Science.gov

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. Desulfoconvexum algidum gen. nov., sp. nov., a psychrophilic sulfate-reducing bacterium isolated from a permanently cold marine sediment.

    PubMed

    Könneke, Martin; Kuever, Jan; Galushko, Alexander; Jørgensen, Bo Barker

    2013-03-01

    A sulfate-reducing bacterium, designated JHA1(T), was isolated from a permanently cold marine sediment sampled in an Artic fjord on the north-west coast of Svalbard. The isolate was originally enriched at 4 °C in a highly diluted liquid culture amended with hydrogen and sulfate. Strain JHA1(T) was a psychrophile, growing fastest between 14 and 16 °C and not growing above 20 °C. Fastest growth was found at neutral pH (pH 7.2-7.4) and at marine concentrations of NaCl (20-30 g l(-1)). Phylogenetic analysis of 16S rRNA gene sequences revealed that strain JHA1(T) was a member of the family Desulfobacteraceae in the Deltaproteobacteria. The isolate shared 99 % 16S rRNA gene sequence similarity with an environmental sequence obtained from permanently cold Antarctic sediment. The closest recognized relatives were Desulfobacula phenolica DSM 3384(T) and Desulfobacula toluolica DSM 7467(T) (both <95 % sequence similarity). In contrast to its closest phylogenetic relatives, strain JHA1(T) grew chemolithoautotrophically with hydrogen as an electron donor. CO dehydrogenase activity indicated the operation of the reductive acetyl-CoA pathway for inorganic carbon assimilation. Beside differences in physiology and morphology, strain JHA1(T) could be distinguished chemotaxonomically from the genus Desulfobacula by the absence of the cellular fatty acid C16 : 0 10-methyl. Phylogenetic differentiation from other genera was further supported by DsrAB and AprBA sequence analysis. Based on the described phylogenetic and phenotypic differences between strain JHA1(T) and its closest relatives, the establishment of a novel genus and a novel species, Desulfoconvexum algidum gen. nov., sp. nov. is proposed. The type strain is JHA1(T) ( = DSM 21856(T)  = JCM 16085(T)).

  3. Dethiosulfatibacter aminovorans gen. nov., sp. nov., a novel thiosulfate-reducing bacterium isolated from coastal marine sediment via sulfate-reducing enrichment with Casamino acids.

    PubMed

    Takii, Susumu; Hanada, Satoshi; Tamaki, Hideyuki; Ueno, Yutaka; Sekiguchi, Yuji; Ibe, Akihiro; Matsuura, Katsumi

    2007-10-01

    A sulfate-reducing enrichment culture originating from coastal marine sediment of the eutrophic Tokyo Bay, Japan, was successfully established with Casamino acids as a substrate. A thiosulfate reducer, strain C/G2(T), was isolated from the enrichment culture after further enrichment with glutamate. Cells of strain C/G2(T) were non-motile rods (0.6-0.8 microm x 2.2-4.8 microm) and were found singly or in pairs and sometimes in short chains. Spores were not formed. Cells of strain C/G2(T) stained Gram-negatively, despite possessing Gram-positive cell walls. The optimum temperature for growth was 28-30 degrees C, the optimum pH was around 7.8 and the optimum salt concentration was 20-30 g l(-1). Lactate, pyruvate, serine, cysteine, threonine, glutamate, histidine, lysine, arginine, Casamino acids, peptone and yeast extract were fermented as single substrates and no sugar was used as a fermentative substrate. A Stickland reaction was observed with some pairs of amino acids. Fumarate, alanine, proline, phenylalanine, tryptophan, glutamine and aspartate were utilized only in the presence of thiosulfate. Strain C/G2(T) fermented glutamate to H2, CO2, acetate and propionate. Thiosulfate and elemental sulfur were reduced to sulfide. Sulfate, sulfite and nitrate were not utilized as electron acceptors. The growth of strain C/G2(T) on Casamino acids or glutamate was enhanced by co-culturing with Desulfovibrio sp. isolated from the original mixed culture enriched with Casamino acids. The DNA G+C content of strain C/G2(T) was 41.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain C/G2(T) formed a distinct cluster with species of the genus Sedimentibacter. The closest relative was Sedimentibacter hydroxybenzoicus (with a gene sequence similarity of 91 %). On the basis of its phylogenetic and phenotypic properties, strain C/G2(T) (=JCM 13356(T)=NBRC 101112(T)=DSM 17477(T)) is proposed as representing a new genus and novel species, Dethiosulfatibacter

  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. 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

  6. 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

  7. Sulfur isotope enrichment during maintenance metabolism in the thermophilic sulfate-reducing bacterium Desulfotomaculum putei.

    PubMed

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

    2009-09-01

    Values of Delta(34)S (=delta(34)S(HS)-delta(34)S(SO(4)), where delta(34)S(HS) and delta(34)S(SO(4)) indicate the differences in the isotopic compositions of the HS(-) and SO(4)(2-) in the eluent, respectively) for many modern marine sediments are in the range of -55 to -75 per thousand, much greater than the -2 to -46 per thousand epsilon(34)S (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 SO(4) 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 delta(34)S values of the sulfate and sulfide eluting from the retentostat were significantly larger, attaining a maximum Delta(34)S of -20.9 per thousand, than the -9.7 per thousand observed during the batch culture experiment, but differences did not attain the values observed in marine sediments.

  8. 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.

  9. A Cultured Greigite-Producing Magnetotactic Bacterium in a Novel Group of Sulfate-Reducing Bacteria

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

    Magnetotactic bacteria contain magnetosomes—intracellular, membrane-bounded, magnetic nanocrystals of magnetite (Fe3O4) or greigite (Fe3S4)—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.

  10. Distribution of Sulfate-Reducing Communities from Estuarine to Marine Bay Waters.

    PubMed

    Colin, Yannick; Goñi-Urriza, Marisol; Gassie, Claire; Carlier, Elisabeth; Monperrus, Mathilde; Guyoneaud, Rémy

    2017-01-01

    Estuaries are highly dynamic ecosystems in which freshwater and seawater mix together. Depending on tide and river inflows, particles originating from rivers or from the remobilization of sediments accumulate in the water column. Due to the salinity gradient and the high heterotrophic activity in the estuarine plume, hypoxic and anoxic microniches may form in oxygenated waters, sustaining favorable conditions for resuspended anaerobic microorganisms. In this context, we tested the hypothesis that anaerobic sulfate-reducing prokaryotes may occur in the water column of the Adour River. Using 16S ribosomal RNA (rRNA) and dsrAB-based terminal restriction fragment length polymorphism (T-RFLP) techniques, we characterized total prokaryotic and sulfate-reducing communities along a gradient from estuarine to marine bay waters. Sulfate-reducing prokaryotes were further characterized by the description of dsrB genes and the cultivation of sulfidogenic anaerobic microorganisms. As a result, physical-chemical parameters had a significant effect on water bacterial diversity and community structure along the studied gradient. The concentration of cultured sulfidogenic microorganisms ranged from 1 to 60 × 10(3) cells l(-1) in the water column. Sulfate-reducing prokaryotes occurring in estuarine waters were closely related to microorganisms previously detected in freshwater sediments, suggesting an estuarine origin, mainly by the remobilization of the sediments. In the marine bay station, sediment-derived sulfate-reducing prokaryotes were not cultured anymore, probably due to freshwater dilution, increasing salinity and extended oxic stress. Nevertheless, isolates related to the type strain Desulfovibrio oceani were cultured from the diluted plume and deep marine waters, indicating the occurrence of autochthonous sulfate-reducing bacteria offshore.

  11. Function of periplasmic hydrogenases in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough.

    PubMed

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

    2007-09-01

    The sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough possesses four periplasmic hydrogenases to facilitate the oxidation 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 their cellular functions, we have compared the growth rates of existing (hyd and hyn1) and newly constructed (hys and hyn-1 hyd) mutants to those of the wild type in defined media in which lactate or hydrogen at either 5 or 50% (vol/vol) was used as the sole electron donor for sulfate reduction. Only strains missing the [Fe] hydrogenase were significantly affected during growth with lactate or with 50% (vol/vol) hydrogen as the sole electron donor. When the cells were grown at low (5% [vol/vol]) hydrogen concentrations, those missing the [NiFeSe] hydrogenase suffered the greatest impairment. The growth rate data correlated strongly with gene expression results obtained from microarray hybridizations and real-time PCR using mRNA extracted from cells grown under the three conditions. Expression of the hys genes followed the order 5% hydrogen>50% hydrogen>lactate, whereas expression of the hyd genes followed the reverse order. These results suggest that growth with lactate and 50% hydrogen is associated with high intracellular hydrogen concentrations, which are best captured by the higher activity, lower affinity [Fe] hydrogenase. In contrast, growth with 5% hydrogen is associated with a low intracellular hydrogen concentration, requiring the lower activity, higher affinity [NiFeSe] hydrogenase.

  12. Function of Periplasmic Hydrogenases in the Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough▿ †

    PubMed Central

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

    2007-01-01

    The sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough possesses four periplasmic hydrogenases to facilitate the oxidation 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 their cellular functions, we have compared the growth rates of existing (hyd and hyn1) and newly constructed (hys and hyn-1 hyd) mutants to those of the wild type in defined media in which lactate or hydrogen at either 5 or 50% (vol/vol) was used as the sole electron donor for sulfate reduction. Only strains missing the [Fe] hydrogenase were significantly affected during growth with lactate or with 50% (vol/vol) hydrogen as the sole electron donor. When the cells were grown at low (5% [vol/vol]) hydrogen concentrations, those missing the [NiFeSe] hydrogenase suffered the greatest impairment. The growth rate data correlated strongly with gene expression results obtained from microarray hybridizations and real-time PCR using mRNA extracted from cells grown under the three conditions. Expression of the hys genes followed the order 5% hydrogen > 50% hydrogen > lactate, whereas expression of the hyd genes followed the reverse order. These results suggest that growth with lactate and 50% hydrogen is associated with high intracellular hydrogen concentrations, which are best captured by the higher activity, lower affinity [Fe] hydrogenase. In contrast, growth with 5% hydrogen is associated with a low intracellular hydrogen concentration, requiring the lower activity, higher affinity [NiFeSe] hydrogenase. PMID:17601789

  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. Desulfonatronum thiodismutans sp. nov., a novel alkaliphilic, sulfate-reducing bacterium capable of lithoautotrophic growth.

    PubMed

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

    2003-09-01

    A novel alkaliphilic, sulfate-reducing bacterium, strain MLF1(T), was isolated from sediments of soda Mono Lake, California. Gram-negative vibrio-shaped cells were observed, which were 0.6-0.7x1.2-2.7 micro m in size, motile by a single polar flagellum and occurred singly, in pairs or as short spirilla. Growth was observed at 15-48 degrees C (optimum, 37 degrees C), >1-7 % NaCl, 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(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(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(T), exhibited 51 % homology. Also, the genome size (1.6x10(9) Da) and T(m) value of the genomic DNA (71+/-2 degrees C) for strain MLF1(T) were significantly different from the genome size (2.1x10(9) Da) and T(m) value (63+/-2 degrees C) for Desulfonatronum lacustre Z-7951(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(T)=ATCC BAA-395(T)=DSM 14708(T)).

  15. 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.

  16. Comparative Analysis of Methane-Oxidizing Archaea and Sulfate-Reducing Bacteria in Anoxic Marine Sediments

    PubMed Central

    Orphan, V. J.; Hinrichs, K.-U.; Ussler, W.; Paull, C. K.; Taylor, L. T.; Sylva, S. P.; Hayes, J. M.; Delong, E. F.

    2001-01-01

    The oxidation of methane in anoxic marine sediments is thought to be mediated by a consortium of methane-consuming archaea and sulfate-reducing bacteria. In this study, we compared results of rRNA gene (rDNA) surveys and lipid analyses of archaea and bacteria associated with methane seep sediments from several different sites on the Californian continental margin. Two distinct archaeal lineages (ANME-1 and ANME-2), peripherally related to the order Methanosarcinales, were consistently associated with methane seep marine sediments. The same sediments contained abundant 13C-depleted archaeal lipids, indicating that one or both of these archaeal groups are members of anaerobic methane-oxidizing consortia. 13C-depleted lipids and the signature 16S rDNAs for these archaeal groups were absent in nearby control sediments. Concurrent surveys of bacterial rDNAs revealed a predominance of δ-proteobacteria, in particular, close relatives of Desulfosarcina variabilis. Biomarker analyses of the same sediments showed bacterial fatty acids with strong 13C depletion that are likely products of these sulfate-reducing bacteria. Consistent with these observations, whole-cell fluorescent in situ hybridization revealed aggregations of ANME-2 archaea and sulfate-reducing Desulfosarcina and Desulfococcus species. Additionally, the presence of abundant 13C-depleted ether lipids, presumed to be of bacterial origin but unrelated to ether lipids of members of the order Desulfosarcinales, suggests the participation of additional bacterial groups in the methane-oxidizing process. Although the Desulfosarcinales and ANME-2 consortia appear to participate in the anaerobic oxidation of methane in marine sediments, our data suggest that other bacteria and archaea are also involved in methane oxidation in these environments. PMID:11282650

  17. Effects of biocides on gene expression in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough.

    PubMed

    Lee, Meng-Hsin Phoebe; Caffrey, Sean M; Voordouw, Johanna K; Voordouw, Gerrit

    2010-07-01

    Although sulfate-reducing bacteria (SRB), such as Desulfovibrio vulgaris Hildenborough (DvH) are often eradicated in oil and gas operations with biocides, such as glutaraldehyde (Glut), tetrakis (hydroxymethyl) phosphonium sulfate (THPS), and benzalkonium chloride (BAC), their response to these agents is not well known. Whole genome microarrays of D. vulgaris treated with biocides well below the minimum inhibitory concentration showed that 256, 96, and 198 genes were responsive to Glut, THPS, and BAC, respectively, and that these three commonly used biocides affect the physiology of the cell quite differently. Glut induces expression of genes required to degrade or refold proteins inactivated by either chemical modification or heat shock, whereas BAC appears to target ribosomal structure. THPS appears to primarily affect energy metabolism of SRB. Mutants constructed for genes strongly up-regulated by Glut, were killed by Glut to a similar degree as the wild type. Hence, it is difficult to achieve increased sensitivity to this biocide by single gene mutations, because Glut affects so many targets. Our results increase understanding of the biocide's mode of action, allowing a more intelligent combination of mechanistically different agents. This can reduce stress on budgets for chemicals and on the environment.

  18. 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.

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

    DOE PAGES

    Price, Morgan N.; Ray, Jayashree; Wetmore, Kelly M.; ...

    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

  20. 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

  1. 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.

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

    PubMed

    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.

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

    PubMed

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

    2013-08-13

    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.

  4. Candidatus Desulfofervidus auxilii, a hydrogenotrophic sulfate-reducing bacterium involved in the thermophilic anaerobic oxidation of methane.

    PubMed

    Krukenberg, Viola; Harding, Katie; Richter, Michael; Glöckner, Frank Oliver; Gruber-Vodicka, Harald R; Adam, Birgit; Berg, Jasmine S; Knittel, Katrin; Tegetmeyer, Halina E; Boetius, Antje; Wegener, Gunter

    2016-09-01

    The anaerobic oxidation of methane (AOM) is mediated by consortia of anaerobic methane-oxidizing archaea (ANME) and their specific partner bacteria. In thermophilic AOM consortia enriched from Guaymas Basin, members of the ANME-1 clade are associated with bacteria of the HotSeep-1 cluster, which likely perform direct electron exchange via nanowires. The partner bacterium was enriched with hydrogen as sole electron donor and sulfate as electron acceptor. Based on phylogenetic, genomic and metabolic characteristics we propose to name this chemolithoautotrophic sulfate reducer Candidatus Desulfofervidus auxilii. Ca. D. auxilii grows on hydrogen at temperatures between 50°C and 70°C with an activity optimum at 60°C and doubling time of 4-6 days. Its genome draft encodes for canonical sulfate reduction, periplasmic and soluble hydrogenases and autotrophic carbon fixation via the reductive tricarboxylic acid cycle. The presence of genes for pili formation and cytochromes, and their similarity to genes of Geobacter spp., indicate a potential for syntrophic growth via direct interspecies electron transfer when the organism grows in consortia with ANME. This first ANME-free enrichment of an AOM partner bacterium and its characterization opens the perspective for a deeper understanding of syntrophy in anaerobic methane oxidation.

  5. 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

  6. Genome sequence of Desulfovibrio sp. A2, a highly copper resistant, sulfate-reducing bacterium isolated from effluents of a zinc smelter at the Urals.

    PubMed

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

    2011-12-01

    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.

  7. 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

  8. Evidence-based annotation of transcripts and proteins in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough.

    PubMed

    Price, Morgan N; Deutschbauer, Adam M; Kuehl, Jennifer V; Liu, Haichuan; Witkowska, H Ewa; Arkin, Adam P

    2011-10-01

    We used high-resolution tiling microarrays and 5' RNA sequencing to identify transcripts in Desulfovibrio vulgaris Hildenborough, a model sulfate-reducing bacterium. We identified the first nucleotide position for 1,124 transcripts, including 54 proteins with leaderless transcripts and another 72 genes for which a major transcript initiates within the upstream protein-coding gene, which confounds measurements of the upstream gene's expression. Sequence analysis of these promoters showed that D. vulgaris prefers -10 and -35 boxes different from those preferred by Escherichia coli. A total of 549 transcripts ended at intrinsic (rho-independent) terminators, but most of the other transcripts seemed to have variable ends. We found low-level antisense expression of most genes, and the 5' ends of these transcripts mapped to promoter-like sequences. Because antisense expression was reduced for highly expressed genes, we suspect that elongation of nonspecific antisense transcripts is suppressed by transcription of the sense strand. Finally, we combined the transcript results with comparative analysis and proteomics data to make 505 revisions to the original annotation of 3,531 proteins: we removed 255 (7.5%) proteins, changed 123 (3.6%) start codons, and added 127 (3.7%) proteins that had been missed. Tiling data had higher coverage than shotgun proteomics and hence led to most of the corrections, but many errors probably remain. Our data are available at http://genomics.lbl.gov/supplemental/DvHtranscripts2011/.

  9. Purification and characterization of homo- and hetero-dimeric acetate kinases from the sulfate-reducing bacterium Desulfovibrio vulgaris.

    PubMed

    Yu, L; Ishida, T; Ozawa, K; Akutsu, H; Horiike, K

    2001-03-01

    Two distinct forms of acetate kinase were purified to homogeneity from a sulfate-reducing bacterium Desulfovibrio vulgaris Miyazaki F. The enzymes were separated from the soluble fraction of the cells on anion exchange columns. One acetate kinase (AK-I) was a homodimer (alpha(S)(2)) and the other (AK-II) was a heterodimer (alpha(S)alpha(L)). On SDS-PAGE, alpha(L) and alpha(S) subunits migrated as bands of 49.3 and 47.8 kDa, respectively, but they had an identical N-terminal amino acid sequence. A rapid HPLC method was developed to directly measure ADP and ATP in assay mixtures. Initial velocity data for AK-I and AK-II were collected by this method and analyzed based on a random sequential mechanism, assuming rapid equilibrium for the substrate binding steps. All kinetic parameters for both the forward acetyl phosphate formation and the reverse ATP formation catalyzed by AK-I and AK-II were successfully determined. The two enzymes showed similar kinetic properties in Mg(2+) requirement, pH-dependence and magnitude of kinetic parameters. These results suggest that two forms of acetate kinase are produced to finely regulate the enzyme function by post-translational modifications of a primary gene product in Desulfovibrio vulgaris.

  10. 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).

  11. Desulfovibrio marrakechensis sp. nov., a 1,4-tyrosol-oxidizing, sulfate-reducing bacterium isolated from olive mill wastewater.

    PubMed

    Chamkh, Fatima; Spröer, Cathrin; Lemos, Paulo Costa; Besson, Stephane; El Asli, Abdel-Ghani; Bennisse, Rhizlane; Labat, Marc; Reis, Maria; Qatibi, Abdel-Illah

    2009-05-01

    A novel mesophilic sulfate-reducing bacterium, EMSSDQ(4)(T), was isolated from olive mill wastewater in the semi-arid region of Morocco (Marrakech). Cells were Gram-negative, catalase-positive, straight rods that were non-motile and non-spore-forming and contained cytochrome c(3) and desulfoviridin. The DNA G+C content was 65.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was a member of the genus Desulfovibrio with Desulfovibrio carbinoliphilus D41(T), Desulfovibrio alcoholivorans SPSN(T), Desulfovibrio fructosivorans JJ(T) and Desulfovibrio carbinolicus EDK82(T) as the most closely related strains with validly published names. In addition to the classical substrates used by Desulfovibrio species, the isolate oxidized 1,4-tyrosol, one of the most abundant phenolic compounds occurring in olive mill wastewater, to 4-hydroxyphenylacetate without ring cleavage. D. alcoholivorans SPSN(T) was also found to carry out this reaction. Under air, strain EMSSDQ(4)(T) exhibited limited growth on lactate and yeast extract in the absence of sulfate. On the basis of genotypic and phenotypic characteristics, it is proposed that the isolate represents a novel species, Desulfovibrio marrakechensis sp. nov. The type strain is EMSSDQ(4)(T) (=DSM 19337(T) =ATCC BAA-1562(T)).

  12. 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.

  13. 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.

  14. Desulfosporosinus burensis sp. nov., a spore-forming, mesophilic, sulfate-reducing bacterium isolated from a deep clay environment.

    PubMed

    Mayeux, Bruno; Fardeau, Marie-Laure; Bartoli-Joseph, Manon; Casalot, Laurie; Vinsot, Agnès; Labat, Marc

    2013-02-01

    A novel anaerobic, gram-positive, spore-forming, curved rod-shaped, mesophilic and sulfate-reducing bacterium was isolated from pore water collected in a borehole at -490 m in Bure (France). This strain, designated BSREI1(T), grew at temperatures between 5 °C and 30 °C (optimum 25 °C) and at a pH between 6 and 8 (optimum 7). It did not require NaCl for growth, but tolerated it up to 1.5 % NaCl. Sulfate, thiosulfate and elemental sulfur were used as terminal electron acceptors. Strain BSREI1(T) used crotonate, formate, lactate, pyruvate, fructose, glycerol and yeast extract as electron donors in the presence of sulfate. The sole quinone was MK-7. The G+C content of the genomic DNA was 43.3 mol%. Strain BSREI1(T) had the type strains of Desulfosporosinus lacus (16S rRNA gene sequence similarity of 96.83 %), Desulfosporosinus meridiei (96.31 %) and Desulfosporosinus hippei (96.16 %) as its closest phylogenetic relatives. On the basis of phylogenetic and physiological properties, strain BSREI1(T) is proposed as a representative of a novel species of the genus Desulfosporosinus, Desulfosporosinus burensis sp. nov.; the type strain is BSREI1(T) ( = DSM 24089(T) = JCM 17380(T)).

  15. Desulfovibrio brasiliensis sp. nov., a moderate halophilic sulfate-reducing bacterium from Lagoa Vermelha (Brazil) mediating dolomite formation.

    PubMed

    Warthmann, Rolf; Vasconcelos, Crisogono; Sass, Henrik; McKenzie, Judith A

    2005-06-01

    A novel halotolerant sulfate-reducing bacterium, Desulfovibrio brasiliensis strain LVform1, was isolated from sediments of a dolomite-forming hypersaline coastal lagoon, Lagoa Vermelha, in the state of Rio de Janeiro, Brazil. The cells are vibrio-shaped and 0.30 to 0.45 microm by 1.0 to 3.5 microm in size. These bacteria mediate the precipitation of dolomite [CaMg(CO3)2] in culture experiments. The strain was identified as a member of the genus Desulfovibrio in the delta-subclass of the Proteobacteria on the basis of its 16S rRNA gene sequence, its physiological and morphological properties. Strain LVform1 is obligate sodium-dependent and grows at NaCl concentrations of up to 15%. The 16S rRNA sequence revealed that this strain is closely related to Desulfovibrio halophilus (96.2% similarity) and to Desulfovibrio oxyclinae (96.8% similarity), which were both isolated from Solar Lake, a hypersaline coastal lake in the Sinai, Egypt. Strain LVform1 is barotolerant, growing under pressures of up to 370 bar (37 MPa). We propose strain LVform1 to be the type strain of a novel species of the genus Desulfovibrio, Desulfovibrio brasiliensis (type strain LVform1 = DSMZ No. 15816 and JCM No. 12178). The GenBank/EMBL accession number for the 16S rDNA sequence of strain LVform1 is AJ544687.

  16. Marine sulfate-reducing bacteria cause serious corrosion of iron under electroconductive biogenic mineral crust

    PubMed Central

    Enning, Dennis; Venzlaff, Hendrik; Garrelfs, Julia; Dinh, Hang T; Meyer, Volker; Mayrhofer, Karl; Hassel, Achim W; Stratmann, Martin; Widdel, Friedrich

    2012-01-01

    Iron (Fe0) corrosion in anoxic environments (e.g. inside pipelines), a process entailing considerable economic costs, is largely influenced by microorganisms, in particular sulfate-reducing bacteria (SRB). The process is characterized by formation of black crusts and metal pitting. The mechanism is usually explained by the corrosiveness of formed H2S, and scavenge of ‘cathodic’ H2 from chemical reaction of Fe0 with H2O. Here we studied peculiar marine SRB that grew lithotrophically with metallic iron as the only electron donor. They degraded up to 72% of iron coupons (10 mm × 10 mm × 1 mm) within five months, which is a technologically highly relevant corrosion rate (0.7 mm Fe0 year−1), while conventional H2-scavenging control strains were not corrosive. The black, hard mineral crust (FeS, FeCO3, Mg/CaCO3) deposited on the corroding metal exhibited electrical conductivity (50 S m−1). This was sufficient to explain the corrosion rate by electron flow from the metal (4Fe0 → 4Fe2+ + 8e−) through semiconductive sulfides to the crust-colonizing cells reducing sulfate (8e− + SO42− + 9H+ → HS− + 4H2O). Hence, anaerobic microbial iron corrosion obviously bypasses H2 rather than depends on it. SRB with such corrosive potential were revealed at naturally high numbers at a coastal marine sediment site. Iron coupons buried there were corroded and covered by the characteristic mineral crust. It is speculated that anaerobic biocorrosion is due to the promiscuous use of an ecophysiologically relevant catabolic trait for uptake of external electrons from abiotic or biotic sources in sediments. PMID:22616633

  17. Marine sulfate-reducing bacteria cause serious corrosion of iron under electroconductive biogenic mineral crust.

    PubMed

    Enning, Dennis; Venzlaff, Hendrik; Garrelfs, Julia; Dinh, Hang T; Meyer, Volker; Mayrhofer, Karl; Hassel, Achim W; Stratmann, Martin; Widdel, Friedrich

    2012-07-01

    Iron (Fe(0) ) corrosion in anoxic environments (e.g. inside pipelines), a process entailing considerable economic costs, is largely influenced by microorganisms, in particular sulfate-reducing bacteria (SRB). The process is characterized by formation of black crusts and metal pitting. The mechanism is usually explained by the corrosiveness of formed H(2) S, and scavenge of 'cathodic' H(2) from chemical reaction of Fe(0) with H(2) O. Here we studied peculiar marine SRB that grew lithotrophically with metallic iron as the only electron donor. They degraded up to 72% of iron coupons (10 mm × 10 mm × 1 mm) within five months, which is a technologically highly relevant corrosion rate (0.7 mm Fe(0) year(-1) ), while conventional H(2) -scavenging control strains were not corrosive. The black, hard mineral crust (FeS, FeCO(3) , Mg/CaCO(3) ) deposited on the corroding metal exhibited electrical conductivity (50 S m(-1) ). This was sufficient to explain the corrosion rate by electron flow from the metal (4Fe(0)  → 4Fe(2+)  + 8e(-) ) through semiconductive sulfides to the crust-colonizing cells reducing sulfate (8e(-)  + SO(4) (2-)  + 9H(+)  → HS(-)  + 4H(2) O). Hence, anaerobic microbial iron corrosion obviously bypasses H(2) rather than depends on it. SRB with such corrosive potential were revealed at naturally high numbers at a coastal marine sediment site. Iron coupons buried there were corroded and covered by the characteristic mineral crust. It is speculated that anaerobic biocorrosion is due to the promiscuous use of an ecophysiologically relevant catabolic trait for uptake of external electrons from abiotic or biotic sources in sediments.

  18. 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

  19. Thermodesulfatator atlanticus sp. nov., a thermophilic, chemolithoautotrophic, sulfate-reducing bacterium isolated from a Mid-Atlantic Ridge hydrothermal vent.

    PubMed

    Alain, Karine; Postec, Anne; Grinsard, Elodie; Lesongeur, Françoise; Prieur, Daniel; Godfroy, Anne

    2010-01-01

    A novel, strictly anaerobic, thermophilic, sulfate-reducing bacterium, designated strain AT1325(T), was isolated from a deep-sea hydrothermal vent at the Rainbow site on the Mid-Atlantic Ridge. This strain was subjected to a polyphasic taxonomic analysis. Cells were Gram-negative motile rods (approximately 2.4 x 0.6 microm) with a single polar flagellum. Strain AT1325(T) grew at 55-75 degrees C (optimum, 65-70 degrees C), at pH 5.5-8.0 (optimum, 6.5-7.5) and in the presence of 1.5-4.5 % (w/v) NaCl (optimum, 2.5 %). Cells grew chemolithoautotrophically with H2 as an energy source and SO4(2-) as an electron acceptor. Alternatively, the novel isolate was able to use methylamine, peptone or yeast extract as carbon sources. The dominant fatty acids (>5 % of the total) were C(16 : 0), C(18 : 1)omega7c, C(18 : 0) and C(19 : 0) cyclo omega8c. The G+C content of the genomic DNA of strain AT1325(T) was 45.6 mol%. Phylogenetic analyses based on 16S rRNA gene sequences placed strain AT1325(T) within the family Thermodesulfobacteriaceae, in the bacterial domain. Comparative 16S rRNA gene sequence analysis indicated that strain AT1325(T) belonged to the genus Thermodesulfatator, sharing 97.8 % similarity with the type strain of Thermodesulfatator indicus, the unique representative species of this genus. On the basis of the data presented, it is suggested that strain AT1325(T) represents a novel species of the genus Thermodesulfatator, for which the name Thermodesulfatator atlanticus sp. nov. is proposed. The type strain is AT1325(T) (=DSM 21156(T)=JCM 15391(T)).

  20. Gene expression by the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough grown on an iron electrode under cathodic protection conditions.

    PubMed

    Caffrey, Sean M; Park, Hyung Soo; Been, Jenny; Gordon, Paul; Sensen, Christoph W; Voordouw, Gerrit

    2008-04-01

    The genome sequence of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough was reanalyzed to design unique 70-mer oligonucleotide probes against 2,824 probable protein-coding regions. These included three genes not previously annotated, including one that encodes a c-type cytochrome. Using microarrays printed with these 70-mer probes, we analyzed the gene expression profile of wild-type D. vulgaris grown on cathodic hydrogen, generated at an iron electrode surface with an imposed negative potential of -1.1 V (cathodic protection conditions). The gene expression profile of cells grown on cathodic hydrogen was compared to that of cells grown with gaseous hydrogen bubbling through the culture. Relative to the latter, the electrode-grown cells overexpressed two hydrogenases, the hyn-1 genes for [NiFe] hydrogenase 1 and the hyd genes, encoding [Fe] hydrogenase. The hmc genes for the high-molecular-weight cytochrome complex, which allows electron flow from the hydrogenases across the cytoplasmic membrane, were also overexpressed. In contrast, cells grown on gaseous hydrogen overexpressed the hys genes for [NiFeSe] hydrogenase. Cells growing on the electrode also overexpressed genes encoding proteins which promote biofilm formation. Although the gene expression profiles for these two modes of growth were distinct, they were more closely related to each other than to that for cells grown in a lactate- and sulfate-containing medium. Electrochemically measured corrosion rates were lower for iron electrodes covered with hyn-1, hyd, and hmc mutant biofilms than for wild-type biofilms. This confirms the importance, suggested by the gene expression studies, of the corresponding gene products in D. vulgaris-mediated iron corrosion.

  1. 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.

  2. Genome sequence of Desulfosporosinus sp. OT, an acidophilic sulfate-reducing bacterium from copper mining waste in Norilsk, Northern Siberia.

    PubMed

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

    2011-11-01

    We have sequenced the genome of Desulfosporosinus sp. OT, a Gram-positive, acidophilic sulfate-reducing Firmicute isolated from copper tailing sediment in the Norilsk mining-smelting area in Northern Siberia, Russia. This represents the first sequenced genome of a Desulfosporosinus species. The genome has a size of 5.7 Mb and encodes 6,222 putative proteins.

  3. 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

  4. 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

  5. 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.

  6. Complete genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812T)

    PubMed Central

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

    2012-01-01

    Thermodesulfatator indicus Moussard et al. 2004 is a member of the Thermodesulfobacteriaceae, a family in the phylum Thermodesulfobacteria that is currently poorly characterized at the genome level. 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. PMID:22768359

  7. 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%.

  8. 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.

  9. 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.

  10. Desulfosporomusa polytropa gen. nov., sp. nov., a novel sulfate-reducing bacterium from sediments of an oligotrophic lake.

    PubMed

    Sass, Henrik; Overmann, Jörg; Rütters, Heike; Babenzien, Hans-Dietrich; Cypionka, Heribert

    2004-10-01

    Five strains of sulfate-reducing bacteria were isolated from the highest positive dilutions of a most probable number (MPN) series supplemented with lactate and inoculated with sediments from the oligotrophic Lake Stechlin. The isolates were endospore-forming and were motile by means of laterally inserted flagella. They stained Gram-negative and contained b-type cytochromes. CO difference spectra indicated the presence of P582 as a sulfite reductase. Phylogenetic analyses of the 16S rDNA sequences revealed that the isolates were very closely affiliated with the genus Sporomusa. However, sulfate and amorphous Fe(OH)(3), but not sulfite, elemental sulfur, MnO(2), or nitrate were used as terminal electron acceptors. Homoacetogenic growth was found with H(2)/CO(2) gas mixture, formate, methanol, ethanol, and methoxylated aromatic compounds. The strains grew autotrophically with H(2) plus CO(2) in the presence or absence of sulfate. Formate, butyrate, several alcohols, organic acids, carbohydrates, some amino acids, choline, and betaine were also utilized as substrates. The growth yield with lactate and sulfate as substrate was 7.0 g dry mass/mol lactate and thus two times higher than in sulfate-free fermenting cultures. All isolates were able to grow in a temperature range of 4-37 degrees C. Physiologically and by the presence of a Gram-negative cell wall, the new isolates resemble known Desulfosporosinus species. However, phylogenetically they are affiliated with the Gram-negative genus Sporomusa belonging to the Selenomonas subgroup of the Firmicutes. Therefore, the new isolates reveal a new phylogenetic lineage of sulfate-reducing bacteria. A new genus and species, Desulfosporomusa polytropa gen. nov., sp. nov. is proposed.

  11. Thermodesulfobium acidiphilum sp. nov., a new thermoacidophilic sulfate-reducing chemoautotrophic bacterium from a Kamchatkan thermal site.

    PubMed

    Frolov, Evgenii N; Kublanov, Ilya V; Toshchakov, Stepan V; Samarov, Nazar I; Novikov, Andrei A; Lebedinsky, Alexander V; Bonch-Osmolovskaya, Elizaveta A; Chernyh, Nikolai A

    2016-12-20

    A new obligately anaerobic sulfate-reducing microorganism, strain 3127-1T, was isolated from geothermally heated soil (Oil Site, Uzon Caldera, Kamchatka, Russia). The new isolate was a moderately thermoacidophilic anaerobe able to grow on H2 or formate by sulfate or thiosulfate respiration. The pH range for growth was 3.7 - 6.5, with an optimum at 4.8-5.0. The temperature range for growth was 37 - 65 °C, with an optimum at 55 °C. The G+C content of genomic DNA was 33.7%. The genome of strain 3127-1T contained two almost identical 16S rRNA genes, differing by a single nucleotide substitution. The closest 16S rRNA gene sequence of a validly published species belonged to Thermodesulfobium narugense Na82T (99.5% identity). However, the average nucleotide identity of genomes of strain 3127-1T and T. narugense Na82T and the predicted DNA-DNA hybridization value (GGDC 2.1 BLAST+, formula 2) were as low as 86% and 32.5 ± 2.5%, respectively. This, together with phenotypic data, showed the new isolate to belong to a new species, for which we propose the name Thermodesulfobium acidiphilum sp. nov., with the type strain 3127-1T (=DSM 102892 T =VKM B-3043 T).

  12. Interactions of polyacrylamides used for enhanced oil recovery and reservoir isolates of the sulfate-reducing bacterium Desulfovibrio

    SciTech Connect

    Sewell, G.W.

    1987-01-01

    The interactions of partially hydrolyzed polyacrylamides utilized in enhanced oil recovery as mobility control agents and reservoir isolates of Desulfovibrio were examined. Produced waters from reservoirs undergoing polymer flooding were sampled to determine the presence and numbers of sulfate-reducing bacteria. The influence of polyacrylamide on the growth of Desulfovibrio under a number of conditions was studied. Brookfield viscosity and screen factor measurements were used to screen for adverse changes in the rheological properties of polyacrylamide solutions which had been exposed to Desulfovibrio. Partially hydrolyzed polyacrylamides stimulated the growth of Desulfovibrio under laboratory conditions. The polymer may act as a nitrogen source or as an incomplete substrate under certain conditions, but is apparently not utilizable as a carbon source. Desulfovibrio caused a loss in screen factor of polyacrylamide solutions under anaerobic conditions, but no significant loss in solution viscosity was observed. No decrease in polymer concentration was detected. Labelled polyacrylamide was not incorporated in Desulfovibrio. The authors conclude that the observed screen factor losses are probably not the result of enzymatic degradation of the polymer, and are most likely a physical/chemical interaction of polymer molecules with some product of Desulfovibrio metabolism.

  13. 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

  14. 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.

  15. 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.

  16. Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide

    PubMed Central

    Strittmatter, Axel W; Liesegang, Heiko; Rabus, Ralf; Decker, Iwona; Amann, Judith; Andres, Sönke; Henne, Anke; Fricke, Wolfgang Florian; Martinez-Arias, Rosa; Bartels, Daniela; Goesmann, Alexander; Krause, Lutz; Pühler, Alfred; Klenk, Hans-Peter; Richter, Michael; Schüler, Margarete; Glöckner, Frank Oliver; Meyerdierks, Anke; Gottschalk, Gerhard; Amann, Rudolf

    2009-01-01

    Sulfate-reducing bacteria (SRB) belonging to the metabolically versatile Desulfobacteriaceae are abundant in marine sediments and contribute to the global carbon cycle by complete oxidation of organic compounds. Desulfobacterium autotrophicum HRM2 is the first member of this ecophysiologically important group with a now available genome sequence. With 5.6 megabasepairs (Mbp) the genome of Db. autotrophicum HRM2 is about 2 Mbp larger than the sequenced genomes of other sulfate reducers (SRB). A high number of genome plasticity elements (> 100 transposon-related genes), several regions of GC discontinuity and a high number of repetitive elements (132 paralogous genes Mbp−1) point to a different genome evolution when comparing with Desulfovibrio spp. The metabolic versatility of Db. autotrophicum HRM2 is reflected in the presence of genes for the degradation of a variety of organic compounds including long-chain fatty acids and for the Wood–Ljungdahl pathway, which enables the organism to completely oxidize acetyl-CoA to CO2 but also to grow chemolithoautotrophically. The presence of more than 250 proteins of the sensory/regulatory protein families should enable Db. autotrophicum HRM2 to efficiently adapt to changing environmental conditions. Genes encoding periplasmic or cytoplasmic hydrogenases and formate dehydrogenases have been detected as well as genes for the transmembrane TpII-c3, Hme and Rnf complexes. Genes for subunits A, B, C and D as well as for the proposed novel subunits L and F of the heterodisulfide reductases are present. This enzyme is involved in energy conservation in methanoarchaea and it is speculated that it exhibits a similar function in the process of dissimilatory sulfate reduction in Db. autotrophicum HRM2. PMID:19187283

  17. Anaerobic degradation pathway of linear Alkylbenzene sulfonates (LAS) in sulfate-reducing marine sediments.

    PubMed

    Lara-Martín, Pablo A; Gómez-Parra, Abelardo; Sanz, José Luis; González-Mazo, Eduardo

    2010-03-01

    Linear alkylbenzene sulfonates (LAS) are among the principal synthetic surfactants used worldwide. Their presence in the environment has been reported in a significant number of studies, and it has been generally assumed that LAS are not biotransformed in the absence of oxygen. However, laboratory experiments performed by our group using anoxic marine sediments have reported LAS degradation percentages that can reach up to 79% in 165 days. Here, we show for the first time the initial reaction metabolites (generated via fumarate addition to the LAS molecules), their biotransformation into sulfophenyl carboxylic acids (SPC), and the progressive degradation of these by successive beta-oxidation reactions. Advanced mass spectrometry has been used to carry out the identification of these compounds. This is the first time that an anaerobic degradation pathway for LAS is described, and these results represent a significant advance in understanding the final fate of these and other similar compounds in anoxic environments.

  18. Impact of copper on the abundance and diversity of sulfate-reducing prokaryotes in two chilean marine sediments.

    PubMed

    Besaury, Ludovic; Ouddane, Baghdad; Pavissich, Juan Pablo; Dubrulle-Brunaud, Carole; González, Bernardo; Quillet, Laurent

    2012-10-01

    We studied the abundance and diversity of the sulfate-reducing prokaryotes (SRPs) in two 30-cm marine chilean sediment cores, one with a long-term exposure to copper-mining residues, the other being a non-exposed reference sediment. The abundance of SRPs was quantified by qPCR of the dissimilatory sulfite reductase gene β-subunit (dsrB) and showed that SRPs are sensitive to high copper concentrations, as the mean number of SRPs all along the contaminated sediment was two orders of magnitude lower than in the reference sediment. SRP diversity was analyzed by using the dsrB-sequences-based PCR-DGGE method and constructing gene libraries for dsrB-sequences. Surprisingly, the diversity was comparable in both sediments, with dsrB sequences belonging to Desulfobacteraceae, Syntrophobacteraceae, and Desulfobulbaceae, SRP families previously described in marine sediments, and to a deep branching dsrAB lineage. The hypothesis of the presence of horizontal transfer of copper resistance genes in the microbial population of the polluted sediment is discussed.

  19. 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

  20. 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.

  1. Genome analysis of Desulfotomaculum gibsoniae strain Groll(T) a highly versatile Gram-positive sulfate-reducing bacterium.

    PubMed

    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

    2014-06-15

    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 Groll(T) 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.

  2. Antimicrobial activity and determination of bioactive components from marine Alcaligenes faecalis extract against a sulfate-reducing bacteria

    NASA Astrophysics Data System (ADS)

    AbdSharad, Ali; Usup, Gires; Sahrani, Fathul Karim; Ahmad, Asmat

    2016-11-01

    Biogenic souring and microbial-influenced corrosion is a common scenario in petroleum reservoir. The serious threat normally comes from sulfate-reducing bacteria (SRB). Alcaligenes faecalis was tested in this study for the ability to inhibit the growth of SRB. Ethyl acetate extraction of A. faecalis grown in marine broth was carried out to produce crude ethyl acetate of A. faecalis (CEAF). CEAF was diluted at concentrations 0.2-12.8 mg/mL and was tested for anti-microbial activity by microdilution susceptibility tests in 96-wells plate. CEAF was then analyzed by Gas Chromatography Mass Spectrometry (GC-MS). The microdilution susceptibility tests showed that the crude have anti- microbial activities on SRB. CEAF showed immediate killing effect against SRB in liquid medium which suggest the presence of active chemical compounds with antimicrobial activity. The GC-MS analysis showed the presence of 20 different chemical compounds in CEAF, The major components in CEAF can be related to antimicrobial, antifungal, antioxidant, pesticide, metabolism, toxicity, anticancer and corrosion inhibition activities. In conclusion, crude ethyl acetate extract of A. faecalis has the ability to inhibit SRB growth.

  3. Desulfoplanes formicivorans gen. nov., sp. nov., a novel sulfate-reducing bacterium isolated from a blackish meromictic lake, and emended description of the family Desulfomicrobiaceae.

    PubMed

    Watanabe, Miho; Kojima, Hisaya; Fukui, Manabu

    2015-06-01

    A novel sulfate-reducing bacterium, designated strain Pf12BT, was isolated from sediment of meromictic Lake Harutori in Japan. Cells were vibroid (1.0 × 3.0-4.0 μm), motile and Gram-stain-negative. For growth, the optimum pH was 7.0-7.5 and the optimum temperature was 42-45 °C. Strain Pf12BT used sulfate, thiosulfate and sulfite as electron acceptors. The G+C content of the genomic DNA was 55.4 mol%. Major cellular fatty acids were C16 : 0 and C18 : 0. The strain was desulfoviridin-positive. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel strain belonged to the order Desulfovibrionales in the class Deltaproteobacteria. The closest relative was Desulfomicrobium baculatum DSM 4028T with which it shared 91 % 16S rRNA gene sequence similarity. On the basis of phylogenetic and phenotypic characterization, a novel species of a new genus belonging to the family Desulfomicrobiaceae is proposed, Desulfoplanes formicivorans gen. nov., sp. nov. The type strain of Desulfoplanes formicivorans is Pf12BT ( = NBRC 110391T = DSM 28890T).

  4. Isolation and characterization of a mesophilic heavy-metals-tolerant sulfate-reducing bacterium Desulfomicrobium sp. from an enrichment culture using phosphogypsum as a sulfate source.

    PubMed

    Azabou, Samia; Mechichi, Tahar; Patel, Bharat K C; Sayadi, Sami

    2007-02-09

    A sulfate-reducing bacterium, was isolated from a 6 month trained enrichment culture in an anaerobic media containing phosphogypsum as a sulfate source, and, designated strain SA2. Cells of strain SA2 were rod-shaped, did not form spores and stained Gram-negative. Phylogenetic analysis of the 16S rRNA gene sequence of the isolate revealed that it was related to members of the genus Desulfomicrobium (average sequence similarity of 98%) with Desulfomicrobium baculatum being the most closely related (sequence similarity of 99%). Strain SA2 used thiosulfate, sulfate, sulfite and elemental sulfur as electron acceptors and produced sulfide. Strain SA2 reduced sulfate contained in 1-20g/L phosphogypsum to sulfide with reduction of sulfate contained in 2g/L phosphogypsum being the optimum concentration. Strain SA2 grew with metalloid, halogenated and non-metal ions present in phosphogypsum and with added high concentrations of heavy metals (125ppm Zn and 100ppm Ni, W, Li and Al). The relative order for the inhibitory metal concentrations, based on the IC(50) values, was Cu, Te>Cd>Fe, Co, Mn>F, Se>Ni, Al, Li>Zn.

  5. Desulfotomaculum arcticum sp. nov., a novel spore-forming, moderately thermophilic, sulfate-reducing bacterium isolated from a permanently cold fjord sediment of Svalbard.

    PubMed

    Vandieken, Verona; Knoblauch, Christian; Jørgensen, Bo Barker

    2006-04-01

    Strain 15T is a novel spore-forming, sulfate-reducing bacterium isolated from a permanently cold fjord sediment of Svalbard. Sulfate could be replaced by sulfite or thiosulfate. Hydrogen, formate, lactate, propionate, butyrate, hexanoate, methanol, ethanol, propanol, butanol, pyruvate, malate, succinate, fumarate, proline, alanine and glycine were used as electron donors in the presence of sulfate. Growth occurred with pyruvate as sole substrate. Optimal growth was observed at pH 7.1-7.5 and concentrations of 1-1.5 % NaCl and 0.4 % MgCl2. Strain 15T grew between 26 and 46.5 degrees C and optimal growth occurred at 44 degrees C. Therefore, strain 15T apparently cannot grow at in situ temperatures of Arctic sediments from where it was isolated, and it was proposed that it was present in the sediment in the form of spores. The DNA G+C content was 48.9 mol%. Strain 15T was most closely related to Desulfotomaculum thermosapovorans MLF(T) (93.5 % 16S rRNA gene sequence similarity). Strain 15T represents a novel species, for which the name Desulfotomaculum arcticum sp. nov. is proposed. The type strain is strain 15T (=DSM 17038T = JCM 12923T).

  6. Sulfate-reducing bacteria in marine sediment (Aarhus Bay, Denmark): abundance and diversity related to geochemical zonation.

    PubMed

    Leloup, Julie; Fossing, Henrik; Kohls, Katharina; Holmkvist, Lars; Borowski, Christian; Jørgensen, Bo Barker

    2009-05-01

    In order to better understand the main factors that influence the distribution of sulfate-reducing bacteria (SRB), their population size and their metabolic activity in high- and low-sulfate zones, we studied the SRB diversity in 3- to 5-m-deep sediment cores, which comprised the entire sulfate reduction zone and the upper methanogenic zone. By combining EMA (ethidium monoazide that can only enter damaged/dead cells and may also bind to free DNA) treatment with real-time PCR, we determined the distributions of total intact bacteria (16S rDNA genes) and intact SRB (dsrAB gene), their relative population sizes, and the proportion of dead cells or free DNA with depth. The abundance of SRB corresponded in average to 13% of the total bacterial community in the sulfate zone, 22% in the sulfate-methane transition zone and 8% in the methane zone. Compared with the total bacterial community, there were relatively less dead/damaged cells and free DNA present than among the SRB and this fraction did not change systematically with depth. By DGGE analysis, based on the amplification of the dsrA gene (400 bp), we found that the richness of SRB did not change with depth through the geochemical zones; but the clustering was related to the chemical zonation. A full-length clone library of the dsrAB gene (1900 bp) was constructed from four different depths (20, 110, 280 and 500 cm), and showed that the dsrAB genes in the near-surface sediment (20 cm) was mainly composed of sequences close to the Desulfobacteraceae, including marine complete and incomplete oxidizers such as Desulfosarcina, Desulfobacterium and Desulfococcus. The three other libraries were predominantly composed of Gram-positive SRB.

  7. Desulfonauticus autotrophicus sp. nov., a novel thermophilic sulfate-reducing bacterium isolated from oil-production water and emended description of the genus Desulfonauticus.

    PubMed

    Mayilraj, Shanmugam; Kaksonen, Anna H; Cord-Ruwisch, Ralf; Schumann, Peter; Spröer, Cathrin; Tindall, Brian J; Spring, Stefan

    2009-03-01

    A novel moderately thermophilic and halophilic sulfate-reducing bacterium, strain TeSt(T), was isolated from production water of an oil field in Northern Germany near Hamburg. The cells were Gram-negative, straight to slightly curved rods and motile by a single polar flagellum. Only hydrogen and formate served as electron donors, whereas a wide variety of organic substrates and CO(2) could be used as carbon sources. Sulfate, sulfite, thiosulfate and sulfur were used as electron acceptors, but not nitrate or ferric iron. The novel isolate was negative for oxidase, catalase and desulfoviridin enzyme activity. Cytochromes were present and predominantly of the c-type. Whole-cells fatty acid patterns were dominated by the branched-chain fatty acids anteiso-C(15:0), iso-C(15:0), iso-C(17:0) and anteiso-C(17:0). As major respiratory lipoquinones partially saturated derivates of menaquinone 6 [MK-6(H(2)) and probably MK-6(H(4))] were identified. The G + C content of the genomic DNA was 41.3 mol% (HPLC method). An analysis of the 16S rRNA gene sequence indicated that strain TeSt(T) belongs to the family Desulfohalobiaceae within the class Deltaproteobacteria. The most closely related species with a sequence similarity of 95.0% was Desulfonauticus submarinus suggesting an affiliation of TeSt(T) to the genus Desulfonauticus. The novel isolate could be clearly distinguished from Desulfonauticus submarinus by its ability to grow chemolithoautotrophically and hence should be assigned to a novel species for which the name Desulfonauticus autotrophicus sp. nov. is proposed. The type strain is TeSt(T) (=DSM 4206(T)=JCM 13028(T)).

  8. Gene Expression by the Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough Grown on an Iron Electrode under Cathodic Protection Conditions▿ †

    PubMed Central

    Caffrey, Sean M.; Park, Hyung Soo; Been, Jenny; Gordon, Paul; Sensen, Christoph W.; Voordouw, Gerrit

    2008-01-01

    The genome sequence of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough was reanalyzed to design unique 70-mer oligonucleotide probes against 2,824 probable protein-coding regions. These included three genes not previously annotated, including one that encodes a c-type cytochrome. Using microarrays printed with these 70-mer probes, we analyzed the gene expression profile of wild-type D. vulgaris grown on cathodic hydrogen, generated at an iron electrode surface with an imposed negative potential of −1.1 V (cathodic protection conditions). The gene expression profile of cells grown on cathodic hydrogen was compared to that of cells grown with gaseous hydrogen bubbling through the culture. Relative to the latter, the electrode-grown cells overexpressed two hydrogenases, the hyn-1 genes for [NiFe] hydrogenase 1 and the hyd genes, encoding [Fe] hydrogenase. The hmc genes for the high-molecular-weight cytochrome complex, which allows electron flow from the hydrogenases across the cytoplasmic membrane, were also overexpressed. In contrast, cells grown on gaseous hydrogen overexpressed the hys genes for [NiFeSe] hydrogenase. Cells growing on the electrode also overexpressed genes encoding proteins which promote biofilm formation. Although the gene expression profiles for these two modes of growth were distinct, they were more closely related to each other than to that for cells grown in a lactate- and sulfate-containing medium. Electrochemically measured corrosion rates were lower for iron electrodes covered with hyn-1, hyd, and hmc mutant biofilms than for wild-type biofilms. This confirms the importance, suggested by the gene expression studies, of the corresponding gene products in D. vulgaris-mediated iron corrosion. PMID:18310429

  9. Isolation and characterization of Desulfocurvus thunnarius sp. nov., a sulfate-reducing bacterium isolated from an anaerobic sequencing batch reactor treating cooking wastewater.

    PubMed

    Hamdi, Olfa; Ben Hania, Wajdi; Postec, Anne; Bartoli, Manon; Hamdi, Moktar; Bouallagui, Hassib; Fauque, Guy; Ollivier, Bernard; Fardeau, Marie-Laure

    2013-11-01

    A novel anaerobic, chemo-organotrophic, sulfate-reducing bacterium, designated strain Olac 40(T), was isolated from a Tunisian wastewater digestor. Cells were curved, motile rods or vibrios (5.0-7.0×0.5 µm). Strain Olac 40(T) grew at temperatures between 15 and 50 °C (optimum 40 °C), and between pH 5.0 and 9.0 (optimum pH 7.1). It did not require NaCl for growth but tolerated it up to 50 g l(-1) (optimum 2 g l(-1)). In the presence of sulfate or thiosulfate, strain Olac 40(T) used lactate, pyruvate and formate as energy sources. Growth was observed on H2 only in the presence of acetate as carbon source. In the presence of sulfate or thiosulfate, the end products of lactate oxidation were acetate, sulfide and CO2. Sulfate, thiosulfate and sulfite were used as terminal electron acceptors, but not elemental sulfur, nitrate or nitrite. The genomic DNA G+C content of strain Olac 40(T) was 70 mol%. The profile of polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, aminophospholipid and four phospholipids. The main fatty acids were C16 : 0, anteiso-C15 : 0 and iso-C15 : 0. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain Olac 40(T) was affiliated with the family Desulfovibrionaceae within the class Deltaproteobacteria. On the basis of 16S rRNA gene sequence comparisons and physiological characteristics, strain Olac 40(T) is proposed to be assigned to a novel species of the genus Desulfocurvus, for which the name Desulfocurvus thunnarius is proposed. The type strain is Olac 40(T) ( = DSM 26129(T) = JCM 18546(T)).

  10. Pseudodesulfovibrio indicus gen. nov., sp. nov., a piezophilic sulfate-reducing bacterium from the Indian Ocean and reclassification of four species of the genus Desulfovibrio.

    PubMed

    Cao, Junwei; Gayet, Nicolas; Zeng, Xiang; Shao, Zongze; Jebbar, Mohamed; Alain, Karine

    2016-10-01

    A novel sulfate-reducing bacterium, strain J2T, was isolated from a serpentinized peridotite sample from the Indian Ocean. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain J2T clustered with the genus Desulfovibrio within the family Desulfovibrionaceae, but it showed low similarity (87.95 %) to the type species Desulfovibrio desulfuricans DSM 642T. It was most closely related to Desulfovibrio portus MSL79T (96.96 %), followed by Desulfovibrio aespoeensis Aspo-2T (96.11 %), Desulfovibrio piezophilus C1TLV30T (96.04 %) and Desulfovibrio profundus DSM 11384T (95.17 %). Other available sequences shared less than 93.33 % 16S rRNA gene sequence similarity. Cells were Gram-staining-negative, anaerobic, motile vibrios (2-6×0.4-0.6 µm). Growth was observed at salinities ranging from 0.2 to 6 % (optimum 2.5 %), from pH 5 to 8 (optimum pH 6.5-7) and at temperatures between 9 and 40 °C (optimum 30-35 °C). J2T was piezophilic, growing optimally at 10 MPa (range 0-30 MPa). J2T used lactate, malate, pyruvate, formate and hydrogen as energy sources. Sulfate, thiosulfate, sulfite, fumarate and nitrate were used as terminal electron acceptors. Lactate and pyruvate were fermented. The main fatty acids were iso-C15 : 0, anteiso-C15 : 0, summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl) and iso-C17 : 0. The DNA G+C content of strain J2T was 63.5 mol%. The combined genotypic and phenotypic data show that strain J2T represents a novel species of a novel genus in the family Desulfovibrionaceae, for which the name Pseudodesulfovibrio indicus gen. nov., sp. nov. is proposed, with the type strain J2T (=MCCC 1A01867T = DSM 101483T). We also propose the reclassification of D. piezophilus as Pseudodesulfovibrio piezophilus comb. nov., D. profundus as Pseudodesulfovibrio profundus comb. nov., D. portus as Pseudodesulfovibrio portus comb. nov. and D. aespoeensis as Pseudodesulfovibrio aespoeensis comb. nov.

  11. The impact of temperature change on the activity and community composition of sulfate-reducing bacteria in arctic versus temperate marine sediments.

    PubMed

    Robador, Alberto; Brüchert, Volker; Jørgensen, Bo Barker

    2009-07-01

    Arctic regions may be particularly sensitive to climate warming and, consequently, rates of carbon mineralization in warming marine sediment may also be affected. Using long-term (24 months) incubation experiments at 0°C, 10°C and 20°C, the temperature response of metabolic activity and community composition of sulfate-reducing bacteria were studied in the permanently cold sediment of north-western Svalbard (Arctic Ocean) and compared with a temperate habitat with seasonally varying temperature (German Bight, North Sea). Short-term (35)S-sulfate tracer incubations in a temperature-gradient block (between -3.5°C and +40°C) were used to assess variations in sulfate reduction rates during the course of the experiment. Warming of arctic sediment resulted in a gradual increase of the temperature optima (T(opt)) for sulfate reduction suggesting a positive selection of psychrotolerant/mesophilic sulfate-reducing bacteria (SRB). However, high rates at in situ temperatures compared with maximum rates showed the predominance of psychrophilic SRB even at high incubation temperatures. Changing apparent activation energies (E(a)) showed that increasing temperatures had an initial negative impact on sulfate reduction that was weaker after prolonged incubations, which could imply an acclimatization response rather than a selection process of the SRB community. The microbial community composition was analysed by targeting the 16S ribosomal RNA using catalysed reporter deposition fluorescence in situ hybridization (CARD-FISH). The results showed the decline of specific groups of SRB and confirmed a strong impact of increasing temperatures on the microbial community composition of arctic sediment. Conversely, in seasonally changing sediment sulfate reduction rates and sulfate-reducing bacterial abundance changed little in response to changing temperature.

  12. 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).

  13. 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.

  14. 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.

  15. 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

  16. 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.

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

    PubMed

    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 (13)C-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.

  18. 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

  19. Fe(III)EDTA and Fe(II)EDTA-NO reduction by a sulfate reducing bacterium in NO and SO₂ scrubbing liquor.

    PubMed

    Chen, Mingxiang; Zhou, Jiti; Zhang, Yu; Wang, Xiaojun; Shi, Zhuang; Wang, Xiaowei

    2015-03-01

    A viable process concept, based on NO and SO2 absorption into an alkaline Fe(II)EDTA (EDTA: ethylenediaminetetraacetic acid) solution in a scrubber combined with biological reduction of the absorbed SO2 utilizing sulfate reducing bacteria (SRB) and regeneration of the scrubbing liquor in a single bioreactor, was developed. The SRB, Desulfovibrio sp. CMX, was used and its sulfate reduction performances in FeEDTA solutions and Fe(II)EDTA-NO had been investigated. In this study, the detailed regeneration process of Fe(II)EDTA solution, which contained Fe(III)EDTA and Fe(II)EDTA-NO reduction processes in presence of D. sp. CMX and sulfate, was evaluated. Fe(III)EDTA and Fe(II)EDTA-NO reduction processes were primarily biological, even if Fe(III)EDTA and Fe(II)EDTA-NO could also be chemically convert to Fe(II)EDTA by biogenic sulfide. Regardless presence or absence of sulfate, more than 87 % Fe(III)EDTA and 98 % Fe(II)EDTA-NO were reduced in 46 h, respectively. Sulfate and Fe(III)EDTA had no affection on Fe(II)EDTA-NO reduction. Sulfate enhanced final Fe(III)EDTA reduction. Effect of Fe(III)EDTA on Fe(II)EDTA-NO reduction rate was more obvious than effect of sulfate on Fe(II)EDTA-NO reduction rate before 8 h. To overcome toxicity of Fe(II)EDTA-NO on SRB, Fe(II)EDTA-NO was reduced first and the reduction of Fe(III)EDTA and sulfate occurred after 2 h. First-order Fe(II)EDTA-NO reduction rate and zero-order Fe(III)EDTA reduction rate were detected respectively before 8 h.

  20. 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.

  1. Alkane biodegradation and dynamics of phylogenetic subgroups of sulfate-reducing bacteria in an anoxic coastal marine sediment artificially contaminated with oil.

