Substrates for Sulfate Reduction and Methane Production in Intertidal Sediments

The activity of and potential substrates for methane-producing bacteria and sulfate-reducing bacteria were examined in marsh, estuary, and beach intertidal sediments. Slow rates of methane production were detected in all sediments, although rates of sulfate reduction were 100- to 1,000-fold higher. After sulfate was depleted in sediments, the rates of methane production sharply increased. The addition of methylamine stimulated methanogenesis in the presence of sulfate, and [¹⁴C]methylamine was rapidly converted to ¹⁴CH₄ and ¹⁴CO₂ in freshly collected marsh sediment. Acetate, hydrogen, or methionine additions did not stimulate methanogenesis. [methyl-¹⁴C]methionine and [2-¹⁴C]acetate were converted to ¹⁴CO₂ and not to ¹⁴CH₄ in fresh sediment. No reduction of ¹⁴CO₂ to ¹⁴CH₄ occurred in fresh sediment. Molybdate, an inhibitor of sulfate reduction, inhibited [2-¹⁴C]acetate metabolism by 98.5%. Fluoracetate, an inhibitor of acetate metabolism, inhibited sulfate reduction by 61%. These results suggest that acetate is a major electron donor for sulfate reduction in marine sediments. In the presence of high concentrations of sulfate, methane may be derived from novel substrates such as methylamine.     

Organic Matter Mineralization with Reduction of Ferric Iron in Anaerobic Sediments

The potential for ferric iron reduction with fermentable substrates, fermentation products, and complex organic matter as electron donors was investigated with sediments from freshwater and brackish water sites in the Potomac River Estuary. In enrichments with glucose and hematite, iron reduction was a minor pathway for electron flow, and fermentation products accumulated. The substitution of amorphous ferric oxyhydroxide for hematite in glucose enrichments increased iron reduction 50-fold because the fermentation products could also be metabolized with concomitant iron reduction. Acetate, hydrogen, propionate, butyrate, ethanol, methanol, and trimethylamine stimulated the reduction of amorphous ferric oxyhydroxide in enrichments inoculated with sediments but not in uninoculated or heat-killed controls. The addition of ferric iron inhibited methane production in sediments. The degree of inhibition of methane production by various forms of ferric iron was related to the effectiveness of these ferric compounds as electron acceptors for the metabolism of acetate. The addition of acetate or hydrogen relieved the inhibition of methane production by ferric iron. The decrease of electron equivalents proceeding to methane in sediments supplemented with amorphous ferric oxyhydroxides was compensated for by a corresponding increase of electron equivalents in ferrous iron. These results indicate that iron reduction can outcompete methanogenic food chains for sediment organic matter. Thus, when amorphous ferric oxyhydroxides are available in anaerobic sediments, the transfer of electrons from organic matter to ferric iron can be a major pathway for organic matter decomposition.     

Methanogenesis and Sulfate Reduction: Competitive and Noncompetitive Substrates in Estuarine Sediments

Sulfate ions did not inhibit methanogenesis in estuarine sediments supplemented with methanol, trimethylamine, or methionine. However, sulfate greatly retarded methanogenesis when hydrogen or acetate was the substrate. Sulfate reduction was stimulated by acetate, hydrogen, and acetate plus hydrogen, but not by methanol or trimethylamine. These results indicate that sulfate-reducing bacteria will outcompete methanogens for hydrogen, acetate, or both, but will not compete with methanogens for compounds like methanol, trimethylamine, or methionine, thereby allowing methanogenesis and sulfate reduction to operate simultaneously within anoxic, sulfate-containing sediments.     

Availability of Ferric Iron for Microbial Reduction in Bottom Sediments of the Freshwater Tidal Potomac River

The distribution of Fe(III), its availability for microbial reduction, and factors controlling Fe(III) availability were investigated in sediments from a freshwater site in the Potomac River Estuary. Fe(III) reduction in sediments incubated under anaerobic conditions and depth profiles of oxalate-extractable Fe(III) indicated that Fe(III) reduction was limited to depths of 4 cm or less, with the most intense Fe(III) reduction in the top 1 cm. In incubations of the upper 4 cm of the sediments, Fe(III) reduction was as important as methane production as a pathway for anaerobic electron flow because of the high rates of Fe(III) reduction in the 0- to 0.5-cm interval. Most of the oxalate-extractable Fe(III) in the sediments was not reduced and persisted to a depth of at least 20 cm. The incomplete reduction was not the result of a lack of suitable electron donors. The oxalate-extractable Fe(III) that was preserved in the sediments was considered to be in a form other than amorphous Fe(III) oxyhydroxide, since synthetic amorphous Fe(III) oxyhydroxide, amorphous Fe(III) oxyhydroxide adsorbed onto clay, and amorphous Fe(III) oxyhydroxide saturated with adsorbed phosphate or fulvic acids were all readily reduced. Fe₃O₄ and the mixed Fe(III)-Fe(II) compound(s) that were produced during the reduction of amorphous Fe(III) oxyhydroxide in an enrichment culture were oxalate extractable but were not reduced, suggesting that mixed Fe(III)-Fe(II) compounds might account for the persistence of oxalate-extractable Fe(III) in the sediments. The availability of microbially reducible Fe(III) in surficial sediments demonstrates that microbial Fe(III) reduction can be important to organic matter decomposition and iron geochemistry. However, the overall extent of microbial Fe(III) reduction is governed by the inability of microorganisms to reduce most of the Fe(III) in the sediment.     

Reduction of Ferric Iron in Anaerobic, Marine Sediment and Interaction with Reduction of Nitrate and Sulfate

Studies were carried out to elucidate the nature and importance of Fe³⁺ reduction in anaerobic slurries of marine surface sediment. A constant accumulation of Fe²⁺ took place immediately after the endogenous NO₃⁻ was depleted. Pasteurized controls showed no activity of Fe³⁺ reduction. Additions of 0.2 mM NO₃⁻ and NO₂⁻ to the active slurries arrested the Fe³⁺ reduction, and the process was resumed only after a depletion of the added compounds. Extended, initial aeration of the sediment did not affect the capacity for reduction of NO₃⁻ and Fe³⁺, but the treatments with NO₃⁻ increased the capacity for Fe³⁺ reduction. Addition of 20 mM MoO₄²⁻ completely inhibited the SO₄²⁻ reduction, but did not affect the reduction of Fe³⁺. The process of Fe³⁺ reduction was most likely associated with the activity of facultative anaerobic, NO₃⁻-reducing bacteria. In surface sediment, the bulk of the Fe³⁺ reduction may be microbial, and the process may be important for mineralization in situ if the availability of NO₃⁻ is low.     

Rapid Assay for Microbially Reducible Ferric Iron in Aquatic Sediments

The availability of ferric iron for microbial reduction as directly determined by the activity of iron-reducing organisms was compared with its availability as determined by a newly developed chemical assay for microbially reducible iron. The chemical assay was based on the reduction of poorly crystalline ferric iron by hydroxylamine under acidic conditions. There was a strong correlation between the extent to which hydroxylamine could reduce various synthetic ferric iron forms and the susceptibility of the iron to microbial reduction in an enrichment culture of iron-reducing organisms. When sediments that contained hydroxylamine-reducible ferric iron were incubated under anaerobic conditions, ferrous iron accumulated as the concentration of hydroxylamine-reducible ferric iron declined over time. Ferrous iron production stopped as soon as the hydroxylamine-reducible ferric iron was depleted. In anaerobic incubations of reduced sediments that did not contain hydroxylamine-reducible ferric iron, there was no microbial iron reduction, even though the sediments contained high concentrations of oxalate-extractable ferric iron. A correspondence between the presence of hydroxylamine-reducible ferric iron and the extent of ferric iron reduction in anaerobic incubations was observed in sediments from an aquifer and in fresh- and brackish-water sediments from the Potomac River estuary. The assay is a significant improvement over previously described procedures for the determination of hydroxylamine-reducible ferric iron because it provides a correction for the high concentrations of solid ferrous iron which may also be extracted from sediments with acid. This is a rapid, simple technique to determine whether ferric iron is available for microbial reduction.     

Synergistic Competitive Inhibition of Ferrous Iron Oxidation by Thiobacillus ferrooxidans by Increasing Concentrations of Ferric Iron and Cells

Oxidation of ferrous iron by Thiobacillus ferrooxidans SM-4 was inhibited competitively by increasing concentrations of ferric iron or cells. A kinetic analysis showed that binding of one inhibitor did not exclude binding of the other and led to synergistic inhibition by the two inhibitors. Binding of one inhibitor, however, was affected by the other inhibitor, and the apparent inhibition constant increased with increasing concentrations of the other inhibitor.     

Iron Additions Reduce Sulfate Reduction Rates and Improve Seagrass Growth on Organic-Enriched Carbonate Sediments

Here we demonstrate, through experimental iron additions to a Mediterranean seagrass meadow, that iron plays a pivotal role in seagrass systems on carbonate sediments, directly through its role as a limiting nutrient, and indirectly by stimulating phosphorus recycling through the activity of the enzyme alkaline phosphatase and by buffering the development of reduced conditions in sediments. Iron additions were performed throughout the active root zone (30 cm depth) to two Posidonia oceanica meadows, one on organic-enriched sediments and one on organic poor sediments (Reference). Seagrass growth, nutrient incorporation and sediment biogeochemical conditions were followed for four months. Iron additions had positive effects on seagrass growth (leaf production increased with 55%) and nutrient incorporation (increased 46–91%) in the organic-enriched site, increasing to levels found at the Reference site. There was no effect of iron additions in the Reference seagrass meadow suggesting that iron was not the most important controlling factor at this site. The iron pools were about two times higher compared to the organic-enriched site. The main effect on the sediment biogeochemical conditions at the organic-enriched site was a suppression of sulfate reduction activity to the levels encountered at the Reference site (6.7 mmol m⁻²d⁻¹ vs. 4.7–5.9 mmol m⁻²d⁻¹). This suggests that the sulfide stress on the seagrasses was removed and that the iron availability increased due to reduced precipitation of iron-sulfides and thus improving seagrass growth conditions in these organic-enriched sediments.     

Sulfate Reduction Relative to Methane Production in High-Rate Anaerobic Digestion: Microbiological Aspects

In the high-rate anaerobic reactors studied (ca. 10 g of chemical oxygen demand [COD] removed per liter of reactor per day), the sulfate-reducing bacteria (SRB) were poor competitors of methane-producing bacteria (MPB), scavenging only on the order of 10 to 20% of the total electron flow. The relatively noncompetitive nature of the SRB in this type of reactor is in sharp contrast to the tendency of the SRB to dominate in natural environments and in other types of anaerobic digesters. Various factors such as the feedback inhibition of H₂S on the SRB, iron limitation, the origin of the SRB inocula, biokinetics, and thermodynamics were investigated. The outcome of the SRB-MPB competition under the reactor conditions studied appeared to be particularly determined by two factors. The SRB, as predicted by the V_max-K_m kinetics, competed most effectively at low substrate levels (<0.5 g of COD per liter). The MPB, however, appeared to colonize and adhere much more effectively to the polyurethane carrier matrix present in the reactor, thus compensating for the apparent lower growth rates. Even if the reactor was initially allowed to be predominantly colonized by SRB, the MPB could regain dominance.     

Sulfate Reduction Relative to Methane Production in High-Rate Anaerobic Digestion: Technical Aspects

The effect of different substrates and different levels of sulfate and sulfide on methane production relative to sulfate reduction in high-rate anaerobic digestion was evaluated. Reactors could be acclimated so that sulfate up to a concentration of 5 g of sulfate S per liter did not significantly affect methanogenesis. Higher levels gave inhibition because of salt toxicity. Sulfate reduction was optimal at a relatively low level of sulfate, i.e., 0.5 g of sulfate S per liter, but was also not significantly affected by higher levels. Both acetoclastic and hydrogenotrophic methane-producing bacteria adapted to much higher levels of free H₂S than the values reported in the literature (50% inhibition occurred only at free H₂S levels of more than 1,000 mg/liter). High levels of free H₂S affected the sulfate-reducing bacteria only slightly. Formate and acetate supported the sulfate-reducing bacteria very poorly. In the high-rate reactors studied, intensive H₂S formation occurred only when H₂ gas or an H₂ precursor such as ethanol was supplied.     

Effects of Temperature and Pressure on Sulfate Reduction and Anaerobic Oxidation of Methane in Hydrothermal Sediments of Guaymas Basin

Rates of sulfate reduction (SR) and anaerobic oxidation of methane (AOM) in hydrothermal deep-sea sediments from Guaymas Basin were measured at temperatures of 5 to 200°C and pressures of 1 × 10⁵, 2.2 × 10⁷, and 4.5 × 10⁷ Pa. A maximum SR of several micromoles per cubic centimeter per day was found at between 60 and 95°C and 2.2 × 10⁷ and 4.5 × 10⁷ Pa. Maximal AOM was observed at 35 to 90°C but generally accounted for less than 5% of SR.     

Dynamics of Methane Production, Sulfate Reduction, and Denitrification in a Permanently Waterlogged Alder Swamp

The dynamics of sulfate reduction, methane production, and denitrification were investigated in a permanently waterlogged alder swamp. Molybdate, an inhibitor of sulfate reduction, stimulated methane production in soil slurries, thus suggesting competition for common substrates between sulfate-reducing and methane-producing bacteria. Acetate, hydrogen, and methanol were found to stimulate both sulfate reduction and methane production, while trimethylamine mainly stimulated methane production. Nitrate addition reduced both methane production and sulfate reduction, either as a consequence of competition or poisoning of the bacteria. Sulfate-reducing bacteria were only slightly limited by the availability of electron acceptors, while denitrifying bacteria were seriously limited by low nitrate concentrations. Arrhenius plots of the three processes revealed different responses to temperature changes in the slurries. Methane production was most sensitive to temperature changes, followed by denitrification and sulfate reduction. No significant differences between slope patterns were observed when comparing summer and winter measurements, indicating similar populations regarding temperature responses.     

Microbial Manganese and Sulfate Reduction in Black Sea Shelf Sediments

The microbial ecology of anaerobic carbon oxidation processes was investigated in Black Sea shelf sediments from mid-shelf with well-oxygenated bottom water to the oxic-anoxic chemocline at the shelf-break. At all stations, organic carbon (C_org) oxidation rates were rapidly attenuated with depth in anoxically incubated sediment. Dissimilatory Mn reduction was the most important terminal electron-accepting process in the active surface layer to a depth of ~1 cm, while SO₄²⁻ reduction accounted for the entire C_org oxidation below. Manganese reduction was supported by moderately high Mn oxide concentrations. A contribution from microbial Fe reduction could not be discerned, and the process was not stimulated by addition of ferrihydrite. Manganese reduction resulted in carbonate precipitation, which complicated the quantification of C_org oxidation rates. The relative contribution of Mn reduction to C_org oxidation in the anaerobic incubations was 25 to 73% at the stations with oxic bottom water. In situ, where Mn reduction must compete with oxygen respiration, the contribution of the process will vary in response to fluctuations in bottom water oxygen concentrations. Total bacterial numbers as well as the detection frequency of bacteria with fluorescent in situ hybridization scaled to the mineralization rates. Most-probable-number enumerations yielded up to 10⁵ cells of acetate-oxidizing Mn-reducing bacteria (MnRB) cm⁻³, while counts of Fe reducers were <10² cm⁻³. At two stations, organisms affiliated with Arcobacter were the only types identified from 16S rRNA clone libraries from the highest positive MPN dilutions for MnRB. At the third station, a clone type affiliated with Pelobacter was also observed. Our results delineate a niche for dissimilatory Mn-reducing bacteria in sediments with Mn oxide concentrations greater than ~10 μmol cm⁻³ and indicate that bacteria that are specialized in Mn reduction, rather than known Mn and Fe reducers, are important in this niche.     

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.     

Methane Production in Shallow-Water, Tropical Marine Sediments

The in situ production of methane was monitored in several types of tropical benthic communities. A bed of Thalassia testudinum located in Caesar Creek (Florida Keys) exhibited the highest methanogenic activity (initial rates = 1.81 to 1.86 mumol CH4/m2 per h) as compared with another seagrass (Syringodium sp., 0.15 to 0.33 mumol/m2 per h) and two coral reef environments (Hydro-Lab, 0.016 to 0.10 mumol/m2 per h; Curacao, 0.14 to 0.47 mumol/m2 per h). The results suggest that a wide variety of benthic metabolic processes (e.g., photosynthetic oxygen production) influences methane production rates.     

The Process of Microbial Sulfate Reduction in Sediments of the Coastal Zone and Littoral of the Kandalaksha Bay of the White Sea

Microbiological and biogeochemical investigations of the coastal zone and the littoral of the Kandalaksha Bay of the White Sea were carried out. The material for investigations was obtained in the series of expeditions of the Institute of Microbiology, Russian Academy of Sciences, in August 1999, 2000, 2001, and in March 2003. The studies were conducted on the littoral and in the water area of the Kandalaksha Preserve, the Moscow University Belomorsk Biological Station, and the Zoological Institute Biological Station, Russian Academy of Sciences. Sediment sampling on the littoral was carried out in the typical microlandscapes differing in the sediment properties and macrobenthos distribution. The maximal sulfate reduction rate (SRR) was shown for the shallow part of the Chernorechenskaya Bay (up to 2550 g S/(dm³ day)) and in the Bab'ye More Bay (up to 3191 g S/(dm³ day)). During the winter season, at a temperature of –0.5 × 0.5°C, the SRR in the sediments of the Kartesh Bay was 7.9 × 13 g S/(dm³ day). In the widest limits, the SRR values varied in the sediment cores sampled on the littoral. The minimal values (11 g S/(dm³ day)) were obtained in the core samples on the silt–sandy littoral. The littoral finely dispersed sediments rich in organic matter were characterized by high SRR values (524–1413 g S/(dm³ day)). The maximal SRR values were shown for the sediments present within the stretch of decomposing macrophytes, in local pits at the lower littoral waterline, and in the mouth of a freshwater stream (51–159 mg S/(dm³ day)). A sharp difference in the level of H₂S production in the type microlandscapes was shown. The average hydrogen sulfide production in finely dispersed sediments constituted 125 mg S/(m² day); in stormy discharge deposits, 1950 mg S/(m² day); in depressions under stones and in silted pits, 4300 mg S/(m² day). A calculation made with regard to the area of microlandscapes with increased productivity shows that the daily H₂S production per 1 km² of the littoral (August) is 60.8 to 202 kg S/(km² day), while the organic carbon consumption for sulfate reduction per 1 km² of the littoral is 46 to 152 kg C_org/(km² day).     

Biological Reduction of Ferric Iron by Iron- and Sulfur-oxidizing Bacteria

B-1625 FA_2β, one of the minor acidic actinomycin congeners produced by Streptomyces antibioticus No. B-1625, was produced selectively on the combined use of sarcosine and ferrous sulfate in a complex medium. The FA_2β was further separated into two components, MeOH- insoluble FA_{2β – 1} and MeOH-soluble FA_{2β – 2}, by methanol treatment. After repeating the MeOH treatment, the purified FA_{2β – 1} was examined as to its physicochemical properties, and subjected to amino acid analysis, and ¹³C-, ¹H-NMR and FAB mass spectral measurements. As a result, the structure of FA_{2β – 1} was deduced to be 2-amino-1-carboxyl-4,6-dimethyl-3-phenoxazone-9- carbonyl-threonyl-valyl-sarcosyl-sarcosyl-N-methylvaline. As much as 1 mg/ml of FA_{2β – 1} showed no antibacterial activity against Gram-negative or Gram-positive bacteria, although FA_{2β – 2} shows antibiotic activity.     

Implications of Competitive Inhibition in the Acetylene Reduction Assay for Dinitrogen Fixation

An earlier paper which analysed the implications of diffusionlimitation for acetylene reduction by intact legume noduleshas recently been criticized for ignoring competitive inhibitionof acetylene reduction by dinitrogen. Mathematical analysesof competitive inhibition show that the dependence of acetylenereduction rate on acetylene concentration under atmosphericN₂ is described adequately by an equation functionally equivalentto the Michaelis—Menten equation, despite competitiveinhibition. Therefore, no modification of the original analysisis required. However, competitive inhibition is shown to bea significant factor when experiments under atmospheric N₂ andunder argon are compared. Acetylene reduction, dinitrogen fixation, competitive inhibition, diffusion limitation, legume nodules     

Sulfate Reduction Potential in Sediments in the Norilsk Mining Area,Northern Siberia

Abstract

The purpose of this study was to characterize the distribution and activity of sulfate-reducing bacteria in tailings and sediments impacted by effluents from mining and smelting operations in the Norilsk area in northern Siberia. The Norilsk mining complex involves three smelter operations, a hydrometallurgical plant, and extensive tailings areas located in the permafrost zone. Sulfate reduction rates measured with a ³⁵SO₄ ^2? tracer technique under various in-situ conditions ranged from 0.05 to 30 nmol S cm^?3 day^?1. Acetate and glucose addition greatly stimulated sulfate reduction, whereas lactate had less effect. The most pronounced stimulation of sulfate reduction (6.5-fold) was observed with phosphate amendment. Most-probable-number (MPN) counts of sulfate-reducing bacteria in media with glucose, ethanol, lactate, and acetate as electron donors were generally highest at around 10⁷ cells ml^?1. The actual MPN counts varied with the sample, electron donor, and incubation conditions (pH 7.2 vs. pH 3.5; 28°C vs. 4°C). Enrichment cultures of sulfate-reducing bacteria were established from a sample that showed the highest rate of sulfate reduction. After multiple serial transfers, the dominant sulfate-reducers were identified by fluorescence in situ hybridization using genus and group-specific 16S rRNA-targeted oligonucleotide probes. Desulfobulbus spp. prevailed in ethanol and lactate enrichments and the Desulfosarcina-Desulfococcus group dominated in acetate and benzoate enrichments. Psychrophilic Desulfotalea-Desulfofustis and moderately psychrophilic Desulforhopalus spp. were identified in enrichments incubated at 4°C, but they were also found in mesophilic enrichments.     

铁摄取调节子在细菌铁离子代谢中的调节及其机制

铁离子是大多数细菌生存所必需的营养物质,但是过多的铁离子通过芬顿反应产生的活性氧（reactive oxygen species, ROS）对细菌造成损伤。因此,细菌必须严格控制体内铁离子浓度。铁摄取调节子（ferric uptake regulator,Fur）是细菌铁离子代谢中最重要的调节子。Fur通过抑制或者激活基因的转录,来调节与铁摄取、利用和储存相关的基因,维持胞内铁离子浓度动态平衡。此外,Fur还参与细菌的氧化应激、抗酸能力、毒力和能量代谢等多种生物过程的调节。本文对Fur参与的生物过程及调节机制进行介绍,以期为进一步研究其他细菌Fur的调节机制,以及Fur在细菌应对环境变化中所起作用提供参考。