Low-oxygen and chemical kinetic constraints on the geochemical niche of neutrophilic iron(II) oxidizing microorganisms

Neutrophilic iron oxidizing bacteria (FeOB) must actively compete with rapid abiotic processes governing Fe(II) oxidation and as a result have adapted to primarily inhabit low-O₂ environments where they can more successfully compete with abiotic Fe(II) oxidation. The spatial distribution of these microorganisms can be observed through the chemical gradients they affect, as measured using in situ voltammetric analysis for dissolved Fe(II), Fe(III), O₂, and FeS_(aq). Field and laboratory determination of the chemical environments inhabited by the FeOB were coupled with detailed kinetic competition studies for abiotic and biotic oxidation processes using a pure culture of FeOB to quantify the geochemical niche these organisms inhabit. In gradient culture tubes, the maximum oxygen levels, which were associated with growth bands of Sideroxydans lithotrophicus (ES-1, a novel FeOB), were 15-50 μM. Kinetic measurements made on S. lithotrophicus compared biotic/abiotic (killed control) Fe oxidation rates. The biotic rate can be a significant and measurable fraction of the total Fe oxidation rate below O₂ concentrations of approximately 50 μM, but biotic Fe(II) oxidation (via the biotic/abiotic rate comparison) becomes difficult to detect at higher O₂ levels. These results are further supported by observations of conditions supporting FeOB communities in field settings. Variablity in cell densities and cellular activity as well as variations in hydrous ferrous oxide mineral quantities significantly affect the laboratory kinetic rates. The microbial habitat (or geochemical niche) where FeOB are active is thus largely controlled by the competition between abiotic and biotic kinetics, which are dependent on Fe(II) concentration, P_O2, temperature and pH in addition to the surface area of hydrous ferric oxide minerals and the cell density/activity of FeOB. Additional field and lab culture observations suggest a potentially important role for the iron-sulfide aqueous molecular cluster, FeS_(aq), in the overall cycling of iron associated with the environments these microorganisms inhabit.     

Kinetics and Mechanism of Trithionate and Tetrathionate Oxidation at Low pH by Hydroxyl Radicals

The oxidation kinetics of trithionate (S₃O₆^2- ) and tetrathionate (S₄O ₆ ^2- ) with hydroxyl radicals (OH^*) have been investigated in systems analogous to acid mine drainage (AMD) environments. The discovery of hydroxyl radical (OH^*) formation on pyrite surfaces (Borda et al., 2003) suggests hydroxyl radicals may affect the oxidation kinetics of intermediate sulfur species such as tetrathionate. Cyclic voltammetry experiments in acidic solutions indicate that the reaction of S₄O ₆ ^2- with OH^* goes through an unknown intermediate, tentatively assigned as S₃O ₄ ^n- . An outer-sphere electron transfer mechanism for the reaction of S₄O ₆ ^2- with OH^* to form S₃O ₄ ^n- is proposed based on experimental results. Oxidation rates for trithionate and tetrathionate in the presence of Fenton's reagent (which forms hydroxyl radicals) are too fast to be directly measured using UV-Vis spectrophotometry, electrochemical, or stop-flow spectrophotometry methods. Competitive reaction kinetics within the context of the Haber—Weiss mechanism suggests that the rate constant for the oxidation of trithionate and tetrathionate with OH^* is in excess of 10⁸ M^-1 sec^-1.     

Iron and Sulfur Chemistry in a Stratified Lake: Evidence for Iron-Rich Sulfide Complexes

A four month study of a man-made lake used for hydroelectric power generation in northeastern Pennsylvania USA was conducted to investigate seasonal anoxia and the effects of sulfide species being transported downstream of the power generation equipment. Water column analyses show that the system is iron-rich compared to sulfide. Total Fe(II) concentrations in the hypolimnion are typically at least twice the total sulfide levels. In situ voltammetric analyses show that free Fe(II) as [Fe(H₂O)₆]²⁺ or free H₂S as H₂S/HS^- are either not present or at trace levels and that iron-rich sulfide complexes are present. From the in situ data and total Fe(II) and H₂S measurements, we infer that these iron-rich sulfide complexes may have stoichiometries such as Fe₂SH³⁺ (or polymeric forms of this and other stoichiometries). These iron-rich sulfide complexes appear related to dissolution of the iron-rich FeS mineral, mackinawite, because IAP calculations on data from discrete bottle samples obtained from bottom waters are similar to the pK_sp of mackinawite. Soluble iron-sulfide species are stable in the absence of O₂ (both in lake waters and the pipeline) and transported several miles during power generation. However, iron-sulfide complexes can react with O₂ to oxidize sulfide and can also dissociate releasing volatile H₂S when the waters containing them are exposed to the atmosphere downstream of the powerplant. Sediment analyses show that the lake is rich in oxidized iron solids (both crystalline and amorphous). Fe concentrations in FeS solids are low (<5 μmole/gr_{dry wt}) and the pyrite concentration ranges from about equal to the solid FeS to 30 times the solid FeS concentration. The degree of pyritization is below 0.12 indicating that pyrite formation is limited by free sulfide, which can react with the iron-rich sulfide complexes.     