    PubMed

    Miralles, Gilles; Grossi, Vincent; Acquaviva, Monique; Duran, Robert; Claude Bertrand, Jean; Cuny, Philippe

    2007-07-01

    For 503 days, unoiled control and artificially oiled sediments were incubated in situ at 20m water depth in a Mediterranean coastal area. Degradation of the aliphatic fraction of the oil added was followed by GC-MS. At the same time, terminal restriction fragment length polymorphism (T-RFLP) of 16S rRNA encoding genes was used to detect dynamics in the sulfate-reducing bacteria (SRB) community in response to the oil contamination. Specific polymerase chain reaction (PCR) primer sets for five generic or suprageneric groups of SRB were used for PCR amplification of DNA extracted from sediments. During the experiment, hydrocarbons from C(17) to C(30) were significantly degraded even in strictly anoxic sediment layers. Of the five SRB groups, only two groups were detected in the sediments (control and oiled), namely the Desulfococcus-Desulfonema-Desulfosarcina-like group and the Desulfovibrio-Desulfomicrobium-like group. Statistical analysis of community patterns revealed dynamic changes over time within these two groups following the contamination. Significant differences in community patterns were recorded in artificially oiled compared with control sediments. Cloning and sequencing of 16S rRNA encoding genes performed after 503 days showed that many of the most abundant sequences were closely related to hydrocarbonoclastic SRB which could have played an active role in the observed biodegradation of aliphatic hydrocarbons. Results from the present study provide useful information on the dynamics of dominant SRB in heavily oil-contaminated sediments and their potential for anaerobic biodegradation for the treatment of spilled oil in anoxic marine environments.

  2. 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.

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

    SciTech Connect

    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; 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, Loanna; Woyke, Tanja; Arkin, Adam P.; Dehal, Paramvir; Chivian, Dylan; Criddle, Craig S.; Wu, Weimin; Chakraborty, Romy; Hazen, Terry C.; Fields, Matthew W.

    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.

  4. 5'-MGB probes allow rapid identification of methanogens and sulfate reducers in cold marine sediments by real-time PCR and melting curve analysis.

    PubMed

    Afonina, Irina; Savvichev, Alexander; Ankoudinova, Irina; Mahoney, Walt

    2009-09-01

    The analysis of microorganism communities in uncultured environmental samples requires laborious and cumbersome techniques such as denaturing gradient gel electrophoresis of amplicons generated with 16S rRNA generic primers with subsequent fragment sequencing. We have developed a simple method for genus identification of methanogen archaea and sulfate-reducing bacteria based on a real-time PCR hybridization probe melting curve analysis. The method takes advantage of a recent explosion of microorganism sequencing data conveniently packaged in the Ribosomal Database Project. Specificity of detection is based on a genus-specific real-time PCR fluorescent 5'-MGB-probe melt. As the probes are designed to have destabilizing mismatches with undesired genera, only samples with a proper melting temperature are called positive.

  5. 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

  6. 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.

  7. Uranium Immobilization by Sulfate-reducing Biofilms

    SciTech Connect

    Beyenal, Haluk; Sani, Rajesh K.; Peyton, Brent M.; Dohnalkova, Alice; Amonette, James E.; Lewandowski, Zbigniew

    2004-04-01

    Hexavalent uranium [U(VI)] was immobilized using biofilms of the sulfate-reducing bacterium (SRB) Desulfovibrio desulfuricans G20. The biofilms were grown in flat-plate continuous-flow reactors using lactate as the electron donor and sulfate as the electron acceptor. U(VI) was continuously fed into the reactor for 32 weeks at a concentration of 126 íM. During this time, the soluble U(VI) was removed (between 88 and 96% of feed) from solution and immobilized in the biofilms. The dynamics of U immobilization in the sulfate-reducing biofilms were quantified by estimating: (1) microbial activity in the SRB biofilm, defined as the hydrogen sulfide (H2S) production rate and estimated from the H2S concentration profiles measured using microelectrodes across the biofilms; (2) concentration of dissolved U in the solution; and (3) the mass of U precipitated in the biofilm. Results suggest that U was immobilized in the biofilms as a result of two processes: (1) enzymatically and (2) chemically, by reacting with microbially generated H2S. Visual inspection showed that the dissolved sulfide species reacted with U(VI) to produce a black precipitate. Synchrotron-based U L3-edge X-ray absorption near edge structure (XANES) spectroscopy analysis of U precipitated abiotically by sodium sulfide indicated that U(VI) had been reduced to U(IV). Selected-area electron diffraction pattern and crystallographic analysis of transmission electron microscope lattice-fringe images confirmed the structure of precipitated U as being that of uraninite.

  8. 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.

  9. Isolation of an algal morphogenesis inducer from a marine bacterium.

    PubMed

    Matsuo, Yoshihide; Imagawa, Hiroshi; Nishizawa, Mugio; Shizuri, Yoshikazu

    2005-03-11

    Ulva and Enteromorpha are cosmopolitan and familiar marine algal genera. It is well known that these green macroalgae lose their natural morphology during short-term cultivation under aseptic conditions and during long-term cultivation in nutrient-added seawater and adopt an unusual form instead. These phenomena led to the belief that undefined morphogenetic factors that were indispensable to the foliaceous morphology of macroalgae exist throughout the oceans. We characterize a causative factor, named thallusin, isolated from an epiphytic marine bacterium. Thallusin induces normal germination and morphogenesis of green macroalgae.

  10. 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

    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 10(8)/g sediment close to the sediment surface to less than 10(5)/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 10(4)/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.

  11. 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.

  12. The First Genomic and Proteomic Characterization of a Deep-Sea Sulfate Reducer: Insights into the Piezophilic Lifestyle of Desulfovibrio piezophilus

    PubMed Central

    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 C1TLV30T 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

  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. Fluoroacetate biosynthesis from the marine-derived bacterium Streptomyces xinghaiensis NRRL B-24674.

    PubMed

    Huang, Sheng; Ma, Long; Tong, Ming Him; Yu, Yi; O'Hagan, David; Deng, Hai

    2014-07-21

    Genome sequencing identified a fluorinase gene in the marine bacterium Streptomyces xinghaiensis NRRL B-24674. Fermentation of the organism with inorganic fluoride (2 mM) demonstrated that the organism could biosynthesise fluoroacetate and that fluoroacetate production is sea-salt dependent. This is the first fluorometabolite producing microorganism identified from the marine environment.

  15. 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...

  16. 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.

  17. Vibrio damsela, a Marine Bacterium, Causes Skin Ulcers on the Damselfish Chromis punctipinnis.

    PubMed

    Love, M; Teebken-Fisher, D; Hose, J E; Farmer, J J; Hickman, F W; Fanning, G R

    1981-12-04

    A previously undescribed marine bacterium, Vibrio damsela, was isolated from naturally occurring skin ulcers on a species of temperate-water damselfish, the blacksmith (Chromis punctipinnis). Laboratory infection of the blacksmith with Vibrio damsela produced similar ulcers. Vibrio damsela was pathogenic for four other species of damselfish but not for members of other families of fish. The bacterium has also been isolated from water and from two human wounds and may be a cause of human disease.

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

    SciTech Connect

    Teske, A.; Ramsing, N.B.; Habicht, K.; Kuever, J.; Joergensen, B.B.; Fukui, Manabu; 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{sup 6} and 10{sup 7} cultivable sulfate-reducing bacteria ml{sup {minus}1} day{sup {minus}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{sup 4} and 10{sup 6} cells ml{sup {minus}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 CO{sub 2} from sulfate reduction in the upper 5 mm accounted for 7 to 8% of the total photosynthetic CO{sub 2} demand of the mat.

  19. Pseudomonas natriegens, a marine bacterium with a generation time of less than 10 minutes.

    PubMed

    EAGON, R G

    1962-04-01

    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.

  20. 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.

  1. Impact of elevated nitrate on sulfate-reducing bacteria: a comparative study of Desulfovibrio vulgaris.

    PubMed

    He, Qiang; He, Zhili; Joyner, Dominique C; Joachimiak, Marcin; Price, Morgan N; Yang, Zamin K; Yen, Huei-Che Bill; Hemme, Christopher L; Chen, Wenqiong; Fields, Matthew M; Stahl, David A; Keasling, Jay D; Keller, Martin; Arkin, Adam P; Hazen, Terry C; Wall, Judy D; Zhou, Jizhong

    2010-11-01

    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(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.

  2. 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.

  3. Polaromonas vacuolata gen. nov., sp. nov., a psychrophilic, marine, gas vacuolate bacterium from Antarctica.

    PubMed

    Irgens, R L; Gosink, J J; Staley, J T

    1996-07-01

    Several strains of a novel heterotrophic gas vacuolate bacterium were isolated from antarctic marine waters. The results of phylogenetic analyses in which 16S ribosomal DAN sequencing was used, coupled with phenotypic tests, indicated that strain 34-P(T) (T = type strain) belongs to a new genus and species of the beta subgroup of the Proteobacteria, for which the name Polaromonas vacuolata is proposed. Although the other four strains studied probably belong to this new species, DNA-DNA hybridization tests were not conducted. The closest phylogenetic relatives of P. vacuolata are the photosynthetic nonsulfur purple bacterium Rhodoferax fermentans and the hydrogen autotroph Variovorax paradoxus.

  4. Mutualistic growth of the sulfate-reducer Desulfovibrio vulgaris Hildenborough with different carbohydrates.

    PubMed

    Santana, M M; Portillo, M C; Gonzalez, J M

    2012-01-01

    Desulfovibrio vulgaris Hildenborough genome presents a phosphotransferase system putatively involved in the transport of carbohydrates. However, utilization of sugars by this sulfate-reducing bacterium has never been reported. Herein, we have observed proliferation of D. vulgaris Hildenborough with some carbohydrates, in mutualism with Stenotrophomonas maltophilia, a non-fermentative, gram-negative gammaproteobacterium, or Microbacterium, a gram-positive actinobacterium. These results suggest the importance of feedback interactions between different heterotrophic bacterial species including the alternative for D. vulgaris of exploiting additional organic resources and novel habitats. Thus, D. vulgaris strongly participates in the mineralization of carbohydrates both in complex natural and artificial systems.

  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. Cyclobacterium halophilum sp. nov., a marine bacterium isolated from a coastal-marine wetland.

    PubMed

    Shahinpei, Azadeh; Amoozegar, Mohammad Ali; Sepahy, Abbas Akhavan; Schumann, Peter; Ventosa, Antonio

    2014-03-01

    A novel Gram-stain-negative, slightly halophilic bacterium, designated strain GASx41(T), was isolated from soil of the coastal-marine wetland Gomishan in Iran. Cells of strain GASx41(T) were curved, ring-like or horseshoe-shaped rods and non-motile. Strain GASx41(T) was strictly aerobic, and catalase- and oxidase-positive. The strain was able to grow at NaCl concentrations of 1-10% (w/v), with optimum growth occurring at 2.5-3% (w/v) NaCl. The optimum temperature and pH for growth were 25-30 °C and pH 7.5-8.0. On the basis of 16S rRNA gene sequence analysis, strain GASx41(T) was shown to belong to the genus Cyclobacterium within the phylum Bacteroidetes and showed closest phylogenetic similarity to 'Cyclobacterium jeungdonense' HMD3055 (98.0%). The DNA G+C content of strain GASx41(T) was 48.1 mol%. The major cellular fatty acids of strain GASx41(T) were iso-C15 : 0, summed feature 4 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), anteiso-C15 : 0 2-OH, anteiso-C15 : 0 and iso-C17 : 0 3-OH, and its polar lipid pattern consisted of phosphatidylethanolamine, phosphatidylcholine and 12 unknown lipids. The only quinone present was menaquinone 7 (MK-7). All these features confirmed the placement of isolate GASx41(T) within the genus Cyclobacterium. On the basis of evidence from this study, a novel species of the genus Cyclobacterium, Cyclobacterium halophilum sp. nov., is proposed, with strain GASx41(T) ( = IBRC-M 10761(T) = CECT 8341(T)) as the type strain.

  7. Pseudomonas creosotenesis sp. n., a Creosote-tolerant Marine Bacterium

    PubMed Central

    O'Neill, Thomas B.; Drisko, Richard W.; Hochman, Harry

    1961-01-01

    In a study of the marine biological environment in which creosoted pilings are located, a previously unreported species of bacteria was isolated. This species was detected on creosoted piling from 11 widely differing locations and was the predominant species of bacteria found on these piling. The new organism was identified as a gram-negative rod belonging to the genus Pseudomonas and has been named Pseudomonas creosotensis. It has been completely described by the standard morphological and biochemical tests. Images FIG. 1 PMID:14480909

  8. A Chloroflexi bacterium dechlorinates polychlorinated biphenyls in marine sediments under in situ-like biogeochemical conditions.

    PubMed

    Zanaroli, Giulio; Balloi, Annalisa; Negroni, Andrea; Borruso, Luigimaria; Daffonchio, Daniele; Fava, Fabio

    2012-03-30

    We investigated the reductive dechlorination of Aroclor 1254 PCBs by a coplanar PCB-dechlorinating microbial community enriched from an actual site contaminated marine sediment of the Venice lagoon in sterile slurry microcosms of the same sediment suspended in its site water, i.e., under biogeochemical conditions that closely mime those occurring in situ. The culture dechlorinated more than 75% of the penta- through hepta-chlorinated biphenyls to tri- and tetra-chlorinated congeners in 30 weeks. The dechlorination rate was reduced by the addition of H(2) and short chain fatty acids, which stimulated sulfate-reduction and methane production, and markedly increased by the presence of vancomycin or ampicillin. DGGE analysis of 16S rRNA genes on PCB-spiked and PCB-free cultures ruled out sulfate-reducing and methanogenic bacteria and revealed the presence of a single Chloroflexi phylotype closely related to the uncultured bacteria m-1 and SF1 associated to PCB dechlorination. These findings suggest that a single dechlorinator is responsible for the observed extensive dechlorination of Aroclor 1254 and that a Chloroflexi species similar to those already detected in freshwater and estuarine contaminated sediments mediates PCB dechlorination in the marine sediment adopted in this study under biogeochemical conditions resembling those occurring in situ in the Brentella Canal of Venice Lagoon.

  9. 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

  10. Cadherin domains in the polysaccharide-degrading marine bacterium Saccharophagus degradans 2-40 are carbohydrate-binding modules.

    PubMed

    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.

  11. Draft Genome Sequence of Agarivorans albus Strain MKT 106T, an Agarolytic Marine Bacterium.

    PubMed

    Yasuike, Motoshige; Nakamura, Yoji; Kai, Wataru; Fujiwara, Atushi; Fukui, Youhei; Satomi, Masataka; Sano, Motohiko

    2013-07-18

    Agarivorans albus is a Gram-negative, strictly aerobic, and agar-hydrolyzing marine bacterium. We present the draft genome sequence of the A. albus strain MKT 106(T), which is composed of 67 contigs (>500 bp) totaling 4,734,285 bp and containing 4,397 coding DNA sequences (CDSs), four rRNAs, and 64 tRNA sequences.

  12. Genomic Analysis of a Marine Bacterium: Bioinformatics for Comparison, Evaluation, and Interpretation of DNA Sequences

    PubMed Central

    Khobragade, Chandrahasya N.

    2016-01-01

    A total of five highly related strains of an unidentified marine bacterium were analyzed through their short genome sequences (AM260709–AM260713). Genome-to-Genome Distance (GGDC) showed high similarity to Pseudoalteromonas haloplanktis (X67024). The generated unique Quick Response (QR) codes indicated no identity to other microbial species or gene sequences. Chaos Game Representation (CGR) showed the number of bases concentrated in the area. Guanine residues were highest in number followed by cytosine. Frequency of Chaos Game Representation (FCGR) indicated that CC and GG blocks have higher frequency in the sequence from the evaluated marine bacterium strains. Maximum GC content for the marine bacterium strains ranged 53-54%. The use of QR codes, CGR, FCGR, and GC dataset helped in identifying and interpreting short genome sequences from specific isolates. A phylogenetic tree was constructed with the bootstrap test (1000 replicates) using MEGA6 software. Principal Component Analysis (PCA) was carried out using EMBL-EBI MUSCLE program. Thus, generated genomic data are of great assistance for hierarchical classification in Bacterial Systematics which combined with phenotypic features represents a basic procedure for a polyphasic approach on unambiguous bacterial isolate taxonomic classification. PMID:27882328

  13. Substrate dependent production of extracellular biosurfactant by a marine bacterium.

    PubMed

    Das, Palashpriya; Mukherjee, Soumen; Sen, Ramkrishna

    2009-01-01

    The potential of a marine microorganism to utilize different carbon substrates for the production of an extracellular biosurfactant was evaluated. Among the several carbon substrates tested for this purpose, production of the crude biosurfactant was found to be highest with glycerol (2.9+/-0.11 g L(-1)) followed by starch (2.5+/-0.11 g L(-1)), glucose (1.16+/-0.11 g L(-1)) and sucrose (0.94+/-0.07 g L(-1)). The crude biosurfactant obtained from glycerol, starch and sucrose media had significantly higher antimicrobial action than those obtained from glucose containing medium. RP-HPLC resolved the crude biosurfactants into several fractions one of which had significant antimicrobial action. The antimicrobial fraction was found in higher concentrations in biosurfactant obtained using glycerol, starch and sucrose as compared to the biosurfactants from glucose medium, thereby explaining higher antimicrobial activity. The carbon substrate was thus found to affect biosurfactant production both in a qualitative and quantitative manner.

  14. 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.

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

    SciTech Connect

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

    1986-10-01

    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 ..mu..mol/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.

  16. 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

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

    PubMed Central

    Liu, Bing; Bian, Chao; Huang, Huiwei; Yin, Zhiwei

    2016-01-01

    Pseudomonas pseudoalcaligenes S1, a marine bacterium, exhibited strong resistance to a high concentration of Hg2+ and remarkable Hg2+ 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

  18. 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…

  19. Activity of sulfate-reducing bacteria under simulated reservoir conditions

    SciTech Connect

    Rosnes, J.T.; Graue, A.; Lien, T. )

    1991-05-01

    This paper reports on sulfate-reducing bacteria (SRB) that have been isolated from hot oilfield waters from subsea oil reservoirs in the North Sea. Experiments with these bacteria in a reservoir simulator indicate that SRB may maintain their activity in the conditions found in most North Sea reservoirs and, if precautions are not taken, may contribute to souring of the oil and gas.

  20. 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

  1. Localized sulfate-reducing zones in a coastal plain aquifer

    USGS Publications Warehouse

    Brown, C.J.; Coates, J.D.; Schoonen, M.A.A.

    1999-01-01

    High concentrations of dissolved iron in ground water of coastal plain or alluvial aquifers contribute to the biofouling of public supply wells for which treatment and remediation is costly. Many of these aquifers, however, contain zones in which microbial sulfate reduction and the associated precipitation of iron-sulfide minerals decreases iron mobility. The principal water-bearing aquifer (Magothy Aquifer of Cretaceous age) in Suffolk County, New York, contains localized sulfate-reducing zones in and near lignite deposits, which generally are associated with clay lenses. Microbial analyses of core samples amended with [14C]-acetate indicate that microbial sulfate reduction is the predominant terminal-electron-accepting process (TEAP) in poorly permeable, lignite-rich sediments at shallow depths and near the ground water divide. The sulfate-reducing zones are characterized by abundant lignite and iron-sulfide minerals, low concentrations of Fe(III) oxyhydroxides, and by proximity to clay lenses that contain pore water with relatively high concentrations of sulfate and dissolved organic carbon. The low permeability of these zones and, hence, the long residence time of ground water within them, permit the preservation and (or) allow the formation of iron-sulfide minerals, including pyrite and marcasite. Both sulfate-reducing bacteria (SRB) and iron-reducing bacteria (IRB) are present beneath and beyond the shallow sulfate-reducing zones. A unique Fe(III)-reducing organism, MD-612, was found in core sediments from a depth of 187 m near the southern shore of Long Island. The distribution of poorly permeable, lignite-rich, sulfate-reducing zones with decreased iron concentration is varied within the principal aquifer and accounts for the observed distribution of dissolved sulfate, iron, and iron sulfides in the aquifer. Locating such zones for the placement of production wells would be difficult, however, because these zones are of limited aerial extent.

  2. 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

  3. 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

  4. Genome Sequence of the Marine Bacterium Vibrio campbellii DS40M4, Isolated from Open Ocean Water

    PubMed Central

    Dias, Graciela M.; Thompson, Cristiane C.; Fishman, Brian; Naka, Hiroaki; Haygood, Margo G.; Crosa, Jorge H.

    2012-01-01

    Vibrio sp. strain DS40M4 is a marine bacterium that was isolated from open ocean water. In this work, using genomic taxonomy, we were able to classify this bacterium as V. campbellii. Our genomic analysis revealed that V. campbellii DS40M4 harbors genes related to iron transport, virulence, and environmental fitness, such as those encoding anguibactin and vanchrobactin biosynthesis proteins, type II, III, IV, and VI secretion systems, and proteorhodopsin. PMID:22275102

  5. 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

  6. 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.

  7. 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.

  8. Physiology and ecology of bacteriophages of the marine bacterium Beneckea natriegens: salinity.

    PubMed Central

    Zachary, A

    1976-01-01

    The effects of variation in ionic levels on the stability and replication of two bacteriophages (nt-1 and nt-6) host specific for the marine bacterium Beneckea natriegens were examined. Monovalent cations influenced the adsorption of the nt-1 but not the nt-6 phage; however, one-step growth studies showed that NaCl was required for replication of both phage. The NaCl optimum for nt-1 production was 0.25 M NaCl, the same as the growth optimum for B. natriegens. However, the optimum for nt-6 production was 0.16 M NaCl. These NaCl optima for host and phage are at estuarine rather than oceanic levels. The nt-1 phage was better suited to replicate at NaCl levels typical of higher salinity areas (18-35%) and the nt-6 phage was better suited to replicate at lower salinities (5-18%). The nt phage were more resistant to low NaCl levels than their host bacterium and appeared limited to marine waters by the lower survival salinity of B. natriegens coupled with phage inactivation processes occurring in natural estuarine waters. Images PMID:938035

  9. 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.

  10. 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.

  11. Discovery of a marine bacterium producing 4-hydroxybenzoate and its alkyl esters, parabens.

    PubMed

    Peng, Xue; Adachi, Kyoko; Chen, Choryu; Kasai, Hiroaki; Kanoh, Kaneo; Shizuri, Yoshikazu; Misawa, Norihiko

    2006-08-01

    Chemically synthesized 4-hydroxybenzoate (4HBA) is widely used in the chemical and electrical industries as a material for producing polymers such as those of the liquid crystal type. Its alkyl esters, called parabens, have been the most widely used preservatives by the food and cosmetic industries. We report here for the first time a microorganism, a marine bacterium, which biosynthesizes these petrochemical products. The marine bacterial strain, A4B-17, which was found to belong to the genus Microbulbifer on the basis of its rRNA and gyrB sequences, was isolated from an ascidian in the coastal waters of Palau. Strain A4B-17 was, surprisingly, found to produce 10 mg/liter of 4HBA, together with its butyl (24 mg/liter), heptyl (0.4 mg/liter), and nonyl (6 mg/liter) esters. We therefore characterized 23 other marine bacteria belonging to the genus Microbulbifer, which our institute had previously isolated from various marine environments, and found that these bacteria also produced 4HBA, although with low production levels (less than one-fifth of that produced by A4B-17). We also show that the alkyl esters of 4HBA produced by strain A4B-17 were effective in preventing the growth of yeasts, molds, and gram-positive bacteria.

  12. 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.

  13. Transcriptional Changes Underlying Elemental Stoichiometry Shifts in a Marine Heterotrophic Bacterium

    PubMed Central

    Chan, Leong-Keat; Newton, Ryan J.; Sharma, Shalabh; Smith, Christa B.; Rayapati, Pratibha; Limardo, Alexander J.; Meile, Christof; Moran, Mary Ann

    2012-01-01

    Marine bacteria drive the biogeochemical processing of oceanic dissolved organic carbon (DOC), a 750-Tg C reservoir that is a critical component of the global C cycle. Catabolism of DOC is thought to be regulated by the biomass composition of heterotrophic bacteria, as cells maintain a C:N:P ratio of ∼50:10:1 during DOC processing. Yet a complicating factor in stoichiometry-based analyses is that bacteria can change the C:N:P ratio of their biomass in response to resource composition. We investigated the physiological mechanisms of resource-driven shifts in biomass stoichiometry in continuous cultures of the marine heterotrophic bacterium Ruegeria pomeroyi (a member of the Roseobacter clade) under four element limitation regimes (C, N, P, and S). Microarray analysis indicated that the bacterium scavenged for alternate sources of the scarce element when cells were C-, N-, or P-limited; reworked the ratios of biomolecules when C- and P- limited; and exerted tighter control over import/export and cytoplasmic pools when N-limited. Under S limitation, a scenario not existing naturally for surface ocean microbes, stress responses dominated transcriptional changes. Resource-driven changes in C:N ratios of up to 2.5-fold and in C:P ratios of up to sixfold were measured in R. pomeroyi biomass. These changes were best explained if the C and P content of the cells was flexible in the face of shifting resources but N content was not, achieved through the net balance of different transcriptional strategies. The cellular-level metabolic trade-offs that govern biomass stoichiometry in R. pomeroyi may have implications for global carbon cycling if extendable to other heterotrophic bacteria. Strong homeostatic responses to N limitation by marine bacteria would intensify competition with autotrophs. Modification of cellular inventories in C- and P-limited heterotrophs would vary the elemental ratio of particulate organic matter sequestered in the deep ocean. PMID:22783226

  14. 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

  15. 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.

  16. RecA Expression in Response to Solar UVR in the Marine Bacterium Vibrio natriegens.

    PubMed

    Booth, M.G.; Jeffrey, W.H.; Miller, R.V.

    2001-12-01

    Solar ultraviolet radiation may produce daily stress on marine and estuarine communities as cells are damaged and repair that damage. Reduction in the earth's stratospheric ozone layer has increased awareness of the potential effects that ultraviolet radiation may have in the environment, including how marine bacteria respond to changes in solar radiation. We examined the use of the bacterial RecA protein as an indicator of the potential of bacteria to repair DNA damage caused by solar UV irradiation using the marine bacterium Vibrio natriegens as a model. RecA is universally present in bacteria and is a regulator protein for the so-called Dark Repair Systems, which include excision repair, postreplication recombinational repair, and mutagenic or SOS repair. Solar UVB and UVA both reduced V. natriegens viability in seawater microcosms. After exposure to unfiltered solar radiation or radiation in which UVB was blocked, survival dropped below 1%, whereas visible light from which UVA and UVB had been filtered had no effect on survival. Using a RecA-specific antibody for detection, RecA protein was induced by solar radiation in a diel pattern in marine microcosms conducted in the Gulf of Mexico. Peak induction was observed at dusk each day. Although RecA expression was correlated with the formation of UVB-induced cyclobutyl pyrimidine dimers, longer wavelength UVA radiation also induced recA gene expression. Our results demonstrate that RecA-regulated, light-independent repair is an important component in the ability of marine bacteria to survive exposure to solar ultraviolet radiation and that RecA expression is a useful monitor of bacterial repair after exposure to solar UVR.

  17. 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

  18. 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.

  19. Adhesive properties of a symbolic bacterium from a wood-boreing marine shipworm

    SciTech Connect

    Imam, S.H.; Greene, R.V.; Griffin, H.L. )

    1990-05-01

    Adhesive properties of cellulolytic, nitrogen-fixing bacterium isolated from a marine shipworm are described. {sup 35}S-labeled cells of the shipworm bacterium bound preferentially Whatman no.1 cellulose filter paper, compared with its binding to other cellulose substrata or substrata lacking cellulose. The ability of the bacteria to bind to Whatman no. 1 filter paper was significantly reduced by glutaraldehyde or heat treatment of cells. Pretreatment of cells with azide, valinomycin, gramicidin-D, bis-hexafluoroacetylacetone (1799), or carbonyl cyanide-p-trifluoromethoxyphenylhydrazone inhibited adhesion activity. Cells pretreated with pronase or trypsin also exhibited reduced binding activity, but chymotrypsin and peptidase had no effect on adhesion activity. Cellodextrins and methyl cellulose 15 inhibited the adhesion of the shipworm bacteria to filter paper, whereas glucose, cellobiose, and soluble carboxymethyl cellulose had no significant effect. The divalent cation chelators EDTA and EGTA (ethylene hlycol-bis({beta}-aminoethyl ether)-N,N,N{prime}N{prime}-tetraacetic acid) had little or no effect on adhesive properties of shipworm bacteria. Also, preabsorbing the substratum with extracellular endoglucanase isolated from the ship worm bacterium or 1% bovine serum albumin had no apparent effect on bacterial binding. Low concentration (0.01%) of sodium dodecyl sulfate solubilized a fraction from whole cells, which appeared to be involved in cellular binding activity. After removal of sodium dodecyl, sulfate, several proteins in this fraction associated with intact cells. These cells exhibited up to 50% enhanced binding to filter paper in comparison to cells which had not been exposed to the sodium dodecyl sulfate-solubilized fraction.

  20. Distinguishing iron-reducing from sulfate-reducing conditions

    USGS Publications Warehouse

    Chapelle, F.H.; Bradley, P.M.; Thomas, M.A.; McMahon, P.B.

    2009-01-01

    Ground water systems dominated by iron- or sulfate-reducing conditions may be distinguished by observing concentrations of dissolved iron (Fe2+) and sulfide (sum of H2S, HS-, and S= species and denoted here as "H2S"). This approach is based on the observation that concentrations of Fe2+ and H2S in ground water systems tend to be inversely related according to a hyperbolic function. That is, when Fe2+ concentrations are high, H2S concentrations tend to be low and vice versa. This relation partly reflects the rapid reaction kinetics of Fe2+ with H2S to produce relatively insoluble ferrous sulfides (FeS). This relation also reflects competition for organic substrates between the iron- and the sulfate-reducing microorganisms that catalyze the production of Fe2+ and H 2S. These solubility and microbial constraints operate in tandem, resulting in the observed hyperbolic relation between Fe2+ and H 2S concentrations. Concentrations of redox indicators, including dissolved hydrogen (H2) measured in a shallow aquifer in Hanahan, South Carolina, suggest that if the Fe2+/H2S mass ratio (units of mg/L) exceeded 10, the screened interval being tapped was consistently iron reducing (H2 ???0.2 to 0.8 nM). Conversely, if the Fe 2+/H2S ratio was less than 0.30, consistent sulfate-reducing (H2 ???1 to 5 nM) conditions were observed over time. Concomitantly high Fe2+ and H2S concentrations were associated with H2 concentrations that varied between 0.2 and 5.0 nM over time, suggesting mixing of water from adjacent iron- and sulfate-reducing zones or concomitant iron and sulfate reduction under nonelectron donor-limited conditions. These observations suggest that Fe2+/H2S mass ratios may provide useful information concerning the occurrence and distribution of iron and sulfate reduction in ground water systems. ?? 2009 National Ground Water Association.

  1. 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.

  2. Characterization of a Marine Bacterium Associated with Crassostrea virginica (the Eastern Oyster)

    PubMed Central

    Weiner, Ronald M.; Segall, Anca M.; Colwell, Rita R.

    1985-01-01

    A gram-negative bacterium found to be closely associated with oysters has been isolated and characterized. The organism, designated LST, has a generation time of 106 min in Marine broth under optimal growth conditions at 25°C. During the decline phase of growth, it exhibits a morphological transition from a motile rod (ca. 1 μm in length) to an elongated, 3- to 40-μm, nonmotile, tightly coiled helix. LST synthesizes and releases a pigment in the stationary and decline phases of growth. Identified as melanin on the basis of chemical properties and UV absorbance maxima, the pigment comprises polymers of heterogeneous molecular weights, ranging from 12,000 to 120,000. The guanosine-plus-cytosine content of the LST DNA is 46%, and results of phenetic analysis and DNA-DNA hybridization indicate that this bacterium represents a new species. LST adheres to a variety of surfaces, including glass, plastics, and oyster shell, and has been shown to promote the settlement of oyster larvae. Images PMID:16346712

  3. 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.

  4. Biosynthesis and characterization of polyhydroxyalkanoates in the polysaccharide-degrading marine bacterium Saccharophagus degradans ATCC 43961.

    PubMed

    González-García, Yolanda; Nungaray, Jesús; Córdova, Jesús; González-Reynoso, Orfil; Koller, Martin; Atlic, Aid; Braunegg, Gerhart

    2008-06-01

    The marine bacterium Saccharophagus degradans was investigated for the synthesis of polyhydroxyalkanoates (PHAs), using glucose as the sole source of carbon in a two-step batch culture. In the first step the microorganism grew under nutrient balanced conditions; in the second step the cells were cultivated under limitation of nitrogen source. The biopolymer accumulated in S. degradans cells was detected by Nile red staining and FT-IR analysis. From GC-MS analysis, it was found that this strain produced a homopolymer of 3-hydroxybutyric acid. The cellular polymer concentration, its molecular mass, glass transition temperature, melting point and heat of fusion were 17.2+/-2.7% of dry cell weight, 54.2+/-0.6 kDa, 37.4+/-6.0 degrees C, 165.6+/-5.5 degrees C and 59.6+/-2.2 J g(-1), respectively. This work is the first report determining the capacity of S. degradans to synthesize PHAs.

  5. Expression of multiple complex polysaccharide-degrading enzyme systems by marine bacterium strain 2-40.

    PubMed

    Ensor; Stosz; Weiner

    1999-08-01

    Saprophytic marine bacterium strain 2-40 (2-40) can degrade numerous complex polysaccharides (CP) including agar, alginic acid, carrageenan, carboxymethylcellulose, chitin, beta-glucan, laminarin, pectin, pullulan, starch, and xylan. The growth of 2-40 was assessed in minimal media containing one of 16 CP or simple carbohydrates, with the result that all supported growth. Each of the carbohydrase systems was elicited at highest levels by the homologous substrate. Each, excluding amylase, was repressed when 2-40 was cultured in glucose minimal synthetic media. Cyclic adenosine monophosphate alleviated the repression. Agarose as sole carbon source supported the synthesis of the most heterologous complex carbohydrase systems, although, generally, at a lower level of activity than the homologous CP.

  6. 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.

  7. 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

  8. 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

    2016-05-05

    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.

  9. Enhanced carboxymethylcellulase production by a newly isolated marine bacterium, Cellulophaga lytica LBH-14, using rice bran.

    PubMed

    Gao, Wa; Lee, Eun-Jung; Lee, Sang-Un; Li, Jianhong; Chung, Chung-Han; Lee, Jin-Woo

    2012-10-01

    The aim of this work was to establish the optimal conditions for production of carboxymethylcellulase (CMCase) by a newly isolated marine bacterium using response surface methodology (RSM). A microorganism producing CMCase, isolated from seawater, was identified as Cellulophaga lytica based 16S rDNA sequencing and the neighborjoining method. The optimal conditions of rice bran, ammonium chloride, and initial pH of the medium for cell growth were 100.0 g/l, 5.00 g/l, and 7.0, respectively, whereas those for production of CMCase were 79.9 g/l, 8.52 g/l, and 6.1. The optimal concentrations of K2HPO4, NaCl, MgSO4·7H2O, and (NH4)2SO4 for cell growth were 6.25, 0.62, 0.28, and 0.42 g/l, respectively, whereas those for production of CMCase were 3.72, 0.54, 0.70, and 0.34 g/l. The optimal temperature for cell growth and the CMCase production by C. lytica LBH-14 were 35 degrees C and 25 degrees C, respectively. The maximal production of CMCase under optimized condition for 3 days was 110.8 U/ml, which was 5.3 times higher than that before optimization. In this study, rice bran and ammonium chloride were developed as carbon and nitrogen sources for the production of CMCase by C. lytica LBH-14. The time for production of CMCase by a newly isolated marine bacterium with submerged fermentations reduced to 3 days, which resulted in enhanced productivity of CMCase and a decrease in its production cost.

  10. 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

  11. Effects of Ultraviolet Radiation on the Gram-positive marine bacterium Microbacterium maritypicum.

    PubMed

    Williams, Patrick D; Eichstadt, Shaundra L; Kokjohn, Tyler A; Martin, Eugene L

    2007-07-01

    Although extensive information is available on the effect ultraviolet (UV) radiation has on Gram-negative marine bacteria, there is a scarcity of data concerning UV radiation and Gram-positive marine bacteria. The focus of this paper is on Microbacterium maritypicum, with the Gram-negative Vibrio natriegens being used as a standard of comparison. M. maritypicum exhibited growth over a NaCl range of 0-1000 mM: , with optimum growth occurring between 0 and 400 mM: NaCl. In contrast, V. natriegens grew over a NaCl span of 250-1000 mM: , with best growth being observed between 250 and 600 mM: NaCl. UV radiation experiments were done using the medium with 250 mM: NaCl. For solar (UV-A and B) radiation and log-phase cells, M. maritypicum was determined to be three times more resistant than V. natriegens. For germicidal (UV-C) radiation, the pattern of resistance of the log-phase cells to the lethal effects of the radiation was even more pronounced, with the Gram-positive bacterium being more than 12 to 13 times more resistant. Similar data to the solar and germicidal log-phase UV kill curves were obtained for stationary-phase cells of both organisms. Photoreactivation was observed for both types of cells exposed to UV-C but none for cells treated with UV-A and B. When log phase cells of M.maritypicum were grown at 0.0 and 0.6 M: NaCl and exposed to UV-C radiation, no difference in survivorship patterns was noted from that of 0.25 M: NaCl grown cells. Although this study has only focused on two marine bacteria, our results indicate that the Gram-positive M. maritypicum could have a built-in advantage for survival in some marine ecosystems.

  12. 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.

  13. 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.

  14. Aurantibacter crassamenti gen. nov., sp. nov., a bacterium isolated from marine sediment.

    PubMed

    Yoon, Jaewoo; Kasai, Hiroaki

    2017-01-01

    A Gram-stain-negative, strictly aerobic, orange-colored, rod-shaped, chemoheterotrophic bacterium, designated HG732(T), was isolated from marine sediment 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 (94.1 %) sequence similarity with Kriegella aquimaris KMM 3665(T). The strain could be differentiated phenotypically from related members of the family Flavobacteriaceae. Major fatty acids of strain HG732(T) were iso-C15:1 G, iso-C15:0 and iso-C17:0 3-OH. The polar lipid profile consisted of phosphatidylglycerol, three unidentidied aminolipids and two unidentified lipids. The DNA G+C content of the strain was determined to be 35.2 mol%, and the major respiratory quinone was identified as menaquinone 6 (MK-6). From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel genus in the family Flavobacteriaceae, for which the name Aurantibacter crassamenti gen. nov., sp. nov. is proposed. The type strain of A. crassamenti gen. nov., sp. nov. is HG732(T) (= KCTC 52207(T) = NBRC 112211(T)).

  15. Hydrogen peroxide-dependent uptake of iodine by marine Flavobacteriaceae bacterium strain C-21.

    PubMed

    Amachi, Seigo; Kimura, Koh; Muramatsu, Yasuyuki; Shinoyama, Hirofumi; Fujii, Takaaki

    2007-12-01

    The cells of the marine bacterium strain C-21, which is phylogenetically closely related to Arenibacter troitsensis, accumulate iodine in the presence of glucose and iodide (I-). In this study, the detailed mechanism of iodine uptake by C-21 was determined using a radioactive iodide tracer, 125I-. In addition to glucose, oxygen and calcium ions were also required for the uptake of iodine. The uptake was not inhibited or was only partially inhibited by various metabolic inhibitors, whereas reducing agents and catalase strongly inhibited the uptake. When exogenous glucose oxidase was added to the cell suspension, enhanced uptake of iodine was observed. The uptake occurred even in the absence of glucose and oxygen if hydrogen peroxide was added to the cell suspension. Significant activity of glucose oxidase was found in the crude extracts of C-21, and it was located mainly in the membrane fraction. These findings indicate that hydrogen peroxide produced by glucose oxidase plays a key role in the uptake of iodine. Furthermore, enzymatic oxidation of iodide strongly stimulated iodine uptake in the absence of glucose. Based on these results, the mechanism was considered to consist of oxidation of iodide to hypoiodous acid by hydrogen peroxide, followed by passive translocation of this uncharged iodine species across the cell membrane. Interestingly, such a mechanism of iodine uptake is similar to that observed in iodine-accumulating marine algae.

  16. Proteome Analysis of the UVB-Resistant Marine Bacterium Photobacterium angustum S14

    PubMed Central

    Matallana-Surget, Sabine; Joux, Fabien; Wattiez, Ruddy; Lebaron, Philippe

    2012-01-01

    The proteome of the marine bacterium Photobacterium angustum S14 was exposed to UVB and analyzed by the implementation of both the post-digest ICPL labeling method and 2D-DIGE technique using exponentially growing cells. A total of 40 and 23 proteins were quantified in all replicates using either the ICPL or 2D-DIGE methods, respectively. By combining both datasets from 8 biological replicates (4 biological replicates for each proteomics technique), 55 proteins were found to respond significantly to UVB radiation in P. angustum. A total of 8 UVB biomarkers of P. angustum were quantified in all replicates using both methods. Among them, the protein found to present the highest increase in abundance (almost a 3-fold change) was RecA, which is known to play a crucial role in the so-called recombinational repair process. We also observed a high number of antioxidants, transport proteins, metabolism-related proteins, transcription/translation regulators, chaperonins and proteases. We also discuss and compare the UVB response and global protein expression profiles obtained for two different marine bacteria with trophic lifestyles: the copiotroph P. angustum and oligotroph Sphingopyxis alaskensis. PMID:22870314

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. 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

  4. Fibrinolytic enzyme from newly isolated marine bacterium Bacillus subtilis ICTF-1: media optimization, purification and characterization.

    PubMed

    Mahajan, Prafulla M; Nayak, Shubhada; Lele, Smita S

    2012-03-01

    Fibrinolytic enzymes are important in treatment of cardiovascular diseases. The present work reports isolation, screening and identification of marine cultures for production of fibrinolytic enzymes. A potent fibrinolytic enzyme-producing bacterium was isolated from marine niches and identified as Bacillus subtilis ICTF-1 on the basis of the 16S rRNA gene sequencing and biochemical properties. Further, media optimization using L(18)-orthogonal array method resulted in enhanced production of fibrinolytic enzyme (8814 U/mL) which was 2.6 fold higher than in unoptimized medium (3420 U/mL). In vitro assays revealed that the enzyme could catalyze blood clot lysis effectively, indicating that this enzyme could be a useful thrombolytic agent. A fibrinolytic enzyme was purified from the culture supernatant to homogeneity by three step procedures with a 34.42-fold increase in specific activity and 7.5% recovery. This purified fibrinolytic enzyme had molecular mass of 28 kDa, optimal temperature and pH at 50 °C and 9, respectively. It was stable at pH 5.0-11.0 and temperature of 25-37 °C. The enzyme activity was activated by Ca(2+) and obviously inhibited by Zn(2+), Fe(3)(+), Hg(2+) and PMSF. The purified fibrinolytic enzyme showed high stability towards various surfactants and was relatively stable towards oxidizing agent. Considering these properties purified fibrinolytic enzyme also finds potential application in laundry detergents in addition to thrombolytic agent. The gene encoding fibrinolytic enzyme was isolated and its DNA sequence was determined. Compared the full DNA sequence with those in NCBI, it was considered to be a subtilisin like serine-protease.

  5. Genome shuffling of marine derived bacterium Nocardia sp. ALAA 2000 for improved ayamycin production.

    PubMed

    El-Gendy, Mervat M A; El-Bondkly, Ahmed M A

    2011-05-01

    Genome shuffling is a recent development in microbiology. The advantage of this technique is that genetic changes can be made in a microorganism without knowing its genetic background. Genome shuffling was applied to the marine derived bacterium Nocardia sp. ALAA 2000 to achieve rapid improvement of ayamycin production. The initial mutant population was generated by treatment with ethyl methane sulfonate (EMS) combined with UV irradiation of the spores, resulting in an improved population (AL/11, AL/136, AL/213 and AL/277) producing tenfold (150 μg/ml) more ayamycin than the original strain. These mutants were used as the starting strains for three rounds of genome shuffling and after each round improved strains were screened and selected based on their ayamycin productivity. The population after three rounds of genome shuffling exhibited an improved ayamycin yield. Strain F3/22 yielded 285 μg/ml of ayamycin, which was 19-fold higher than that of the initial strain and 1.9-fold higher than the mutants used as the starting point for genome shuffling. We evaluated the genetic effect of UV + EMS-mutagenesis and three rounds of genome shuffling on the nucleotide sequence by random amplified polymorphic DNA (RAPD) analysis. Many differences were noticed in mutant and recombinant strains compared to the wild type strain. These differences in RAPD profiles confirmed the presence of genetic variations in the Nocardia genome after mutagenesis and genome shuffling.

  6. A serine hydroxymethyltransferase from marine bacterium Shewanella algae: Isolation, purification, characterization and l-serine production.

    PubMed

    Jiang, Wei; Xia, Bingzhao; Liu, Ziduo

    2013-10-01

    Currently, l-serine is mainly produced by enzymatic conversion, in which serine hydroxymethyltransferase (SHMT) is the key enzyme, suggesting the importance of searching for a SHMT with high activity. Shewanella algae, a methanol-utilizing marine bacterium showing high SHMT activity, was selected based on screening bacterial strains and comparison of the activities of SHMTs. A glyA was isolated from the S. algae through thermal asymmetric interlaced PCR (TAIL-PCR) and it encoded a 417 amino acid polypeptide. The SaSHMT, encoded by the glyA, showed the optimal activity at 50°C and pH 7.0, and retained over 45% of its maximal activity after incubation at 40°C for 3h. The enzyme showed better stability under alkaline environment (pH 6.5-9.0) than Hyphomicrobium methylovorum GM2's SHMT (pH 6.0-7.5). The SaSHMT can produce 77.76mM of l-serine by enzymatic conversion, with the molecular conversion rate in catalyzing glycine to l-serine being 1.41-fold higher than that of Escherichia coli. Therefore, the SaSHMT has the potential for industrial applications due to its tolerance of alkaline environment and a relatively high enzymatic conversion rate.

  7. 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.

  8. Capture of Arginine at Low Concentrations by a Marine Psychrophilic Bacterium

    PubMed Central

    Geesey, Gill G.; Morita, Richard Y.

    1979-01-01

    The cells of the marine bacterium Ant-300 were found to take up arginine when this substrate was at low concentrations. The cells possessed an uptake system(s) that specifically transported l-arginine. The kinetic parameters for uptake appeared to differ when the cells were exposed to nanomolar and micromolar concentrations of the amino acid. Uptake over this concentration range functioned in the absence of an exogenous energy source, even after the cells had been preincubated in unsupplemented artificial seawater. Respiratory activity appeared to be a more important driving force for arginine uptake than adenosine 5′-triphosphate hydrolysis. The cells also exhibited chemotaxis toward l-arginine. The minimum arginine concentration needed to elicit a chemotactic response was between 10−5 and 10−6 M. It is proposed that the capture of arginine by cells of Ant-300 in nutrient-depleted waters, which are typical of the open ocean, proceeds via high-affinity active transport, whereas in substrate-enriched seawater, capture involves chemotaxis and an active transport mechanism with reduced affinity for the substrate. PMID:16345475

  9. 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.

  10. 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.

  11. Phage resistance of a marine bacterium, Roseobacter denitrificans OCh114, as revealed by comparative proteomics.

    PubMed

    Huang, Chunxiao; Zhang, Yongyu; Jiao, Nianzhi

    2010-08-01

    Roseobacter is a dominant lineage in the marine environment. This group of bacteria is diverse in terms of both their phylogenetic composition and their physiological potential. Roseobacter denitrificans OCh114 is one of the most studied bacteria of the Roseobacter lineage. Recently, a lytic phage (RDJLPhi1) that infects this bacterium was isolated and a mutant strain (M1) of OCh114 that is resistant to RDJLPhi1 was also obtained. Here, we investigate the mechanisms supporting phage resistance of M1. Our results excluded the possibilities of several phage resistance mechanisms, including abortive infection, lysogeny, and the clustered regularly interspaced short palindromic repeats (CRISPRs) related mechanism. Adsorption kinetics assays revealed that adsorption inhibition might be a potential cause for the phage resistance of M1. Comparative proteomic analysis of M1 and OCh114 revealed significant changes in the membrane protein compliment of these bacteria. Five membrane proteins with important biological functions were significantly down-regulated in the phage-resistant M1. Meanwhile, several outer membrane porins with different modifications and an OmpA family domain protein were markedly up-regulated. We hypothesize that the down-regulated membrane proteins in M1 may serve as the potential phage receptors, whose absence prevented the adsorption of phage RDJLPhi1 to host cells and subsequent infection.

  12. 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.

  13. Characterization of giant spheroplasts generated from the aerobic anoxygenic photosynthetic marine bacterium Roseobacter litoralis.

    PubMed

    Nojiri, Akane; Ogita, Shinjiro; Isogai, Yasuhiro; Nishida, Hiromi

    2015-01-01

    We generated and characterized giant spheroplasts from the aerobic anoxygenic photosynthetic marine bacterium Roseobacter litoralis. The giant spheroplasts contained vacuole-like structures within the cells, mainly consisting of a single membrane. The in vivo absorption spectrum of the giant spheroplasts did not have peaks typically observed for bacteriochlorophyll a. The culture media pH decreased during the growth of the giant spheroplasts. The change in the pH profile for cells grown under light was no different from that for cells grown in the dark. These results showed that the R. litoralis giant spheroplasts formed lost their photosynthetic apparatus in culture. Most of the giant spheroplasts returned to their original size, likely via filamentous cells. The culture media pH increased during the growth of the filamentous cells. Some filamentous cells had septum-like structures. In such filamentous cells, DNA was separated. Initially, the color of the separated cells was white. Two weeks later, the cells changed to red in the dark, and the in vivo absorption spectrum of the cells had peaks typically observed for bacteriochlorophyll a. Our findings strongly suggest that the giant spheroplasts of R. litoralis can control the genetic information, return to their original cell size, and regain their original functions.

  14. Purification and Characterization of a New Alginate Lyase from Marine Bacterium Vibrio sp. SY08

    PubMed Central

    Li, Shangyong; Wang, Linna; Hao, Jianhua; Xing, Mengxin; Sun, Jingjing; Sun, Mi

    2016-01-01

    Unsaturated alginate disaccharides (UADs), enzymatically derived from the degradation of alginate polymers, are considered powerful antioxidants. In this study, a new high UAD-producing alginate lyase, AlySY08, has been purified from the marine bacterium Vibrio sp. SY08. AlySY08, with a molecular weight of about 33 kDa and a specific activity of 1070.2 U/mg, showed the highest activity at 40 °C in phosphate buffer at pH 7.6. The enzyme was stable over a broad pH range (6.0–9.0) and retained about 75% activity after incubation at 40 °C for 2 h. Moreover, the enzyme was active in the absence of salt ions and its activity was enhanced by the addition of NaCl and KCl. AlySY08 resulted in an endo-type alginate lyase that degrades both polyM and polyG blocks, yielding UADs as the main product (81.4% of total products). All these features made AlySY08 a promising candidate for industrial applications in the production of antioxidants from alginate polysaccharides. PMID:28025527

  15. 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.

  16. Three alginate lyases from marine bacterium Pseudomonas fluorescens HZJ216: purification and characterization.

    PubMed

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

    2011-06-01

    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 Mg(2+) ions can enhance the enzyme activities while Fe(2+), Fe(3+), Ba(2+), and Zn(2+) 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.

  17. Relationship between ion requirements for respiration and membrane transport in a marine bacterium.

    PubMed

    Khanna, G; DeVoe, L; Brown, L; Niven, D F; MacLeod, R A

    1984-01-01

    Intact cells of the marine bacterium Alteromonas haloplanktis 214 oxidized NADH, added to the suspending medium, by a process which was stimulated by Na+ or Li+ but not K+. Toluene-treated cells oxidized NADH at three times the rate of untreated cells by a mechanism activated by Na+ but not by Li+ or K+. In the latter reaction, K+ spared the requirement for Na+. Intact cells of A. haloplanktis oxidized ethanol by a mechanism stimulated by either Na+ or Li+. The uptake of alpha-aminoisobutyric acid by intact cells of A. haloplanktis in the presence of either NADH or ethanol as an oxidizable substrate required Na+, and neither Li+ nor K+ could replace it. The results indicate that exogenous and endogenous NADH and ethanol are oxidized by A. haloplanktis by processes distinguishable from one another by their requirements for alkali metal ions and from the ion requirements for membrane transport. Intact cells of Vibrio natriegens and Photobacterium phosphoreum oxidized NADH, added externally, by an Na+-activated process, and intact cells of Vibrio fischeri oxidized NADH, added externally, by a K+-activated process. Toluene treatment caused the cells of all three organisms to oxidize NADH at much faster rates than untreated cells by mechanisms which were activated by Na+ and spared by K+.

  18. 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.

  19. Prosthecochloris indica sp. nov., a novel green sulfur bacterium from a marine aquaculture pond, Kakinada, India.

    PubMed

    Anil Kumar, Pinnaka; Naga Radha Srinivas, Tanuku; Sasikala, Chintalapati; Venkata Ramana, Chintalapati; Süling, Jorg; Imhoff, Johannes

    2009-04-01

    A green sulfur bacterium, strain JAGS6T was isolated from a marine aquaculture pond located near Kakinada on the east coast of India. Cells of strain JAGS6T were Gram-negative, non-motile, coccoid, 1-1.2 microm in diameter, with prosthecae. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JAGS6T clusters with members of the genus Prosthecochloris and the sequence similarity with the nearest relative, Prosthecochloris vibrioformis, is 96.7%. Cultures of strain JAGS6T are green in color and the cells contain bacteriochlorophyll c and most likely carotenoids of the chlorobactene series as photosynthetic pigments. Strain JAGS6T is mesophilic, halotolerant (up to 7% NaCl) and is obligately phototrophic, utilizing sulfide but not thiosulfate as a photosynthetic electron donor. Sulfur globules are deposited outside the cells during oxidation of sulfide. On the basis of 16S rRNA gene sequence analysis and its morphological and physiological characteristics, strain JAGS6T is distinct from described species of the genus Prosthecochloris and we propose to describe it as a new species, Prosthecochloris indica, sp. nov. The type strain is JAGS6T (=JCM 13299T=ATCC BAA1214T).

  20. 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

  1. Hydrogenases in sulfate-reducing bacteria function as chromium reductase.

    PubMed

    Chardin, B; Giudici-Orticoni, M-T; De Luca, G; Guigliarelli, B; Bruschi, M

    2003-12-01

    The ability of sulfate-reducing bacteria (SRB) to reduce chromate VI has been studied for possible application to the decontamination of polluted environments. Metal reduction can be achieved both chemically, by H(2)S produced by the bacteria, and enzymatically, by polyhemic cytochromes c(3). We demonstrate that, in addition to low potential polyheme c-type cytochromes, the ability to reduce chromate is widespread among [Fe], [NiFe], and [NiFeSe] hydrogenases isolated from SRB of the genera Desulfovibrio and Desulfomicrobium. Among them, the [Fe] hydrogenase from Desulfovibrio vulgaris strain Hildenborough reduces Cr(VI) with the highest rate. Both [Fe] and [NiFeSe] enzymes exhibit the same K(m) towards Cr(VI), suggesting that Cr(VI) reduction rates are directly correlated with hydrogen consumption rates. Electron paramagnetic resonance spectroscopy enabled us to probe the oxidation by Cr(VI) of the various metal centers in both [NiFe] and [Fe] hydrogenases. These experiments showed that Cr(VI) is reduced to paramagnetic Cr(III), and revealed inhibition of the enzyme at high Cr(VI) concentrations. The significant decrease of both hydrogenase and Cr(VI)-reductase activities in a mutant lacking [Fe] hydrogenase demonstrated the involvement of this enzyme in Cr(VI) reduction in vivo. Experiments with [3Fe-4S] ferredoxin from Desulfovibrio gigas demonstrated that the low redox [Fe-S] (non-heme iron) clusters are involved in the mechanism of metal reduction by hydrogenases.

  2. Biogeography of sulfate-reducing prokaryotes in river floodplains.

    PubMed

    Miletto, Marzia; Loy, Alexander; Antheunisse, A Martijn; Loeb, Roos; Bodelier, Paul L E; Laanbroek, Hendrikus J

    2008-06-01

    In this study, a large-scale field survey was conducted to describe the biogeography of sulfate-reducing prokaryotes (SRPs) in river floodplains. Fingerprints obtained with three methods, i.e. 16S rRNA gene-based oligonucleotide microarray, dsrB-based denaturing gradient gel electrophoresis (DGGE) and polar lipid-derived fatty acid (PLFA) analyses, were used as a proxy to describe the SRPs community diversity. Each set of profiles was subjected to a combined multivariate/correlation analysis in order to compare SRP community profiles and to highlight the environmental variables influencing the SRPs distribution along environmental gradients. Floodplain soils harbored distinct SRP communities displaying biogeographic patterns. Nearly all profiles from the tidal sites consistently separated from the nontidal sites, independently from the screening method and the multivariate statistics used. The distribution of the microarray/DGGE/PLFA-based fingerprints in the principal component plots could be correlated to eight soil variables, i.e. soil organic matter, total nitrogen, total phosphorous and total potassium, and extractable ammonium, nitrate, phosphate and sulfate, as well as seven pore water variables, i.e. phosphate, sulfate, sulfide, chloride, sodium, potassium and magnesium ions. Indication of a salinity- and plant nutrient-dependent distribution of SRPs related to Desulfosarcina, Desulfomonile and Desulfobacter was suggested by microarray, DGGE and PLFA analyses.

  3. Anaerobic Naphthalene Degradation by a Sulfate-Reducing Enrichment Culture†

    PubMed Central

    Meckenstock, Rainer U.; Annweiler, Eva; Michaelis, Walter; Richnow, Hans H.; Schink, Bernhard

    2000-01-01

    Anaerobic naphthalene degradation by a sulfate-reducing enrichment culture was studied by substrate utilization tests and identification of metabolites by gas chromatography-mass spectrometry. In substrate utilization tests, the culture was able to oxidize naphthalene, 2-methylnaphthalene, 1- and 2-naphthoic acids, phenylacetic acid, benzoic acid, cyclohexanecarboxylic acid, and cyclohex-1-ene-carboxylic acid with sulfate as the electron acceptor. Neither hydroxylated 1- or 2-naphthoic acid derivatives and 1- or 2-naphthol nor the monoaromatic compounds ortho-phthalic acid, 2-carboxy-1-phenylacetic acid, and salicylic acid were utilized by the culture within 100 days. 2-Naphthoic acid accumulated in all naphthalene-grown cultures. Reduced 2-naphthoic acid derivatives could be identified by comparison of mass spectra and coelution with commercial reference compounds such as 1,2,3,4-tetrahydro-2-naphthoic acid and chemically synthesized decahydro-2-naphthoic acid. 5,6,7,8-Tetrahydro-2-naphthoic acid and octahydro-2-naphthoic acid were tentatively identified by their mass spectra. The metabolites identified suggest a stepwise reduction of the aromatic ring system before ring cleavage. In degradation experiments with [1-13C]naphthalene or deuterated D8-naphthalene, all metabolites mentioned derived from the introduced labeled naphthalene. When a [13C]bicarbonate-buffered growth medium was used in conjunction with unlabeled naphthalene, 13C incorporation into the carboxylic group of 2-naphthoic acid was shown, indicating that activation of naphthalene by carboxylation was the initial degradation step. No ring fission products were identified. PMID:10877763

  4. 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.

  5. 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

  6. 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

    2013-04-11

    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.

  7. 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.

  8. 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.

  9. The metagenome of the marine anammox bacterium ‘Candidatus Scalindua profunda’ illustrates the versatility of this globally important nitrogen cycle bacterium

    PubMed Central

    van de Vossenberg, Jack; Woebken, Dagmar; Maalcke, Wouter J; Wessels, Hans J C T; Dutilh, Bas E; Kartal, Boran; Janssen-Megens, Eva M; Roeselers, Guus; Yan, Jia; Speth, Daan; Gloerich, Jolein; Geerts, Wim; van der Biezen, Erwin; Pluk, Wendy; Francoijs, Kees-Jan; Russ, Lina; Lam, Phyllis; Malfatti, Stefanie A; Tringe, Susannah Green; Haaijer, Suzanne C M; Op den Camp, Huub J M; Stunnenberg, Henk G; Amann, Rudi; Kuypers, Marcel M M; Jetten, Mike S M

    2013-01-01

    Anaerobic ammonium-oxidizing (anammox) bacteria are responsible for a significant portion of the loss of fixed nitrogen from the oceans, making them important players in the global nitrogen cycle. To date, marine anammox bacteria found in marine water columns and sediments worldwide belong almost exclusively to the ‘Candidatus Scalindua’ species, but the molecular basis of their metabolism and competitive fitness is presently unknown. We applied community sequencing of a marine anammox enrichment culture dominated by ‘Candidatus Scalindua profunda’ to construct a genome assembly, which was subsequently used to analyse the most abundant gene transcripts and proteins. In the S. profunda assembly, 4756 genes were annotated, and only about half of them showed the highest identity to the only other anammox bacterium of which a metagenome assembly had been constructed so far, the freshwater ‘Candidatus Kuenenia stuttgartiensis’. In total, 2016 genes of S. profunda could not be matched to the K. stuttgartiensis metagenome assembly at all, and a similar number of genes in K. stuttgartiensis could not be found in S. profunda. Most of these genes did not have a known function but 98 expressed genes could be attributed to oligopeptide transport, amino acid metabolism, use of organic acids and electron transport. On the basis of the S. profunda metagenome, and environmental metagenome data, we observed pronounced differences in the gene organization and expression of important anammox enzymes, such as hydrazine synthase (HzsAB), nitrite reductase (NirS) and inorganic nitrogen transport proteins. Adaptations of Scalindua to the substrate limitation of the ocean may include highly expressed ammonium, nitrite and oligopeptide transport systems and pathways for the transport, oxidation, and assimilation of small organic compounds that may allow a more versatile lifestyle contributing to the competitive fitness of Scalindua in the marine realm. PMID:22568606

  10. 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.

