Biomedical subjects

J M Suflita

Publications and source records attributed to J M Suflita.

At least 19 recordsLinked to original sources

PubMed2004

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

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 Desulfovibrio vulgaris. 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-microm 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 Al2O3 content 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.

Aluminum Oxide↗

PubMed2003

Characterization of microbial activities and U reduction in a shallow aquifer contaminated by uranium mill tailings.

A characterization of the Shiprock, NM, uranium mill tailing site focused on the geochemical and microbiological factors governing in-situ uranium-redox reactions. Groundwater and aqueous extracts of sediment samples contained a wide concentration range of sulfate, nitrate, and U(VI) with median values of 21.2 mM, 16.1 micro M, and 2.7 micro M, respectively. Iron(III) was not detected in groundwater, but a median value of 0.3 mM in sediment extracts was measured. Bacterial diversity down gradient from the disposal pile reflected the predominant geochemistry with relatively high numbers of sulfate- and nitrate-reducing microorganisms, and smaller numbers of acetogenic, methanogenic, nitrate-dependent Fe(II)-oxidizing, Fe(III)-reducing, and sulfide-oxidizing bacteria. In aquifer slurry incubations, nitrate reduction was always preferred and had a negative impact on sulfate-, Fe(III)-, and U-reduction rates. We also found that sulfate-reduction rates decreased sharply in the presence of clay, while Fe(III)-reduction increased with no clear impact on U reduction. In the absence of clay, iron and sulfate reduction correlated with concentrations of Fe(III) and sulfate, respectively. Rates of U(VI) loss did not correlate with the concentration of any electron acceptor. With the exception of Fe(III), electron donor amendment was largely unsuccessful in stimulating electron acceptor loss over a 2-week incubation period, suggesting that endogenous forms of organic matter were sufficient to support microbial activity. Our findings suggest that efforts to accelerate biological U reduction should initially focus on stimulating nitrate removal.

Bacteria↗

PubMed2001

Signature metabolites attesting to the in situ attenuation of alkylbenzenes in anaerobic environments.

Accurate assessment of the fate of hydrocarbons spilt in aquifers is essential for gauging associated health and ecological risks. Regulatory pressure to actively remediate such contaminated ecosystems can be substantially diminished if solid evidence for in situ microbial destruction of pollutants is obtained. In laboratory incubations, sediment-associated microorganisms from a gas condensate-contaminated aquifer anaerobically biodegraded toluene, ethylbenzene, xylene, and toluic acid isomers with stoichiometric amounts of sulfate consumed or methane produced. The activation of the alkylated aromatic contaminants involved conversion to their corresponding benzylsuccinic acid derivatives, a reaction known to occur for toluene and m-xylene decay, but one previously unrecognized for ethylbenzene, o- and p-xylene, and m-toluate metabolism. Benzylsuccinates were further biodegraded to toluates, phthalates, and benzoate. In laboratory incubations, these metabolites were transiently produced. Several of the metabolites were also detected in groundwater samples from an aquifer where alkylbenzene concentrations decreased over time, suggesting that anaerobic microbial metabolism of these contaminants also occurs in situ. Our studies confirm the utility of the aforementioned compounds as signature metabolites attesting to the natural attenuation of aromatic hydrocarbons in anaerobic environments.

Bacteria, Anaerobic↗

PubMed2001

The influence of nitrate on microbial processes in oil industry production waters.

Sulfide accumulation due to bacterial sulfate reduction is responsible for a number of serious problems in the oil industry. Among the strategies to control the activity of sulfate-reducing bacteria (SRB) is the use of nitrate, which can exhibit a variety of effects. We investigated the relevance of this approach to souring oil fields in Oklahoma and Alberta in which water flooding is used to enhance oil recovery. SRB and nitrate-reducing bacteria (NRB) were enumerated in produced waters from both oil fields. In the Oklahoma field, the rates of sulfate reduction ranged from 0.05 to 0.16 microM S day(-1) at the wellheads, and an order of magnitude higher at the oil-water separator. Sulfide production was greatest in the water storage tanks in the Alberta field. Microbial counts alone did not accurately reflect the potential for microbial activities. The majority of the sulfide production appeared to occur after the oil was pumped aboveground, rather than in the reservoir. Laboratory experiments showed that adding 5 and 10 mM nitrate to produced waters from the Oklahoma and Alberta oil fields, respectively, decreased the sulfide content to negligible levels and increased the numbers of NRB. This work suggests that sulfate reduction control measures can be concentrated on aboveground facilities, which will decrease the amount of sulfide reinjected into reservoirs during the disposal of oil field production waters.

Alberta↗

PubMed2000

Anaerobic oxidation of n-dodecane by an addition reaction in a sulfate-reducing bacterial enrichment culture.

We identified trace metabolites produced during the anaerobic biodegradation of H(26)- and D(26)-n-dodecane by an enrichment culture that mineralizes these compounds in a sulfate-dependent fashion. The metabolites are dodecylsuccinic acids that, in the case of the perdeuterated substrate, retain all of the deuterium atoms. The deuterium retention and the gas chromatography-mass spectrometry fragmentation patterns of the derivatized metabolites suggest that they are formed by C---H or C---D addition across the double bond of fumarate. As trimethylsilyl esters, two nearly coeluting metabolites of equal abundance with nearly identical mass spectra were detected from each of H(26)- and D(26)-dodecane, but as methyl esters, only a single metabolite peak was detected for each parent substrate. An authentic standard of protonated n-dodecylsuccinic acid that was synthesized and derivatized by the two methods had the same fragmentation patterns as the metabolites of H(26)-dodecane. However, the standard gave only a single peak for each ester type and gas chromatographic retention times different from those of the derivatized metabolites. This suggests that the succinyl moiety in the dodecylsuccinic acid metabolites is attached not at the terminal methyl group of the alkane but at a subterminal position. The detection of two equally abundant trimethylsilyl-esterified metabolites in culture extracts suggests that the analysis is resolving diastereomers which have the succinyl moiety located at the same subterminal carbon in two different absolute configurations. Alternatively, there may be more than one methylene group in the alkane that undergoes the proposed fumarate addition reaction, giving at least two structural isomers in equal amounts.

Alkanes↗

PubMed1999

Estimation of methanogen biomass by quantitation of coenzyme M.

Determination of the role of methanogenic bacteria in an anaerobic ecosystem often requires quantitation of the organisms. Because of the extreme oxygen sensitivity of these organisms and the inherent limitations of cultural techniques, an accurate biomass value is very difficult to obtain. We standardized a simple method for estimating methanogen biomass in a variety of environmental matrices. In this procedure we used the thiol biomarker coenzyme M (CoM) (2-mercaptoethanesulfonic acid), which is known to be present in all methanogenic bacteria. A high-performance liquid chromatography-based method for detecting thiols in pore water (A. Vairavamurthy and M. Mopper, Anal. Chim. Acta 78:363-370, 1990) was modified in order to quantify CoM in pure cultures, sediments, and sewage water samples. The identity of the CoM derivative was verified by using liquid chromatography-mass spectroscopy. The assay was linear for CoM amounts ranging from 2 to 2,000 pmol, and the detection limit was 2 pmol of CoM/ml of sample. CoM was not adsorbed to sediments. The methanogens tested contained an average of 19.5 nmol of CoM/mg of protein and 0.39 +/- 0.07 fmol of CoM/cell. Environmental samples contained an average of 0.41 +/- 0.17 fmol/cell based on most-probable-number estimates. CoM was extracted by using 1% tri-(N)-butylphosphine in isopropanol. More than 90% of the CoM was recovered from pure cultures and environmental samples. We observed no interference from sediments in the CoM recovery process, and the method could be completed aerobically within 3 h. Freezing sediment samples resulted in 46 to 83% decreases in the amounts of detectable CoM, whereas freezing had no effect on the amounts of CoM determined in pure cultures. The method described here provides a quick and relatively simple way to estimate methanogenic biomass.

Biomass↗

PubMed1999

Characterization of two subsurface H2-utilizing bacteria, Desulfomicrobium hypogeium sp. nov. and Acetobacterium psammolithicum sp. nov., and their ecological roles.

We examined the relative roles of acetogenic and sulfate-reducing bacteria in H2 consumption in a previously characterized subsurface sandstone ecosystem. Enrichment cultures originally inoculated with ground sandstone material obtained from a Cretaceous formation in central New Mexico were grown with hydrogen in a mineral medium supplemented with 0.02% yeast extract. Sulfate reduction and acetogenesis occurred in these cultures, and the two most abundant organisms carrying out the reactions were isolated. Based on 16S rRNA analysis data and on substrate utilization patterns, these organisms were named Desulfomicrobium hypogeium sp. nov. and Acetobacterium psammolithicum sp. nov. The steady-state H2 concentrations measured in sandstone-sediment slurries (threshold concentration, 5 nM), in pure cultures of sulfate reducers (threshold concentration, 2 nM), and in pure cultures of acetogens (threshold concentrations 195 to 414 nM) suggest that sulfate reduction is the dominant terminal electron-accepting process in the ecosystem examined. In an experiment in which direct competition for H2 between D. hypogeium and A. psammolithicum was examined, sulfate reduction was the dominant process.

DNA, Bacterial↗

PubMed1999

Cresol metabolism by the sulfate-reducing bacterium Desulfotomaculum sp. strain Groll.

The metabolism of cresols under sulfate-reducing conditions was investigated in Desulfotomaculum sp. strain Groll. This strain grows on a variety of aromatic compounds, including para- and meta- but not ortho-cresol. Degradation of p-cresol proceeded by oxidation reactions of the methyl group to yield p-hydroxybenzoate, which was then dehydroxylated to benzoate. The aromatic intermediates expected for this pathway, p-hydroxybenzyl alcohol, p-hydroxybenzaldehyde, p-hydroxybenzoate, and benzoate, were readily metabolized by strain Groll. Utilization of these intermediates generally preceded and inhibited the degradation of p-cresol. p-Hydroxybenzoate and benzoate were detected in culture fluid as metabolites of p-cresol. p-Hydroxybenzaldehyde and p-hydroxybenzoate were detected in cultures degrading p-hydroxybenzyl alcohol. Enzyme activities responsible for utilization of p- and m-cresol, induced by growth on the respective cresol, were detected in cell-free extracts of strain Groll. The compounds detected in culture fluids and the enzyme activities detected in cell-free extracts indicate that the pathways for the degradation of p- and m-cresol converge on benzoate, followed by metabolism to benzoyl-coenzyme A (CoA). Strain Groll can utilize both cresol isomers under sulfate-reducing conditions by similar reactions, but the enzyme activities catalyzing these transformations of the two isomers appear distinct.

Anaerobiosis↗

PubMed1997

Anaerobic aquifer transformations of 2,4-dinitrophenol under different terminal electron accepting conditions.

We evaluated the susceptibility of 2,4-dinitrophenol (2,4-DNP) and 2,4-diaminophenol to anaerobic biodegradation in aquifer slurries. Aquifer microorganisms depleted 2,4-DNP at rates of 25, 9 and 0.4 microM/day under methanogenic, sulfate-reducing and nitrate-reducing conditions, respectively. Rates of abiotic, 2,4-DNP loss in autoclaved control incubations were 7.2, 6.2 and 0.95 microM/day respectively. Abiotic, 2,4-DNP reduction was especially important as the first step in its transformation. 2-Amino-4-nitrophenol was produced by this process, but this compound was further metabolized in methanogenic and sulfate-reducing aquifer slurries. This partially reduced compound persisted in autoclaved controls and in the nitrate-reducing aquifer slurries. Aquifer slurries incubated with either 2,4-DNP or 2,4-diaminophenol produced methane when incubated with no other electron acceptor suggesting that mineralization had occurred under these conditions. In parallel experiments, aquifer slurries amended with 2,6-dinitrophenol or picric acid did not produce methane at levels above the substrate unamended controls.

