Kinetic Analysis of Competition Between Sulfate Reducers and Methanogens for Hydrogen in Sediments

The competition between sulfate-reducing and methanogenic bacteria for hydrogen was investigated in eutrophic lake sediments that contained low in situ sulfate concentrations and in sulfate-amended sediments. Sulfate reduction and methane production coexisted in situ in lake surface sediments (0 to 2 cm), but methane production was the dominant terminal process. Addition of 10 to 20 mM sulfate to sediments resulted in a decrease in the hydrogen partial pressure and a concomitant inhibition of methane production over time. Molybdate inhibition of sulfate reduction in sulfate-amended sediments was followed by an increase in the hydrogen partial pressure and the methane production rate to values comparable to those in sediments not amended with sulfate. The sulfate reducer population had a half-saturation constant for hydrogen uptake of 141 pascals versus 597 pascals for the methanogen population. Thus, when sulfate was not limiting, the lower half-saturation constant of sulfate reducers enabled them to inhibit methane production by lowering the hydrogen partial pressure below levels that methanogens could effectively utilize. However, methanogens coexisted with sulfate reducers in the presence of sulfate, and the outcome of competition at any time was a function of the rate of hydrogen production, the relative population sizes, and sulfate availability.     

Methylmercury Decomposition in Sediments and Bacterial Cultures: Involvement of Methanogens and Sulfate Reducers in Oxidative Demethylation

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.     

Penetration of Sulfate Reducers through a Porous North Sea Oil Reservoir

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.     

Estimation of Bacterial Nitrate Reduction Rates at In Situ Concentrations in Freshwater Sediments

A method was developed to follow bacterial nitrate reduction in freshwater sediments by using common high-performance liquid chromatographic equipment. The low detection limit (14 pmol) of the method enabled us to study concentration profiles and reaction kinetics under natural conditions. Significant nitrate concentrations (1 to 27 μM) were observed in the sediment of Lake Vechten during the nonstratified period; the concentration profiles showed a successive depletion of oxygen, nitrate, and sulfate with depth. The profiles were restricted to the upper 3 cm of the sediment which is rich in organics and loosely structured. Nitrate reduction in the sediment-water interface followed first-order reaction kinetics at in situ concentrations. Remarkably high potential nitrate-reducing activity was observed in the part of the sediment in which nitrate did not diffuse. This activity was also observed throughout the whole year. Estimates of K_m varied between 17 and 100 μM and V_max varied between 7.2 and 36 μmol cm⁻³ day⁻¹ for samples taken at different depths. The diffusion coefficient of nitrate ([10 ± 0.4] × 10⁻⁶ cm² s⁻¹) across the sediment-water interface was estimated by a constant-source technique and applied to a mathematical model to estimate the net nitrate reduction during the nonstratified period. In this period, observed nitrate reduction rates by the model, 0.2 to 0.4 mmol m⁻² day⁻¹, were lower than those found for oxygen (27 mmol m⁻² day⁻¹) and sulfate (0.4 mmol m⁻² day⁻¹). During the summer stratification, nitrate was absent in the sediment and reduction could not be estimated by the model.     

Membrane Na+-pyrophosphatases Can Transport Protons at Low Sodium Concentrations

Membrane-bound Na⁺-pyrophosphatase (Na⁺-PPase), working in parallel with the corresponding ATP-energized pumps, catalyzes active Na⁺ transport in bacteria and archaea. Each ∼75-kDa subunit of homodimeric Na⁺-PPase forms an unusual funnel-like structure with a catalytic site in the cytoplasmic part and a hydrophilic gated channel in the membrane. Here, we show that at subphysiological Na⁺ concentrations (<5 mm), the Na⁺-PPases of Chlorobium limicola, four other bacteria, and one archaeon additionally exhibit an H⁺-pumping activity in inverted membrane vesicles prepared from recombinant Escherichia coli strains. H⁺ accumulation in vesicles was measured with fluorescent pH indicators. At pH 6.2–8.2, H⁺ transport activity was high at 0.1 mm Na⁺ but decreased progressively with increasing Na⁺ concentrations until virtually disappearing at 5 mm Na⁺. In contrast, ²²Na⁺ transport activity changed little over a Na⁺ concentration range of 0.05–10 mm. Conservative substitutions of gate Glu²⁴² and nearby Ser²⁴³ and Asn⁶⁷⁷ residues reduced the catalytic and transport functions of the enzyme but did not affect the Na⁺ dependence of H⁺ transport, whereas a Lys⁶⁸¹ substitution abolished H⁺ (but not Na⁺) transport. All four substitutions markedly decreased PPase affinity for the activating Na⁺ ion. These results are interpreted in terms of a model that assumes the presence of two Na⁺-binding sites in the channel: one associated with the gate and controlling all enzyme activities and the other located at a distance and controlling only H⁺ transport activity. The inherent H⁺ transport activity of Na⁺-PPase provides a rationale for its easy evolution toward specific H⁺ transport.     

Low-Molecular-Weight Sulfonates, a Major Substrate for Sulfate Reducers in Marine Microbial Mats

Several low-molecular-weight sulfonates were added to microbial mat slurries to investigate their effects on sulfate reduction. Instantaneous production of sulfide occurred after taurine and cysteate were added to all of the microbial mats tested. The rates of production in the presence of taurine and cysteate were 35 and 24 μM HS⁻ h⁻¹ in a stromatolite mat, 38 and 36 μM HS⁻ h⁻¹ in a salt pond mat, and 27 and 18 μM HS⁻ h⁻¹ in a salt marsh mat, respectively. The traditionally used substrates lactate and acetate stimulated the rate of sulfide production 3 to 10 times more than taurine and cysteate stimulated the rate of sulfide production in all mats, but when ethanol, glycolate, and glutamate were added to stromatolite mat slurries, the resulting increases were similar to the increases observed with taurine and cysteate. Isethionate, sulfosuccinate, and sulfobenzoate were tested only with the stromatolite mat slurry, and these compounds had much smaller effects on sulfide production. Addition of molybdate resulted in a greater inhibitory effect on acetate and lactate utilization than on sulfonate use, suggesting that different metabolic pathways were involved. In all of the mats tested taurine and cysteate were present in the pore water at nanomolar to micromolar concentrations. An enrichment culture from the stromatolite mat was obtained on cysteate in a medium lacking sulfate and incubated anaerobically. The rate of cysteate consumption by this enrichment culture was 1.6 pmol cell⁻¹ h⁻¹. Compared to the results of slurry studies, this rate suggests that organisms with properties similar to the properties of this enrichment culture are a major constituent of the sulfidogenic population. In addition, taurine was consumed at some of highest dilutions obtained from most-probable-number enrichment cultures obtained from stromatolite samples. Based on our comparison of the sulfide production rates found in various mats, low-molecular-weight sulfonates are important sources of C and S in these ecosystems.     

Sulfur-containing Compounds in Lemna perpusilla 6746 Grown at a Range of Sulfate Concentrations

Lemna perpusilla 6746, grown photoautotrophically at a series of sulfate concentrations ranging from 0.32 to 1,000 μm, was labeled to radioisotopic equilibrium with ³⁵SO₄²⁻. Sulfur-containing compounds were isolated and purified from the colonies. Radioactivity in each compound was a measure of the amount of that compound present in the tissue. The following compounds were identified and quantitated: inorganic sulfate, glutathione, homocyst(e)ine, cyst(e)ine, methionine, S-methylmethionine sulfonium, S-adenosylmethionine, S-adenosylhomocysteine, cystathionine, chloroformsoluble (presumed to be sulfolipid), protein cyst(e)ine, and protein methionine. γ-Glutamylcyst(e)ine, erythro- and threo-thiothreonine, and S-methylcysteine were not detected. No volatile ³⁵S compounds were formed during plant growth at 1,000 μm sulfate, nor were significant amounts of ³⁵S compounds excreted into the medium.     

Kinetics of Acetate Oxidation by Two Sulfate Reducers Isolated from Anaerobic Granular Sludge

Kinetic parameters of acetate oxidation were determined for the sulfate reducers Desulforhabdus amnigenus and Desulfobacca acetoxidans. Based on these parameters, both sulfate reducers seem to be able to outcompete Methanosaeta spp. for acetate in acetate-fed anaerobic bioreactors. Mixed-substrate studies showed that D. amnigenus degraded acetate and hydrogen simultaneously but preferred lactate, propionate, and ethanol over acetate.     

Sulfate Reduction in Freshwater Sediments Receiving Acid Mine Drainage

One arm of Lake Anna, Va., receives acid mine drainage (AMD) from Contrary Creek (SO₄²⁻ concentration = 2 to 20 mM, pH = 2.5 to 3.5). Acid-volatile sulfide concentrations, SO₄²⁻ reduction rates, and interstitial SO₄²⁻ concentrations were measured at various depths in the sediment at four stations in four seasons to assess the effects of the AMD-added SO₄²⁻ on bacterial SO₄²⁻ reduction. Acid-volatile sulfide concentrations were always an order of magnitude higher at the stations receiving AMD than at a control station in another arm of the lake that received no AMD. Summer SO₄²⁻ reduction rates were also an order of magnitude higher at stations that received AMD than at the control station (226 versus 13.5 mmol m⁻² day⁻¹), but winter values were inconclusive, probably due to low sediment temperature (6°C). Profiles of interstitial SO₄²⁻ concentrations at the AMD stations showed a rapid decrease with depth (from 1,270 to 6 μM in the top 6 cm) due to rapid SO₄²⁻ reduction. Bottom-water SO₄²⁻ concentrations in the AMD-receiving arm were highest in winter and lowest in summer. These data support the conclusion that there is a significant enhancement of SO₄²⁻ reduction in sediments receiving high SO₄²⁻ inputs from AMD.     

Role of Methanogens and Other Bacteria in Degradation of Dimethyl Sulfide and Methanethiol in Anoxic Freshwater Sediments

The roles of several trophic groups of organisms (methanogens and sulfate- and nitrate-reducing bacteria) in the microbial degradation of methanethiol (MT) and dimethyl sulfide (DMS) were studied in freshwater sediments. The incubation of DMS- and MT-amended slurries revealed that methanogens are the dominant DMS and MT utilizers in sulfate-poor freshwater systems. In sediment slurries, which were depleted of sulfate, 75 μmol of DMS was stoichiometrically converted into 112 μmol of methane. The addition of methanol or MT to DMS-degrading slurries at concentrations similar to that of DMS reduced DMS degradation rates. This indicates that the methanogens in freshwater sediments, which degrade DMS, are also consumers of methanol and MT. To verify whether a competition between sulfate-reducing and methanogenic bacteria for DMS or MT takes place in sulfate-rich freshwater systems, the effects of sulfate and inhibitors, like bromoethanesulfonic acid, molybdate, and tungstate, on the degradation of MT and DMS were studied. The results for these sulfate-rich and sulfate-amended slurry incubations clearly demonstrated that besides methanogens, sulfate-reducing bacteria take part in MT and DMS degradation in freshwater sediments, provided that sulfate is available. The possible involvement of an interspecies hydrogen transfer in these processes is discussed. In general, our study provides evidence for methanogenesis as a major sink for MT and DMS in freshwater sediments.     

Tropical Strains of Ralstonia solanacearum Outcompete Race 3 Biovar 2 Strains at Lowland Tropical Temperatures

Bacterial wilt, caused by members of the heterogenous Ralstonia solanacearum species complex, is an economically important vascular disease affecting many crops. Human activity has widely disseminated R. solanacearum strains, increasing their global agricultural impact. However, tropical highland race 3 biovar 2 (R3bv2) strains do not cause disease in tropical lowlands, even though they are virulent at warm temperatures. We tested the hypothesis that differences in temperature adaptation and competitive fitness explain the uneven geographic distribution of R. solanacearum strains. Using three phylogenetically and ecologically distinct strains, we measured competitive fitness at two temperatures following paired-strain inoculations of their shared host, tomato. Lowland tropical strain GMI1000 was only weakly virulent on tomato under temperate conditions (24°C for day and 19°C for night [24/19°C]), but highland tropical R3bv2 strain UW551 and U.S. warm temperate strain K60 were highly virulent at both 24/19°C and 28°C. Strain K60 was significantly more competitive than both GMI1000 and UW551 in tomato rhizospheres and stems at 28°C, and GMI1000 also outcompeted UW551 at 28°C. The results were reversed at cooler temperatures, at which highland strain UW551 generally outcompeted GMI1000 and K60 in planta. The superior competitive index of UW551 at 24/19°C suggests that adaptation to cool temperatures could explain why only R3bv2 strains threaten highland agriculture. Strains K60 and GMI1000 each produced different bacteriocins that inhibited growth of UW551 in culture. Such interstrain inhibition could explain why R3bv2 strains do not cause disease in tropical lowlands.     

Freshwater Bacteria Can Methylate Selenium through the Thiopurine Methyltransferase Pathway

Involvement of the bacterial thiopurine methyltransferase (bTPMT) in natural selenium methylation by freshwater was investigated. A freshwater environment that had no known selenium contamination but exhibited reproducible emission of dimethyl selenide (DMSe) or dimethyl diselenide (DMDSe) when it was supplemented with an organic form of selenium [(methyl)selenocysteine] or an inorganic form of selenium (sodium selenite) was used. The distribution of the bTPMT gene (tpm) in the microflora was studied. Freshwater bacteria growing on 10 μM sodium selenite and 10 μM sodium selenate were isolated, and 4.5 and 10% of the strains, respectively, were shown by colony blot hybridization to hybridize with a Pseudomonas syringae tpm DNA probe. Ribotyping showed that these strains are closely related. The complete rrs sequence of one of the strains, designated Hsa.28, was obtained and analyzed. Its closest phyletic neighbor was found to be the Pseudomonas anguilliseptica rrs sequence. The Hsa.28 strain grown with sodium selenite or (methyl)selenocysteine produced significant amounts of DMSe and DMDSe. The Hsa.28 tpm gene was isolated by genomic DNA library screening and sequencing. BLASTP comparisons of the deduced Hsa.28 bTPMT sequence with P. syringae, Pseudomonas aeruginosa, Vibrio cholerae, rat, and human thiopurine methyltransferase sequences revealed that the levels of similarity were 52 to 71%. PCR-generated Escherichia coli subclones containing the Hsa.28 tpm open reading frame were constructed. E. coli cells harboring the constructs and grown with sodium selenite or (methyl)selenocysteine produced significant levels of DMSe and DMDSe, confirming that the gene plays a role in selenium methylation. The effect of strain Hsa.28 population levels on freshwater DMSe and DMDSe emission was investigated. An increase in the size of the Hsa.28 population was found to enhance significantly the emission of methyl selenides by freshwater samples supplemented with sodium selenite or (methyl)selenocysteine. These data suggest that bTPMT can play a role in natural freshwater selenium methylation processes.     

High-Temperature Microbial Sulfate Reduction Can Be Accompanied by Magnetite Formation

The hyperthermophilic sulfate-reducing archaeon Archaeoglobus fulgidus was found to be capable of lithoautotrophic growth on medium containing molecular hydrogen, sulfate, and amorphous Fe(III) oxide. During the growth of this microorganism, amorphous Fe(III) oxide was transformed into black strongly magnetic precipitate rich in magnetite, as shown by Moessbauer studies. Experiments involving inhibition of microbial sulfate reduction and abiotic controls revealed that magnetite production resulted from chemical reactions proceeding at elevated temperatures (83°C) between molecular hydrogen, amorphous Fe(III) oxide, and sulfide formed enzymatically in the course of dissimilatory sulfate reduction. It follows that magnetite production in this system can be characterized as biologically mediated mineralization. This is the first report on magnetite formation as a result of activity of sulfate-reducing microorganisms.     

Effect of Low Sulfate Concentrations on Lactate Oxidation and Isotope Fractionation during Sulfate Reduction by Archaeoglobus fulgidus Strain Z

The effect of low substrate concentrations on the metabolic pathway and sulfur isotope fractionation during sulfate reduction was investigated for Archaeoglobus fulgidus strain Z. This archaeon was grown in a chemostat with sulfate concentrations between 0.3 mM and 14 mM at 80°C and with lactate as the limiting substrate. During sulfate reduction, lactate was oxidized to acetate, formate, and CO₂. This is the first time that the production of formate has been reported for A. fulgidus. The stoichiometry of the catabolic reaction was strongly dependent on the sulfate concentration. At concentrations of more than 300 μM, 1 mol of sulfate was reduced during the consumption of 1 mol of lactate, whereas only 0.6 mol of sulfate was consumed per mol of lactate oxidized at a sulfate concentration of 300 μM. Furthermore, at low sulfate concentrations acetate was the main carbon product, in contrast to the CO₂ produced at high concentrations. We suggest different pathways for lactate oxidation by A. fulgidus at high and low sulfate concentrations. At about 300 μM sulfate both the growth yield and the isotope fractionation were limited by sulfate, whereas the sulfate reduction rate was not limited by sulfate. We suggest that the cell channels more energy for sulfate uptake at sulfate concentrations below 300 to 400 μM than it does at higher concentrations. This could explain the shift in the metabolic pathway and the reduced growth yield and isotope fractionation at low sulfate levels.     

Kinetic Studies of Bacterial Sulfate Reduction in Freshwater Sediments by High-Pressure Liquid Chromatography and Microdistillation

Indirect photometric chromatography and microdistillation enabled a simultaneous measurement of sulfate depletion and sulfide production in the top 3 cm of freshwater sediments to be made. The simultaneous measurement of sulfate depletion and sulfide production rates provided added insight into microbial sulfur metabolism. The lower sulfate reduction rates, as derived from the production of acid-volatile ³⁵S²⁻ only, were explained by a conversion of this pool to an undistillable fraction under acidic conditions during incubation. A mathematical model was applied to calculate sulfate reduction from sulfate gradients at the sediment-water interface. To avoid disturbance of these gradients, the sample volume was reduced to 0.2 g (wet weight) of sediment. Sulfate diffusion coefficients in the model were determined (D_s = 0.3 × 10⁻⁵ cm² s⁻¹ at 6°C). The results of the model were compared with those of radioactive sulfate turnover experiments by assessing the actual turnover rate constants (2 to 5 day⁻¹) and pool sizes of sulfate at different sediment depths.     

Glucose in Freshwater of Central Amazon Lakes: Natural Substrate Concentrations Determined by Dilution Bioassay

A bioassay method has been employed to measure concentrations of glucose in the Central Amazon lakes. Michaelis-Menten enzyme kinetics parameters from the 14 bioassay measurements were made during this study. Concentrations of glucose found in Lago Tupé (10–485 μg/1)., Lago Cristalino (8–393 μg/1). and Lago Janauari (1-485 μg/1). are greater than anticipated. The bioassay method is applicable in determining concentrations of glucose in freshwater of the Central Amazon.