  11. 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

  12. 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.

  13. 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

  14. 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.

  15. Trimethylamine and trimethylamine N-oxide are supplementary energy sources for a marine heterotrophic bacterium: implications for marine carbon and nitrogen cycling.

    PubMed

    Lidbury, Ian D E A; Murrell, J Colin; Chen, Yin

    2015-03-01

    Bacteria of the marine Roseobacter clade are characterised by their ability to utilise a wide range of organic and inorganic compounds to support growth. Trimethylamine (TMA) and trimethylamine N-oxide (TMAO) are methylated amines (MA) and form part of the dissolved organic nitrogen pool, the second largest source of nitrogen after N2 gas, in the oceans. We investigated if the marine heterotrophic bacterium, Ruegeria pomeroyi DSS-3, could utilise TMA and TMAO as a supplementary energy source and whether this trait had any beneficial effect on growth. In R. pomeroyi, catabolism of TMA and TMAO resulted in the production of intracellular ATP which in turn helped to enhance growth rate and growth yield as well as enhancing cell survival during prolonged energy starvation. Furthermore, the simultaneous use of two different exogenous energy sources led to a greater enhancement of chemoorganoheterotrophic growth. The use of TMA and TMAO primarily as an energy source resulted in the remineralisation of nitrogen in the form of ammonium, which could cross feed into another bacterium. This study provides greater insight into the microbial metabolism of MAs in the marine environment and how it may affect both nutrient flow within marine surface waters and the flux of these climatically important compounds into the atmosphere.

  16. Genome sequence of Vibrio sp. strain EJY3, an agarolytic marine bacterium metabolizing 3,6-anhydro-L-galactose as a sole carbon source.

    PubMed

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

    2012-05-01

    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.

  17. 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.

  18. Cyclobacterium qasimii sp. nov., a psychrotolerant bacterium isolated from Arctic marine sediment.

    PubMed

    Shivaji, S; Reddy, P Vishnu Vardhan; Rao, S S S Nageshwara; Begum, Zareena; Manasa, Poorna; Srinivas, T N R

    2012-09-01

    A novel Gram-stain-negative, horseshoe-shaped, non-motile bacterium, designated strain M12-11B(T), was isolated from a marine sediment sample collected at a depth of 200 m from Kongsfjorden, Svalbard. The colony colour was orangish red due to the presence of carotenoids. Fatty acids were dominated by branched and unsaturated fatty acids (90.8 %), with a high abundance of iso-C(15 : 0) (14.9 %), anteiso-C(15 : 0) (11.4 %), iso-C(15 : 1) G (13.1 %), C(15 : 1)ω6c (5.4 %), C(17 : 1)ω6c (6.7 %), summed feature 3 (C(16 : 1)ω7c and/or C(16 : 1)ω6c; 9.3 %) and summed feature 9 (10-methyl C(16 : 0) and/or iso-C(17 : 1)ω9c; 5.9 %). Strain M12-11B(T) contained MK-7 as the major respiratory quinone. The polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, one unidentified aminolipid and three unidentified lipids. Based on 16S rRNA gene sequence similarities, the type strains of Cyclobacterium amurskyense, Cyclobacterium marinum and Cyclobacterium lianum were most closely related to M12-11B(T) with sequence similarities of 98.2, 96.8 and 93.3 %, respectively. Other members of the family Cyclobacteriaceae had sequence similarities of <92.0 %. However, DNA-DNA hybridization with Cyclobacterium amurskyense KCTC 12363(T) and Cyclobacterium marinum DSM 745(T) showed relatedness values of only 24.5 and 32.5 % with respect to strain M12-11B(T). Based on the results of DNA-DNA hybridization experiments and phenotypic and chemotaxonomic data, it appears that strain M12-11B(T) represents a novel species of the genus Cyclobacterium, for which the name Cyclobacterium qasimii sp. nov. is proposed; the type strain is M12-11B(T) (= KCTC 23011(T) = NBRC 106168(T)) and it has a DNA G+C content of 40.5 mol%.

  19. Production of electrically-conductive nanoscale filaments by sulfate-reducing bacteria in the microbial fuel cell.

    PubMed

    Eaktasang, Numfon; Kang, Christina S; Lim, Heejun; Kwean, Oh Sung; Cho, Suyeon; Kim, Yohan; Kim, Han S

    2016-06-01

    This study reports that the obligate anaerobic microorganism, Desulfovibrio desulfuricans, a predominant sulfate-reducing bacterium (SRB) in soils and sediments, can produce nanoscale bacterial appendages for extracellular electron transfer. These nanofilaments were electrically-conductive (5.81S·m(-1)) and allowed SRBs to directly colonize the surface of insoluble or solid electron acceptors. Thus, the direct extracellular electron transfer to the insoluble electrode in the microbial fuel cell (MFC) was possible without inorganic electron-shuttling mediators. The production of nanofilaments was stimulated when only insoluble electron acceptors were available for cellular respiration. These results suggest that when availability of a soluble electron acceptor for SRBs (SO4(2-)) is limited, D. desulfuricans initiates the production of conductive nanofilaments as an alternative strategy to transfer electrons to insoluble electron acceptors. The findings of this study contribute to understanding of the role of SRBs in the biotransformation of various substances in soils and sediments and in the MFC.

  20. Investigation of the mechanism of iron acquisition by the marine bacterium Alteromonas luteoviolaceus: Characterization of siderophore production

    SciTech Connect

    Reid, R.T.; Butler, A. )

    1991-12-01

    Iron availability in the ocean ranges from one to four orders of magnitude below typical growth requirements of bacteria. The discrepancy between Fe availability and requirements raises questions about the mechanisms that marine bacteria use to sequester Fe{sup 3+}. Surprisingly little is known about the siderophores produced by marine bacteria. Growth conditions of an open-ocean bacterial isolate, Alteromonas luteoviolaceus, were investigated to determine the conditions which enhance siderophore production. Methods to isolate and purify the siderophores were determined. The siderophores produced by A. luteoviolaceus were partially characterized by mass spectral analysis, amino acid analysis, qualitative analytical tests, chemical degradation, and nuclear magnetic resonance. A new set of outer membrane proteins was also produced when the bacterium was grown under Fe-limited conditions.

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

    PubMed

    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

    2014-08-01

    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.

  3. Characterization of cytochrome c3 from the thermophilic sulfate reducer Thermodesulfobacterium commune.

    PubMed Central

    Hatchikian, E C; Papavassiliou, P; Bianco, P; Haladjian, J

    1984-01-01

    A c3 type cytochrome has been purified from the thermophilic, non-spore-forming, sulfate-reducing bacterium Thermodesulfobacterium commune. The purified protein was homogeneous as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, gel filtration, and isoelectric focusing. A pI of 6.83 was observed. The molecular weight of the cytochrome was estimated to be ca. 13,000 from both gel filtration and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The hemoprotein exhibited absorption maxima at 530, 408.5, and 351 nm in the oxidized form and 551.5 (alpha band), 522.5 (beta band), and 418.5 nm (gamma band) in the reduced form. The extinction coefficients of T. commune cytochrome c3 were 130,000, 74,120, and 975,000 M-1 cm-1 at 551.5, 522.5, and 418.5 nm, respectively. It contains four hemes per molecule, on the basis of both the iron estimation and the extinction coefficient value of its pyridine hemochrome. The amino acid composition showed the presence of eight cysteine residues involved in heme binding. T. commune cytochrome c3 had low threonine, serine, and glycine contents and high glutamic acid and hydrophobic residue contents. The electrochemical study of T. commune cytochrome c3 by cyclic voltammetry and differential pulse polarography has shown that the cytochrome system behaves like a reversible system. Four redox potential values at Eh1 = -0.140 +/- 0.010 V, Eh2 = Eh3 = Eh4 = -0.280 +/- 0.010 V have been determined. T. commune cytochrome c3, which acts as the physiological electron carrier of hydrogenase, is similar in most respects to the multiheme low-potential cytochrome c3 which is characteristic of the genus Desulfovibrio. PMID:6090384

  4. 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

  5. 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

  6. 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.

  7. Enrichment and Physiological Characterization of a Novel Nitrospira-Like Bacterium Obtained from a Marine Sponge ▿

    PubMed Central

    Off, Sandra; Alawi, Mashal; Spieck, Eva

    2010-01-01

    Members of the nitrite-oxidizing genus Nitrospira are most likely responsible for the second step of nitrification, the conversion of nitrite (NO2−) to nitrate (NO3−), 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°C and 30°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

  8. In vitro antiplasmodial activity of bacterium RJAUTHB 14 associated with marine sponge Haliclona Grant against Plasmodium falciparum.

    PubMed

    Jacob Inbaneson, Samuel; Ravikumar, Sundaram

    2012-06-01

    Malaria is the most important parasitic disease, leading to annual death of about one million people, and the Plasmodium falciparum develops resistance to well-established antimalarial drugs. The newest antiplasmodial drug from a marine microorganism helps in addressing this problem. In the present study, Haliclona Grant were collected and subjected for enumeration and isolation of associated bacteria. The count of bacterial isolates was maximum in November 2007 (18 × 10(4) colony-forming units (CFU) g(-1), and the average count was maximum during the monsoon season (117 × 10(3) CFU g(-1)). Thirty-three morphologically different bacterial isolates were isolated from Haliclona Grant, and the extracellular ethyl acetate extracts were screened for antiplasmodial activity against P. falciparum. The antiplasmodial activity of bacterium RJAUTHB 14 (11.98 μg[Symbol: see text]ml(-1)) is highly comparable with the positive control chloroquine (IC(50) 19.59 μg[Symbol: see text]ml(-1)), but the other 21 bacterial extracts showed an IC(50) value of more than 100 μg[Symbol: see text]ml(-1). Statistical analysis reveals that significant in vitro antiplasmodial activity (P < 0.05) was observed between the concentrations and time of exposure. The chemical injury to erythrocytes showed no morphological changes in erythrocytes by the ethyl acetate extract of bacterial isolates after 48 h of incubation. The in vitro antiplasmodial activity might be due to the presence of reducing sugars and alkaloids in the ethyl acetate extracts of bacterium RJAUTHB 14. The 16S rRNA gene partial sequence of bacterium RJAUTHB 14 is deposited in NCBI (GenBank accession no. GU269569). It is concluded from the present study that the ethyl acetate extracts of bacterium RJAUTHB 14 possess lead compounds for the development of antiplasmodial drugs.

  9. 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...

  10. 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

  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. Aerobic and anoxic growth and nitrate removal capacity of a marine denitrifying bacterium isolated from a recirculation aquaculture system.

    PubMed

    Borges, Maria-Teresa; Sousa, André; De Marco, Paolo; Matos, Ana; Hönigová, Petra; Castro, Paula M L

    2008-01-01

    Bacterial biofilters used in marine recirculation aquaculture systems need improvements to enhance nitrogen removal efficiency. Relatively little is known about biofilter autochthonous population structure and function. The present study was aimed at isolating and characterizing an autochthonous denitrifying bacterium from a marine biofilter installed at a recirculation aquaculture system. Colonization of four different media in a marine fish farm was followed by isolation of various denitrifying strains and molecular classification of the most promising one, strain T2, as a novel member of the Pseudomonas fluorescens cluster. This strain exhibits high metabolic versatility regarding N and C source utilization and environmental conditions for growth. It removed nitrate through aerobic assimilatory metabolism at a specific rate of 116.2 mg NO(3)-N g dw(-1) h(-1). Dissimilatory NO(3)-N removal was observed under oxic conditions at a limited rate, where transient NO(2)-N formed represented 22% (0.17 mg L(-1)) of the maximum transient NO(2)-N observed under anoxic conditions. Dissimilatory NO(3)-N removal under anoxic conditions occurred at a specific rate of 53.5 mg NO(3)-N g dw(-1) h(-1). The isolated denitrifying strain was able to colonize different materials, such as granular activated carbon (GAC), Filtralite and Bioflow plastic rings, which allow the development of a prototype bioreactor for strain characterization under dynamic conditions and mimicking fish-farm operating conditions.

  13. Differentiation of Chitinase-Active and Non-Chitinase-Active Subpopulations of a Marine Bacterium during Chitin Degradation

    PubMed Central

    Baty, Ace M.; Eastburn, Callie C.; Diwu, Zhenjun; Techkarnjanaruk, Somkiet; Goodman, Amanda E.; Geesey, Gill G.

    2000-01-01

    The ability of marine bacteria to adhere to detrital particulate organic matter and rapidly switch on metabolic genes in an effort to reproduce is an important response for bacterial survival in the pelagic marine environment. The goal of this investigation was to evaluate the relationship between chitinolytic gene expression and extracellular chitinase activity in individual cells of the marine bacterium Pseudoalteromonas sp. strain S91 attached to solid chitin. A green fluorescent protein reporter gene under the control of the chiA promoter was used to evaluate chiA gene expression, and a precipitating enzyme-linked fluorescent probe, ELF-97–N-acetyl-β-d-glucosaminide, was used to evaluate extracellular chitinase activity among cells in the bacterial population. Evaluation of chiA expression and ELF-97 crystal location at the single-cell level revealed two physiologically distinct subpopulations of S91 on the chitin surface: one that was chitinase active and remained associated with the surface and another that was non-chitinase active and released daughter cells into the bulk aqueous phase. It is hypothesized that the surface-associated, non-chitinase-active population is utilizing chitin degradation products that were released by the adjacent chitinase-active population for cell replication and dissemination into the bulk aqueous phase. PMID:10919822

  14. 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

  15. 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.

  16. Cloning and Characterization of a Novel Chondroitin Sulfate/Dermatan Sulfate 4-O-Endosulfatase from a Marine Bacterium*

    PubMed Central

    Wang, Wenshuang; Han, Wenjun; Cai, Xingya; Zheng, Xiaoyu; Sugahara, Kazuyuki; Li, Fuchuan

    2015-01-01

    Sulfatases are potentially useful tools for structure-function studies of glycosaminoglycans (GAGs). To date, various GAG exosulfatases have been identified in eukaryotes and prokaryotes. However, endosulfatases that act on GAGs have rarely been reported. Recently, a novel HA and CS lyase (HCLase) was identified for the first time from a marine bacterium (Han, W., Wang, W., Zhao, M., Sugahara, K., and Li, F. (2014) J. Biol. Chem. 289, 27886–27898). In this study, a putative sulfatase gene, closely linked to the hclase gene in the genome, was recombinantly expressed and characterized in detail. The recombinant protein showed a specific N-acetylgalactosamine-4-O-sulfatase activity that removes 4-O-sulfate from both disaccharides and polysaccharides of chondroitin sulfate (CS)/dermatan sulfate (DS), suggesting that this sulfatase represents a novel endosulfatase. The novel endosulfatase exhibited maximal reaction rate in a phosphate buffer (pH 8.0) at 30 °C and effectively removed 17–65% of 4-O-sulfates from various CS and DS and thus significantly inhibited the interactions of CS and DS with a positively supercharged fluorescent protein. Moreover, this endosulfatase significantly promoted the digestion of CS by HCLase, suggesting that it enhances the digestion of CS/DS by the bacterium. Therefore, this endosulfatase is a potential tool for use in CS/DS-related studies and applications. PMID:25648894

  17. Draft Genome Sequence of Aeromonas caviae CH129, a Marine-Derived Bacterium Isolated from the Coast of São Paulo State, Brazil

    PubMed Central

    Alfonso Vargas, Nadia Catalina; Zimpel, Cristina Kraemer; Pessoa, Adalberto; Rivera, Irma Nelly Gutierrez

    2016-01-01

    We report here the draft genome sequence of Aeromonas caviae CH129, a marine-derived bacterium isolated from the coast of São Paulo state, Brazil. Genomic analysis revealed genes encoding enzymes involved in binding, transport, and chitin metabolism and different virulence-associated factors. PMID:27908996

  18. Draft Genome Sequence of Aeromonas caviae CH129, a Marine-Derived Bacterium Isolated from the Coast of São Paulo State, Brazil.

    PubMed

    Cardozo, Flávio Augusto; Alfonso Vargas, Nadia Catalina; Zimpel, Cristina Kraemer; Pessoa, Adalberto; Rivera, Irma Nelly Gutierrez

    2016-12-01

    We report here the draft genome sequence of Aeromonas caviae CH129, a marine-derived bacterium isolated from the coast of São Paulo state, Brazil. Genomic analysis revealed genes encoding enzymes involved in binding, transport, and chitin metabolism and different virulence-associated factors.

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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)).

  4. Purification and characterization of a novel alginate lyase from the marine bacterium Cobetia sp. NAP1 isolated from brown algae.

    PubMed

    Yagi, Hisashi; Fujise, Asako; Itabashi, Narumi; Ohshiro, Takashi

    2016-12-01

    The application of marine resources, instead of fossil fuels, for biomass production is important for building a sustainable society. Seaweed is valuable as a source of marine biomass for producing biofuels such as ethanol, and can be used in various fields. Alginate is an anionic polysaccharide that forms the main component of brown algae. Various alginate lyases (e.g. exo- and endo-types and oligoalginate lyase) are generally used to degrade alginate. We herein describe a novel alginate lyase, AlgC-PL7, which belongs to the polysaccharide lyase 7 family. AlgC-PL7 was isolated from the halophilic Gram-negative bacterium Cobetia sp. NAP1 collected from the brown algae Padina arborescens Holmes. The optimal temperature and pH for AlgC-PL7 activity were 45 °C and 8, respectively. Additionally, AlgC-PL7 was thermostable and salt-tolerant, exhibited broad substrate specificity, and degraded alginate into monosaccharides. Therefore, AlgC-PL7 is a promising enzyme for the production of biofuels.

  5. Isolation and characterization of aggregate-forming sulfate-reducing and purple sulfur bacteria from the chemocline of meromictic Lake Cadagno, Switzerland.

    PubMed

    Peduzzi, Sandro; Tonolla, Mauro; Hahn, Dittmar

    2003-07-01

    Abstract In situ hybridization with specific oligonucleotide probes was used to monitor enrichment cultures of yet uncultured populations of sulfate-reducing and small-celled purple sulfur bacteria found to associate into aggregates in the chemocline of meromictic Lake Cadagno, Switzerland, and to select potential isolates. Enrichment and isolation conditions resembled those of their nearest cultured relatives, the sulfate-reducing bacterium Desulfocapsa thiozymogenes and small-celled purple sulfur bacteria belonging to the genus Lamprocystis, respectively. Based on comparative 16S rRNA analysis and physiological characterization, isolate Cad626 was found to resemble D. thiozymogenes although it differed from the type strain by its ability to grow on lactate and pyruvate. Like D. thiozymogenes, isolate Cad626 was able to disproportionate inorganic sulfur compounds (sulfur, thiosulfate, sulfite) and to grow, although growth on sulfur required a sulfide scavenger (FeOOH). Isolate Cad16 represented small-celled purple sulfur bacteria that belonged to a previously detected, but uncultured population designated F and was related to Lamprocystis purpurea as evidenced by comparative 16S rRNA analysis and the presence of bacteriochlorophyll a and the carotenoid okenone. Mixed cultures of isolates Cad626 and Cad16 resulted in their association in aggregates similar to those observed in the chemocline of Lake Cadagno. Concomitant growth enhancement of both isolates in mixed culture suggested synergistic interactions that presumably resemble a source-sink relationship for sulfide between the sulfate-reducing bacterium growing by sulfur disproportionation and the purple sulfur bacteria acting as biotic scavenger.

  6. Simultaneous sulfate reduction and copper removal by a PVA-immobilized sulfate reducing bacterial culture.

    PubMed

    Hsu, Hsiu-Feng; Jhuo, Yu-Sheng; Kumar, Mathava; Ma, Ying-Shih; Lin, Jih-Gaw

    2010-06-01

    The effect of a sulfate reducing bacteria immobilized in polyvinyl alcohol (PVA) on simultaneous sulfate reduction and copper removal was investigated. Batch experiments were designed using central composite design (CCD) with two parameters, i.e. the copper concentration (10-100mg/L), and the quantity of immobilized SRB in culture solution (19-235 mg of VSS/L). Response surface methodology (RSM) was used to model the experimental data, and to identify optimal conditions for the maximum sulfate reduction and copper removal. Under optimum condition, i.e. approximately 138.5mg VSS/L of sulfate reducing bacteria immobilized in PVA, and approximately 51.5mg/L of copper, the maximum sulfate reduction rate was 1.57 d(-1) as based on the first-order kinetic equation. The data demonstrate that immobilizing sulfate reducing bacteria in PVA can enhance copper removal and the resistance of the bacteria towards copper toxicity.

  7. Complete Genome Sequence of Rhodococcus sp. Strain WMMA185, a Marine Sponge-Associated Bacterium

    PubMed Central

    Adnani, Navid; Braun, Doug R.; McDonald, Bradon R.; Chevrette, Marc G.; Currie, Cameron R.

    2016-01-01

    The Rhodococcus strain WMMA185 was isolated from the marine sponge Chondrilla nucula as part of ongoing drug discovery efforts. Analysis of the 4.44-Mb genome provides information regarding interspecies interactions as pertains to regulation of secondary metabolism and natural product biosynthetic potentials. PMID:27979952

  8. Streptomyces lunalinharesii 235 prevents the formation of a sulfate-reducing bacterial biofilm.

    PubMed

    Rosa, Juliana Pacheco da; Tibúrcio, Samyra Raquel Gonçalves; Marques, Joana Montezano; Seldin, Lucy; Coelho, Rosalie Reed Rodrigues

    2016-01-01

    Streptomyces lunalinharesii strain 235 produces an antimicrobial substance that is active against sulfate reducing bacteria, the major bacterial group responsible for biofilm formation and biocorrosion in petroleum reservoirs. The use of this antimicrobial substance for sulfate reducing bacteria control is therefore a promising alternative to chemical biocides. In this study the antimicrobial substance did not interfere with the biofilm stability, but the sulfate reducing bacteria biofilm formation was six-fold smaller in carbon steel coupons treated with the antimicrobial substance when compared to the untreated control. A reduction in the most probable number counts of planktonic cells of sulfate reducing bacteria was observed after treatments with the sub-minimal inhibitory concentration, minimal inhibitory concentration, and supra-minimal inhibitory concentration of the antimicrobial substance. Additionally, when the treated coupons were analyzed by scanning electron microscopy, the biofilm formation was found to be substantially reduced when the supra-minimal inhibitory concentration of the antimicrobial substance was used. The coupons used for the biofilm formation had a small weight loss after antimicrobial substance treatment, but corrosion damage was not observed by scanning electron microscopy. The absence of the dsrA gene fragment in the scraped cell suspension after treatment with the supra-minimal inhibitory concentration of the antimicrobial substance suggests that Desulfovibrio alaskensis was not able to adhere to the coupons. This is the first report on an antimicrobial substance produced by Streptomyces active against sulfate reducing bacteria biofilm formation. The application of antimicrobial substance as a potential biocide for sulfate reducing bacteria growth control could be of great interest to the petroleum industry.

  9. Crassaminicella profunda gen. nov., sp. nov., an anaerobic marine bacterium isolated from deep-sea sediments.

    PubMed

    Lakhal, Raja; Pradel, Nathalie; Postec, Anne; Ollivier, Bernard; Cayol, Jean-Luc; Godfroy, Anne; Fardeau, Marie-Laure; Galés, Grégoire

    2015-09-01

    A novel, anaerobic, chemo-organotrophic bacterium, designated strain Ra1766H(T), was isolated from sediments of the Guaymas basin (Gulf of California, Mexico) taken from a depth of 2002  m. Cells were thin, motile, Gram-stain-positive, flexible rods forming terminal endospores. Strain Ra1766H(T) grew at temperatures of 25-45 °C (optimum 30 °C), pH 6.7-8.1 (optimum 7.5) and in a salinity of 5-60 g l(-1) NaCl (optimum 30 g l(-1)). It was an obligate heterotrophic bacterium fermenting carbohydrates (glucose and mannose) and organic acids (pyruvate and succinate). Casamino acids and amino acids (glutamate, aspartate and glycine) were also fermented. The main end products from glucose fermentation were acetate, butyrate, ethanol, H2 and CO2. Sulfate, sulfite, thiosulfate, elemental sulfur, fumarate, nitrate, nitrite and Fe(III) were not used as terminal electron acceptors. The predominant cellular fatty acids were C14  : 0, C16 : 1ω7, C16 : 1ω7 DMA and C16 : 0. The main polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phospholipids. The G+C content of the genomic DNA was 33.7 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain Ra1766H(T) was affiliated to cluster XI of the order Clostridiales, phylum Firmicutes. The closest phylogenetic relative of Ra1766H(T) was Geosporobacter subterraneus (94.2% 16S rRNA gene sequence similarity). On the basis of phylogenetic inference and phenotypic properties, strain Ra1766H(T) ( = DSM 27501(T) = JCM 19377(T)) is proposed to be the type strain of a novel species of a novel genus, named Crassaminicella profunda.

  10. A substantial fraction of phytoplankton-derived DON is resistant to degradation by a metabolically versatile, widely distributed marine bacterium

    PubMed Central

    Kimmance, Susan; McCormack, Paul

    2017-01-01

    The capacity of bacteria for degrading dissolved organic nitrogen (DON) and remineralising ammonium is of importance for marine ecosystems, as nitrogen availability frequently limits productivity. Here, we assess the capacity of a widely distributed and metabolically versatile marine bacterium to degrade phytoplankton-derived dissolved organic carbon (DOC) and nitrogen. To achieve this, we lysed exponentially growing diatoms and used the derived dissolved organic matter (DOM) to support an axenic culture of Alteromonas sp.. Bacterial biomass (as particulate carbon and nitrogen) was monitored for 70 days while growth dynamics (cell count), DOM (DOC, DON) and dissolved nutrient concentrations were monitored for up to 208 days. Bacterial biomass increased rapidly within the first 7 days prior to a period of growth/death cycles potentially linked to rapid nutrient recycling. We found that ≈75% of the initial DOC and ≈35% of the initial DON were consumed by bacteria within 40 and 4 days respectively, leaving a significant fraction of DOM resilient to degradation by this bacterial species. The different rates and extents to which DOC and DON were accessed resulted in changes in DOM stoichiometry and the iterative relationship between DOM quality and bacterial growth over time influenced bacterial cell C:N molar ratio. C:N values increased to 10 during the growth phase before decreasing to values of ≈5, indicating a change from relative N-limitation/C-sufficiency to relative C-limitation/N-sufficiency. Consequently, despite its reported metabolic versatility, we demonstrate that Alteromonas sp. was unable to access all phytoplankton derived DOM and that a bacterial community is likely to be required. By making the relatively simple assumption that an experimentally derived fraction of DOM remains resilient to bacterial degradation, these experimental results were corroborated by numerical simulations using a previously published model describing the interaction

  11. A halotolerant thermostable lipase from the marine bacterium Oceanobacillus sp. PUMB02 with an ability to disrupt bacterial biofilms

    PubMed Central

    Seghal Kiran, George; Nishanth Lipton, Anuj; Kennedy, Jonathan; Dobson, Alan DW; Selvin, Joseph

    2014-01-01

    A halotolerant thermostable lipase was purified and characterized from the marine bacterium Oceanobacillus sp. PUMB02. This lipase displayed a high degree of stability over a wide range of conditions including pH, salinity, and temperature. It was optimally active at 30 °C and pH 8.0 respectively and was stable at higher temperatures (50–70 °C) and alkaline pH. The molecular mass of the lipase was approximately 31 kDa based on SDS-PAGE and MALDI-ToF fingerprint analysis. Conditions for enhanced production of lipase by Oceanobacillus sp. PUMB02 were attained in response surface method-guided optimization with factors such as olive oil, sucrose, potassium chromate, and NaCl being evaluated, resulting in levels of 58.84 U/ml being achieved. The biofilm disruption potential of the PUMB02 lipase was evaluated and compared with a marine sponge metagenome derived halotolerant lipase Lpc53E1. Good biofilm disruption activity was observed with both lipases against potential food pathogens such as Bacillus cereus MTCC1272, Listeria sp. MTCC1143, Serratia sp. MTCC4822, Escherichia coli MTCC443, Pseudomonas fluorescens MTCC1748, and Vibrio parahemolyticus MTCC459. Phase contrast microscopy, scanning electron microscopy, and confocal laser scanning microscopy showed very effective disruption of pathogenic biofilms. This study reveals that marine derived hydrolytic enzymes such as lipases may have potential utility in inhibiting biofilm formation in a food processing environment and is the first report of the potential application of lipases from the genus Oceanobacillus in biofilm disruption strategies. PMID:25482232

  12. Benzylsuccinate Formation as a Means of Anaerobic Toluene Activation by Sulfate-Reducing Strain PRTOL1

    PubMed Central

    Beller, H. R.; Spormann, A. M.

    1997-01-01

    Permeabilized cells of toluene-mineralizing, sulfate-reducing strain PRTOL1 catalyzed the addition of toluene to fumarate to form benzylsuccinate under anaerobic conditions. Recent in vitro studies with two toluene-mineralizing, denitrifying bacteria demonstrated the same fumarate addition reaction and indicated that it may be the first step of anaerobic toluene degradation. This study with strain PRTOL1 shows that anaerobic toluene activation by fumarate addition occurs in bacteria as disparate as sulfate-reducing and denitrifying species (members of the delta and beta subclasses of the Proteobacteria, respectively). PMID:16535701

  13. Sulfate-reducing bacteria in rice field soil and on rice roots.

    PubMed

    Wind, T; Stubner, S; Conrad, R

    1999-05-01

    Rice plants that were grown in flooded rice soil microcosms were examined for their ability to exhibit sulfate reducing activity. Washed excised rice roots showed sulfate reduction potential when incubated in anaerobic medium indicating the presence of sulfate-reducing bacteria. Rice plants, that were incubated in a double-chamber (phylloshpere and rhizosphere separated), showed potential sulfate reduction rates in the anoxic rhizosphere compartment. These rates decreased when oxygen was allowed to penetrate through the aerenchyma system of the plants into the anoxic root compartment, indicating that sulfate reducers on the roots were partially inhibited by oxygen or that sulfate was regenerated by oxidation of reduced S-compounds. The potential activity of sulfate reducers on rice roots was consistent with MPN enumerations showing that H2-utilizing sulfate-reducing bacteria were present in high numbers on the rhizoplane (4.1 x 10(7) g-1 root fresh weight) and in the adjacent rhizosperic soil (2.5 x 10(7) g-1 soil dry weight). Acetate-oxidizing sulfate reducers, on the other hand, showed highest numbers in the unplanted bulk soil (1.9 x 10(6) g-1 soil dry weight). Two sulfate reducing bacteria were isolated from the highest dilutions of the MPN series and were characterized physiologically and phylogenetically. Strain F1-7b which was isolated from the rhizoplane with H2 as electron donor was related to subgroup II of the family Desulfovibrionaceae. Strain EZ-2C2, isolated from the rhizoplane on acetate, grouped together with Desulforhabdus sp. and Syntrophobacter wolinii. Other strains of sulfate-reducing bacteria originated from bulk soil of rice soil microcosms and were isolated using different electron donors. From these isolates, strains R-AcA1, R-IbutA1, R-PimA1 and R-AcetonA170 were Gram-positive bacteria which were affiliated with the genus Desulfotomaculum. The other isolates were members of subgroup II of the Desulfovibrionaceae (R-SucA1 and R-LacA1), were

  14. Biogeochemistry. Sulfate reducers--dominant players in a low-oxygen world?

    PubMed

    Vasconcelos, C; McKenzie, J A

    2000-12-01

    Sulfate reducing bacteria can adapt to extreme physical and chemical conditions and play an important role in global geochemical cycles, but their role in the formation of ore deposits has remained controversial. Strong support for such a role is provided by Labrenz et al., who have discovered sulfate-reducing bacteria that can tolerate low levels of oxygen and can precipitate zinc sulfide minerals. The results may have implications for bioremediation and may provide clues to processes that may have been more widespread in the geologic past.

  15. The effect of humic acid on uptake/adsorption of copper by a marine bacterium and two marine ciliates.

    PubMed

    Lores, E M; Snyder, R A; Pennock, J R

    1999-01-01

    The effect of humic acid (HA) on Cu uptake by a bacterium and two bacterivorus ciliates was investigated. The presence of HA resulted in a statistically significant (p<0.001) decrease in Cu associated with bacteria that were exposed to 67 microg Cu L(-1). Complexation of Cu appears to lower the availability of Cu with respect to bacterial cell surface binding and uptake. For ciliates, 10 mg HA L(-1) significantly reduced uptake of Cu by Uronema, but did not reduce uptake of Cu by Pleuronema. Uronema exposed to 67 microg Cu L(-1) accumulated 54% less Cu when 10 mg HA L(-1) was present (0.50 pg ciliate(-1) vs 0.23 pg ciliate(-1)). Uronema feeding on V. natriegens, took up less than half as much Cu as unfed Uronema when exposed to Cu without HA (0.41 pg Cu fed ciliate(-1) vs 0.86 pg Cu unfed ciliate(-1), but only 40% less when exposed to Cu and HA (0.31 pg Cu fed ciliate(-1) vs 0.51 pg Cu unfed ciliate(-1)). The lower % reduction attributable to fed ciliates in the presence of HA suggests that some of the Cu associated with HA is available through trophic processes.

  16. Genome Sequence of the Agar-Degrading Marine Bacterium Alteromonadaceae sp. Strain G7

    PubMed Central

    Kwak, Min-Jung; Song, Ju Yeon; Kim, Byung Kwon; Chi, Won-Jae; Kwon, Soon-Kyeong; Choi, Soobeom; Chang, Yong-Keun

    2012-01-01

    Here, we present the high-quality draft genome sequence of the agar-degrading marine gammaproteobacterium Alteromonadaceae sp. strain G7, which was isolated from coastal seawater to be utilized as a bioresource for production of agar-derived biofuels. The 3.91-Mb genome contains a number of genes encoding algal polysaccharide-degrading enzymes such as agarases and sulfatases. PMID:23209220

  17. Biogeography of the ubiquitous marine bacterium Alteromonas macleodii determined by multilocus sequence analysis.

    PubMed

    Ivars-Martínez, Elena; D'Auria, Giuseppe; Rodríguez-Valera, Francisco; Sânchez-Porro, Cristina; Ventosa, Antonio; Joint, Ian; Mühling, Martin

    2008-09-01

    Twenty-three isolates of the widely distributed marine bacteria Alteromonas macleodii have been analysed by multilocus sequence analysis combined with phylogenetic and multivariate statistical analyses. The strains originated from the Pacific Ocean, Mediterranean Sea, English Channel, Black Sea and Thailand. Using the nucleotide sequences of nine loci for each of the 23 isolates, a robust identification was achieved of different clades within the single species. Strains generally clustered with the depth in the water column from which the isolate originated. Strains also showed more recombination with isolates from the same vicinity, suggesting that genetic exchange plays a role in diversification of planktonic marine prokaryotes. This study thus shows for the first time for a large set of isolates of a species of planktonic marine prokaryotes that multilocus sequence analysis overcomes the problems associated with the analysis of individual marker genes or presence of extensive recombination events. It can thus achieve intraspecific identification to the level of genotypes and, by comparison with relevant environmental data, ecotypes.

  18. Pseudomonas glareae sp. nov., a marine sediment-derived bacterium with antagonistic activity.

    PubMed

    Romanenko, Lyudmila A; Tanaka, Naoto; Svetashev, Vassilii I; Mikhailov, Valery V

    2015-06-01

    An aerobic, Gram-negative, motile, rod-shaped bacterium designated KMM 9500(T) was isolated from a sediment sample collected from the Sea of Japan seashore. Comparative 16S rRNA gene sequence analysis affiliated strain KMM 9500(T) to the genus Pseudomonas as a distinct subline clustered with Pseudomonas marincola KMM 3042(T) and Pseudomonas segetis KCTC 12331(T) sharing the highest similarities of 98 and 97.9 %, respectively. Strain KMM 9500(T) was characterized by mainly possessing ubiquinone Q-9, and by the predominance of C18:1 ω7c, C16:1 ω7c, and C16:0 followed by C12:0 in its fatty acid profile. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unknown aminophospholipid, and unknown phospholipids. Strain KMM 9500(T) was found to inhibit growth of Gram-negative and Gram-positive indicatory microorganisms. Based on the phylogenetic analysis and distinctive phenotypic characteristics, strain 9500(T) is concluded to represent a novel species of the genus Pseudomonas, for which the name Pseudomonas glareae sp. nov. is proposed. The type strain of the species is strain KMM 9500(T) (=NRIC 0939(T)).

  19. Extracellular haem peroxidases mediate Mn(II) oxidation in a marine Roseobacter bacterium via superoxide production.

    PubMed

    Andeer, Peter F; Learman, Deric R; McIlvin, Matt; Dunn, James A; Hansel, Colleen M

    2015-10-01

    Manganese (Mn) oxides are among the strongest sorbents and oxidants in environmental systems. A number of biotic and abiotic pathways induce the oxidation of Mn(II) to Mn oxides. Here, we use a combination of proteomic analyses and activity assays, to identify the enzyme(s) responsible for extracellular superoxide-mediated Mn oxide formation by a bacterium within the ubiquitous Roseobacter clade. We show that animal haem peroxidases (AHPs) located on the outer membrane and within the secretome are responsible for Mn(II) oxidation. These novel peroxidases have previously been implicated in direct Mn(II) oxidation by phylogenetically diverse bacteria. Yet, we show that in this Roseobacter species, AHPs mediate Mn(II) oxidation not through a direct reaction but by producing superoxide and likely also by degrading hydrogen peroxide. These findings point to a eukaryotic-like oscillatory oxidative-peroxidative enzymatic cycle by these AHPs that leads to Mn oxide formation by this organism. AHP expression appears unaffected by Mn(II), yet the large energetic investment required to produce and secrete these enzymes points to an as yet unknown physiological function. These findings are further evidence that bacterial peroxidases and secreted enzymes, in general, are unappreciated controls on the cycling of metals and reactive oxygen species (ROS), and by extension carbon, in natural systems.

  20. DESIGNING SULFATE-REDUCING BACTERIA FIELD BIOREACTORS USING THE BEST MODEL

    EPA Science Inventory

    BEST (bioreactor economics, size and time of operation) is a spreadsheet-based model that is used in conjunction with a public domain computer software package, PHREEQCI. BEST is intended to be used in the design process of sulfate-reducing bacteria (SRB)field bioreactors to pas...

  1. DESIGNING SULFATE-REDUCING BACTERIA FIELD-BIOREACTORS USING THE BEST MODEL

    EPA Science Inventory

    DESIGNING SULFATE-REDUCING BACTERIA FIELD-BIOREACTORS USING THE BEST MODEL

    Marek H. Zaluski1,3, Brian T. Park1, Diana R. Bless2

    1 MSE Technology Applications; 200 Technology Way, Butte, Montana 59701, USA
    2 U.S. EPA, Office of Research and Development, Cincinna...

  2. Temperature-Dependent Variations in Sulfate-Reducing Communities Associated with a Terrestrial Hydrocarbon Seep

    PubMed Central

    Cheng, Ting-Wen; Lin, Li-Hung; Lin, Yue-Ting; Song, Sheng-Rong; Wang, Pei-Ling

    2014-01-01

    Terrestrial hydrocarbon seeps are an important source of naturally emitted methane over geological time. The exact community compositions responsible for carbon cycling beneath these surface features remain obscure. As sulfate reduction represents an essential process for anoxic organic mineralization, this study collected muddy fluids from a high-temperature hydrocarbon seep in Taiwan and analyzed community structures of sulfate-supplemented sediment slurries incubated anoxically at elevated temperatures. The results obtained demonstrated that sulfate consumption occurred between 40°C and 80°C. Dominant potential sulfate reducers included Desulfovibrio spp., Desulfonatronum spp., Desulforhabdus spp., and Desulfotomaculum spp. at 40°C, Thermodesulfovibrio spp. at 50°C, Thermodesulfovibrio spp. and Thermacetogenium spp. at 60°C, Thermacetogenium spp. and Archaeoglobus spp. at 70°C, and Archaeoglobus spp. at 80°C. None of these potential sulfate reducers exceeded 7% of the community in the untreated sample. Since no exogenous electron donor was provided during incubation, these sulfate reducers appeared to rely on the degradation of organic matter inherited from porewater and sediments. Aqueous chemistry indicated that fluids discharged in the region represented a mixture of saline formation water and low-salinity surface water; therefore, these lines of evidence suggest that deeply-sourced, thermophilic and surface-input, mesophilic sulfate-reducing populations entrapped along the subsurface fluid transport could respond rapidly once the ambient temperature is adjusted to a range close to their individual optima. PMID:25273230

  3. Response And Recovery Of Sulfate-Reducing Biochemical Reactors From Aerobic Stress Events

    EPA Science Inventory

    Microbially-mediated treatment of mining-influenced water (MIW) through the implementation of sulfate-reducing biochemical reactors (BCRs) is an attractive option for passive, in situ remediation with low operating costs and reduced maintenance requirements. However, BCRs can be...

  4. Response And Recovery Of Sulfate-Reducing Biochemical Reactors From Aerobic Stress Events (Presentation)

    EPA Science Inventory

    Microbially-mediated treatment of mining-influenced water (MIW) through the implementation of sulfate-reducing biochemical reactors (BCR) is an attractive option for passive, in situ remediation with low operating costs and reduced maintenance requirements. However, BCRs can be ...

  5. Mine Waste Technology Program. In Situ Source Control Of Acid Generation Using Sulfate-Reducing Bacteria

    EPA Science Inventory

    This report summarizes the results of the Mine Waste Technology Program (MWTP) Activity III, Project 3, In Situ Source Control of Acid Generation Using Sulfate-Reducing Bacteria, funded by the U.S. Environmental Protection Agency (EPA) and jointly administered by EPA and the U.S....

  6. COMPUTER SIMULATOR (BEST) FOR DESIGNING SULFATE-REDUCING BACTERIA FIELD BIOREACTORS

    EPA Science Inventory

    BEST (bioreactor economics, size and time of operation) is a spreadsheet-based model that is used in conjunction with public domain software, PhreeqcI. BEST is used in the design process of sulfate-reducing bacteria (SRB) field bioreactors to passively treat acid mine drainage (A...

  7. Structural and Functional Dynamics of Sulfate-Reducing Populations in Bacterial Biofilms

    PubMed Central

    Santegoeds, Cecilia M.; Ferdelman, Timothy G.; Muyzer, Gerard; de Beer, Dirk

    1998-01-01

    We describe the combined application of microsensors and molecular techniques to investigate the development of sulfate reduction and of sulfate-reducing bacterial populations in an aerobic bacterial biofilm. Microsensor measurements for oxygen showed that anaerobic zones developed in the biofilm within 1 week and that oxygen was depleted in the top 200 to 400 μm during all stages of biofilm development. Sulfate reduction was first detected after 6 weeks of growth, although favorable conditions for growth of sulfate-reducing bacteria (SRB) were present from the first week. In situ hybridization with a 16S rRNA probe for SRB revealed that sulfate reducers were present in high numbers (approximately 108 SRB/ml) in all stages of development, both in the oxic and anoxic zones of the biofilm. Denaturing gradient gel electrophoresis (DGGE) showed that the genetic diversity of the microbial community increased during the development of the biofilm. Hybridization analysis of the DGGE profiles with taxon-specific oligonucleotide probes showed that Desulfobulbus and Desulfovibrio were the main sulfate-reducing bacteria in all biofilm samples as well as in the bulk activated sludge. However, different Desulfobulbus and Desulfovibrio species were found in the 6th and 8th weeks of incubation, respectively, coinciding with the development of sulfate reduction. Our data indicate that not all SRB detected by molecular analysis were sulfidogenically active in the biofilm. PMID:9758792

  8. Microbial Activity In The Peerless Jenny King Sulfate Reducing Bioreactor System (Presentation)

    EPA Science Inventory

    The Peerless Jenny King treatment system is a series of four sulfate reducing bioreactor cells installed to treat acid mine drainage in the Upper Tenmile Creek Superfund Site located in the Rimini Mining District, near Helena MT. The system consists of a wetland pretreatment fol...

  9. Microbial Activity In The Peerless Jenny King Sulfate Reducing Bioreactors System

    EPA Science Inventory

    The Peerless Jenny King treatment system is a series of four sulfate reducing bioreactor cells installed to treat acid mine drainage in the Upper Tenmile Creek Superfund Site located in the Rimini Mining District, near Helena, MT. The system consists of a wetland pretreatment fo...

  10. Vibrio psychroerythrus sp. n.: Classification of the Psychrophilic Marine Bacterium, NRC 1004

    PubMed Central

    D'aoust, J. Y.; Kushner, D. J.

    1972-01-01

    A red-pigmented organism, formerly known as marine psychrophile NRC 1004, has been classified as Vibrio psychroerythrus sp. n. Classification was mainly based on morphology, the ability of the organism to oxidize and ferment glucose, its sensitivity to vibriostat 0/129, and its deoxyribonucleic acid base composition of 40.0 moles% guanine plus cytosine, determined by thermal denaturation. The organism gave positive reactions for catalase, oxidase, and starch hydrolysis and produced acid from maltose and dextrin but not from arabinose. It was indole- and citrate-negative and reduced nitrate to nitrite without producing gas. PMID:5053463

  11. Dimethylsulfide is an energy source for the heterotrophic marine bacterium Sagittula stellata.

    PubMed

    Boden, Rich; Murrell, J Colin; Schäfer, Hendrik

    2011-09-01

    Dimethylsulfide (DMS) is a volatile organosulfur compound, ubiquitous in the oceans, that has been credited with various roles in biogeochemical cycling and in climate control. Various oceanic sinks of DMS are known - both chemical and biological - although they are poorly understood. In addition to the utilization of DMS as a carbon or a sulfur source, some Bacteria are known to oxidize it to dimethylsulfoxide (DMSO). Sagittula stellata is a heterotrophic member of the Alphaproteobacteria found in marine environments. It has been shown to oxidize DMS during heterotrophic growth on sugars, but the reasons for and the mechanisms of this oxidation have not been investigated. Here, we show that the oxidation of DMS to DMSO is coupled to ATP synthesis in S. stellata and that DMS acts as an energy source during chemoorganoheterotrophic growth of the organism on fructose and on succinate. DMS dehydrogenase (which is responsible for the oxidation of DMS to DMSO in other marine Bacteria) and DMSO reductase activities were absent from cells grown in the presence of DMS, indicating an alternative route of DMS oxidation in this organism.

  12. Antiangiogenic activity of low-temperature lysozyme from a marine bacterium in vivo and in vitro

    NASA Astrophysics Data System (ADS)

    Wang, Zhenhua; Liu, Jincheng; Su, Ai; Sun, Mi; Wang, Chunbo

    2009-11-01

    We extracted marine low-temperature lysozyme (MLTL), a novel lysozyme, from a marine microorganism through fermentation. Our previous study suggested that a low molecular weight (16 kDa) may exert anti-tumor activity through antiangiogenesis. In this study, we extracted a high weight (39 kDa) and investigated its antiangiogenic activity in vivo and in vitro. Using zebrafish embryos as an in vivo study model, we found that treatment with MLTL significantly inhibited the growth of subintestinal vessels (SIVs) in a dose-dependent manner and that 400 µg/ml MLTL was sufficient to block the growth of SIVs. An in vitro study conducted using human umbilical vein endothelial cells (HUVECs) revealed that MLTL suppressed the proliferation, migration and tube formation of HUVECs in a dose-dependent manner. Interestingly, assays by flow cytometry and DNA electrophoresis indicated that MLTL was able to induce apoptosis of HUVECs. Moreover, further study demonstrated that the disruption of intracellular Ca2+ homeostasis may play an important role in MLTL induced apoptosis of HUVECs. Taken together, the results of this study demonstrate for the first time that MLTL inhibits angiogenesis through its pleiotropic effects on vascular endothelial cells and induces apoptosis through regulation of cellular Ca2+ levels. The results of this study also revealed a possible mechanism underlying the antiangiogenic effect of MLTL and suggested that MLTL may be a promising new antiangiogenic agent for use in cancer therapy.

  13. Dealing with salinity extremes and nitrogen limitation - an unexpected strategy of the marine bacterium Dinoroseobacter shibae.

    PubMed

    Kleist, Sarah; Ulbrich, Marcus; Bill, Nelli; Schmidt-Hohagen, Kerstin; Geffers, Robert; Schomburg, Dietmar

    2017-03-01

    Having the right coping strategy for changes in osmolarity or desiccation is essential for the survival of every cell. So far, nothing is known about compatible solutes and the salt adaptation of the marine Rhodobacteraceae. The family member Dinoroseobacter shibae DFL12(T) is shown here to form the compatible solutes α-glucosylglycerol (GG) and α-glucosylglycerate (GGA). To our knowledge, this is the first experimental evidence for GGA formation within the α-proteobacteria. Together with glutamate and putrescine, these substances enable good growth in salinity ranging from 0.3% to 5%. A salinity of 5% leads to a biomass share of 7.6% of compatible solutes and the very low salt level of 0.3% results in an 18-fold increased putrescine concentration compared with environmental conditions. Additionally, the substitution of glutamate by GGA has been shown during exposure to nitrogen limitation and in the stationary growth phase of the organism. Salt shock transcriptome analysis of D. shibae has revealed the essential role of its 153 kb chromid, which carries the genes for GG biosynthesis and several transport and exchange systems. Within the family of Rhodobacteraceae, the genomic capability of forming GG and GGA is strictly restricted to marine family members.

  14. The Distribution of Thermophilic Sulfate-reducing Bacteria Along an Estuarine Gradient Reveals Multiple Origins of Endospores in Estuarine Sediments

    NASA Astrophysics Data System (ADS)

    Bell, E.

    2015-12-01

    Cold marine sediments harbour inactive spores of thermophilic bacteria. These misplaced thermophiles are genetically similar to microorganisms detected in deep biosphere environments, leading to the hypothesis that seabed fluid flow transports thermophiles out of warm subsurface environments and into the ocean. Estuaries form the transition between the marine and the terrestrial biosphere and are influenced by tidal currents, surface run-off and groundwater seepage. Endospores from thermophilic bacteria present in estuarine sediments could therefore originate from a number of sources that may influence the estuary differently. We have therefore tested the hypothesis that this will lead to a gradient in the composition of thermophilic endospore populations in estuarine sediments. The distribution of thermophilic spore-forming sulfate-reducing bacteria along an estuarine gradient from freshwater (River Tyne, UK) to marine (North Sea) was investigated. Microbial community analysis by 16S rRNA gene amplicon sequencing revealed changes in the thermophilic population enriched at different locations within the estuary. Certain species were only detected at the marine end, highlighting possible links to deep marine biosphere habitats such as oil reservoirs that harbour closely related Desulfotomaculum spp. Conversely, other taxa were predominantly observed in the freshwater reaches of the estuary indicating dispersal from an upstream or terrestrial source. Different endospore populations were enriched dependent on incubation temperature and spore heat-resistance. Microcosms incubated at 50, 60 or 70°C showed a shift in the dominant species of Desulfotomaculum enriched as the temperature increased. Microcosms triple-autoclaved at 121°C prior to incubation still showed rapid and reproducible sulfate-reduction and some Desulfotomaculum spp. remained active after autoclaving at 130°C. These results show that temperature physiology and biogeographic patterns can be used to

  15. Shewanella algicola sp. nov., a marine bacterium isolated from brown algae.

    PubMed

    Kim, Ji-Young; Yoo, Han-Su; Lee, Dong-Heon; Park, So-Hyun; Kim, Young-Ju; Oh, Duck-Chul

    2016-06-01

    A Gram-stain-negative, aerobic, rod-shaped bacterium motile by means of a single polar flagella, strain ST-6T, was isolated from a brown alga (Sargassum thunbergii) collected in Jeju, Republic of Korea. Strain ST-6T was psychrotolerant, growing at 4-30 °C (optimum 20 °C). Phylogenetic analysis based on 16S rRNA and gyrB gene sequences revealed that strain ST-6T belonged to a distinct lineage in the genus Shewanella. Strain ST-6T was related most closely to Shewanella basaltis J83T, S. gaetbuli TF-27T, S. arctica IT12T, S. vesiculosa M7T and S. aestuarii SC18T, showing 96-97 % and 85-70 % 16S rRNA and gyrB gene sequences similarities, respectively. DNA-DNA relatedness values between strain ST-6T and the type strains of two species of the genus Shewanella were <22.6 %. The major cellular fatty acids (>5 %) were summed feature 3 (comprising C16:1ω7c and/ or iso-C15:0 2-OH), C16:0, iso-C13:0 and C17:1ω8c. The DNA G+C content of strain ST-6Twas 42.4 mol%, and the predominant isoprenoid quinones were menaquinone MK-7 and ubiquinones Q-7 and Q-8. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain ST-6T is considered to represent a novel species of the genus Shewanella, for which the name Shewanella algicola sp. nov. is proposed. The type strain is ST-6T (= KCTC 23253T = JCM 31091T).

  16. Complete Genome Sequence of the Marine, Chemolithoautotrophic, Ammonia-Oxidizing Bacterium Nitrosococcus oceani ATCC 19707

    SciTech Connect

    Klots, Martin G.; Arp, D J; Chain, Patrick S; El-Sheikh, Amal F.; Hauser, Loren John; Hommes, Norman G.; Larimer, Frank W; Malfatti, Stephanie; Norton, Jeanette M.; Poret-Peterson, Amisha T.; Vergez, Lisa; Ward, Bess B.

    2006-01-01

    The gammaproteobacterium Nitrosococcus oceani (ATCC 19707) is a gram-negative obligate chemolithoautotroph capable of extracting energy and reducing power from the oxidation of ammonia to nitrite. Sequencing and annotation of the genome revealed a single circular chromosome (3,481,691 bp; G+C content of 50.4%) and a plasmid (40,420 bp) that contain 3,052 and 41 candidate protein-encoding genes, respectively. The genes encoding proteins necessary for the function of known modes of lithotrophy and autotrophy were identified. Contrary to betaproteobacterial nitrifier genomes, the N. oceani genome contained two complete rrn operons. In contrast, only one copy of the genes needed to synthesize functional ammonia monooxygenase and hydroxylamine oxidoreductase, as well as the proteins that relay the extracted electrons to a terminal electron acceptor, were identified. The N. oceani genome contained genes for 13 complete two-component systems. The genome also contained all the genes needed to reconstruct complete central pathways, the tricarboxylic acid cycle, and the Embden-Meyerhof-Parnass and pentose phosphate pathways. The N. oceani genome contains the genes required to store and utilize energy from glycogen inclusion bodies and sucrose. Polyphosphate and pyrophosphate appear to be integrated in this bacterium's energy metabolism, stress tolerance, and ability to assimilate carbon via gluconeogenesis. One set of genes for type I ribulose-1,5-bisphosphate carboxylase/oxygenase was identified, while genes necessary for methanotrophy and for carboxysome formation were not identified. The N. oceani genome contains two copies each of the genes or operons necessary to assemble functional complexes I and IV as well as ATP synthase (one H+-dependent F0F1 type, one Na+-dependent V type).

  17. Complete Genome Sequence of the Marine, Chemolithoautotrophic, Ammonia-Oxidizing Bacterium Nitrosococcus oceani ATCC 19707†

    PubMed Central

    Klotz, Martin G.; Arp, Daniel J.; Chain, Patrick S. G.; El-Sheikh, Amal F.; Hauser, Loren J.; Hommes, Norman G.; Larimer, Frank W.; Malfatti, Stephanie A.; Norton, Jeanette M.; Poret-Peterson, Amisha T.; Vergez, Lisa M.; Ward, Bess B.

    2006-01-01

    The gammaproteobacterium Nitrosococcus oceani (ATCC 19707) is a gram-negative obligate chemolithoautotroph capable of extracting energy and reducing power from the oxidation of ammonia to nitrite. Sequencing and annotation of the genome revealed a single circular chromosome (3,481,691 bp; G+C content of 50.4%) and a plasmid (40,420 bp) that contain 3,052 and 41 candidate protein-encoding genes, respectively. The genes encoding proteins necessary for the function of known modes of lithotrophy and autotrophy were identified. Contrary to betaproteobacterial nitrifier genomes, the N. oceani genome contained two complete rrn operons. In contrast, only one copy of the genes needed to synthesize functional ammonia monooxygenase and hydroxylamine oxidoreductase, as well as the proteins that relay the extracted electrons to a terminal electron acceptor, were identified. The N. oceani genome contained genes for 13 complete two-component systems. The genome also contained all the genes needed to reconstruct complete central pathways, the tricarboxylic acid cycle, and the Embden-Meyerhof-Parnass and pentose phosphate pathways. The N. oceani genome contains the genes required to store and utilize energy from glycogen inclusion bodies and sucrose. Polyphosphate and pyrophosphate appear to be integrated in this bacterium's energy metabolism, stress tolerance, and ability to assimilate carbon via gluconeogenesis. One set of genes for type I ribulose-1,5-bisphosphate carboxylase/oxygenase was identified, while genes necessary for methanotrophy and for carboxysome formation were not identified. The N. oceani genome contains two copies each of the genes or operons necessary to assemble functional complexes I and IV as well as ATP synthase (one H+-dependent F0F1 type, one Na+-dependent V type). PMID:16957257

  18. The Complete Genome Sequence of the Marine, Chemolithoautotrophic, Ammonia-Oxidizing Bacterium Nitrosococcus oceani ATCC19707

    SciTech Connect

    Klotz, M G; Arp, D J; Chain, P S; El-Sheikh, A F; Hauser, L J; Hommes, N G; Larimer, F W; Malfatti, S A; Norton, J M; Poret-Peterson, A T; Vergez, L M; Ward, B B

    2006-08-03

    The Gammaproteobacterium, Nitrosococcus oceani (ATCC 19707), is a Gram-negative obligate chemolithoautotroph capable of extracting energy and reducing power from the oxidation of ammonia to nitrite. Sequencing and annotation of the genome revealed a single circular chromosome (3,481,691 bp; 50.4% G+C) and a plasmid (40,420 bp) that contain 3052 and 41 candidate protein-encoding genes, respectively. The genes encoding proteins necessary for the function of known modes of lithotrophy and autotrophy were identified. In contrast to betaproteobacterial nitrifier genomes, the N. oceani genome contained two complete rrn operons. In contrast, only one copy of the genes needed to synthesize functional ammonia monooxygenase and hydroxylamine oxidoreductase, as well as the proteins that relay the extracted electrons to a terminal electron acceptor were identified. The N. oceani genome contained genes for 13 complete two-component systems. The genome also contained all the genes needed to reconstruct complete central pathways, the tricarboxylic acid cycle and the Embden-Meyerhof-Parnass and pentose phosphate pathways. The N. oceani genome contains the genes required to store and utilize energy from glycogen inclusion bodies and sucrose. Polyphosphate and pyrophosphate appear to be integrated in this bacterium's energy metabolism, stress tolerance and the ability to assimilate carbon via gluconeogenesis. One set of genes for type I RuBisCO was identified, while genes necessary for methanotrophy and for carboxysome formation were not identified. The N. oceani genome contains two copies each of the genes or operons necessary to assemble functional complexes I and IV as well as ATP synthase (one H{sup +}-dependent F{sub 0}F{sub 1}-type, one Na{sup +}-dependent V-type).

  19. Phosphate Limitation Triggers the Dissolution of Precipitated Iron by the Marine Bacterium Pseudovibrio sp. FO-BEG1

    PubMed Central

    Romano, Stefano; Bondarev, Vladimir; Kölling, Martin; Dittmar, Thorsten; Schulz-Vogt, Heide N.

    2017-01-01

    Phosphorus is an essential nutrient for all living organisms. In bacteria, the preferential phosphorus source is phosphate, which is often a limiting macronutrient in many areas of the ocean. The geochemical cycle of phosphorus is strongly interconnected with the cycles of other elements and especially iron, because phosphate tends to adsorb onto iron minerals, such as iron oxide formed in oxic marine environments. Although the response to either iron or phosphate limitation has been investigated in several bacterial species, the metabolic interplay between these two nutrients has rarely been considered. In this study we evaluated the impact of phosphate limitation on the iron metabolism of the marine bacterium Pseudovibrio sp. FO-BEG1. We observed that phosphate limitation led to an initial decrease of soluble iron in the culture up to three times higher than under phosphate surplus conditions. Similarly, a decrease in soluble cobalt was more pronounced under phosphate limitation. These data point toward physiological changes induced by phosphate limitation that affect either the cellular surface and therefore the metal adsorption onto it or the cellular metal uptake. We discovered that under phosphate limitation strain FO-BEG1, as well as selected strains of the Roseobacter clade, secreted iron-chelating molecules. This leads to the hypothesis that these bacteria might release such molecules to dissolve iron minerals, such as iron-oxyhydroxide, in order to access the adsorbed phosphate. As the adsorption of phosphate onto iron minerals can significantly decrease phosphate concentrations in the environment, the observed release of iron-chelators might represent an as yet unrecognized link between the biogeochemical cycle of phosphorus and iron, and it suggests another biological function of iron-chelating molecules in addition to metal-scavenging. PMID:28352252

  20. Isolation and identification of a bacterium from marine shrimp digestive tract: A new degrader of starch and protein

    NASA Astrophysics Data System (ADS)

    Li, Jiqiu; Tan, Beiping; Mai, Kangsen

    2011-09-01

    It is a practical approach to select candidate probiotic bacterial stains on the basis of their special traits. Production of digestive enzyme was used as a trait to select a candidate probiotic bacterial strain in this study. In order to select a bacterium with the ability to degrade both starch and protein, an ideal bacterial strain STE was isolated from marine shrimp ( Litopenaeus vannamei) intestines by using multiple selective media. The selected isolate STE was identified on the basis of its morphological, physiological, and biochemical characteristics as well as molecular analyses. Results of degradation experiments confirmed the ability of the selected isolate to degrade both starch and casein. The isolate STE was aerobic, Gram-negative, rod-shaped, motile and non-spore-forming, and had catalase and oxidase activities but no glucose fermentation activity. Among the tested carbon/nitrogen sources, only Tween40, alanyl-glycine, aspartyl-glycine, and glycyl-l-glutamic acid were utilized by the isolate STE. Results of homology comparison analyses of the 16S rDNA sequences showed that the isolate STE had a high similarity to several Pseudoalteromonas species and, in the phylogenetic tree, grouped with P. ruthenica with maximum bootstrap support (100%). In conclusion, the isolate STE was characterized as a novel strain belonging to the genus Pseudoalteromonas. This study provides a further example of a probiotic bacterial strain with specific characteristics isolated from the host gastrointestinal tract.

  1. A CMP-N-acetylneuraminic acid synthetase purified from a marine bacterium, Photobacterium leiognathi JT-SHIZ-145.

    PubMed

    Kajiwara, Hitomi; Mine, Toshiki; Miyazaki, Tatsuo; Yamamoto, Takeshi

    2011-01-01

    A cytidine 5'-monophospho-N-acetylneuraminic acid (CMP-Neu5Ac) synthetase was found in a crude extract prepared from Photobacterium leiognathi JT-SHIZ-145, a marine bacterium that also produces a β-galactoside α2,6-sialyltransferase. The CMP-Neu5Ac synthetase was purified from the crude extract of the cells by a combination of anion-exchange and gel filtration column chromatography. The purified enzyme migrated as a single band (60 kDa) on sodium dodecylsulfate-polyacrylamide gel electrophoresis. The activity of the enzyme was maximal at 35 °C at pH 9.0, and the synthetase required Mg(2+) for activity. Although these properties are similar to those of other CMP-Neu5Ac synthetases isolated from bacteria, this synthetase produced not only CMP-Neu5Ac from cytidine triphosphate and Neu5Ac, but also CMP-N-glycolylneuraminic acid from cytidine triphosphate and N-glycolylneuraminic acid, unlike CMP-Neu5Ac synthetase purified from Escherichia coli.

  2. Enhancing production of a 24-membered ring macrolide compound by a marine bacterium using response surface methodology*

    PubMed Central

    Chen, Hua; Wu, Mian-bin; Chen, Zheng-jie; Wang, Ming-lu; Lin, Jian-ping; Yang, Li-rong

    2013-01-01

    A 24-membered ring macrolide compound, macrolactin A has potential applications in pharmaceuticals for its anti-infectious and antiviral activity. In this study, macrolactin A was produced by a marine bacterium, which was identified as Bacillus subtilis by 16S ribosomal RNA (rRNA) sequence analysis. Electrospray ionization mass spectrometry (ESI/MS) and nuclear magnetic resonance (NMR) spectroscopy analyses were used to characterize this compound. To improve the production, response surface methodology (RSM) involving Box-Behnken design (BBD) was employed. Faeces bombycis, the main by-product in sericulture, was used as a nitrogen source in fermentation. The interactions between three significant factors, F. bombycis, soluble starch, and (NH4)2SO4 were investigated. A quadratic model was constructed to fit the production and the factors. Optimum medium composition was obtained by analysis of the model. When cultivated in the optimum medium, the production of macrolactin A was increased to 851 mg/L, 2.7 times as compared to the original. This study is also useful to find another way in utilizing F. bombycis. PMID:23549852

  3. Interaction of Pb(II) and biofilm associated extracellular polymeric substances of a marine bacterium Pseudomonas pseudoalcaligenes NP103

    NASA Astrophysics Data System (ADS)

    Kumari, Supriya; Mangwani, Neelam; Das, Surajit

    2017-02-01

    Three-dimensional excitation-emission matrix (3D EEM) fluorescence spectroscopy and attenuated total reflectance fourier-transformed infrared spectroscopy (ATR-FTIR) was used to evaluate the interaction of biofilm associated extracellular polymeric substances (EPS) of a marine bacterium Pseudomonas pseudoalcaligenes NP103 with lead [Pb(II)]. EEM fluorescence spectroscopic analysis revealed the presence of one protein-like fluorophore in the EPS of P. pseudoalcaligenes NP103. Stern-Volmer equation indicated the existence of only one binding site (n = 0.789) in the EPS of P. pseudoalcaligenes NP103. The interaction of Pb(II) with EPS was spontaneous at room temperature (∆ G = - 2.78 kJ/K/mol) having binding constant (Kb) of 2.59 M- 1. ATR-FTIR analysis asserted the involvement of various functional groups such as sulphydryl, phosphate and hydroxyl and amide groups of protein in Pb(II) binding. Scanning electron microscopy (SEM) and fluorescence microscopy analysis displayed reduced growth of biofilm with altered surface topology in Pb(II) supplemented medium. Energy dispersive X-ray spectroscopy (EDX) analysis revealed the entrapment of Pb in the EPS. Uronic acid, a characteristic functional group of biofilm, was observed in 1H NMR spectroscopy. The findings suggest that biofilm associated EPS are perfect organic ligands for Pb(II) complexation and may significantly augment the bioavailability of Pb(II) in the metal contaminated environment for subsequent sequestration.

  4. Aerobic-heterotrophic nitrogen removal through nitrate reduction and ammonium assimilation by marine bacterium Vibrio sp. Y1-5.

    PubMed

    Li, Yating; Wang, Yanru; Fu, Lin; Gao, Yizhan; Zhao, Haixia; Zhou, Weizhi

    2017-04-01

    An aerobic marine bacterium Vibrio sp. Y1-5 was screened to achieve efficient nitrate and ammonium removal simultaneously and fix nitrogen in cells without N loss. Approximately 98.0% of nitrate (100mg/L) was removed in 48h through assimilatory nitrate reduction and nitrate reductase was detected in the cytoplasm. Instead of nitrification, the strain assimilated ammonium directly, and it could tolerate as high as 1600mg/L ammonium concentration while removing 844.6mg/L. In addition, ammonium assimilation occurred preferentially in the medium containing nitrate and ammonium with a total nitrogen (TN) removal efficiency of 80.4%. The results of nitrogen balance and Fourier infrared spectra illustrated that the removed nitrogen was all transformed to protein or stored as organic nitrogen substances in cells and no N was lost in the process. Toxicological studies with the brine shrimp species Artemia naupliia indicated that Vibrio sp. Y1-5 can be applied in aquatic ecosystems safely.

  5. Ieodoglucomide C and Ieodoglycolipid, New Glycolipids from a Marine-Derived Bacterium Bacillus licheniformis 09IDYM23.

    PubMed

    Tareq, Fakir Shahidullah; Lee, Hyi-Seung; Lee, Yeon-Ju; Lee, Jong Seok; Shin, Hee Jae

    2015-05-01

    Chemical examination of the ethyl acetate extract from the fermentation broth of the marine-derived bacterium Bacillus licheniformis resulted in the isolation of two new glycolipids, ieodoglucomide C (1) and ieodoglycolipid (2). The structural characterization of 1 and 2 was achieved by extensive spectroscopic evidence, including 2D NMR experiments. A combination of chemical derivatization techniques followed by NMR studies, LC-MS data analysis and a literature review was deployed for the establishment of the stereo-configurations of 1 and 2. Compounds 1 and 2 exhibited good antibiotic properties against Staphylococcus aureus, Bacillus subtilis, Bacillus cereus, Salmonella typhi, Escherichia coli and Pseudomonas aeruginosa with MICs ranging from 0.01 to 0.05 μM. Furthermore, the antifungal activity of 1 and 2 was evaluated against plant pathogenic fungi Aspergillus niger, Rhizoctonia solani, Botrytis cinerea and Colletotrichum acutatum as well as the human pathogen Candida albicans. Compounds 1 and 2 inhibited the mycelial growth of these pathogens with MIC values of 0.03-0.05 μM, revealing that these compounds are good candidates for the development of new fungicides.

  6. Genome Sequence of Polycyclovorans algicola Strain TG408, an Obligate Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic Phytoplankton

    PubMed Central

    Thompson, Haydn F.; Angelova, Angelina; Whitman, William B.; Huntemann, Marcel; Copeland, Alex; Chen, Amy; Kyrpides, Nikos; Markowitz, Victor; Palaniappan, Krishnaveni; Ivanova, Natalia; Mikhailova, Natalia; Ovchinnikova, Galina; Andersen, Evan; Pati, Amrita; Stamatis, Dimitrios; Reddy, T. B. K.; Ngan, Chew Yee; Chovatia, Mansi; Daum, Chris; Shapiro, Nicole; Cantor, Michael N.; Woyke, Tanja

    2015-01-01

    Polycyclovorans algicola strain TG408 is a recently discovered bacterium associated with marine eukaryotic phytoplankton and exhibits the ability to utilize polycyclic aromatic hydrocarbons (PAHs) almost exclusively as sole sources of carbon and energy. Here, we present the genome sequence of this strain, which is 3,653,213 bp, with 3,477 genes and an average G+C content of 63.8%. PMID:25814607

  7. Genome Sequence of Porticoccus hydrocarbonoclasticus Strain MCTG13d, an Obligate Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic Phytoplankton.

    PubMed

    Gutierrez, Tony; Whitman, William B; Huntemann, Marcel; Copeland, Alex; Chen, Amy; Kyrpides, Nikos; Markowitz, Victor; Pillay, Manoj; Ivanova, Natalia; Mikhailova, Natalia; Ovchinnikova, Galina; Andersen, Evan; Pati, Amrita; Stamatis, Dimitrios; Reddy, T B K; Ngan, Chew Yee; Chovatia, Mansi; Daum, Chris; Shapiro, Nicole; Cantor, Michael N; Woyke, Tanja

    2015-06-18

    Porticoccus hydrocarbonoclasticus strain MCTG13d is a recently discovered bacterium that is associated with marine eukaryotic phytoplankton and that almost exclusively utilizes polycyclic aromatic hydrocarbons (PAHs) as the sole source of carbon and energy. Here, we present the genome sequence of this strain, which is 2,474,654 bp with 2,385 genes and has an average G+C content of 53.1%.

  8. Genome Sequence of Polycyclovorans algicola Strain TG408, an Obligate Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic Phytoplankton.

    PubMed

    Gutierrez, Tony; Thompson, Haydn F; Angelova, Angelina; Whitman, William B; Huntemann, Marcel; Copeland, Alex; Chen, Amy; Kyrpides, Nikos; Markowitz, Victor; Palaniappan, Krishnaveni; Ivanova, Natalia; Mikhailova, Natalia; Ovchinnikova, Galina; Andersen, Evan; Pati, Amrita; Stamatis, Dimitrios; Reddy, T B K; Ngan, Chew Yee; Chovatia, Mansi; Daum, Chris; Shapiro, Nicole; Cantor, Michael N; Woyke, Tanja

    2015-03-26

    Polycyclovorans algicola strain TG408 is a recently discovered bacterium associated with marine eukaryotic phytoplankton and exhibits the ability to utilize polycyclic aromatic hydrocarbons (PAHs) almost exclusively as sole sources of carbon and energy. Here, we present the genome sequence of this strain, which is 3,653,213 bp, with 3,477 genes and an average G+C content of 63.8%.

  9. Genome Sequence of Porticoccus hydrocarbonoclasticus Strain MCTG13d, an Obligate Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic Phytoplankton

    PubMed Central

    Whitman, William B.; Huntemann, Marcel; Copeland, Alex; Chen, Amy; Kyrpides, Nikos; Markowitz, Victor; Pillay, Manoj; Ivanova, Natalia; Mikhailova, Natalia; Ovchinnikova, Galina; Andersen, Evan; Pati, Amrita; Stamatis, Dimitrios; Reddy, T. B. K.; Ngan, Chew Yee; Chovatia, Mansi; Daum, Chris; Shapiro, Nicole; Cantor, Michael N.; Woyke, Tanja

    2015-01-01

    Porticoccus hydrocarbonoclasticus strain MCTG13d is a recently discovered bacterium that is associated with marine eukaryotic phytoplankton and that almost exclusively utilizes polycyclic aromatic hydrocarbons (PAHs) as the sole source of carbon and energy. Here, we present the genome sequence of this strain, which is 2,474,654 bp with 2,385 genes and has an average G+C content of 53.1%. PMID:26089431

  10. Bile acids are new products of a marine bacterium, Myroides sp. strain SM1.

    PubMed

    Maneerat, Suppasil; Nitoda, Teruhiko; Kanzaki, Hiroshi; Kawai, Fusako

    2005-06-01

    Strain SM1 was isolated as a biosurfactant-producing microorganism from seawater and presumptively identified as Myroides sp., based on morphology, biochemical characteristics and 16S rDNA sequence. The strain produced surface-active compounds in marine broth, which were purified, using emulsification activity for n-hexadecane as an indicator. The purified compounds were identified by thin-layer chromatography, (1)H- and (13)C-NMR spectra and fast atom bombardment mass spectrometry as cholic acid, deoxycholic acid and their glycine conjugates. Type strains of the genus Myroides, M. odoratus JCM7458 and M. odoramitimus JCM7460, also produced these compounds. Myroides sp. strain SM1 possessed a biosynthetic route to cholic acid from cholesterol. Thus, bile acids were found as new products of prokaryotic cells, genus Myroides.

  11. The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol.

    PubMed

    Sun, Jing; Todd, Jonathan D; Thrash, J Cameron; Qian, Yanping; Qian, Michael C; Temperton, Ben; Guo, Jiazhen; Fowler, Emily K; Aldrich, Joshua T; Nicora, Carrie D; Lipton, Mary S; Smith, Richard D; De Leenheer, Patrick; Payne, Samuel H; Johnston, Andrew W B; Davie-Martin, Cleo L; Halsey, Kimberly H; Giovannoni, Stephen J

    2016-05-16

    Marine phytoplankton produce ∼10(9) tonnes of dimethylsulfoniopropionate (DMSP) per year(1,2), an estimated 10% of which is catabolized by bacteria through the DMSP cleavage pathway to the climatically active gas dimethyl sulfide(3,4). SAR11 Alphaproteobacteria (order Pelagibacterales), the most abundant chemo-organotrophic bacteria in the oceans, have been shown to assimilate DMSP into biomass, thereby supplying this cell's unusual requirement for reduced sulfur(5,6). Here, we report that Pelagibacter HTCC1062 produces the gas methanethiol, and that a second DMSP catabolic pathway, mediated by a cupin-like DMSP lyase, DddK, simultaneously shunts as much as 59% of DMSP uptake to dimethyl sulfide production. We propose a model in which the allocation of DMSP between these pathways is kinetically controlled to release increasing amounts of dimethyl sulfide as the supply of DMSP exceeds cellular sulfur demands for biosynthesis.

  12. Antibiofilm Activity of the Marine Bacterium Pseudoalteromonas sp. Strain 3J6▿

    PubMed Central

    Dheilly, Alexandra; Soum-Soutéra, Emmanuelle; Klein, Géraldine L.; Bazire, Alexis; Compère, Chantal; Haras, Dominique; Dufour, Alain

    2010-01-01

    Biofilm formation results in medical threats or economic losses and is therefore a major concern in a variety of domains. In two-species biofilms of marine bacteria grown under dynamic conditions, Pseudoalteromonas sp. strain 3J6 formed mixed biofilms with Bacillus sp. strain 4J6 but was largely predominant over Paracoccus sp. strain 4M6 and Vibrio sp. strain D01. The supernatant of Pseudoalteromonas sp. 3J6 liquid culture (SN3J6) was devoid of antibacterial activity against free-living Paracoccus sp. 4M6 and Vibrio sp. D01 cells, but it impaired their ability to grow as single-species biofilms and led to higher percentages of nonviable cells in 48-h biofilms. Antibiofilm molecules of SN3J6 were able to coat the glass surfaces used to grow biofilms and reduced bacterial attachment about 2-fold, which might partly explain the biofilm formation defect but not the loss of cell viability. SN3J6 had a wide spectrum of activity since it affected all Gram-negative marine strains tested except other Pseudoalteromonas strains. Biofilm biovolumes of the sensitive strains were reduced 3- to 530-fold, and the percentages of nonviable cells were increased 3- to 225-fold. Interestingly, SN3J6 also impaired biofilm formation by three strains belonging to the human-pathogenic species Pseudomonas aeruginosa, Salmonella enterica, and Escherichia coli. Such an antibiofilm activity is original and opens up a variety of applications for Pseudoalteromonas sp. 3J6 and/or its active exoproducts in biofilm prevention strategies. PMID:20363799

  13. Toxic Effect of a Marine Bacterium on Aquatic Organisms and Its Algicidal Substances against Phaeocystis globosa

    PubMed Central

    Yang, Qiuchan; Chen, Lina; Hu, Xiaoli; Zhao, Ling; Yin, Pinghe; Li, Qiang

    2015-01-01

    Harmful algal blooms have caused enormous damage to the marine ecosystem and the coastal economy in China. In this paper, a bacterial strain B1, which had strong algicidal activity against Phaeocystis globosa, was isolated from the coastal waters of Zhuhai in China. The strain B1 was identified as Bacillus sp. on the basis of 16S rDNA gene sequence and morphological characteristics. To evaluate the ecological safety of the algicidal substances produced by strain B1, their toxic effects on marine organisms were tested. Results showed that there were no adverse effects observed in the growth of Chlorella vulgaris, Chaetoceros muelleri, and Isochrystis galbana after exposure to the algicidal substances at a concentration of 1.0% (v/v) for 96 h. The 48h LC50 values for Brachionus plicatilis, Moina mongolica Daday and Paralichthys olivaceus were 5.7, 9.0 and 12.1% (v/v), respectively. Subsequently, the algicidal substances from strain B1 culture were isolated and purified by silica gel column, Sephadex G-15 column and high-performance liquid chromatography. Based on quadrupole time-of-flight mass spectrometry and PeakView Software, the purified substances were identified as prolyl-methionine and hypoxanthine. Algicidal mechanism indicated that prolyl-methionine and hypoxanthine inhibited the growth of P. globosa by disrupting the antioxidant systems. In the acute toxicity assessment using M. mongolica, 24h LC50 values of prolyl-methionine and hypoxanthine were 7.0 and 13.8 g/L, respectively. The active substances produced by strain B1 can be considered as ecologically and environmentally biological agents for controlling harmful algal blooms. PMID:25646807

  14. Molecular characterization of sulfate-reducing bacteria community in surface sediments from the adjacent area of Changjiang Estuary

    NASA Astrophysics Data System (ADS)

    Zhang, Yu; Zhen, Yu; Mi, Tiezhu; He, Hui; Yu, Zhigang

    2016-02-01

    Sulfate-reducing bacteria (SRB), which obtain energy from dissimilatory sulfate reduction, play a vital role in the carbon and sulfur cycles. The dissimilatory sulfite reductase (Dsr), catalyzing the last step in the sulfate reduction pathway, has been found in all known SRB that have been tested so far. In this study, the diversity of SRB was investigated in the surface sediments from the adjacent area of Changjiang Estuary by PCR amplification, cloning and sequencing of the dissimilatory sulfite reductase beta subunit gene ( dsrB). Based on dsrB clone libraries constructed in this study, diversified SRB were found, represented by 173 unique OTUs. Certain cloned sequences were associated with Desulfobacteraceae, Desulfobulbaceae, and a large fraction (60%) of novel sequences that have deeply branched groups in the dsrB tree, indicating that novel SRB inhabit the surface sediments. In addition, correlations of the SRB assemblages with environmental factors were analyzed by the linear model-based redundancy analysis (RDA). The result revealed that temperature, salinity and the content of TOC were most closely correlated with the SRB communities. More information on SRB community was obtained by applying the utility of UniFrac to published dsrB gene sequences from this study and other 9 different kinds of marine environments. The results demonstrated that there were highly similar SRB genotypes in the marine and estuarine sediments, and that geographic positions and environmental factors influenced the SRB community distribution.

  15. Polycyclovorans algicola gen. nov., sp. nov., an Aromatic-Hydrocarbon-Degrading Marine Bacterium Found Associated with Laboratory Cultures of Marine Phytoplankton

    PubMed Central

    Green, David H.; Nichols, Peter D.; Whitman, William B.; Semple, Kirk T.; Aitken, Michael D.

    2013-01-01

    A strictly aerobic, halotolerant, rod-shaped bacterium, designated strain TG408, was isolated from a laboratory culture of the marine diatom Skeletonema costatum (CCAP1077/1C) by enrichment with polycyclic aromatic hydrocarbons (PAHs) as the sole carbon source. 16S rRNA gene sequence analysis placed this organism within the order Xanthomonadales of the class Gammaproteobacteria. Its closest relatives included representatives of the Hydrocarboniphaga-Nevskia-Sinobacter clade (<92% sequence similarity) in the family Sinobacteraceae. The strain exhibited a narrow nutritional spectrum, preferring to utilize aliphatic and aromatic hydrocarbon compounds and small organic acids. Notably, it displayed versatility in degrading two- and three-ring PAHs. Moreover, catechol 2,3-dioxygenase activity was detected in lysates, indicating that this strain utilizes the meta-cleavage pathway for aromatic compound degradation. Cells produced surface blebs and contained a single polar flagellum. The predominant isoprenoid quinone of strain TG408 was Q-8, and the dominant fatty acids were C16:0, C16:1 ω7c, and C18:1 ω7c. The G+C content of the isolate's DNA was 64.3 mol% ± 0.34 mol%. On the basis of distinct phenotypic and genotypic characteristics, strain TG408 represents a novel genus and species in the class Gammaproteobacteria for which the name Polycyclovorans algicola gen. nov., sp. nov., is proposed. Quantitative PCR primers targeting the 16S rRNA gene of this strain were developed and used to show that this organism is found associated with other species of marine phytoplankton. Phytoplankton may be a natural biotope in the ocean where new species of hydrocarbon-degrading bacteria await discovery and which contribute significantly to natural remediation processes. PMID:23087039

  16. Cloning and characterization of three epoxide hydrolases from a marine bacterium, Erythrobacter litoralis HTCC2594.

    PubMed

    Woo, Jung-Hee; Hwang, Young-Ok; Kang, Sung Gyun; Lee, Hyun Sook; Cho, Jang-Cheon; Kim, Sang-Jin

    2007-08-01

    Previously, we reported that ten strains belonging to Erythrobacter showed epoxide hydrolase (EHase) activities toward various epoxide substrates. Three genes encoding putative EHases were identified by analyzing open reading frames of Erythrobacter litoralis HTCC2594. Despite low similarities to reported EHases, the phylogenetic analysis of the three genes showed that eeh1 was similar to microsomal EHase, while eeh2 and eeh3 could be grouped with soluble EHases. The three EHase genes were cloned, and the recombinant proteins (rEEH1, rEEH2, and rEEH3) were purified. The functionality of purified proteins was proved by hydrolytic activities toward styrene oxide. EEH1 preferentially hydrolyzed (R)-styrene oxide, whereas EEH3 preferred to hydrolyze (S)-styrene oxide, representing enantioselective hydrolysis of styrene oxide. On the other hand, EEH2 could hydrolyze (R)- and (S)-styrene oxide at an equal rate. The optimal pH and temperature for the EHases occurred largely at neutral pHs and 40-55 degrees C. The substrate selectivity of rEEH1, rEEH2, and rEEH3 toward various epoxide substrates were also investigated. This is the first representation that a strict marine microorganism possessed three EHases with different enantioselectivity toward styrene oxide.

  17. Proteomic Analysis of Stationary Phase in the Marine Bacterium 'Candidatus Pelagibacter ubique'

    SciTech Connect

    Sowell, Sarah M.; Norbeck, Angela D.; Lipton, Mary S.; Nicora, Carrie D.; Callister, Stephen J.; Smith, Richard D.; Barofsky, Douglas F.; Giovannoni, Stephen J.

    2008-05-01

    Candidatus Pelagibacter ubique, an abundant marine alphaproteobacterium, subsists in nature at low ambient nutrient concentrations and may often be exposed to nutrient limitation, but its genome revealed no evidence of global regulatory adaptations to stationary phase. We used high-resolution capillary liquid chromatography (LC) coupled online to an LTQ mass spectrometer to build an Accurate Mass and Time (AMT) tag library, and employed the AMT tag approach to quantitatively examine proteome differences between exponentially growing and stationary phase Cand. P. ubique cells cultivated in a seawater medium. The AMT tag library represented 72% of the predicted protein coding genes. Stationary phase protein abundance increased for OsmC, which mitigates oxidative damage, and for molecular chaperones, enzymes involved in methionine and cysteine biosynthesis, proteins involved in rho-dependent transcription termination, and the signal transduction enzymes CheY-FisH and ChvG. Our findings indicate that Cand. P. ubique responds adaptively to stationary phase by increasing the abundance of a suite of proteins that contribute to homeostasis, but does not undergo major proteome remodeling. We speculate that this limited response may enable Cand. P. ubique to cope with ambient conditions in which nutrients are often insufficient for short periods, and the ability to resume growth overrides the capacity for long term survival afforded by more comprehensive global stationary phase responses.

  18. Glaciecola agarilytica sp. nov., an agar-digesting marine bacterium from the East Sea, Korea.

    PubMed

    Yong, Jeong-Joong; Park, Soo-Je; Kim, Hyeon-Ju; Rhee, Sung-Keun

    2007-05-01

    A taxonomic study was carried out on an isolate, strain NO2(T), from marine sediment collected from the East Sea, Korea. Comparative 16S rRNA gene sequence studies showed that this strain belonged to the Gammaproteobacteria and was most closely related to Glaciecola mesophila KMM 241(T) and Glaciecola polaris LMG 21857(T) (98.6 and 98.0 % 16S rRNA gene sequence similarity, respectively). The isolate was Gram-negative, aerobic and slightly halophilic and grew in 2-8 % NaCl and at 7-30 degrees C. Strain NO2(T) shared some physiological and biochemical properties with G. mesophila KMM 241(T) and G. polaris LMG 21857(T). The G+C content of the genomic DNA of strain NO2(T) was 45 mol%. Strain NO2(T) possessed C(16 : 0), summed feature 4 (C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH) and summed feature 7 (C(18 : 1)omega9c/omega12t/omega7c) as the major cellular fatty acids. DNA-DNA relatedness data indicated that strain NO2(T) represents a distinct species that is separate from G. mesophila and G. polaris. On the basis of polyphasic evidence, it is proposed that strain NO2(T) (=KCTC 12755(T)=LMG 23762(T)) represents the type strain of a novel species, Glaciecola agarilytica sp. nov.

  19. Shimia sagamensis sp. nov., a marine bacterium isolated from cold-seep sediment.

    PubMed

    Nogi, Yuichi; Mori, Kozue; Uchida, Hiromi; Hatada, Yuji

    2015-09-01

    A novel marine bacterial strain designated JAMH 011(T) was isolated from the cold-seep sediment in Sagami Bay, Japan. Cells were Gram-stain-negative, rod-shaped, non-spore-forming, aerobic chemo-organotrophs and motile by means of a single polar flagellum. Growth occurred at temperatures below 31 °C, with the optimum at 25 °C. The major respiratory quinone was Q-10. The predominant fatty acid was C18 : 1ω7c. On the basis of 16S rRNA gene sequence analysis, the isolated strain was closely affiliated with members of the genus Shimia in the class Alphaproteobacteria, and the 16S rRNA gene sequence similarity of the novel isolate with the type strain of the closest related species, Shimia haliotis WM35(T), was 98.1%. The DNA G+C content of the novel strain was 57.3 mol%. The hybridization values for DNA-DNA relatedness between strain JAMH 011(T) and reference strains belonging to the genus Shimia were less than 9.4 ± 0.7%. Based on differences in taxonomic characteristics, the isolated strain represents a novel species of the genus Shimia, for which the name Shimia sagamensis sp. nov. is proposed. The type strain is JAMH 011(T) ( = JCM 30583(T) = DSM 29734(T)).

  20. Thalassobius abyssi sp. nov., a marine bacterium isolated from the cold-seep sediment.

    PubMed

    Nogi, Yuichi; Mori, Kozue; Makita, Hiroko; Hatada, Yuji

    2015-11-09

    A novel marine bacterial strain designated JAMH 043T was isolated from the cold-seep sediment in Sagami Bay, Japan. Cells were Gram-negative, rod-shaped, non-motile and aerobic chemo-organotrophs. The cells of the isolate grew optimally at 25 °C, pH 7.0-7.5, and with 3% (w/v) NaCl. The major respiratory quinone was Q-10. The predominant fatty acid was C18:1ω7c. On the basis of 16S rRNA gene sequence analysis, the isolated strain was closely affiliated with members of the genus Thalassobius in the class Alphaproteobacteria, and the 16S rRNA gene sequence similarity of the novel isolate with the type strain of closest related species, Thalassobius aestuarii JC2049T, was 98.4 %. The DNA G+C content of the novel strain was 58.0 mol%. The hybridization values for DNA-DNA relatedness between strain JAMH043T and reference strains belonging to the genus Thalassobius were less than 14.1±2.2 %. Based on differences in taxonomic characteristics, the isolated strain represents a novel species of the genus Thalassobius, for which the name Thalassobius abyssi sp. nov. is proposed. Type strain is JAMH 043T (=JCM 30900T =DSMZ 100673T).

  1. Structural properties of the tubular appendage spinae from marine bacterium Roseobacter sp. strain YSCB

    PubMed Central

    Bernadac, A.; Wu, L.-F.; Santini, C.-L.; Vidaud, C.; Sturgis, J. N.; Menguy, N.; Bergam, P.; Nicoletti, C.; Xiao, T.

    2012-01-01

    Spinae are tubular surface appendages broadly found in Gram-negative bacteria. Little is known about their architecture, function or origin. Here, we report structural characterization of the spinae from marine bacteria Roseobacter sp. YSCB. Electron cryo-tomography revealed that a single filament winds into a hollow flared base with progressive change to a cylinder. Proteinase K unwound the spinae into proteolysis-resistant filaments. Thermal treatment ripped the spinae into ribbons that were melted with prolonged heating. Circular dichroism spectroscopy revealed a dominant beta-structure of the spinae. Differential scanning calorimetry analyses showed three endothermic transformations at 50–85°C, 98°C and 123°C, respectively. The heating almost completely disintegrated the spinae, abolished the 98°C transition and destroyed the beta-structure. Infrared spectroscopy identified the amide I spectrum maximum at a position similar to that of amyloid fibrils. Therefore, the spinae distinguish from other bacterial appendages, e.g. flagella and stalks, in both the structure and mechanism of assembly. PMID:23230515

  2. The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol

    SciTech Connect

    Sun, Jing; Todd, Jonathan D.; Thrash, J. Cameron; Qian, Yanping; Qian, Michael C.; Temperton, Ben; Guo, Jiazhen; Fowler, Emily K.; Aldrich, Joshua T.; Nicora, Carrie D.; Lipton, Mary S.; Smith, Richard D.; De Leenheer, Patrick; Payne, Samuel H.; Johnston, Andrew W. B.; Davie-Martin, Cleo L.; Halsey, Kimberly H.; Giovannoni, Stephen J.

    2016-05-16

    Marine phytoplankton produce ~109 tons of dimethylsulfoniopropionate (DMSP) per year1,2, an estimated 10% of which is catabolized by bacteria through the DMSP cleavage pathway to the climatically active gas dimethyl sulfide (DMS)3,4. SAR11 Alphaproteobacteria (order Pelagibacterales), the most abundant chemoorganotrophic bacteria in the oceans, have been shown to assimilate DMSP into biomass, thereby supplying this cell’s unusual requirement for reduced sulfur5,6. Here we report that Pelagibacter HTCC1062 produces the gas methanethiol (MeSH) and that simultaneously a second DMSP catabolic pathway, mediated by a DMSP lyase, shunts as much as 59% of DMSP uptake to DMS production. We propose a model in which the allocation of DMSP between these pathways is kinetically controlled to release increasing amounts of DMS as the supply of DMSP exceeds cellular sulfur demands for biosynthesis. These findings suggest that DMSP supply and demand relationships in Pelagibacter metabolism are important to determining rates of oceanic DMS production.

  3. Characterization of the first alginolytic operons in a marine bacterium: from their emergence in marine Flavobacteriia to their independent transfers to marine Proteobacteria and human gut Bacteroides.

    PubMed

    Thomas, François; Barbeyron, Tristan; Tonon, Thierry; Génicot, Sabine; Czjzek, Mirjam; Michel, Gurvan

    2012-09-01

    Alginate constitutes a significant part of seaweed biomass and thus a crucial nutrient for numerous marine heterotrophic bacteria. However, the mechanisms for alginate assimilation remain largely unknown in marine microorganisms. We show here that the genome of the marine flavobacterium Zobellia galactanivorans contains seven putative alginate lyase genes, five of them localized within two clusters comprising additional carbohydrate-related genes. The transcription of these genes and the alginolytic activity were strongly induced when Z. galactanivorans used alginate as sole carbon source. These clusters were shown to be transcribed as polycistronic mRNAs and thus to constitute operons. Several candidate enzymes were successfully overexpressed in Escherichia coli, purified and their activity tested. Particularly, AlyA1, AlyA4, AlyA5 and AlyA7 are confirmed as active alginate lyases. Zg2622 and Zg2614 are a dehydrogenase and a kinase, respectively, further converting the terminal unsaturated monosaccharides released by alginate lyases into 2-keto-3-deoxy-6-phosphogluconate. In-depth phylogenomic analyses reveal that such alginolytic operons originated from an ancestral marine flavobacterium and were independently transferred to marine proteobacteria and Japanese gut Bacteroides. These bacteria thus gained the capacity to assimilate the main polysaccharide of brown algae, an adaptive advantage in coastal environments but also in the gut microbiota of specific human population.

  4. Uranium immobilization by sulfate-reducing biofilms grown on hematite, dolomite, and calcite.

    SciTech Connect

    Marsili, E.; Beyenal, Haluk; Di Palma, L.; Merli, C.; Dohnalkova, Alice; Amonette, James E.; Lewandowski, Zbigniew

    2007-12-15

    Biofilms of sulfate-reducing bacteria Desulfovibrio desulfuricans G20 wereused to reduce dissolved U(VI)and subsequently immobilize U(IV) in the presence of uranium-complexing carbonates. The biofilms were grown in three identically operated fixed bed reactors, filled with three types of minerals: one noncarbonate-bearing mineral(hematite) and two carbonate-bearing minerals (calcite and dolomite). The source of carbonates in the reactors filled with calcite and dolomite were the minerals, while in the reactor filled with hematite it was a 10 mM carbonate buffer, pH 7.2, which we added to the growth medium. Our five-month study demonstrated that the sulfate-reducing biofilms grown in all reactors were able to immobilize/reduce uranium efficiently, despite the presence of uranium-complexing carbonates.

  5. Anaerobic biodegradation of soybean biodiesel and diesel blends under sulfate-reducing conditions.

    PubMed

    Wu, Shuyun; Yassine, Mohamad H; Suidan, Makram T; Venosa, Albert D

    2016-10-01

    Biotransformation of soybean biodiesel and its biodiesel/petrodiesel blends were investigated under sulfate-reducing conditions. Three blends of biodiesel, B100, B50, and B0, were treated using microbial cultures pre-acclimated to B100 (biodiesel only) and B80 (80% biodiesel and 20% petrodiesel). Results indicate that the biodiesel could be effectively biodegraded in the presence or absence of petrodiesel, whereas petrodiesel could not be biodegraded at all under sulfate-reducing conditions. The kinetics of biodegradation of individual Fatty Acid Methyl Ester (FAME) compounds and their accompanying sulfate-reduction rates were studied using a serum bottle test. As for the biodegradation of individual FAME compounds, the biodegradation rates for the saturated FAMEs decreased with increasing carbon chain length. For unsaturated FAMEs, biodegradation rates increased with increasing number of double bonds. The presence of petrodiesel had a greater effect on the rate of biodegradation of biodiesel than on the extent of removal.

  6. Complete genome sequence of the acetate-degrading sulfate reducer Desulfobacca acetoxidans type strain (ASRB2).

    PubMed

    Göker, Markus; Teshima, Hazuki; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Huntemann, Marcel; Liolios, Konstantinos; Ivanova, Natalia; Pagani, Ioanna; Mavromatis, Konstantinos; Ovchinikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Brambilla, Evelyne-Marie; Rohde, Manfred; Spring, Stefan; Detter, John C; Woyke, Tanja; Bristow, James; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2011-07-01

    Desulfobacca acetoxidans Elferink et al. 1999 is the type species of the genus Desulfobacca, which belongs to the family Syntrophaceae in the class Deltaproteobacteria. The species was first observed in a study on the competition of sulfate-reducers and acetoclastic methanogens for acetate in sludge. D. acetoxidans is considered to be the most abundant acetate-degrading sulfate reducer in sludge. It is of interest due to its isolated phylogenetic location in the 16S rRNA-based tree of life. This is the second completed genome sequence of a member of the family Syntrophaceae to be published and only the third genome sequence from a member of the order Syntrophobacterales. The 3,282,536 bp long genome with its 2,969 protein-coding and 54 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  7. Uranium immobilization by sulfate-reducing biofilms grown on hematite, dolomite, and calcite.

    PubMed

    Marsili, Enrico; Beyenal, Haluk; Di Palma, Luca; Merli, Carlo; Dohnalkova, Alice; Amonette, James E; Lewandowski, Zbigniew

    2007-12-15

    Biofilms of sulfate-reducing bacteria Desulfovibrio desulfuricans G20 were used to reduce dissolved U(VI) and subsequently immobilize U(IV) in the presence of uranium-complexing carbonates. The biofilms were grown in three identically operated fixed bed reactors, filled with three types of minerals: one noncarbonate-bearing mineral (hematite) and two carbonate-bearing minerals (calcite and dolomite). The source of carbonates in the reactors filled with calcite and dolomite were the minerals, while in the reactor filled with hematite it was a 10 mM carbonate buffer, pH 7.2, which we added to the growth medium. Our five-month study demonstrated that the sulfate-reducing biofilms grown in all reactors were able to immobilize/reduce uranium efficiently, despite the presence of uranium-complexing carbonates.

  8. Kordia ulvae sp. nov., a bacterium isolated from the surface of green marine algae Ulva sp.

    PubMed

    Qi, Feng; Huang, Zhaobin; Lai, Qiliang; Li, Dengfeng; Shao, Zongze

    2016-04-20

    A novel bacterial strain SC2T was isolated from Ulva sp. a green marine algae. Strain SC2T was Gram-negative, aerobic, rod-shaped and had no flagellum. Oxidase and catalase were positive. Strain SC2T can degrade skim milk, agar, soluble starch, Tween 20 and Tween 80. The optimal salinity and temperature of strain SC2T were 2% and 30 °C, respectively. Phylogenetic analysis based on the 16S rRNA gene indicated that strain SC2T was affiliated to the genus Kordia, with highest sequence similarity to Kordia algicida OT-1T (97.23%), Kordia antarctica IMCC3317T (97.23%) and Kordia jejudonensis SSK3-3T (97.02%); other species of the genus Kordia shared 93.98%-95.78% sequence similarity. The ANI value and the DNA-DNA hybridization estimated value between strain SC2T and three type strains (K. algicida OT-1T, K. antarctica IMCC3317T and K. jejudonensis SSK3-3T) were found to be 79.4%-82.4% and 24.2%-27.0%, respectively. The predominant fatty acids (>5.0%) were C16:0, iso-C15:0, iso-C15:0 3-OH, iso-C17:0 3-OH, summed feature 3 (comprised C16:1 ω7c/C16:1 ω6c), summed feature 8 (comprised C18:1 ω7c/C18:1 ω6c) and summed feature 9 (comprised iso-C17:1 ω9c/C16:0 10-methyl). The respiratory quinone was Menaquinone-6 (MK-6). The polar lipid profile consisted of four unknown lipids, three unidentified phospholipids, one unidentified aminolipid and one phosphatidylethanolamine. The G+C content of the genomic DNA was 34.5 mol%. The combined genotypic and phenotypic data showed that strain SC2T represents a novel species within the genus Kordia, for which the name Kordia ulvae sp. nov. is proposed, with the type strain SC2T (= KCTC 42872T = MCCC 1A01772T = LMG 29123T).

  9. Winogradskyella psychrotolerans sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from Arctic sediment.

    PubMed

    Begum, Z; Srinivas, T N R; Manasa, P; Sailaja, B; Sunil, B; Prasad, S; Shivaji, S

    2013-05-01

    A novel Gram-negative, rod-coccus shaped, non-motile, strain, RS-3(T), was isolated from a sediment sample collected from the marine transect of Kongsfjorden, Ny-Ålesund, Svalbard, Arctic. Colonies and broth cultures were yellowish in colour due to the presence of carotenoids. Strain RS-3(T) was positive for oxidase, aesculinase, caseinase, gelatinase and urease activities and negative for amylase, catalase, lipase, lysine decarboxylase, ornithine decarboxylase, DNase and β-galactosidase activities. The predominant fatty acids were iso-C15 : 0 (18.0), anteiso-C15 : 0 (16.8), iso-C15 : 1 G (14.2), anteiso-C15 : 1 A (6.0) and iso-C15 : 0 3-OH (6.8). Strain RS-3(T) contained MK-6 (72.42 %) and MK-7 (27.58 %) as the major respiratory quinones and phosphatidylethanolamine, two unidentified aminolipids and two unidentified lipids make up the polar lipid composition. The DNA G+C content of strain RS-3(T) was 34.7±1.2 mol%. The 16S rRNA gene sequence analysis indicated that Winogradskyella pacifica and Winogradskyella thalassocola are the most closely related species with sequence similarities to the type strains of these species of 98.5 and 97.7 %, respectively. However, DNA-DNA hybridization with Winogradskyella pacifica KCTC 22997(T) and Winogradskyella thalassocola DSM 15363(T) showed a relatedness of 22 and 42.5 % with respect to strain RS-3(T). Based on the DNA-DNA hybridization values, phenotypic and chemotaxonomic characteristics and phylogenetic inference, strain RS-3(T) is proposed as a novel species of the genus Winogradskyella, for which the name Winogradskyella psychrotolerans sp. nov. is proposed. The type strain of Winogradskyella psychrotolerans sp. nov. is RS-3(T) ( = CIP 110154(T) = NBRC 106169(T)). An emended description of the genus Winogradskyella is provided.

  10. Shewanella arctica sp. nov., an iron-reducing bacterium isolated from Arctic marine sediment.

    PubMed

    Kim, So-Jeong; Park, Soo-Je; Oh, Yong-Sik; Lee, Sang-Ah; Shin, Kee-Sun; Roh, Dong-Hyun; Rhee, Sung-Keun

    2012-05-01

    Two strains of dissimilatory iron-reducing bacteria, which could couple lactate oxidation to iron reduction for energy conservation, were isolated from Arctic marine sediment. The strains, IR12(T) and IR26, were both Gram-staining-negative, catalase- and oxidase-positive and facultative anaerobes. Their cells were rod-shaped and motile by means of a polar flagellum. Both strains grew in the presence of 0.5-3.5 % (w/v) NaCl, with an absolute requirement for Na(+). Both were psychrotolerant since they could grow at 4-28 °C but had an optimum growth temperature of 20 °C. Both grew at pH 4.5-9.0 (optimum, pH 7.5). The major fatty acids of strains IR12(T) and IR26 were summed feature 3 (C(16 : 1)ω6c and/or C(16 : 1)ω7c) and C(16 : 0). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strains IR12(T) and IR26 belonged to the class Gammaproteobacteria and were most closely related to Shewanella vesiculosa M7(T), Shewanella livingstonensis NF22(T) and Shewanella frigidimarina ACAM 591(T) (with 98.5 and 98.8 %, 98.5 and 98.8 %, and 98.5 and 98.8 % sequence similarities, respectively). The genomic DNA G+C contents of strains IR12(T) and IR26 were 40.0 and 40.3 mol%, respectively. DNA-DNA relatedness data indicated that the two novel strains represented a single species that was distinct from S. vesiculosa M7(T), S. livingstonensis NF22(T) and S. frigidimarina ACAM 591(T). Based on the phylogenetic, phenotypic and DNA-DNA relatedness data, the two new strains represent a single novel species of the genus Shewanella, for which the name Shewanella arctica sp. nov. is proposed. The type strain is IR12(T) ( = KCTC 23109(T) = JCM 16723(T)).

  11. Development of Microarrays-Based Metagenomics Technology for Monitoring Sulfate-Reducing Bacteria in Subsurface Environments

    SciTech Connect

    Cindy, Shi

    2015-07-17

    At the contaminated DOE sites, sulfate-reducing bacteria (SRB) are a significant population and play an important role in the microbial community during biostimulation for metal reduction. However, the diversity, structure and dynamics of SRB communities are poorly understood. Therefore, this project aims to use high throughput sequencing-based metagenomics technologies for characterizing the diversity, structure, functions, and activities of SRB communities by developing genomic and bioinformatics tools to link the SRB biodiversity with ecosystem functioning.

  12. Sulfate-reducing bacteria mediate thionation of diphenylarsinic acid under anaerobic conditions.

    PubMed

    Guan, Ling; Shiiya, Ayaka; Hisatomi, Shihoko; Fujii, Kunihiko; Nonaka, Masanori; Harada, Naoki

    2015-02-01

    Diphenylarsinic acid (DPAA) is often found as a toxic intermediate metabolite of diphenylchloroarsine or diphenylcyanoarsine that were produced as chemical warfare agents and were buried in soil after the World Wars. In our previous study Guan et al. (J Hazard Mater 241-242:355-362, 2012), after application of sulfate and carbon sources, anaerobic transformation of DPAA in soil was enhanced with the production of diphenylthioarsinic acid (DPTAA) as a main metabolite. This study aimed to isolate and characterize anaerobic soil microorganisms responsible for the metabolism of DPAA. First, we obtained four microbial consortia capable of transforming DPAA to DPTAA at a high transformation rate of more than 80% after 4 weeks of incubation. Sequencing for the bacterial 16S rRNA gene clone libraries constructed from the consortia revealed that all the positive consortia contained Desulfotomaculum acetoxidans species. In contrast, the absence of dissimilatory sulfite reductase gene (dsrAB) which is unique to sulfate-reducing bacteria was confirmed in the negative consortia showing no DPAA reduction. Finally, strain DEA14 showing transformation of DPAA to DPTAA was isolated from one of the positive consortia. The isolate was assigned to D. acetoxidans based on the partial 16S rDNA sequence analysis. Thionation of DPAA was also carried out in a pure culture of a known sulfate-reducing bacterial strain, Desulfovibrio aerotolerans JCM 12613(T). These facts indicate that sulfate-reducing bacteria are microorganisms responsible for the transformation of DPAA to DPTAA under anaerobic conditions.

  13. Evaluation of redox indicators for determining sulfate-reducing and dechlorinating conditions.

    PubMed

    Jones, Brian D; Ingle, James D

    2005-11-01

    An in situ methodology based on covalently bonded redox indicators has been developed for determining when sulfate-reducing conditions exist in environmental samples. Three immobilized redox indicators [thionine (Thi, formal potential at pH 7 (E(0')7) equals 52 mV), cresyl violet (CV, E(0')7 = -81 mV), and phenosafranine (PSaf, E(0')7 = -267 mV)] were tested for their response to sulfide in synthetic solutions and under sulfate-reducing conditions in wastewater slurries. The byproduct of the sulfate-reducing process, sulfide, was found to couple well to CV in the concentration range of 1-100 microM total sulfide ([S(-II)]) and the pH range of 6-8. Thi, the indicator with the highest formal potential, reacts rapidly with sulfide at levels well below 1 microM while PSaf, the indicator with the lowest formal potential, does not couple to sulfide at levels in excess of 100 microM [S(-II)]. The degree of reduction of the indicators (i.e., the fraction of cresyl violet oxidized) in contact with a given level of sulfide can be modeled qualitatively with an equilibrium expression for [S(-II)]-indicator based on the Nernst equation assuming that rhombic sulfur is the product of sulfide oxidation. In a groundwater sample with dechlorinating microbes, reduction of Thi and partial reduction of CV correlated with dechlorination of TCE to cis-DCE.

  14. Evidence of the activity of dissimilatory sulfate-reducing prokaryotes in nonsulfidogenic tropical mobile muds.

    PubMed

    Madrid, Vanessa M; Aller, Robert C; Aller, Josephine Y; Chistoserdov, Andrei Y

    2006-08-01

    In spite of the nonsulfidic conditions and abundant reactive iron(III) commonly found in mobile tropical deltaic muds, genes encoding dissimilatory sulfite reductase (dsr) were successfully amplified from the upper approximately 1 m of coastal deposits sampled along French Guiana and in the Gulf of Papua. The dsr sequences retrieved were highly diverse, were generally represented in both study regions and fell into six large phylogenetic groupings: Deltaproteobacteria, Thermodesulfovibrio groups, Firmicutes and three groups without known cultured representatives. The spatial and temporal distribution of dsr sequences strongly supports the contention that the sulfate-reducing prokaryote communities in mobile mud environments are cosmopolitan and stable over a period of years. The decrease in the (35)SO(4) (2-) tracer demonstrates that, despite abundant reactive sedimentary iron(III) ( approximately 350-400 mumol g(-1)), the sulfate-reducing prokaryotes present are active, with the highest levels of sulfide being generated in the upper zones of the cores (0-30 cm). Both the time course of the (35)S-sulfide tracer activity and the lack of reduced sulfur in sediments demonstrate virtually complete anaerobic loss of solid phase sulfides. We propose a pathway of organic matter oxidation involving at least 5-25% of the remineralized carbon, wherein sulfide produced by sulfate-reducing prokaryotes is cyclically oxidized biotically or abiotically by metal oxides.

  15. Carbon isotope fractionation by sulfate-reducing bacteria using different pathways for the oxidation of acetate.

    PubMed

    Goevert, Dennis; Conrad, Ralf

    2008-11-01

    Acetate is a key intermediate in the anaerobic degradation of organic matter. In anoxic environments, available acetate is a competitive substrate for sulfate-reducing bacteria (SRB) and methane-producing archaea. Little is known about the fractionation of carbon isotopes by sulfate reducers. Therefore, we determined carbon isotope compositions in cultures of three acetate-utilizing SRB, Desulfobacter postgatei, Desulfobacter hydrogenophilus, and Desulfobacca acetoxidans. We found that these species showed strong differences in their isotope enrichment factors (epsilon) of acetate. During the consumption of acetate and sulfate, acetate was enriched in 13C by 19.3% per hundred in Desulfobacca acetoxidans. By contrast, both D. postgatei and D. hydrogenophilus showed a slight depletion of 13C resulting in epsilon(ac)-values of 1.8 and 1.5% per hundred, respectively. We suggest that the different isotope fractionation is due to the different metabolic pathways for acetate oxidation. The strongly fractionating Desulfobacca acetoxidans uses the acetyl-CoA/carbon monoxide dehydrogenase pathway, which is also used by acetoclastic methanogens that show a similar fractionation of acetate (epsilon(ac) = -21 to -27% per hundred). In contrast, Desulfobacter spp. oxidize acetate to CO2 via the tricarboxylic acid (TCA) cycle and apparently did not discriminate against 13C. Our results suggestthat carbon isotope fractionation in environments with sulfate reduction will strongly depend on the composition of the sulfate-reducing bacterial community oxidizing acetate.

  16. Molecular characterization of a homolog of the ferric-uptake regulator, Fur, from the marine bacterium Marinobacter algicola DG893

    PubMed Central

    Barker, Ryan A.; Tisnado, Jerrell; Lambert, Lisa A.; Gärdes, Astrid; Carrano, Mary W.; Carrano, Paul N.; Gillian, Christopher

    2016-01-01

    Full length recombinant iron regulatory protein, Fur, has been isolated and characterized from the algal-associated marine bacterium Marinobacter algicola DG893. Under nondenaturing conditions the Fur protein behaves on size exclusion chromatography as a dimer while it is monomeric under SDS PAGE conditions. ICP-MS and fluorescence quenching experiments show that Mb-Fur binds a single metal ion (Zn, Mn, or Co) per monomer. Electrophoretic mobility shift assays were used to probe the interaction of Mb-Fur with the purported Fur box in the promoter region upstream of the vibrioferrin biosynthetic operon. Interaction of Mb-Fur with a 100 bp DNA fragment containing the Fur box in the presence of 10 μM Mn, Co or Zn(II) resulted in decreased migration of DNA on a 7.5 % polyacrylamide gel. In the absence of the Fur protein or the metal, no interaction is seen. The presence of EDTA in the binding, loading or running buffers also abolished all activity demonstrating the importance of the metal in formation of the promoter-repressor complex. Based on a high degree of similarity between Mb-Fur and its homolog from Pseudomonas aeruginosa (PA) whose X-ray structure is known we developed a structural model for the former which suggested that only one of the several metal binding sites found in other Fur’s would be functional. This is consistent with the single metal binding stoichiometry we observed. Since the purported metal binding site was one that has been described as “structural” rather than “functional” in PA and yet the monometallic Mb-Fur retains DNA Fur box binding ability it reopens the question of which site is which, or if different species have adapted the sites for different purposes. PMID:25528647

  17. Molecular characterization of a homolog of the ferric-uptake regulator, Fur, from the marine bacterium Marinobacter algicola DG893.

    PubMed

    Barker, Ryan A; Tisnado, Jerrell; Lambert, Lisa A; Gärdes, Astrid; Carrano, Mary W; Carrano, Paul N; Gillian, Christopher; Carrano, Carl J

    2015-02-01

    Full length recombinant iron regulatory protein, Fur, has been isolated and characterized from the algal-associated marine bacterium Marinobacter algicola DG893. Under nondenaturing conditions the Fur protein behaves on size exclusion chromatography as a dimer while it is monomeric under SDS PAGE conditions. ICP-MS and fluorescence quenching experiments show that Mb-Fur binds a single metal ion (Zn, Mn, or Co) per monomer. Electrophoretic mobility shift assays were used to probe the interaction of Mb-Fur with the purported Fur box in the promoter region upstream of the vibrioferrin biosynthetic operon. Interaction of Mb-Fur with a 100 bp DNA fragment containing the Fur box in the presence of 10 µM Mn, Co or Zn(II) resulted in decreased migration of DNA on a 7.5% polyacrylamide gel. In the absence of the Fur protein or the metal, no interaction is seen. The presence of EDTA in the binding, loading or running buffers also abolished all activity demonstrating the importance of the metal in formation of the promoter-repressor complex. Based on a high degree of similarity between Mb-Fur and its homolog from Pseudomonas aeruginosa (PA) whose X-ray structure is known we developed a structural model for the former which suggested that only one of the several metal binding sites found in other Fur's would be functional. This is consistent with the single metal binding stoichiometry we observed. Since the purported metal binding site was one that has been described as "structural" rather than "functional" in PA and yet the monometallic Mb-Fur retains DNA Fur box binding ability it reopens the question of which site is which, or if different species have adapted the sites for different purposes.

  18. Lutibacter litoralis gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from tidal flat sediment.

    PubMed

    Choi, Dong H; Cho, Byung C

    2006-04-01

    A rod-shaped marine bacterium, designated strain CL-TF09T, isolated from a tidal flat in Ganghwa, Korea, was characterized based on its physiological and biochemical features, fatty acid profile and phylogenetic position. 16S rRNA gene sequence analysis revealed a clear affiliation with the family Flavobacteriaceae. Strain CL-TF09T showed the closest phylogenetic relationship with the genera Tenacibaculum and Polaribacter; sequence similarities between CL-TF09T and the type strains of Tenacibaculum and Polaribacter species ranged from 90.7 to 91.8 %. Cells of strain CL-TF09T were non-motile and grew on solid media as yellow colonies. The strain grew in the presence of 1-5 % sea salts, within a temperature range of 5-30 degrees C and at pH 7-8. The strain had iso-C(15 : 0) 3-OH (17.4 %), iso-C(15 : 0) (16.7 %), anteiso-C(15 : 0) (15.1 %) and iso-C(16 : 0) 3-OH (13.4 %) as predominant fatty acids. The DNA G+C content was 33.9 mol%. Based on the physiological, fatty acid composition and phylogenetic data presented, strain CL-TF09T is considered to represent a novel genus and species of the family Flavobacteriaceae, for which the name Lutibacter litoralis gen. nov., sp. nov. is proposed. The type strain is CL-TF09T (=KCCM 42118T = JCM 13034T).

  19. Lacinutrix gracilariae sp. nov., a bacterium isolated from the surface of a marine red alga Gracilaria sp.

    PubMed

    Huang, Zhaobin; Li, Guizhen; Lai, Qiliang; Gu, Li; Shao, Zongze

    2015-11-09

    A Gram-negative, aerobic, non-flagellated, rod-shaped bacterium, designated as strain Lxc1T, was isolated from the surface of a marine red alga, Gracilaria sp., which was collected from the coastal regions in Jinjiang, Fujian Province, China. The colony of the strain was orange-yellow, circular and smooth. The 16S rRNA gene of Lxc1T had maximum sequence similarity with Lacinutrix himadriensis E4-9aT (97.1%), followed by L. jangbogonensis PAMC 27137T, L. copepodicola DJ3T, L. algicola AKS293T, and L. mariniflava AKS 432T (similarities <96.4%). Phylogenetic analysis showed strain Lxc1T formed a tight cluster with L. himadriensis E4-9aT and L. copepodicola DJ3T, but represented a novel lineage belonging to the genus Lacinutrix. The predominant fatty acids were iso-C15:1 G (18.3%), iso-C15:0 (16.7%), iso-C17:0-3OH (10.6%), and iso-C15:0-3OH (8.6%). Menaquinone-6 (MK-6) was the only respiratory quinone present. The DNA G+C content of Lxc1T was 31.7 mol%. Combining the results above, it was ascertained that the strain Lxc1T represented a novel species of the genus Lacinutrix, for which the name Lacinutrix gracilariae sp. nov. is proposed. The type strain is Lxc1T (=MCCC 1A01567T=KCTC 42808T).

  20. Identification of a cyclic-di-GMP-modulating response regulator that impacts biofilm formation in a model sulfate reducing bacterium

    PubMed Central

    Rajeev, Lara; Luning, Eric G.; Altenburg, Sara; Zane, Grant M.; Baidoo, Edward E. K.; Catena, Michela; Keasling, Jay D.; Wall, Judy D.; Fields, Matthew W.; Mukhopadhyay, Aindrila

    2014-01-01

    We surveyed the eight putative cyclic-di-GMP-modulating response regulators (RRs) in Desulfovibrio vulgaris Hildenborough that are predicted to function via two-component signaling. Using purified proteins, we examined cyclic-di-GMP (c-di-GMP) production or turnover in vitro of all eight proteins. The two RRs containing only GGDEF domains (DVU2067, DVU0636) demonstrated c-di-GMP production activity in vitro. Of the remaining proteins, three RRs with HD-GYP domains (DVU0722, DVUA0086, and DVU2933) were confirmed to be Mn2+-dependent phosphodiesterases (PDEs) in vitro and converted c-di-GMP to its linear form, pGpG. DVU0408, containing both c-di-GMP production (GGDEF) and degradation domains (EAL), showed c-di-GMP turnover activity in vitro also with production of pGpG. No c-di-GMP related activity could be assigned to the RR DVU0330, containing a metal-dependent phosphohydrolase HD-OD domain, or to the HD-GYP domain RR, DVU1181. Studies included examining the impact of overexpressed cyclic-di-GMP-modulating RRs in the heterologous host E. coli and led to the identification of one RR, DVU0636, with increased cellulose production. Evaluation of a transposon mutant in DVU0636 indicated that the strain was impaired in biofilm formation and demonstrated an altered carbohydrate:protein ratio relative to the D. vulgaris wild type biofilms. However, grown in liquid lactate/sulfate medium, the DVU0636 transposon mutant showed no growth impairment relative to the wild-type strain. Among the eight candidates, only the transposon disruption mutant in the DVU2067 RR presented a growth defect in liquid culture. Our results indicate that, of the two diguanylate cyclases (DGCs) that function as part of two-component signaling, DVU0636 plays an important role in biofilm formation while the function of DVU2067 has pertinence in planktonic growth. PMID:25120537

  1. Effect of Na+ Concentration and Nutritional Factors on the Lag Phase and Exponential Growth Rates of the Marine Bacterium Deleya aesta and of Other Marine Species

    PubMed Central

    Berthelet, Marc; MacLeod, Robert A.

    1989-01-01

    Growth of the marine bacterium Deleya aesta in a succinate minimal medium showed increasingly long lag phases as Na+ was decreased below the optimum (200 to 500 mM). The minimum Na+ concentration permitting growth consistently was 15 mM. Supplementation of the medium with KHCO3 (as a source of CO2) or yeast extract, especially in combination, reduced the lag phase, increased the rate of exponential growth, and allowed growth at 8 mM Na+. KHCO3 did not reduce the lag period but did increase the rate of exponential growth of Deleya venusta, Deleya pacifica, and Alteromonas haloplanktis 214. Yeast extract was active for all three. The effect of yeast extract on D. aesta could be reproduced by a mixture of amino acids approximating its amino acid composition. l-Alanine, l-aspartate, and l-methionine, in combination, were the most effective in reducing the lag phase, although not as effective as the complete mixture. Succinate, l-aspartate, and l-alanine were transported into the cells by largely independent pathways and oxidized at rates which were much lower at 10 than at 200 mM Na+. l-Methionine was transported at a low rate in the absence of Na+ and at a higher rate at 10 mM but was not oxidized. Above 25 mM Na+, the rate of transport of the carbon source was not the rate-limiting step for growth. It is concluded that a combination of transportable carbon sources reduced the lag period and increased the rate of exponential growth because they can be taken up independently and at low Na+ utilized simultaneously. PMID:16347969

  2. Genome sequence of the pink–pigmented marine bacterium Loktanella hongkongensis type strain (UST950701–009PT), a representative of the Roseobacter group

    DOE PAGES

    Lau, Stanley CK; Riedel, Thomas; Fiebig, Anne; ...

    2015-08-11

    Loktanella hongkongensis UST950701-009PT is a Gram-negative, non-motile and rod-shaped bacterium isolated from a marine biofilm in the subtropical seawater of Hong Kong. When growing as a monospecies biofilm on polystyrene surfaces, this bacterium is able to induce larval settlement and metamorphosis of a ubiquitous polychaete tubeworm Hydroides elegans. The inductive cues are low-molecular weight compounds bound to the exopolymeric matrix of the bacterial cells. In the present study we describe the features of L. hongkongensis strain DSM 17492T together with its genome sequence and annotation and novel aspects of its phenotype. The 3,198,444 bp long genome sequence encodes 3104 protein-codingmore » genes and 57 RNA genes. Lastly, the two unambiguously identified extrachromosomal replicons contain replication modules of the RepB and the Rhodobacteraceae-specific DnaA-like type, respectively.« less

  3. Genome sequence of the pink–pigmented marine bacterium Loktanella hongkongensis type strain (UST950701–009PT), a representative of the Roseobacter group

    SciTech Connect

    Lau, Stanley CK; Riedel, Thomas; Fiebig, Anne; Han, James; Huntemann, Marcel; Petersen, Jörn; Ivanova, Natalia N.; Markowitz, Victor; Woyke, Tanja; Göker, Markus; Kyrpides, Nikos C.; Klenk, Hans-Peter; Qian, Pei-Yuan

    2015-08-11

    Loktanella hongkongensis UST950701-009PT is a Gram-negative, non-motile and rod-shaped bacterium isolated from a marine biofilm in the subtropical seawater of Hong Kong. When growing as a monospecies biofilm on polystyrene surfaces, this bacterium is able to induce larval settlement and metamorphosis of a ubiquitous polychaete tubeworm Hydroides elegans. The inductive cues are low-molecular weight compounds bound to the exopolymeric matrix of the bacterial cells. In the present study we describe the features of L. hongkongensis strain DSM 17492T together with its genome sequence and annotation and novel aspects of its phenotype. The 3,198,444 bp long genome sequence encodes 3104 protein-coding genes and 57 RNA genes. Lastly, the two unambiguously identified extrachromosomal replicons contain replication modules of the RepB and the Rhodobacteraceae-specific DnaA-like type, respectively.

  4. Genome sequence of the pink-pigmented marine bacterium Loktanella hongkongensis type strain (UST950701-009P(T)), a representative of the Roseobacter group.

    PubMed

    Lau, Stanley Ck; Riedel, Thomas; Fiebig, Anne; Han, James; Huntemann, Marcel; Petersen, Jörn; Ivanova, Natalia N; Markowitz, Victor; Woyke, Tanja; Göker, Markus; Kyrpides, Nikos C; Klenk, Hans-Peter; Qian, Pei-Yuan

    2015-01-01

    Loktanella hongkongensis UST950701-009P(T) is a Gram-negative, non-motile and rod-shaped bacterium isolated from a marine biofilm in the subtropical seawater of Hong Kong. When growing as a monospecies biofilm on polystyrene surfaces, this bacterium is able to induce larval settlement and metamorphosis of a ubiquitous polychaete tubeworm Hydroides elegans. The inductive cues are low-molecular weight compounds bound to the exopolymeric matrix of the bacterial cells. In the present study we describe the features of L. hongkongensis strain DSM 17492(T) together with its genome sequence and annotation and novel aspects of its phenotype. The 3,198,444 bp long genome sequence encodes 3104 protein-coding genes and 57 RNA genes. The two unambiguously identified extrachromosomal replicons contain replication modules of the RepB and the Rhodobacteraceae-specific DnaA-like type, respectively.

  5. Electron-bifurcating transhydrogenase is central to hydrogen isotope fractionation during lipid biosynthesis in sulfate reducing bacteria

    NASA Astrophysics Data System (ADS)

    Leavitt, W.; Flynn, T. M.; Suess, M.; Bradley, A. S.

    2015-12-01

    A significant range in microbial lipid 2H/1H ratios is observed in modern marine sediments [Li et al. 2009. GCA]. The magnitude of hydrogen isotope fractionation between microbial lipids and growth water (2ɛlipid-H2O) is hypothesized to relate to the central carbon and energy metabolism [Zhang et al. 2009. PNAS]. These observations have raised the intriguing possibility for culture independent identification of the dominant metabolic pathways operating in environments critical to the geological record. One such metabolism we would like to track for its global significance in sedimentary carbon cycling is bacterial sulfate reduction [Jørgensen. 1982. Nature]. To-date, heterotrophic sulfate reducing bacteria (SRB) have been observed to produce lipids that are depleted in fatty acid H-isotope composition, relative to growth water (2ɛlipid-H2O ~ -125 to -175 ‰), with experiments on different substrates yielding little variability [Campbell et al. 2009. GCA; Osburn. 2013; Dawson et al. 2015. Geobiology]. In stark contrast, aerobic heterotrophs show a wide range in fractionations (2ɛlipid-H2O ~ +300 to -125‰) which seems to scale with the route cellular carbon metabolism [Zhang et al. 2009. PNAS; Heinzelmann et al. 2015. Front Microbio]. Recent work in aerobic methylotrophs [Bradley et al. 2014. AGU] implicates transhydrogenase (TH) activity as a critical control on 2ɛlipid-H2O. This work suggests a specific driving mechanism for this range in fractionation is the ratio of intracellular NADPH/NADH, and more fundamentally, the intracellular redox state. In SRB a key component of energy metabolism is the activity of electron-bifurcating TH [Price et al. 2014. Front Microbio], for which a recent transposon mutant library has generated a number of knockouts in the target gene [Kuehl et al. 2014. mBio] in the model organism Desulfovibrio alaskensis strain G20. In this study we compare growth rates, fatty acid concentrations and 2ɛlipid-H2O from wild type and TH

  6. Spore-Forming Thermophilic Sulfate-Reducing Bacteria Isolated from North Sea Oil Field Waters

    PubMed Central

    Rosnes, Jan Thomas; Torsvik, Terje; Lien, Torleiv

    1991-01-01

    Thermophilic sulfate-reducing bacteria were isolated from oil field waters from oil production platforms in the Norwegian sector of the North Sea. Spore-forming rods dominated in the enrichments when lactate, propionate, butyrate, or a mixture of aliphatic fatty acids (C4 through C6) was added as a carbon source and electron donor. Representative strains were isolated and characterized. The isolates grew autotrophically on H2-CO2 and heterotrophically on fatty acids such as formate, propionate, butyrate, caproate, valerate, pyruvate, and lactate and on alcohols such as methanol, ethanol, and propanol. Sulfate, sulfite, and thiosulfate but not nitrate could be used as an electron acceptor. The temperature range for growth was 43 to 78°C; the spores were extremely heat resistant and survived 131°C for 20 min. The optimum pH was 7.0. The isolates grew well in salt concentrations ranging from 0 to 800 mmol of NaCl per liter. Sulfite reductase P582 was present, but cytochrome c and desulfoviridin were not found. Electron micrographs revealed a gram-positive cell organization. The isolates were classified as a Desulfotomaculum sp. on the basis of spore formation, general physiological characteristics, and submicroscopic organization. To detect thermophilic spore-forming sulfate-reducing bacteria in oil field water, polyvalent antisera raised against antigens from two isolates were used. These bacteria were shown to be widespread in oil field water from different platforms. The origin of thermophilic sulfate-reducing bacteria in the pore water of oil reservoirs is discussed. Images PMID:16348538

  7. A Novel Type II NAD+-Specific Isocitrate Dehydrogenase from the Marine Bacterium Congregibacter litoralis KT71.

    PubMed

    Wu, Ming-Cai; Tian, Chang-Qing; Cheng, Hong-Mei; Xu, Lei; Wang, Peng; Zhu, Guo-Ping

    2015-01-01

    In most living organisms, isocitrate dehydrogenases (IDHs) convert isocitrate into ɑ-ketoglutarate (ɑ-KG). Phylogenetic analyses divide the IDH protein family into two subgroups: types I and II. Based on cofactor usage, IDHs are either NAD+-specific (NAD-IDH) or NADP+-specific (NADP-IDH); NADP-IDH evolved from NAD-IDH. Type I IDHs include NAD-IDHs and NADP-IDHs; however, no type II NAD-IDHs have been reported to date. This study reports a novel type II NAD-IDH from the marine bacterium Congregibacter litoralis KT71 (ClIDH, GenBank accession no. EAQ96042). His-tagged recombinant ClIDH was produced in Escherichia coli and purified; the recombinant enzyme was NAD+-specific and showed no detectable activity with NADP+. The Km values of the enzyme for NAD+ were 262.6±7.4 μM or 309.1±11.2 μM with Mg2+ or Mn2+ as the divalent cation, respectively. The coenzyme specificity of a ClIDH Asp487Arg/Leu488His mutant was altered, and the preference of the mutant for NADP+ was approximately 24-fold higher than that for NAD+, suggesting that ClIDH is an NAD+-specific ancestral enzyme in the type II IDH subgroup. Gel filtration and analytical ultracentrifugation analyses revealed the homohexameric structure of ClIDH, which is the first IDH hexamer discovered thus far. A 163-amino acid segment of CIIDH is essential to maintain its polymerization structure and activity, as a truncated version lacking this region forms a non-functional monomer. ClIDH was dependent on divalent cations, the most effective being Mn2+. The maximal activity of purified recombinant ClIDH was achieved at 35°C and pH 7.5, and a heat inactivation experiment showed that a 20-min incubation at 33°C caused a 50% loss of ClIDH activity. The discovery of a NAD+-specific, type II IDH fills a gap in the current classification of IDHs, and sheds light on the evolution of type II IDHs.

  8. Lacinutrix himadriensis sp. nov., a psychrophilic bacterium isolated from a marine sediment, and emended description of the genus Lacinutrix.

    PubMed

    Srinivas, T N R; Prasad, S; Manasa, P; Sailaja, B; Begum, Z; Shivaji, S

    2013-02-01

    A novel gram-negative, rod-shaped, non-motile, psychrophilic bacterium, designated strain E4-9a(T), was isolated from a marine sediment sample collected at a depth of 276 m from Kongsfjorden, Svalbard, in the Arctic Ocean. The colony colour was golden yellow. Strain E4-9a(T) was positive for amylase activity at 5 °C. The predominant fatty acids were iso-C(15 : 1) G (21.8 %), anteiso-C(15 : 0) (19.1 %), anteiso-C(15 : 1) A (18.6 %), iso-C(15 : 0) (13.8 %) and iso-C(16 : 1) H (6.4 %). Strain E4-9a(T) contained MK-6 as the major respiratory quinone. The polar lipids consisted of phosphatidylethanolamine, three unidentified aminolipids (AL1, AL4 and AL5), an unidentified phospholipid and four unidentified lipids (L1, L4 to L6). Based on 16S rRNA gene sequence similarity, it was ascertained that the closest related species to E4-9a(T) were Lacinutrix copepodicola, L. algicola and L. mariniflava, with sequence similarity to the respective type strains of 98.5, 96.5 and 95.8 %. Phylogenetic analysis showed that strain E4-9a(T) clustered with the type strain of L. copepodicola and with those of L. algicola and L. mariniflava at distances of 1.5 and 4.8 % (98.5 and 95.2 % similarity), respectively. However, DNA-DNA hybridization with L. copepodicola DJ3(T) showed 59 % relatedness with respect to strain E4-9a(T). The DNA G+C content of strain E4-9a(T) was 29 mol%. Based on the results of DNA-DNA hybridization and phenotypic data, it appears that strain E4-9a(T) represents a novel species of the genus Lacinutrix, for which the name Lacinutrix himadriensis sp. nov. is proposed. The type strain is E4-9a(T) ( = CIP 110310(T)  = KCTC 23612(T)).

  9. Recombinant expression of Toluene o-Xylene Monooxygenase (ToMO) from Pseudomonas stutzeri OX1 in the marine Antarctic bacterium Pseudoalteromonas haloplanktis TAC125.

    PubMed

    Siani, Loredana; Papa, Rosanna; Di Donato, Alberto; Sannia, Giovanni

    2006-11-10

    The psychrophilic bacterium Pseudoalteromonas haloplanktis TAC125, isolated from Antarctic seawater, was used as recipient for a biodegradative gene of the mesophilic Pseudomonas stutzeri OX1. tou cluster, coding for Toluene o-Xylene Monooxygenase (ToMO), was successfully cloned and expressed into a "cold expression" vector. Apparent catalytic parameters of the recombinant microorganisms on three different substrates were determined and compared with those exhibited by Escherichia coli recombinant cells expressing ToMO. Production of a catalytically efficient TAC/tou microorganism supports the possibility of developing specific degradative capabilities for the bioremediation of chemically contaminated marine environments and of industrial effluents characterised by low temperatures.

  10. Immobilizing U from solution by immobilized sulfate-reducing bacteria of desulfovibrio desulfuricans

    NASA Astrophysics Data System (ADS)

    Xu, Hulfang; Barton, Larry L.

    2000-07-01

    As determined by transmission electron microscopy, the reduction of uranyl accetate 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 metabolically active sulfate-reducing bacteria. The nanocrystals have an average diameter of 5 nm and have anhedral shape. It is proposed that cytochrome in these cells has an important role in the reduction of uranyl through transferring electron from molecular hydrogen or lactic acid to uranyl ions.

  11. Penetration of Sulfate Reducers through a Porous North Sea Oil Reservoir

    PubMed Central

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

    1996-01-01

    The presence of mesophilic benzoate-degrading sulfate-reducing bacteria in the water systems of three Norwegian oil platforms was investigated. Strain 4502 was isolated from the injection water system, and specific antibodies were produced against this isolate. It was present in the injection water system during a period of 3 years, but not in the in situ reservoir water. Later it was found in water samples collected from the oil field production system. This showed that strain 4502 had penetrated the reservoir together with the injection water and eventually reached the production well. PMID:16535415

  12. Treatment of acid mine drainage by sulfate reducing bacteria with iron in bench scale runs.

    PubMed

    Bai, He; Kang, Yong; Quan, Hongen; Han, Yang; Sun, Jiao; Feng, Ying

    2013-01-01

    In order to treat acid mine drainage (AMD) effectively using sulfate-reducing bacteria (SRB) at high concentration of sulfate and heavy metals, Fe(0) was added to enhance the activity of SRB. When AMD was treated by SRB and Fe(0) at 25 °C, more than 61% of sulfate was removed and the effluent pH was improved from 2.75 to 6.20 during the operation. Cu(2+) was removed effectively with the removal efficiency at 99%, while only 86% of Fe(2+) was removed during the AMD treatment, without conspicuous change of Mn(2+) in the effluent in the process.

  13. Genes for Uranium Bioremediation in the Anaerobic Sulfate-Reducing Bacteria

    SciTech Connect

    Wall, Judy D.

    1999-06-01

    Objective A: Electron transfer components necessary for uranium reduction. Objective B: Possible FNR-analog in the sulfate-reducing bacteria. Attempts to isolate FNR or FIKJ analogs from Desuflovibrio through the design of degenerate primers for amplification of portions of the genes has not been successful. In contrast, several amplicons have been generated for the genes encoding the regulators of two-component signal sequences. Since several global regulators fall into this class, we are attempting to obtain sufficient sequence information to indicate what metabolic pathways are affected by the regulators. Cloning and sequencing of two such amplicons has revealed that bona fide two-component regulators are present in Desulfovibrio.

  14. Preparative isolation and purification of macrolactin antibiotics from marine bacterium Bacillus amyloliquefaciens using high-speed counter-current chromatography in stepwise elution mode.

    PubMed

    He, Shan; Wang, Hongqiang; Yan, Xiaojun; Zhu, Peng; Chen, Juanjuan; Yang, Rui

    2013-01-11

    Preparative high-speed counter-current chromatography (HSCCC) was successfully applied to the isolation and purification of two macrolactin antibiotics from marine bacterium Bacillus amyloliquefaciens for the first time using stepwise elution with a pair of two-phase solvent systems composed of n-hexane-ethyl acetate-methanol-water at (1:4:1:4, v/v) and (3:4:3:4, v/v). The preparative HSCCC separation was performed on 300 mg of crude sample yielding macrolactin B (22.7 mg) and macrolactin A (40.4 mg) in a one-step separation, with purities over 95% as determined by HPLC. The structures of these compounds were identified by MS, (1)H NMR and (13)C NMR. Our results demonstrated that HSCCC was an efficient technique to separate marine antibiotics, which provide an approach to solve the problem of their sample availability for drug development.

  15. Formation of diphenylthioarsinic acid from diphenylarsinic acid under anaerobic sulfate-reducing soil conditions.

    PubMed

    Hisatomi, Shihoko; Guan, Ling; Nakajima, Mami; Fujii, Kunihiko; Nonaka, Masanori; Harada, Naoki

    2013-11-15

    Diphenylarsinic acid (DPAA) is a toxic phenylarsenical compound often found around sites contaminated with phenylarsenic chemical warfare agents, diphenylcyanoarsine or diphenylchloroarsine, which were buried in soil after the World Wars. This research concerns the elucidation of the chemical structure of an arsenic metabolite transformed from DPAA under anaerobic sulfate-reducing soil conditions. In LC/ICP-MS analysis, the retention time of the metabolite was identical to that of a major phenylarsenical compound synthesized by chemical reaction of DPAA and hydrogen sulfide. Moreover the mass spectra for the two compounds measured using LC/TOF-MS were similar. Subsequent high resolution mass spectral analysis indicated that two major ions at m/z 261 and 279, observed on both mass spectra, were attributable to C12H10AsS and C12H12AsSO, respectively. These findings strongly suggest that the latter ion is the molecular-related ion ([M+H](+)) of diphenylthioarsinic acid (DPTA; (C6H5)2AsS(OH)) and the former ion is its dehydrated fragment. Thus, our results reveal that DPAA can be transformed to DPTA, as a major metabolite, under sulfate-reducing soil conditions. Moreover, formation of diphenyldithioarsinic acid and subsequent dimerization were predicted by the chemical reaction analysis of DPAA with hydrogen sulfide. This is the first report to elucidate the occurrence of DPAA-thionation in an anaerobic soil.

  16. Heavy metal removal from multicomponent system by sulfate reducing bacteria: Mechanism and cell surface characterization.

    PubMed

    Kiran, M Gopi; Pakshirajan, Kannan; Das, Gopal

    2017-02-15

    This study evaluated the combined effect of Cd(II), Cu(II), Ni(II), Fe(III), Pb(II) and Zn(II) on each other removal by anaerobic biomass under sulfate reducing condition. Statistically valid Plackett-Burman design of experiments was employed to carry out this mixture study. The results obtained showed a maximum removal of Cu(II) (98.9%), followed by Ni(II) (97%), Cd(II) (94.8%), Zn(II) (94.6%), Pb(II) (94.4%) and Fe(III) (93.9%). Analysis of variance (ANOVA) of the sulfate and chemical oxygen demand (COD) reduction revealed that the effect due to copper was highly significant (P value<0.05) on sulfate and COD removal. To establish the role of sulfate reducing bacteria (SRB) in the metal removal process, surface morphology and composition of the metal loaded biomass were analyzed by transmission electron microscopy (TEM) equipped with energy dispersive spectroscopy (EDS) and by field emission scanning electron microscopy (FESEM) integrated with energy dispersive X-ray spectroscopy (EDX). The results obtained revealed that the metal precipitates are associated with the outer and inner cell surface of the SRB as a result of the sulfide generated by SRB.

  17. Biologically-Induced Precipitation of Minerals in a Medium with Zinc Under Sulfate-Reducing Conditions.

    PubMed

    Wolicka, Dorota; Borkowski, Andrzej; Jankiewicz, Urszula; Stępień, Wojciech; Kowalczyk, Paweł

    2015-01-01

    Sulfate-reducing microbial communities were enriched from soils collected in areas with crude-oil exploitation. Cultures were grown in modified Postgate C medium and minimal medium, with ethanol or lactate as an electron donor. The batch cultures were grown with addition of zinc in concentrations of 100-700 mg/l. A lack of increased protein concentration in the solutions compared with the control batch, was noted in cultures containing over 200 mg Zn2+/l. The 16S rRNA method was applied to determine the specific composition of the selected microorganism communities. The analysis indicated the presence of Desulfovibrio spp., Desulfobulbus spp. and Desulfotomaculum spp. in the communities. Diffractometric analysis indicated the presence of biogenic sphalerite in cultures with 100 and 200 mg Zn2+/l and elemental sulfur in cultures with 200 mg Zn2+/l. Other post culture sediments (300-700 mg Zn2+/l) contained only hopeite [Zn3(PO4)2·4H2O] formed abiotically during the experiment, which was confirmed by studies of the activity of sulfate-reducing microbial communities.

  18. Impact of clay minerals on sulfate-reducing activity in aquifers

    USGS Publications Warehouse

    Wong, D.; Suflita, J.M.; McKinley, J.P.; Krumholz, L.R.

    2004-01-01

    Previous studies have shown that sulfate-reduction activity occurs in a heterogeneous manner throughout the terrestrial subsurface. Low-activity regions are often observed in the presence of clay minerals. Here we report that clays inhibit sulfate reduction activity in sediments and in a pure culture of Desulfovibriovulgaris. Clay minerals including bentonite and kaolinite inhibited sulfate reduction by 70–90% in sediments. Intact clays and clay colloids or soluble components, capable of passing through a 0.2-µm filter, were also inhibitory to sulfate-reducing bacteria. Other adsorbent materials, including anion or cation exchangers and a zeolite, did not inhibit sulfate reduction in sediments, suggesting that the effect of clays was not due to their cation-exchange capacity. We observed a strong correlation between the Al2O3content of clays and their relative ability to inhibit sulfate reduction in sediments (r2 = 0.82). This suggested that inhibition might be a direct effect of Al3+ (aq) on the bacteria. We then tested pure aluminum oxide (Al2O3) and showed it to act in a similar manner to clay. As dissolved aluminum is known to be toxic to a variety of organisms at low concentrations, our results suggest that the effects of clay on sulfate-reducing bacteria may be directly due to aluminum. Thus, our experiments provide an explanation for the lack of sulfate-reduction activity in clay-rich regions and presents a mechanism for the effect.

  19. BASE COMPOSITION OF THE DEOXYRIBONUCLEIC ACID OF SULFATE-REDUCING BACTERIA.

    PubMed

    SIGAL, N; SENEZ, J C; LEGALL, J; SEBALD, M

    1963-06-01

    Sigal, Nicole (Laboratoire de Chimie Bactérienne du CNRS, Marseille, France), Jacques C. Senez, Jean Le Gall, and Madeleine Sebald. Base composition of the deoxyribonucleic acid of sulfate-reducing bacteria. J. Bacteriol. 85:1315-1318. 1963-The deoxyribonucleic acid constitution of several strains of sulfate-reducing bacteria has been analytically determined. The results of these studies show that this group of microorganisms includes at least four subgroups characterized by significantly different values of the adenine plus thymine to guanine plus cytosine ratio. The nonsporulated forms with polar flagellation, containing both cytochrome c(3) and desulfoviridin, are divided into two subgroups. One includes the fresh-water, nonhalophilic strains with base ratio from 0.54 to 0.59, and the other includes the halophilic or halotolerant strains with base ratio from 0.74 to 0.77. The sporulated, peritrichous strains without cytochrome and desulfoviridin ("nigrificans" and "orientis") are distinct from the above two types and differ from each other, having base ratios of 1.20 and 1.43, respectively.

  20. Cultivation of high-rate sulfate reducing sludge by pH-based electron donor dosage.

    PubMed

    Paulo, Paula L; Kleerebezem, Robbert; Lettinga, Gatze; Lens, Piet N L

    2005-07-21

    A novel self-regulating bioreactor concept for sulfate reduction is proposed aiming for high biomass concentrations and treatment capacities. The system consists of a cell suspension of sulfate reducing bacteria in a continuous stirred tank reactor (30 degrees C) fed with a mixture of both electron donor and electron acceptor (formic acid and sulfuric acid, respectively), nutrients and phosphate buffer via a pH controller. The pH rise due to sulfate reduction is balanced with dosage of the sulfate reducing substrates as acids. The reactor concept was shown to be capable of full sulfate reduction without competition for the electron donor by methanogens and acetogens. Activity assays revealed that hardly any methanogenic activity on formate was left in the suspension by the end of the continuous run (130 days). In addition, the sulfidogenic activity with formate and H2/CO2 had increased, respectively, 3.9 and 11.6 times at the end of the experimental run. The evolution of the particle size distribution of the cell suspension over time indicated that newly grown cells have the tendency to attach together in flocs or to the existing agglomerates.

  1. Molecular diversity of sulfate-reducing bacteria from two different continental margin habitats.

    PubMed

    Liu, Xueduan; Bagwell, Christopher E; Wu, Liyou; Devol, Allan H; Zhou, Jizhong

    2003-10-01

    This study examined the natural diversity and distributions of sulfate-reducing bacteria along a natural carbon gradient extending down the shelf-slope transition zone of the eastern Pacific continental margin. Dissimilatory (bi)sulfite reductase gene sequences (dsrAB) were PCR amplified and cloned from five different sampling sites, each at a discrete depth, from two different margin systems, one off the Pacific coast of Mexico and another off the coast of Washington State. A total of 1,762 clones were recovered and evaluated by restriction fragment length polymorphism (RFLP) analysis. The majority of the gene sequences recovered showed site and depth restricted distributions; however, a limited number of gene sequences were widely distributed within and between the margin systems. Cluster analysis identified 175 unique RFLP patterns, and nucleotide sequences were determined for corresponding clones. Several different continental margin DsrA sequences clustered with those from formally characterized taxa belonging to the delta subdivision of the class Proteobacteria (Desulfobulbus propionicus, Desulfosarcina variabilis) and the Bacillus-Clostridium (Desulfotomaculum putei) divisions, although the majority of the recovered sequences were phylogenetically divergent relative to all of the other DsrA sequences available for comparison. This study revealed extensive new genetic diversity among sulfate-reducing bacteria in continental margin sedimentary habitats, which appears to be tightly coupled to slope depth, specifically carbon bioavailability.

  2. Inhibition of sulfate-reducing bacteria by metal sulfide formation in bioremediation of acid mine drainage.

    PubMed

    Utgikar, Vivek P; Harmon, Stephen M; Chaudhary, Navendu; Tabak, Henry H; Govind, Rakesh; Haines, John R

    2002-02-01

    Acid mine drainage (AMD) containing high concentrations of sulfate and heavy metal ions can be treated by biological sulfate reduction. It has been reported that the effect of heavy metals on sulfate-reducing bacteria (SRB) can be stimulatory at lower concentrations and toxic/inhibitory at higher concentrations. The quantification of the toxic/inhibitory effect of dissolved heavy metals is critical for the design and operation of an effective AMD bioremediation process. Serum bottle and batch reactor studies on metal toxicity to SRB indicate that insoluble metal sulfides can inhibit the SRB activity as well. The mechanism of inhibition is postulated to be external to the bacterial cell. The experimental data indicate that the metal sulfides formed due to the reaction between the dissolved metal and biogenic sulfide act as barriers preventing the access of the reactants (sulfate, organic matter) to the necessary enzymes. Scanning electron micrographs of the SRB cultures exposed to copper and zinc provide supporting evidence for this hypothesis. The SRB cultures retained their ability to effect sulfate reduction indicating that the metal sulfides were not lethally toxic to the SRB. This phenomenon of metal sulfide inhibition of the SRB has to be taken into account while designing a sulfate-reducing bioreator, and subsequently an efficient biotreatment strategy for AMD. Any metal sulfide formed in the bioreactor needs to be removed immediately from the system to maintain the efficiency of the process of sulfate reduction.

  3. Analyses of spatial distributions of sulfate-reducing bacteria and their activity in aerobic wastewater biofilms

    SciTech Connect

    Okabe, Satoshi; Itoh, Tsukasa; Satoh, Hisashi; Watanabe, Yoshimasa

    1999-11-01

    The vertical distribution of sulfate-reducing bacteria (SRB) in aerobic wastewater biofilms grown on rotating disk reactors was investigated by fluorescent in situ hybridization (FISH) with 16S rRNA-targeted oligonucleotide probes. To correlate the vertical distribution of SRB populations with their activity, the microprofiles of O{sub 2}, H{sub 2}S, NO{sub 2}{minus}, NH{sub 2}{sup +}, and pH were measured with microelectrodes. In addition, a cross-evaluation of the FISH and microelectrode analyses was performed by comparing them with culture-based approaches and biogeochemical measurements. In situ hybridization revealed that a relatively high abundance of the probe SRB385-stained cells were evenly distributed throughout the biofilm, even in the toxic surface. The probe SRB660-stained Desulfobulbus spp. were found to be numerically important members of SRB populations. The result of microelectrode measurements showed that a high sulfate-reducing activity was found in a narrow anaerobic zone located about 150 to 300 {micro}m below the biofilm surface and above which an intensive sulfide oxidation zone was found. The biogeochemical measurements showed that elemental sulfur (S{degree}) was an important intermediate of the sulfide reoxidation in such thin wastewater biofilms, which accounted for about 75% of the total S pool in the biofilm. The contribution of an internal Fe-sulfur cycle to the overall sulfur cycle in aerobic wastewater biofilms was insignificant (less than 1%) due to the relatively high sulfate reduction rate.

  4. Promotion of Ni2+ Removal by Masking Toxicity to Sulfate-Reducing Bacteria: Addition of Citrate

    PubMed Central

    Qian, Junwei; Zhu, Xiaoyu; Tao, Yong; Zhou, Yan; He, Xiaohong; Li, Daping

    2015-01-01

    The sulfate-reducing bioprocess is a promising technology for the treatment of heavy metal-containing wastewater. This work was conducted to investigate the possibility of promoting heavy metal removal by the addition of citrate to mask Ni2+ toxicity to sulfate-reducing bacteria (SRB) in batch reactors. SRB growth was completely inhibited in Ni2+-containing medium (1 mM) when lactate served as the sole carbon resource, leading to no sulfate reduction and Ni2+ removal. However, after the addition of citrate, SRB grew well, and sulfate was quickly reduced to sulfide. Simultaneously, the Ni-citrate complex was biodegraded to Ni2+ and acetate. The NiS precipitate was then formed, and Ni2+ was completely removed from the solution. It was suggested that the addition of citrate greatly alleviates Ni2+ toxicity to SRB and improves the removal of Ni2+, which was confirmed by quantitative real-time PCR targeting dissimilatory sulfite reductase (dsrAB) genes. Analysis of the carbon metabolism indicated that lactate instead of acetate served as the electron donor for sulfate reduction. This study offers a potential approach to increase the removal of heavy metals from wastewater in the single stage SRB-based bioprocess. PMID:25860948

  5. Inhibitory activity of an extract from a marine bacterium Halomonas sp. HSB07 against the red-tide microalga Gymnodinium sp. (Pyrrophyta)

    NASA Astrophysics Data System (ADS)

    Liu, Juan; Li, Fuchao; Liu, Ling; Jiang, Peng; Liu, Zhaopu

    2013-11-01

    In recent years, red tides occurred frequently in coastal areas worldwide. Various methods based on the use of clay, copper sulfate, and bacteria have been successful in controlling red tides to some extent. As a new defensive agent, marine microorganisms are important sources of compounds with potent inhibitory bioactivities against red-tide microalgae, such as Gymnodinium sp. (Pyrrophyta). In this study, we isolated a marine bacterium, HSB07, from seawater collected from Hongsha Bay, Sanya, South China Sea. Based on its 16S rRNA gene sequence and biochemical characteristics, the isolated strain HSB07 was identified as a member of the genus Halomonas. A crude ethyl acetate extract of strain HSB07 showed moderate inhibition activity against Gymnodinium sp. in a bioactive prescreening experiment. The extract was further separated into fractions A, B, and C by silica gel column chromatography. Fractions B and C showed strong inhibition activities against Gymnodinium. This is the first report of inhibitory activity of secondary metabolites of a Halomonas bacterium against a red-tide-causing microalga.

  6. A putative siderophore-interacting protein from the marine bacterium Shewanella frigidimarina NCIMB 400: cloning, expression, purification, crystallization and X-ray diffraction analysis

    SciTech Connect

    Trindade, Inês B.; Fonseca, Bruno M.; Matias, Pedro M.; Louro, Ricardo O.; Moe, Elin

    2016-08-09

    The gene encoding a putative siderophore-interacting protein from the marine bacterium S. frigidimarina was successfully cloned, followed by expression and purification of the gene product. Optimized crystals diffracted to 1.35 Å resolution and preliminary crystallographic analysis is promising with respect to structure determination and increased insight into the poorly understood molecular mechanisms underlying iron acquisition. Siderophore-binding proteins (SIPs) perform a key role in iron acquisition in multiple organisms. In the genome of the marine bacterium Shewanella frigidimarina NCIMB 400, the gene tagged as SFRI-RS12295 encodes a protein from this family. Here, the cloning, expression, purification and crystallization of this protein are reported, together with its preliminary X-ray crystallographic analysis to 1.35 Å resolution. The SIP crystals belonged to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 48.04, b = 78.31, c = 67.71 Å, α = 90, β = 99.94, γ = 90°, and are predicted to contain two molecules per asymmetric unit. Structure determination by molecular replacement and the use of previously determined ∼2 Å resolution SIP structures with ∼30% sequence identity as templates are ongoing.

  7. Identification and distribution of sulfate reducing bacteria and sulphur-oxidising bacteria in northern South China Sea

    NASA Astrophysics Data System (ADS)

    Mao, S.; Zhu, X.; Guan, H.; Wu, D.; Wu, N.

    2015-12-01

    Fatty acids are one of the major components in modern marine sediments. It is well known that the saturated short-chain FAs were typically to be from vascular plants, algae, bacteria, and other sources, while the saturated long-chain FAs are the major components found in leaf waxes, suberin, and cutin in terrestrial higher plants. So the lipid biomarkers of fatty acids in Site 4B from Shenhu Area, northern South China Sea were investigated in Recent research supported from the 973 Program (2009CB219506), and the resources of branched fatty acids and monounsaturated fatty acids were mainly discussed. The results reveal that i/a15:0, i/a17:0, 16:1ω5, 18:1ω9 and 10me16:0 are derived from sulfate reducing bacteria (SRB), while 16:1ω7t/c and 18:1ω7 are originated from sulphur-oxidising bacteria (SOB). The biomakers of methanotrophs such as 16:1ω6/8 and 18:1ω6/8 were not detected in the sediments which coincide with more positive carbon isotope values of the fatty acids in the sediments. The stable relationship between SRB and SOB below 97cm in the sediments reflects the relative stable oxidative and reductive depositional environment which may be connected with the sulphur cycle in the sediments, that is carried out as sulfate is reduced to sulfide, and then sulfide is oxidized to sulfate and elemental sulfur, at last elemental sulfur is disproportionated to sulfide and sulfate. The frequently changed relationship of SRB and SOB above 97cm in the sediments indicates intensely changing oxidative and reductive sedimental environment, that may related with diapir structure around Site 4B, which also brings about hydrocarbon seepage leading to increasing biomass at 97cm.

  8. Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DLT)

    PubMed Central

    Spring, Stefan; Visser, Michael; Lu, Megan; Copeland, Alex; Lapidus, Alla; Lucas, Susan; Cheng, Jan-Fang; Han, Cliff; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Ivanova, Natalia; Land, Miriam; Hauser, Loren; Larimer, Frank; Rohde, Manfred; Göker, Markus; Detter, John C.; Kyrpides, Nikos C.; Woyke, Tanja; Schaap, Peter J.; Plugge, Caroline M.; Muyzer, Gerard; Kuever, Jan; Pereira, Inês A. C.; Parshina, Sofiya N.; Bernier-Latmani, Rizlan; Stams, Alfons J.M.; Klenk, Hans-Peter

    2012-01-01

    Desulfotomaculum ruminis Campbell and Postgate 1965 is a member of the large genus Desulfotomaculum which contains 30 species and is contained in the family Peptococcaceae. This species is of interest because it represents one of the few sulfate-reducing bacteria that have been isolated from the rumen. Here we describe the features of D. ruminis together with the complete genome sequence and annotation. The 3,969,014 bp long chromosome with a total of 3,901 protein-coding and 85 RNA genes is the second completed genome sequence of a type strain of the genus Desulfotomaculum to be published, and was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2009. PMID:23408247

  9. Suitability of different growth substrates as source of nitrogen for sulfate reducing bacteria.

    PubMed

    Dev, Subhabrata; Patra, Aditya Kumar; Mukherjee, Abhijit; Bhattacharya, Jayanta

    2015-11-01

    Sulfate reducing bacteria (SRB) mediated treatment of acid mine drainage is considered as a globally accepted technology. However, inadequate information on the role of nitrogen source in the augmentation of SRB significantly affects the overall treatment process. Sustenance of SRB depends on suitable nitrogen source which is considered as an important nutrient. This review focuses on the different nitrogen rich growth substrates for their effectiveness to support SRB growth and sulfate reduction in passive bioreactors. Compounds like NH4Cl, NH4HCO3, NO3 (-), aniline, tri-nitrotoluene, cornsteep liquor, peptone, urea, and chitin are reported to have served as nitrogen source for SRB. In association with fermentative bacteria, SRB can metabolize these complex compounds to NH4 (+), amines, and amino acids. After incorporation into cells, these compounds take part in the biosynthesis of nucleic acids, amino acids and enzyme co-factor. This work describes the status of current and the probable directions of the future research.

  10. Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DLT)

    SciTech Connect

    Spring, Stefan; Visser, Michael; Lu, Megan; Copeland, Alex; Lapidus, Alla; Lucas, Susan; Cheng, Jan-Fang; Han, Cliff; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Ivanova, Natalia; Land, Miriam; Hauser, Loren; Larimer, Frank; Rohde, Manfred; Göker, Markus; Detter, John C.; Kyrpides, Nikos C.; Woyke, Tanja; Schaap, Peter J.; Plugge, Caroline M.; Muyzer, Gerard; Kuever, Jan; Pereira, Inês A. C.; Parshina, Sofiya N.; Bernier-Latmani, Rizlan; Stams, Alfons J. M.; Klenk, Hans-Peter

    2012-12-11

    Desulfotomaculum ruminis Campbell and Postgate 1965 is a member of the large genus Desulfotomaculum which contains 30 species and is contained in the family Peptococcaceae. This species is of interest because it represents one of the few sulfate- reducing bacteria that have been isolated from the rumen. Here we describe the features of D. ruminis together with the complete genome sequence and annotation. The 3,969,014 bp long chromosome with a total of 3,901 protein-coding and 85 RNA genes is the second completed genome sequence of a type strain of the genus Desulfotomaculum to be pub- lished, and was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2009.

  11. Hydrogen sulfide production by sulfate-reducing bacteria utilizing additives eluted from plastic resins.

    PubMed

    Tsuchida, Daisuke; Kajihara, Yusuke; Shimidzu, Nobuhiro; Hamamura, Kengo; Nagase, Makoto

    2011-06-01

    In the present study it was demonstrated that organic additives eluted from plastic resins could be utilized as substrates by sulfate-reducing bacteria. Two laboratory-scale experiments, a microcosm experiment and a leaching experiment, were conducted using polyvinyl chloride (PVC) as a model plastic resin. In the former experiment, the conversion of sulfate to sulfide was evident in microcosms that received plasticized PVC as the sole carbon source, but not in those that received PVC homopolymer. Additionally, dissolved organic carbon accumulated only in microcosms that received plasticized PVC, indicating that the dissolved organic carbon originated from additives. In the leaching experiment, phenol and bisphenol A were found in the leached solutions. These results suggest that the disposal of waste plastics in inert waste landfills may result in the production of H(2)S.

  12. Styrene N-vinylpyrrolidone metal-nanocomposites as antibacterial coatings against Sulfate Reducing Bacteria.

    PubMed

    Fathy, M; Badawi, A; Mazrouaa, A M; Mansour, N A; Ghazy, E A; Elsabee, M Z

    2013-10-01

    Copolymer of styrene, and vinylpyrrolidone was prepared by various techniques. Different nanometals and nanometal oxides were added into the copolymer as antimicrobial agents against Sulfate Reducing Bacteria (SRB). The nanocomposite chemical structure was confirmed by using FTIR, (1)H NMR spectroscopy and thermogravimetric analysis (TGA). The biocidal action of these nanocomposites against the SRB was detected using sulfide determination method in Postgate medium B. The data indicated that the nanocomposites had an inhibitory effect on the growth of SRB and reduced the bacterial corrosion rate of mild steel coupons. The prepared nanocomposites have high inhibition efficiency when applied as coatings and show less efficiency when applied as solids or solution into SRB medium. The copolymer and its nanocomposites effectively reduced the total corrosion rate as determined by total weight loss method.

  13. Isolation of Sulfate-Reducing Bacteria from Sediments Above the Deep-Subseafloor Aquifer

    PubMed Central

    Fichtel, Katja; Mathes, Falko; Könneke, Martin; Cypionka, Heribert; Engelen, Bert

    2011-01-01

    On a global scale, crustal fluids fuel a large part of the deep-subseafloor biosphere by providing electron acceptors for microbial respiration. In this study, we examined bacterial cultures from sediments of the Juan de Fuca Ridge, Northeast Pacific (IODP Site U1301). The sediments comprise three distinctive compartments: an upper sulfate-containing zone, formed by bottom-seawater diffusion, a sulfate-depleted zone, and a second (∼140 m thick) sulfate-containing zone influenced by fluid diffusion from the basaltic aquifer. In order to identify and characterize sulfate-reducing bacteria, enrichment cultures from different sediment layers were set up, analyzed by molecular screening, and used for isolating pure cultures. The initial enrichments harbored specific communities of heterotrophic microorganisms. Strains affiliated to Desulfosporosinus lacus, Desulfotomaculum sp., and Desulfovibrio aespoeensis were isolated only from the top layers (1.3–9.1 meters below seafloor, mbsf), while several strains of Desulfovibrio indonesiensis and a relative of Desulfotignum balticum were obtained from near-basement sediments (240–262 mbsf). Physiological tests on three selected strains affiliated to Dv. aespoeensis, Dv. indonesiensis, and Desulfotignum balticum indicated that all reduce sulfate with a limited number of short-chain n-alcohols or fatty acids and were able to ferment either ethanol, pyruvate, or betaine. All three isolates shared the capacity of growing chemolithotrophically with H2 as sole electron donor. Strain P23, affiliating with Dv. indonesiensis, even grew autotrophically in the absence of any organic compounds. Thus, H2 might be an essential electron donor in the deep-subseafloor where the availability of organic substrates is limited. The isolation of non-sporeforming sulfate reducers from fluid-influenced layers indicates that they have survived the long-term burial as active populations even after the separation from the seafloor hundreds

  14. Acetate production from oil under sulfate-reducing conditions in bioreactors injected with sulfate and nitrate.

    PubMed

    Callbeck, Cameron M; Agrawal, Akhil; Voordouw, Gerrit

    2013-08-01

    Oil production by water injection can cause souring in which sulfate in the injection water is reduced to sulfide by resident sulfate-reducing bacteria (SRB). Sulfate (2 mM) in medium injected at a rate of 1 pore volume per day into upflow bioreactors containing residual heavy oil from the Medicine Hat Glauconitic C field was nearly completely reduced to sulfide, and this was associated with the generation of 3 to 4 mM acetate. Inclusion of 4 mM nitrate inhibited souring for 60 days, after which complete sulfate reduction and associated acetate production were once again observed. Sulfate reduction was permanently inhibited when 100 mM nitrate was injected by the nitrite formed under these conditions. Pulsed injection of 4 or 100 mM nitrate inhibited sulfate reduction temporarily. Sulfate reduction resumed once nitrate injection was stopped and was associated with the production of acetate in all cases. The stoichiometry of acetate formation (3 to 4 mM formed per 2 mM sulfate reduced) is consistent with a mechanism in which oil alkanes and water are metabolized to acetate and hydrogen by fermentative and syntrophic bacteria (K. Zengler et al., Nature 401:266-269, 1999), with the hydrogen being used by SRB to reduce sulfate to sulfide. In support of this model, microbial community analyses by pyrosequencing indicated SRB of the genus Desulfovibrio, which use hydrogen but not acetate as an electron donor for sulfate reduction, to be a major community component. The model explains the high concentrations of acetate that are sometimes found in waters produced from water-injected oil fields.

  15. Acetate Production from Oil under Sulfate-Reducing Conditions in Bioreactors Injected with Sulfate and Nitrate

    PubMed Central

    Callbeck, Cameron M.; Agrawal, Akhil

    2013-01-01

    Oil production by water injection can cause souring in which sulfate in the injection water is reduced to sulfide by resident sulfate-reducing bacteria (SRB). Sulfate (2 mM) in medium injected at a rate of 1 pore volume per day into upflow bioreactors containing residual heavy oil from the Medicine Hat Glauconitic C field was nearly completely reduced to sulfide, and this was associated with the generation of 3 to 4 mM acetate. Inclusion of 4 mM nitrate inhibited souring for 60 days, after which complete sulfate reduction and associated acetate production were once again observed. Sulfate reduction was permanently inhibited when 100 mM nitrate was injected by the nitrite formed under these conditions. Pulsed injection of 4 or 100 mM nitrate inhibited sulfate reduction temporarily. Sulfate reduction resumed once nitrate injection was stopped and was associated with the production of acetate in all cases. The stoichiometry of acetate formation (3 to 4 mM formed per 2 mM sulfate reduced) is consistent with a mechanism in which oil alkanes and water are metabolized to acetate and hydrogen by fermentative and syntrophic bacteria (K. Zengler et al., Nature 401:266–269, 1999), with the hydrogen being used by SRB to reduce sulfate to sulfide. In support of this model, microbial community analyses by pyrosequencing indicated SRB of the genus Desulfovibrio, which use hydrogen but not acetate as an electron donor for sulfate reduction, to be a major community component. The model explains the high concentrations of acetate that are sometimes found in waters produced from water-injected oil fields. PMID:23770914

  16. Immobilization of cobalt by sulfate-reducing bacteria in subsurface sediments

    USGS Publications Warehouse

    Krumholz, Lee R.; Elias, Dwayne A.; Suflita, Joseph M.

    2003-01-01

    We investigated the impact of sulfate-reduction on immobilization of metals in subsurface aquifers. Co 2+ was used as a model for heavy metals. Factors limiting sulfate-reduction dependent Co 2+ immobilization were tested on pure cultures of sulfate-reducing bacteria, and in sediment columns from a landfill leachate contaminated aquifer. In the presence of 1 mM Co 2+ , the growth of pure cultures of sulfate-reducing bacteria was not impacted. Cultures of Desulfovibrio desulfuricans, Desulfotomaculum gibsoniae , and Desulfomicrobium hypogeia removed greater than 99.99% of the soluble Co 2+ when CoCl 2 was used with no chelators. The above cultures and Desulfoarcula baarsi removed 98-99.94% of the soluble Co(II) when the metal was complexed with the model ligand nitrilotriacetate (Co-NTA). Factors controlling the rate of sulfate-reduction based Co 2+ precipitation were investigated in sediment-cobalt mixtures. Several electron donors were tested and all but toluene accelerated soluble Co 2+ loss. Ethanol and formate showed the greatest stimulation. All complex nitrogen sources tested slowed and decreased the extent of Co 2+ removal from solution relative to formate-amended sediment incubations. A range of pH values were tested (6.35-7.81), with the more alkaline incubations exhibiting the largest precipitation of Co 2+ . The immobilization of Co 2+ in sediments was also investigated with cores to monitor the flow of Co 2+ through undisturbed sediments. An increase in the amount of Co 2+ immobilized as CoS was observed as sulfate reduction activity was stimulated in flow through columns. Both pure culture and sediment incubation data indicate that stimulation of sulfate reduction is a viable strategy in the immobilization of contaminating metals in subsurface systems.

  17. The use of magnesium peroxide for the inhibition of sulfate-reducing bacteria under anoxic conditions.

    PubMed

    Chang, Yu-Jie; Chang, Yi-Tang; Hung, Chun-Hsiung

    2008-11-01

    Sulfate-reducing bacteria (SRB), which cause microbiologically influenced material corrosion under anoxic conditions, form one of the major groups of microorganisms responsible for the generation of hydrogen sulfide. In this study, which is aimed at reducing the presence of SRB, a novel alternative approach involving the addition of magnesium peroxide (MgO2) compounds involving the use of reagent-grade MgO2 and a commercial product (ORC) was evaluated as a means of inhibiting SRB in laboratory batch columns. Different concentrations of MgO2 were added in the columns when black sulfide sediment had appeared in the columns. The experimental results showed that MgO2 is able to inhibit biogenic sulfide. The number of SRB, the sulfide concentration and the sulfate reducing rate (SRR) were decreased. ORCtrade mark as an additive was able to decrease more effectively the concentration of sulfide in water and the SRB-control effect was maintained over a longer time period when ORCtrade mark was used. The level of oxidation-reduction potential (ORP), which has a linear relationship to the sulfide/sulfate ratio, is a good indicator of SRB activity. As determined by fluorescence in-situ hybridization (FISH), most SRB growth was inhibited under increasing amounts of added MgO2. The concentration of sulfide reflected the abundance of the SRB. Utilization of organic matter greater than the theoretical SRB utilization rate indicated that facultative heterotrophs became dominant after MgO2 was added. The results of this study could supply the useful information for further study on evaluating the solution to biocorrosion problems in practical situations.

  18. Application Of Immobilized Sulfate Reducing Bacteria For Permeable Reactive Barriers In Abandoned Coal Mines

    NASA Astrophysics Data System (ADS)

    Kim, K.; Hur, W.; Choi, S.; Min, K.; Baek, H.

    2006-05-01

    The decline of the Korean coal industry has been drastic in production and consumption. This has been resulted mainly from the environmental concern and the collapse of commercial viability, which has eventually necessitated the government to implement the coal industry rationalization policies to reduce coal production and close down uneconomical mines. The overall drainage rates from abandoned coal mines reaches up to 80,000 ton/day. As a measure of controlling the acid mine drainage from abandoned coal mines, reactive materials in the pathways of drainage, designed to intercept and to transform the contaminants into environmentally acceptable forms can be applied at mines with small drainage rates. The main objective of this study is to design a permeable reactive barrier(PRB) to treat low flow and/or low contaminant loads of acid mine drainage. The PRB is comprised of immobilized sulfate reducing bacteria in hard beads and limestone to remove heavy metals and to raise the pH of AMD. A laboratory reactor was used to prepare a mixed culture of sulfate reducing bacteria. The microbes were separated and mixed with biodegradable matrix to form spherical beads. In order to maintain the viability of micro-organisms for a prolonged period, substrates such as saw dust, polysaccharide or glycerol was supplemented for the beads preparation. The strength of beads fortified by powered limestone to control the permeability of PRB. Different mixtures of limestone and the immobilized beads were tested to determine hydraulic conductivity and AMD treatment capacities. The characteristics of the spherical beads at various pH of AMD was investigated.

  19. Assessing the Role of Iron Sulfides in the Long Term Sequestration of Uranium by Sulfate-Reducing Bacteria

    SciTech Connect

    Hayes, Kim F.; Bi, Yuqiang; Carpenter, Julian; Hyng, Sung Pil; Rittmann, Bruce E.; Zhou, Chen; Vannela, Raveender; Davis, James A.

    2014-01-01

    This overarching aim of this project was to identify the role of biogenic and synthetic iron-sulfide minerals in the long-term sequestration of reduced U(IV) formed under sulfate-reducing conditions when subjected to re-oxidizing conditions. The work reported herein was achieved through the collaborative research effort conducted at Arizona State University (ASU) and the University of Michigan (UM). Research at ASU, focused on the biogenesis aspects, examined the biogeochemical bases for iron-sulfide production by Desulfovibrio vulgaris, a Gram-negative bacterium that is one of the most-studied strains of sulfate-reducing bacteria. A series of experimental studies were performed to investigate comprehensively important metabolic and environmental factors that affect the rates of sulfate reduction and iron-sulfide precipitation, the mineralogical characteristics of the iron sulfides, and how uranium is reduced or co-reduced by D. vulagaris. FeS production studies revealed that controlling the pH affected the growth of D. vulgaris and strongly influenced the formation and growth of FeS solids. In particular, lower pH produced larger-sized mackinawite (Fe1+xS). Greater accumulation of free sulfide, from more sulfate reduction by D. vulgaris, also led to larger-sized mackinawite and stimulated mackinawite transformation to greigite (Fe3S4) when the free sulfide concentration was 29.3 mM. On the other hand, using solid Fe(III) (hydr)oxides as the iron source led to less productivity of FeS due to their slow and incomplete dissolution and scavenging of sulfide. Furthermore, sufficient free Fe2+, particularly during Fe(III) (hydr)oxide reductions, led to the additional formation of vivianite [Fe3(PO4)2•8(H2O)]. The U(VI) reduction studies revealed that D. vulgaris reduced U(VI) fastest when accumulating sulfide from concomitant sulfate reduction, since direct enzymatic and sulfide-based reductions of U(VI) occurred in parallel. The UO2 produced in presence of ferrous

  20. Influence of nitrogen substrates and substrate C:N ratios on the nitrogen isotopic composition of amino acids from the marine bacterium Vibrio harveyi

    NASA Astrophysics Data System (ADS)

    Maki, K.; Ohkouchi, N.; Chikaraishi, Y.; Fukuda, H.; Miyajima, T.; Nagata, T.

    2014-09-01

    Nitrogen (N) isotopic compositions of individual hydrolysable amino acids (δ15NAAs) in N pools have been increasingly used for trophic position assessment and evaluation of sources and transformation processes of organic matter in marine environments. However, there are limited data about variability in δ15NAAs patterns and how this variability influences marine bacteria, an important mediator of trophic transfer and organic matter transformation. We explored whether marine bacterial δ15NAAs profiles change depending on the type and C:N ratio of the substrate. The δ15NAAs profile of a marine bacterium, Vibrio harveyi, was examined using medium containing either glutamate, alanine or ammonium as the N source [substrate C:N ratios (range, 3 to 20) were adjusted with glucose]. The data were interpreted as a reflection of isotope fractionations associated with de novo synthesis of amino acids by bacteria. Principal component analysis (PCA) using the δ15N offset values normalized to glutamate + glutamine δ15N revealed that δ15NAAs profiles differed depending on the N source and C:N ratio of the substrate. High variability in the δ15N offset of alanine and valine largely explained this bacterial δ15NAAs profile variability. PCA was also conducted using bacterial and phytoplankton (cyanobacteria and eukaryotic algae) δ15NAAs profile data reported previously. The results revealed that bacterial δ15NAAs patterns were distinct from those of phytoplankton. Therefore, the δ15NAAs profile is a useful indicator of biochemical responses of bacteria to changes in substrate conditions, serving as a potentially useful method for identifying organic matter sources in marine environments.

  1. Sulfate-reducing bacteria release barium and radium from naturally occurring radioactive material in oil-field barite

    USGS Publications Warehouse

    Phillips, E.J.P.; Landa, E.R.; Kraemer, T.; Zielinski, R.

    2001-01-01

    Scale and sludge deposits formed during oil production can contain elevated levels of Ra, often coprecipitated with barium sulfate (barite). The potential for sulfate-reducing bacteria to release 226 Ra and Ba (a Ra analog) from oil-field barite was evaluated. The concentration of dissolved Ba increased when samples containing pipe scale, tank sludge, or oil-field brine pond sediment were incubated with sulfate-reducing bacteria Desulfovibrio sp., Str LZKI, isolated from an oil-field brine pond. However, Ba release was not stoichiometric with sulfide production in oil-field samples, and <0.1% of the Ba was released. Potential for the release of 226Ra was demonstrated, and the 226 Ra release associated with sulfate-reducing activity was predictable from the amount of Ba released. As with Ba, only a fraction of the 226Ra expected from the amount of sulfide produced was released, and most of the Ra remained associated with the solid material.

  2. Proton efflux coupled to dark H/sub 2/ oxidation in whole cells of a marine sulfur photosynthetic bacterium (Chromatium sp. strain Miami PBS1071)

    SciTech Connect

    Kumazawa, S.; Izawa, S.; Mitsui, A.

    1983-04-01

    Whole cells of photoanaerobically grown Chromatium sp. strain Miami PBS1071, a marine sulfur purple bacterium, oxidized H/sub 2/ in the dark through the oxyhydrogen reaction at rates of up to 59 nmol of H/sub 2/ per mg (dry weight) per min. H/sub 2/ oxidation was routinely measured in H/sub 2/ pulse experiments with air-equilibrated cells. The reaction was accompanied by a reversible H/sup +/ efflux from the cells, suggesting an outward H/sup +/ translocation reaction coupled to H/sub 2/ oxidation. Anaerobic H/sub 2/ uptake with 2,5-dimethyl-p-benzoguinone as an oxidant also showed a weak H/sup +/-translocating activity. Carbonylcyanide 3-chlorophenylhydrazone (1 ..mu..M) stimulated H/sub 2/ oxidation and abolished the associated H/sup +/ changes when H/sub 2/ oxidation was observed in O/sub 2/ pulse experiments with H/sub 2/-Ar-equilibrated cells. However, the uncoupler inhibited both H/sub 2/ oxidation and H/sup +/ changes when measurements were made in H/sub 2/ pulse experiments with air-equilibrated cells. It is suggested that in this bacterium the susceptibility of hydrogenase to reversible O/sub 2/ inactivation in situ is enhanced by the presence of uncoupling agents.

  3. Secondary Metabolites Produced by the Marine Bacterium Halobacillus salinus That Inhibit Quorum Sensing-Controlled Phenotypes in Gram-Negative Bacteria▿

    PubMed Central

    Teasdale, Margaret E.; Liu, Jiayuan; Wallace, Joselynn; Akhlaghi, Fatemeh; Rowley, David C.

    2009-01-01

    Certain bacteria use cell-to-cell chemical communication to coordinate community-wide phenotypic expression, including swarming motility, antibiotic biosynthesis, and biofilm production. Here we present a marine gram-positive bacterium that secretes secondary metabolites capable of quenching quorum sensing-controlled behaviors in several gram-negative reporter strains. Isolate C42, a Halobacillus salinus strain obtained from a sea grass sample, inhibits bioluminescence production by Vibrio harveyi in cocultivation experiments. With the use of bioassay-guided fractionation, two phenethylamide metabolites were identified as the active agents. The compounds additionally inhibit quorum sensing-regulated violacein biosynthesis by Chromobacterium violaceum CV026 and green fluorescent protein production by Escherichia coli JB525. Bacterial growth was unaffected at concentrations below 200 μg/ml. Evidence is presented that these nontoxic metabolites may act as antagonists of bacterial quorum sensing by competing with N-acyl homoserine lactones for receptor binding. PMID:19060172

  4. A putative siderophore-interacting protein from the marine bacterium Shewanella frigidimarina NCIMB 400: cloning, expression, purification, crystallization and X-ray diffraction analysis

    PubMed Central

    Trindade, Inês B.; Fonseca, Bruno M.; Matias, Pedro M.; Louro, Ricardo O.; Moe, Elin

    2016-01-01

    Siderophore-binding proteins (SIPs) perform a key role in iron acquisition in multiple organisms. In the genome of the marine bacterium Shewanella frigidimarina NCIMB 400, the gene tagged as SFRI_RS12295 encodes a protein from this family. Here, the cloning, expression, purification and crystallization of this protein are reported, together with its preliminary X-ray crystallographic analysis to 1.35 Å resolution. The SIP crystals belonged to the monoclinic space group P21, with unit-cell parameters a = 48.04, b = 78.31, c = 67.71 Å, α = 90, β = 99.94, γ = 90°, and are predicted to contain two molecules per asymmetric unit. Structure determination by molecular replacement and the use of previously determined ∼2 Å resolution SIP structures with ∼30% sequence identity as templates are ongoing. PMID:27599855

  5. Wound healing and antibacterial activities of chondroitin sulfate- and acharan sulfate-reduced silver nanoparticles

    NASA Astrophysics Data System (ADS)

    Im, A.-Rang; Kim, Jee Young; Kim, Hyun-Seok; Cho, Seonho; Park, Youmie; Kim, Yeong Shik

    2013-10-01

    For topical applications in wound healing, silver nanoparticles (AgNPs) have attracted much attention as antibacterial agents. Herein, we describe a green-synthetic route for the production of biocompatible and crystalline AgNPs using two glycosaminoglycans, chondroitin sulfate (CS) and acharan sulfate (AS), as reducing agents. The synthetic approach avoids the use of toxic chemicals, and the yield of AgNPs formation is found to be 98.1% and 91.1% for the chondroitin sulfate-reduced silver nanoparticles (CS-AgNPs) and the acharan sulfate-reduced silver nanoparticles (AS-AgNPs), respectively. Nanoparticles with mostly spherical and amorphous shapes were observed, with an average diameter of 6.16 ± 2.26 nm for CS-AgNPs and 5.79 ± 3.10 nm for AS-AgNPs. Images of the CS-AgNPs obtained from atomic force microscopy revealed the self-assembled structure of CS was similar to a densely packed woven mat with AgNPs sprinkled on the CS. These nanoparticles were stable under cell culture conditions without any noticeable aggregation. An approximately 128-fold enhancement of the antibacterial activities of the AgNPs was observed against Enterobacter cloacae and Escherichia coli when compared to CS and AS alone. In addition, an in vivo animal model of wound healing activity was tested using mice that were subjected to deep incision wounds. In comparison to the controls, the ointments containing CS-AgNPs and AS-AgNPs stimulated wound closure under histological examination and accelerated the deposition of granulation tissue and collagen in the wound area. The wound healing activity of the ointments containing CS-AgNPs and AS-AgNPs are comparable to that of a commercial formulation of silver sulfadiazine even though the newly prepared ointments contain a lower silver concentration. Therefore, the newly prepared AgNPs demonstrate potential for use as an attractive biocompatible nanocomposite for topical applications in the treatment of wounds.

  6. Wound healing and antibacterial activities of chondroitin sulfate- and acharan sulfate-reduced silver nanoparticles.

    PubMed

    Im, A-Rang; Kim, Jee Young; Kim, Hyun-Seok; Cho, Seonho; Park, Youmie; Kim, Yeong Shik

    2013-10-04

    For topical applications in wound healing, silver nanoparticles (AgNPs) have attracted much attention as antibacterial agents. Herein, we describe a green-synthetic route for the production of biocompatible and crystalline AgNPs using two glycosaminoglycans, chondroitin sulfate (CS) and acharan sulfate (AS), as reducing agents. The synthetic approach avoids the use of toxic chemicals, and the yield of AgNPs formation is found to be 98.1% and 91.1% for the chondroitin sulfate-reduced silver nanoparticles (CS-AgNPs) and the acharan sulfate-reduced silver nanoparticles (AS-AgNPs), respectively. Nanoparticles with mostly spherical and amorphous shapes were observed, with an average diameter of 6.16 ± 2.26 nm for CS-AgNPs and 5.79 ± 3.10 nm for AS-AgNPs. Images of the CS-AgNPs obtained from atomic force microscopy revealed the self-assembled structure of CS was similar to a densely packed woven mat with AgNPs sprinkled on the CS. These nanoparticles were stable under cell culture conditions without any noticeable aggregation. An approximately 128-fold enhancement of the antibacterial activities of the AgNPs was observed against Enterobacter cloacae and Escherichia coli when compared to CS and AS alone. In addition, an in vivo animal model of wound healing activity was tested using mice that were subjected to deep incision wounds. In comparison to the controls, the ointments containing CS-AgNPs and AS-AgNPs stimulated wound closure under histological examination and accelerated the deposition of granulation tissue and collagen in the wound area. The wound healing activity of the ointments containing CS-AgNPs and AS-AgNPs are comparable to that of a commercial formulation of silver sulfadiazine even though the newly prepared ointments contain a lower silver concentration. Therefore, the newly prepared AgNPs demonstrate potential for use as an attractive biocompatible nanocomposite for topical applications in the treatment of wounds.

  7. Chromopeptide A, a highly cytotoxic depsipeptide from the marine sediment-derived bacterium Chromobacterium sp. HS-13-94

    PubMed Central

    Zhou, Zhenfang; Wang, Xin; Zhang, Hui; Sun, Jingya; Zheng, Linghui; Liu, Hongchun; Wang, Jidong; Shen, Aijun; Geng, Meiyu; Guo, Yuewei

    2015-01-01

    A bicyclic depsipeptide, chromopeptide A (1), was isolated from a deep-sea-derived bacterium Chromobacterium sp. HS-13-94. Its structure was determined by extensive spectroscopic analysis and by comparison with a related known compound. The absolute configuration of chromopeptide A was established by X-ray diffraction analysis employing graphite monochromated Mo Kα radiation (λ=0.71073 Å) with small Flack parameter 0.03. Chromopeptide A suppressed the proliferation of HL-60, K-562, and Ramos cells with average IC50 values of 7.7, 7.0, and 16.5 nmol/L, respectively. PMID:26579426

  8. Reduction and precipitation of neptunium(V) by sulfate-reducing bacteria.

    SciTech Connect

    Banaszak, J. E.; Rittmann, B. E.; Reed, D. T.

    1999-10-21

    Migration of neptunium, as NpO{sub 2}{sup +}, has been identified as a potentially important pathway for actinide release at nuclear waste repositories and existing sites of subsurface contamination. Reduction of Np(V) to Np(IV) will likely reduce its volubility, resulting in lowered subsurface migration. The ability of sulfate-reducing bacteria (SRB) to utilize Np(V) as an electron acceptor was investigated, because these bacteria are active in many anaerobic aquifers and are known to facilitate the reduction of metals and radionuclides. Pure and mixed cultures of SRB were able to precipitate neptunium during utilization of pyruvate, lactate, and hydrogen as electron donors in the presence and absence of sulfate. The neptunium in the precipitate was identified as Np(IV) using X-ray absorption near edge spectroscopy (XANES) analysis. In mixed-culture studies, the addition of hydrogen to consortia grown by pyruvate fermentation stimulated neptunium reduction and precipitation. Experiments with pure cultures of Desulfovibrio vulgaris, growing by lactate fermentation in the absence of sulfate or by sulfate reduction, confirm that the organism is active in neptunium reduction and precipitation. Based on our results, the activity of SRB in the subsurface may have a significant, and potentially beneficial, impact on actinide mobility by reducing neptunium volubility.

  9. Uranium removal by sulfate reducing biofilms in the presence of carbonates

    SciTech Connect

    Marsili, E.; Beyenal, Haluk; Di Palma, L.; Merli, C.; Dohnalkova, Alice; Amonette, James E.; Lewandowski, Zbigniew

    2005-12-01

    Hexavalent uranium [U(VI)] was immobilized in biofilms composed of the sulfate reducing bacteria (SRB), Desulfovibrio desulfuricans G20. The biofilms were grown in two flat-plate, continuous-flow reactors using lactate as the electron donor and sulfate as the electron acceptor. The growth medium contained uranium U(VI) and the pH was maintained constant using bicarbonate buffer. The reactors were operated for 5 months, and during that time biofilm activity and uranium removal were evaluated. The efficiency of uranium removal strongly depended on the concentration of uranium in the influent, and was estimated to be 30.4% in the reactor supplied with 3 mg/L of U(VI) and 73.9% in the reactor supplied with 30 mg/L of U(VI). TEM and SAED analysis showed that uranium in both reactors accumulated mostly on microbial cell membranes and in the periplasmic space. The deposits had amorphous or poor nanocrystalline structures.

  10. Leaching of 226Ra from U mill tailings by sulfate-reducing bacteria.

    PubMed

    Landa, E R; Miller, C L; Updegraff, D M

    1986-10-01

    Relatively insoluble sulfate precipitates appear to be a major host for Ra in sulfuric acid-treated, U mill tailings. The dissolution of such precipitates by natural processes, such as metabolism by sulfate-reducing bacteria (SRB), creates the potential for release of Ra to contacting waters. Significant leaching of Ra by SRB was achieved in the laboratory during the anaerobic incubation (1 to 119 days) of U mill tailings with pure cultures of Desulfovibrio desulfuricans and mixed cultures containing SRB isolated from the tailings, all grown on a lactate medium at room temperature. While the maximum 226Ra concentration reached in a sterile media control was 0.44 Bq/L (12 pCi/L), that in the SRB systems was 61 Bq/L (1640 pCi/L) or about 20% of the total Ra inventory in the original tailings sample. The leaching of Ra in SRB systems was accompanied by a decrease in soluble sulfate concentration, an increase in total sulfide concentration, and an increase in the number of SRB. The observed leaching effect does not appear to be due to the action of microbial chelates or to binding to cell walls. Potential implications of these findings to the management of U mill tailings and other radioactive wastes are discussed.

  11. Immunomagnetically Captured Thermophilic Sulfate-Reducing Bacteria from North Sea Oil Field Waters

    PubMed Central

    Christensen, Bjørn; Torsvik, Terje; Lien, Torleiv

    1992-01-01

    Immunomagnetic beads (IMB) were used to recover thermophilic sulfate-reducing bacteria from oil field waters from oil production platforms in the Norwegian sector of the North Sea. IMB coated with polyclonal antibodies against whole-cell antigens of the thermophilic Thermodesulfobacterium mobile captured strains GFA1, GFA2, and GFA3. GFA1 was serologically and morphologically identical to T. mobile. GFA2 and GFA3 were spore forming and similar to the Desulfotomaculum strains T90A and T93B previously isolated from North Sea oil field waters by a classical enrichment procedure. Western blots (immunoblots) of whole cells showed that GFA2, GFA3, T90A, and T93B are different serotypes of the same Desulfotomaculum species. Monoclonal antibodies (MAb) against T. mobile type strain cells were produced and used as capture agents on IMB. These MAb, named A4F4, were immunoglobulin M; they were specific to T. mobile and directed against lipopolysaccharides. The prevailing cells immunocaptured with MAb A4F4 were morphologically and serologically similar to T. mobile type strain cells. T. mobile was not detected in these oil field waters by classical enrichment procedures. Furthermore, extraction with antibody-coated IMB allowed pure strains to be isolated directly from primary enrichment cultures without prior time-consuming subculturing and consecutive transfers to selective media. Images PMID:16348693

  12. Biodegradation of munitions compounds by a sulfate reducing bacterial enrichment culture

    SciTech Connect

    Boopathy, R.; Manning, J.

    1997-08-01

    The degradation of several munitions compounds was studied. The compounds included 2,4,6-trinitrotoluene (TNT), hexahydro-1,3,5-trinitro-1,3,5-triazine, octahydro-1,3,5,7-tetranitro-1,3,5,7-tetraazocine, 2,4,6-trinitrobenzene (TNB), and 2,4-dinitrotoluene. All of the compounds studied were degraded by the sulfate reducing bacterial (SRB) enrichment culture. The SRB culture did not use the munitions compounds as their sole source of carbon. However, all the munitions compounds tested served as the sole source of nitrogen for the SRB culture. Degradation of munitions compounds was achieved by a co-metabolic process. The SRB culture used a variety of carbon sources including pyruvate, ethanol, formate, lactate, and H{sub 2}-CO{sub 2}. The SRB culture was an incomplete oxidizer, unable to carry out the terminal oxidation of organic substrates to CO{sub 2} as the sole product, and it did not use acetate or methanol as a carbon source. In addition to serving as nitrogen sources, the munitions compounds also served as electron acceptors in the absence of sulfate. A soil slurry experiment with 5% and 10% munitions compounds-contaminated soil showed that the contaminant TNT was metabolized by the SRB culture in the presence of pyruvate as electron donor. This culture may be useful in decontaminating munitions compounds-contaminated soil and water under anaerobic conditions.

  13. Preparation of metal-resistant immobilized sulfate reducing bacteria beads for acid mine drainage treatment.

    PubMed

    Zhang, Mingliang; Wang, Haixia; Han, Xuemei

    2016-07-01

    Novel immobilized sulfate-reducing bacteria (SRB) beads were prepared for the treatment of synthetic acid mine drainage (AMD) containing high concentrations of Fe, Cu, Cd and Zn using up-flow anaerobic packed-bed bioreactor. The tolerance of immobilized SRB beads to heavy metals was significantly enhanced compared with that of suspended SRB. High removal efficiencies of sulfate (61-88%) and heavy metals (>99.9%) as well as slightly alkaline effluent pH (7.3-7.8) were achieved when the bioreactor was fed with acidic influent (pH 2.7) containing high concentrations of multiple metals (Fe 469 mg/L, Cu 88 mg/L, Cd 92 mg/L and Zn 128 mg/L), which showed that the bioreactor filled with immobilized SRB beads had tolerance to AMD containing high concentrations of heavy metals. Partially decomposed maize straw was a carbon source and stabilizing agent in the initial phase of bioreactor operation but later had to be supplemented by a soluble carbon source such as sodium lactate. The microbial community in the bioreactor was characterized by denaturing gradient gel electrophoresis (DGGE) and sequencing of partial 16S rDNA genes. Synergistic interaction between SRB (Desulfovibrio desulfuricans) and co-existing fermentative bacteria could be the key factor for the utilization of complex organic substrate (maize straw) as carbon and nutrients source for sulfate reduction.

  14. Diversity of functional genes of methanogens, methanotrophs and sulfate reducers in deep-sea hydrothermal environments.

    PubMed

    Nercessian, Olivier; Bienvenu, Nadège; Moreira, David; Prieur, Daniel; Jeanthon, Christian

    2005-01-01

    To contribute to the identification of methanogens, methanotrophs and sulfate-reducing bacteria (SRB) in microbial communities from the 13 degrees N (East Pacific Rise) and Rainbow (Mid-Atlantic Ridge) hydrothermal vent fields, we investigated the diversity of mcrA, pmoA and dsrAB genes sequences. Clone libraries were obtained using DNA isolated from fragments of diffuse vents, sediment and in situ samplers. The clones were categorized by restriction fragment length polymorphism, and representatives of each group were sequenced. Sequences were related to that of hyperthermophilic (order Methanopyrales and family Methanocaldococcaceae), thermophilic and mesophilic (family Methanococcaceae) methanogens, thermophilic (proposed genus 'Methylothermus') and mesophilic type I methanotrophs, and hyperthermophilic (order Archaeoglobales), thermophilic (order Thermodesulfobacteriales) and mesophilic (family Desulfobulbaceae) SRB. Several of the obtained sequences were distantly related to the genes of cultivated organisms, providing evidence of the existence of novel lineages in the three functional groups. This study provides for the first time an insight into the diversity of several functional genes of deep-sea hydrothermal system microorganisms.

  15. Treatment of acid rock drainage using a sulfate-reducing bioreactor with zero-valent iron.

    PubMed

    Ayala-Parra, Pedro; Sierra-Alvarez, Reyes; Field, James A

    2016-05-05

    This study assessed the bioremediation of acid rock drainage (ARD) in flow-through columns testing zero-valent iron (ZVI) for the first time as the sole exogenous electron donor to drive sulfate-reducing bacteria in permeable reactive barriers. Columns containing ZVI, limestone or a mixture of both materials were inoculated with an anaerobic mixed culture and fed a synthetic ARD containing sulfuric acid and heavy metals (initially copper, and later also cadmium and lead). ZVI significantly enhanced sulfate reduction and the heavy metals were extensively removed (>99.7%). Solid-phase analyses showed that heavy metals were precipitated with biogenic sulfide in the columns packed with ZVI. Excess sulfide was sequestered by iron, preventing the discharge of dissolved sulfide. In the absence of ZVI, heavy metals were also significantly removed (>99.8%) due to precipitation with hydroxide and carbonate ions released from the limestone. Vertical-profiles of heavy metals in the columns packing, at the end of the experiment, demonstrated that the ZVI columns still had excess capacity to remove heavy metals, while the capacity of the limestone control column was approaching saturation. The ZVI provided conditions that enhanced sulfate reduction and generated alkalinity. Collectively, the results demonstrate an innovative passive ARD remediation process using ZVI as sole electron-donor.

  16. Bioremediation of copper-containing wastewater by sulfate reducing bacteria coupled with iron.

    PubMed

    Bai, He; Kang, Yong; Quan, Hongen; Han, Yang; Sun, Jiao; Feng, Ying

    2013-11-15

    In order to treat copper-containing wastewater effectively using sulfate reducing bacteria (SRB), iron (Fe(0)) was added to enhance the activity of SRB. The SRB system and the SRB + Fe(0) system were operated under continuous operation. The sulfate reduction efficiency of the SRB + Fe(0) system was twice as much as that of the SRB system with the sulfate loading rate at 125  mg L(-1) h(-1). The effect of COD/SO4(2-) on sulfate reduction indicates an enhanced activity of SRB by adding Fe(0). 99% of total sulfate was deducted in both systems at pH 4.0-7.0, and temperature slightly influenced the removal of sulfate in the SRB + Fe(0) system. In the copper-containing wastewater treatment, the SRB + Fe(0) system shows a better performance since sulfate removal in this system was higher than the SRB system, and the removal ratio of Cu(2+) was held above 95% in SRB + Fe(0) system at all influent Cu(2+) concentrations.

  17. Component analysis and heavy metal adsorption ability of extracellular polymeric substances (EPS) from sulfate reducing bacteria.

    PubMed

    Yue, Zheng-Bo; Li, Qing; Li, Chuan-chuan; Chen, Tian-hu; Wang, Jin

    2015-10-01

    Extracellular polymeric substances (EPS) play an important role in the treatment of acid mine drainage (AMD) by sulfate-reducing bacteria (SRB). In this paper, Desulfovibrio desulfuricans was used as the test strain to explore the effect of heavy metals on the components and adsorption ability of EPS. Fourier-transform infrared (FTIR) spectroscopy analysis results showed that heavy metals did not influence the type of functional groups of EPS. Potentiometric titration results indicated that the acidic constants (pKa) of the EPS fell into three ranges of 3.5-4.0, 5.9-6.7, and 8.9-9.8. The adsorption site concentrations of the surface functional groups also increased. Adsorption results suggested that EPS had a specific binding affinity for the dosed heavy metal, and that EPS extracted from the Zn(2+)-dosed system had a higher binding affinity for all heavy metals. Additionally, Zn(2+) decreased the inhibitory effects of Cd(2+) and Cu(2+) on the SRB.

  18. Evaluation of organic substrates to enhance the sulfate-reducing activity in phosphogypsum.

    PubMed

    Castillo, Julio; Pérez-López, Rafael; Sarmiento, Aguasanta M; Nieto, José M

    2012-11-15

    Several experiments were conducted to evaluate the activity and growth of sulfate-reducing bacteria (SRB) in a metal-rich culture medium (approx. 250 mg/L Fe, 75 mg/L Zn and Cu, 10mg/L Cd) with phosphogypsum as bacterial inoculum. Phosphogypsum was collected from the stack covering the salt-marshes of the Tinto river (SW Spain). Three organic amendments were used as carbon sources, two low-cost wastes (horse manure and legume compost) and one sample of natural soil (vegetal cover). In the experiments, sulfate was reduced to sulfide during the growth of SRB populations, and concentrations were decreased in the solution. Metal concentrations also decreased to values below the detection limit. Metal removal took place by precipitation of newly-formed sulfides. Pyrite-S was the main sulfide component (approx. 200 μmol/g and 80% of pyritization) and occurred mainly as framboidal grains and rarely as isolated polyhedral crystals. Horse manure was the most successful organic substrate to promote SRB activity (sulfate removal of 61%), followed by vegetal cover (49%) and legume compost (31%). These findings propose the possibility of using naturally-occurring SRB in the phosphogypsum for bioremediation strategies based on natural soil covers with organic amendments.

  19. Identification of population dynamics in sulfate-reducing consortia on exposure to sulfate.

    PubMed

    Icgen, Bulent; Harrison, Sue

    2006-12-01

    The microbial population structure and function of a mixed culture of sulfate-reducing bacteria (SRB) maintained in anaerobic continuous bioreactors were tracked before and after a major perturbation, which involved the addition of sulfate to the influent of a bioreactor when operated at steady state at 35 degrees C, pH 7.8 and a 2.5 day residence time with feed stream containing 10 and 15 kg m(-3) sulfate as terminal electron acceptor and 19.6 and 29.4 kg m(-3) ethanol as carbon source and electron donor, respectively. The population structure determined by fluorescence in situ hybridization (FISH), by using 16S rRNA-targeted oligonucleotide probes, was linked to the functional performance of the SRB in the reactor. Hybridization analysis using these 16S rRNA-targeted oligonucleotide probes revealed that a high concentration of sulfate was toxic for Desulfobacterium and Desulfobulbus. On the other hand, the Desulfococcus group was found to be the most dominant group of SRB in the feed stream containing 15 kg m(-3) sulfate as terminal electron acceptor and 29.4 kg m(-3) ethanol as carbon source and electron donor.

  20. Improved method for enumerating sulfate-reducing bacteria using optical density

    PubMed Central

    Bernardez, L.A.; de Andrade Lima, L.R.P.

    2015-01-01

    The photometric determination of bacterial concentration can be affected by secondary scattering and other interferences. The conventional growth medium for sulfate-reducing bacteria (SRB) has iron that precipitates as iron sulfides, a dark precipitate which is useful to indicate bacterial activity. However, iron hydroxides also precipitate at high pH values and the presence of these precipitates interferes considerably in the optical density of the solution affecting estimates of the cell population thus seriously limiting the use of the conventional method. In this method a modification of the current method improves the measurement of the optical density of a solution with SRB cells. • The method consists of an acidification with hydrochloric acid of a sample of a mixed culture of SRB enriched from the produced water from oil fields to pH below 2. • The results show that the relationship between the bacterial dry mass and absorbance is exponential in the observed range. It was observed a large slope in the linearized fit equation, and the acidified solution does not change the integrity of the SRB cells after the treatment. • The results of the kinetic experiments, including the bacterial growth time evolution, demonstrate the applicability of the method. PMID:26150995

  1. Sulfate-reducing bacteria in a denitrification reactor packed with wood as a carbon source.

    PubMed

    Yamashita, Takahiro; Yamamoto-Ikemoto, Ryoko; Zhu, Jianqing

    2011-02-01

    A denitrification reactor packed with wood as a carbon source was operated using synthetic inorganic wastewater. The maximum denitrification rate was 62.4 g-NO(3)(-)/m(3)/day at HRT of 24 h. The nitrate removal continued after 1500 days. The denitrification efficiency was assumed to enhance sulfur denitrification via wood degradation by sulfate reduction. The achieved sulfate reduction rate was 468 mg-SO(4)(2-)/kg-dry weight wood/day after 419 days of operation. The sulfate reduction rate in the deep-layer biofilm inside the wood was higher than that in the total biofilm inside the wood. The sulfate-reducing bacteria segregated inside the wood. This study suggested that Desulfobulbus spp. and Desulfomicrobium spp. grown in the deep-layer degraded the wood incompletely, and the produced organic acids were utilized by the heterotrophic denitrifying bacteria, Desulfobacter spp. and Desulfonema spp., grown in the surface layer, and that these surface bacteria complete the degradation of the organic acids from the wood.

  2. Diversity of sulfate-reducing bacteria in a plant using deep geothermal energy

    NASA Astrophysics Data System (ADS)

    Alawi, Mashal; Lerm, Stephanie; Vetter, Alexandra; Wolfgramm, Markus; Seibt, Andrea; Würdemann, Hilke

    2011-06-01

    Enhanced process understanding of engineered geothermal systems is a prerequisite to optimize plant reliability and economy. We investigated microbial, geochemical and mineralogical aspects of a geothermal groundwater system located in the Molasse Basin by fluid analysis. Fluids are characterized by temperatures ranging from 61°C to 103°C, salinities from 600 to 900 mg/l and a dissolved organic carbon content (DOC) between 6.4 to 19.3 mg C/l. The microbial population of fluid samples was analyzed by genetic fingerprinting techniques based on PCR-amplified 16S rRNA- and dissimilatory sulfite reductase genes. Despite of the high temperatures, microbes were detected in all investigated fluids. Fingerprinting and DNA sequencing enabled a correlation to metabolic classes and biogeochemical processes. The analysis revealed a broad diversity of sulfate-reducing bacteria. Overall, the detection of microbes known to be involved in biocorrosion and mineral precipitation indicates that microorganisms could play an important role for the understanding of processes in engineered geothermal systems.

  3. Comparative study of cellulose waste versus organic waste as substrate in a sulfate reducing bioreactor.

    PubMed

    Choudhary, R P; Sheoran, A S

    2011-03-01

    The biodegradability and comparative effectiveness in treatment of acid mine drainage of ten locally available organic waste materials were examined. pH of AMD increased from 2.70 to 6.25, 7.10 and 7.50 with buffalo, cow and goat manures whereas cellulosic wastes increased the pH within the range of 4.83-5.32 in laboratory scale single substrate bioreactors. Significant reduction was observed in Eh, acidity and sulfate with manures in treated AMD. Maximum metal removal efficiency was 99.3%, 99.9%, 99.8%, 99.1%, 99.1%, and 73.8% for Fe, Cu, Zn, Ni, Co and Mn in maximum retention period of 10 days. The highest efficiency of metal removal was observed in bioreactors with manures as single substrate. The effectiveness of substrate depends on its biodegradation ability, the results with cellulosic waste indicates it may need more than 10 days to biodegrade. Biodegradability of organic waste was evaluated according to COD/SO(4)(2-) and C/N ratio and the ratios of 0.48-0.57 and 22.22-23.00 respectively were adequate parameters for activity of sulfate reducing bacteria and pollutant removal efficiency.

  4. Anaerobic oxidation of dimethylsulfide and methanethiol in mangrove sediments is dominated by sulfate-reducing bacteria.

    PubMed

    Lyimo, Thomas J; Pol, Arjan; Harhangi, Harry R; Jetten, Mike S M; Op den Camp, Huub J M

    2009-12-01

    The oxidation of dimethylsulfide and methanethiol by sulfate-reducing bacteria (SRB) was investigated in Tanzanian mangrove sediments. The rate of dimethylsulfide and methanethiol accumulation in nonamended sediment slurry (control) incubations was very low while in the presence of the inhibitors tungstate and bromoethanesulfonic acid (BES), the accumulation rates ranged from 0.02-0.34 to 0.2-0.4 nmol g FW sediment(-1) h(-1), respectively. Degradation rates of methanethiol and dimethylsulfide added were 2-10-fold higher. These results point to a balance of production and degradation. Degradation was inhibited much stronger by tungstate than by BES, which implied that SRB were more important. In addition, a new species of SRB, designated strain SD1, was isolated. The isolate was a short rod able to utilize a narrow range of substrates including dimethylsulfide, methanethiol, pyruvate and butyrate. Strain SD1 oxidized dimethylsulfide and methanethiol to carbon dioxide and hydrogen sulfide with sulfate as the electron acceptor and exhibited a low specific growth rate of 0.010 +/- 0.002 h(-1), but a high affinity for its substrates. The isolated microorganism could be placed in the genus Desulfosarcina (the most closely related cultured species was Desulfosarcina variabilis, 97% identity). Strain SD1 represents a member of the dimethylsulfide/methanethiol-consuming SRB population in mangrove sediments.

  5. Linked redox precipitation of sulfur and selenium under anaerobic conditions by sulfate-reducing bacterial biofilms.

    PubMed

    Hockin, Simon L; Gadd, Geoffrey M

    2003-12-01

    A biofilm-forming strain of sulfate-reducing bacteria (SRB), isolated from a naturally occurring mixed biofilm and identified by 16S rDNA analysis as a strain of Desulfomicrobium norvegicum, rapidly removed 200 micro M selenite from solution during growth on lactate and sulfate. Elemental selenium and elemental sulfur were precipitated outside SRB cells. Precipitation occurred by an abiotic reaction with bacterially generated sulfide. This appears to be a generalized ability among SRB, arising from dissimilatory sulfide biogenesis, and can take place under low redox conditions and in the dark. The reaction represents a new means for the deposition of elemental sulfur by SRB under such conditions. A combination of transmission electron microscopy, environmental scanning electron microscopy, and cryostage field emission scanning electron microscopy were used to reveal the hydrated nature of SRB biofilms and to investigate the location of deposited sulfur-selenium in relation to biofilm elements. When pregrown SRB biofilms were exposed to a selenite-containing medium, nanometer-sized selenium-sulfur granules were precipitated within the biofilm matrix. Selenite was therefore shown to pass through the biofilm matrix before reacting with bacterially generated sulfide. This constitutes an efficient method for the removal of toxic concentrations of selenite from solution. Implications for environmental cycling and the fate of sulfur and selenium are discussed, and a general model for the potential action of SRB in selenium transformations is presented.

  6. Alkaline textile wastewater biotreatment: A sulfate-reducing granular sludge based lab-scale study.

    PubMed

    Zeng, Qian; Hao, Tianwei; Mackey, Hamish Robert; Wei, Li; Guo, Gang; Chen, Guanghao

    2017-03-06

    In this study the feasibility of treating dyeing wastewater with sulfate reducing granular sludge was explored, focusing on decolorization/degradation of azo dye (Procion Red HE-7B) and the performance of microbial consortia under alkaline conditions (pH=11). Efficiency of HE-7B degradation was influenced strongly by the chemical oxygen demand (COD) concentration which was examined in the range of 500-3000mg/L. COD removal efficiency was reduced at high COD concentration, while specific removal rate was enhanced to 17.5 mg-COD/gVSSh(-1). HE-7B removal was also improved at higher organic strength with more than 90% removal efficiency and a first-rate removal constant of 5.57h(-1) for dye degradation. Three dye-degradation metabolites were identified by HPLC-MS. The granular structure provided enhanced removal performance for HE-7B and COD in comparison to a near-identical floc SRB system and the key functional organisms were identified by high throughput sequencing. This study demonstrates an example of a niche application where SRB granules can be applied for high efficient and cost-effective treatment of a wastewater under adverse environmental conditions.

  7. Purification and Characterization of N-Acetylglucosamine-6-phosphate Deacetylase from a Psychrotrophic Marine Bacterium, Alteromonas Species.

    PubMed

    Yamano; Higashida; Endo; Sakata; Fujishima; Maruyama; Higashihara

    2000-01-01

    A psychrotrophic bacterium, strain Mct-9, which produced an N-acetylglucosamine-6-phosphate deacetylase, was isolated from a deep-seawater sample in the Mariana Trough. The Mct-9 strain was identified as Alteromonas sp. The native enzyme had a molecular mass of 164,000 Da, and was predicted to be composed of four identical subunits with molecular masses of 41,000 Da. The purified enzyme hydrolyzed N-acetylglucosamine (GlcNAc), GlcNAc-6-phosphate, and GlcNAc-6-sulfate. Considering the low K(m) and high k(cat)/K(m) for GlcNAc-6-phosphate, it probably acts as a GlcNAc-6-phosphate deacetylase in vivo. The enzyme was functional in the temperature range of 5 degrees to 70 degrees C and displayed optimal activity at 55 degrees C. The optimal temperature was higher than that of the deacetylase from the mesophilic bacterium Vibrio cholerae non-O1. The characteristics of the GlcNAc-6-phosphate deacetylase from Alteromonas sp. are unique among psychrotrophs and psychrophiles, whose intracellular enzymes are mostly thermolabile.

  8. Photoinhibition of Phaeocystis globosa resulting from oxidative stress induced by a marine algicidal bacterium Bacillus sp. LP-10

    PubMed Central

    Guan, Chengwei; Guo, Xiaoyun; Li, Yi; Zhang, Huajun; Lei, Xueqian; Cai, Guanjing; Guo, Jiajia; Yu, Zhiming; Zheng, Tianling

    2015-01-01

    Harmful algal blooms caused by Phaeocystis globosa have resulted in staggering losses to coastal countries because of their world-wide distribution. Bacteria have been studied for years to control the blooms of harmful alga, however, the action mechanism of them against harmful algal cells is still not well defined. Here, a previously isolated algicidal bacterium Bacillus sp. LP-10 was used to elucidate the potential mechanism involved in the dysfunction of P. globosa algal cells at physiological and molecular levels. Our results showed Bacillus sp. LP-10 induced an obvious rise of reactive oxygen species (ROS), which was supposed to be major reason for algal cell death. Meanwhile, the results revealed a significant decrease of photosynthetic physiological indexes and apparent down-regulated of photosynthesis-related genes (psbA and rbcS) and protein (PSII reaction center protein D1), after treated by Bacillus sp. LP-10 filtrates, suggesting photoinhibition occurred in the algal cells. Furthermore, our results indicated that light played important roles in the algal cell death. Our work demonstrated that the major lethal reason of P. globosa cells treated by the algicidal bacterium was the photoinhibition resulted from oxidative stress induced by Bacillus sp. LP-10. PMID:26601700

  9. Quorum sensing in marine snow and its possible influence on production of extracellular hydrolytic enzymes in marine snow bacterium Pantoea ananatis B9.

    PubMed

    Jatt, Abdul Nabi; Tang, Kaihao; Liu, Jiwen; Zhang, Zenghu; Zhang, Xiao-Hua

    2015-02-01

    Marine snow is a continuous shower of organic and inorganic detritus, and plays a crucial role in transporting materials from the sea surface to the deep ocean. The aims of the current study were to identify N-acyl homoserine lactone (AHL)-based quorum sensing (QS) signaling molecules directly from marine snow particles and to investigate the possible regulatory link between QS signals and extracellular hydrolytic enzymes produced by marine snow bacteria. The marine snow samples were collected from the surface water of China marginal seas. Two AHLs, i.e. 3OC6-HSL and C8-HSL, were identified directly from marine snow particles, while six different AHL signals, i.e. C4-HSL, 3OC6-HSL, C6-HSL, C10-HSL, C12-HSL and C14-HSL were produced by Pantoea ananatis B9 inhabiting natural marine snow particles. Of the extracellular hydrolytic enzymes produced by P. ananatis B9, alkaline phosphatase activity was highly enhanced in growth medium supplemented with exogenous AHL (C10-HSL), while quorum quenching enzyme (AiiA) drastically reduced the enzyme activity. To our knowledge, this is the first report revealing six different AHL signals produced by P. ananatis B9 and AHL-based QS system enhanced the extracellular hydrolytic enzyme in P. ananatis B9. Furthermore, this study first time revealing 3OC6-HSL production by Paracoccus carotinifaciens affiliated with Alphaproteobacteria.

  10. Identification of Distinct Communities of Sulfate-Reducing Bacteria in Oil Fields by Reverse Sample Genome Probing

    PubMed Central

    Voordouw, Gerrit; Voordouw, Johanna K.; Jack, Thomas R.; Foght, Julia; Fedorak, Phillip M.; Westlake, Donald W. S.

    1992-01-01

    Thirty-five different standards of sulfate-reducing bacteria, identified by reverse sample genome probing and defined as bacteria with genomes showing little or no cross-hybridization, were in part characterized by Southern blotting, using 16S rRNA and hydrogenase gene probes. Samples from 56 sites in seven different western Canadian oil field locations were collected and enriched for sulfate-reducing bacteria by using different liquid media containing one of the following carbon sources: lactate, ethanol, benzoate, decanoate, propionate, or acetate. DNA was isolated from the enrichments and probed by reverse sample genome probing using master filters containing denatured chromosomal DNAs from the 35 sulfate-reducing bacterial standards. Statistical analysis of the microbial compositions at 44 of the 56 sites indicated the presence of two distinct communities of sulfate-reducing bacteria. The discriminating factor between the two communities was the salt concentration of the production waters, which were either fresh water or saline. Of 34 standards detected, 10 were unique to the fresh water and 18 were unique to the saline oil field environment, while only 6 organisms were cultured from both communities. Images PMID:16348801

  11. Field Tests of “In-Situ” Remediation of Groundwater From Dissolved Mercury Utilizing Sulfate Reducing Bacteria

    EPA Science Inventory

    Field tests of biologically active filters have been conducted at groundwater mercury pollution site in Pavlodar, Kazakhstan. The biofilters represented cultures of sulfate-reducing bacteria (SRB) immobilized on claydite imbedded in wells drilled down to basalt clay layer (14-17 ...

  12. Stable Carbon Isotope Ratios of Lipid Biomarkers and Biomass for Sulfate-reducing Bacteria Grown with Different Substrates

    NASA Technical Reports Server (NTRS)

    Londry, K. L.; Jahnke, L. L.; Des Marais, D. J.

    2001-01-01

    We have determined isotope ratios of biomass and Fatty Acids Methyl Esters (FAME) for four Sulfate-Reducing Bacteria (SRB) grown lithotrophically and heterotrophically, and are investigating whether these biomarker signatures can reveal the ecological role and distribution of SRB within microbial mats. Additional information is contained in the original extended abstract.

  13. Isolation and identification of sulfate reducing bacteria (SRB) from the sediment pond after a coal mine in Samarinda, East Kalimantan

    NASA Astrophysics Data System (ADS)

    Kusumawati, Eko; Sudrajat, Putri, Junita Susilaning

    2017-02-01

    Title isolation and identification of sulfate reducing bacteria (SRB) of sediment pond former coal mine in Samarinda, East Kalimantan. Sulfate reducing bacteria (SRB) is a group of microbes that can be used to improve the quality of sediment former coal mine. In the metabolic activities, the SRB can reduce sulfate to H2S which immediately binds to metals that are widely available on mined lands and precipitated in the form of metal sulfides reductive. Isolation and identification of sulfate reducing bacteria carried out in the Laboratory of Microbiology and Molecular Genetics, Faculty of Mathematics and Natural Sciences, University of Mulawarman, Samarinda. Postgate B is a liquid medium used for isolation through serial dilution. Physiological and biochemical characterization was done by Bergey's Manual of Determinative Bacteriology. Six isolates of sulfate reducing bacteria were isolated from the sediment pond former coal mine in Samarinda. Several groups of bacteria can grow at 14 days of incubation, however, another group of bacteria which takes 21 days to grow. The identification results showed that two isolates belong to the genus Desulfotomaculum sp., and each of the other isolates belong to the genus Desulfococcus sp., Desulfobacter sp., Desulfobulbus sp. and Desulfobacterium sp.

  14. USING RESPIROMETRY TO MEASURE HYDROGEN UTILIZATION IN SULFATE REDUCING BACTERIA IN THE PRESENCE OF COPPER AND ZINC

    EPA Science Inventory

    A respirometric method has been developed to measure hydrogen utilization by sulfate reducing bacteria (SRB). One application of this method has been to test inhibitory metals effects on the SRB culture used in a novel acid mine drainage treatment technology. As a control param...

  15. BIOREACTOR ECONOMICS, SIZE AND TIME OF OPERATION (BEST) COMPUTER SIMULATOR FOR DESIGNING SULFATE-REDUCING BACTERIA FIELD BIOREACTORS

    EPA Science Inventory

    BEST (bioreactor economics, size and time of operation) is an Excel™ spreadsheet-based model that is used in conjunction with the public domain geochemical modeling software, PHREEQCI. The BEST model is used in the design process of sulfate-reducing bacteria (SRB) field bioreacto...

  16. Characterization of Fe (III)-reducing enrichment culture and isolation of Fe (III)-reducing bacterium Enterobacter sp. L6 from marine sediment.

    PubMed

    Liu, Hongyan; Wang, Hongyu

    2016-07-01

    To enrich the Fe (III)-reducing bacteria, sludge from marine sediment was inoculated into the medium using Fe (OH)3 as the sole electron acceptor. Efficiency of Fe (III) reduction and composition of Fe (III)-reducing enrichment culture were analyzed. The results indicated that the Fe (III)-reducing enrichment culture with the dominant bacteria relating to Clostridium and Enterobacter sp. had high Fe (III) reduction of (2.73 ± 0.13) mmol/L-Fe (II). A new Fe (III)-reducing bacterium was isolated from the Fe (III)-reducing enrichment culture and identified as Enterobacter sp. L6 by 16S rRNA gene sequence analysis. The Fe (III)-reducing ability of strain L6 under different culture conditions was investigated. The results indicated that strain L6 had high Fe (III)-reducing activity using glucose and pyruvate as carbon sources. Strain L6 could reduce Fe (III) at the range of NaCl concentrations tested and had the highest Fe (III) reduction of (4.63 ± 0.27) mmol/L Fe (II) at the NaCl concentration of 4 g/L. This strain L6 could reduce Fe (III) with unique properties in adaptability to salt variation, which indicated that it can be used as a model organism to study Fe (III)-reducing activity isolated from marine environment.

  17. Distribution of Sulfate-Reducing and Methanogenic Bacteria in Anaerobic Aggregates Determined by Microsensor and Molecular Analyses

    PubMed Central

    Santegoeds, Cecilia M.; Damgaard, Lars Riis; Hesselink, Gijs; Zopfi, Jakob; Lens, Piet; Muyzer, Gerard; de Beer, Dirk

    1999-01-01

    Using molecular techniques and microsensors for H2S and CH4, we studied the population structure of and the activity distribution in anaerobic aggregates. The aggregates originated from three different types of reactors: a methanogenic reactor, a methanogenic-sulfidogenic reactor, and a sulfidogenic reactor. Microsensor measurements in methanogenic-sulfidogenic aggregates revealed that the activity of sulfate-reducing bacteria (2 to 3 mmol of S2− m−3 s−1 or 2 × 10−9 mmol s−1 per aggregate) was located in a surface layer of 50 to 100 μm thick. The sulfidogenic aggregates contained a wider sulfate-reducing zone (the first 200 to 300 μm from the aggregate surface) with a higher activity (1 to 6 mmol of S2− m−3 s−1 or 7 × 10−9 mol s−1 per aggregate). The methanogenic aggregates did not show significant sulfate-reducing activity. Methanogenic activity in the methanogenic-sulfidogenic aggregates (1 to 2 mmol of CH4 m−3 s−1 or 10−9 mmol s−1 per aggregate) and the methanogenic aggregates (2 to 4 mmol of CH4 m−3 s−1 or 5 × 10−9 mmol s−1 per aggregate) was located more inward, starting at ca. 100 μm from the aggregate surface. The methanogenic activity was not affected by 10 mM sulfate during a 1-day incubation. The sulfidogenic and methanogenic activities were independent of the type of electron donor (acetate, propionate, ethanol, or H2), but the substrates were metabolized in different zones. The localization of the populations corresponded to the microsensor data. A distinct layered structure was found in the methanogenic-sulfidogenic aggregates, with sulfate-reducing bacteria in the outer 50 to 100 μm, methanogens in the inner part, and Eubacteria spp. (partly syntrophic bacteria) filling the gap between sulfate-reducing and methanogenic bacteria. In methanogenic aggregates, few sulfate-reducing bacteria were detected, while methanogens were found in the core. In the sulfidogenic aggregates, sulfate-reducing bacteria were

  18. Draft Genome Sequence of a Selenite- and Tellurite-Reducing Marine Bacterium, Lysinibacillus sp. Strain ZYM-1

    PubMed Central

    Zhao, Yonghe; Dong, Yuxuan; Zhang, Yiwen; Che, Lin; Pan, Haixia

    2016-01-01

    Lysinibacillus sp. ZYM-1, a Gram-positive strain isolated from marine sediments, reduces selenite and tellurite efficiently. Meanwhile, it also exhibits high resistance to Zn2+ and Mn2+. Here, we report the draft genome sequence of strain ZYM-1, which contains genes related to selenite and tellurite reduction and also metal resistance. PMID:26769938

  19. Antimicrobial action and anti-corrosion effect against sulfate reducing bacteria by lemongrass (Cymbopogon citratus) essential oil and its major component, the citral.

    PubMed

    Korenblum, Elisa; Regina de Vasconcelos Goulart, Fátima; de Almeida Rodrigues, Igor; Abreu, Fernanda; Lins, Ulysses; Alves, Péricles Barreto; Blank, Arie Fitzgerald; Valoni, Erika; Sebastián, Gina V; Alviano, Daniela Sales; Alviano, Celuta Sales; Seldin, Lucy

    2013-08-10

    The anti-corrosion effect and the antimicrobial activity of lemongrass essential oil (LEO) against the planktonic and sessile growth of a sulfate reducing bacterium (SRB) were evaluated. Minimum inhibitory concentration (MIC) of LEO and its major component, the citral, was 0.17 mg ml-1. In addition, both LEO and citral showed an immediate killing effect against SRB in liquid medium, suggesting that citral is responsible for the antimicrobial activity of LEO against SRB. Transmission electron microscopy revealed that the MIC of LEO caused discernible cell membrane alterations and formed electron-dense inclusions. Neither biofilm formation nor corrosion was observed on carbon steel coupons after LEO treatment. LEO was effective for the control of the planktonic and sessile SRB growth and for the protection of carbon steel coupons against biocorrosion. The application of LEO as a potential biocide for SRB growth control in petroleum reservoirs and, consequently, for souring prevention, and/or as a coating protection against biocorrosion is of great interest for the petroleum industries.

  20. Antimicrobial action and anti-corrosion effect against sulfate reducing bacteria by lemongrass (Cymbopogon citratus) essential oil and its major component, the citral

    PubMed Central

    2013-01-01

    The anti-corrosion effect and the antimicrobial activity of lemongrass essential oil (LEO) against the planktonic and sessile growth of a sulfate reducing bacterium (SRB) were evaluated. Minimum inhibitory concentration (MIC) of LEO and its major component, the citral, was 0.17 mg ml-1. In addition, both LEO and citral showed an immediate killing effect against SRB in liquid medium, suggesting that citral is responsible for the antimicrobial activity of LEO against SRB. Transmission electron microscopy revealed that the MIC of LEO caused discernible cell membrane alterations and formed electron-dense inclusions. Neither biofilm formation nor corrosion was observed on carbon steel coupons after LEO treatment. LEO was effective for the control of the planktonic and sessile SRB growth and for the protection of carbon steel coupons against biocorrosion. The application of LEO as a potential biocide for SRB growth control in petroleum reservoirs and, consequently, for souring prevention, and/or as a coating protection against biocorrosion is of great interest for the petroleum industries. PMID:23938023

  1. Desulfotomaculum alcoholivorax sp. nov., a moderately thermophilic, spore-forming, sulfate-reducer isolated from a fluidized-bed reactor treating acidic metal- and sulfate-containing wastewater.

    PubMed

    Kaksonen, Anna H; Spring, Stefan; Schumann, Peter; Kroppenstedt, Reiner M; Puhakka, Jaakko A

    2008-04-01

    A moderately thermophilic, Gram-positive, endospore-forming, sulfate-reducing bacterium was isolated from a fluidized-bed reactor treating acidic water containing metal and sulfate. The strain, designated RE35E1T, was rod-shaped and motile. The temperature range for growth was 33-51 degrees C (optimum 44-46 degrees C) and the pH range was 6.0-7.5 (optimum pH 6.4-7.3). The strain grew optimally without additional NaCl. The electron acceptors were 10 mM sulfate, thiosulfate and elemental sulfur and 1 mM (but not 10 mM) sulfite. Various alcohols and carboxylic acids were utilized as electron donors. Fermentative growth occurred on pyruvate. The cell wall contained meso-diaminopimelic acid, and the major respiratory isoprenoid quinone was menaquinone MK-7. The major whole-cell fatty acids were iso-C15 : 0, iso-C17 : 1 omega 10c and iso-C17 : 0. Strain RE35E1T was related to representatives of the genera Desulfotomaculum and Sporotomaculum, the closest relatives being Desulfotomaculum arcticum DSM 17038T (96.3 % 16S rRNA gene sequence similarity) and Sporotomaculum hydroxybenzoicum DSM 5475T (92.0 % similarity). Strain RE35E1T represents a novel species, for which the name Desulfotomaculum alcoholivorax sp. nov. is proposed. The type strain is RE35E1T (=DSM 16058T=JCM 14019T).

  2. Membrane-bound oxygen reductases of the anaerobic sulfate-reducing Desulfovibrio vulgaris Hildenborough: roles in oxygen defence and electron link with periplasmic hydrogen oxidation.

    PubMed

    Ramel, F; Amrani, A; Pieulle, L; Lamrabet, O; Voordouw, G; Seddiki, N; Brèthes, D; Company, M; Dolla, A; Brasseur, G

    2013-12-01

    Cytoplasmic membranes of the strictly anaerobic sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough contain two terminal oxygen reductases, a bd quinol oxidase and a cc(b/o)o3 cytochrome oxidase (Cox). Viability assays pointed out that single Δbd, Δcox and double ΔbdΔcox deletion mutant strains were more sensitive to oxygen exposure than the WT strain, showing the involvement of these oxygen reductases in the detoxification of oxygen. The Δcox strain was slightly more sensitive than the Δbd strain, pointing to the importance of the cc(b/o)o3 cytochrome oxidase in oxygen protection. Decreased O2 reduction rates were measured in mutant cells and membranes using lactate, NADH, ubiquinol and menadiol as substrates. The affinity for oxygen measured with the bd quinol oxidase (Km, 300 nM) was higher than that of the cc(b/o)o3 cytochrome oxidase (Km, 620 nM). The total membrane activity of the bd quinol oxidase was higher than that of the cytochrome oxidase activity in line with the higher expression of the bd oxidase genes. In addition, analysis of the ΔbdΔcox mutant strain indicated the presence of at least one O2-scavenging membrane-bound system able to reduce O2 with menaquinol as electron donor with an O2 affinity that was two orders of magnitude lower than that of the bd quinol oxidase. The lower O2 reductase activity in mutant cells with hydrogen as electron donor and the use of specific inhibitors indicated an electron transfer link between periplasmic H2 oxidation and membrane-bound oxygen reduction via the menaquinol pool. This linkage is crucial in defence of the strictly anaerobic bacterium Desulfovibrio against oxygen stress.

  3. Mo enrichment in black shale and reduction of molybdate by sulfate-reducing bacteria (SRB) (Invited)

    NASA Astrophysics Data System (ADS)

    Xu, H.; Barton, L. L.

    2010-12-01

    The Lower Cambrian Black shale in Zunyi area of Guizhou Province, Southern China contains significant amount of Mo, As, and sulfide minerals. Additionally, Mo and sulfides are closely associated with organic matter of kerogen. Transmission electron microscopy (TEM) results show pyrite micro-crystals and Mo-As-S-bearing carbon (kerogen). High-resolution TEM image shows that Mo-rich areas are Mo-sulfide (molybdenite) layers that form poorly crystalline structures in organic carbon matrix. X-ray energy-dispersive spectra (EDS) indicate composition from the pyrite and the Mo-rich area. The black shale is very unique because of its high Mo concentration. One possible mechanism for enriching Mo from paleo-seawater is the involvement of SRB. Molybdate is an essential trace element required by biological systems including the anaerobic sulfate-reducing bacteria (SRB); however, detrimental consequences may occur if molybdate is present in high concentrations in the environment. We followed the growth of Desulfovibrio gigas ATCC 19364, D. vulgaris Hildenborough, D. desulfuricans DSM 642, and D. desulfuricans DSM 27774 in media containing sub-lethal levels of molybdate and observed a red-brown color in the culture fluid. Spectral analysis of the culture fluid revealed absorption peaks at 467 nm, 395 nm and 314 nm and this color is proposed to be a molybdate-sulfide complex. Reduction of molybdate with the formation of molybdate disulfide occurs in the periplasm D. gigas and D. desulfuricans DSM 642. From these results we suggest that the occurrence of poorly crystalline Mo-sulfides in black shale may be a result from SRB reduction and selective enrichment of Mo in paleo-seawater. We suggest that similar SRB mechanism could cause the Mo enrichment in a ~ 2.5 billion years old late Archean McRae Shale, which is related to the great oxidation event of early earth atmosphere.

  4. Diversity and Characterization of Sulfate-Reducing Bacteria in Groundwater at a Uranium Mill Tailings Site

    PubMed Central

    Chang, Yun-Juan; Peacock, Aaron D.; Long, Philip E.; Stephen, John R.; McKinley, James P.; Macnaughton, Sarah J.; Hussain, A. K. M. Anwar; Saxton, Arnold M.; White, David C.

    2001-01-01

    Microbially mediated reduction and immobilization of U(VI) to U(IV) plays a role in both natural attenuation and accelerated bioremediation of uranium-contaminated sites. To realize bioremediation potential and accurately predict natural attenuation, it is important to first understand the microbial diversity of such sites. In this paper, the distribution of sulfate-reducing bacteria (SRB) in contaminated groundwater associated with a uranium mill tailings disposal site at Shiprock, N.Mex., was investigated. Two culture-independent analyses were employed: sequencing of clone libraries of PCR-amplified dissimilatory sulfite reductase (DSR) gene fragments and phospholipid fatty acid (PLFA) biomarker analysis. A remarkable diversity among the DSR sequences was revealed, including sequences from δ-Proteobacteria, gram-positive organisms, and the Nitrospira division. PLFA analysis detected at least 52 different mid-chain-branched saturate PLFA and included a high proportion of 10me16:0. Desulfotomaculum and Desulfotomaculum-like sequences were the most dominant DSR genes detected. Those belonging to SRB within δ-Proteobacteria were mainly recovered from low-uranium (≤302 ppb) samples. One Desulfotomaculum-like sequence cluster overwhelmingly dominated high-U (>1,500 ppb) sites. Logistic regression showed a significant influence of uranium concentration over the dominance of this cluster of sequences (P = 0.0001). This strong association indicates that Desulfotomaculum has remarkable tolerance and adaptation to high levels of uranium and suggests the organism's possible involvement in natural attenuation of uranium. The in situ activity level of Desulfotomaculum in uranium-contaminated environments and its comparison to the activities of other SRB and other functional groups should be an important area for future research. PMID:11425735

  5. Diversity and characterization of sulfate-reducing bacteria in groundwater at a uranium mill tailings site.

    PubMed

    Chang, Y J; Peacock, A D; Long, P E; Stephen, J R; McKinley, J P; Macnaughton, S J; Hussain, A K; Saxton, A M; White, D C

    2001-07-01

    Microbially mediated reduction and immobilization of U(VI) to U(IV) plays a role in both natural attenuation and accelerated bioremediation of uranium-contaminated sites. To realize bioremediation potential and accurately predict natural attenuation, it is important to first understand the microbial diversity of such sites. In this paper, the distribution of sulfate-reducing bacteria (SRB) in contaminated groundwater associated with a uranium mill tailings disposal site at Shiprock, N.Mex., was investigated. Two culture-independent analyses were employed: sequencing of clone libraries of PCR-amplified dissimilatory sulfite reductase (DSR) gene fragments and phospholipid fatty acid (PLFA) biomarker analysis. A remarkable diversity among the DSR sequences was revealed, including sequences from delta-Proteobacteria, gram-positive organisms, and the Nitrospira division. PLFA analysis detected at least 52 different mid-chain-branched saturate PLFA and included a high proportion of 10me16:0. Desulfotomaculum and Desulfotomaculum-like sequences were the most dominant DSR genes detected. Those belonging to SRB within delta-Proteobacteria were mainly recovered from low-uranium (< or =302 ppb) samples. One Desulfotomaculum-like sequence cluster overwhelmingly dominated high-U (>1,500 ppb) sites. Logistic regression showed a significant influence of uranium concentration over the dominance of this cluster of sequences (P = 0.0001). This strong association indicates that Desulfotomaculum has remarkable tolerance and adaptation to high levels of uranium and suggests the organism's possible involvement in natural attenuation of uranium. The in situ activity level of Desulfotomaculum in uranium-contaminated environments and its comparison to the activities of other SRB and other functional groups should be an important area for future research.

  6. Fermentation couples Chloroflexi and sulfate-reducing bacteria to Cyanobacteria in hypersaline microbial mats

    PubMed Central

    Lee, Jackson Z.; Burow, Luke C.; Woebken, Dagmar; Everroad, R. Craig; Kubo, Mike D.; Spormann, Alfred M.; Weber, Peter K.; Pett-Ridge, Jennifer; Bebout, Brad M.; Hoehler, Tori M.

    2013-01-01

    Past studies of hydrogen cycling in hypersaline microbial mats have shown an active nighttime cycle, with production largely from Cyanobacteria and consumption from sulfate-reducing bacteria (SRB). However, the mechanisms and magnitude of hydrogen cycling have not been extensively studied. Two mats types near Guerrero Negro, Mexico—permanently submerged Microcoleus microbial mat (GN-S), and intertidal Lyngbya microbial mat (GN-I)—were used in microcosm diel manipulation experiments with 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), molybdate, ammonium addition, and physical disruption to understand the processes responsible for hydrogen cycling between mat microbes. Across microcosms, H2 production occurred under dark anoxic conditions with simultaneous production of a suite of organic acids. H2 production was not significantly affected by inhibition of nitrogen fixation, but rather appears to result from constitutive fermentation of photosynthetic storage products by oxygenic phototrophs. Comparison to accumulated glycogen and to CO2 flux indicated that, in the GN-I mat, fermentation released almost all of the carbon fixed via photosynthesis during the preceding day, primarily as organic acids. Across mats, although oxygenic and anoxygenic phototrophs were detected, cyanobacterial [NiFe]-hydrogenase transcripts predominated. Molybdate inhibition experiments indicated that SRBs from a wide distribution of DsrA phylotypes were responsible for H2 consumption. Incubation with 13C-acetate and NanoSIMS (secondary ion mass-spectrometry) indicated higher uptake in both Chloroflexi and SRBs relative to other filamentous bacteria. These manipulations and diel incubations confirm that Cyanobacteria were the main fermenters in Guerrero Negro mats and that the net flux of nighttime fermentation byproducts (not only hydrogen) was largely regulated by the interplay between Cyanobacteria, SRBs, and Chloroflexi. PMID:24616716

  7. Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm.

    PubMed

    Probst, Alexander J; Holman, Hoi-Ying N; DeSantis, Todd Z; Andersen, Gary L; Birarda, Giovanni; Bechtel, Hans A; Piceno, Yvette M; Sonnleitner, Maria; Venkateswaran, Kasthuri; Moissl-Eichinger, Christine

    2013-03-01

    Archaea are usually minor components of a microbial community and dominated by a large and diverse bacterial population. In contrast, the SM1 Euryarchaeon dominates a sulfidic aquifer by forming subsurface biofilms that contain a very minor bacterial fraction (5%). These unique biofilms are delivered in high biomass to the spring outflow that provides an outstanding window to the subsurface. Despite previous attempts to understand its natural role, the metabolic capacities of the SM1 Euryarchaeon remain mysterious to date. In this study, we focused on the minor bacterial fraction in order to obtain insights into the ecological function of the biofilm. We link phylogenetic diversity information with the spatial distribution of chemical and metabolic compounds by combining three different state-of-the-art methods: PhyloChip G3 DNA microarray technology, fluorescence in situ hybridization (FISH) and synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectromicroscopy. The results of PhyloChip and FISH technologies provide evidence for selective enrichment of sulfate-reducing bacteria, which was confirmed by the detection of bacterial dissimilatory sulfite reductase subunit B (dsrB) genes via quantitative PCR and sequence-based analyses. We further established a differentiation of archaeal and bacterial cells by SR-FTIR based on typical lipid and carbohydrate signatures, which demonstrated a co-localization of organic sulfate, carbonated mineral and bacterial signatures in the biofilm. All these results strongly indicate an involvement of the SM1 euryarchaeal biofilm in the global cycles of sulfur and carbon and support the hypothesis that sulfidic springs are important habitats for Earth's energy cycles. Moreover, these investigations of a bacterial minority in an Archaea-dominated environment are a remarkable example of the great power of combining highly sensitive microarrays with label-free infrared imaging.

  8. Integrative analysis of Geobacter spp. and sulfate-reducing bacteria during uranium bioremediation

    NASA Astrophysics Data System (ADS)

    Barlett, M.; Zhuang, K.; Mahadevan, R.; Lovley, D.

    2012-03-01

    Enhancing microbial U(VI) reduction with the addition of organic electron donors is a promising strategy for immobilizing uranium in contaminated groundwaters, but has yet to be optimized because of a poor understanding of the factors controlling the growth of various microbial communities during bioremediation. In previous field trials in which acetate was added to the subsurface, there were two distinct phases: an initial phase in which acetate-oxidizing, U(VI)-reducing Geobacter predominated and U(VI) was effectively reduced and a second phase in which acetate-oxidizing sulfate reducing bacteria (SRB) predominated and U(VI) reduction was poor. The interaction of Geobacter and SRB was investigated both in sediment incubations that mimicked in situ bioremediation and with in silico metabolic modeling. In sediment incubations, Geobacter grew quickly but then declined in numbers as the microbially reducible Fe(III) was depleted whereas the SRB grow more slowly and reached dominance after 30-40 days. Modeling predicted a similar outcome. Additional modeling in which the relative initial percentages of the Geobacter and SRB were varied indicated that there was little to no competitive interaction between Geobacter and SRB when acetate was abundant. Further simulations suggested that the addition of Fe(III) would revive the Geobacter, but have little to no effect on the SRB. This result was confirmed experimentally. The results demonstrate that it is possible to predict the impact of amendments on important components of the subsurface microbial community during groundwater bioremediation. The finding that Fe(III) availability, rather than competition with SRB, is the key factor limiting the activity of Geobacter during in situ uranium bioremediation will aid in the design of improved uranium bioremediation strategies.

  9. Integrative analysis of the interactions between Geobacter spp. and sulfate-reducing bacteria during uranium bioremediation

    NASA Astrophysics Data System (ADS)

    Barlett, M.; Zhuang, K.; Mahadevan, R.; Lovley, D. R.

    2011-11-01

    Enhancing microbial U(VI) reduction with the addition of organic electron donors is a promising strategy for immobilizing uranium in contaminated groundwaters, but has yet to be optimized because of a poor understanding of the factors controlling the growth of various microbial communities during bioremediation. In previous field trials in which acetate was added to the subsurface, there were two distinct phases: an initial phase in which acetate-oxidizing, U(VI)-reducing Geobacter predominated and U(VI) was effectively reduced and a second phase in which acetate-oxidizing sulfate reducing bacteria (SRB) predominated and U(VI) reduction was poor. The interaction of Geobacter and SRB was investigated both in sediment incubations that mimicked in situ bioremediation and with in silico metabolic modeling. In sediment incubations, Geobacter grew quickly but then declined in numbers as the microbially reducible Fe(III) was depleted whereas the SRB grow more slowly and reached dominance after 30-40 days. Modeling predicted a similar outcome. Additional modeling in which the relative initial percentages of the Geobacter and SRB were varied indicated that there was little to no competitive interaction between Geobacter and SRB when acetate was abundant. Further simulations suggested that the addition of Fe(III) would revive the Geobacter, but have little to no effect on the SRB. This result was confirmed experimentally. The results demonstrate that it is possible to predict the impact of amendments on important components of the subsurface microbial community during groundwater bioremediation. The finding that Fe(III) availability, rather than competition with SRB, is the key factor limiting the activity of Geobacter during in situ uranium bioremediation will aid in the design of improved uranium bioremediation strategies.

  10. Distribution, Activities, and Interactions of Methanogens and Sulfate-Reducing Prokaryotes in the Florida Everglades

    PubMed Central

    Bae, Hee-Sung; Holmes, M. Elizabeth; Chanton, Jeffrey P.; Reddy, K. Ramesh

    2015-01-01

    To gain insight into the mechanisms controlling methanogenic pathways in the Florida Everglades, the distribution and functional activities of methanogens and sulfate-reducing prokaryotes (SRPs) were investigated in soils (0 to 2 or 0 to 4 cm depth) across the well-documented nutrient gradient in the water conservation areas (WCAs) caused by runoff from the adjacent Everglades Agricultural Area. The methyl coenzyme M reductase gene (mcrA) sequences that were retrieved from WCA-2A, an area with relatively high concentrations of SO42− (≥39 μM), indicated that methanogens inhabiting this area were broadly distributed within the orders Methanomicrobiales, Methanosarcinales, Methanocellales, Methanobacteriales, and Methanomassiliicoccales. In more than 3 years of monitoring, quantitative PCR (qPCR) using newly designed group-specific primers revealed that the hydrogenotrophic Methanomicrobiales were more numerous than the Methanosaetaceae obligatory acetotrophs in SO42−-rich areas of WCA-2A, while the Methanosaetaceae were dominant over the Methanomicrobiales in WCA-3A (with relatively low SO42− concentrations; ≤4 μM). qPCR of dsrB sequences also indicated that SRPs are present at greater numbers than methanogens in the WCAs. In an incubation study with WCA-2A soils, addition of MoO42− (a specific inhibitor of SRP activity) resulted in increased methane production rates, lower apparent fractionation factors [αapp; defined as (amount of δ13CO2 + 1,000)/(amount of δ13CH4 + 1,000)], and higher Methanosaetaceae mcrA transcript levels compared to those for the controls without MoO42−. These results indicate that SRPs play crucial roles in controlling methanogenic pathways and in shaping the structures of methanogen assemblages as a function of position along the nutrient gradient. PMID:26276115

  11. Methylmercury decomposition in sediments and bacterial cultures: Involvement of methanogens and sulfate reducers in oxidative demethylation

    USGS Publications Warehouse

    Oremland, R.S.; Culbertson, C.W.; Winfrey, M.R.

    1991-01-01

    Demethylation of monomethylmercury in freshwater and estuarine sediments and in bacterial cultures was investigated with 14CH3HgI. Under anaerobiosis, results with inhibitors indicated partial involvement of both sulfate reducers and methanogens, the former dominating estuarine sediments, while both were active in freshwaters. Aerobes were the most significant demethylators in estuarine sediments, but were unimportant in freshwater sediments. Products of anaerobic demethylation were mainly 14CO2 as well as lesser amounts of 14CH4. Acetogenic activity resulted in fixation of some 14CO2 produced from 14CH3HgI into acetate. Aerobic demethylation in estuarine sediments produced only 14CH4, while aerobic demethylation in freshwater sediments produced small amounts of both 14CH4 and 14CO2. Two species of Desulfovibrio produced only traces of 14CH4 from 14CH3HgI, while a culture of a methylotrophic methanogen formed traces of 14CO2 and 14CH4 when grown on trimethylamine in the presence of the 14CH3HgI. These results indicate that both aerobes and anaerobes demethylate mercury in sediments, but that either group may dominate in a particular sediment type. Aerobic demethylation in the estuarine sediments appeared to proceed by the previously characterized organomercurial-lyase pathway, because methane was the sole product. However, aerobic demethylation in freshwater sediments as well as anaerobic demethylation in all sediments studied produced primarily carbon dioxide. This indicates the presence of an oxidative pathway, possibly one in which methylmercury serves as an analog of one-carbon substrates.

  12. Mercury Methylation Independent of the Acetyl-Coenzyme A Pathway in Sulfate-Reducing Bacteria

    PubMed Central

    Ekstrom, Eileen B.; Morel, François M. M.; Benoit, Janina M.

    2003-01-01

    Sulfate-reducing bacteria (SRB) in anoxic waters and sediments are the major producers of methylmercury in aquatic systems. Although a considerable amount of work has addressed the environmental factors that control methylmercury formation and the conditions that control bioavailability of inorganic mercury to SRB, little work has been undertaken analyzing the biochemical mechanism of methylmercury production. The acetyl-coenzyme A (CoA) pathway has been implicated as being key to mercury methylation in one SRB strain, Desulfovibrio desulfuricans LS, but this result has not been extended to other SRB species. To probe whether the acetyl-CoA pathway is the controlling biochemical process for methylmercury production in SRB, five incomplete-oxidizing SRB strains and two Desulfobacter strains that do not use the acetyl-CoA pathway for major carbon metabolism were assayed for methylmercury formation and acetyl-CoA pathway enzyme activities. Three of the SRB strains were also incubated with chloroform to inhibit the acetyl-CoA pathway. So far, all species that have been found to have acetyl-CoA activity are complete oxidizers that require the acetyl-CoA pathway for basic metabolism, as well as methylate mercury. Chloroform inhibits Hg methylation in these species either by blocking the methylating enzyme or by indirect effects on metabolism and growth. However, we have identified four incomplete-oxidizing strains that clearly do not utilize the acetyl-CoA pathway either for metabolism or mercury methylation (as confirmed by the absence of chloroform inhibition). Hg methylation is thus independent of the acetyl-CoA pathway and may not require vitamin B12 in some and perhaps many incomplete-oxidizing SRB strains. PMID:12957930

  13. Distribution, activities, and interactions of methanogens and sulfate-reducing prokaryotes in the Florida Everglades.

    PubMed

    Bae, Hee-Sung; Holmes, M Elizabeth; Chanton, Jeffrey P; Reddy, K Ramesh; Ogram, Andrew

    2015-11-01

    To gain insight into the mechanisms controlling methanogenic pathways in the Florida Everglades, the distribution and functional activities of methanogens and sulfate-reducing prokaryotes (SRPs) were investigated in soils (0 to 2 or 0 to 4 cm depth) across the well-documented nutrient gradient in the water conservation areas (WCAs) caused by runoff from the adjacent Everglades Agricultural Area. The methyl coenzyme M reductase gene (mcrA) sequences that were retrieved from WCA-2A, an area with relatively high concentrations of SO4 (2-) (≥39 μM), indicated that methanogens inhabiting this area were broadly distributed within the orders Methanomicrobiales, Methanosarcinales, Methanocellales, Methanobacteriales, and Methanomassiliicoccales. In more than 3 years of monitoring, quantitative PCR (qPCR) using newly designed group-specific primers revealed that the hydrogenotrophic Methanomicrobiales were more numerous than the Methanosaetaceae obligatory acetotrophs in SO4 (2-)-rich areas of WCA-2A, while the Methanosaetaceae were dominant over the Methanomicrobiales in WCA-3A (with relatively low SO4 (2-) concentrations; ≤4 μM). qPCR of dsrB sequences also indicated that SRPs are present at greater numbers than methanogens in the WCAs. In an incubation study with WCA-2A soils, addition of MoO4 (2-) (a specific inhibitor of SRP activity) resulted in increased methane production rates, lower apparent fractionation factors [αapp; defined as (amount of δ(13)CO2 + 1,000)/(amount of δ(13)CH4 + 1,000)], and higher Methanosaetaceae mcrA transcript levels compared to those for the controls without MoO4 (2-). These results indicate that SRPs play crucial roles in controlling methanogenic pathways and in shaping the structures of methanogen assemblages as a function of position along the nutrient gradient.

  14. Sulfate Reducing Bacteria and Mycobacteria Dominate the Biofilm Communities in a Chloraminated Drinking Water Distribution System.

    PubMed

    Gomez-Smith, C Kimloi; LaPara, Timothy M; Hozalski, Raymond M

    2015-07-21

    The quantity and composition of bacterial biofilms growing on 10 water mains from a full-scale chloraminated water distribution system were analyzed using real-time PCR targeting the 16S rRNA gene and next-generation, high-throughput Illumina sequencing. Water mains with corrosion tubercles supported the greatest amount of bacterial biomass (n = 25; geometric mean = 2.5 × 10(7) copies cm(-2)), which was significantly higher (P = 0.04) than cement-lined cast-iron mains (n = 6; geometric mean = 2.0 × 10(6) copies cm(-2)). Despite spatial variation of community composition and bacterial abundance in water main biofilms, the communities on the interior main surfaces were surprisingly similar, containing a core group of operational taxonomic units (OTUs) assigned to only 17 different genera. Bacteria from the genus Mycobacterium dominated all communities at the main wall-bulk water interface (25-78% of the community), regardless of main age, estimated water age, main material, and the presence of corrosion products. Further sequencing of the mycobacterial heat shock protein gene (hsp65) provided species-level taxonomic resolution of mycobacteria. The two dominant Mycobacteria present, M. frederiksbergense (arithmetic mean = 85.7% of hsp65 sequences) and M. aurum (arithmetic mean = 6.5% of hsp65 sequences), are generally considered to be nonpathogenic. Two opportunistic pathogens, however, were detected at low numbers: M. hemophilum (arithmetic mean = 1.5% of hsp65 sequences) and M. abscessus (arithmetic mean = 0.006% of hsp65 sequences). Sulfate-reducing bacteria from the genus Desulfovibrio, which have been implicated in microbially influenced corrosion, dominated all communities located underneath corrosion tubercules (arithmetic mean = 67.5% of the community). This research provides novel insights into the quantity and composition of biofilms in full-scale drinking water distribution systems, which is critical for assessing the risks to public health and to the

  15. Corrosion of iron by sulfate-reducing bacteria: new views of an old problem.

    PubMed

    Enning, Dennis; Garrelfs, Julia

    2014-02-01

    About a century ago, researchers first recognized a connection between the activity of environmental microorganisms and cases of anaerobic iron corrosion. Since then, such microbially influenced corrosion (MIC) has gained prominence and its technical and economic implications are now widely recognized. Under anoxic conditions (e.g., in oil and gas pipelines), sulfate-reducing bacteria (SRB) are commonly considered the main culprits of MIC. This perception largely stems from three recurrent observations. First, anoxic sulfate-rich environments (e.g., anoxic seawater) are particularly corrosive. Second, SRB and their characteristic corrosion product iron sulfide are ubiquitously associated with anaerobic corrosion damage, and third, no other physiological group produces comparably severe corrosion damage in laboratory-grown pure cultures. However, there remain many open questions as to the underlying mechanisms and their relative contributions to corrosion. On the one hand, SRB damage iron constructions indirectly through a corrosive chemical agent, hydrogen sulfide, formed by the organisms as a dissimilatory product from sulfate reduction with organic compounds or hydrogen ("chemical microbially influenced corrosion"; CMIC). On the other hand, certain SRB can also attack iron via withdrawal of electrons ("electrical microbially influenced corrosion"; EMIC), viz., directly by metabolic coupling. Corrosion of iron by SRB is typically associated with the formation of iron sulfides (FeS) which, paradoxically, may reduce corrosion in some cases while they increase it in others. This brief review traces the historical twists in the perception of SRB-induced corrosion, considering the presently most plausible explanations as well as possible early misconceptions in the understanding of severe corrosion in anoxic, sulfate-rich environments.

  16. Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm

    PubMed Central

    Probst, Alexander J; Holman, Hoi-Ying N; DeSantis, Todd Z; Andersen, Gary L; Birarda, Giovanni; Bechtel, Hans A; Piceno, Yvette M; Sonnleitner, Maria; Venkateswaran, Kasthuri; Moissl-Eichinger, Christine

    2013-01-01

    Archaea are usually minor components of a microbial community and dominated by a large and diverse bacterial population. In contrast, the SM1 Euryarchaeon dominates a sulfidic aquifer by forming subsurface biofilms that contain a very minor bacterial fraction (5%). These unique biofilms are delivered in high biomass to the spring outflow that provides an outstanding window to the subsurface. Despite previous attempts to understand its natural role, the metabolic capacities of the SM1 Euryarchaeon remain mysterious to date. In this study, we focused on the minor bacterial fraction in order to obtain insights into the ecological function of the biofilm. We link phylogenetic diversity information with the spatial distribution of chemical and metabolic compounds by combining three different state-of-the-art methods: PhyloChip G3 DNA microarray technology, fluorescence in situ hybridization (FISH) and synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectromicroscopy. The results of PhyloChip and FISH technologies provide evidence for selective enrichment of sulfate-reducing bacteria, which was confirmed by the detection of bacterial dissimilatory sulfite reductase subunit B (dsrB) genes via quantitative PCR and sequence-based analyses. We further established a differentiation of archaeal and bacterial cells by SR-FTIR based on typical lipid and carbohydrate signatures, which demonstrated a co-localization of organic sulfate, carbonated mineral and bacterial signatures in the biofilm. All these results strongly indicate an involvement of the SM1 euryarchaeal biofilm in the global cycles of sulfur and carbon and support the hypothesis that sulfidic springs are important habitats for Earth's energy cycles. Moreover, these investigations of a bacterial minority in an Archaea-dominated environment are a remarkable example of the great power of combining highly sensitive microarrays with label-free infrared imaging. PMID:23178669

  17. Corrosion of Iron by Sulfate-Reducing Bacteria: New Views of an Old Problem

    PubMed Central

    Garrelfs, Julia

    2014-01-01

    About a century ago, researchers first recognized a connection between the activity of environmental microorganisms and cases of anaerobic iron corrosion. Since then, such microbially influenced corrosion (MIC) has gained prominence and its technical and economic implications are now widely recognized. Under anoxic conditions (e.g., in oil and gas pipelines), sulfate-reducing bacteria (SRB) are commonly considered the main culprits of MIC. This perception largely stems from three recurrent observations. First, anoxic sulfate-rich environments (e.g., anoxic seawater) are particularly corrosive. Second, SRB and their characteristic corrosion product iron sulfide are ubiquitously associated with anaerobic corrosion damage, and third, no other physiological group produces comparably severe corrosion damage in laboratory-grown pure cultures. However, there remain many open questions as to the underlying mechanisms and their relative contributions to corrosion. On the one hand, SRB damage iron constructions indirectly through a corrosive chemical agent, hydrogen sulfide, formed by the organisms as a dissimilatory product from sulfate reduction with organic compounds or hydrogen (“chemical microbially influenced corrosion”; CMIC). On the other hand, certain SRB can also attack iron via withdrawal of electrons (“electrical microbially influenced corrosion”; EMIC), viz., directly by metabolic coupling. Corrosion of iron by SRB is typically associated with the formation of iron sulfides (FeS) which, paradoxically, may reduce corrosion in some cases while they increase it in others. This brief review traces the historical twists in the perception of SRB-induced corrosion, considering the presently most plausible explanations as well as possible early misconceptions in the understanding of severe corrosion in anoxic, sulfate-rich environments. PMID:24317078

  18. Methylmercury decomposition in sediments and bacterial cultures: Involvement of methanogens and sulfate reducers in oxidative demethylation

    SciTech Connect

    Oremland, R.S.; Culbertson, C.W. ); Winfrey, M.R. )

    1991-01-01

    The biogeochemical cycling of mercury has received considerable attention because of the toxicity of methylmercury, its bioaccumulation in biota, and its biomagnification in aquatic food chains. The formation of methylmercury is mediated primarily by microorganisms. Demethylation of monomethylmercury in freshwater and estuarine sediments and in bacterial cultures was investigated with {sup 14}CH{sub 3}HgI. Under anaerobiosis, results with inhibitors indicated partial involvement of both sulfate reducers and methanogens, the former dominated estuarine sediments, while both were active in freshwaters. Aerobes were the most significant demethylators in estuarine sediments, but were unimportant in freshwater sediments. Products of anaerobic demthylation were mainly {sup 14}CO{sub 2} as well as lesser amounts of {sup 14}CH{sub 4}. Acetogenic activity resulted in fixation of some {sup 14}CO{sub 2} produced from {sup 14}CH{sub 3}HgI into acetate. Aerobic demethylation in estuarine sediments produced only {sup 14}CH{sub 4}, while aerobic demethylation in freshwater sediments produced small amounts of both {sup 14}CH{sub 4} and {sup 14}CO{sub 2}. Two species of Desulfovibrio produced only traces of {sup 14}CH{sub 4} from {sup 14}CH{sub 3}HgI, while a culture of a methylotrophic methanogen formed traces of {sup 14}CO{sub 2} and {sup 14}CH{sub 4} when grown on trimethylamine in the presence of the {sup 14}CH{sub 3}HgI. These results indicate that both aerobes and anaerobes demethylate mercury in sediments, but that either group may dominate in a particular sediment type. Aerobic demethylation in the estuarine sediments appeared to proceed by the previously characterized organomercurial-lyase pathway, because methane was the sole product. This indicates the presence of an oxidative pathway, possibly one in which methylmercury serves as an analog of one-carbon substrates.

  19. Quorum Sensing in Vibrio fischeri Cell Density-Dependent Activation of Symbiosis-Related Genes in a Marine Bacterium

    DTIC Science & Technology

    2007-11-02

    Washington, DC 20503. 1. AGENCY USE ONLY (Leave blank) 2. REPORT DATE August 3, 1998 4. TITLE AND SUBTITLE Quorum Sensing in Vibrio fischeri Cell...of the proposed research is to fully elucidate the mechanism of quorum sensing and response in bacteria by continuing investigations of the most well...Regulation/Marine bacteria/Symbiosis Genes/ Transcriptional activation/ Quorum Sensing 17. SECURITY CLASSIFICATION OF REPORT u NSN 7540-01-280

  20. O-heterocyclic derivatives with antibacterial properties from marine bacterium Bacillus subtilis associated with seaweed, Sargassum myriocystum.

    PubMed

    Chakraborty, Kajal; Thilakan, Bini; Chakraborty, Rekha Devi; Raola, Vamshi Krishna; Joy, Minju

    2017-01-01

    The brown seaweed, Sargassum myriocystum associated with heterotrophic bacterium, Bacillus subtilis MTCC 10407 (JF834075) exhibited broad-spectra of potent antibacterial activities against pathogenic bacteria Aeromonas hydrophila, Vibrio vulnificus, and Vibrio parahaemolyticus. B. subtilis MTCC 10407 was found to be positive for polyketide synthetase (pks) gene, and therefore, was considered to characterize secondary metabolites bearing polyketide backbone. Using bioassay-guided fractionation, two new antibacterial O-heterocyclic compounds belonging to pyranyl benzoate analogs of polyketide origin, with activity against pathogenic bacteria, have been isolated from the ethyl acetate extract of B. subtilis MTCC 10407. In the present study, the secondary metabolites of B. subtilis MTCC 10407 with potent antibacterial action against bacterial pathogens was recognized to represent the platform of pks-1 gene-encoded products. Two homologous compounds 3 (3-(methoxycarbonyl)-4-(5-(2-ethylbutyl)-5,6-dihydro-3-methyl-2H-pyran-2-yl)-butyl benzoate) and 4 [2-(8-butyl-3-ethyl-3,4,4a,5,6,8a-hexahydro-2H-chromen-6-yl)-ethyl benzoate] also have been isolated from the ethyl acetate extract of host seaweed S. myriocystum. The two compounds isolated from ethyl acetate extract of S. myriocystum with lesser antibacterial properties shared similar structures with the compounds purified from B. subtilis that suggested the ecological and metabolic relationship between these compounds in seaweed-bacterial relationship. Tetrahydropyran-2-one moiety of the tetrahydropyrano-[3,2b]-pyran-2(3H)-one system of 1 might be cleaved by the metabolic pool of seaweeds to afford methyl 3-(dihydro-3-methyl-2H-pyranyl)-propanoate moiety of 3, which was found to have no significant antibacterial activity. It is therefore imperative that the presence of dihydro-methyl-2H-pyran-2-yl propanoate system is essentially required to impart the greater activity. The direct involvement of polarisability (Pl) with

  1. Flavobacterium ahnfeltiae sp. nov., a new marine polysaccharide-degrading bacterium isolated from a Pacific red alga.

    PubMed

    Nedashkovskaya, Olga I; Balabanova, Larissa A; Zhukova, Natalia V; Kim, So-Jeong; Bakunina, Irina Y; Rhee, Sung-Keun

    2014-10-01

    A Gram-negative, aerobic, rod-shaped, motile by gliding and yellow-pigmented bacterium, designated strain 10Alg 130(T), that displayed the ability to destroy polysaccharides of red and brown algae, was isolated from the red alga Ahnfeltia tobuchiensis. The phylogenetic analysis based on 16S rRNA gene sequence placed the novel strain within the genus Flavobacterium, the type genus of the family Flavobacteriaceae, the phylum Bacteroidetes, with sequence similarities of 96.2 and 95.7 % to Flavobacterium jumunjiense KCTC 23618(T) and Flavobacterium ponti CCUG 58402(T), and 95.3-92.5 % to other recognized Flavobacterium species. The prevalent fatty acids of strain 10Alg 130(T) were iso-C15:0, iso-C15:0 3-OH, iso-C17:0 3-OH, C15:0 and iso-C17:1ω9c. The polar lipid profile consisted of phosphatidylethanolamine, two unknown aminolipids and three unknown lipids. The DNA G+C content of the type strain was 34.3 mol%. The new isolate and the type strains of recognized species of the genus Flavobacterium could strongly be distinguished by a number of phenotypic characteristics. A combination of the genotypic and phenotypic data showed that the algal isolate represents a novel species of the genus Flavobacterium, for which the name Flavobacterium ahnfeltiae sp. nov. is proposed. The type strain is 10Alg 130(T) (=KCTC 32467(T) = KMM 6686(T)).

  2. Inorganic carbon fixation by sulfate-reducing bacteria in the Black Sea water column.

    PubMed

    Neretin, Lev N; Abed, Raeid M M; Schippers, Axel; Schubert, Carsten J; Kohls, Katharina; Kuypers, Marcel M M

    2007-12-01

    The Black Sea is the largest anoxic water basin on Earth and its stratified water column comprises an upper oxic, middle suboxic and a lower permanently anoxic, sulfidic zone. The abundance of sulfate-reducing bacteria (SRB) in water samples was determined by quantifying the copy number of the dsrA gene coding for the alpha subunit of the dissimilatory (bi)sulfite reductase using real-time polymerase chain reaction. The dsrA gene was detected throughout the whole suboxic and anoxic zones. The maximum dsrA copy numbers were 5 x 10(2) and 6.3 x 10(2) copies ml(-1) at 95 m in the suboxic and at 150 m in the upper anoxic zone, respectively. The proportion of SRB to total Bacteria was 0.1% in the oxic, 0.8-1.9% in the suboxic and 1.2-4.7% in the anoxic zone. A phylogenetic analysis of 16S rDNA clones showed that most clones from the anoxic zone formed a coherent cluster within the Desulfonema-Desulfosarcina group. A similar depth profile as for dsrA copy numbers was obtained for the concentration of non-isoprenoidal dialkyl glycerol diethers (DGDs), which are most likely SRB-specific lipid biomarkers. Three different DGDs were found to be major components of the total lipid fractions from the anoxic zone. The DGDs were depleted in (13)C relative to the delta(13)C values of dissolved CO(2) (delta(13)C(CO2)) by 14-19 per thousand. Their delta(13)C values [delta(13)C(DGD(II-III))] co-varied with depth showing the least (13)C-depleted values in the top of the sulfidic, anoxic zone and the most (13)C-depleted values in the deep anoxic waters at 1500 m. This co-variation provides evidence for CO(2) incorporation by the DGD(II-III)-producing SRB, while the 1:2 relationship between delta(13)C(CO2) and delta(13)C(DGD(II-III)) indicates the use of an additional organic carbon source.

  3. Biogeochemistry of a Field-Scale Sulfate Reducing Bioreactor Treating Mining Influenced Water

    NASA Astrophysics Data System (ADS)

    Drennan, D.; Lee, I.; Landkamer, L.; Figueroa, L. A.; Webb, S.; Sharp, J. O.

    2012-12-01

    Acidity, metal release, and toxicity may be environmental health concerns in areas influenced by mining. Mining influenced waters (MIW) can be remediated through the establishment of Sulfate Reducing Bioreactors (SRBRs) as part of engineered passive treatment systems. The objective of our research is an enhanced understanding of the biogeochemistry in SRBRs by combining molecular biological and geochemical techniques. Bioreactor reactive substrate, settling pond water, and effluent (from the SRBR) were collected from a field scale SRBR in Arizona, which has been in operation for approximately 3 years. Schematically, the water passes through the SRBR; combines with flow that bypasses the SRBR into the and goes into the mixing pond, and finally is released as effluent to aerobic polishing cells. High throughput sequencing of extracted DNA revealed that Proteobacteria dominated the reactive substrate (61%), settling pond (93%), and effluent (50%), with the next most abundant phylum in all samples (excluding uncultured organisms) being Bacteriodes (1-17%). However, at the superclass level, the three samples were more variable. Gammaproteobacteria dominated the reactive substrate (35%), Betaproteobacteria in the settling pond (63%) and finally the effluent was dominated by Epsilonproteobacteria (Helicobacteraceae) (43%). Diversity was most pronounced in association with the reactor matrix, and least diverse in the settling pond. Putative functional analysis revealed a modest presence of sulfate/sulfur reducing bacteria (SRB) (>5%) in both the matrix and settling pond but a much higher abundance (43%) of sulfur reducing bacteria in the effluent. Interestingly this effluent population was composed entirely of the family Helicobacteraceae (sulfur reduction II via polysulfide pathway). Other putative functions of interest include metal reduction in the matrix (3%) and effluent (3%), as well as polysaccharide degradation, which was largely abundant in all samples (21

  4. Enzymatic catalysis of mercury methylation by planktonic and biofilm cultures of sulfate- reducing bacteria

    NASA Astrophysics Data System (ADS)

    Lin, C.; Kampalath, R.; Jay, J.

    2007-12-01

    While biofilms are now known to be the predominant form of microbial growth in nature, little is known about their role in environmental mercury (Hg) methylation. Due to its long-range atmospheric transport, Hg contamination of food chains is a worldwide problem, impacting even pristine areas. Among different forms of mercury species, methylmercury (MeHg) is an extremely neurotoxic and biomagnification-prone compound that can lead to severely adverse health effects on wildlife and humans. Considerable studies have shown that in the aquatic environment the external supply of MeHg is not sufficient to account for MeHg accumulation in biota and in situ biological MeHg formation plays a critical role in determining the amount of MeHg in food webs; moreover, sulfate-reducing bacteria (SRB) has been identified as the principal Hg-methylating organisms in nature. In a wide range of aquatic systems wetlands are considered important sites for Hg methylation mostly because of the environmental factors that promote microbial activity within, and biofilms are especially important in wetland ecosystems due to large amount of submerged surfaces. Although recent work has focused on the environmental factors that control MeHg production and the conditions that affect the availability of inorganic Hg to SRB, much remains to be understood about the biochemical mechanism of the Hg methylation process in SRB, especially in the biofilm-growth of these microbes. Data from our previous study with SRB strains isolated from a coastal wetland suggested that the specific Hg methylation rate found was approximately an order of magnitude higher in biofilm cells than in planktonic cells. In order to investigate possible reasons for this observed difference, and to test if this phenomenon is observed in other strains, we conducted chloroform, fluroacetate and molybdate inhibition assays in both complete and incomplete-oxidizing SRB species (Desulfovibrio desulfuricans M8, Desulfococcus sp

  5. Hydrocarbon activation under sulfate-reducing and methanogenic conditions proceeds by different mechanisms.

    NASA Astrophysics Data System (ADS)

    Head, Ian; Gray, Neil; Aitken, Caroline; Sherry, Angela; Jones, Martin; Larter, Stephen

    2010-05-01

    Microbial degradation of alkanes typically involves their conversion to fatty acids which are then catabolised by beta-oxidation. The critical step in this process is activation of the hydrocarbon. Under oxic conditions this is catalyzed by monooxygenase enzymes with the formation of long chain alcohols. In the absence of oxygen alternative alkane activation mechanisms have been observed or proposed. Fumarate addition to alkanes to form alkyl succinates is considered a central process in anaerobic hydrocarbon degradation. Comparative studies of crude oil degradation under sulphate-reducing and methanogenic conditions revealed distinctive patterns of compound class removal and metabolite formation. Alkyl succinates derived from C7 to C26 n-alkanes and branched chain alkanes were found in abundance in sulfate-reducing systems but these were not detected during methanogenic crude oil degradation. Only one other mechanism of alkane activation has been elucidated to date. This involves addition of carbon derived from bicarbonate/CO2 to C-3 of an alkane chain to form a 2-ethylalkane with subsequent removal of the ethyl group leading to the formation of a fatty acid 1 carbon shorter than the original alkane. 2-ethylalkanes have never been detected as metabolites of anaerobic alkane degradation and were not detected in crude oil-degrading methanogenic systems. Due to the range of alkanes present in crude oil it was not possible to infer the generation of C-odd acids from C-even alkanes which is characteristic of the C-3 carboxylation mechanism. Furthermore genes homologous to alkysuccinate synthetases were not detected in the methanogenic hydrocarbon degrading community by pyrosequencing of total DNA extracted from methanogenic enrichments cultures. beta-oxidation genes were detected and intriguingly, alcohol and aldehyde dehydrogenase genes were present. This offers the possibility that alkane activation in the methanogenic system does not proceed via acid metabolites

  6. Thiocapsa marina sp. nov., a novel, okenone-containing, purple sulfur bacterium isolated from brackish coastal and marine environments.

    PubMed

    Caumette, Pierre; Guyoneaud, Remy; Imhoff, Johannes F; Süling, Jörg; Gorlenko, Vladimir

    2004-07-01

    Four marine, phototrophic, purple sulfur bacteria (strains 5811T, 5812, BM-3 and BS-1) were isolated in pure culture from different brackish to marine sediments in the Mediterranean Sea, the White Sea and the Black Sea. Single cells of these strains were coccus-shaped, non-motile and did not contain gas vesicles. The colour of cell suspensions that were grown in the light was purple-red. Bacteriochlorophyll a and carotenoids of the okenone series were present as photosynthetic pigments. Photosynthetic membrane systems were of the vesicular type. Hydrogen sulfide, thiosulfate, elemental sulfur and molecular hydrogen were used as electron donors during photolithotrophic growth under anoxic conditions; carbon dioxide was utilized as the carbon source. During growth on sulfide, elemental sulfur globules were stored inside the cells. In the presence of hydrogen sulfide, several organic substances could be photoassimilated. Comparative 16S rDNA sequence analysis revealed an affiliation of these four strains to the genus Thiocapsa. Both phylogenetic analysis and the results of DNA-DNA hybridization studies revealed that these strains formed a separate cluster within the genus Thiocapsa. Thus, according to phenotypic characteristics and mainly the carotenoid composition, 16S rDNA sequence analysis and DNA-DNA hybridization data, it is proposed that these strains should be classified as a novel species, Thiocapsa marina sp. nov., with strain 5811T (=DSM 5653T=ATCC 43172T) as the type strain.

  7. Characterisation of a marine bacterium Vibrio brasiliensis T33 producing N-acyl homoserine lactone quorum sensing molecules.

    PubMed

    Tan, Wen-Si; Yunos, Nina Yusrina Muhamad; Tan, Pui-Wan; Mohamad, Nur Izzati; Adrian, Tan-Guan-Sheng; Yin, Wai-Fong; Chan, Kok-Gan

    2014-07-08

    N-acylhomoserine lactones (AHL) plays roles as signal molecules in quorum sensing (QS) in most Gram-negative bacteria. QS regulates various physiological activities in relation with population density and concentration of signal molecules. With the aim of isolating marine water-borne bacteria that possess QS properties, we report here the preliminary screening of marine bacteria for AHL production using Chromobacterium violaceum CV026 as the AHL biosensor. Strain T33 was isolated based on preliminary AHL screening and further identified by using 16S rDNA sequence analysis as a member of the genus Vibrio closely related to Vibrio brasiliensis. The isolated Vibrio sp. strain T33 was confirmed to produce N-hexanoyl-L-homoserine lactone (C6-HSL) and N-(3-oxodecanoyl)-L-homoserine lactone (3-oxo-C10 HSL) through high resolution tandem mass spectrometry analysis. We demonstrated that this isolate formed biofilms which could be inhibited by catechin. To the best of our knowledge, this is the first report that documents the production of these AHLs by Vibrio brasiliensis strain T33.

  8. Complete genome sequence of the acetate-degrading sulfate reducer Desulfobacca acetoxidans type strain (ASRB2T)

    SciTech Connect

    Goker, Markus; Teshima, Hazuki; Lapidus, Alla L.; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Pitluck, Sam; Huntemann, Marcel; Liolios, Konstantinos; Ivanova, N; Pagani, Ioanna; Mavromatis, K; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Brambilla, Evelyne-Marie; Rohde, Manfred; Spring, Stefan; Detter, J. Chris; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2011-01-01

    Desulfobacca acetoxidans Elferink et al. 1999 is the type species of the genus Desulfobacca, which belongs to the family Syntrophaceae in the class Deltaproteobacteria. The species was first observed in a study on the competition of sulfate-reducers and acetoclastic methanogens for acetate in sludge. D. acetoxidans is considered to be the most abundant acetate-degrading sulfate reducer in sludge. It is of interest due to its isolated phylogenetic location in the 16S rRNA-based tree of life. This is the second completed genome sequence of a member of the family Syntrophaceae to be published and only the third genome sequence from a member of the order Syntrophobacterales. The 3,282,536 bp long genome with its 2,969 protein-coding and 54 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  9. Optimization of culture conditions and medium composition for the marine algicidal bacterium Alteromonas sp. DH46 by uniform design

    NASA Astrophysics Data System (ADS)

    Lin, Jing; Zheng, Wei; Tian, Yun; Wang, Guizhong; Zheng, Tianling

    2013-09-01

    Harmful algal blooms (HABs) have led to extensive ecological and environmental issues and huge economic losses. Various HAB control techniques have been developed, and biological methods have been paid more attention. Algicidal bacteria is a general designation for bacteria which inhibit algal growth in a direct or indirect manner, and kill or damage the algal cells. A metabolite which is strongly toxic to the dinoflagellate Alexandrium tamarense was produced by strain DH46 of the alga-lysing bacterium Alteromonas sp. The culture conditions were optimized using a single-factor test method. Factors including carbon source, nitrogen source, temperature, initial pH value, rotational speed and salinity were studied. The results showed that the cultivation of the bacteria at 28°C and 180 r min-1 with initial pH 7 and 30 salt contcentration favored both the cell growth and the lysing effect of strain DH46. The optimal medium composition for strain DH46 was determined by means of uniform design experimentation, and the most important components influencing the cell density were tryptone, yeast extract, soluble starch, NaNO3 and MgSO4. When the following culture medium was used (tryptone 14.0g, yeast extract 1.63g, soluble starch 5.0 g, NaNO3 1.6 g, MgSO4 2.3 g in 1L), the largest bacterial dry weight (7.36 g L-1) was obtained, which was an enhancement of 107% compared to the initial medium; and the algal lysis rate was as high as 98.4% which increased nearly 10% after optimization.

  10. Physiological and Genetic Description of Dissimilatory Perchlorate Reduction by the Novel Marine Bacterium Arcobacter sp. Strain CAB

    PubMed Central

    Carlström, Charlotte I.; Wang, Ouwei; Melnyk, Ryan A.; Bauer, Stefan; Lee, Joyce; Engelbrektson, Anna; Coates, John D.

    2013-01-01

    ABSTRACT A novel dissimilatory perchlorate-reducing bacterium (DPRB), Arcobacter sp. strain CAB, was isolated from a marina in Berkeley, CA. Phylogenetically, this halophile was most closely related to Arcobacter defluvii strain SW30-2 and Arcobacter ellisii. With acetate as the electron donor, strain CAB completely reduced perchlorate (ClO4−) or chlorate (ClO3−) [collectively designated (per)chlorate] to innocuous chloride (Cl−), likely using the perchlorate reductase (Pcr) and chlorite dismutase (Cld) enzymes. When grown with perchlorate, optimum growth was observed at 25 to 30°C, pH 7, and 3% NaCl. Transmission electron microscopy (TEM) and scanning electron microscopy (SEM) preparations were dominated by free-swimming straight rods with 1 to 2 polar flagella per cell. Strain CAB utilized a variety of organic acids, fructose, and hydrogen as electron donors coupled to (per)chlorate reduction. Further, under anoxic growth conditions strain CAB utilized the biogenic oxygen produced as a result of chlorite dismutation to oxidize catechol via the meta-cleavage pathway of aerobic catechol degradation and the catechol 2,3-dioxygenase enzyme. In addition to (per)chlorate, oxygen and nitrate were alternatively used as electron acceptors. The 3.48-Mb draft genome encoded a distinct perchlorate reduction island (PRI) containing several transposases. The genome lacks the pcrC gene, which was previously thought to be essential for (per)chlorate reduction, and appears to use an unrelated Arcobacter c-type cytochrome to perform the same function. PMID:23695836

  11. A new recombinant endo-1,3-β-D-glucanase from the marine bacterium Formosa algae KMM 3553: enzyme characteristics and transglycosylation products analysis.

    PubMed

    Kusaykin, Mikhail I; Belik, Alexey A; Kovalchuk, Svetlana N; Dmitrenok, Pavel S; Rasskazov, Valerii A; Isakov, Vladimir V; Zvyagintseva, Tatyana N

    2017-02-01

    A specific endo-1,3-β-D-glucanase (GFA) gene was found in genome of marine bacterium Formosa algae KMM 3553. For today this is the only characterized endo-1,3-β-D-glucanase (EC 3.2.1.39) in Formosa genus and the only bacterial EC 3.2.1.39 GH16 endo-1,3-β-D-glucanase with described transglycosylation activity. It was expressed in E. coli and isolated in homogeneous state. Investigating the products of polysaccharides digestion with GFA allowed to establish it's substrate specificity and classify this enzyme as glucan endo-1,3-β-D-glucosidase (EC 3.2.1.39). The amino-acid sequence of GFA consists of 556 residues and shows sequence similarity of 45-85% to β-1,3-glucanases of bacteria belonging to the CAZy 16th structural family of glycoside hydrolases GH16. Enzyme has molecular weight 61 kDa, exhibits maximum of catalytic activity at 45 °C, pH 5.5. Half-life period at 45 °С is 20 min, complete inactivation happens at 55 °C within 10 min. Km for hydrolysis of laminarin is 0.388 mM. GFA glucanase from marine bacteria F. algae is one of rare enzymes capable to catalyze reactions of transglycosylation. It catalyzed transfer of glyconic part of substrate molecule on methyl-β-D-xylopyranoside, glycerol and methyl-α-D-glucopyranoside. The enzyme can be used in structure determination of β-1,3-glucans (or mixed 1,3;1,4- and 1,3;1,6-β-D-glucans) and enzymatic synthesis of new carbohydrate-containing compounds.

  12. A thermophilic, hydrogenogenic and carboxydotrophic bacterium, Calderihabitans maritimus gen. nov., sp. nov., from a marine sediment core of an undersea caldera.

    PubMed

    Yoneda, Yasuko; Yoshida, Takashi; Yasuda, Hisato; Imada, Chiaki; Sako, Yoshihiko

    2013-10-01

    A hydrogenogenic, carboxydotrophic marine bacterium, strain KKC1(T), was isolated from a sediment core sample taken from a submerged marine caldera. Cells were non-motile, Gram-stain-negative, 1.0-3.0 µm straight rods, often observed with round endospores. Strain KKC1(T) grew at 55-68 °C, pH 5.2-9.2 and 0.8-14 % (w/v) salinity. Optimum growth occurred at 65 °C, pH 7.0-7.5 and 2.46 % salinity with a doubling time of 3.7 h. The isolate grew chemolithotrophically, producing H2 from carbon monoxide (CO) oxidation with reduction of various electron acceptors, e.g. sulfite, thiosulfate, fumarate, ferric iron and AQDS (9,10-anthraquinone 2,6-disulfonate). KKC1(T) grew heterotrophically on pyruvate, lactate, fumarate, glucose, fructose and mannose with thiosulfate as an electron acceptor. When grown mixotrophically on CO and pyruvate, C16 : 0 constituted almost half of the total cellular fatty acids. The DNA G+C content was 50.6 mol%. The 16S rRNA gene sequence of KKC1(T) was most closely related to those of members of the genus Moorella with similarity ranging from 91 to 89 %. Based on physiological and phylogenetic novelty, we propose the isolate as a representative of a new genus and novel species with the name Calderihabitans maritimus gen. nov., sp. nov.; the type strain of the type species is KKC1(T) ( = DSM 26464(T) = NBRC 109353(T)).

  13. Resilience of sulfate-reducing granular sludge against temperature, pH, oxygen, nitrite, and free nitrous acid.

    PubMed

    Hao, Tianwei; Mackey, Hamish R; Guo, Gang; Liu, Rulong; Chen, Guanghao

    2016-10-01

    Sulfate-reducing granular sludge has recently been developed and characterized in detail as part of the development of the sulfate reduction, autotrophic denitrification, nitrification integrated (SANI) process. However, information regarding temperature of granules to environmental fluctuation is lacking, an aspect that is important in dealing with real wastewater. A comprehensive assessment of sulfate-reducing granular sludge performance under various environmental conditions was thus conducted in this study, including temperature, pH, oxygen, nitrite, and free nitrous acid (FNA) as possible encountering conditions in the removal of organics and/or nitrate. Specific chemical oxygen demand removal rate of the granules was determined to be reduced by 65 % when the temperature varied between 10-15 °C, reduced by 70 % when dissolved oxygen (DO) was 0.5 mg/L or greater, and at least, reduced by 75 % when nitrite was 30 mg N/L or above. Nevertheless, the sludge activity recovered by 82, 100, and 86 % from exposure to high oxygen and nitrite and low temperature levels, respectively. Combined inhibition of nitrite and FNA on the sludge is strong and complex, while FNA alone reduced cell viability from 60 to 40 % when its concentration increased to 2.3 mg N/L. The present study demonstrates that sulfate-reducing bacteria (SRB) granules possess high resilience against varying environmental conditions, showing the high application potential of sulfate-reducing granular sludge in dealing with brackish and saline industrial or domestic wastewaters.

  14. Assessing the Role of Iron Sulfides in the Long Term Sequestration of U by Sulfate Reducing Bacteria

    SciTech Connect

    Rittman, Bruce; Zhou, Chen; Vannela, Raveender

    2013-12-31

    This four-year project’s overarching aim was to identify the role of biogenic and synthetic iron-sulfide minerals in the long-term sequestration of reduced U(IV) formed under sulfate-reducing conditions when subjected to re-oxidizing conditions. As stated in this final report, significant progress was achieved through the collaborative research effort conducted at Arizona State University (ASU) and the University of Michigan (UM).

  15. Reverse Sample Genome Probing, a New Technique for Identification of Bacteria in Environmental Samples by DNA Hybridization, and Its Application to the Identification of Sulfate-Reducing Bacteria in Oil Field Samples

    PubMed Central

    Voordouw, Gerrit; Voordouw, Johanna K.; Karkhoff-Schweizer, Roxann R.; Fedorak, Phillip M.; Westlake, Donald W. S.

    1991-01-01

    A novel method for the identification of bacteria in environmental samples by DNA hybridization is presented. It is based on the fact that, even within a genus, the genomes of different bacteria may have little overall sequence homology. This allows the use of the labeled genomic DNA of a given bacterium (referred to as a “standard”) to probe for its presence and that of bacteria with highly homologous genomes in total DNA obtained from an environmental sample. Alternatively, total DNA extracted from the sample can be labeled and used to probe filters on which denatured chromosomal DNA from relevant bacterial standards has been spotted. The latter technique is referred to as reverse sample genome probing, since it is the reverse of the usual practice of deriving probes from reference bacteria for analyzing a DNA sample. Reverse sample genome probing allows identification of bacteria in a sample in a single step once a master filter with suitable standards has been developed. Application of reverse sample genome probing to the identification of sulfate-reducing bacteria in 31 samples obtained primarily from oil fields in the province of Alberta has indicated that there are at least 20 genotypically different sulfate-reducing bacteria in these samples. Images PMID:16348574

  16. Anaerobic Oxidation of o-Xylene, m-Xylene, and Homologous Alkylbenzenes by New Types of Sulfate-Reducing Bacteria

    PubMed Central

    Harms, Gerda; Zengler, Karsten; Rabus, Ralf; Aeckersberg, Frank; Minz, Dror; Rosselló-Mora, Ramon; Widdel, Friedrich

    1999-01-01

    Various alkylbenzenes were depleted during growth of an anaerobic, sulfate-reducing enrichment culture with crude oil as the only source of organic substrates. From this culture, two new types of mesophilic, rod-shaped sulfate-reducing bacteria, strains oXyS1 and mXyS1, were isolated with o-xylene and m-xylene, respectively, as organic substrates. Sequence analyses of 16S rRNA genes revealed that the isolates affiliated with known completely oxidizing sulfate-reducing bacteria of the δ subclass of the class Proteobacteria. Strain oXyS1 showed the highest similarities to Desulfobacterium cetonicum and Desulfosarcina variabilis (similarity values, 98.4 and 98.7%, respectively). Strain mXyS1 was less closely related to known species, the closest relative being Desulfococcus multivorans (similarity value, 86.9%). Complete mineralization of o-xylene and m-xylene was demonstrated in quantitative growth experiments. Strain oXyS1 was able to utilize toluene, o-ethyltoluene, benzoate, and o-methylbenzoate in addition to o-xylene. Strain mXyS1 oxidized toluene, m-ethyltoluene, m-isoproyltoluene, benzoate, and m-methylbenzoate in addition to m-xylene. Strain oXyS1 did not utilize m-alkyltoluenes, whereas strain mXyS1 did not utilize o-alkyltoluenes. Like the enrichment culture, both isolates grew anaerobically on crude oil with concomitant reduction of sulfate to sulfide. PMID:10049854

  17. Biochemical characterization and structural analysis of a new cold-active and salt-tolerant esterase from the marine bacterium Thalassospira sp.

    PubMed

    De Santi, Concetta; Leiros, Hanna-Kirsti S; Di Scala, Alessia; de Pascale, Donatella; Altermark, Bjørn; Willassen, Nils-Peder

    2016-05-01

    A gene encoding an esterase, ThaEst2349, was identified in the marine psychrophilic bacterium Thalassospira sp. GB04J01. The gene was cloned and overexpressed in E. coli as a His-tagged fusion protein. The recombinant enzyme showed optimal activity at 45 °C and the thermal stability displayed a retention of 75 % relative activity at 40 °C after 2 h. The optimal pH was 8.5 but the enzyme kept more than 75 % of its maximal activity between pH 8.0 and 9.5. ThaEst2349 also showed remarkable tolerance towards high concentrations of salt and it was active against short-chain p-nitrophenyl esters, displaying optimal activity with the acetate. The enzyme was tested for tolerance of organic solvents and the results are suggesting that it could function as an interesting candidate for biotechnological applications. The crystal structure of ThaEst2349 was determined to 1.69 Å revealing an asymmetric unit containing two chains, which also is the biological unit. The structure has a characteristic cap domain and a catalytic triad comprising Ser158, His285 and Asp255. To explain the cold-active nature of the enzyme, we compared it against thermophilic counterparts. Our hypothesis is that a high methionine content, less hydrogen bonds and less ion pairs render the enzyme more flexible at low temperatures.

  18. A new alkaliphilic cold-active esterase from the psychrophilic marine bacterium Rhodococcus sp.: functional and structural studies and biotechnological potential.

    PubMed

    De Santi, Concetta; Tedesco, Pietro; Ambrosino, Luca; Altermark, Bjørn; Willassen, Nils-Peder; de Pascale, Donatella

    2014-03-01

    The special features of cold-adapted lipolytic biocatalysts have made their use possible in several industrial applications. In fact, cold-active enzymes are known to be able to catalyze reactions at low temperatures, avoiding side reactions taking place at higher temperatures and preserving the integrity of products. A lipolytic gene was isolated from the Arctic marine bacterium Rhodococcus sp. AW25M09 and expressed in Escherichia coli as inclusion bodies. The recombinant enzyme (hereafter called RhLip) showed interesting cold-active esterase activity. The refolded purified enzyme displayed optimal activity at 30 °C and was cold-active with retention of 50% activity at 10 °C. It is worth noting that the optimal pH was 11, and the low relative activity below pH 10 revealed that RhLip was an alkaliphilic esterase. The enzyme was active toward short-chain p-nitrophenyl esters (C2-C6), displaying optimal activity with the butyrate (C4) ester. In addition, the enzyme revealed a good organic solvent and salt tolerance. These features make this an interesting enzyme for exploitation in some industrial applications.

  19. Construction and use of a broad-host-range plasmid expressing the lamB gene for utilization of bacteriophage lambda vectors in the marine bacterium Vibrio harveyi.

    PubMed

    Jasiecki, J; Czy, A; Gabig, M; Wegrzyn, G

    2001-07-01

    The remarkable success of Escherichia coli as a model organism in molecular genetics was dependent, among other things, on its susceptibility to genetic manipulation. Many versatile and sophisticated genetic tools for molecular biology studies are derived from bacteriophage lambda. However, this bacteriophage is specific for E. coli, and thus lambda-based techniques have been restricted to this bacterium. Plasmids expressing the E. coli gene coding for bacteriophage lambda receptor were reported previously, and introduction of such plasmids into cells of some other bacteria made them sensitive to phage lambda infection. However, we found that these systems were not efficient for Vibrio harveyi, one of the most frequently investigated species of marine bacteria. Here we describe construction of a broad-host-range plasmid expressing the lamB gene. Introduction of this plasmid to V. harveyi cells and expression of lamB made this strain susceptible to bacteriophage lambda adsorption and lambda DNA injection. Foreign genetic material could be introduced into cells of this strain using a cosmid vector.

  20. Proteomic characterization of plasmid pLA1 for biodegradation of polycyclic aromatic hydrocarbons in the marine bacterium, Novosphingobium pentaromativorans US6-1.

    PubMed

    Yun, Sung Ho; Choi, Chi-Won; Lee, Sang-Yeop; Lee, Yeol Gyun; Kwon, Joseph; Leem, Sun Hee; Chung, Young Ho; Kahng, Hyung-Yeel; Kim, Sang Jin; Kwon, Kae Kyoung; Kim, Seung Il

    2014-01-01

    Novosphingobium pentaromativorans US6-1 is a halophilic marine bacterium able to degrade polycyclic aromatic hydrocarbons (PAHs). Genome sequence analysis revealed that the large plasmid pLA1 present in N. pentaromativorans US6-1 consists of 199 ORFs and possess putative biodegradation genes that may be involved in PAH degradation. 1-DE/LC-MS/MS analysis of N. pentaromativorans US6-1 cultured in the presence of different PAHs and monocyclic aromatic hydrocarbons (MAHs) identified approximately 1,000 and 1,400 proteins, respectively. Up-regulated biodegradation enzymes, including those belonging to pLA1, were quantitatively compared. Among the PAHs, phenanthrene induced the strongest up-regulation of extradiol cleavage pathway enzymes such as ring-hydroxylating dioxygenase, putative biphenyl-2,3-diol 1,2-dioxygenase, and catechol 2,3-dioxygenase in pLA1. These enzymes lead the initial step of the lower catabolic pathway of aromatic hydrocarbons through the extradiol cleavage pathway and participate in the attack of PAH ring cleavage, respectively. However, N. pentaromativorans US6-1 cultured with p-hydroxybenzoate induced activation of another extradiol cleavage pathway, the protocatechuate 4,5-dioxygenase pathway, that originated from chromosomal genes. These results suggest that N. pentaromativorans US6-1 utilizes two different extradiol pathways and plasmid pLA1 might play a key role in the biodegradation of PAH in N. pentaromativorans US6-1.

  1. Fijiolides A and B, inhibitors of TNF-alpha-induced NFkappaB activation, from a marine-derived sediment bacterium of the genus Nocardiopsis.

    PubMed

    Nam, Sang-Jip; Gaudêncio, Susana P; Kauffman, Christopher A; Jensen, Paul R; Kondratyuk, Tamara P; Marler, Laura E; Pezzuto, John M; Fenical, William

    2010-06-25

    Fijiolide A, a potent inhibitor of TNF-alpha-induced NFkappaB activation, along with fijiolide B, were isolated from a marine-derived bacterium of the genus Nocardiopsis. The planar structures of fijiolides A (1) and B (2) were elucidated by interpretation of 2D NMR spectroscopic data, while the absolute configurations of these compounds were defined by interpretation of circular dichroism and 2D NMR data combined with application of the advanced Mosher's method. Fijiolides A and B are related to several recently isolated chloroaromatic compounds, which appear to be the Bergman cyclization products of enediyne precursors. Fijiolide A reduced TNF-alpha-induced NFkappaB activation by 70.3%, with an IC(50) value of 0.57 micro-M. Fijiolide B demonstrated less inhibition, only 46.5%, without dose dependence. The same pattern was also observed with quinone reductase (QR) activity: fijiolide A was found to induce quinone reductase-1 (QR1) with an induction ratio of 3.5 at a concentration of 20 microg/mL (28.4 microM). The concentration required to double the activity was 1.8 microM. Fijiolide B did not affect QR1 activity, indicating the importance of the nitrogen substitution pattern for biological activity. On the basis of these data, fijiolide A is viewed as a promising lead for more advanced anticancer testing.

  2. Assessment of bioflocculant production by Bacillus sp. Gilbert, a marine bacterium isolated from the bottom sediment of Algoa Bay.

    PubMed

    Nontembiso, Piyo; Sekelwa, Cosa; Leonard, Mabinya V; Anthony, Okoh I

    2011-01-01

    The bioflocculant-producing potentials of a marine bacteria isolated from the bottom sediment of Algoa Bay was investigated using standard methods. The 16S rDNA sequence analysis revealed 98% similarity to that of Bacillus sp. HXG-C1 and the nucleotide sequence was deposited in GenBank as Bacillus sp. Gilbert with accession number HQ537128. Bioflocculant was optimally produced when sucrose (72% flocculating activity) and ammonium chloride (91% flocculating activity) were used as sole sources of carbon and nitrogen, respectively; an initial pH 6.2 of the production medium; and Mg²⁺ as cation. Chemical analysis of the purified bioflocculant revealed the compound to be a polysaccharide.

  3. Assessment of Bioflocculant Production by Bacillus sp. Gilbert, a Marine Bacterium Isolated from the Bottom Sediment of Algoa Bay

    PubMed Central

    Nontembiso, Piyo; Sekelwa, Cosa; Leonard, Mabinya V.; Anthony, Okoh I.

    2011-01-01

    The bioflocculant-producing potentials of a marine bacteria isolated from the bottom sediment of Algoa Bay was investigated using standard methods. The 16S rDNA sequence analysis revealed 98% similarity to that of Bacillus sp. HXG-C1 and the nucleotide sequence was deposited in GenBank as Bacillus sp. Gilbert with accession number HQ537128. Bioflocculant was optimally produced when sucrose (72% flocculating activity) and ammonium chloride (91% flocculating activity) were used as sole sources of carbon and nitrogen, respectively; an initial pH 6.2 of the production medium; and Mg2+ as cation. Chemical analysis of the purified bioflocculant revealed the compound to be a polysaccharide. PMID:21822413

  4. Comparative study of MnO2 nanoparticle synthesis by marine bacterium Saccharophagus degradans and yeast Saccharomyces cerevisiae.

    PubMed

    Salunke, Bipinchandra K; Sawant, Shailesh S; Lee, Sang-Ill; Kim, Beom Soo

    2015-07-01

    Microorganisms are one of the most attractive and simple sources for the synthesis of different types of metal nanoparticles. The synthesis of manganese dioxide nanoparticles (MnO2 NPs) by microorganisms from reducing potassium permanganate was investigated for the first time in the present study. The microbial supernatants of the bacterium Saccharophagus degradans ATCC 43961 (Sde 2-40) and of the yeast Saccharomyces cerevisiae showed positive reactions to the synthesis of MnO2 NPs by displaying a change of color in the permanganate solution from purple to yellow. KMnO4-specific peaks also disappeared and MnO2-specific peaks emerged at an absorption maximum of 365 nm in UV-visible spectrophotometry. The washed Sde 2-40 cells did not show any ability to synthesize MnO2 NPs. The medium and medium constituents of Sde 2-40 showed similar positive reactions as supernatants, which indicate the role of the Sde 2-40 medium constituents in the synthesis of MnO2 NPs. This suggests that microorganisms without nanoparticle synthesis ability can be misreported for their abilities to synthesize nanoparticles. S. cerevisiae washed cells showed an ability to synthesize MnO2 NPs. The strategies of keeping yeast cells in tea bags and dialysis membranes showed positive tests for the synthesis of MnO2 NPs. A Fourier transform-infrared spectroscopy study suggested roles for the proteins, alcoholic compounds, and cell walls of S. cerevisiae cells in the synthesis of MnO2 NPs. Electron-dispersive X-ray spectroscopy analyses confirmed the presence of Mn and O in the sample. X-ray photoelectron spectroscopy revealed characteristic binding energies for MnO2 NPs. Transmission electron microscopy micrographs revealed the presence of uniformly dispersed hexagonal- and spherical-shaped particles with an average size of 34.4 nm. The synthesis approach using yeast is possible by a simple reaction at low temperature without any need for catalysts, templates, or expensive and precise equipment

  5. Biomarkers of sulfate reducing bacteria from a variety of different aged samples including a modern microbial mat

    NASA Astrophysics Data System (ADS)

    Pages, A.; Grice, K.; Lockhart, R.; Holman, A.; Melendez, I.; Van Kranendonk, M.; Jaraula, C.

    2011-12-01

    Most biomarkers present in sediments occur in only trace concentrations, trapped in kerogen or may be highly functionalised especially in recent sedimentary deposits making them difficult to chromatographically resolve, thus presenting considerable analytical challenges, especially for isotope studies. Innovative hydro (Hy) pyrolysis (Py) techniques are able to target or convert many of these compounds into free hydrocarbons more amenable to gas chromatography mass-spectrometry (GC-MS) and compound-specific isotope analysis (CSIA). HyPy has been applied to a modern layered smooth mat from Shark Bay, Western Australia. Saturate and aromatic fractions from different layers of the mat have been analysed by GC-MS and CSIA. After HyPy, an even-odd distribution of n-alkanes has been revealed as well as very long-chain n-alkanes up to n-C38. Stable carbon isotopic values of the n-alkanes indicated the presence of at least two bacterial communities. The short-chain n-alkanes were likely to be representative of a cyanobacteria community (δ13C, C15-C23, - 18 to -25 %VPDB) while the carbon isotopic values of the long-chain n-alkanes supported the presence of sulfate reducing bacteria (δ13C, C25-C33, - 30 to - 34 %VPDB). Long-chain fatty acids have been previously reported in sulfate reducing bacteria. It is hypothesised that this distribution and isotopic character representing sulfate reducing bacteria consortia may be preserved in the rock record. This hypothesis has been tested in Australian rocks: a Devonian carbonaceous concretion containing an exceptionally well preserved fossil invertebrate from the Canning Basin, Western Australia, a Paleoproterozoic sample (1.6 billion years old) from a lead-zinc ore deposit from the McArthur Basin, Northern Territories and a Paleoproterozoic chert (2.3 billion years old) from the Pilbara, Western Australia. Biomarkers of these samples showed a strong predominance of long-chain n-alkanes, up to n-C38 with an even-odd distribution

  6. Electron microscopic characterization of the sulfate reducer Desulfovibrio vulgaris: biofilms and clumps

    NASA Astrophysics Data System (ADS)

    Auer, M.; Remis, J.; Jorgens, D.; Zemla, M.; Singer, M.; Schmitt, J.; Gorby, Y.; Hazen, T.; Wall, J.; Elias, D.; Torok, T.

    2008-12-01

    Numerous studies have helped characterize the stress response of the anaerobic sulfate reducer Desulfovibrio vulgaris Hildenborough (DvH). Yet all of these techniques represent bulk analyses of cells grown mostly under liquid culture conditions in large reactors. Such results represent an average over a large variety of individual cellular responses, hence assuming a homogeneous distribution of physiological traits. Moreover, only recently are those techniques applied to the environmentally more relevant condition of microbial communities (biofilms). What is missing is a detailed ultrastructural analysis of such biofilms in order to determine biofilm organization and its extracellular metal deposition distribution. Using sophisticated sample cryo-preparation approaches such as high-pressure freezing, freeze-substitution or microwave- assisted processing, followed serial section TEM imaging, we have found a large heterogeneity with respect to metal precipitation with some cells being surrounded by metal precipitates whereas neighboring cells, being genetically identical and seeing virtually the exact same microenvironment, completely lack extracellular metal deposits. Interestingly, apart from metal deposits near cell surfaces, we also found string- and sheet- like metal deposits in between neighboring cells that in mature biofilms can extend for hundreds of micrometers. In mature DvH biofilms such deposits were predominantly associated with areas of intact cells in biofilms, with areas devoid of such metal deposits displayed predominantly cell debris, suggesting a role of such deposits for cell survival, which may be of high significance to biofilms at DOE sites. Upon tomographic imaging we found that extracellular metal deposits were often associated with thin filaments and vesicle-like features. To complement our serial section 2D analysis of resin-embedded samples and the resulting limitation of sampling 3D biofilm as thin sections of arbitrary orientation, we

  7. Microbial methanogenesis in the sulfate-reducing zone of surface sediments traversing the Peruvian margin

    NASA Astrophysics Data System (ADS)

    Maltby, J.; Sommer, S.; Dale, A. W.; Treude, T.

    2015-09-01

    We studied the concurrence of methanogenesis and sulfate reduction in surface sediments (0-25 cm below sea floor, cmbsf) at six stations (70, 145, 253, 407, 770 and 1024 m) along the Peruvian margin (12° S). This oceanographic region is characterized by high carbon export to the seafloor, creating an extensive oxygen minimum zone (OMZ) on the shelf, both factors that could favor surface methanogenesis. Sediments sampled along the depth transect traversed areas of anoxic and oxic conditions in the bottom-near water. Net methane production (batch incubations) and sulfate reduction (35S-sulfate radiotracer incubation) were determined in the upper 0-25 cmbsf of multicorer cores from all stations, while deep hydrogenotrophic methanogenesis (> 30 cmbsf, 14C-bicarbonate radiotracer incubation) was determined in two gravity cores at selected sites (78 and 407 m). Furthermore, stimulation (methanol addition) and inhibition (molybdate addition) experiments were carried out to investigate the relationship between sulfate reduction and methanogenesis. Highest rates of methanogenesis and sulfate reduction in the surface sediments, integrated over 0-25 cmbsf, were observed on the shelf (70-253 m, 0.06-0.1 and 0.5-4.7 mmol m-2 d-1, respectively), while lowest rates were discovered at the deepest site (1024 m, 0.03 and 0.2 mmol m-2 d-1, respectively). The addition of methanol resulted in significantly higher surface methanogenesis activity, suggesting that the process was mostly based on non-competitive substrates, i.e., substrates not used by sulfate reducers. In the deeper sediment horizons, where competition was probably relieved due to the decline of sulfate, the usage of competitive substrates was confirmed by the detection of hydrogenotrophic activity in the sulfate-depleted zone at the shallow shelf station (70 m). Surface methanogenesis appeared to be correlated to the availability of labile organic matter (C / N ratio) and organic carbon degradation (DIC production

  8. Microbial methanogenesis in the sulfate-reducing zone of surface sediments traversing the Peruvian margin

    NASA Astrophysics Data System (ADS)

    Maltby, J.; Sommer, S.; Dale, A. W.; Treude, T.

    2016-01-01

    We studied the concurrence of methanogenesis and sulfate reduction in surface sediments (0-25 cm below sea floor) at six stations (70, 145, 253, 407, 990 and 1024 m) along the Peruvian margin (12° S). This oceanographic region is characterized by high carbon export to the seafloor creating an extensive oxygen minimum zone (OMZ) on the shelf, both factors that could favor surface methanogenesis. Sediments sampled along the depth transect traversed areas of anoxic and oxic conditions in the bottom-near water. Net methane production (batch incubations) and sulfate reduction (35S-sulfate radiotracer incubation) were determined in the upper 0-25 cm b.s.f. of multiple cores from all stations, while deep hydrogenotrophic methanogenesis (> 30 cm b.s.f., 14C-bicarbonate radiotracer incubation) was determined in two gravity cores at selected sites (78 and 407 m). Furthermore, stimulation (methanol addition) and inhibition (molybdate addition) experiments were carried out to investigate the relationship between sulfate reduction and methanogenesis.

    Highest rates of methanogenesis and sulfate reduction in the surface sediments, integrated over 0-25 cm b.s.f., were observed on the shelf (70-253 m, 0.06-0.1 and 0.5-4.7 mmol m-2 d-1, respectively), while lowest rates were discovered at the deepest site (1024 m, 0.03 and 0.2 mmol m-2 d-1, respectively). The addition of methanol resulted in significantly higher surface methanogenesis activity, suggesting that the process was mostly based on non-competitive substrates - i.e., substrates not used by sulfate reducers. In the deeper sediment horizons, where competition was probably relieved due to the decrease of sulfate, the usage of competitive substrates was confirmed by the detection of hydrogenotrophic activity in the sulfate-depleted zone at the shallow shelf station (70 m).

    Surface methanogenesis appeared to be correlated to the availability of labile organic matter (C / N ratio) and organic carbon

  9. Algivirga pacifica gen. nov., sp. nov., a novel agar-degrading marine bacterium of the family Flammeovirgaceae isolated from Micronesia.

    PubMed

    Kim, Jennifer Jooyoun; Kim, Ji Hyung; Kwon, Young-Kyung; Kwon, Kae Kyoung; Yang, Sung-Hyun; Jang, Jiyi; Heo, Soo-Jin; Park, Heung-Sik; Jung, Won-Kyo; Lee, Youngdeuk; Kang, Do-Hyung; Oh, Chulhong

    2013-12-01

    An aerobic, Gram-negative, coccoid to short rod-shaped and non-flagellated marine bacterial strain S354(T) was isolated from seawater of Micronesia. The strain was capable to degrade agar-forming slight depression into agar plate. Growth occurred at a temperature range of 12-44 °C, a pH range of 5-9, and a salinity range of 1-7 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences suggested that S354(T) belongs to the family Flammeovirgaceae. The novel strain was most closely related to Limibacter armeniacum YM 11-185(T) with similarity of 92.5 %. The DNA G+C content was 43.8 mol%. The major fatty acids (>10 %) were iso-C15:0 and C16:1 ω5c. The predominant isoprenoid quinone was determined to be MK-7. Polar lipid profile of S354(T) consisted of phosphatidylethanolamine, unknown polar lipid, and unknown glycolipids. Based on the phenotypic, phylogenetic, biochemical, and physiological tests conducted in this study, S354(T) is proposed to represent a type strain of a novel genus and species. The 16S rRNA gene sequence of S354(T) is registered in GenBank under the accession number JQ639084. The type of strain Algivirga pacifica gen. nov., sp. nov. is S354(T) (=KCCM 90107(T)=JCM 18326(T)).

  10. Bacillus toyonensis strain AEMREG6, a bacterium isolated from South African marine environment sediment samples produces a glycoprotein bioflocculant.

    PubMed

    Okaiyeto, Kunle; Nwodo, Uchechukwu U; Mabinya, Leonard V; Okoh, Anthony I

    2015-03-23

    A bioflocculant-producing bacteria, isolated from sediment samples of a marine environment in the Eastern Cape Province of South Africa demonstrated a flocculating activity above 60% for kaolin clay suspension. Analysis of the 16S ribosomal deoxyribonucleic acid (rDNA) nucleotide sequence of the isolate in the GenBank database showed 99% similarity to Bacillus toyonensis strain BCT-7112 and it was deposited in the GenBank as Bacillus toyonensis strain AEMREG6 with accession number KP406731. The bacteria produced a bioflocculant (REG-6) optimally in the presence of glucose and NH4NO3 as the sole carbon and nitrogen source, respectively, initial medium pH of 5 and Ca2+ as the cation of choice. Chemical analysis showed that purified REG-6 was a glycoprotein mainly composed of polysaccharide (77.8%) and protein (11.5%). It was thermally stable and had strong flocculating activity against kaolin suspension over a wide range of pH values (3-11) with a relatively low dosage requirement of 0.1 mg/mL in the presence of Mn2+. Fourier transform infrared spectroscopy (FTIR) revealed the presence of hydroxyl, carboxyl and amide groups preferred for flocculation. Scanning electron microscopy (SEM) revealed that bridging was the main flocculation mechanism of REG-6. The outstanding flocculating performance of REG-6 holds great potential to replace the hazardous chemical flocculants currently used in water treatment.

  11. Transcriptional and translational regulatory responses to iron limitation in the globally distributed marine bacterium Candidatus Pelagibacter ubique

    SciTech Connect

    Smith, Daniel P.; Kitner, J. B.; Norbeck, Angela D.; Clauss, Therese RW; Lipton, Mary S.; Schwalbach, M. S.; Steindler, L.; Nicora, Carrie D.; Smith, Richard D.; Giovannoni, Stephen J.

    2010-05-05

    Abstract Background: Iron is recognized as an important micronutrient that limits microbial plankton productivity over vast regions of the oceans. We investigated the gene expression responses of Candidatus Pelagibacter ubique cultures to iron limitation in natural seawater media supplemented with a siderophore to chelate iron. Methodology/Principal Findings: Microarray data indicated transcription of the periplasmic iron binding protein sfuC increased by 16-fold, and iron transporter subunits, iron-sulfur center assembly genes, and the putative ferroxidase rubrerythrin transcripts increased to a lesser extent. Quantitative peptide mass spectrometry revealed that sfuC protein abundance increased 27-fold, despite an average decrease of 59% across the global proteome. Two RNA-binding proteins, CspE and CspL, correlated well with iron availability, suggesting that they may contribute to the observed differences between the transcriptome and proteome. Conclusions/Significance: We propose sfuC as a marker gene for indicating iron limitation in marine metatranscriptomic and metaproteomic ecological surveys. The marked proteome reduction was not directly correlated to changes in the transcriptome, implicating post-transcriptional regulatory mechanisms as modulators of protein expression. We propose a model in which the RNA-binding activity of cspE and cspL selectively enables protein synthesis of the iron acquisition protein sfuC during transient growth-limiting episodes of iron scarcity.

  12. Production of cryoprotectant extracellular polysaccharide substances (EPS) by the marine psychrophilic bacterium Colwellia psychrerythraea strain 34H under extreme conditions.

    PubMed

    Marx, Joseph G; Carpenter, Shelly D; Deming, Jody W

    2009-01-01

    Extracellular polysaccharide substances (EPS) play critical roles in microbial ecology, including the colonization of extreme environments in the ocean, from sea ice to the deep sea. After first developing a sugar-free growth medium, we examined the relative effects of temperature, pressure, and salinity on EPS production (on a per cell basis) by the obligately marine and psychrophilic gamma-proteobacterium, Colwellia psychrerythraea strain 34H. Over growth-permissive temperatures of approximately 10 to -4 degrees C, EPS production did not change, but from -8 to -14 degrees C when samples froze, EPS production rose dramatically. Similarly, at growth-permissive hydrostatic pressures of 1-200 atm (1 atm = 101.325 kPa) (at -1 and 8 degrees C), EPS production was unchanged, but at higher pressures of 400 and 600 atm EPS production rose markedly. In salinity tests at 10-100 parts per million (and -1 and 5 degrees C), EPS production increased at the freshest salinity tested. Extreme environmental conditions thus appear to stimulate EPS production by this strain. Furthermore, strain 34H recovered best from deep-freezing to -80 degrees C (not found for Earthly environments) if first supplemented with a preparation of its own EPS, rather than other cryoprotectants like glycerol, suggesting EPS production as both a survival strategy and source of compounds with potentially novel properties for biotechnological and other applications.

  13. Biosorption and Biomineralization of U(VI) by the Marine Bacterium Idiomarina loihiensis MAH1: Effect of Background Electrolyte and pH

    PubMed Central

    Morcillo, Fernando; González-Muñoz, María T.; Reitz, Thomas; Romero-González, María E.; Arias, José M.; Merroun, Mohamed L.

    2014-01-01

    The main goal of this study is to compare the effects of pH, uranium concentration, and background electrolyte (seawater and NaClO4 solution) on the speciation of uranium(VI) associated with the marine bacterium Idiomarina loihiensis MAH1. This was done at the molecular level using a multidisciplinary approach combining X-ray Absorption Spectroscopy (XAS), Time-Resolved Laser-Induced Fluorescence Spectroscopy (TRLFS), and High Resolution Transmission Electron Microscopy (HRTEM). We showed that the U(VI)/bacterium interaction mechanism is highly dependent upon pH but also the nature of the used background electrolyte played a role. At neutral conditions and a U concentration ranging from 5·10−4 to 10−5 M (environmentally relevant concentrations), XAS analysis revealed that uranyl phosphate mineral phases, structurally resembling meta-autunite [Ca(UO2)2(PO4)2 2–6H2O] are precipitated at the cell surfaces of the strain MAH1. The formation of this mineral phase is independent of the background solution but U(VI) luminescence lifetime analyses demonstrated that the U(VI) speciation in seawater samples is more intricate, i.e., different complexes were formed under natural conditions. At acidic conditions, pH 2, 3 and 4.3 ([U] = 5·10−4 M, background electrolyte  = 0.1 M NaClO4), the removal of U from solution was due to biosorption to Extracellular Polysaccharides (EPS) and cell wall components as evident from TEM analysis. The LIII-edge XAS and TRLFS studies showed that the biosorption process observed is dependent of pH. The bacterial cell forms a complex with U through organic phosphate groups at pH 2 and via phosphate and carboxyl groups at pH 3 and 4.3, respectively. The differences in the complexes formed between uranium and bacteria on seawater compared to NaClO4 solution demonstrates that the actinide/microbe interactions are influenced by the three studied factors, i.e., the pH, the uranium concentration and the chemical composition of the

  14. Responses of the marine bacterium Pseudomonas fluorescens to an excess of heavy metals: physiological and biochemical aspects.

    PubMed

    Poirier, I; Jean, N; Guary, J C; Bertrand, M

    2008-11-15

    A Pseudomonas fluorescens strain was isolated from oxic marine sediments obtained from the strand zone of the St Anne Bay (a moderately metal-contaminated site to the west of Cherbourg harbour). The strain, which exhibited a high tolerance to metal contamination when cultivated (minimal inhibitory concentration=950 microM [62 mg L(-1)] for Zn, 660 microM [42 mg L(-1)] for Cu, and 505 microM [57 mg L(-1)] for Cd), was further characterized by its physiological and biochemical responses to metal additions to the culture medium. Bacterial growth was significantly disturbed by 380 microM Zn (25 mg L(-1)), 315 microM Cu (20 mg L(-1)) and 90 microM Cd (10 mg L(-1)). The Zn-containing alkaline phosphatase was studied as an intoxication biomarker. Its activity was stimulated (+9%) by an excess of Zn, but inhibited by Cd (-55%) and Cu (-10%), these two elements could displace the native Zn or/and disturb the enzyme 3D-structure. Bacterial O(2) consumption was recorded as a global physiological response to metal stress. This parameter dropped with increasing Cd and Cu contamination (-49% and -45%, respectively, at 20 mg L(-1)). By contrast, Zn increased O2 consumption (approximately +40% for the different tested concentrations). The proteomes of bacteria grown in the presence or absence of 20 mg metal L(-1) were characterized by 2D-gel electrophoresis. The number of spots exhibiting a difference in intensity between the contaminated sample and the control was 65, 68, and 103, for Zn, Cu and Cd, respectively. Among them, 45, 61 and 82 spots respectively appeared de novo or increased in intensity, indicative of metal-stimulated synthesis, particularly for Cu and Cd. In summary, whereas Cd and Cu treatments both stressed cells and slowed down primary metabolism to differing extents, Zn has a stimulating action on several physiological and biochemical parameters.

  15. Microbial diversity in polluted harbor sediments II: Sulfate-reducing bacterial community assessment using terminal restriction fragment length polymorphism and clone library of dsrAB gene

    NASA Astrophysics Data System (ADS)

    Zhang, Wen; Song, Lin-sheng; Ki, Jang-Seu; Lau, Chun-Kwan; Li, Xiang-Dong; Qian, Pei-Yuan

    2008-02-01

    Sulfate-reducing bacteria (SRB) are important regulators of a variety of processes in coastal marine sediments regarding organic matter turnover, biodegradation of pollutants, and sulfur and carbon cycles. Yet their community compositions have not been investigated in polluted harbor sediments. This study described the diversity and spatial variation of SRB communities in surface sediments in Victoria Harbor, Hong Kong. The spatial variation of SRB communities was described by terminal restriction fragment length polymorphism (T-RFLP). The results showed that the most diversified terminal restriction fragments were found at polluted sites. In addition, cluster analysis indicated that although the SRB communities were different at the two polluted sites, they were still more similar to each other than to the two more distant reference sites. Based on a dsrAB clone library constructed at a polluted site, diversified SRB were found, represented by 30 Operational Taxonomic Units (OTUs). Upon comparisons among the SRB sequences detected from this study and those in the GenBank, five clades of SRB were found. Three clades belonged to the known families Desulfobacteraceae, Desulfobulbaceae, and Syntrophobacteriaceae. The majority of sequenced clones, which distantly related to sequences in the GenBank, constituted the remaining two unclassified groups, suggesting unique SRB members related to the polluted harbor environment. Statistical analyses indicated that estimated SRB richness correlated with environment factors such as sulfur content, acid volatile sulfate, and redox potential.

  16. [NO3-/NO2- inhibits sulfate-reducing activity of the enrichment culture of sulfate-reducing prokaryotes from an off-shore oil reservoir at Bohai Bay, China].

    PubMed

    Liu, Hong-Yu; Shi, Rong-Jiu; Zhang, Ying; Shi, Zhen-Guo; Zhang, Ying-Yue; Yu, Liang; Zhang, Xiao-Bo; Tan, Tao

    2014-08-01

    Long-term injection of sulfate-rich water into oil reservoirs stimulates the proliferation of sulfate-reducing prokaryotes (SRP) therein and results in production of a great amount of H2S, leading to souring in oil reservoirs and related environmental problems. In this study, we first, using modified API RP 38 medium, enriched SRP present in production water from a producing well at Bohai Bay, China, and then examined the inhibitory effects of nitrate or nitrite on sulfate reduction activity of the SRP. Results showed that the enriched SRP culture exhibited a high sulfate reduction activity as indicated by a sulfate-reducing rate of 10.4 mmol SO4(2-) x d(-1) x g(-1) dry cell. In presence of 0.4, 0.8, 1.8, and 4.2 mmol x L(-1) nitrate, sulfate reduction was inhibited for 5, 9, 20, and over 35 days, respectively. With the addition of 0.6, 0.9, 1.4, 2.6 and 4.6 mmol x L(-1) of nitrite, the inhibitory period lasted 3, 12, 22, and over 39 days, respectively. The SRP enrichment culture could dissimilatorily reduce nitrate to ammonium. When sulfate, nitrate and nitrite coexisted, nitrate or nitrite was preferentially used over sulfate as electron acceptor by the enriched SRP. This competitive use of electron acceptor and the strong inhibitory effect of nitrite possibly accounted for the suppression of nitrate and nitrite on the sulfate-reducing activity of the enriched SRP cultures from offshore oil reservoir at Bohai Bay.

  17. Desulfurispora thermophila gen. nov., sp. nov., a thermophilic, spore-forming sulfate-reducer isolated from a sulfidogenic fluidized-bed reactor.

    PubMed

    Kaksonen, Anna H; Spring, Stefan; Schumann, Peter; Kroppenstedt, Reiner M; Puhakka, Jaakko A

    2007-05-01

    A thermophilic, Gram-positive, endospore-forming, sulfate-reducing bacterium was isolated from a sulfidogenic fluidized-bed reactor treating acidic metal- and sulfate-containing water. The strain, designated RA50E1(T), was rod-shaped and motile. The strain grew at 40-67 degrees C (optimum growth at 59-61 degrees C) and pH 6.4-7.9 (optimum growth at pH 7.0-7.3). The strain tolerated up to 1 % NaCl. Sulfate, sulfite, thiosulfate and elemental sulfur were used as electron acceptors, but not nitrate, nitrite or iron(III). Electron donors utilized were H(2)/CO(2) (80 : 20, v/v), alcohols, various carboxylic acids and some sugars. Fermentative growth occurred on lactate and pyruvate. The cell wall contained meso-diaminopimelic acid and the major respiratory isoprenoid quinone was menaquinone MK-7. Major whole-cell fatty acids were iso-C(15 : 0) and iso-C(17 : 0). Strain RA50E1(T) was distantly related to representatives of the genera Desulfotomaculum, Pelotomaculum, Sporotomaculum and Cryptanaerobacter. On the basis of 16S rRNA gene sequence data, the strain cannot be assigned to any known genus. Based on the phenotypic and phylogenetic features of strain RA50E1(T), it is proposed that the strain represents a novel species in a new genus, for which the name Desulfurispora thermophila gen. nov., sp. nov. is proposed. The type strain of Desulfurispora thermophila is RA50E1(T) (=DSM 16022(T)=JCM 14018(T)).

  18. The chitin catabolic cascade in the marine bacterium Vibrio cholerae: characterization of a unique chitin oligosaccharide deacetylase.

    PubMed

    Li, Xibing; Wang, Lai-Xi; Wang, Xuesong; Roseman, Saul

    2007-12-01

    Chitin, one of the most abundant organic substances in nature, is consumed by marine bacteria, such as Vibrio cholerae, via a multitude of tightly regulated genes (Li and Roseman 2004, Proc Natl Acad Sci USA. 101:627-631). One such gene, cod, is reported here. It encodes a chitin oligosaccharide deacetylase (COD), when cells are induced by chitobiose, (GlcNH(2))(2), or crude crab shells. COD was molecularly cloned (COD-6His), overproduced, and purified to apparent homogeneity. COD is secreted at all stages of growth by induced V. cholerae. The gene sequence predicts a 26 N-terminal amino acid signal peptide not found in the isolated protein. COD is very active with chitin oligosaccharides, is virtually inactive with GlcNAc, and slightly active with colloidal ([(3)H]-N-acetyl)-chitin. The oligosaccharides are converted almost quantitatively to products lacking one acetyl group. The latter were characterized by mass spectrometry (ESI-MS), and treatment with nitrous acid. COD catalyzes the following reactions (n = 2-6): (GlcNAc)(n)--> GlcNAc-GlcNH(2)-(GlcNAc)(n-2) + Ac(-). That is, COD hydrolyzes the N-acetyl groups attached to the penultimate GlcNAc residue. The gene bank sequence data show that cod is highly conserved in Vibrios and Photobacteria. One such gene encodes a deacetylase isolated from V. alginolytics (Ohishi et al. 1997, Biosci Biotech Biochem. 61:1113-1117; Ohishi et al. 2000, J Biosci Bioeng. 90:561-563), that is specific for (GlcNAc)(2), but inactive with higher oligosaccharides. The COD enzymatic products, GlcNAc-GlcNH(2)-(GlcNAc)(n), closely resemble those obtained by hydrolysis of the chitooligosaccharides with Nod B: GlcNH(2)-(GlcNAc)(3-4). The latter are key intermediates in the biosynthesis of Nod factors, critically important in communications between the symbiotic nitrogen fixing bacteria and plants. Conceivably, the COD products play equally important roles in cellular communications that remain to be defined.

  19. Transposon mutagenesis identified chromosomal and plasmid genes essential for adaptation of the marine bacterium Dinoroseobacter shibae to anaerobic conditions.

    PubMed

    Ebert, Matthias; Laaß, Sebastian; Burghartz, Melanie; Petersen, Jörn; Koßmehl, Sebastian; Wöhlbrand, Lars; Rabus, Ralf; Wittmann, Christoph; Tielen, Petra; Jahn, Dieter

    2013-10-01

    Anaerobic growth and survival are integral parts of the life cycle of many marine bacteria. To identify genes essential for the anoxic life of Dinoroseobacter shibae, a transposon library was screened for strains impaired in anaerobic denitrifying growth. Transposon insertions in 35 chromosomal and 18 plasmid genes were detected. The essential contribution of plasmid genes to anaerobic growth was confirmed with plasmid-cured D. shibae strains. A combined transcriptome and proteome approach identified oxygen tension-regulated genes. Transposon insertion sites of a total of 1,527 mutants without an anaerobic growth phenotype were determined to identify anaerobically induced but not essential genes. A surprisingly small overlap of only three genes (napA, phaA, and the Na(+)/Pi antiporter gene Dshi_0543) between anaerobically essential and induced genes was found. Interestingly, transposon mutations in genes involved in dissimilatory and assimilatory nitrate reduction (napA, nasA) and corresponding cofactor biosynthesis (genomic moaB, moeB, and dsbC and plasmid-carried dsbD and ccmH) were found to cause anaerobic growth defects. In contrast, mutation of anaerobically induced genes encoding proteins required for the later denitrification steps (nirS, nirJ, nosD), dimethyl sulfoxide reduction (dmsA1), and fermentation (pdhB1, arcA, aceE, pta, acs) did not result in decreased anaerobic growth under the conditions tested. Additional essential components (ferredoxin, cccA) of the anaerobic electron transfer chain and central metabolism (pdhB) were identified. Another surprise was the importance of sodium gradient-dependent membrane processes and genomic rearrangements via viruses, transposons, and insertion sequence elements for anaerobic growth. These processes and the observed contributions of cell envelope restructuring (lysM, mipA, fadK), C4-dicarboxylate transport (dctM1, dctM3), and protease functions to anaerobic growth require further investigation to unravel the

  20. Nutrition and Metabolism of Marine Bacteria XVI. Formation of Protoplasts, Spheroplasts, and Related Forms from a Gram-negative Marine Bacterium1

    PubMed Central

    Costerton, J. W.; Forsberg, Cecil; Matula, Tibor I.; Buckmire, F. L. A.; MacLeod, Robert A.

    1967-01-01

    When cells of a marine pseudomonad were washed and suspended in 0.5 m sucrose, they retained their rod shape, but thin sections, when examined in an electron microscope, revealed that the outer layer of the cell wall had separated a considerable distance from the cytoplasmic membrane. Treatment of such cells with lysozyme alone produced no obvious change, but treatment with ethylenediaminetetraacetic acid (EDTA) alone caused the outer wall to disappear. A combination of EDTA and lysozyme resulted in the rapid formation of spheres essentially free from hexosamine and indistinguishable from protoplasts of gram-positive bacteria. When cells were washed with 0.5 m NaCl and then suspended in 0.5 m sucrose, they also retained their rod shape, but in this case the outer layer separated from the cells completely and could be recovered from the suspending medium. Such cells were converted to protoplasts by the action of lysozyme alone. Cells washed and finally suspended in 0.5 m NaCl, when treated with EDTA and lysozyme, slowly became spherical. Thin sections revealed typical spheroplasts of gram-negative bacteria in which the outer wall remained intact. Protoplasts took up α-aminoisobutyric acid by a Na+-dependent process. Images PMID:4965199

  1. Bacillus mesophilus sp. nov., an alginate-degrading bacterium isolated from a soil sample collected from an abandoned marine solar saltern.

    PubMed

    Zhou, Yan-Xia; Liu, Guo-Hong; Liu, Bo; Chen, Guan-Jun; Du, Zong-Jun

    2016-07-01

    A novel Gram-stain positive, endospore-forming bacterium, designated SA4(T), was isolated from a soil sample collected from an abandoned marine solar saltern at Wendeng, Shandong Province, PR China. Cells were observed to be rod shaped, alginase positive, catalase positive and motile. The strain was found to grow at temperatures ranging from 15 to 40 °C (optimum 35 °C), and pH 5.0-11.0 (optimum pH 8.0) with 0-7.0 % (w/v) NaCl concentration (optimum NaCl 3.0 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SA4(T) belongs to the genus Bacillus and exhibits 16S rRNA gene sequence similarities of 96.6, 96.5, 96.3 and 96.2 % with Bacillus horikoshii DSM 8719(T), Bacillus acidicola 105-2(T), Bacillus shackletonii LMG 18435(T) and Bacillus pocheonensis Gsoil 420(T), respectively. The menaquinone was identified as MK-7 and the major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids detected were anteiso-C15:0 (22.3 %), iso-C15:0 (22.6 %), iso-C16:0 (14.8 %) and iso-C14:0 (14.7 %). The DNA G+C content was determined to be 42.4 mol %. Phenotypic, chemotaxonomic and genotypic properties clearly indicated that isolate SA4(T) represents a novel species within the genus Bacillus, for which the name Bacillus mesophius sp. nov. is proposed. The type strain is SA4(T) (=DSM 101000(T)=CCTCC AB 2015209(T)).

  2. Marinilactibacillus piezotolerans sp. nov., a novel marine lactic acid bacterium isolated from deep sub-seafloor sediment of the Nankai Trough.

    PubMed

    Toffin, Laurent; Zink, Klaus; Kato, Chiaki; Pignet, Patricia; Bidault, Adeline; Bienvenu, Nadège; Birrien, Jean-Louis; Prieur, Daniel

    2005-01-01

    A piezotolerant, mesophilic, marine lactic acid bacterium (strain LT20T) was isolated from a deep sub-seafloor sediment core collected at Nankai Trough, off the coast of Japan. Cells were Gram-positive, rod-shaped, non-sporulating and non-motile. The NaCl concentration range for growth was 0-120 g l(-1), with the optimum at 10-20 g l(-1). The temperature range for growth at pH 7.0 was 4-50 degrees C, with the optimum at 37-40 degrees C. The optimum pH for growth was 7.0-8.0. The optimum pressure for growth was 0.1 MPa with tolerance up to 30 MPa. The main cellular phospholipids were phosphatidylglycerols (25 %), diphosphatidylglycerols (34 %) and a group of compounds tentatively identified as ammonium-containing phosphatidylserines (32 %); phosphatidylethanolamines (9 %) were minor components. The fatty acid composition was dominated by side chains of 16 : 0, 14 : 0 and 16 : 1. The G+C content of the genomic DNA was 42 mol%. On the basis of 16S rRNA gene sequence analysis and the secondary structure of the V6 region, this organism was found to belong to the genus Marinilactibacillus and was closely related to Marinilactibacillus psychrotolerans M13-2(T) (99 %), Marinilactibacillus sp. strain MJYP.25.24 (99 %) and Alkalibacterium olivapovliticus strain ww2-SN4C (97 %). Despite the high similarity between their 16S rRNA gene sequences (99 %), the DNA-DNA hybridization levels were less than 20 %. On the basis of physiological and genetic characteristics, it is proposed that this organism be classified as a novel species, Marinilactibacillus piezotolerans sp. nov. The type strain is LT20T (=DSM 16108T=JCM 12337T).

  3. Structural flexibility of the heme cavity in the cold-adapted truncated hemoglobin from the Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125.

    PubMed

    Giordano, Daniela; Pesce, Alessandra; Boechi, Leonardo; Bustamante, Juan Pablo; Caldelli, Elena; Howes, Barry D; Riccio, Alessia; di Prisco, Guido; Nardini, Marco; Estrin, Dario; Smulevich, Giulietta; Bolognesi, Martino; Verde, Cinzia

    2015-08-01

    Truncated hemoglobins build one of the three branches of the globin protein superfamily. They display a characteristic two-on-two α-helical sandwich fold and are clustered into three groups (I, II and III) based on distinct structural features. Truncated hemoglobins are present in eubacteria, cyanobacteria, protozoa and plants. Here we present a structural, spectroscopic and molecular dynamics characterization of a group-II truncated hemoglobin, encoded by the PSHAa0030 gene from Pseudoalteromonas haloplanktis TAC125 (Ph-2/2HbO), a cold-adapted Antarctic marine bacterium hosting one flavohemoglobin and three distinct truncated hemoglobins. The Ph-2/2HbO aquo-met crystal structure (at 2.21 Å resolution) shows typical features of group-II truncated hemoglobins, namely the two-on-two α-helical sandwich fold, a helix Φ preceding the proximal helix F, and a heme distal-site hydrogen-bonded network that includes water molecules and several distal-site residues, including His(58)CD1. Analysis of Ph-2/2HbO by electron paramagnetic resonance, resonance Raman and electronic absorption spectra, under varied solution conditions, shows that Ph-2/2HbO can access diverse heme ligation states. Among these, detection of a low-spin heme hexa-coordinated species suggests that residue Tyr(42)B10 can undergo large conformational changes in order to act as the sixth heme-Fe ligand. Altogether, the results show that Ph-2/2HbO maintains the general structural features of group-II truncated hemoglobins but displays enhanced conformational flexibility in the proximity of the heme cavity, a property probably related to the functional challenges, such as low temperature, high O2 concentration and low kinetic energy of molecules, experienced by organisms living in the Antarctic environment.

  4. Performance and microbial community dynamics of a sulfate-reducing bioreactor treating coal generated acid mine drainage.

    PubMed

    Burns, Andrew S; Pugh, Charles W; Segid, Yosief T; Behum, Paul T; Lefticariu, Liliana; Bender, Kelly S

    2012-06-01

    The effectiveness of a passive flow sulfate-reducing bioreactor processing acid mine drainage (AMD) generated from an abandoned coal mine in Southern Illinois was evaluated using geochemical and microbial community analysis 10 months post bioreactor construction. The results indicated that the treatment system was successful in both raising the pH of the AMD from 3.09 to 6.56 and in lowering the total iron level by 95.9%. While sulfate levels did decrease by 67.4%, the level post treatment (1153 mg/l) remained above recommended drinking water levels. Stimulation of biological sulfate reduction was indicated by a +2.60‰ increase in δ(34)S content of the remaining sulfate in the water post-treatment. Bacterial community analysis targeting 16S rRNA and dsrAB genes indicated that the pre-treated samples were dominated by bacteria related to iron-oxidizing Betaproteobacteria, while the post-treated water directly from the reactor outflow was dominated by sequences related to sulfur-oxidizing Epsilonproteobacteria and complex carbon degrading Bacteroidetes and Firmicutes phylums. Analysis of the post-treated water, prior to environmental release, revealed that the community shifted back to predominantly iron-oxidizing Betaproteobacteria. DsrA analysis implied limited diversity in the sulfate-reducing population present in both the bioreactor outflow and oxidation pond samples. These results support the use of passive flow bioreactors to lower the acidity, metal, and sulfate levels present in the AMD at the Tab-Simco mine, but suggest modifications of the system are necessary to both stimulate sulfate-reducing bacteria and inhibit sulfur-oxidizing bacteria.

  5. Multiple sulfur isotope signatures of sulfite and thiosulfate reduction by the model dissimilatory sulfate-reducer, Desulfovibrio alaskensis str. G20

    PubMed Central

    Leavitt, William D.; Cummins, Renata; Schmidt, Marian L.; Sim, Min S.; Ono, Shuhei; Bradley, Alexander S.; Johnston, David T.

    2014-01-01

    Dissimilatory sulfate reduction serves as a key metabolic carbon remineralization process in anoxic marine environments. Sulfate reducing microorganisms can impart a wide range in mass-dependent sulfur isotopic fractionation. As such, the presence and relative activity of these organisms is identifiable from geological materials. By extension, sulfur isotope records are used to infer the redox balance of marine sedimentary environments, and the oxidation state of Earth's oceans and atmosphere. However, recent work suggests that our understanding of microbial sulfate reduction (MSRs) may be missing complexity associated with the presence and role of key chemical intermediates in the reductive process. This study provides a test of proposed metabolic models of sulfate reduction by growing an axenic culture of the well-studied MSRs, Desulfovibrio alaskensis strain G20, under electron donor limited conditions on the terminal electron acceptors sulfate, sulfite or thiosulfate, and tracking the multiple S isotopic consequences of each condition set. The dissimilatory reduction of thiosulfate and sulfite produce unique minor isotope effects, as compared to the reduction of sulfate. Further, these experiments reveal a complex biochemistry associated with sulfite reduction. That is, under high sulfite concentrations, sulfur is shuttled to an intermediate pool of thiosulfate. Site-specific isotope fractionation (within thiosulfate) is very large (34ε ~ 30‰) while terminal product sulfide carries only a small fractionation from the initial sulfite (34ε < 10‰): a signature similar in magnitude to sulfate and thiosulfate reduction. Together these findings show that microbial sulfate reduction (MSR) is highly sensitive to the concentration of environmentally important sulfur-cycle intermediates (sulfite and thiosulfate), especially when thiosulfate and the large site-specific isotope effects are involved. PMID:25505449

  6. Multiple sulfur isotope signatures of sulfite and thiosulfate reduction by the model dissimilatory sulfate-reducer, Desulfovibrio alaskensis str. G20.

    PubMed

    Leavitt, William D; Cummins, Renata; Schmidt, Marian L; Sim, Min S; Ono, Shuhei; Bradley, Alexander S; Johnston, David T

    2014-01-01

    Dissimilatory sulfate reduction serves as a key metabolic carbon remineralization process in anoxic marine environments. Sulfate reducing microorganisms can impart a wide range in mass-dependent sulfur isotopic fractionation. As such, the presence and relative activity of these organisms is identifiable from geological materials. By extension, sulfur isotope records are used to infer the redox balance of marine sedimentary environments, and the oxidation state of Earth's oceans and atmosphere. However, recent work suggests that our understanding of microbial sulfate reduction (MSRs) may be missing complexity associated with the presence and role of key chemical intermediates in the reductive process. This study provides a test of proposed metabolic models of sulfate reduction by growing an axenic culture of the well-studied MSRs, Desulfovibrio alaskensis strain G20, under electron donor limited conditions on the terminal electron acceptors sulfate, sulfite or thiosulfate, and tracking the multiple S isotopic consequences of each condition set. The dissimilatory reduction of thiosulfate and sulfite produce unique minor isotope effects, as compared to the reduction of sulfate. Further, these experiments reveal a complex biochemistry associated with sulfite reduction. That is, under high sulfite concentrations, sulfur is shuttled to an intermediate pool of thiosulfate. Site-specific isotope fractionation (within thiosulfate) is very large ((34)ε ~ 30‰) while terminal product sulfide carries only a small fractionation from the initial sulfite ((34)ε < 10‰): a signature similar in magnitude to sulfate and thiosulfate reduction. Together these findings show that microbial sulfate reduction (MSR) is highly sensitive to the concentration of environmentally important sulfur-cycle intermediates (sulfite and thiosulfate), especially when thiosulfate and the large site-specific isotope effects are involved.

  7. Marine Bacteria from Danish Coastal Waters Show Antifouling Activity against the Marine Fouling Bacterium Pseudoalteromonas sp. Strain S91 and Zoospores of the Green Alga Ulva australis Independent of Bacteriocidal Activity▿†

    PubMed Central

    Bernbom, Nete; Ng, Yoke Yin; Kjelleberg, Staffan; Harder, Tilmann; Gram, Lone

    2011-01-01

    The aims of this study were to determine if marine bacteria from Danish coastal waters produce antifouling compounds and if antifouling bacteria could be ascribed to specific niches or seasons. We further assess if antibacterial effect is a good proxy for antifouling activity. We isolated 110 bacteria with anti-Vibrio activity from different sample types and locations during a 1-year sampling from Danish coastal waters. The strains were identified as Pseudoalteromonas, Phaeobacter, and Vibrionaceae based on phenotypic tests and partial 16S rRNA gene sequence similarity. The numbers of bioactive bacteria were significantly higher in warmer than in colder months. While some species were isolated at all sampling locations, others were niche specific. We repeatedly isolated Phaeobacter gallaeciensis at surfaces from one site and Pseudoalteromonas tunicata at two others. Twenty-two strains, representing the major taxonomic groups, different seasons, and isolation strategies, were tested for antiadhesive effect against the marine biofilm-forming bacterium Pseudoalteromonas sp. strain S91 and zoospores of the green alga Ulva australis. The antiadhesive effects were assessed by quantifying the number of strain S91 or Ulva spores attaching to a preformed biofilm of each of the 22 strains. The strongest antifouling activity was found in Pseudoalteromonas strains. Biofilms of Pseudoalteromonas piscicida, Pseudoalteromonas tunicata, and Pseudoalteromonas ulvae prevented Pseudoalteromonas S91 from attaching to steel surfaces. P. piscicida killed S91 bacteria in the suspension cultures, whereas P. tunicata and P. ulvae did not; however, they did prevent adhesion by nonbactericidal mechanism(s). Seven Pseudoalteromonas species, including P. piscicida and P. tunicata, reduced the number of settling Ulva zoospores to less than 10% of the number settling on control surfaces. The antifouling alpP gene was detected only in P. tunicata strains (with purple and yellow pigmentation), so

  8. Evidence that crude oil alkane activation proceeds by different mechanisms under sulfate-reducing and methanogenic conditions

    NASA Astrophysics Data System (ADS)

    Aitken, C. M.; Jones, D. M.; Maguire, M. J.; Gray, N. D.; Sherry, A.; Bowler, B. F. J.; Ditchfield, A. K.; Larter, S. R.; Head, I. M.

    2013-05-01

    Fumarate addition has been widely proposed as an initial step in the anaerobic oxidation of both aromatic and aliphatic hydrocarbons. Alkyl and aryl succinates have been reported as metabolites of hydrocarbon degradation in laboratory studies with both pure and enrichment cultures of sulfate-, nitrate-, and iron-reducing bacteria. In addition these compounds have been reported in samples from environments such as hydrocarbon contaminated aquifers where, in addition to the above redox processes, hydrocarbon degradation linked to methanogenesis was observed. Here we report data from anaerobic crude oil degrading microcosms which revealed significant differences between the acid metabolite profiles of crude oil degraded under sulfate-reducing or methanogenic conditions. Under sulfate-reducing conditions fumarate addition and the formation of alkylsuccinate metabolites was the principal mechanism for the anaerobic degradation of n-alkanes and branched chain alkanes. Other than alkyl succinates that represent indigenous metabolites in the sediment inoculum, alkyl succinate metabolites were never detected in sediment microcosms where methane generation was quantitatively linked to n-alkane degradation. This indicates that alternative mechanisms of alkane activation may operate under methanogenic conditions.

  9. [Inhibition of the activity of sulfate-reducing bacteria in produced water from oil reservoir by nitrate].

    PubMed

    Yang, De-Yu; Zhang, Ying; Shi, Rong-Jiu; Han, Si-Qin; Li, Guang-Zhe; Li, Guo-Qiao; Zhao, Jin-Yi

    2014-01-01

    Growth and metabolic activity of sulfate-reducing bacteria (SRB) can result in souring of oil reservoirs, leading to various problems in aspects of environmental pollution and corrosion. Nitrate addition and management of nitrate-reducing bacteria (NRB) offer potential solutions to controlling souring in oil reservoirs. In this paper, a facultive chemolithotrophic NRB, designated as DNB-8, was isolated from the produced fluid of a water-flooded oil reservoir at Daqing oilfield. Then the efficacies and mechanisms of various concentrations of nitrate in combination with DNB-8 in the inhibition of the activity of SRB enriched culture were compared. Results showed that 1.0 mmol x L(-1) of nitrate or 0.45 mmol x L(-1) of nitrite inhibited the sulfate-reducing activity of SRB enrichments; the competitive reduction of nitrate by DNB-8 and the nitrite produced were responsible for the suppression. Besides, the SRB enrichment cultures showed a metabolic pathway of dissimilatory nitrate reduction to ammonium (DNRA) via nitrite. The SRB cultures could possibly alleviate the nitrite inhibition by DNRA when they were subjected to high-strength nitrate.

  10. Example study for granular bioreactor stratification: Three-dimensional evaluation of a sulfate-reducing granular bioreactor

    PubMed Central

    Hao, Tian-wei; Luo, Jing-hai; Su, Kui-zu; Wei, Li; Mackey, Hamish R.; Chi, Kun; Chen, Guang-Hao

    2016-01-01

    Recently, sulfate-reducing granular sludge has been developed for application in sulfate-laden water and wastewater treatment. However, little is known about biomass stratification and its effects on the bioprocesses inside the granular bioreactor. A comprehensive investigation followed by a verification trial was therefore conducted in the present work. The investigation focused on the performance of each sludge layer, the internal hydrodynamics and microbial community structures along the height of the reactor. The reactor substratum (the section below baffle 1) was identified as the main acidification zone based on microbial analysis and reactor performance. Two baffle installations increased mixing intensity but at the same time introduced dead zones. Computational fluid dynamics simulation was employed to visualize the internal hydrodynamics. The 16S rRNA gene of the organisms further revealed that more diverse communities of sulfate-reducing bacteria (SRB) and acidogens were detected in the reactor substratum than in the superstratum (the section above baffle 1). The findings of this study shed light on biomass stratification in an SRB granular bioreactor to aid in the design and optimization of such reactors. PMID:27539264

  11. Removal of chromium and lead by a sulfate-reducing consortium using peat moss as carbon source.

    PubMed

    Márquez-Reyes, Julia Mariana; López-Chuken, Ulrico Javier; Valdez-González, Arcadio; Luna-Olvera, Hugo Alberto

    2013-09-01

    The effect of pre-treated peat moss on the ability of a sulfate-reducing microbial consortium to remove chromium and lead in solution was evaluated. The most active bacterial community (235.7 mmol H2S/g VSS) was selected from among eight consortia. The peat moss was pre-treated with different HCl concentrations and contact times. The best combination of treatments was 20% HCl for 10 min. The constant substrate affinity Ks was 740 mg COD/L and the ratio COD/SO4(2-) was 0.71. At pH 5, higher production of biogenic sulfide was observed. The up-flowpacked bed bioreactor operated at a flow of 8.3 mL/min for 180 h to obtain removal efficiency (by sulfate-reducing activity) of 90% lead and 65% chromium. It is important to consider that peat moss is a natural adsorbent that further influences the removal efficiency of metal ions.

  12. Sulfur Isotropic Studies of Archean Slate and Graywacke from Northern Minnesota: Evidence for the Existence of Sulfate Reducing Bacteria

    NASA Technical Reports Server (NTRS)

    Ripley, E. M.; Nicol, D. L.

    1979-01-01

    Sulfur isotopic studies of pyrite from metasediments in the 2.6 b.y. old Deer Lake greenstone sequence, Minnesota, were conducted in order to evaluate the possible importance of sulfate reducing bacteria in sulfide formation. Pyrite occurs as ovules up to 2 cm in diameter within graphitic slates, and as fine disseminations in metagraywacke units. SEM studies indicate the pyrite is framboidal in morphology. Delta notation values of pyrite from the Deer Lake sediments range from -2.3 to 11.1 0/00, with a peak at approximately +2 o/oo. Isotopic data is consistent with either high temperature inorganic reduction of circulating seawater sulfate, or low temperature bacterial reduction. However, the lack of sulfide bands or massive occurrences in the sediments, the restriction of pyrite mineralization to the sediments, and the absence of evidence for hot spring activity suggest that a diagenetic origin of pyrite is more feasible. Sulfide in such an environment would be produced principally by the action of sulfate reducing bacteria.

  13. Enhanced bioremediation of heavy metal from effluent by sulfate-reducing bacteria with copper-iron bimetallic particles support.

    PubMed

    Zhou, Qin; Chen, Yongzhe; Yang, Ming; Li, Wenkai; Deng, Le

    2013-05-01

    The purpose of this study was to investigate the potential of copper-iron bimetallic particles supported sulfate-reducing bacteria (SRB) in enhancing the reduction of Cu(2+) and Zn(2+) in effluent. The results showed that the copper-iron bimetallic particles can enhance Cu(2+) and Zn(2+) removal and the resistance of the sulfate-reducing bacteria towards metals toxicity, the inhibiting concentration of Cu(2+) and Zn(2+) for SRB was significantly increased (from 100 to 200 mg/L for Cu(2+) and 300 to 400 mg/L for Zn(2+)). The removal efficiencies of Cu(2+) and Zn(2+) (initial concentration 100 mg/L) were 98.17% and 99.67% in SRB-Cu/Fe system after 48 h, while only 29.83% Cu(2+), 90.88% Zn(2+) and 63.81% Cu(2+), 72.63% Zn(2+) were removed in the SRB and Cu/Fe system at the same condition.

  14. Example study for granular bioreactor stratification: Three-dimensional evaluation of a sulfate-reducing granular bioreactor

    NASA Astrophysics Data System (ADS)

    Hao, Tian-Wei; Luo, Jing-Hai; Su, Kui-Zu; Wei, Li; Mackey, Hamish R.; Chi, Kun; Chen, Guang-Hao

    2016-08-01

    Recently, sulfate-reducing granular sludge has been developed for application in sulfate-laden water and wastewater treatment. However, little is known about biomass stratification and its effects on the bioprocesses inside the granular bioreactor. A comprehensive investigation followed by a verification trial was therefore conducted in the present work. The investigation focused on the performance of each sludge layer, the internal hydrodynamics and microbial community structures along the height of the reactor. The reactor substratum (the section below baffle 1) was identified as the main acidification zone based on microbial analysis and reactor performance. Two baffle installations increased mixing intensity but at the same time introduced dead zones. Computational fluid dynamics simulation was employed to visualize the internal hydrodynamics. The 16S rRNA gene of the organisms further revealed that more diverse communities of sulfate-reducing bacteria (SRB) and acidogens were detected in the reactor substratum than in the superstratum (the section above baffle 1). The findings of this study shed light on biomass stratification in an SRB granular bioreactor to aid in the design and optimization of such reactors.

  15. Evaluating zinc isotope fractionation under sulfate reducing conditions using a flow-through cell and in situ XAS analysis

    NASA Astrophysics Data System (ADS)

    Jamieson-Hanes, Julia H.; Shrimpton, Heather K.; Veeramani, Harish; Ptacek, Carol J.; Lanzirotti, Antonio; Newville, Matthew; Blowes, David W.

    2017-04-01

    A flow-through cell experiment was conducted to evaluate Zn isotope fractionation during ZnS precipitation under microbially-mediated sulfate-reducing conditions. Synthetic groundwater containing 0.90 mM Zn was pumped through a cell containing creek sediment that was biostimulated to promote sulfate reducing conditions. Real-time, in situ X-ray absorption spectroscopy (XAS) was applied at the Zn K-edge to collect spectra via a Kapton® window in the front of the cell over the course of the experiment. Aqueous effluent samples were collected and analysed to determine concentrations of anions and cations, and Zn isotope ratios. The flow rate was increased step-wise during the experiment to modify the residence time and produce changes in the extent of sulfate reduction, which in turn controlled the extent of ZnS precipitation. Greater enrichment in the heavier isotope in the aqueous phase relative to the input solution was associated with more extensive Zn removal. A Rayleigh curve was fit to the isotope data, where ε = -0.27 ± 0.06‰ (2σ). Evaluation of Zn isotope fractionation under controlled flow conditions is critical to improve the efficacy of this powerful analytical technique when applied to natural systems or remediation projects in the field.

  16. Temperature and pressure adaptation of a sulfate reducer from the deep subsurface

    PubMed Central

    Fichtel, Katja; Logemann, Jörn; Fichtel, Jörg; Rullkötter, Jürgen; Cypionka, Heribert; Engelen, Bert

    2015-01-01

    Microbial life in deep marine subsurface faces increasing temperatures and hydrostatic pressure with depth. In this study, we have examined growth characteristics and temperature-related adaptation of the Desulfovibrio indonesiensis strain P23 to the in situ pressure of 30 MPa. The strain originates from the deep subsurface of the eastern flank of the Juan de Fuca Ridge (IODP Site U1301). The organism was isolated at 20°C and atmospheric pressure from ~61°C-warm sediments approximately 5 m above the sediment–basement interface. In comparison to standard laboratory conditions (20°C and 0.1 MPa), faster growth was recorded when incubated at in situ pressure and high temperature (45°C), while cell filamentation was induced by further compression. The maximum growth temperature shifted from 48°C at atmospheric pressure to 50°C under high-pressure conditions. Complementary cellular lipid analyses revealed a two-step response of membrane viscosity to increasing temperature with an exchange of unsaturated by saturated fatty acids and subsequent change from branched to unbranched alkyl moieties. While temperature had a stronger effect on the degree of fatty acid saturation and restructuring of main phospholipids, pressure mainly affected branching and length of side chains. The simultaneous decrease of temperature and pressure to ambient laboratory conditions allowed the cultivation of our moderately thermophilic strain. This may in turn be one key to a successful isolation of microorganisms from the deep subsurface adapted to high temperature and pressure. PMID:26500624

  17. A genomic island of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough promotes survival under stress conditions while decreasing the efficiency of anaerobic growth.

    PubMed

    Johnston, Shawna; Lin, Shiping; Lee, Phoebe; Caffrey, Sean M; Wildschut, Janine; Voordouw, Johanna K; da Silva, Sofia M; Pereira, Ines A C; Voordouw, Gerrit

    2009-04-01

    A 47 kb genomic island (GEI) bracketed by 50 bp direct repeats, containing 52 annotated genes, was found to delete spontaneously from the genome of Desulfovibrio vulgaris Hildenborough. The island contains genes for site-specific recombinases and transposases, rubredoxin:oxygen oxidoreductase-1 (Roo1) and hybrid cluster protein-1 (Hcp1), which promote survival in air and nitrite stress. The numbering distinguishes these from the Roo2 and Hcp2 homologues for which the genes are located elsewhere in the genome. Cells with and without the island (GEI(+) and GEI(-) cells respectively) were obtained by colony purification. GEI(-) cells arise in anaerobic cultures of colony-purified GEI(+) cells, indicating that the site-specific recombinases encoded by the island actively delete this region. GEI(+) cells survive better in microaerophilic conditions due to the presence of Roo1, whereas the Hcps appear to prevent inhibition by sulfur and polysulfide, which are formed by chemical reaction of sulfide and nitrite. Hence, the island confers resistance to oxygen and nitrite stress. However, GEI(-) cells have a higher growth rate in anaerobic media. Microarrays and enzyme activity stains indicated that the GEI(-) cells have increased expression of genes, which promote anaerobic energy conservation, explaining the higher growth rate. Hence, while lowering the efficiency of anaerobic metabolism, the GEI increases the fitness of D. vulgaris under stress conditions, a feature reminiscent of pathogenicity islands which allow more effective colonization of environments provided by the targeted hosts.

  18. Purification, crystallization and preliminary X-ray diffraction analysis of adenosine triphosphate sulfurylase (ATPS) from the sulfate-reducing bacterium Desulfovibrio desulfuricans ATCC 27774

    SciTech Connect

    Gavel, Olga Yu.; Kladova, Anna V.; Bursakov, Sergey A.; Dias, João M.; Texeira, Susana; Shnyrov, Valery L.; Moura, José J. G.; Moura, Isabel; Romão, Maria J.; Trincão, José

    2008-07-01

    Native zinc-containing ATP sulfurylase from D. desulfuricans ATCC 27774 was purified to homogeneity and crystallized. Diffraction data were collected to 2.5 Å resolution. Native zinc/cobalt-containing ATP sulfurylase (ATPS; EC 2.7.7.4; MgATP:sulfate adenylyltransferase) from Desulfovibrio desulfuricans ATCC 27774 was purified to homogeneity and crystallized. The orthorhombic crystals diffracted to beyond 2.5 Å resolution and the X-ray data collected should allow the determination of the structure of the zinc-bound form of this ATPS. Although previous biochemical studies of this protein indicated the presence of a homotrimer in solution, a dimer was found in the asymmetric unit. Elucidation of this structure will permit a better understanding of the role of the metal in the activity and stability of this family of enzymes.

  19. Identification of bacteria in enrichment cultures of sulfate reducers in the Cariaco Basin water column employing Denaturing Gradient Gel Electrophoresis of 16S ribosomal RNA gene fragments

    PubMed Central

    2013-01-01

    Background The Cariaco Basin is characterized by pronounced and predictable vertical layering of microbial communities dominated by reduced sulfur species at and below the redox transition zone. Marine water samples were collected in May, 2005 and 2006, at the sampling stations A (10°30′ N, 64°40′ W), B (10°40′ N, 64°45′ W) and D (10°43’N, 64°32’W) from different depths, including surface, redox interface, and anoxic zones. In order to enrich for sulfate reducing bacteria (SRB), water samples were inoculated into anaerobic media amended with lactate or acetate as carbon source. To analyze the composition of enrichment cultures, we performed DNA extraction, PCR-DGGE, and sequencing of selected bands. Results DGGE results indicate that many bacterial genera were present that are associated with the sulfur cycle, including Desulfovibrio spp., as well as heterotrophs belonging to Vibrio, Enterobacter, Shewanella, Fusobacterium, Marinifilum, Mariniliabilia, and Spirochaeta. These bacterial populations are related to sulfur coupling and carbon cycles in an environment of variable redox conditions and oxygen availability. Conclusions In our studies, we found an association of SRB-like Desulfovibrio with Vibrio species and other genera that have a previously defined relevant role in sulfur transformation and coupling of carbon and sulfur cycles in an environment where there are variable redox conditions and oxygen availability. This study provides new information about microbial species that were culturable on media for SRB at anaerobic conditions at several locations and water depths in the Cariaco Basin. PMID:23981583

  20. Mono- and Dialkyl Glycerol Ether Lipids in Anaerobic Bacteria: Biosynthetic Insights from the Mesophilic Sulfate Reducer Desulfatibacillum alkenivorans PF2803T

    PubMed Central

    Mollex, Damien; Vinçon-Laugier, Arnauld; Hakil, Florence; Pacton, Muriel; Cravo-Laureau, Cristiana

    2015-01-01

    Bacterial glycerol ether lipids (alkylglycerols) have received increasing attention during the last decades, notably due to their potential role in cell resistance or adaptation to adverse environmental conditions. Major uncertainties remain, however, regarding the origin, biosynthesis, and modes of formation of these uncommon bacterial lipids. We report here the preponderance of monoalkyl- and dialkylglycerols (1-O-alkyl-, 2-O-alkyl-, and 1,2-O-dialkylglycerols) among the hydrolyzed lipids of the marine mesophilic sulfate-reducing proteobacterium Desulfatibacillum alkenivorans PF2803T grown on n-alkenes (pentadec-1-ene or hexadec-1-ene) as the sole carbon and energy source. Alkylglycerols account for one-third to two-thirds of the total cellular lipids (alkylglycerols plus acylglycerols), depending on the growth substrate, with dialkylglycerols contributing to one-fifth to two-fifths of the total ether lipids. The carbon chain distribution of the lipids of D. alkenivorans also depends on that of the substrate, but the chain length and methyl-branching patterns of fatty acids and monoalkyl- and dialkylglycerols are systematically congruent, supporting the idea of a biosynthetic link between the three classes of compounds. Vinyl ethers (1-alken-1′-yl-glycerols, known as plasmalogens) are not detected among the lipids of strain PF2803T. Cultures grown on different (per)deuterated n-alkene, n-alkanol, and n-fatty acid substrates further demonstrate that saturated alkylglycerols are not formed via the reduction of hypothetic alken-1′-yl intermediates. Our results support an unprecedented biosynthetic pathway to monoalkyl/monoacyl- and dialkylglycerols in anaerobic bacteria and suggest that n-alkyl compounds present in the environment can serve as the substrates for supplying the building blocks of ether phospholipids of heterotrophic bacteria. PMID:25724965

  1. Genes for Uranium Bioremediation in the Anaerobic Sulfate-Reducing Bacteria: Desulfovibrio mutants with altered sensitivity to oxidative stress

    SciTech Connect

    Payne, Rayford B.; Ringbauer, Joseph A., Jr.; Wall, Judy D.

    2006-04-05

    Sulfate-reducing bacteria of the genus Desulfovibrio are ubiquitous in anaerobic environments such as groundwater, sediments, and the gastrointestinal tract of animals. Because of the ability of Desulfovibrio to reduce radionuclides and metals through both enzymatic and chemical means, they have been proposed as a means to bioremediate heavy metal contaminated sites. Although classically thought of as strict anaerobes, Desulfovibrio species are surprisingly aerotolerant. Our objective is to understand the response of Desulfovibrio to oxidative stress so that we may more effectively utilize them in bioremediation of heavy metals in mixed aerobic-anaerobic environments. The enzymes superoxide dismutase, superoxide reductase, catalase, and rubrerythrin have been shown by others to be involved in the detoxification of reactive oxygen species in Desulfovibrio. Some members of the genus Desulfovibrio can even reduce molecular oxygen to water via a membrane bound electron transport chain with the concomitant production of ATP, although their ability to grow with oxygen as the sole electron acceptor is still questioned.

  2. Enhanced performance of sulfate reducing bacteria based biocathode using stainless steel mesh on activated carbon fabric electrode.

    PubMed

    Sharma, Mohita; Jain, Pratiksha; Varanasi, Jhansi L; Lal, Banwari; Rodríguez, Jorge; Lema, Juan M; Sarma, Priyangshu M

    2013-12-01

    An anoxic biocathode was developed using sulfate-reducing bacteria (SRB) consortium on activated carbon fabric (ACF) and the effect of stainless steel (SS) mesh as additional current collector was investigated. Improved performance of biocathode was observed with SS mesh leading to nearly five folds increase in power density (from 4.79 to 23.11 mW/m(2)) and threefolds increase in current density (from 75 to 250 mA/m(2)). Enhanced redox currents and lower Tafel slopes observed from cyclic voltammograms of ACF with SS mesh indicated the positive role of uniform electron collecting points. Differential pulse voltammetry technique was employed as an additional tool to assess the redox carriers involved in bioelectrochemical reactions. SRB biocathode was also tested for reduction of volatile fatty acids (VFA) present in the fermentation effluent stream and the results indicated the possibility of integration of this system with anaerobic fermentation for efficient product recovery.

  3. Tailoring partially reduced graphene oxide as redox mediator for enhanced biotransformation of iopromide under methanogenic and sulfate-reducing conditions.

    PubMed

    Toral-Sánchez, Eduardo; Rangel-Mendez, J Rene; Ascacio Valdés, Juan A; Aguilar, Cristóbal N; Cervantes, Francisco J

    2016-10-22

    This work reports the first successful application of graphene oxide (GO) and partially reduced GO (rGO) as redox mediator (RM) to increase the biotransformation of the recalcitrant iodinated contrast medium, iopromide (IOP). Results showed that GO-based materials promoted up to 5.5 and 2.8-fold faster biotransformation of IOP by anaerobic sludge under methanogenic and sulfate-reducing conditions, respectively. Correlation between the extent of reduction of GO and its redox-mediating capacity was demonstrated, which was reflected in faster removal and greater extent of biotransformation of IOP. Further analysis indicated that the biotransformation pathway of IOP involved multiple reactions including deiodination, decarboxylation, demethylation, dehydration and N-dealkylation. GO-based materials could be strategically tailored and integrated in biological treatment systems to effectively enhance the redox conversion of recalcitrant pollutants commonly found in wastewater treatment systems and industrial effluents.

  4. Quorum Sensing and the Use of Quorum Quenchers as Natural Biocides to Inhibit Sulfate-Reducing Bacteria

    PubMed Central

    Scarascia, Giantommaso; Wang, Tiannyu; Hong, Pei-Ying

    2016-01-01

    Sulfate-reducing bacteria (SRB) are one of the main protagonist groups of biocorrosion in the seawater environment. Given their principal role in biocorrosion, it remains a crucial task to develop strategies to reduce the abundance of SRBs. Conventional approaches include the use of biocides and antibiotics, which can impose health, safety, and environmental concerns. This review examines an alternative approach to this problem. This is achieved by reviewing the role of quorum sensing (QS) in SRB populations and its impact on the biofilm formation process. Genome databases of SRBs are mined to look for putative QS systems and homologous protein sequences representative of autoinducer receptors or synthases. Subsequently, this review puts forward the potential use of quorum quenchers as natural biocides against SRBs and outlines the potential strategies for the implementation of this approach. PMID:27983678

  5. Growth of Anaerobic Methane-Oxidizing Archaea and Sulfate-Reducing Bacteria in a High-Pressure Membrane Capsule Bioreactor

    PubMed Central

    Gieteling, Jarno; Widjaja-Greefkes, H. C. Aura; Plugge, Caroline M.; Stams, Alfons J. M.; Lens, Piet N. L.; Meulepas, Roel J. W.

    2014-01-01

    Communities of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB) grow slowly, which limits the ability to perform physiological studies. High methane partial pressure was previously successfully applied to stimulate growth, but it is not clear how different ANME subtypes and associated SRB are affected by it. Here, we report on the growth of ANME-SRB in a membrane capsule bioreactor inoculated with Eckernförde Bay sediment that combines high-pressure incubation (10.1 MPa methane) and thorough mixing (100 rpm) with complete cell retention by a 0.2-μm-pore-size membrane. The results were compared to previously obtained data from an ambient-pressure (0.101 MPa methane) bioreactor inoculated with the same sediment. The rates of oxidation of labeled methane were not higher at 10.1 MPa, likely because measurements were done at ambient pressure. The subtype ANME-2a/b was abundant in both reactors, but subtype ANME-2c was enriched only at 10.1 MPa. SRB at 10.1 MPa mainly belonged to the SEEP-SRB2 and Eel-1 groups and the Desulfuromonadales and not to the typically found SEEP-SRB1 group. The increase of ANME-2a/b occurred in parallel with the increase of SEEP-SRB2, which was previously found to be associated only with ANME-2c. Our results imply that the syntrophic association is flexible and that methane pressure and sulfide concentration influence the growth of different ANME-SRB consortia. We also studied the effect of elevated methane pressure on methane production and oxidation by a mixture of methanogenic and sulfate-reducing sludge. Here, methane oxidation rates decreased and were not coupled to sulfide production, indicating trace methane oxidation during net methanogenesis and not anaerobic methane oxidation, even at a high methane partial pressure. PMID:25501484

  6. Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions.

    PubMed

    Kwon, Man Jae; O'Loughlin, Edward J; Boyanov, Maxim I; Brulc, Jennifer M; Johnston, Eric R; Kemner, Kenneth M; Antonopoulos, Dionysios A

    2016-01-01

    Although iron- and sulfate-reducing bacteria in subsurface environments have crucial roles in biogeochemical cycling of C, Fe, and S, how specific electron donors impact the compositional structure and activity of native iron- and/or sulfate-reducing communities is largely unknown. To understand this better, we created bicarbonate-buffered batch systems in duplicate with three different electron donors (acetate, lactate, or glucose) paired with ferrihydrite and sulfate as the electron acceptors and inoculated them with subsurface sediment as the microbial inoculum. Sulfate and ferrihydrite reduction occurred simultaneously and were faster with lactate than with acetate. 16S rRNA-based sequence analysis of the communities over time revealed that Desulfotomaculum was the major driver for sulfate reduction coupled with propionate oxidation in lactate-amended incubations. The reduction of sulfate resulted in sulfide production and subsequent abiotic reduction of ferrihydrite. In contrast, glucose promoted faster reduction of ferrihydrite, but without reduction of sulfate. Interestingly, the glucose-amended incubations led to two different biogeochemical trajectories among replicate bottles that resulted in distinct coloration (white and brown). The two outcomes in geochemical evolution might be due to the stoc