Geochemistry of Flooded Underground Mine Workings Influenced by Bacterial Sulfate Reduction

Unlike the majority of the water in the flooded mine complex of Butte Montana, which includes the highly acidic Berkeley pit lake, groundwater in the flooded West Camp underground mine workings has a circum-neutral pH and contains at least 8 μM aqueous sulfide. This article examines the geochemistry and stable isotope composition of this unusual H₂S-rich mine water, and also discusses problems related to the colorimetric analysis of sulfide in waters that contain FeS_(aq) cluster compounds. The West Camp mine pool is maintained at a constant elevation by continuous pumping, with discharge water that contains elevated Mn (90 μM), Fe (16 μM), and As (1.3 μM) but otherwise low metal concentrations. Dissolved inorganic carbon in the mine water is in chemical and isotopic equilibrium with rhodochrosite in the mineralized veins. The mine water is under-saturated with mackinawite and amorphous FeS, but is supersaturated with Cu- and Zn-sulfides. However, voltammetry studies show that much of the dissolved sulfide and ferrous iron are present as FeS_(aq) cluster molecules: as a result, the free concentration of the West Camp water is poorly constrained. Concentrations of dissolved sulfide determined by colorimetry were lower than gravimetric assays obtained by AgNO₃ addition, implying that the FeS_(aq) clusters are not completely extracted by the Methylene Blue reagent. In contrast, the clusters are quantitatively extracted as Ag₂S after addition of AgNO₃. Isotopic analysis of co-existing aqueous sulfide and sulfate confirms that the sulfide was produced by sulfate-reducing bacteria (SRB). The H₂S-rich mine water is not confined to the immediate vicinity of the extraction well, but is also present in flooded mine shafts up to 3 km away, and in samples bailed from mine shafts at depths up to 300 m below static water level. This illustrates that SRB are well established throughout the southwestern portion of the extensive (>15 km³) Butte flooded mine complex.     

Sulfur geochemistry of hydrothermal waters in Yellowstone National Park,Wyoming, USA. III. An anion-exchange resin technique for sampling and preservation of sulfoxyanions in natural waters

A sampling protocol for the retention, extraction, and analysis of sulfoxyanions in hydrothermal waters has been developed in the laboratory and tested at Yellowstone National Park and Green Lake, NY. Initial laboratory testing of the anion-exchange resin Bio-Rad™ AG1-X8 indicated that the resin was well suited for the sampling, preservation, and extraction of sulfate and thiosulfate. Synthetic solutions containing sulfate and thiosulfate were passed through AG1-X8 resin columns and eluted with 1 and 3 M KCl, respectively. Recovery ranged from 89 to 100%. Comparison of results for water samples collected from five pools in Yellowstone National Park between on-site IC analysis (U.S. Geological Survey mobile lab) and IC analysis of resin-stored sample at SUNY-Stony Brook indicates 96 to 100% agreement for three pools (Cinder, Cistern, and an unnamed pool near Cistern) and 76 and 63% agreement for two pools (Sulfur Dust and Frying Pan). Attempts to extract polythionates from the AG1-X8 resin were made using HCl solutions, but were unsuccessful. Bio-Rad™ AG2-X8, an anion-exchange resin with weaker binding sites than the AG1-X8 resin, is better suited for polythionate extraction. Sulfate and thiosulfate extraction with this resin has been accomplished with KCl solutions of 0.1 and 0.5 M, respectively. Trithionate and tetrathionate can be extracted with 4 M KCl. Higher polythionates can be extracted with 9 M hydrochloric acid. Polythionate concentrations can then be determined directly using ion chromatographic methods, and laboratory results indicate recovery of up to 90% for synthetic polythionate solutions using AG2-X8 resin columns.     

