq outcome values are also discussed in the data analysis focusing on low probability outcomes.

  15. Antagonistic effect of monovalent cations in maintenance of cellular integrity of a marine bacterium.

    PubMed

    De Voe, I W; Oginsky, E L

    1969-06-01

    The susceptibility of a marine bacterium, designated isolate c-A1, to lysis in distilled water and in salt solutions has been found to be a function of Na(+) concentration. Optical densities of cells pre-exposed to 0.05 m MgCl(2) were maintained in 1.0 m KCl, whereas those of cells pre-exposed to 1.0 m NaCl were not maintained at any KCl concentration tested. Cells transferred from MgCl(2) to low concentrations of NaCl underwent more extensive lysis than did those transferred to distilled water. The degree of disruption of cells transferred to distilled water from mixtures of 0.05 m MgCl(2) and NaCl (0 to 1.0 m) was dependent on the concentration of NaCl; similar results were obtained with LiCl, but not with KCl. In electron micrographs of thin sections, c-A1 cell envelopes consisted of two double-track layers which fractured and peeled apart on lysis after pre-exposure to NaCl-MgCl(2) mixtures. Envelope eruptions or "hernias" occurred only in lysed cells pre-exposed to NaCl alone. No evidence for a functional lytic enzyme was found. Comparative studies on a terrestrial pseudomonad with a multilayered envelope indicated that preexposure to NaCl did not enhance the susceptibility of this cell to lysis in distilled water. The lytic susceptibility of the marine bacterium is considered to be the consequence of competition between specific monovalent cations and Mg(++) for electrostatic interactions with components of the cell envelope of this organism. PMID:5788707

  16. Antagonistic Effect of Monovalent Cations in Maintenance of Cellular Integrity of a Marine Bacterium1

    PubMed Central

    De Voe, Irving W.; Oginsky, Evelyn L.

    1969-01-01

    The susceptibility of a marine bacterium, designated isolate c-A1, to lysis in distilled water and in salt solutions has been found to be a function of Na+ concentration. Optical densities of cells pre-exposed to 0.05 m MgCl2 were maintained in 1.0 m KCl, whereas those of cells pre-exposed to 1.0 m NaCl were not maintained at any KCl concentration tested. Cells transferred from MgCl2 to low concentrations of NaCl underwent more extensive lysis than did those transferred to distilled water. The degree of disruption of cells transferred to distilled water from mixtures of 0.05 m MgCl2 and NaCl (0 to 1.0 m) was dependent on the concentration of NaCl; similar results were obtained with LiCl, but not with KCl. In electron micrographs of thin sections, c-A1 cell envelopes consisted of two double-track layers which fractured and peeled apart on lysis after pre-exposure to NaCl-MgCl2 mixtures. Envelope eruptions or “hernias” occurred only in lysed cells pre-exposed to NaCl alone. No evidence for a functional lytic enzyme was found. Comparative studies on a terrestrial pseudomonad with a multilayered envelope indicated that preexposure to NaCl did not enhance the susceptibility of this cell to lysis in distilled water. The lytic susceptibility of the marine bacterium is considered to be the consequence of competition between specific monovalent cations and Mg++ for electrostatic interactions with components of the cell envelope of this organism. Images PMID:5788707

  17. Corrosion control in the presence of sulfate-reducing bacteria

    SciTech Connect

    Schick, G. )

    1990-07-01

    Impressed current and magnesium anode-type cathodic protection usually provide appreciable protection to the buried and underground telephone plant. However, in the laboratory, a medium containing sulfate-reducing bacteria (SRB) strongly reduces the output current from the magnesium anode. This explains the lack of success with magnesium anodes in the field where the ratio of protected surface area to current output is orders of magnitude higher than in the laboratory test. Low concentrations of sodium hypochlorite (NaOCl) additive to the solution provide minimal protection. However, high concentrations and/or aeration can eliminate the high concentration of SRB in the aqueous medium.

  18. A Novel Eliminase from a Marine Bacterium That Degrades Hyaluronan and Chondroitin Sulfate*

    PubMed Central

    Han, Wenjun; Wang, Wenshuang; Zhao, Mei; Sugahara, Kazuyuki; Li, Fuchuan

    2014-01-01

    Lyases cleave glycosaminoglycans (GAGs) in an eliminative mechanism and are important tools for the structural analysis and oligosaccharide preparation of GAGs. Various GAG lyases have been identified from terrestrial but not marine organisms even though marine animals are rich in GAGs with unique structures and functions. Herein we isolated a novel GAG lyase for the first time from the marine bacterium Vibrio sp. FC509 and then recombinantly expressed and characterized it. It showed strong lyase activity toward hyaluronan (HA) and chondroitin sulfate (CS) and was designated as HA and CS lyase (HCLase). It exhibited the highest activities to both substrates at pH 8.0 and 0.5 m NaCl at 30 °C. Its activity toward HA was less sensitive to pH than its CS lyase activity. As with most other marine enzymes, HCLase is a halophilic enzyme and very stable at temperatures from 0 to 40 °C for up to 24 h, but its activity is independent of divalent metal ions. The specific activity of HCLase against HA and CS reached a markedly high level of hundreds of thousands units/mg of protein under optimum conditions. The HCLase-resistant tetrasaccharide Δ4,5HexUAα1-3GalNAc(6-O-sulfate)β1-4GlcUA(2-O-sulfate)β1-3GalNAc(6-O-sulfate) was isolated from CS-D, the structure of which indicated that HCLase could not cleave the galactosaminidic linkage bound to 2-O-sulfated d-glucuronic acid (GlcUA) in CS chains. Site-directed mutagenesis indicated that HCLase may work via a catalytic mechanism in which Tyr-His acts as the Brønsted base and acid. Thus, the identification of HCLase provides a useful tool for HA- and CS-related research and applications. PMID:25122756

  19. Suitability of fluorescence measurements to quantify sulfate-reducing bacteria.

    PubMed

    Barton, Larry L; Carpenter, Claire M

    2013-06-01

    Fluorescence activity has been used to identify Desulfovibrio and has been termed the 'desulfoviridin test'. This fluorescence is attributed to the prosthetic group of bisulfite reductase, a key enzyme in dissimilatory sulfate reduction. We have pursued the use of fluorescence measurements to quantify sulfate-reducing bacteria. Cells of D. desulfuricans and D. gigas were treated with NaOH and produced two fluorescence spectra: one with maximum fluorescence with an excitation at 395 nm and an emission at 605 nm and another with an excitation at 320 nm and emission at 360 nm. Using the fluorescence with excitation at 395 nm and emission at 605 nm, we explored a series of parameters to measure Desulfovibrio in pure cultures and environmental samples. Fluorescence measurements are reliable provided the cells are treated with 1.75 N NaOH and the chromophore released from the cells is not exposed to strong light intensity, and is not exposed to temperatures greater than 20 °C, and measurements are done within a few minutes of extraction. Bleaching of fluorescence was attributed to metal ions in solution which was not observed until metal concentrations reached 1.5mM. We propose that D. desulfuricans is appropriate as the reference organism for measurement of sulfate-reducing bacteria by fluorescence and by using fluorescence intensity, 10(5) cells/ml can be readily detected in environmental samples. PMID:23566827

  20. Pathway of Fermentative Hydrogen Production by Sulfate-reducing Bacteria

    SciTech Connect

    Wall, Judy D.

    2015-02-16

    Biofuels are a promising source of sustainable energy. Such biofuels are intermediate products of microbial metabolism of renewable substrates, in particular, plant biomass. Not only are alcohols and solvents produced in this degradative process but energy-rich hydrogen as well. Non photosynthetic microbial hydrogen generation from compounds other than sugars has not been fully explored. We propose to examine the capacity of the abundant soil anaerobes, sulfate-reducing bacteria, for hydrogen generation from organic acids. These apparently simple pathways have yet to be clearly established. Information obtained may facilitate the exploitation of other microbes not yet readily examined by molecular tools. Identification of the flexibility of the metabolic processes to channel reductant to hydrogen will be useful in consideration of practical applications. Because the tools for genetic and molecular manipulation of sulfate-reducing bacteria of the genus Desulfovibrio are developed, our efforts will focus on two strains, D. vulgaris Hildenborough and Desulfovibrio G20.Therefore total metabolism, flux through the pathways, and regulation are likely to be limiting factors which we can elucidate in the following experiments.

  1. Improved Methodology for Bioremoval of Black Crusts on Historical Stone Artworks by Use of Sulfate-Reducing Bacteria

    PubMed Central

    Cappitelli, Francesca; Zanardini, Elisabetta; Ranalli, Giancarlo; Mello, Emilio; Daffonchio, Daniele; Sorlini, Claudia

    2006-01-01

    An improved methodology to remove black crusts from stone by using Desulfovibrio vulgaris subsp. vulgaris ATCC 29579, a sulfate-reducing bacterium, is presented. The strain removed 98% of the sulfates of the crust in a 45-h treatment. Precipitation of black iron sulfide was avoided using filtration of a medium devoid of iron. Among three cell carriers, Carbogel proved to be superior to both sepiolite and Hydrobiogel-97, as it allowed an easy application of the bacteria, kept the system in a state where microbial activity was maintained, and allowed easy removal of the cells after the treatment. PMID:16672524

  2. Against the rules: a marine bacterium, Loktanella rosea, possesses a unique lipopolysaccharide.

    PubMed

    Ieranò, Teresa; Silipo, Alba; Nazarenko, Evgeny L; Gorshkova, Raisa P; Ivanova, Elena P; Garozzo, Domenico; Sturiale, Luisa; Lanzetta, Rosa; Parrilli, Michelangelo; Molinaro, Antonio

    2010-05-01

    Bacteria are an inimitable source of new glyco-structures potentially useful in medicinal and environmental chemistry. Lipopolysaccharides (LPS; endotoxins) are the major components of the outer membrane of Gram-negative bacteria; being exposed toward the external environment they can undergo structural changes and thus, they often possess peculiar chemical features that allow them to thrive in harsh chemical and physical environments. Marine bacteria have evolved and adapted over millions of years in order to succeed in different environments, finding a niche for their survival characterized by severe physical or chemical parameters. The present work focuses on the structural investigation of the LPS from Loktanella rosea, a marine Gram-negative bacterium. Through chemical analysis, 2D nuclear magnetic resonance and matrix-assisted laser desorption ionization mass spectrometry investigations, a unique LPS carbohydrate backbone has been defined. The lipid A skeleton consists of a trisaccharide backbone lacking the typical phosphate groups and is characterized by two beta-glucosamines and an alpha-galacturonic acid. The core region is built up of three ulosonic acids, with two 3-deoxy-d-manno-oct-2-ulopyranosonic acid residues, one of which is carrying a neuraminic acid. This carbohydrate structure is an exceptional variation from the typical architectural skeleton of endotoxins which consequently implies a very different biosynthesis. PMID:20093711

  3. Genome sequence of Enterobacter sp. ST3, a quorum sensing bacterium associated with marine dinoflagellate

    PubMed Central

    Zhou, Jin; Lao, Yong-Min; Ma, Zhi-Ping; Cai, Zhong-Hua

    2016-01-01

    Phycosphere environment is a typical marine niche, harbor diverse populations of microorganisms, which are thought to play a critical role in algae host and influence mutualistic and competitive interactions. Understanding quorum sensing-based acyl-homoserine lactone (AHL) language may shed light on the interaction between algal-associated microbial communities in the native environment. In this work, we isolated an epidermal bacterium (was tentatively named Enterobacter sp. ST3, and deposited in SOA China, the number is MCCC1K02277-ST3) from the marine dinoflagellate Scrippsiella trochoidea, and found it has the ability to produce short-chain AHL signal. In order to better understand its communication information at molecular level, the genomic map was investigated. The genome size was determined to be 4.81 Mb with a G + C content of 55.59%, comprising 6 scaffolds of 75 contigs containing 4647 protein-coding genes. The functional proteins were predicted, and 3534 proteins were assigned to COG functional categories. An AHL-relating gene, LuxR, was found in upstream position at contig 1. This genome data may provide clues to increase understanding of the chemical characterization and ecological behavior of strain ST3 in the phycosphere microenvironment. PMID:26981407

  4. Complete Cellulase System in the Marine Bacterium Saccharophagus degradans Strain 2-40T

    PubMed Central

    Taylor, Larry E.; Henrissat, Bernard; Coutinho, Pedro M.; Ekborg, Nathan A.; Hutcheson, Steven W.; Weiner, Ronald M.

    2006-01-01

    Saccharophagus degradans strain 2-40 is a representative of an emerging group of marine complex polysaccharide (CP)-degrading bacteria. It is unique in its metabolic versatility, being able to degrade at least 10 distinct CPs from diverse algal, plant and invertebrate sources. The S. degradans genome has been sequenced to completion, and more than 180 open reading frames have been identified that encode carbohydrases. Over half of these are likely to act on plant cell wall polymers. In fact, there appears to be a full array of enzymes that degrade and metabolize plant cell walls. Genomic and proteomic analyses reveal 13 cellulose depolymerases complemented by seven accessory enzymes, including two cellodextrinases, three cellobiases, a cellodextrin phosphorylase, and a cellobiose phosphorylase. Most of these enzymes exhibit modular architecture, and some contain novel combinations of catalytic and/or substrate binding modules. This is exemplified by endoglucanase Cel5A, which has three internal family 6 carbohydrate binding modules (CBM6) and two catalytic modules from family five of glycosyl hydrolases (GH5) and by Cel6A, a nonreducing-end cellobiohydrolase from family GH6 with tandem CBM2s. This is the first report of a complete and functional cellulase system in a marine bacterium with a sequenced genome. PMID:16707677

  5. Production of polyhydroxybutyrate by the marine photosynthetic bacterium Rhodovulum sulfidophilum P5

    NASA Astrophysics Data System (ADS)

    Cai, Jinling; Wei, Ying; Zhao, Yupeng; Pan, Guanghua; Wang, Guangce

    2012-07-01

    The effects of different NaCl concentrations, nitrogen sources, carbon sources, and carbon to nitrogen molar ratios on biomass accumulation and polyhydroxybutyrate (PHB) production were studied in batch cultures of the marine photosynthetic bacterium Rhodovulum sulfidophilum P5 under aerobic-dark conditions. The results show that the accumulation of PHB in strain P5 is a growth-associated process. Strain P5 had maximum biomass and PHB accumulation at 2%-3% NaCl, suggesting that the bacterium can maintain growth and potentially produce PHB at natural seawater salinity. In the nitrogen source test, the maximum biomass accumulation (8.10±0.09 g/L) and PHB production (1.11±0.13 g/L and 14.62%±2.2 of the cell dry weight) were observed when peptone and ammonium chloride were used as the sole nitrogen source. NH{4/+}-N was better for PHB production than other nitrogen sources. In the carbon source test, the maximum biomass concentration (7.65±0.05 g/L) was obtained with malic acid as the sole carbon source, whereas the maximum yield of PHB (5.03±0.18 g/L and 66.93%±1.69% of the cell dry weight) was obtained with sodium pyruvate as the sole carbon source. In the carbon to nitrogen ratios test, sodium pyruvate and ammonium chloride were selected as the carbon and nitrogen sources, respectively. The best carbon to nitrogen molar ratio for biomass accumulation (8.77±0.58 g/L) and PHB production (6.07±0.25 g/L and 69.25%±2.05% of the cell dry weight) was 25. The results provide valuable data on the production of PHB by R. sulfidophilum P5 and further studies are on-going for best cell growth and PHB yield.

  6. Structure and morphology of magnetite anaerobically-produced by a marine magnetotactic bacterium and a dissimilatory iron-reducing bacterium

    USGS Publications Warehouse

    Sparks, N.H.C.; Mann, S.; Bazylinski, D.A.; Lovley, D.R.; Jannasch, H.W.; Frankel, R.B.

    1990-01-01

    Intracellular crystals of magnetite synthesized by cells of the magnetotactic vibroid organism, MV-1, and extracellular crystals of magnetite produced by the non-magnetotactic dissimilatory iron-reducing bacterium strain GS-15, were examined using high-resolution transmission electron microscopy, electron diffraction and 57Fe Mo??ssbauer spectroscopy. The magnetotactic bacterium contained a single chain of approximately 10 crystals aligned along the long axis of the cell. The crystals were essentially pure stoichiometric magnetite. When viewed along the crystal long axis the particles had a hexagonal cross-section whereas side-on they appeared as rectangules or truncated rectangles of average dimension, 53 ?? 35 nm. These findings are explained in terms of a three-dimensional morphology comprising a hexagonal prism of {110} faces which are capped and truncated by {111} end faces. Electron diffraction and lattice imaging studies indicated that the particles were structurally well-defined single crystals. In contrast, magnetite particles produced by the strain, GS-15 were irregular in shape and had smaller mean dimensions (14 nm). Single crystals were imaged but these were not of high structural perfection. These results highlight the influence of intracellular control on the crystallochemical specificity of bacterial magnetites. The characterization of these crystals is important in aiding the identification of biogenic magnetic materials in paleomagnetism and in studies of sediment magnetization. ?? 1990.

  7. Effects of iron-reducing bacteria on carbon steel corrosion induced by thermophilic sulfate-reducing consortia.

    PubMed

    Valencia-Cantero, Eduardo; Peña-Cabriales, Juan José

    2014-02-28

    Four thermophilic bacterial species, including the iron-reducing bacterium Geobacillus sp. G2 and the sulfate-reducing bacterium Desulfotomaculum sp. SRB-M, were employed to integrate a bacterial consortium. A second consortium was integrated with the same bacteria, except for Geobacillus sp. G2. Carbon steel coupons were subjected to batch cultures of both consortia. The corrosion induced by the complete consortium was 10 times higher than that induced by the second consortium, and the ferrous ion concentration was consistently higher in iron-reducing consortia. Scanning electronic microscopy analysis of the carbon steel surface showed mineral films colonized by bacteria. The complete consortium caused profuse fracturing of the mineral film, whereas the non-iron-reducing consortium did not generate fractures. These data show that the iron-reducing activity of Geobacillus sp. G2 promotes fracturing of mineral films, thereby increasing steel corrosion. PMID:24225375

  8. Stereochemical course of hydrolytic reaction catalyzed by alpha-galactosidase from cold adaptable marine bacterium of genus Pseudoalteromonas

    NASA Astrophysics Data System (ADS)

    Bakunina, Irina; Balabanova, Larissa; Golotin, Vasiliy; Slepchenko, Lyubov; Isakov, Vladimir; Rasskazov, Valeriy

    2014-10-01

    The recombinant α-galactosidase of the marine bacterium (α-PsGal) was synthesized with the use of the plasmid 40Gal, consisting of plasmid pET-40b (+) (Novagen) and the gene corresponding to the open reading frame of the mature α-galactosidase of marine bacterium Pseudoalteromonas sp. KMM 701, transformed into the E. coli Rosetta(DE3) cells. In order to understand the mechanism of action, the stereochemistry of hydrolysis of 4-nitrophenyl α-D-galactopyranoside (4-NPGP) by α-PsGal was measured by 1H NMR spectroscopy. The kinetics of formation of α- and β-anomer of galactose showed that α-anomer initially formed and accumulated, and then an appreciable amount of β-anomer appeared as a result of mutarotation. The data clearly show that the enzymatic hydrolysis of 4-NPGP proceeds with the retention of anomeric configuration, probably, due to a double displacement mechanism of reaction.

  9. Draft Genome Sequence of Providencia sneebia Strain ST1, a Quorum Sensing Bacterium Associated with Marine Microalgae

    PubMed Central

    Zhou, Jin; Lao, Yong-Min; Cai, Zhong-Hua

    2016-01-01

    Providencia sneebia strain ST1 is a symbiotic bacterium (belonging to phylum gammaproteobacteria) with marine microalgae. This bacterium exhibits the ability to produce N-Acyl homoserine lactone signal molecule. To date, no genome that originates from marine Providencia spp. has been reported. In this study, we present the genome sequence of this strain. It has a genome size of 4.89 M, with 19 contigs and an average G+C of 51.97%. The function of 4,631 proteins was predicted, and 3,652 proteins were assigned to COG functional categories. Among them, 407 genes are involved in carbohydrate metabolism, 306 genes participate in nitrogen utilization and energy conversion, and 185 genes related to signal transduction process. Thus, this strain plays an active role in the biogeochemical cycle in algal life history. The whole-genome of this isolate and annotation will help enhance understanding of bacterial ecological behavior in the phycosphere. PMID:27026792

  10. Purification and Characterization of a Fucoidanase (FNase S) from a Marine Bacterium Sphingomonas paucimobilis PF-1

    PubMed Central

    Kim, Woo Jung; Park, Joo Woong; Park, Jae Kweon; Choi, Doo Jin; Park, Yong Il

    2015-01-01

    The Search for enzyme activities that efficiently degrade marine polysaccharides is becoming an increasingly important area for both structural analysis and production of lower-molecular weight oligosaccharides. In this study, an endo-acting fucoidanase that degrades Miyeokgui fucoidan (MF), a sulfated galactofucan isolated from the sporophyll (called Miyeokgui in Korean) of Undaria pinnatifida, into smaller-sized galactofuco-oligosaccharides (1000–4000 Da) was purified from a marine bacterium, Sphingomonas paucimobilis PF-1, by ammonium sulfate precipitation, diethylaminoethyl (DEAE)-Sepharose column chromatography, and chromatofocusing. The specific activity of this enzyme was approximately 112-fold higher than that of the crude enzyme, and its molecular weight was approximately 130 kDa (FNase S), as determined by native gel electrophoresis and 130 (S1), 70 (S2) and 60 (S3) kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The optimum pH and temperature of FNase S were pH 6.0–7.0 and 40–45 °C, respectively. FNase S activity was enhanced by Mn2+ and Na+ (115.7% and 131.2%), but it was inhibited by Ca2+, K+, Ba2+, Cu2+ (96%, 83.7%, 84.3%, and 89.3%, respectively), each at 1 mM. The Km, Vmax and Kcat values of FNase S on MF were 1.7 mM, 0.62 mg·min−1, and 0.38·S−1, respectively. This enzyme could be a valuable tool for the structural analysis of fucoidans and production of bioactive fuco-oligosaccharides. PMID:26193285

  11. Comprehensive insights into the response of Alexandrium tamarense to algicidal component secreted by a marine bacterium

    PubMed Central

    Lei, Xueqian; Li, Dong; Li, Yi; Chen, Zhangran; Chen, Yao; Cai, Guanjing; Yang, Xujun; Zheng, Wei; Zheng, Tianling

    2015-01-01

    Harmful algal blooms occur throughout the world, threatening human health, and destroying marine ecosystems. Alexandrium tamarense is a globally distributed and notoriously toxic dinoflagellate that is responsible for most paralytic shellfish poisoning incidents. The culture supernatant of the marine algicidal bacterium BS02 showed potent algicidal effects on A. tamarense ATGD98-006. In this study, we investigated the effects of this supernatant on A. tamarense at physiological and biochemical levels to elucidate the mechanism involved in the inhibition of algal growth by the supernatant of the strain BS02. Reactive oxygen species (ROS) levels increased following exposure to the BS02 supernatant, indicating that the algal cells had suffered from oxidative damage. The levels of cellular pigments, including chlorophyll a and carotenoids, were significantly decreased, which indicated that the accumulation of ROS destroyed pigment synthesis. The decline of the maximum photochemical quantum yield (Fv/Fm) and relative electron transport rate (rETR) suggested that the photosynthesis systems of algal cells were attacked by the BS02 supernatant. To eliminate the ROS, the activities of antioxidant enzymes, including superoxide dismutase (SOD) and catalase (CAT), increased significantly within a short period of time. Real-time PCR revealed changes in the transcript abundances of two target photosynthesis-related genes (psbA and psbD) and two target respiration-related genes (cob and cox). The transcription of the respiration-related genes was significantly inhibited by the treatments, which indicated that the respiratory system was disturbed. Our results demonstrate that the BS02 supernatant can affect the photosynthesis process and might block the PS II electron transport chain, leading to the production of excessive ROS. The increased ROS can further destroy membrane integrity and pigments, ultimately inducing algal cell death. PMID:25667582

  12. Comprehensive insights into the response of Alexandrium tamarense to algicidal component secreted by a marine bacterium.

    PubMed

    Lei, Xueqian; Li, Dong; Li, Yi; Chen, Zhangran; Chen, Yao; Cai, Guanjing; Yang, Xujun; Zheng, Wei; Zheng, Tianling

    2015-01-01

    Harmful algal blooms occur throughout the world, threatening human health, and destroying marine ecosystems. Alexandrium tamarense is a globally distributed and notoriously toxic dinoflagellate that is responsible for most paralytic shellfish poisoning incidents. The culture supernatant of the marine algicidal bacterium BS02 showed potent algicidal effects on A. tamarense ATGD98-006. In this study, we investigated the effects of this supernatant on A. tamarense at physiological and biochemical levels to elucidate the mechanism involved in the inhibition of algal growth by the supernatant of the strain BS02. Reactive oxygen species (ROS) levels increased following exposure to the BS02 supernatant, indicating that the algal cells had suffered from oxidative damage. The levels of cellular pigments, including chlorophyll a and carotenoids, were significantly decreased, which indicated that the accumulation of ROS destroyed pigment synthesis. The decline of the maximum photochemical quantum yield (Fv/Fm) and relative electron transport rate (rETR) suggested that the photosynthesis systems of algal cells were attacked by the BS02 supernatant. To eliminate the ROS, the activities of antioxidant enzymes, including superoxide dismutase (SOD) and catalase (CAT), increased significantly within a short period of time. Real-time PCR revealed changes in the transcript abundances of two target photosynthesis-related genes (psbA and psbD) and two target respiration-related genes (cob and cox). The transcription of the respiration-related genes was significantly inhibited by the treatments, which indicated that the respiratory system was disturbed. Our results demonstrate that the BS02 supernatant can affect the photosynthesis process and might block the PS II electron transport chain, leading to the production of excessive ROS. The increased ROS can further destroy membrane integrity and pigments, ultimately inducing algal cell death. PMID:25667582

  13. Tenacibactins A-D, hydroxamate siderophores from a marine-derived bacterium, Tenacibaculum sp. A4K-17.

    PubMed

    Jang, Jae-Hyuk; Kanoh, Kaneo; Adachi, Kyoko; Matsuda, Satoru; Shizuri, Yoshikazu

    2007-04-01

    Four new hydroxamate siderophores, tenacibactins A-D (1-4), were isolated from a culture broth of the marine-derived bacterium Tenacibaculum sp. A4K-17. The structures of these tenacibactins were determined by NMR analyses and ESIMS/MS experiments. The iron-binding (chelating) activity of 1-4 was evaluated by the chrome azurol sulfonate (CAS) assay. PMID:17319723

  14. Transcriptional response of the photoheterotrophic marine bacterium Dinoroseobacter shibae to changing light regimes

    PubMed Central

    Tomasch, Jürgen; Gohl, Regina; Bunk, Boyke; Diez, Maria Suarez; Wagner-Döbler, Irene

    2011-01-01

    Bacterial aerobic anoxygenic photosynthesis (AAP) is an important mechanism of energy generation in aquatic habitats, accounting for up to 5% of the surface ocean's photosynthetic electron transport. We used Dinoroseobacter shibae, a representative of the globally abundant marine Roseobacter clade, as a model organism to study the transcriptional response of a photoheterotrophic bacterium to changing light regimes. Continuous cultivation of D. shibae in a chemostat in combination with time series microarray analysis was used in order to identify gene-regulatory patterns after switching from dark to light and vice versa. The change from heterotrophic growth in the dark to photoheterotrophic growth in the light was accompanied by a strong but transient activation of a broad stress response to the formation of singlet oxygen, an immediate downregulation of photosynthesis-related genes, fine-tuning of the expression of ETC components, as well as upregulation of the transcriptional and translational apparatus. Furthermore, our data suggest that D. shibae might use the 3-hydroxypropionate cycle for CO2 fixation. Analysis of the transcriptome dynamics after switching from light to dark showed relatively small changes and a delayed activation of photosynthesis gene expression, indicating that, except for light other signals must be involved in their regulation. Providing the first analysis of AAP on the level of transcriptome dynamics, our data allow the formulation of testable hypotheses on the cellular processes affected by AAP and the mechanisms involved in light- and stress-related gene regulation. PMID:21654848

  15. Purification and characterization of catalase from marine bacterium Acinetobacter sp. YS0810.

    PubMed

    Fu, Xinhua; Wang, Wei; Hao, Jianhua; Zhu, Xianglin; Sun, Mi

    2014-01-01

    The catalase from marine bacterium Acinetobacter sp. YS0810 (YS0810CAT) was purified and characterized. Consecutive steps were used to achieve the purified enzyme as follows: ethanol precipitation, DEAE Sepharose ion exchange, Superdex 200 gel filtration, and Resource Q ion exchange. The active enzyme consisted of four identical subunits of 57.256 kDa. It showed a Soret peak at 405 nm, indicating the presence of iron protoporphyrin IX. The catalase was not apparently reduced by sodium dithionite but was inhibited by 3-amino-1,2,4-triazole, hydroxylamine hydrochloride, and sodium azide. Peroxidase-like activity was not found with the substrate o-phenylenediamine. So the catalase was determined to be a monofunctional catalase. N-terminal amino acid of the catalase analysis gave the sequence SQDPKKCPVTHLTTE, which showed high degree of homology with those of known catalases from bacteria. The analysis of amino acid sequence of the purified catalase by matrix-assisted laser desorption ionization time-of-flight mass spectrometry showed that it was a new catalase, in spite of its high homology with those of known catalases from other bacteria. The catalase showed high alkali stability and thermostability. PMID:25045672

  16. A polysaccharide-degrading marine bacterium Flammeovirga sp. MY04 and its extracellular agarase system

    NASA Astrophysics Data System (ADS)

    Han, Wenjun; Gu, Jingyan; Yan, Qiujie; Li, Jungang; Wu, Zhihong; Gu, Qianqun; Li, Yuezhong

    2012-09-01

    Bacteria of the genus Flammeovirga can digest complex polysaccharides (CPs), but no details have been reported regarding the CP depolymerases of these bacteria. MY04, an agarolytic marine bacterium isolated from coastal sediments, has been identified as a new member of the genus Flammeovirga. The MY04 strain is able to utilize multiple CPs as a sole carbon source and grows well on agarose, mannan, or xylan. This strain produces high concentrations of extracellular proteins (490 mg L-1 ± 18.2 mg L-1 liquid culture) that exhibit efficient and extensive degradation activities on various polysaccharides, especially agarose. These proteins have an activity of 310 U mg-1 ± 9.6 U mg-1 proteins. The extracellular agarase system (EAS) in the crude extracellular enzymes contains at least four agarose depolymerases, which are with molecular masses of approximately 30-70 kDa. The EAS is stable at a wide range of pH values (6.0-11.0), temperatures (0-50°C), and sodium chloride (NaCl) concentrations (0-0.9 mol L-1). Two major degradation products generated from agarose by the EAS are identified to be neoagarotetraose and neoagarohexaose, suggesting that β-agarases are the major constituents of the MY04 EAS. These results suggest that the Flammeovirga strain MY04 and its polysaccharide-degradation system hold great promise in industrial applications.

  17. Copper-induced production of copper-binding supernatant proteins by the marine bacterium Vibrio alginolyticus

    SciTech Connect

    Harwood-Sears, V.; Gordon, A.S. )

    1990-05-01

    Growth of the marine bacterium Vibrio alginolyticus is temporarily inhibited by micromolar levels of copper. During the copper-induced lag phase, supernatant compounds and detoxify copper are produced. In this study two copper-inducible supernatant proteins having molecular masses of ca. 21 and 19 kilodaltons (CuBP1 and CuPB2) were identified; these proteins were, respectively, 25 and 46 times amplified in supernatants of copper-challenged cultures compared with controls. Experiments in which chloramphenicol was added to cultures indicated that there was de novo synthesis of these proteins in response to copper. When supernatants were separated by gel permeation chromatography, CuBP1 and CuPB2 coeluted with a copper-induced peak in copper-binding activity. CuBP1 and CuBP2 from whole supernatants were concentrated and partially purified by using a copper-charged immobilized metal ion affinity chromatography column, confirming the affinity of these proteins for copper. A comparison of cell pellets and supernatants demonstrated that CuBP1 was more concentrated in supernatants than in cells. Our data are consistent with a model for a novel mechanism of copper detoxification in which excretion of copper-binding protein is induced by copper.

  18. A new κ-carrageenase CgkS from marine bacterium Shewanella sp. Kz7

    NASA Astrophysics Data System (ADS)

    Wang, Linna; Li, Shangyong; Zhang, Shilong; Li, Jiejing; Yu, Wengong; Gong, Qianhong

    2015-08-01

    A new κ-carrageenase gene cgkS was cloned from marine bacterium Shewanella sp. Kz7 by using degenerate and site-finding PCR. The gene was comprised of an open reading frame of 1224 bp, encoding 407 amino acid residues, with a signal peptide of 24 residues. Based on the deduced amino acid sequence, the κ-carrageenase CgkS was classified into the Glycoside Hydrolase family 16. The cgkS gene was expressed in Escherichia coli, and the recombinant enzyme was purified to homogeneity with a specific activity of 716.8 U mg-1 and a yield of 69%. Recombinant CgkS was most active at 45°C and pH 8.0. It was stable at pH 6.0-9.0 and below 30°C. The enzyme did not require NaCl for activity, although its activity was enhanced by NaCl. CgkS degraded κ-carrageenan in an endo-fashion releasing tetrasaccharides and disaccharides as main hydrolysis products.

  19. Three Alginate Lyases from Marine Bacterium Pseudomonas fluorescens HZJ216: Purification and Characterization

    SciTech Connect

    Liyan, Li; Jiang, Xiaolu; Wang, Peng; Guan, Huashi; Guo, Hong

    2010-01-01

    Three alginate lyases (A, B, and C) from an alginate-degrading marine bacterium strain HZJ216 isolated from brown seaweed in the Yellow Sea of China and identified preliminarily as Pseudomonas fluorescens are purified, and their biochemical properties are described. Molecular masses of the three enzymes are determined by SDS-PAGE to be 60.25, 36, and 23 kDa with isoelectric points of 4, 4.36, and 4.59, respectively. Investigations of these enzymes at different pH and temperatures show that they are most active at pH 7.0 and 35 C. Alginate lyases A and B are stable in the pH range of 5.0 9.0, while alginate lyase C is stable in the pH range of 5.0 7.0. Among the metal ions tested, additions of Na+, K+, and Mg2+ ions can enhance the enzyme activities while Fe2+, Fe3+, Ba2+, and Zn2+ ions show inhibitory effects. The substrate specificity results demonstrate that alginate lyase C has the specificity for G block while alginate lyases A and B have the activities for both M and G blocks. It is the first report about extracellular alginate lyases with high alginate-degrading activity from P. fluorescens.

  20. Recombinant α-NAcetylgalactosaminidase from Marine Bacterium-Modifying A Erythrocyte Antigens

    PubMed Central

    Balabanova, L. A.; Golotin, V. A.; Bakunina, I. Y.; Slepchenko, L. V.; Isakov, V. V.; Podvolotskaya, A. B.; Rasskazov, V. A.

    2015-01-01

    A plasmid based on pET-40b was constructed to synthesize recombinant α-N-acetylgalactosaminidase of the marine bacterium Arenibacter latericius KMM 426T (α-AlNaGal) in Escherichia coli cells. The yield of α-Al- NaGal attains 10 mg/ml with activity of 49.7 ± 1.3 U at 16°C, concentration of inductor 2 mM, and cultivation for 12 h. Techniques such as anion exchange, metal affinity and gel filtration chromatography to purify α-AlNaGal were applied. α-AlNaGal is a homodimer with a molecular weight of 164 kDa. This enzyme is stable at up to 50°C with a temperature range optimum activity of 20–37°C. Furthermore, its activity is independent of the presence of metal ions in the incubation medium. 1H NMR spectroscopy revealed that α-AlNaGal catalyzes the hydrolysis of the O-glycosidic bond with retention of anomeric stereochemistry and possesses a mechanism of action identical to that of other glycoside hydrolases of the 109 family. α-AlNaGal reduces the serological activity of A erythrocytes at pH 7.3. This property of α-AlNaGal can potentially be used for enzymatic conversion of A and AB erythrocytes to blood group O erythrocytes. PMID:25927009

  1. Recombinant α-NAcetylgalactosaminidase from Marine Bacterium-Modifying A Erythrocyte Antigens.

    PubMed

    Balabanova, L A; Golotin, V A; Bakunina, I Y; Slepchenko, L V; Isakov, V V; Podvolotskaya, A B; Rasskazov, V A

    2015-01-01

    A plasmid based on pET-40b was constructed to synthesize recombinant α-N-acetylgalactosaminidase of the marine bacterium Arenibacter latericius KMM 426T (α-AlNaGal) in Escherichia coli cells. The yield of α-Al- NaGal attains 10 mg/ml with activity of 49.7 ± 1.3 U at 16°C, concentration of inductor 2 mM, and cultivation for 12 h. Techniques such as anion exchange, metal affinity and gel filtration chromatography to purify α-AlNaGal were applied. α-AlNaGal is a homodimer with a molecular weight of 164 kDa. This enzyme is stable at up to 50°C with a temperature range optimum activity of 20-37°C. Furthermore, its activity is independent of the presence of metal ions in the incubation medium. 1H NMR spectroscopy revealed that α-AlNaGal catalyzes the hydrolysis of the O-glycosidic bond with retention of anomeric stereochemistry and possesses a mechanism of action identical to that of other glycoside hydrolases of the 109 family. α-AlNaGal reduces the serological activity of A erythrocytes at pH 7.3. This property of α-AlNaGal can potentially be used for enzymatic conversion of A and AB erythrocytes to blood group O erythrocytes. PMID:25927009

  2. Effects of Inorganic Particles on Metabolism by a Periphytic Marine Bacterium

    PubMed Central

    Gordon, Andrew S.; Gerchakov, Sol M.; Millero, Frank J.

    1983-01-01

    Measurements were made of adsorption of a periphytic marine bacterium, glucose, and glutamic acid to inorganic particles in seawater and defined bacterial growth medium. Measurements of the metabolism of bacteria were made in the presence and absence of particles by microcalorimetry and radiorespirometry. It was found that hydroxyapatite adsorbs glutamic acid, but not glucose, from the experimental medium. It was also found that hydroxyapatite adsorbs essentially all of the bacteria from the medium when the bacterial concentration is approximately 6 × 105 bacteria per ml. If the bacterial concentration is approximately 6 × 107, then only a small fraction of cells become attached. It was therefore possible to select bacterial concentrations and organic nutrients so that bacterial attachment, organic nutrient adsorption, or both would occur in different experiments. In this experimental system the metabolism by attached and nonattached bacteria of adsorbing and nonadsorbing organic nutrients was measured. The results show that bacterial activity in this model system was not enhanced by the particles, regardless of whether the bacteria, the organic nutrient, or both were associated with the surface. In fact, the respiratory activity of the attached bacteria was diminished in comparison with that of free bacteria. PMID:16346191

  3. Cloning, expression, purification and application of a novel chitinase from a thermophilic marine bacterium Paenibacillus barengoltzii.

    PubMed

    Yang, Shaoqing; Fu, Xing; Yan, Qiaojuan; Guo, Yu; Liu, Zhuqing; Jiang, Zhengqiang

    2016-02-01

    A novel chitinase gene (PbChi70) from a marine bacterium Paenicibacillus barengoltzii was cloned and functionally expressed in Escherichia coli. The recombinant enzyme (PbChi70) was purified to homogeneity with a recovery yield of 51.9%. The molecular mass of purified enzyme was estimated to be 70.0 kDa by SDS-PAGE. PbChi70 displayed maximal activity at pH 5.5 and 55 °C, respectively. It exhibited strict substrate specificity for colloidal chitin, glycol chitin, powdery chitin, and N-acetyl chitooligosaccharides with degrees of polymerization above three. The enzyme exhibited an endo-type cleavage pattern and hydrolyzed colloidal chitin to yield mainly (GlcNAc)2. Furthermore, colloidal chitin was hydrolyzed by PbChi70 to produce 21.6 mg mL(-1) (GlcNAc)2 with the highest conversion yield of 89.5% (w/w). (GlcNAc)2 was further separated by an active charcoal column with a purity of 99% and a final yield of 61%. The unique enzymatic properties of the chitinase may make it a good candidate for (GlcNAc)2 production. PMID:26304445

  4. Colwellia asteriadis sp. nov., a marine bacterium isolated from the starfish Asterias amurensis.

    PubMed

    Choi, Eun Ju; Kwon, Hak Cheol; Koh, Hye Yeon; Kim, Young Sug; Yang, Hyun Ok

    2010-08-01

    A marine bacterial strain, KMD 002T, was isolated from an Amur starfish, Asterias amurensis, collected in the East Sea of Korea. Strain KMD 002T was a Gram-negative, beige-pigmented, rod-shaped bacterium. The strain was capable of growth at relatively low temperatures (4-25 degrees C) and over a broad pH range (pH 4.0-10.0). The major fatty acids were C16:1omega7c and/or iso-C15:0 2-OH and C16:0 and the predominant isoprenoid quinone was Q-8. The DNA G+C content of strain KMD 002T was 40.3 mol%. Phylogenetic analysis using 16S rRNA gene sequences revealed that strain KMD 002T belonged to the genus Colwellia. However, various phenotypic properties as well as low 16S rRNA gene sequence similarities to members of the genus Colwellia (94.1-96.7%) suggested that strain KMD 002T is a representative of a novel species, for which the name Colwellia asteriadis sp. nov. is proposed. The type strain is KMD 002T (=KCCM 90077T =JCM 15608T). PMID:19801395

  5. Regulation of iron transport related genes by boron in the marine bacterium Marinobacter algicola DG893.

    PubMed

    Romano, Ariel; Trimble, Lyndsay; Hobusch, Ashtian R; Schroeder, Kristine J; Amin, Shady A; Hartnett, Andrej D; Barker, Ryan A; Crumbliss, Alvin L; Carrano, Carl J

    2013-08-01

    While there has been extensive interest in the use of boron isotope ratios as a surrogate of pH in paleoclimate studies in the context of climate change-related questions, the high (0.4 mM) concentration and the depth-independent (conservative or non-nutrient-like) concentration profile of this element have led to boron being neglected as a potentially biologically relevant element in the modern ocean. Here we report that boron affects the expression of a number of protein and genes in the "algal-associated" Gram-negative marine bacterium Marinobacter algicola DG893. Most intriguingly, a number of these proteins and genes are related to iron uptake. In a recent separate publication we have shown that boron regulates one such iron transport related protein, i.e. the periplasmic iron binding protein FbpA via a direct interaction of the metalloid with this protein. Here we show that a number of other iron uptake related genes are also affected by boron but in the opposite way i.e. they are up-regulated. We propose that the differential effect of boron on FbpA expression relative to other iron transport related genes is a result of an interaction between boron and the global iron regulatory protein Fur. PMID:23775459

  6. Evidence for the subcellular localization and specificity of chlordane inhibition in the marine bacterium Aeromonas proteolytica.

    PubMed Central

    Nakas, J P; Litchfield, C D

    1979-01-01

    Sublethal levels (10 to 100 micrograms/ml) of the chlorinated insecticide chlordane (1,2,4,5,6,7,8,8-octachloro-3a,4,7,7a-tetrahydro-4,7-methanoindan) were introduced into the growth medium of the marine bacterium, Aeromonas proteolytica. Chlordane inhibited the synthesis of an extracellular endopeptidase by almost 40% but exhibited no such inhibition of the extracellular aminopeptidase also produced during the growth cycle. Studied with 14C-labeled chlordane demonstrated that the insecticide was not biologically degraded under the test conditions used and that up to 75% of the recoverable chlordane was cell associated within 48 h. Studied with uniformly labeled L[14C]valine and [2-14C]uracil established that neither the transport nor the incorporation of these protein and ribonucleic acid precursors was inhibited by chlordane. Separation of the membrane fractions using isopycnic centrifugation localized 14C-labeled chlordane in the cytoplasmic membrane. Also, chlordane inhibited the membrane-bound adenosine 5'-triphosphatase while the soluble (released) form of this enzyme remained unaffected. These data indicate that chlordane resides in the cytoplasmic membrane and may cause specific alterations in membrane-associated activities. PMID:156517

  7. Aerobic and anaerobic degradation of a range of alkyl sulfides by a denitrifying marine bacterium

    USGS Publications Warehouse

    Visscher, P.T.; Taylor, B.F.

    1993-01-01

    A pure culture of a bacterium was obtained from a marine microbial mat by using an anoxic medium containing dimethyl sulfide (DMS) and nitrate. The isolate grew aerobically or anaerobically as a denitrifier on alkyl sulfides, including DMS, dimethyl disulfide, diethyl sulfide (DES), ethyl methyl sulfide, dipropyl sulfide, dibutyl sulfide, and dibutyl disulfide. Cells grown on an alkyl sulfide or disulfide also oxidized the corresponding thiols, namely, methanethiol, ethanethiol, propanethiol, or butanethiol. Alkyl sulfides were metabolized by induced or derepressed cells with oxygen, nitrate, or nitrite as electron acceptor. Cells grown on DMS immediately metabolized DMS, but there was a lag before DES was consumed; with DES-grown cells, DES was immediately used but DMS was used only after a lag. Chloramphenicol prevented the eventual use of DES by DMS-grown cells and DMS use by DES-grown cells, respectively, indicating separate enzymes for the metabolism of methyl and ethyl groups. Growth was rapid on formate, acetate, propionate, and butyrate but slow on methanol. The organism also grew chemolithotrophically on thiosulfate with a decrease in pH; growth required carbonate in the medium. Growth on sulfide was also carbonate dependent but slow. The isolate was identified as a Thiobacillus sp. and designated strain ASN-1. It may have utility for removing alkyl sulfides, and also nitrate, nitrite, and sulfide, from wastewaters.

  8. A cold-adapted, solvent and salt tolerant esterase from marine bacterium Psychrobacter pacificensis.

    PubMed

    Wu, Gaobing; Zhang, Xiangnan; Wei, Lu; Wu, Guojie; Kumar, Ashok; Mao, Tao; Liu, Ziduo

    2015-11-01

    Lipolytic enzymes with unique physico-chemical characteristics are gaining more attention for their immense industrial importance. In this study, a novel lipolytic enzyme (Est11) was cloned from the genomic library of a marine bacterium Psychrobacter pacificensis. The enzyme was expressed in Escherichia coli and purified to homogeneity with molecular mass of 32.9kDa. The recombinant Est11 was able to hydrolyze short chain esters (C2-C8) and displayed an optimum activity against butyrate ester (C4). The optimal temperature and pH were 25°C and 7.5, respectively. Est11 retained more than 70% of its original activity at 10°C, suggesting that it was a cold-active esterase. The enzyme was highly active and stable at high concentration of NaCl (5M). Further, incubation with ethanol, isopropanol, propanediol, DMSO, acetonitrile, and glycerol rendered remarkable positive effects on Est11 activity. Typically, even at the concentration of 30% (v/v), ethanol, DMSO, and propanediol increased Est11 activity by 1.3, 2.0, and 2.4-folds, respectively. This new robust enzyme with remarkable properties like cold-adaptability, exceptional tolerance to salt and organic solvents provides us a promising candidate to meet the needs of some harsh industrial processes. PMID:26231332

  9. Iridescence of a Marine Bacterium and Classification of Prokaryotic Structural Colors

    PubMed Central

    Vukusic, Peter; Luke, Stephen

    2012-01-01

    Iridescence is a property of structural color that is occasionally encountered in higher eukaryotes but that has been poorly documented in the prokaryotic kingdom. In the present work, we describe a marine bacterium, identified as Cellulophaga lytica, isolated from the surface of an anemone, that exhibits bright green iridescent colonies under direct epi-illumination. This phenomenon has not previously been investigated in detail. In this study, color changes of C. lytica colonies were observed at various angles of direct illumination or observation. Its iridescent green appearance was dominant on various growth media. Red and violet colors were also discerned on colony edges. Remarkable C. lytica bacterial iridescence was revealed and characterized using high-resolution optical spectrometry. In addition to this, by culturing other bacterial strains to which various forms of faintly iridescent traits have previously been attributed, we identify four principal appearance characteristics of structural color in prokaryotes. A new general classification of bacterial iridescence is therefore proposed in this study. Furthermore, a specific separate class is described for iridescent C. lytica strains because they exhibit what is so far a unique intense glitter-like iridescence in reflection. C. lytica is the first prokaryote discovered to produce the same sort of intense iridescence under direct illumination as that associated with higher eukaryotes, like some insects and birds. Due to the nature of bacterial biology, cultivation, and ubiquity, this discovery may be of significant interest for both ecological and nanoscience endeavors. PMID:22267664

  10. Affinity purification of metalloprotease from marine bacterium using immobilized metal affinity chromatography.

    PubMed

    Li, Shangyong; Wang, Linna; Yang, Juan; Bao, Jing; Liu, Junzhong; Lin, Shengxiang; Hao, Jianhua; Sun, Mi

    2016-06-01

    In this study, an efficient affinity purification protocol for an alkaline metalloprotease from marine bacterium was developed using immobilized metal affinity chromatography. After screening and optimization of the affinity ligands and spacer arm lengths, Cu-iminmodiacetic acid was chosen as the optimal affinity ligand, which was coupled to Sepharose 6B via a 14-atom spacer arm. The absorption analysis of this medium revealed a desorption constant Kd of 21.5 μg/mL and a theoretical maximum absorption Qmax of 24.9 mg/g. Thanks to this affinity medium, the enzyme could be purified by only one affinity purification step with a purity of approximately 95% pure when analyzed by high-performance liquid chromatography and reducing sodium dodecyl sulfate polyacrylamide gel electrophoresis. The recovery of the protease activity reached 74.6%, which is much higher than the value obtained by traditional protocols (8.9%). These results contribute to the industrial purifications and contribute a significant reference for the purification of other metalloproteases. PMID:27058973

  11. Aerobic and anaerobic degradation of a range of alkyl sulfides by a denitrifying marine bacterium.

    PubMed Central

    Visscher, P T; Taylor, B F

    1993-01-01

    A pure culture of a bacterium was obtained from a marine microbial mat by using an anoxic medium containing dimethyl sulfide (DMS) and nitrate. The isolate grew aerobically or anaerobically as a denitrifier on alkyl sulfides, including DMS, dimethyl disulfide, diethyl sulfide (DES), ethyl methyl sulfide, dipropyl sulfide, dibutyl sulfide, and dibutyl disulfide. Cells grown on an alkyl sulfide or disulfide also oxidized the corresponding thiols, namely, methanethiol, ethanethiol, propanethiol, or butanethiol. Alkyl sulfides were metabolized by induced or derepressed cells with oxygen, nitrate, or nitrite as electron acceptor. Cells grown on DMS immediately metabolized DMS, but there was a lag before DES was consumed; with DES-grown cells, DES was immediately used but DMS was used only after a lag. Chloramphenicol prevented the eventual use of DES by DMS-grown cells and DMS use by DES-grown cells, respectively, indicating separate enzymes for the metabolism of methyl and ethyl groups. Growth was rapid on formate, acetate, propionate, and butyrate but slow on methanol. The organism also grew chemolithotrophically on thiosulfate with a decrease in pH; growth required carbonate in the medium. Growth on sulfide was also carbonate dependent but slow. The isolate was identified as a Thiobacillus sp. and designated strain ASN-1. It may have utility for removing alkyl sulfides, and also nitrate, nitrite, and sulfide, from wastewaters. PMID:8285707

  12. Biochemistry, physiology and biotechnology of sulfate-reducing bacteria.

    PubMed

    Barton, Larry L; Fauque, Guy D

    2009-01-01

    Chemolithotrophic bacteria that use sulfate as terminal electron acceptor (sulfate-reducing bacteria) constitute a unique physiological group of microorganisms that couple anaerobic electron transport to ATP synthesis. These bacteria (220 species of 60 genera) can use a large variety of compounds as electron donors and to mediate electron flow they have a vast array of proteins with redox active metal groups. This chapter deals with the distribution in the environment and the major physiological and metabolic characteristics of sulfate-reducing bacteria (SRB). This chapter presents our current knowledge of soluble electron transfer proteins and transmembrane redox complexes that are playing an essential role in the dissimilatory sulfate reduction pathway of SRB of the genus Desulfovibrio. Environmentally important activities displayed by SRB are a consequence of the unique electron transport components or the production of high levels of H(2)S. The capability of SRB to utilize hydrocarbons in pure cultures and consortia has resulted in using these bacteria for bioremediation of BTEX (benzene, toluene, ethylbenzene and xylene) compounds in contaminated soils. Specific strains of SRB are capable of reducing 3-chlorobenzoate, chloroethenes, or nitroaromatic compounds and this has resulted in proposals to use SRB for bioremediation of environments containing trinitrotoluene and polychloroethenes. Since SRB have displayed dissimilatory reduction of U(VI) and Cr(VI), several biotechnology procedures have been proposed for using SRB in bioremediation of toxic metals. Additional non-specific metal reductase activity has resulted in using SRB for recovery of precious metals (e.g. platinum, palladium and gold) from waste streams. Since bacterially produced sulfide contributes to the souring of oil fields, corrosion of concrete, and discoloration of stonework is a serious problem, there is considerable interest in controlling the sulfidogenic activity of the SRB. The

  13. Linking Microbial Ecology to Geochemistry in Sulfate Reducing Systems

    NASA Astrophysics Data System (ADS)

    Drennan, D. M.; Lee, I.; Landkamer, L.; Almstrand, R.; Figueroa, L. A.; Sharp, J. H.

    2013-12-01

    Sulfate reducing bioreactors (SRBRs) can serve as passive treatment systems for mining influenced waters (MIW). An enhanced understanding of the biogeochemistry and efficacy of SRBRs can be achieved by combining molecular biological and geochemical techniques in both field and column settings. To this end, a spatial and temporal sequence of eight pilot-scale columns were analyzed employing a multidisciplinary approach using ICP-AES, next-generation sequencing, and SEM-EDX to explore the effects of variable substrate on community structure and performance (measured by Zn removal). All pilot scale reactors contained 30% limestone by mass, 7 of the 8 had variable amounts of woodchips, sawdust, and alfalfa hay, and an 8th column where the only carbon source was walnut shells. High throughput sequencing of DNA extracted from liquid in pilot-scale columns reveals, similarly to an analogous field system in Arizona, a dominance of Proteobacteria. However, after the first pore volume, performance differences between substrate permutations emerged, where columns containing exclusively walnut shells or sawdust exhibited a more effective startup and metal removal than did columns containing exclusively woodchips or alfalfa hay. SEM-EDX analysis revealed the initial formation of gypsum (CaSO4) precipitates regardless of substrate. Zn was observed in the presence of Ca, S, and O in some column samples, suggesting there was co-precipitation of Zn and CaSO4. This is congruent with micro-XAS analysis of field data suggesting iron sulfides were co-precipitating with gypsum. A SEM-EDX analysis from a subsequent sampling event (8 months into operation) indicated that precipitation may be shifting to ZnS and ZnCO3. Biplots employing Canonical Correspondence Analysis (CCA) describe how diversity scales with performance and substrate selection, and how community shifts may result in differential performance and precipitation in response to selective pressure of bioreactor material on

  14. Abiotic transformation of dinitrophenols under sulfate-reducing conditions

    SciTech Connect

    Gui, L.; Bouwer, E.J.

    1996-10-01

    Dinitrophenols are hazardous chemicals commonly detected in the environment. Little is known about their fate under sulfate-reducing conditions (SRC) where H{sub 2}S level is elevated due to microbial activity. Dinitrophenols are susceptible to both biotic and abiotic transformation under SRC. The objectives of this research are to investigate dinitrophenol transformation using hydrogen sulfide as a reductant, and to determine factors that affect the abiotic transformation kinetics under SRC. Dinitrophenols studied were 2,4-dinitrophenol (DNP), 4,6-dinitro-o-cresol (DNOC), and 2-sec-butyl-4,6-dinitrophenol (dinoseb). All three dinitrophenols were transformed through an ortho-nitroreduction pathway. In the presence of H{sub 2}S as the bulk reductant and a small amount of trace metals (10{sup -6} to 10{sup -7} M), pseudo-first-order kinetics was observed. Addition of yeast extract (YE, 0.02%) enhanced dinoseb transformation rate significantly. An increase in HS concentration resulted in Michaelis-Menton type kinetics for dinoseb in the presence of trace metals and YE, suggesting that trace metals and YE functioned as electron mediators.

  15. Complete Genome Sequence of the Hyperthermophilic Sulfate-Reducing Bacterium Thermodesulfobacterium geofontis OPF15T

    PubMed Central

    Hamilton-Brehm, Scott D.; Lucas, Susan; Han, James; Lapidus, Alla; Cheng, Jan-Fang; Goodwin, Lynne A.; Pitluck, Sam; Peters, Lin; Mikhailova, Natalia; Davenport, Karen W.; Detter, John C.; Han, Cliff S.; Tapia, Roxanne; Land, Miriam L.; Hauser, Loren; Kyrpides, Nikos C.; Ivanova, Natalia N.; Pagani, Ioanna; Bruce, David; Woyke, Tanja; Cottingham, Robert W.

    2013-01-01

    Thermodesulfobacterium geofontis OPF15T (ATCC BAA-2454, JCM 18567) was isolated from Obsidian Pool, Yellowstone National Park, and grows optimally at 83°C. The 1.6-Mb genome sequence was finished at the Joint Genome Institute and has been deposited for future genomic studies pertaining to microbial processes and nutrient cycles in high-temperature environments. PMID:23580711

  16. Complete Genome Sequence of the Hyperthermophilic Sulfate-Reducing Bacterium Thermodesulfobacterium geofontis OPF15T.

    PubMed

    Elkins, James G; Hamilton-Brehm, Scott D; Lucas, Susan; Han, James; Lapidus, Alla; Cheng, Jan-Fang; Goodwin, Lynne A; Pitluck, Sam; Peters, Lin; Mikhailova, Natalia; Davenport, Karen W; Detter, John C; Han, Cliff S; Tapia, Roxanne; Land, Miriam L; Hauser, Loren; Kyrpides, Nikos C; Ivanova, Natalia N; Pagani, Ioanna; Bruce, David; Woyke, Tanja; Cottingham, Robert W

    2013-01-01

    Thermodesulfobacterium geofontis OPF15(T) (ATCC BAA-2454, JCM 18567) was isolated from Obsidian Pool, Yellowstone National Park, and grows optimally at 83°C. The 1.6-Mb genome sequence was finished at the Joint Genome Institute and has been deposited for future genomic studies pertaining to microbial processes and nutrient cycles in high-temperature environments. PMID:23580711

  17. Complete Genome Sequence of the hyperthermophilic sulfate-reducing bacterium Thermodesulfobacterium geofontis OPF15T

    SciTech Connect

    Elkins, James G.; Hamilton-Brehm, Scott; Lucas, Susan; Han, James; Lapidus, Alla; Cheng, Jan-Fang; Goodwin, Lynne A.; Pitluck, Sam; Peters, Lin; Mikhailova, Natalia; Walston Davenport, Karen; Detter, John C.; Han, Cliff S.; Tapia, Roxanne; Land, Miriam L.; Hauser, Loren; Kyrpides, Nikos C.; Ivanova, Natalia N.; Pagani, Ioanna; Bruce, David; Woyke, Tanja; Cottingham, Robert W.

    2013-04-11

    Thermodesulfobacterium geofontis OPF15T was isolated from Obsidian Pool, Yellowstone National Park and grows optimally at 83 oC. The OPF15T genome was finished at the Joint Genome Institute and the 1.6 Mb sequence has been annotated and deposited for future genomic studies aimed at understanding microbial processes and nutrient cycles in high-temperature environments.

  18. Genome Sequence of the Piezophilic, Mesophilic Sulfate-Reducing Bacterium Desulfovibrio indicus J2T.

    PubMed

    Cao, Junwei; Maignien, Lois; Shao, Zongze; Alain, Karine; Jebbar, Mohamed

    2016-01-01

    The complete genome sequence ofDesulfovibrio indicusJ2(T), a member of the familyDesulfovibrionaceae, consists of 3,966,573-bp in one contig and encodes 3,461 predicted genes, 5 noncoding RNAs, 3 rRNAs operons, and 52 tRNA-encoding genes. The genome is consistent with a heterotrophic, anaerobic lifestyle including the sulfate reduction pathway. PMID:27056223

  19. Bacterial Growth Phase Influences Methylmercury Production by the Sulfate-Reducing Bacterium Desulfovibrio desulfuricans ND132

    SciTech Connect

    Biswas, Abir; Brooks, Scott C; Miller, Carrie L; Mosher, Jennifer J; Yin, Xiangping Lisa; Drake, Meghan M

    2011-01-01

    The effect of bacterial growth phase is an aspect of mercury (Hg) methylation that previous studies have not investigated in detail. Here we consider the effect of growth phase (mid-log, late-log and late stationary phase) on Hg methylation by the known methylator Desulfovibrio desulfuricans ND132. We tested the addition of Hg alone (chloride-complex), Hg with Suwannee River natural organic matter (SRNOM) (unequilibrated), and Hg equilibrated with SRNOM on monomethylmercury (MMHg) production by ND132 over a growth curve in pyruvate-fumarate media. This NOM did not affect MMHg production even under very low Hg:SRNOM ratios, where Hg binding is predicted to be dominated by high energy sites. Adding Hg or Hg-NOM to growing cultures 24h before sampling (late addition) resulted in {approx}2x greater net fraction of Hg methylated than for comparably aged cultures exposed to Hg from the initial culture inoculation (early addition). Mid- and late-log phase cultures produced similar amounts of MMHg, but late stationary phase cultures (both under early and late Hg addition conditions) produced up to {approx}3x more MMHg, indicating the potential importance of growth phase in studies of MMHg production.

  20. Genome Sequence of the Piezophilic, Mesophilic Sulfate-Reducing Bacterium Desulfovibrio indicus J2T

    PubMed Central

    Maignien, Lois; Shao, Zongze; Alain, Karine

    2016-01-01

    The complete genome sequence of Desulfovibrio indicus J2T, a member of the family Desulfovibrionaceae, consists of 3,966,573-bp in one contig and encodes 3,461 predicted genes, 5 noncoding RNAs, 3 rRNAs operons, and 52 tRNA-encoding genes. The genome is consistent with a heterotrophic, anaerobic lifestyle including the sulfate reduction pathway. PMID:27056223

  1. Bacterial Growth Phase Influences Methylmercury Production by the Sulfate-Reducing Bacterium Desulfovibrio desulfuricans ND132

    SciTech Connect

    Biswas, Abir; Brooks, Scott C; Miller, Carrie L; Mosher, Jennifer J; Yin, Xiangping Lisa; Drake, Meghan M

    2011-01-01

    The effect of bacterial growth phase is an aspect of mercury (Hg) methylation that previous studies have not investigated in detail. Here we consider the effect of growth phase (mid-log, late-log and late stationary phase) on Hg methylation by the known methylator Desulfovibrio desulfuricans ND132. We tested the addition of Hg alone (chloride-complex), Hg with Suwannee River natural organic matter (SRNOM) (unequilibrated), and Hg equilibrated with SRNOM on monomethylmercury (MMHg) production by ND132 over a growth curve in pyruvate fumarate media. This NOM did not affect MMHg production even under very low Hg: SRNOM ratios, where Hg binding is predicted to be dominated by high energy sites. Adding Hg or Hg NOM to growing cultures 24 h before sampling (late addition) resulted in ~2 greater net fraction of Hg methylated than for comparably aged cultures exposed to Hg from the initial culture inoculation (early addition). Mid-and late-log phase cultures produced similar amounts of MMHg, but late stationary phase cultures (both under early and late Hg addition conditions) produced up to ~3 more MMHg, indicating the potential importance of growth phase in studies of MMHg production.

  2. Draft genome sequence of the first acid-tolerant sulfate-reducing deltaproteobacterium Desulfovibrio sp. TomC having potential for minewater treatment.

    PubMed

    Karnachuk, Olga V; Mardanov, Andrey V; Avakyan, Marat R; Kadnikov, Vitaly V; Vlasova, Maria; Beletsky, Alexey V; Gerasimchuk, Anna L; Ravin, Nikolai V

    2015-02-01

    The sulfidogenic bacterium Desulfovibrio sp. TomC was isolated from acidic waste at the abandoned gold ore mining site in the Martaiga gold ore belt, Western Siberia. This bacterium, being the first reported acid-tolerant gram-negative sulfate-reducer of the order Deltaproteobacteria, is able to grow at pH as low as 2.5 and is resistant to high concentrations of metals. The draft 5.3 Mb genome sequence of Desulfovibrio sp. TomC has been established and provides the genetic basis for application of this microorganism in bioreactors and other bioremediation schemes for the treatment of metal-containing wastewater. PMID:25724779

  3. Novel processes for anaerobic sulfate production from elemental sulfur by sulfate-reducing bacteria

    USGS Publications Warehouse

    Lovley, D.R.; Phillips, E.J.P.

    1994-01-01

    Sulfate reducers and related organisms which had previously been found to reduce Fe(III) with H2 or organic electron donors oxidized S0 to sulfate when Mn(IV) was provided as an electron acceptor. Organisms catalyzing this reaction in washed cell suspensions included Desulfovibrio desulfuricans, Desulfomicrobium baculatum. Desulfobacterium autotrophicum, Desulfuromonas acetoxidans, and Geobacter metallireducens. These organisms produced little or no sulfate from S0 with Fe(III) as a potential electron acceptor or in the absence of an electron acceptor. In detailed studies with Desulfovibrio desulfuricans, the stoichiometry of sulfate and Mn(II) production was consistent with the reaction S0 + 3 MnO2 + 4H+ ???SO42- + 3Mn(II) + 2H2O. None of the organisms evaluated could be grown with S0 as the sole electron donor and Mn(IV) as the electron acceptor. In contrast to the other sulfate reducers evaluated, Desulfobulbus propionicus produced sulfate from S0 in the absence of an electron acceptor and Fe(III) oxide stimulated sulfate production. Sulfide also accumulated in the absence of Mn(IV) or Fe(III). The stoichiometry of sulfate and sulfide production indicated that Desulfobulbus propionicus disproportionates S0 as follows: 4S0 + 4H2O???SO42- + 3HS- + 5 H+. Growth of Desulfobulbus propionicus with S0 as the electron donor and Fe(III) as a sulfide sink and/or electron acceptor was very slow. The S0 oxidation coupled to Mn(IV) reduction described here provides a potential explanation for the Mn(IV)-dependent sulfate production that previous studies have observed in anoxic marine sediments. Desulfobulbus propionicus is the first example of a pure culture known to disproportionate S0.

  4. Biomass Yield Efficiency of the Marine Anammox Bacterium, “Candidatus Scalindua sp.,” is Affected by Salinity

    PubMed Central

    Awata, Takanori; Kindaichi, Tomonori; Ozaki, Noriatsu; Ohashi, Akiyoshi

    2015-01-01

    The growth rate and biomass yield efficiency of anaerobic ammonium oxidation (anammox) bacteria are markedly lower than those of most other autotrophic bacteria. Among the anammox bacterial genera, the growth rate and biomass yield of the marine anammox bacterium “Candidatus Scalindua sp.” is still lower than those of other anammox bacteria enriched from freshwater environments. The activity and growth of marine anammox bacteria are generally considered to be affected by the presence of salinity and organic compounds. Therefore, in the present study, the effects of salinity and volatile fatty acids (VFAs) on the anammox activity, inorganic carbon uptake, and biomass yield efficiency of “Ca. Scalindua sp.” enriched from the marine sediments of Hiroshima Bay, Japan, were investigated in batch experiments. Differences in VFA concentrations (0–10 mM) were observed under varying salinities (0.5%–4%). Anammox activity was high at 0.5%–3.5% salinity, but was 30% lower at 4% salinity. In addition, carbon uptake was higher at 1.5%–3.5% salinity. The results of the present study clearly demonstrated that the biomass yield efficiency of the marine anammox bacterium “Ca. Scalindua sp.” was significantly affected by salinity. On the other hand, the presence of VFAs up to 10 mM did not affect anammox activity, carbon uptake, or biomass yield efficiency. PMID:25740428

  5. Phylogenetic Characteristics of Sulfate-reducing Bacteria Having Ability to Reduce Polysulfide

    SciTech Connect

    Takahashi, Yui; Suto, Koichi; Inoue, Chihiro; Chida, Tadashi

    2006-05-15

    To find an efficient bacterium, which has the strong capacity to produce hydrogen sulfide from polysulfide as the waste of process generating hydrogen from hydrogen sulfide by photocatalytic reaction using sun light, is very important for constructing hydrogen producing system. 10 strains of sulfate-reducing bacteria (SRB), which can reduce polysulfide directly, have been isolated from various natural samples such as TCE contaminated soil, soil and sludge around hot spring environment, and the cooling tower of a geothermal plant. This study describes physiological and phylogenetic characterization of SRB which can reduce polysulfide. All of isolates had the ability to reduce polusulfide but these reduction rates were difference depend on isolates. Phylogetetically, all of isolates located difference position for general SRB including Desulfovibrio desulfuricans, which is used standard strain in this study, so they do not belong to Proteobacteria. These have close relation to the genus Desulfotomaculum which can reduce elemental sulfur. It suggests that the ability of reducing elemental sulfur is important for reducing polysulfide to hydrogen sulfide.

  6. Phylogenetic Characteristics of Sulfate-reducing Bacteria Having Ability to Reduce Polysulfide

    NASA Astrophysics Data System (ADS)

    Takahashi, Yui; Suto, Koichi; Inoue, Chihiro; Chida, Tadashi

    2006-05-01

    To find an efficient bacterium, which has the strong capacity to produce hydrogen sulfide from polysulfide as the waste of process generating hydrogen from hydrogen sulfide by photocatalytic reaction using sun light, is very important for constructing hydrogen producing system. 10 strains of sulfate-reducing bacteria (SRB), which can reduce polysulfide directly, have been isolated from various natural samples such as TCE contaminated soil, soil and sludge around hot spring environment, and the cooling tower of a geothermal plant. This study describes physiological and phylogenetic characterization of SRB which can reduce polysulfide. All of isolates had the ability to reduce polusulfide but these reduction rates were difference depend on isolates. Phylogetetically, all of isolates located difference position for general SRB including Desulfovibrio desulfuricans, which is used standard strain in this study, so they do not belong to Proteobacteria. These have close relation to the genus Desulfotomaculum which can reduce elemental sulfur. It suggests that the ability of reducing elemental sulfur is important for reducing polysulfide to hydrogen sulfide.

  7. Genetics and Molecular Biology of Hydrogen Metabolism in Sulfate-Reducing Bacteria

    SciTech Connect

    Wall, Judy D.

    2014-12-23

    The degradation of our environment and the depletion of fossil fuels make the exploration of alternative fuels evermore imperative. Among the alternatives is biohydrogen which has high energy content by weight and produces only water when combusted. Considerable effort is being expended to develop photosynthetic systems -- algae, cyanobacteria, and anaerobic phototrophs -- for sustainable H2 production. While promising, this approach also has hurdles such as the harvesting of light in densely pigmented cultures that requires costly constant mixing and large areas for exposure to sunlight. Little attention is given to fermentative H2 generation. Thus understanding the microbial pathways to H2 evolution and metabolic processes competing for electrons is an essential foundation that may expand the variety of fuels that can be generated or provide alternative substrates for fine chemical production. We studied a widely found soil anaerobe of the class Deltaproteobacteria, a sulfate-reducing bacterium to determine the electron pathways used during the oxidation of substrates and the potential for hydrogen production.

  8. Antibiofilm Activity of an Exopolysaccharide from Marine Bacterium Vibrio sp. QY101

    PubMed Central

    Han, Feng; Duan, Gaofei; Lu, Xinzhi; Gu, Yuchao; Yu, Wengong

    2011-01-01

    Bacterial exopolysaccharides have always been suggested to play crucial roles in the bacterial initial adhesion and the development of complex architecture in the later stages of bacterial biofilm formation. However, Escherichia coli group II capsular polysaccharide was characterized to exert broad-spectrum biofilm inhibition activity. In this study, we firstly reported that a bacterial exopolysaccharide (A101) not only inhibits biofilm formation of many bacteria but also disrupts established biofilm of some strains. A101 with an average molecular weight of up to 546 KDa, was isolated and purified from the culture supernatant of the marine bacterium Vibrio sp. QY101 by ethanol precipitation, iron-exchange chromatography and gel filtration chromatography. High performance liquid chromatography traces of the hydrolyzed polysaccharides showed that A101 is primarily consisted of galacturonic acid, glucuronic acid, rhamnose and glucosamine. A101 was demonstrated to inhibit biofilm formation by a wide range of Gram-negative and Gram-positive bacteria without antibacterial activity. Furthermore, A101 displayed a significant disruption on the established biofilm produced by Pseudomonas aeruginosa, but not by Staphylococcus aureus. Importantly, A101 increased the aminoglycosides antibiotics' capability of killing P. aeruginosa biofilm. Cell primary attachment to surfaces and intercellular aggregates assays suggested that A101 inhibited cell aggregates of both P. aeruginosa and S. aureus, while the cell-surface interactions inhibition only occurred in S. aureus, and the pre-formed cell aggregates dispersion induced by A101 only occurred in P. aeruginosa. Taken together, these data identify the antibiofilm activity of A101, which may make it potential in the design of new therapeutic strategies for bacterial biofilm-associated infections and limiting biofilm formation on medical indwelling devices. The found of A101 antibiofilm activity may also promote a new recognition

  9. Purification and characterization of the oxidase from the marine bacterium Pseudomonas nautica 617.

    PubMed

    Arnaud, S; Malatesta, F; Guigliarelli, B; Gayda, J P; Bertrand, P; Miraglio, R; Denis, M

    1991-06-01

    The aerobic respiratory system of the hydrocarbonoclastic marine bacterium Pseudomonas nautica 617 ends with a single terminal oxidase. It is a heme-containing membranous protein which has been demonstrated only to reduce molecular oxygen to hydrogen peroxide [Denis, M., Arnaud S. & Malatesta, F. (1989) FEBS Lett. 247, 475-479]. The purification of this oxidase was achieved in a single step through by DEAE-Trisacryl chromatography. SDS/PAGE showed the presence of four subunits. The pI was found to be 4.45 and a Mr of 130,000 was determined by gel filtration. The amino acid composition of the purified terminal oxidase has been determined. About 52% of the residues are hydrophobic, strengthening the membranous nature of this bacterial oxidase. Room temperature optical spectra are typical of heme b with a 560-nm band for the reduced form in the alpha range. The prosthetic group is made of two hemes b, one high-spin (S = 5/2, gl = 5.9, g parallel approximately 2.0), the other low-spin (S = 1/2, gz = 2.94, gy = 2.27). No other metal centre was detected by EPR. The two hemes remained unresolved in optical spectra, even at low temperature, and throughout redox titration. They behaved potentiometrically like a one-electron, single redox couple, with Em = 87 +/- 10 mV at pH 7.2 and 293 K. The purified oxidase did not oxidize ferrocytochrome c, but displayed quinol oxidase activity both with the native quinone (2419 nmol O2.min-1.mg protein-1 and commercially available coenzyme (101.74 nmol O2.min-1.mg protein-1). Exposure of the reduced enzyme to CO induced the collapse of alpha and beta bands as occurred during reoxidation. In contrast, NaCN and NaN3 fully inhibited the oxidase activity. Results are discussed with respect to other purified quinol oxidases. PMID:1645655

  10. Biochemical and Structural Characterization of the Complex Agarolytic Enzyme System from the Marine Bacterium Zobellia galactanivorans*

    PubMed Central

    Hehemann, Jan-Hendrik; Correc, Gaëlle; Thomas, François; Bernard, Thomas; Barbeyron, Tristan; Jam, Murielle; Helbert, William; Michel, Gurvan; Czjzek, Mirjam

    2012-01-01

    Zobellia galactanivorans is an emerging model bacterium for the bioconversion of algal biomass. Notably, this marine Bacteroidetes possesses a complex agarolytic system comprising four β-agarases and five β-porphyranases, all belonging to the glycoside hydrolase family 16. Although β-agarases are specific for the neutral agarobiose moieties, the recently discovered β-porphyranases degrade the sulfated polymers found in various quantities in natural agars. Here, we report the biochemical and structural comparison of five β-porphyranases and β-agarases from Z. galactanivorans. The respective degradation patterns of two β-porphyranases and three β-agarases are analyzed by their action on defined hybrid oligosaccharides. In light of the high resolution crystal structures, the biochemical results allowed a detailed mapping of substrate specificities along the active site groove of the enzymes. Although PorA displays a strict requirement for C6-sulfate in the −2- and +1-binding subsites, PorB tolerates the presence of 3–6-anhydro-l-galactose in subsite −2. Both enzymes do not accept methylation of the galactose unit in the −1 subsite. The β-agarase AgaD requires at least four consecutive agarose units (DP8) and is highly intolerant to modifications, whereas for AgaB oligosaccharides containing C6-sulfate groups at the −4, +1, and +3 positions are still degraded. Together with a transcriptional analysis of the expression of these enzymes, the structural and biochemical results allow proposition of a model scheme for the agarolytic system of Z. galactanivorans. PMID:22778272

  11. Recombinant production and characterization of a highly active alkaline phosphatase from marine bacterium Cobetia marina.

    PubMed

    Golotin, Vasily; Balabanova, Larissa; Likhatskaya, Galina; Rasskazov, Valery

    2015-04-01

    The psychrophilic marine bacterium, Cobetia marina, recovered from the mantle tissue of the marine mussel, Crenomytilus grayanus, which contained a gene encoding alkaline phosphatase (AP) with apparent biotechnology advantages. The enzyme was found to be more efficient than its counterparts and showed k cat value 10- to 100-fold higher than those of all known commercial APs. The enzyme did not require the presence of exogenous divalent cations and dimeric state of its molecule for activity. The recombinant enzyme (CmAP) production and purification were optimized with a final recovery of 2 mg of the homogenous protein from 1 L of the transgenic Escherichia coli Rosetta(DE3)/Pho40 cells culture. CmAP displayed a half-life of 16 min at 45 °C and 27 min at 40 °C in the presence of 2 mM EDTA, thus suggesting its relative thermostability in comparison with the known cold-adapted analogues. A high concentration of EDTA in the incubation mixture did not appreciably inhibit CmAP. The enzyme was stable in a wide range of pH (6.0-11.0). CmAP exhibited its highest activity at the reaction temperature of 40-50 °C and pH 9.5-10.3. The structural features of CmAP could be the reason for the increase in its stability and catalytic turnover. We have modeled the CmAP 3D structure on the base of the high-quality experimental structure of the close homologue Vibrio sp. AP (VAP) and mutated essential residues predicted to break Mg(2+) bonds in CmAP. It seems probable that the intrinsically tight binding of catalytic and structural metal ions together with the flexibility of intermolecular and intramolecular links in CmAP could be attributed to the adapted mutualistic lifestyle in oceanic waters. PMID:25260971

  12. A Comparative biochemical study on two marine endophytes, Bacterium SRCnm and Bacillus sp. JS, Isolated from red sea algae.

    PubMed

    Ahmed, Eman Fadl; Hassan, Hossam Mokhtar; Rateb, Mostafa Ezzat; Abdel-Wahab, Noha; Sameer, Somayah; Aly Taie, Hanan Anwar; Abdel-Hameed, Mohammed Sayed; Hammouda, Ola

    2016-01-01

    Two marine endophytic bacteria were isolated from the Red Sea algae; a red alga; Acanthophora dendroides and the brown alga Sargassum sabrepandum. The isolates were identified based on their 16SrRNA sequences as Bacterium SRCnm and Bacillus sp. JS. The objective of this study was to investigate the potential anti-microbial and antioxidant activities of the extracts of the isolated bacteria grown in different nutrient conditions. Compared to amoxicillin (25μg/disk) and erythromycin (15μg/disk), the extracts of Bacterium SRCn min media II, III, IV and V were potent inhibitors of the gram-positive bacterium Sarcina maxima even at low concentrations. Also, the multidrug resistant Staphylococcus aureus(MRSA) was more sensitive to the metabolites produced in medium (II) of the same endophyte than erythromycin (15μg/disk). A moderate activity of the Bacillus sp. JS extracts of media I and II was obtained against the same pathogen. The total compounds (500ug/ml) of both isolated endophytes showed moderate antioxidant activities (48.9% and 46.1%, respectively). LC/MS analysis of the bacterial extracts was carried out to investigate the likely natural products produced. Cyclo(D-cis-Hyp-L-Leu), dihydrosphingosine and 2-Amino-1,3-hexadecanediol were identified in the fermentation medium of Bacterium SRCnm, whereas cyclo (D-Pro-L-Tyr) and cyclo (L-Leu-L-Pro) were the suggested compounds of Bacillus sp. JS. PMID:26826831

  13. Enrichment and characterization of sulfate reducing, naphthalene degrading microorganisms

    NASA Astrophysics Data System (ADS)

    Steffen, Kümmel; Florian-Alexander, Herbst; Márcia, Duarte; Dietmar, Pieper; Jana, Seifert; Bergen Martin, von; Hans-Hermann, Richnow; Carsten, Vogt

    2014-05-01

    Polycyclic aromatic hydrocarbons (PAH) are pollutants of great concern due to their potential toxicity, mutagenicity and carcinogenicity. PAH are widely distributed in the environment by accidental discharges during the transport, use and disposal of petroleum products, and during forest and grass fires. Caused by their hydrophobic nature, PAH basically accumulate in sediments from where they are slowly released into the groundwater. Although generally limited by the low water solubility of PAH, microbial degradation is one of the major mechanisms leading to the complete clean-up of PAH-contaminated sites. Whereas organisms and biochemical pathways responsible for the aerobic breakdown of PAH are well known, anaerobic PAH biodegradation is less understood; only a few anaerobic PAH degrading cultures have been described. We studied the anaerobic PAH degradation in a microcosm approach to enrich anaerobic PAH degraders. Anoxic groundwater and sediment samples were used as inoculum. Groundwater samples were purchased from the erstwhile gas works facility and a former wood impregnation site. In contrast, sources of sediment samples were a former coal refining area and an old fuel depot. Samples were incubated in anoxic mineral salt medium with naphthalene as sole carbon source and sulfate as terminal electron acceptor. Grown cultures were characterized by feeding with 13C-labeled naphthalene, 16S rRNA gene sequencing using an Illumina® approach, and functional proteome analyses. Finally, six enrichment cultures able to degrade naphthalene under anoxic conditions were established. First results point to a dominance of identified sequences affiliated to the freshwater sulfate-reducing strain N47, which is a known anaerobic naphthalene degrader, in four out of the six enrichments. In those enrichments, peptides related to the pathway of anoxic naphthalene degradation in N47 were abundant. Overall the data underlines the importance of Desulfobacteria for natural

  14. Revisiting Modes of energy generation in sulfate reducing bacteria

    SciTech Connect

    Joachimiak, Marcin; Chakraborty, Romy; Zhou, Aifen; Fortney, Julian; Geller, Jil; Wall, Judy; Zhou, Jizhong; Arkin, Adam; Hazen, Terry; Keasling, Jay; Chhabra, Swapnil

    2010-05-17

    Sulfate reducing bacteria (SRB) play an important role in global sulfur and carbon cycling through their ability to completely mineralize organic matter while respiring sulfate to hydrogen sulfide. They are ubiquitous in anaerobic environments and have the ability to reduce toxic metals like Cr(VI) and U(VI). While SRB have been studied for over three decades, bioenergetic modes of this group of microbes are poorly understood. Desulfovibrio vulgaris strain Hildenborough (DvH) has served as a model SRB over the last decade with the accumulation of transcriptomic, proteomic and metabolic data under a wide variety of stressors. To further investigate the three hypothesized modes of energy generation in this anaerobe we conducted a systematic study involving multiple electron donor and acceptor combinations for growth. DvH was grown at 37oC in a defined medium with (a) lactate + thiosulfate, (b) lactate + sulfite (c) lactate + sulfate, (d) pyruvate + sulfate, (e) H2 + acetate + sulfate, (f) formate + acetate + sulfate, g) formate + sulfate and (h) pyruvate fermentation. Cells were harvested at mid-log phase of growth for all conditions for transcriptomics, when the optical density at 600nm was in the range 0.42-0.5. Initial results indicate that cells grown on lactate do not appear to significantly differentiate their gene expression profiles when presented with different electron acceptors. These profiles however differ significantly from those observed during growth with other electron donors such as H2 and formate, as well as during fermentative growth. Together the gene expression changes in the presence of different electron donors provide insights into the ability of DvH to differentially reduce metals such as Cr(VI). Here we present revised modes of energy generation in DvH in light of this new transcriptomic evidence.

  15. Stable carbon isotope fractionation by sulfate-reducing bacteria

    NASA Technical Reports Server (NTRS)

    Londry, Kathleen L.; Des Marais, David J.

    2003-01-01

    Biogeochemical transformations occurring in the anoxic zones of stratified sedimentary microbial communities can profoundly influence the isotopic and organic signatures preserved in the fossil record. Accordingly, we have determined carbon isotope discrimination that is associated with both heterotrophic and lithotrophic growth of pure cultures of sulfate-reducing bacteria (SRB). For heterotrophic-growth experiments, substrate consumption was monitored to completion. Sealed vessels containing SRB cultures were harvested at different time intervals, and delta(13)C values were determined for gaseous CO(2), organic substrates, and products such as biomass. For three of the four SRB, carbon isotope effects between the substrates, acetate or lactate and CO(2), and the cell biomass were small, ranging from 0 to 2 per thousand. However, for Desulfotomaculum acetoxidans, the carbon incorporated into biomass was isotopically heavier than the available substrates by 8 to 9 per thousand. SRB grown lithoautotrophically consumed less than 3% of the available CO(2) and exhibited substantial discrimination (calculated as isotope fractionation factors [alpha]), as follows: for Desulfobacterium autotrophicum, alpha values ranged from 1.0100 to 1.0123; for Desulfobacter hydrogenophilus, the alpha value was 0.0138, and for Desulfotomaculum acetoxidans, the alpha value was 1.0310. Mixotrophic growth of Desulfovibrio desulfuricans on acetate and CO(2) resulted in biomass with a delta(13)C composition intermediate to that of the substrates. The extent of fractionation depended on which enzymatic pathways were used, the direction in which the pathways operated, and the growth rate, but fractionation was not dependent on the growth phase. To the extent that environmental conditions affect the availability of organic substrates (e.g., acetate) and reducing power (e.g., H(2)), ecological forces can also influence carbon isotope discrimination by SRB.

  16. Toward a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough

    SciTech Connect

    Chhabra, S.R.; Joachimiak, M.P.; Petzold, C.J.; Zane, G.M.; Price, M.N.; Gaucher, S.; Reveco, S.A.; Fok, V.; Johanson, A.R.; Batth, T.S.; Singer, M.; Chandonia, J.M.; Joyner, D.; Hazen, T.C.; Arkin, A.P.; Wall, J.D.; Singh, A.K.; Keasling, J.D.

    2011-05-01

    Protein–protein interactions offer an insight into cellular processes beyond what may be obtained by the quantitative functional genomics tools of proteomics and transcriptomics. The aforementioned tools have been extensively applied to study E. coli and other aerobes and more recently to study the stress response behavior of Desulfovibrio 5 vulgaris Hildenborough, a model anaerobe and sulfate reducer. In this paper we present the first attempt to identify protein-protein interactions in an obligate anaerobic bacterium. We used suicide vector-assisted chromosomal modification of 12 open reading frames encoded by this sulfate reducer to append an eight amino acid affinity tag to the carboxy-terminus of the chosen proteins. Three biological replicates of the 10 ‘pulled-down’ proteins were separated and analyzed using liquid chromatography-mass spectrometry. Replicate agreement ranged between 35% and 69%. An interaction network among 12 bait and 90 prey proteins was reconstructed based on 134 bait-prey interactions computationally identified to be of high confidence. We discuss the biological significance of several unique metabolic features of D. vulgaris revealed by this protein-protein interaction data 15 and protein modifications that were observed. These include the distinct role of the putative carbon monoxide-induced hydrogenase, unique electron transfer routes associated with different oxidoreductases, and the possible role of methylation in regulating sulfate reduction.

  17. Aerobic and anaerobic metabolism of 6,10,14-trimethylpentadecan-2-one by a denitrifying bacterium isolated from marine sediments.

    PubMed Central

    Rontani, J F; Gilewicz, M J; Michotey, V D; Zheng, T L; Bonin, P C; Bertrand, J C

    1997-01-01

    This report describes the metabolism of 6,10,14-trimethylpentadecan-2-one by a denitrifying bacterium (Marinobacter sp. strain CAB) isolated from marine sediments. Under aerobic and denitrifying conditions, this strain efficiently degraded this ubiquitous isoprenoid ketone. Several bacterial metabolites, 4,8,12-trimethyl-tridecan-1-ol, 4,8,12-trimethyltridecanal, 4,8,12-trimethyltridecanoic acid, Z-3,7-dimethylocten-2-oic acid, Z-3,7,11-trimethyldodecen-2-oic acid, and 6,10,14-trimethylpentadecan-2-ol, were formally identified, and different pathways were proposed to explain the formation of such isoprenoid compounds. PMID:9023941

  18. Photobacterium kishitanii sp. nov., a luminous marine bacterium symbiotic with deep-sea fishes.

    PubMed

    Ast, Jennifer C; Cleenwerck, Ilse; Engelbeen, Katrien; Urbanczyk, Henryk; Thompson, Fabiano L; De Vos, Paul; Dunlap, Paul V

    2007-09-01

    Six representatives of a luminous bacterium commonly found in association with deep, cold-dwelling marine fishes were isolated from the light organs and skin of different fish species. These bacteria were Gram-negative, catalase-positive, and weakly oxidase-positive or oxidase-negative. Morphologically, cells of these strains were coccoid or coccoid-rods, occurring singly or in pairs, and motile by means of polar flagellation. After growth on seawater-based agar medium at 22 degrees C for 18 h, colonies were small, round and white, with an intense cerulean blue luminescence. Analysis of 16S rRNA gene sequence similarity placed these bacteria in the genus Photobacterium. Phylogenetic analysis based on seven housekeeping gene sequences (16S rRNA gene, gapA, gyrB, pyrH, recA, rpoA and rpoD), seven gene sequences of the lux operon (luxC, luxD, luxA, luxB, luxF, luxE and luxG) and four gene sequences of the rib operon (ribE, ribB, ribH and ribA), resolved the six strains as members of the genus Photobacterium and as a clade distinct from other species of Photobacterium. These strains were most closely related to Photobacterium phosphoreum and Photobacterium iliopiscarium. DNA-DNA hybridization values between the designated type strain, Photobacterium kishitanii pjapo.1.1(T), and P. phosphoreum LMG 4233(T), P. iliopiscarium LMG 19543(T) and Photobacterium indicum LMG 22857(T) were 51, 43 and 19 %, respectively. In AFLP analysis, the six strains clustered together, forming a group distinct from other analysed species. The fatty acid C(17 : 0) cyclo was present in these bacteria, but not in P. phosphoreum, P. iliopiscarium or P. indicum. A combination of biochemical tests (arginine dihydrolase and lysine decarboxylase) differentiates these strains from P. phosphoreum and P. indicum. The DNA G+C content of P. kishitanii pjapo.1.1(T) is 40.2 %, and the genome size is approximately 4.2 Mbp, in the form of two circular chromosomes. These strains represent a novel species, for

  19. Fermentation Products of Solvent Tolerant Marine Bacterium Moraxella spp. MB1 and Its Biotechnological Applications in Salicylic Acid Bioconversion

    PubMed Central

    Wahidullah, Solimabi; Naik, Deepak N.; Devi, Prabha

    2013-01-01

    As part of a proactive approach to environmental protection, emerging issues with potential impact on the environment is the subject of ongoing investigation. One emerging area of environmental research concerns pharmaceuticals like salicylic acid, which is the main metabolite of various analgesics including aspirin. It is a common component of sewage effluent and also an intermediate in the degradation pathway of various aromatic compounds which are introduced in the marine environment as pollutants. In this study, biotransformation products of salicylic acid by seaweed, Bryopsis plumosa, associated marine bacterium, Moraxella spp. MB1, have been investigated. Phenol, conjugates of phenol and hydroxy cinnamic acid derivatives (coumaroyl, caffeoyl, feruloyl and trihydroxy cinnamyl) with salicylic acid (3–8) were identified as the bioconversion products by electrospray ionization mass spectrometry. These results show that the microorganism do not degrade phenolic acid but catalyses oxygen dependent transformations without ring cleavage. The degradation of salicylic acid is known to proceed either via gentisic acid pathway or catechol pathway but this is the first report of biotransformation of salicylic acid into cinnamates, without ring cleavage. Besides cinnamic acid derivatives (9–12), metabolites produced by the bacterium include antimicrobial indole (13) and β-carbolines, norharman (14), harman (15) and methyl derivative (16), which are beneficial to the host and the environment. PMID:24391802

  20. Fermentation products of solvent tolerant marine bacterium Moraxella spp. MB1 and its biotechnological applications in salicylic acid bioconversion.

    PubMed

    Wahidullah, Solimabi; Naik, Deepak N; Devi, Prabha

    2013-01-01

    As part of a proactive approach to environmental protection, emerging issues with potential impact on the environment is the subject of ongoing investigation. One emerging area of environmental research concerns pharmaceuticals like salicylic acid, which is the main metabolite of various analgesics including aspirin. It is a common component of sewage effluent and also an intermediate in the degradation pathway of various aromatic compounds which are introduced in the marine environment as pollutants. In this study, biotransformation products of salicylic acid by seaweed, Bryopsis plumosa, associated marine bacterium, Moraxella spp. MB1, have been investigated. Phenol, conjugates of phenol and hydroxy cinnamic acid derivatives (coumaroyl, caffeoyl, feruloyl and trihydroxy cinnamyl) with salicylic acid (3-8) were identified as the bioconversion products by electrospray ionization mass spectrometry. These results show that the microorganism do not degrade phenolic acid but catalyses oxygen dependent transformations without ring cleavage. The degradation of salicylic acid is known to proceed either via gentisic acid pathway or catechol pathway but this is the first report of biotransformation of salicylic acid into cinnamates, without ring cleavage. Besides cinnamic acid derivatives (9-12), metabolites produced by the bacterium include antimicrobial indole (13) and β-carbolines, norharman (14), harman (15) and methyl derivative (16), which are beneficial to the host and the environment. PMID:24391802

  1. Visualization of Mercury Methylating Pure-Culture Sulfate-Reducing Biofilms

    NASA Astrophysics Data System (ADS)

    Lin, C.; Reyes, C.; Mendez, C.; Jay, J. A.

    2005-12-01

    Methylmercury is a potent neurotoxin that can accumulate in food chains posing a serious ecological problem in certain aquatic systems. Relatively less toxic inorganic mercury (Hg) is converted to methylmercury (CH3Hg+) by bacteria, and it has been shown that sulfate reducing bacteria (SRB) are the major mediators of this process in many aquatic systems. To date, all laboratory studies on bacterial mercury methylation by SRB have been conducted using planktonic, free floating, bacterial cultures, yet bacteria exist mostly as attached communities or biofilms in the environment. We hypothesized that biofilms composed of different SRB would differ in their ability to bind and methylate mercury compared to planktonic cultures. To test our hypothesis ten SRB isolates capable of producing biofilms in the laboratory were enriched from a marine sediment. We identified the isolates by 16S rDNA sequence analysis, compared pure-culture biofilm structure using fluorescent in situ hybridization (FISH) and confocal microscopy, and measured mercury methylation in biofilms of these SRB.

  2. Anaerobic biodegradation of long-chain n-alkanes under sulfate-reducing conditions

    SciTech Connect

    Caldwell, M.E.; Suflita, J.M.; Garrett, R.M.; Prince, R.C.

    1998-07-15

    The ability of anaerobic microorganisms to degrade a wide variety of crude oil components was investigated using chronically hydrocarbon-contaminated marine sediments as the source of inoculum. When sulfate reduction was the predominant electron-accepting process, gas chromatographic analysis revealed almost complete n-alkane removal (C{sub 15}-C{sub 34}) from a weathered oil within 201 d of incubation. No alteration of the oil was detected in sterile control incubations or when nitrate served as an alternate electron acceptor. The amount of sulfate reduced in the oil-amended nonsterile incubations was more than enough to account for the complete mineralization of the n-alkane fraction of the oil; no loss of this anion was observed in sterile control incubations. The mineralization of the alkanes was confirmed using {sup 14}C-14,15-octacosane (C{sub 28}H{sub 58}), with 97% of the radioactivity recovered as {sup 14}CO{sub 2}. These findings extend the range of hydrocarbons known to be amenable to anaerobic biodegradation. Moreover, the rapid and extensive alteration in the n-alkanes can no longer be considered a defining characteristic of aerobic oil biodegradation processes alone.

  3. Genome sequence of the model sulfate reducer Desulfovibrio gigas: a comparative analysis within the Desulfovibrio genus*

    PubMed Central

    Morais-Silva, Fabio O; Rezende, Antonio Mauro; Pimentel, Catarina; Santos, Catia I; Clemente, Carla; Varela–Raposo, Ana; Resende, Daniela M; da Silva, Sofia M; de Oliveira, Luciana Márcia; Matos, Marcia; Costa, Daniela A; Flores, Orfeu; Ruiz, Jerónimo C; Rodrigues-Pousada, Claudina

    2014-01-01

    Desulfovibrio gigas is a model organism of sulfate-reducing bacteria of which energy metabolism and stress response have been extensively studied. The complete genomic context of this organism was however, not yet available. The sequencing of the D. gigas genome provides insights into the integrated network of energy conserving complexes and structures present in this bacterium. Comparison with genomes of other Desulfovibrio spp. reveals the presence of two different CRISPR/Cas systems in D. gigas. Phylogenetic analysis using conserved protein sequences (encoded by rpoB and gyrB) indicates two main groups of Desulfovibrio spp, being D. gigas more closely related to D. vulgaris and D. desulfuricans strains. Gene duplications were found such as those encoding fumarate reductase, formate dehydrogenase, and superoxide dismutase. Complexes not yet described within Desulfovibrio genus were identified: Mnh complex, a v-type ATP-synthase as well as genes encoding the MinCDE system that could be responsible for the larger size of D. gigas when compared to other members of the genus. A low number of hydrogenases and the absence of the codh/acs and pfl genes, both present in D. vulgaris strains, indicate that intermediate cycling mechanisms may contribute substantially less to the energy gain in D. gigas compared to other Desulfovibrio spp. This might be compensated by the presence of other unique genomic arrangements of complexes such as the Rnf and the Hdr/Flox, or by the presence of NAD(P)H related complexes, like the Nuo, NfnAB or Mnh. PMID:25055974

  4. Factors Governing the Germination of Sulfate-Reducing Desulfotomaculum Endospores Involved in Oil Reservoir Souring.

    NASA Astrophysics Data System (ADS)

    Sherry, A.; Bell, E.; Cueto, G.; Suarez-Suarez, A.; Pilloni, G.; Hubert, C. R.

    2015-12-01

    Reservoir souring is caused by the activity of sulfate-reducing microorganisms (SRM) in subsurface oil reservoirs, and is often induced by seawater injection during secondary oil recovery. Souring can potentially contribute to corrosion of infrastructure, health and safety hazards to the workforce, and reduction in value by increasing refining costs associated with producing the oil resource. Souring causes annual losses in the billions of dollars to the oil industry. Endospore-forming SRM, such as Desulfotomaculum spp., are often suspected culprits in reservoir souring. Endospores can survive unfavourable conditions for long periods, yet remain poised to germinate and become active if conditions become more favourable. Factors governing endospore germination are poorly understood, but are thought to include availability of nutrients, possibly metabolic by products of other anaerobic bioprocesses, and/or variations in temperature. Most research has focused on aerobic Bacillus spp., with very few studies dedicated to spore germination among anaerobes (order Clostridiales) including the sulfate-reducing Desulfotomaculum found in anoxic subsurface petroleum reservoirs. For Desulfotomaculum spores in deep hot oil reservoirs, cold seawater introduction during secondary oil recovery may create thermal viability zones for sulfate reduction near the injection wellbore. To evaluate these processes, sulfate-containing microcosms were prepared with different marine sediments as a source of spores, and amended with organic substrates in the presence or absence of oil. Incubation at 80°C for six days was followed by a down-shift in temperature to 60°C to mimic cold seawater injection into a hot reservoir. Souring did not occur at 80°C, but commenced within hours at 60°C. Microcosms were monitored for sulfate reduction and organic acids in combination with next generation sequencing of 16S rRNA genes (Ion Torrent, Illumina MiSeq). Through a combination of high

  5. Porticoccus hydrocarbonoclasticus sp. nov., an aromatic hydrocarbon-degrading bacterium identified in laboratory cultures of marine phytoplankton.

    PubMed

    Gutierrez, Tony; Nichols, Peter D; Whitman, William B; Aitken, Michael D

    2012-02-01

    A marine bacterium, designated strain MCTG13d, was isolated from a laboratory culture of the dinoflagellate Lingulodinium polyedrum CCAP1121/2 by enrichment with polycyclic aromatic hydrocarbons (PAHs) as the sole carbon source. Based on 16S rRNA gene sequence comparisons, the strain was most closely related to Porticoccus litoralis IMCC2115(T) (96.5%) and to members of the genera Microbulbifer (91.4 to 93.7%) and Marinimicrobium (90.4 to 92.0%). Phylogenetic trees showed that the strain clustered in a distinct phyletic line in the class Gammaproteobacteria for which P. litoralis is presently the sole cultured representative. The strain was strictly aerobic, rod shaped, Gram negative, and halophilic. Notably, it was able to utilize hydrocarbons as sole sources of carbon and energy, whereas sugars did not serve as growth substrates. The predominant isoprenoid quinone of strain MCTG13d was Q-8, and the dominant fatty acids were C(16:1ω7c), C(18:1ω7c), and C(16:0). DNA G+C content for the isolate was 54.9 ± 0.42 mol%. Quantitative PCR primers targeting the 16S rRNA gene of this strain showed that this organism was common in other laboratory cultures of marine phytoplankton. On the basis of phenotypic and genotypic characteristics, strain MCTG13d represents a novel species of Porticoccus, for which the name Porticoccus hydrocarbonoclasticus sp. nov. is proposed. The discovery of this highly specialized hydrocarbon-degrading bacterium living in association with marine phytoplankton suggests that phytoplankton represent a previously unrecognized biotope of novel bacterial taxa that degrade hydrocarbons in the ocean. PMID:22139001

  6. Porticoccus hydrocarbonoclasticus sp. nov., an Aromatic Hydrocarbon-Degrading Bacterium Identified in Laboratory Cultures of Marine Phytoplankton

    PubMed Central

    Nichols, Peter D.; Whitman, William B.; Aitken, Michael D.

    2012-01-01

    A marine bacterium, designated strain MCTG13d, was isolated from a laboratory culture of the dinoflagellate Lingulodinium polyedrum CCAP1121/2 by enrichment with polycyclic aromatic hydrocarbons (PAHs) as the sole carbon source. Based on 16S rRNA gene sequence comparisons, the strain was most closely related to Porticoccus litoralis IMCC2115T (96.5%) and to members of the genera Microbulbifer (91.4 to 93.7%) and Marinimicrobium (90.4 to 92.0%). Phylogenetic trees showed that the strain clustered in a distinct phyletic line in the class Gammaproteobacteria for which P. litoralis is presently the sole cultured representative. The strain was strictly aerobic, rod shaped, Gram negative, and halophilic. Notably, it was able to utilize hydrocarbons as sole sources of carbon and energy, whereas sugars did not serve as growth substrates. The predominant isoprenoid quinone of strain MCTG13d was Q-8, and the dominant fatty acids were C16:1ω7c, C18:1ω7c, and C16:0. DNA G+C content for the isolate was 54.9 ± 0.42 mol%. Quantitative PCR primers targeting the 16S rRNA gene of this strain showed that this organism was common in other laboratory cultures of marine phytoplankton. On the basis of phenotypic and genotypic characteristics, strain MCTG13d represents a novel species of Porticoccus, for which the name Porticoccus hydrocarbonoclasticus sp. nov. is proposed. The discovery of this highly specialized hydrocarbon-degrading bacterium living in association with marine phytoplankton suggests that phytoplankton represent a previously unrecognized biotope of novel bacterial taxa that degrade hydrocarbons in the ocean. PMID:22139001

  7. MOLECULAR PHYLOGENETIC AND BIOGEOCHEMICAL STUDIES OF SULFATE-REDUCING BACTERIA IN THE RHIZOSPHERE OF SPARTINA ALTERNIFLORA

    EPA Science Inventory

    The population composition and biogeochemistry of sulfate-reducing bacteria (SRB) in the rhizosphere of the marsh grass Spartina alterniflora was investigated over two growing seasons using molecular probing, enumerations of culturable SRB, and measurements of SO42- reduction rat...

  8. Molecular analysis of the metabolic rates of discrete subsurface populations of sulfate reducers

    SciTech Connect

    Miletto, M.; Williams, K.H.; N'Guessan, A.L.; Lovley, D.R.

    2011-04-01

    Elucidating the in situ metabolic activity of phylogenetically diverse populations of sulfate-reducing microorganisms that populate anoxic sedimentary environments is key to understanding subsurface ecology. Previous pure culture studies have demonstrated that transcript abundance of dissimilatory (bi)sulfite reductase genes is correlated with the sulfate reducing activity of individual cells. To evaluate whether expression of these genes was diagnostic for subsurface communities, dissimilatory (bi)sulfite reductase gene transcript abundance in phylogenetically distinct sulfate-reducing populations was quantified during a field experiment in which acetate was added to uranium-contaminated groundwater. Analysis of dsrAB sequences prior to the addition of acetate indicated that Desulfobacteraceae, Desulfobulbaceae, and Syntrophaceae-related sulfate reducers were the most abundant. Quantifying dsrB transcripts of the individual populations suggested that Desulfobacteraceae initially had higher dsrB transcripts per cell than Desulfobulbaceae or Syntrophaceae populations, and that the activity of Desulfobacteraceae increased further when the metabolism of dissimilatory metal reducers competing for the added acetate declined. In contrast, dsrB transcript abundance in Desulfobulbaceae and Syntrophaceae remained relatively constant, suggesting a lack of stimulation by added acetate. The indication of higher sulfate-reducing activity in the Desulfobacteraceae was consistent with the finding that Desulfobacteraceae became the predominant component of the sulfate-reducing community. Discontinuing acetate additions resulted in a decline in dsrB transcript abundance in the Desulfobacteraceae. These results suggest that monitoring transcripts of dissimilatory (bi)sulfite reductase genes in distinct populations of sulfate reducers can provide insight into the relative rates of metabolism of different components of the sulfate-reducing community and their ability to respond to

  9. Genome Sequence of Vibrio sp. Strain EJY3, an Agarolytic Marine Bacterium Metabolizing 3,6-Anhydro-l-Galactose as a Sole Carbon Source

    PubMed Central

    Roh, Hanseong; Yun, Eun Ju; Lee, Saeyoung; Ko, Hyeok-Jin; Kim, Sujin; Kim, Byung-Yong; Song, Heesang; Lim, Kwang-il

    2012-01-01

    The metabolic fate of 3,6-anhydro-l-galactose (l-AHG) is unknown in the global marine carbon cycle. Vibrio sp. strain EJY3 is an agarolytic marine bacterium that can utilize l-AHG as a sole carbon source. To elucidate the metabolic pathways of l-AHG, we have sequenced the complete genome of Vibrio sp. strain EJY3. PMID:22535948

  10. Genus- and group-specific hybridization probes for determinative and environmental studies of sulfate-reducing bacteria

    SciTech Connect

    Devereux, R.; Kane, M.D.; Winfrey, J.; Stahl, D.A.

    1992-01-01

    A set of six oligonucleotides, complementary to conserved tracts of 16S rRNA from phylogenetically-defined groups of sulfate-reducing bacteria, was characterized for use as hybridization probes in determinative and environmental microbiology. Four probes were genus specific and identified Desulfobacterium spp., Desulfobacter spp., Desulfobulbus spp., or Desulfovibrio spp. The other two probes encompassed more diverse assemblages. One probe was specific for the phylogenetic lineage composed of Desulfococcus multivorans, Desulfosarcina variabilis, and Desulfobotulus sapovorans. The remaining probe was specific for Desulfobacterium spp., Desulfobacter spp., D. multivorans, D. variabilis, and D. sapovorans. Temperature of dissociation was determined for each probe and the designed specificities of each were evaluated by hybridizations against closely related nontargeted species. In addition, each probe was screened by using a 'phylogrid' membrane which consisted of nucleic acids from sixtyfour non-targeted organisms representing a diverse collection of eukarya, archaea, and bacteria. The value of these probes to studies in environmental microbiology was evaluated by hybridizations to 16S rRNAs of sulfate-reducing bacteria present in marine sediments.

  11. Anaerobic hydrocarbon degradation in petroleum-contaminated harbor sediments under sulfate-reducing and artificially imposed iron-reducing conditions

    USGS Publications Warehouse

    Coates, J.D.; Anderson, R.T.; Woodward, J.C.; Phillips, E.J.P.; Lovley, D.R.

    1996-01-01

    The potential use of iron(III) oxide to stimulate in-situ hydrocarbon degradation in anaerobic petroleum-contaminated harbor sediments was investigated. Previous studies have indicated that Fe(III)-reducing bacteria (FeRB) can oxidize some electron donors more effectively than sulfate- reducing bacteria (SRB). In contrast to previous results in freshwater sediments, the addition of Fe(III) to marine sediments from San Diego Bay, CA did not switch the terminal electron-accepting process (TEAP) from sulfate reduction to Fe-(III) reduction. Addition of Fe(III) also did not stimulate anaerobic hydrocarbon oxidation. Exposure of the sediment to air [to reoxidize Fe(II) to Fe(III)] followed by anaerobic incubation of the sediments, resulted in Fe-(III) reduction as the TEAP, but contaminant degradation was not stimulated and in some instances was inhibited. The difference in the ability of FeRB to compete with the SRB in the different sediment treatments was related to relative population sizes. Although the addition of Fe(III) did not stimulate hydrocarbon degradation, the results presented here as well as other recent studies demonstrate that there may be significant anaerobic hydrocarbon degradation under sulfate-reducing conditions in harbor sediments.

  12. Degradation of o-xylene and m-xylene by a novel sulfate-reducer belonging to the genus Desulfotomaculum.

    PubMed

    Morasch, Barbara; Schink, Bernhard; Tebbe, Christoph C; Meckenstock, Rainer U

    2004-06-01

    A strictly anaerobic bacterium, strain OX39, was isolated with o-xylene as organic substrate and sulfate as electron acceptor from an aquifer at a former gasworks plant contaminated with aromatic hydrocarbons. Apart from o-xylene, strain OX39 grew on m-xylene and toluene and all three substrates were oxidized completely to CO(2). Induction experiments indicated that o-xylene, m-xylene, and toluene degradation were initiated by different specific enzymes. Methylbenzylsuccinate was identified in supernatants of cultures grown on o-xylene and m-xylene, and benzylsuccinate was detected in supernatants of toluene-grown cells, thus indicating that degradation was initiated in all three cases by fumarate addition to the methyl group. Strain OX39 was sensitive towards sulfide and depended on Fe(II) in the medium as a scavenger of the produced sulfide. Analysis of the PCR-amplified 16S rRNA gene revealed that strain OX39 affiliates with the gram-positive endospore-forming sulfate reducers of the genus Desulfotomaculum and is the first hydrocarbon-oxidizing bacterium in this genus. PMID:15127183

  13. Azide anions inhibit GH-18 endochitinase and GH-20 Exo β-N-acetylglucosaminidase from the marine bacterium Vibrio harveyi.

    PubMed

    Sirimontree, Paknisa; Fukamizo, Tamo; Suginta, Wipa

    2016-02-01

    Vibrio harveyi is a bioluminescent marine bacterium that utilizes chitin as its sole source of energy. In the course of chitin degradation, the bacterium primarily secretes an endochitinase A (VhChiA) to hydrolyze chitin, generating chitooligosaccharide fragments that are readily transported into the cell and broken down to GlcNAc monomers by an exo β-N-acetylglucosaminidase (VhGlcNAcase). Here we report that sodium salts, especially sodium azide, inhibit two classes of these chitin-degrading enzymes (VhChiA and VhGlcNAcase) with distinct modes of action. Kinetic analysis of the enzymatic hydrolysis of pNP-glycoside substrates reveals that sodium azide inhibition of VhChiA has a mixed-type mode, but that it inhibits VhGlcNAcase competitively. We propose that azide anions inhibit chitinase activity by acting as strong nucleophiles that attack Cγ of the catalytic Glu or Cβ of the neighbouring Asp residues. Azide anions may bind not only to the catalytic centre, but also to the other subsites in the substrate-binding cleft of VhChiA. In contrast, azide anions may merely occupy the small-binding pocket of VhGlcNAcase, thereby blocking the accessibility of its active site by short-chain substrates. PMID:26330565

  14. Role of Chitin-Binding Proteins in the Specific Attachment of the Marine Bacterium Vibrio harveyi to Chitin

    PubMed Central

    Montgomery, Michael T.; Kirchman, David L.

    1993-01-01

    We examined the mechanism of attachment of the marine bacterium Vibrio harveyi to chitin. Wheat germ agglutinin and chitinase bind to chitin and competitively inhibited the attachment of V. harveyi to chitin, but not to cellulose. Bovine serum albumin and cellulase do not bind to chitin and had no effect on bacterial attachment to chitin. These data suggest that this bacterium recognizes specific attachment sites on the chitin particle. The level of attachment of a chitinase-overproducing mutant of V. harveyi to chitin was about twice as much as that of the uninduced wild type. Detergent-extracted cell membranes inhibited attachment and contained a 53-kDa peptide that was overproduced by the chitinase-overproducing mutant. Three peptides (40, 53, and 150 kDa) were recovered from chitin which had been exposed to membrane extracts. Polyclonal antibodies raised against extracellular chitinase cross-reacted with the 53- and 150-kDa chitin-binding peptides and inhibited attachment, probably by sterically hindering interactions between the chitin-binding peptides and chitin. The 53- and 150-kDa chitin-binding peptides did not have chitinase activity. These results suggest that chitin-binding peptides, especially the 53-kDa chitin-binding peptide and chitinase and perhaps the 150-kDa peptide, mediate the specific attachment of V. harveyi to chitin. Images PMID:16348865

  15. Structure and anticancer activity of sulfated O-polysaccharide from marine bacterium Cobetia litoralis KMM 3880(T).

    PubMed

    Kokoulin, Maxim S; Kuzmich, Alexandra S; Kalinovsky, Anatoly I; Tomshich, Svetlana V; Romanenko, Lyudmila A; Mikhailov, Valery V; Komandrova, Nadezhda A

    2016-12-10

    We presented the structure of the polysaccharide moiety and anticancer activity in vitro of the sulfated lipopolysaccharide isolated from the marine bacterium Cobetia litoralis KMM 3880(T). The structure of O-polysaccharide was investigated by chemical methods along with (1)H and (13)C NMR spectroscopy. The O-polysaccharide was built up of branched trisaccharide repeating units consist of D-glucose (D-Glcр), D-mannose (D-Manр) and sulfated 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo5S): →7-β-Kdoр4Ac5S-(2→4)-[β-d-Glcp-(1→2)-]-β-d-Manр6Ac-1→. We demonstrated that the lipopolysaccharide and О-deacetylated O-polysaccharide from Cobetia litoralis KMM 3880(T) inhibited a colony formation of human melanoma SK-MEL-28 and colorectal carcinoma HTC-116 cells. PMID:27577896

  16. Examining Deep Subsurface Sulfate Reducing Bacterial Diversity to Test Spatial and Temporal Biogeography

    NASA Astrophysics Data System (ADS)

    Mills, H. J.; Reese, B. K.

    2013-12-01

    In this study, we take advantage of the isolation and scale of the deep marine subsurface to examine microbial biogeography. Unlike other environments, deep marine subsurface provides a unique opportunity to study biogeography across four dimensions. These samples are not only isolated by linear space on a global scale, but they are also temporally isolated by, in some cases, tens of millions of years. Through the support of multiple Integrated Ocean Drilling Program expeditions, we characterized the metabolically active fraction of the subsurface microbial community by targeting and sequencing 16S rRNA gene transcripts (RNA-based analysis). By characterizing the metabolically active fraction, we described lineages that were currently under selective environmental pressure and not relic lineages that may have become dormant or dead at some point in the past. This study was narrowed from the total diversity obtained to provide a detailed examination of the distribution and diversity of sulfate reducing bacteria (SRB); a functional group highly important to and ubiquitous in marine systems. The biogeochemical importance of this functional group, compounded with defined clades makes it a valuable and feasible target for a global biogeography study. SRB lineages from the deep subsurface were compared to contemporary lineages collected from multiple shallow sediment sites that had been extracted and sequenced using the same techniques. The SRB sequences acquired from our databases were clustered using 97% sequence similarity and analyzed using a suite of diversity and statistical tools. The geochemical conditions of the sediments sampled were considered when analyzing the resulting dendrograms and datasets. As hypothesized, lineages from the deep subsurface phylogenetically grouped together. However, similarities were detected to lineages from the shallow modern sediments, suggesting novel lineages may have evolved at a slow rate due to predicted lengthened life cycles

  17. The ecophysiology of sulfur isotope fractionation by sulfate reducing bacteria in response to variable environmental conditions

    NASA Astrophysics Data System (ADS)

    Leavitt, W.; Bradley, A. S.; Johnston, D. T.; Pereira, I. A. C.; Venceslau, S.; Wallace, C.

    2014-12-01

    Microbial sulfate reducers (MSR) drive the Earth's biogeochemical sulfur cycle. At the heart of this energy metabolism is a cascade of redox transformations coupling organic carbon and/or hydrogen oxidation to the dissimilatory reduction of sulfate to sulfide. The sulfide produced is depleted in the heavier isotopes of sulfur relative to sulfate. The magnitude of discrimination (fractionation) depends on: i) the cell-specific sulfate reduction rate (csSRR, Kaplan & Rittenberg (1964) Can. J. Microbio.; Chambers et al. (1975) Can. J. Microbio; Sim et al. (2011) GCA; Leavitt et al. (2013) PNAS), ii) the ambient sulfate concentration (Harrison & Thode (1958) Research; Habicht et al. (2002) Science; Bradley et al. in review), iii) both sulfate and electron donor availability, or iv) an intrinsic physiological limitation (e.g. cellular division rate). When neither sulfate nor electron donor limits csSRR a more complex function relates the magnitude of isotope fractionation to cell physiology and environmental conditions. In recent and on-going work we have examined the importance of enzyme-specific fractionation factors, as well as the influence of electron donor or electron acceptor availability under carefully controlled culture conditions (e.g. Leavitt et al. (2013) PNAS). In light of recent advances in MSR genetics and biochemistry we utilize well-characterized mutant strains, along with a continuous-culture methodology (Leavitt et al. (2013) PNAS) to further probe the fractionation capacity of this metabolism under controlled physiological conditions. We present our latest findings on the magnitude of S and D/H isotope fractionation in both wild type and mutant strains. We will discuss these in light of recent theoretical advances (Wing & Halevy (2014) PNAS), examining the mode and relevance of MSR isotope fractionation in the laboratory to modern and ancient environmental settings, particularly anoxic marine sediments.

  18. Sulfate-Reducing Microorganisms in Wetlands – Fameless Actors in Carbon Cycling and Climate Change

    PubMed Central

    Pester, Michael; Knorr, Klaus-Holger; Friedrich, Michael W.; Wagner, Michael; Loy, Alexander

    2012-01-01

    Freshwater wetlands are a major source of the greenhouse gas methane but at the same time can function as carbon sink. Their response to global warming and environmental pollution is one of the largest unknowns in the upcoming decades to centuries. In this review, we highlight the role of sulfate-reducing microorganisms (SRM) in the intertwined element cycles of wetlands. Although regarded primarily as methanogenic environments, biogeochemical studies have revealed a previously hidden sulfur cycle in wetlands that can sustain rapid renewal of the small standing pools of sulfate. Thus, dissimilatory sulfate reduction, which frequently occurs at rates comparable to marine surface sediments, can contribute up to 36–50% to anaerobic carbon mineralization in these ecosystems. Since sulfate reduction is thermodynamically favored relative to fermentative processes and methanogenesis, it effectively decreases gross methane production thereby mitigating the flux of methane to the atmosphere. However, very little is known about wetland SRM. Molecular analyses using dsrAB [encoding subunit A and B of the dissimilatory (bi)sulfite reductase] as marker genes demonstrated that members of novel phylogenetic lineages, which are unrelated to recognized SRM, dominate dsrAB richness and, if tested, are also abundant among the dsrAB-containing wetland microbiota. These discoveries point toward the existence of so far unknown SRM that are an important part of the autochthonous wetland microbiota. In addition to these numerically dominant microorganisms, a recent stable isotope probing study of SRM in a German peatland indicated that rare biosphere members might be highly active in situ and have a considerable stake in wetland sulfate reduction. The hidden sulfur cycle in wetlands and the fact that wetland SRM are not well represented by described SRM species explains their so far neglected role as important actors in carbon cycling and climate change. PMID:22403575

  19. Mechanistic Insight into Trimethylamine N-Oxide Recognition by the Marine Bacterium Ruegeria pomeroyi DSS-3

    PubMed Central

    Li, Chun-Yang; Chen, Xiu-Lan; Shao, Xuan; Wei, Tian-Di; Wang, Peng; Xie, Bin-Bin; Qin, Qi-Long; Zhang, Xi-Ying; Su, Hai-Nan; Song, Xiao-Yan; Shi, Mei; Zhou, Bai-Cheng

    2015-01-01

    ABSTRACT Trimethylamine N-oxide (TMAO) is an important nitrogen source for marine bacteria. TMAO can also be metabolized by marine bacteria into volatile methylated amines, the precursors of the greenhouse gas nitrous oxide. However, it was not known how TMAO is recognized and imported by bacteria. Ruegeria pomeroyi DSS-3, a marine Roseobacter, has an ATP-binding cassette transporter, TmoXWV, specific for TMAO. TmoX is the substrate-binding protein of the TmoXWV transporter. In this study, the substrate specificity of TmoX of R. pomeroyi DSS-3 was characterized. We further determined the structure of the TmoX/TMAO complex and studied the TMAO-binding mechanism of TmoX by biochemical, structural, and mutational analyses. A Ca2+ ion chelated by an extended loop in TmoX was shown to be important for maintaining the stability of TmoX. Molecular dynamics simulations indicate that TmoX can alternate between “open” and “closed” states for binding TMAO. In the substrate-binding pocket, four tryptophan residues interact with the quaternary amine of TMAO by cation-π interactions, and Glu131 forms a hydrogen bond with the polar oxygen atom of TMAO. The π-π stacking interactions between the side chains of Phe and Trp are also essential for TMAO binding. Sequence analysis suggests that the TMAO-binding mechanism of TmoX may have universal significance in marine bacteria, especially in the marine Roseobacter clade. This study sheds light on how marine microorganisms utilize TMAO. IMPORTANCE Trimethylamine N-oxide (TMAO) is an important nitrogen source for marine bacteria. The products of TMAO metabolized by bacteria are part of the precursors of the greenhouse gas nitrous oxide. It is unclear how TMAO is recognized and imported by bacteria. TmoX is the substrate-binding protein of a TMAO-specific transporter. Here, the substrate specificity of TmoX of Ruegeria pomeroyi DSS-3 was characterized. The TMAO-binding mechanism of TmoX was studied by biochemical, structural

  20. Complete genome of a coastal marine bacterium Muricauda lutaonensis KCTC 22339(T).

    PubMed

    Oh, Jeongsu; Choe, Hanna; Kim, Byung Kwon; Kim, Kyung Mo

    2015-10-01

    Muricauda lutaonensis KCTC 22339(T) is a yellow-pigmented, gram-negative, rod-shaped bacterium that was isolated from a coastal hot spring of a volcanic island in the Pacific Ocean, off the eastern coast of Taiwan. We here report the complete genome of M. lutaonensis KCTC 22339(T), which consists of 3,274,259bp with the G+C content of 44.97%. The completion of the M. lutaonensis genome sequence is expected to provide a valuable resource for understanding the secondary metabolic pathways related to bacterial pigmentation. PMID:25986927

  1. Understanding the performance of sulfate reducing bacteria based packed bed reactor by growth kinetics study and microbial profiling.

    PubMed

    Dev, Subhabrata; Roy, Shantonu; Bhattacharya, Jayanta

    2016-07-15

    A novel marine waste extract (MWE) as alternative nitrogen source was explored for the growth of sulfate reducing bacteria (SRB). Variation of sulfate and nitrogen (MWE) showed that SRB growth follows an uncompetitive inhibition model. The maximum specific growth rates (μmax) of 0.085 and 0.124 h(-1) and inhibition constants (Ki) of 56 and 4.6 g/L were observed under optimized sulfate and MWE concentrations, respectively. The kinetic data shows that MWE improves the microbial growth by 27%. The packed bed bioreactor (PBR) under optimized sulfate and MWE regime showed sulfate removal efficiency of 62-66% and metals removal efficiency of 66-75% on using mine wastewater. The microbial community analysis using DGGE showed dominance of SRB (87-89%). The study indicated the optimum dosing of sulfate and cheap organic nitrogen to promote the growth of SRB over other bacteria. PMID:27085153

  2. Anaerobic metabolism of nitroaromatic compounds by sulfate-reducing and methanogenic bacteria

    SciTech Connect

    Boopathy, R.; Kulpa, C.F.

    1994-06-01

    Ecological observations suggest that sulfate-reducing and methanogenic bacteria might metabolize nitroaromatic compounds under anaerobic conditions if appropriate electron donors and electron acceptors are present in the environment, but this ability had not been demonstrated until recently. Most studies on the microbial metabolism of nitroaromatic compounds used aerobic microorganisms. In most cases no mineralization of nitroaromatics occurs, and only superficial modifications of the structures are reported. However, under anaerobic sulfate-reducing conditions, the nitroaromatic compounds reportedly undergo a series of reductions with the formation of amino compounds. For example, trinitrotoluene under sulfate-reducing conditions is reduced to triaminotoluene by the enzyme nitrite reductase, which is commonly found in many Desulfovibrio spp. The removal of ammonia from triaminotoluene is achieved by reductive deamination catalyzed by the enzyme reductive deaminase, with the production of ammonia and toluene. Some sulfate reducers can metabolize toluene to CO{sub 2}. Similar metabolic processes could be applied to other nitroaromatic compounds like nitrobenzene, nitrobenzoic acids, nitrophenols, and aniline. Many methanogenic bacteria can reduce nitroaromatic compounds to amino compounds. In this paper we review the anaerobic metabolic processes of nitroaromatic compounds under sulfate-reducing And methanogenic conditions.

  3. Effects of temperature on anaerobic decomposition of high-molecular weight organic matter under sulfate-reducing conditions

    NASA Astrophysics Data System (ADS)

    Matsui, Takato; Kojima, Hisaya; Fukui, Manabu

    2013-03-01

    Most sedimentary mineralization occurs along coasts under anaerobic conditions. In the absence of oxygen, high-molecular weight organic matter in marine sediments is gradually decomposed by hydrolysis, fermentation and sulfate reduction. Because of the different responses of the respective steps to temperature, degradation may be specifically slowed or stopped in certain step. To evaluate the effect of temperature on cellobiose degradation, culture experiments were performed at six different temperatures (3 °C, 8 °C, 13 °C, 18 °C, 23 °C, and 28 °C) under sulfate-reducing conditions. This study measured the concentrations of sulfide, dissolved organic carbon (DOC), and organic acids during that degradation. Degradation patterns were divided into three temperature groups: 3 °C, 8/13 °C, and 18/23/28 °C. The decrease in DOC proceeded in two steps, except at 3 °C. The length of the stagnant phase separating these two steps differed greatly between temperatures of 8/13 °C and 18/23/28 °C. In the first step, organic carbon was consumed by hydrolysis, fermentation and sulfate reduction. In the second step, acetate accumulated during the first step was oxidized by sulfate reduction. Bacterial communities in the cultures were analyzed by denaturing gradient gel electrophoresis (DGGE); the major differences among the three temperature groups were attributed to shifts in acetate-using sulfate reducers of the genus Desulfobacter. This suggests that temperature characteristics of dominant acetate oxidizers are important factors in determining the response of carbon flow in coastal marine sediments in relation to the changes in temperature.

  4. Respiration and respiratory enzyme activity in aerobic and anaerobic cultures of the marine denitrifying bacterium, Pseudomonas perfectomarinus

    NASA Astrophysics Data System (ADS)

    Packard, T. T.; Garfield, P. C.; Martinez, R.

    1983-03-01

    Oxygen consumption, nitrate reduction, respiratory electron transport activity, and nitrate reductase activity were measured in aerobic and anaerobic cultures of the marine bacterium, Pseudomonas perfectomarinus. The respiratory electron transport activity was closely correlated with oxygen consumption ( r = 0.98) in aerobic cultures and nearly as well correlated with nitrate reductase activity ( r = 0.91) and nitrate reduction ( r = 0.85) in anaerobic cultures. It was also well correlated with biomass in both aerobic ( r = 0.99) and anaerobic ( r = 0.94) cultures supporting the use of tetrazolium reduction as an index of living biomass. Time courses of nitrate and nitrate in the anaerobic cultures demonstrated that at nitrate concentrations above 1 mM, denitrification proceeds stepwise. Time courses of pH in anaerobic cultures revealed a rise from 7 to 8.5 during nitrite reduction indicating net proton utilization. This proton utilization is predicted by the stoichiometry of denitrification. Although the experiments were not under 'simulated in situ' conditions, the results are relevant to studies of denitrification, to bacterial ATP production, and to the respiratory activity of marine plankton in the ocean.

  5. Spongiimicrobium salis gen. nov., sp. nov., a bacterium of the family Flavobacteriaceae isolated from a marine sponge.

    PubMed

    Yoon, Jaewoo; Adachi, Kyoko; Kasai, Hiroaki

    2016-09-01

    A Gram-stain-negative, strictly aerobic, pale-yellow pigmented, rod-shaped, chemoheterotrophic bacterium, designated A6F-11(T), was isolated from a marine sponge collected in Japan. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the novel marine strain was affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and that it shared the highest (92.9 %) sequence similarity with Arenibacter palladensis LMG 21972(T). The strain could be differentiated phenotypically from related members of the family Flavobacteriaceae. The major fatty acids of strain A6F-11(T) were iso-C15:1 G, iso-C15:0, C16:1 ω6c and/or C16:1 ω7c and iso-C17:0 3-OH. The polar lipid profile consisted of phosphatidylglycerol, two unidentified aminolipids and two unidentified lipids. The DNA G+C content was 34.7 mol%, and the major respiratory quinone was menaquinone 6 (MK-6). From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel taxon in the family Flavobacteriaceae, for which the name Spongiimicrobium salis gen. nov., sp. nov. is proposed. The type strain of S. salis gen. nov., sp. nov. is A6F-11(T) (= KCTC 42753(T) = NBRC 111401(T)). PMID:27125652

  6. Pyruvatibacter mobilis gen. nov., sp. nov., a marine bacterium from the culture broth of Picochlorum sp. 122.

    PubMed

    Wang, Guanghua; Tang, Mingxing; Wu, Hualian; Dai, Shikun; Li, Tao; Chen, Chenghao; He, Hui; Fan, Jiewei; Xiang, Wenzhou; Li, Xiang

    2016-01-01

    A Gram-stain-negative, aerobic bacterium, designated strain GYP-11T, was isolated from the culture broth of a marine microalga, Picochloruma sp. 122. Cells were dimorphic rods; free living cells were motile by means of a single polar flagellum, and star-shaped-aggregate-forming cells were attached with stalks and non-motile. Sodium pyruvate or Tween 20 was required for growth on marine agar 2216.16S rRNA gene sequence analysis revealed that this isolate shared 94.07 % similarity with its closest type strain, Parvibaculum hydrocarboniclasticum EPR92T. Phylogenetic analyses indicated that strain GYP-11T represents a distinct lineage in a robust clade consisting of strain GYP-11T, alphaproteobacterium GMD21A06 and Candidatus Phaeomarinobacter ectocarpi Ec32. This clade was close to the genera Parvibaculum and Tepidicaulis in the order Rhizobiales. Chemotaxonomic and physiological characteristics, including cellular fatty acids and carbon source profiles, also readily distinguished strain GYP-11T from all established genera and species. Thus, it is concluded that strain GYP-11T represents a novel species of a new genus in the order Rhizobiales, for which the name Pyruvatibacter mobilis gen. nov., sp. nov. is proposed. The type strain of Pyruvatibacter mobilis is GYP-11T ( = CGMCC 1.15125T = KCTC 42509T). PMID:26476620

  7. Complete Genome Sequence of the Bioluminescent Marine Bacterium Vibrio harveyi ATCC 33843 (392 [MAV]).

    PubMed

    Wang, Zheng; Hervey, W Judson; Kim, Seongwon; Lin, Baochuan; Vora, Gary J

    2015-01-01

    Vibrio harveyi is a Gram-negative marine γ-proteobacterium that is known to be a formidable pathogen of aquatic animals and is a model organism for the study of bacterial bioluminescence and quorum sensing. In this report, we describe the complete genome sequence of the most studied strain of this species: V. harveyi ATCC 33843 (392 [MAV]). PMID:25635019

  8. Complete Genome Sequence of the Bioluminescent Marine Bacterium Vibrio harveyi ATCC 33843 (392 [MAV])

    PubMed Central

    Wang, Zheng; Hervey, W. Judson; Kim, Seongwon; Lin, Baochuan

    2015-01-01

    Vibrio harveyi is a Gram-negative marine γ-proteobacterium that is known to be a formidable pathogen of aquatic animals and is a model organism for the study of bacterial bioluminescence and quorum sensing. In this report, we describe the complete genome sequence of the most studied strain of this species: V. harveyi ATCC 33843 (392 [MAV]). PMID:25635019

  9. Complete Genome Sequence of the Proteorhodopsin-Containing Marine Bacterium Sediminicola sp. YIK13

    PubMed Central

    Kwon, Yong Min

    2016-01-01

    Sediminicola sp. YIK13 is a marine flavobacterium, isolated from tidal flat sediment. Here, we present the first complete genome sequence of this genus, which consists of 3,569,807 bp with 39.4% GC content. This strain contains proteorhodopsin, as well as retinal biosynthesis genes, allowing it to utilize sunlight as an energy source. PMID:26823585

  10. Complete Genome Sequence of the Proteorhodopsin-Containing Marine Bacterium Sediminicola sp. YIK13.

    PubMed

    Kwon, Yong Min; Kim, Sang-Jin

    2016-01-01

    Sediminicola sp. YIK13 is a marine flavobacterium, isolated from tidal flat sediment. Here, we present the first complete genome sequence of this genus, which consists of 3,569,807 bp with 39.4% GC content. This strain contains proteorhodopsin, as well as retinal biosynthesis genes, allowing it to utilize sunlight as an energy source. PMID:26823585