Journal Article↗

PubMed1997

A rapid and simple method for estimating sulfate reduction activity and quantifying inorganic sulfides.

Volume, 63, no. 4, p. 1627-1630. After publication of this article, it was brought to the attention of the authors that an earlier paper, similar in both methodology and salient findings to ours, was published by Y. P. Hsieh and C. H. Yang. Both papers describe a diffusion method for the extraction and recovery of reduced inorganic sulfides from sediment samples placed in sealed reaction vessels. Our paper describes the application of the method to the measurement of sulfate reduction rates. The earlier work contains important information, but unfortunately, the existence of the work was realized only after publication of our paper. We regret this omission, and the following reference should have been cited in our article. 13a.Hsieh, Y. P., and C. H. Yang. 1989. Diffusion methods for the determination of reduced inorganic sulfur species in sediments. Limnol. Oceanogr. 34: 1126-1130. [This corrects the article on p. 1627 in vol. 63.].

Journal Article↗

PubMed1997

A rapid and simple method for estimating sulfate reduction activity and quantifying inorganic sulfides.

A simplified passive extraction procedure for quantifying reduced inorganic sulfur compounds from sediments and water is presented. This method may also be used for the estimation of sulfate reduction rates. Efficient extraction of FeS, FeS(inf2), and S(sup2-) was obtained with this procedure; however, the efficiency for S(sup0) depended on the form that was tested. Passive extraction can be used with samples containing up to 20 mg of reduced sulfur. We demonstrated the utility of this technique in a determination of both sulfate reduction rates and reduced inorganic sulfur pools in marine and freshwater sediments. A side-by-side comparison of the passive extraction method with the established single-step distillation technique yielded comparable results with a fraction of the effort.

Journal Article↗

PubMed1997

Reductive dehalogenation and mineralization of 3-chlorobenzoate in the presence of sulfate by microorganisms from a methanogenic aquifer.

We investigated the anaerobic biodegradation of 3-chlorobenzoate (3CBz) by microorganisms from an aquifer where chloroaromatic compounds were previously found to resist decay in the presence of sulfate. After a lengthy lag period, 3CBz was degraded in the presence of sulfate and concurrently with sulfate reduction. Chlorine removal from 2,5- or 3,5-dichlorobenzoates and the transient appearance of benzoate from 3CBz confirmed that reductive dehalogenation was the initial fate process for these substrates. Sulfate did not influence 3CBz degradation rates in acclimated enrichment cultures but accelerated the development of 3CBz degradation activity in fresh transfers. Benzoate degradation was more rapid in the presence of sulfate regardless of the enrichment history. Nitrate, sulfite, and a headspace of air inhibited 3CBz dehalogenation, while thiosulfate had no effect. Mass balance determinations revealed that 71 to 107% of the theoretically expected amount of methane was produced from 3CBz and benzoate oxidation in the absence of sulfate. In parallel cultures containing 15 mM sulfate, methanogenesis was reduced to 48 to 71% of that theoretically expected, while sulfate reduction accounted for 12 to 50% of the reducing equivalents. In either the presence or absence of sulfate, steady-state dissolved hydrogen concentrations were similar to those reported for sulfate-reducing or methanogenic environments, respectively. Molybdate inhibited sulfate reduction and 3CBz dehalogenation to a similar extent but did not affect benzoate biodegradation. Sulfate-dependent 3CBz biodegradation was not observed. We conclude that reductive dehalogenation and sulfate reduction occur concurrently in these enrichments and that the sulfate-dependent stimulation in fresh transfers was likely due to the acceleration of benzoate oxidation.

Journal Article↗

PubMed1997

Anaerobic Degradation of m-Cresol by a Sulfate-Reducing Bacterium.

m-Cresol metabolism under sulfate-reducing conditions was studied with a pure culture of Desulfotomaculum sp. strain Groll. Previous studies with a sulfate-reducing consortium indicated that m-cresol was degraded via an initial para-carboxylation reaction. However, 4-hydroxy-2-methylbenzoic acid was not degraded by strain Groll, and no evidence for ring carboxylation of m-cresol was found. Strain Groll readily metabolized the putative metabolites of a methyl group oxidation pathway, including 3-hydroxybenzyl alcohol, 3-hydroxybenzaldehyde, 3-hydroxybenzoic acid, and benzoic acid. Degradation of these compounds preceded and inhibited m-cresol decay. 3-Hydroxybenzoic acid was detected in cultures that received either m-cresol or 3-hydroxybenzyl alcohol, and trace amounts of benzoic acid were detected in m-cresol-degrading cultures. Therefore, we propose that strain Groll metabolizes m-cresol by a methyl group oxidation pathway which is an alternate route for the catabolism of this compound under sulfate-reducing conditions.

Journal Article↗

PubMed1997

Influence of sulfur oxyanions on reductive dehalogenation activities in Desulfomonile tiedjei.

The inhibition of aryl reductive dehalogenation reactions by sulfur oxyanions has been demonstrated in environmental samples, dehalogenating enrichments, and the sulfate-reducing bacterium Desulfomonile tiedjei; however, this phenomenon is not well understood. We examined the effects of sulfate, sulfite, and thiosulfate on reductive dehalogenation in the model microorganism D. tiedjei and found separate mechanisms of inhibition due to these oxyanions under growth versus nongrowth conditions. Dehalogenation activity was greatly reduced in extracts of cells grown in the presence of both 3-chlorobenzoate, the substrate or inducer for the aryl dehalogenation activity, and either sulfate, sulfite, or thiosulfate, indicating that sulfur oxyanions repress the requisite enzymes. In extracts of fully induced cells, thiosulfate and sulfite, but not sulfate, were potent inhibitors of aryl dehalogenation activity even in membrane fractions lacking the cytoplasmically located sulfur oxyanion reductase. These results suggest that under growth conditions, sulfur oxyanions serve as preferred electron acceptors and negatively influence dehalogenation activity in D. tiedjei by regulating the amount of active aryl dehalogenase in cells. Additionally, in vitro inhibition by sulfur oxyanions is due to the interaction of the reactive species with enzymes involved in dehalogenation and need not involve competition between two respiratory processes for reducing equivalents. Sulfur oxyanions also inhibited tetrachloroethylene dehalogenation by the same mechanisms, further indicating that chloroethylenes are fortuitously dehalogenated by the aryl dehalogenase. The commonly observed inhibition of reductive dehalogenation reactions under sulfate-reducing conditions may be due to similar regulation mechanisms in other dehalogenating microorganisms that contain multiple respiratory activities.

Anions↗

PubMed1996

Interspecies acetate transfer influences the extent of anaerobic benzoate degradation by syntrophic consortia.

Benzoate degradation by an anaerobic, syntrophic bacterium, strain SB, in coculture with Desulfovibrio sp. strain G-11 reached a threshold value which depended on the amount of acetate added and ranged from about 2.5 to 29.9 (mu)M. Increasing acetate concentrations also uncompetitively inhibited benzoate degradation. The apparent V(infmax) and apparent K(infm) for benzoate degradation decreased with increasing acetate concentration, but the benzoate degradation capacities (V(infmax)/K(infm)) of cell suspensions remained comparable. The addition of an acetate-using bacterium to cocultures after the threshold was reached resulted in the degradation of benzoate to below the detection limit. Mathematical simulations showed that the benzoate threshold was not predicted by the inhibitory effect of acetate on benzoate degradation kinetics. With nitrate instead of sulfate as the terminal electron acceptor, no benzoate threshold was observed in the presence of 20 mM acetate even though the kinetics of benzoate degradation were slower with nitrate rather than sulfate as the electron acceptor. When strain SB was grown with Desulfovibrio sp. strain DG2 that had a fourfold-lower V(infmax) for hydrogen use than strain G-11, the V(infmax) for benzoate degradation was 37-fold lower than that of strain SB-G-11 cocultures. The Gibb's free energy for benzoate degradation was less negative in cell suspensions with a threshold than in suspensions without a threshold. These studies showed that the threshold was not a function of the inhibition of benzoate degradation by acetate or the toxicity of the undissociated form of acetate. Rather, a critical or minimal Gibb's free energy may exist where thermodynamic constraints preclude further benzoate degradation.

Journal Article↗

PubMed1996

The importance of hydrogen in landfill fermentations.

Forty-two samples taken from two landfills were monitored for CH(inf4) production and apparent steady-state H(inf2) concentration. The rates of methanogenesis in these samples ranged from below the detection limit to 1,900 (mu)mol kg (dry weight)(sup-1) day(sup-1), and the median steady-state hydrogen concentration was 1.4 (mu)M in one landfill and 5.2 (mu)M in the other. To further investigate the relationship between hydrogen concentration and methanogenesis, a subset of seven landfill samples was selected on basis of their rates of CH(inf4) production, H(inf2) concentrations, sample pHs, and moisture contents. Samples with H(inf2) concentrations of <20 nM had relatively small amounts of volatile fatty acids (VFAs) (undetectable to 18.6 mmol of VFA kg [dry weight](sup-1)), while samples with H(inf2) concentrations of >100 nM had relatively high VFA levels (133 to 389 mmol of VFA kg [dry weight](sup-1)). Samples with high H(inf2) and VFA contents had relatively low pH values (<=6.3). However, methanogenic and syntrophic bacteria were present in all samples, so the lack of methanogenesis in some samples was not due to a lack of suitable inocula. The low rates of methanogenesis in these samples were probably due to inhibitory effects of low pH and VFA accumulation, resulting from a thermodynamic uncoupling of fatty acid oxidation. As in other anaerobic ecosystems, H(inf2) is a critical intermediate that may be used to monitor the status of landfill fermentations.

Journal Article↗

PubMed1996

Characterization of Chloroethylene Dehalogenation by Cell Extracts of Desulfomonile tiedjei and Its Relationship to Chlorobenzoate Dehalogenation.

We characterized the reductive dehalogenation of tetrachloroethylene in cell extracts of Desulfomonile tiedjei and compared it with this organism's 3-chlorobenzoate dehalogenation activity. Tetrachloroethylene was sequentially dehalogenated to trichloro- and dichloroethylene; there was no evidence for dichloroethylene dehalogenation. Like the previously characterized 3-chlorobenzoate dehalogenation activity, tetrachloroethylene dehalogenation was heat sensitive, not oxygen labile, and increased in proportion to the amount of protein in assay mixtures. In addition, both dehalogenation activities were dependent on hydrogen or formate as an electron donor and had an absolute requirement for either methyl viologen or triquat as an electron carrier in vitro. Both activities appear to be catalyzed by integral membrane proteins with similar solubilization characteristics. Dehalogenation of tetrachloroethylene was inhibited by 3-chlorobenzoate but not by the structural isomers 2- and 4-chlorobenzoate. The last two compounds are not substrates for D. tiedjei. These findings lead us to suggest that the dehalogenation of tetrachloroethylene in D. tiedjei is catalyzed by a dehalogenase previously thought to be specific for meta-halobenzoates.

Journal Article↗

PubMed1994

Anaerobic biodegradation of methyl esters by Acetobacterium woodii and Eubacterium limosum.

The ability of Acetobacterium woodii and Eubacterium limosum to degrade methyl esters of acetate, propionate, butyrate, and isobutyrate was examined under growing and resting-cell conditions. Both bacteria hydrolyzed the esters to the corresponding carboxylates and methanol under either condition. Methanol was further oxidized to formate under growing but not resting conditions. Unlike the metabolism of phenylmethylethers, no H2 requirement was evident for ester biotransformation. The hydrolysis of methyl carboxylates is thermodynamically favorable under standard conditions and the mixotrophic metabolism of ester/CO2 allowed for bacterial growth. These results suggest that the degradation of methyl carboxylates may be a heretofore unrecognized nutritional option for acetogenic bacteria.

Acetates↗