Acid mine drainage biogeochemistry at Iron Mountain,California

The Richmond Mine at Iron Mountain, Shasta County, California, USA provides an excellent opportunity to study the chemical and biological controls on acid mine drainage (AMD) generation in situ, and to identify key factors controlling solution chemistry. Here we integrate four years of field-based geochemical data with 16S rRNA gene clone libraries and rRNA probe-based studies of microbial population structure, cultivation-based metabolic experiments, arsenopyrite surface colonization experiments, and results of intermediate sulfur species kinetics experiments to describe the Richmond Mine AMD system. Extremely acidic effluent (pH between 0.5 and 0.9) resulting from oxidation of approximately 1 × 10⁵ to 2 × 10⁵ moles pyrite/day contains up to 24 g/1 Fe, several g/1 Zn and hundreds of mg/l Cu. Geochemical conditions change markedly over time, and are reflected in changes in microbial populations. Molecular analyses of 232 small subunit ribosomal RNA (16S rRNA) gene sequences from six sites during a sampling time when lower temperature (<32°C), higher pH (>0.8) conditions predominated show the dominance of Fe-oxidizing prokaryotes such as Ferroplasma and Leptospirillum in the primary drainage communities. Leptospirillum group III accounts for the majority of Leptospirillum sequences, which we attribute to anomalous physical and geochemical regimes at that time. A couple of sites peripheral to the main drainage, "Red Pool" and a pyrite "Slump," were even higher in pH (>1) and the community compositions reflected this change in geochemical conditions. Several novel lineages were identified within the archaeal Thermoplasmatales order associated with the pyrite slump, and the Red Pool (pH 1.4) contained the only population of Acidithiobacillus. Relatively small populations of Sulfobacillus spp. and Acidithiobacillus caldus may metabolize elemental sulfur as an intermediate species in the oxidation of pyritic sulfide to sulfate. Experiments show that elemental sulfur which forms on pyrite surfaces is resistant to most oxidants; its solublization by unattached cells may indicate involvement of a microbially derived electron shuttle. The detachment of thiosulfate (S₂O₃^2-) as a leaving group in pyrite oxidation should result in the formation and persistence of tetrathionate in low pH ferric iron-rich AMD solutions. However, tetrathionate is not observed. Although a S₂O₃^2--like species may form as a surface-bound intermediate, data suggest that Fe³⁺ oxidizes the majority of sulfur to sulfate on the surface of pyrite. This may explain why microorganisms that can utilize intermediate sulfur species are scarce compared to Fe-oxidizing taxa at the Richmond Mine site.

     

Use of voltammetric solid-state (micro)electrodes for studying biogeochemical processes: Laboratory measurements to real time measurements with an in situ electrochemical analyzer (ISEA)

Solid-state voltammetric (micro)electrodes have been used in a variety of environments to study biogeochemical processes. Here we show the wealth of information that has been obtained in the study of sediments, microbial mats, cultures and the water column including hydrothermal vents. Voltammetric analyzers have been developed to function with operator guidance and in unattended mode for temporal studies with an in situ electrochemical analyzer (ISEA). The electrodes can detect the presence (or absence) of a host of redox species and trace metals simultaneously. The multi-species capacity of the voltammetric electrode can be used to examine complex heterogeneous environments such as the root zone of salt marsh sediments. The data obtained with these systems clearly show that O₂ and Mn²⁺ profiles in marine sedimentary porewaters and in microbial biofilms on metal surfaces rarely overlap indicating that O₂ is not a direct oxidant for Mn²⁺. This lack of overlap was suggested originally by Joris Gieskes' group. In waters emanating from hydrothermal vents, Fe²⁺, H₂S and soluble molecular FeS clusters (FeS_aq) are detected indicating that the reactants for the pyrite formation reaction are H₂S and soluble molecular FeS clusters. Using the ISEA with electrodes at fixed positions, data collected continuously over three days near a Riftia pachyptila tubeworm field generally show that O₂ and H₂S anti-correlate and that H₂S and temperature generally correlate. Unlike sedimentary environments, the data clearly show that Riftia live in areas where both O₂ and H₂S co-exist so that its endosymbiont bacteria can perform chemosynthesis. However, physical mixing of diffuse flow vent waters with oceanic bottom waters above or to the side of the tubeworm field can dampen these correlations or even reverse them. Voltammetry is a powerful technique because it provides chemical speciation data (e.g.; oxidation state and different elemental compounds/ions) as well as quantitative data. Because (micro)organisms occupy environmental niches due to the system's chemistry, it is necessary to know chemical speciation. Voltammetric methods allow us to study how chemistry drives biology and how biology can affect chemistry for its own benefit.     

Kinetics and mechanism of polythionate oxidation to sulfate at low pH by O2 and Fe

Polythionates (S_xO₆²⁻) are important in redox transformations involving many sulfur compounds. Here we investigate the oxidation kinetics and mechanisms of trithionate and tetrathionate oxidation between pH 0.4 and pH 2 in the presence of Fe³⁺ and/or oxygen. In these solutions, Fe³⁺ plus oxygen oxidizes tetrathionate and trithionate at least an order of magnitude faster than oxygen alone. Kinetic measurements, coupled with density functional calculations, suggest that the rate-limiting step for tetrathionate oxidation involves Fe³⁺ attachment, followed by electron density shifts that result in formation of a sulfite radical and S₃O₃⁰ derivatives. The overall reaction orders for trithionate and tetrathionate are fractional due to rearrangement reactions and side reactions between reactants and intermediate products. The pseudo-first order rate coefficients for tetrathionate range from 10⁻¹¹ s⁻¹ at 25°C to 10⁻⁸ s⁻¹ at 70°C, compared to 2 × 10⁻⁷ s⁻¹ at 35 °C for trithionate. The apparent activation energy (E_A) for tetrathionate oxidation at pH 1.5 is 104.5 ± 4.13 kJ/mol. A rate law at pH 1.5 and 70°C between 0.5 and 5 millimolar [Fe³⁺] is of the form: