Reductive dissolution of fe(III) oxides byPseudomonas sp. 200

First Insight into the Mobilization and Sequestration of Arsenic in a Karstic Soil during Redox Changes

Karst terrains provide drinking water for about 25% of the people on our planet, particularly in the southwest of China. Pollutants such as arsenic (As) in the soil can infiltrate groundwater through sinkholes and bedrock fractures in karst terrains. Despite this, the underlying mechanisms responsible for As release from karst soils under redox changes remain largely unexplored. Here, we used multiple synchrotron-based spectroscopic analyses to explore As mobilization and sequestration in As-polluted karstic soil under biogeochemical conditions that mimic field-validated redox conditions. We observed that As in the soil exists primarily as As(V), which is mainly associated with Fe(oxyhydr)oxides. The concentration of the dissolved As was high (294 μM) and As(III) was dominant (∼95%) at low Eh (≤-100 mV), indicating the high risk of As leaching under reducing conditions. This As mobilization was attributed to the fact that the dissolution of ferrihydrite and calcite promoted the release and reduction of associated As(V). The concentration of the dissolved As was low (17.0 μM) and As(V) was dominant (∼68%) at high Eh (≥+100 mV), which might be due to the oxidation and/or sequestration of As(III) by the recrystallized ferric phase. Our results showed that the combined effects of the reductive release of As(V) from both ferric and nonferric phases, along with the recrystallization of the ferric phase, govern the redox-induced mobilization and potential leaching of As in soils within karst environments.

Weathered granites and soils harbour microbes with lanthanide-dependent methylotrophic enzymes

BACKGROUND

Prior to soil formation, phosphate liberated by rock weathering is often sequestered into highly insoluble lanthanide phosphate minerals. Dissolution of these minerals releases phosphate and lanthanides to the biosphere. Currently, the microorganisms involved in phosphate mineral dissolution and the role of lanthanides in microbial metabolism are poorly understood.

RESULTS

Although there have been many studies of soil microbiology, very little research has investigated microbiomes of weathered rock. Here, we sampled weathered granite and associated soil to identify the zones of lanthanide phosphate mineral solubilisation and genomically define the organisms implicated in lanthanide utilisation. We reconstructed 136 genomes from 11 bacterial phyla and found that gene clusters implicated in lanthanide-based metabolism of methanol (primarily xoxF3 and xoxF5) are surprisingly common in microbial communities in moderately weathered granite. Notably, xoxF3 systems were found in Verrucomicrobia for the first time, and in Acidobacteria, Gemmatimonadetes and Alphaproteobacteria. The xoxF-containing gene clusters are shared by diverse Acidobacteria and Gemmatimonadetes, and include conserved hypothetical proteins and transporters not associated with the few well studied xoxF systems. Given that siderophore-like molecules that strongly bind lanthanides may be required to solubilise lanthanide phosphates, it is notable that candidate metallophore biosynthesis systems were most prevalent in bacteria in moderately weathered rock, especially in Acidobacteria with lanthanide-based systems.

CONCLUSIONS

Phosphate mineral dissolution, putative metallophore production and lanthanide utilisation by enzymes involved in methanol oxidation linked to carbonic acid production co-occur in the zone of moderate granite weathering. In combination, these microbial processes likely accelerate the conversion of granitic rock to soil.

Anaerobic methane-oxidizing activity in a deep underground borehole dominantly colonized by Ca. Methanoperedenaceae

The family Ca. Methanoperedenaceae archaea mediates the anaerobic oxidation of methane (AOM) in different terrestrial environments. Using a newly developed high-pressure laboratory incubation system, we investigated 214- and 249-m deep groundwater samples at Horonobe Underground Research Laboratory, Japan, where the high and low abundances of Ca. Methanoperedenaceae archaea have been shown by genome-resolved metagenomics, respectively. The groundwater samples amended with 13 C-labelled methane and amorphous Fe(III) were incubated at a pressure of 1.6 MPa. After 3-7 days of incubation, the AOM rate was 45.8 ± 19.8 nM/day in 214-m groundwater. However, almost no activity was detected from 249-m groundwater. Based on the results from 16S rRNA gene analysis, the abundance of Ca. Methanoperedenaceae archaea was high in the 214-m deep groundwater sample, whereas Ca. Methanoperedenaceae archaea was undetected in the 249-m deep groundwater sample. These results support the in situ AOM activity of Ca. Methanoperedenaceae archaea in the 214-m deep subsurface borehole interval. Although the presence of Fe-bearing phyllosilicates was demonstrated in the 214-m deep groundwater, it needs to be determined whether Ca. Methanoperedenaceae archaea use the Fe-bearing phyllosilicates as in situ electron acceptors by high-pressure incubation amended with the Fe-bearing phyllosilicates.

Effects of microplastics on nitrogen and phosphorus cycles and microbial communities in sediments

Sediments are the long-term sinks of microplastics (MPs) and nutrients in freshwater ecosystems. Therefore, understanding the effect of MPs on sediment nutrients is crucial. However, few studies have discussed the effects of MPs on nitrogen and phosphorus cycles in freshwater sediments. Herein, 0.5% (w/w) polyvinyl chloride (PVC), polylactic acid (PLA), and polypropylene (PP) MPs were added to freshwater sediments to evaluate their effects on microbial communities and nitrogen and phosphorus release. The potential biochemical functions of the bacterial communities in the sediments were predicted and assessed via 16S rRNA gene sequencing. The results showed that MPs significantly affected the microbial community composition and nutrient cycling in the sediments. PVC and PP MPs can promote microbial nitrification and nitrite oxidation, while PP can significantly promote alkaline phosphatase (ALP) activity and the abundance of the phosphorus-regulation (phoR) gene. PLA MPs had the potential to promote the abundance of microbial phosphorus transporter (ugpB), nitrogen fixation (nifD, nifH, and nifX), and denitrification (nirS, napA, and norB) genes and inhibit nitrification, resulting in massive accumulation and release of ammonia nitrogen. Although PLA MPs inhibited the activity of ALP and the abundance of the organophosphorus mineralization (phoD) gene, it could enhance dissimilatory iron and sulfite reduction, which may promote the release of sedimentary phosphorus. Our findings may help understand the mechanisms of nitrogen and phosphorus cycles and microbial communities driven by MPs in sediments and provide a basis for future assessments of the environmental behavior of MPs in freshwater ecosystems.

Iron acquisition and mineral transformation by cyanobacteria living in extreme environments

Iron is an essential micronutrient for most living organisms, including cyanobacteria. These microorganisms have been found in Earth's driest polar and non-polar deserts, including the Atacama Desert, Chile. Iron-containing minerals were identified in colonized rock substrates from the Atacama Desert, however, the interactions between microorganisms and iron minerals remain unclear. In the current study, we determined that colonized gypsum rocks collected from the Atacama Desert contained both magnetite and hematite phases. A cyanobacteria isolate was cultured on substrates consisting of gypsum with embedded magnetite nanoparticles. Transmission electron microscopy imaging revealed a significant reduction in the size of magnetite nanoparticles due to their dissolution, which occurred around the microbial biofilms. Concurrently, hematite was detected, likely from the oxidation of the magnetite nanoparticles. Higher cell counts and production of siderophores were observed in cultures with magnetite nanoparticles suggesting that cyanobacteria were actively acquiring iron from the magnetite nanoparticles. Magnetite dissolution and iron acquisition by the cyanobacteria was further confirmed using large bulk magnetite crystals, uncovering a survival strategy of cyanobacteria in these extreme environments.

Genome-Resolved Metagenomic Analysis of Groundwater: Insights into Arsenic Mobilization in Biogeochemical Interaction Networks

High-arsenic (As) groundwaters, a worldwide issue, are critically controlled by multiple interconnected biogeochemical processes. However, there is limited information on the complex biogeochemical interaction networks that cause groundwater As enrichment in aquifer systems. The western Hetao basin was selected as a study area to address this knowledge gap, offering an aquifer system where groundwater flows from an oxidizing proximal fan (low dissolved As) to a reducing flat plain (high dissolved As). The key microbial interaction networks underpinning the biogeochemical pathways responsible for As mobilization along the groundwater flow path were characterized by genome-resolved metagenomic analysis. Genes associated with microbial Fe(II) oxidation and dissimilatory nitrate reduction were noted in the proximal fan, suggesting the importance of nitrate-dependent Fe(II) oxidation in immobilizing As. However, genes catalyzing microbial Fe(III) reduction (omcS) and As(V) detoxification (arsC) were highlighted in groundwater samples downgradient flow path, inferring that reductive dissolution of As-bearing Fe(III) (oxyhydr)oxides mobilized As(V), followed by enzymatic reduction to As(III). Genes associated with ammonium oxidation (hzsABC and hdh) were also positively correlated with Fe(III) reduction (omcS), suggesting a role for the Feammox process in driving As mobilization. The current study illustrates how genomic sequencing tools can help dissect complex biogeochemical systems, and strengthen biogeochemical models that capture key aspects of groundwater As enrichment.

Spatiotemporal dynamics in soil iron affected by wetland conversion on the Sanjiang Plain

Since the 1950s, nearly 80% of wetlands in the Sanjiang Plain have been converted into paddy fields. The conversion might affect the solubility and mobility of soil iron, influencing the export of iron into the Amur River and the primary production of the Okhotsk Sea. However, information regarding long‐term studies of the spatiotemporal dynamics of soil iron after cultivation is limited. In this study, six regions, including 18 plots in the Sanjiang Plain, were selected as sampling sites covering natural wetlands and paddy fields with planting ages of 2, 5, 11, 18, and 25 years after conversion from the wetland. Samples were collected at six different depths (0–10, 10–20, 20–40, 40–60, 60–90, and 90–120 cm) analyzed for water‐soluble ferrous iron (Fe[II]), water‐soluble iron (Few), complex iron (Fep), amorphous iron oxides (Feo), free iron oxides (Fed), and total iron (Fet) and six soil physicochemical characteristics. Two years after the conversion of wetlands to rice fields led to an immediate decrease in Fe(II), Few, Fep/Fed, and Feo/Fed, while the Fep and Feo contents decreased at 5 years. Both the concentrations and stocks of soil Fet increased gradually during the first 18 years. The findings in the Sanjiang Plain suggest that the function of wetlands after conversion as a source of iron might decrease with increasing time, with potential ecological effects on the neighboring marine environment. Recently initiated wetland restoration would protect the land ecosystems in the Sanjiang Plain and promote the future sustainability of the Amur Basin.

Enhancing anaerobic degradation of phenol to methane via solubilizing Fe(III) oxides for dissimilatory iron reduction with organic chelates

The improved performances during anaerobic degradation of phenol to methane with Fe(OH)₃ were usually inapparent, due to its lower solubility (unaccessible to dissimilatory iron reduction) and more positive reduction potential of Fe(III)/Fe(II) (unfavorable for enriching Fe(III)-reducing bacteria [IRBs]). In this study, citrate, the organic chelates, were used to solubilize Fe(III) with the aim of improving the phenol degradation and declining the reduction potential of Fe(III)/Fe(II). Results showed that, in the co-occurrence of citrate and Fe(OH)₃, the degradation rates of phenol were about 1.3-fold rapider than that with sole Fe(OH)₃. Analysis of cyclic voltammetry demonstrated that the reduction potential of Fe(III)/Fe(II) in the form of Fe(OH)₃ (-0.41 to -0.28 V vs Ag/AgCl) declined to -0.61 to -0.41 V. As a result, the Fe(III)-reducing genera, such as Petrimonas and Shewanella, which held a great potential of proceeding syntrophic metabolism via direct interspecies electron transfer (DIET), were significantly enriched.

Self-standing Electrochemical Set-up to Enrich Anode-respiring Bacteria On-site

Anaerobic respiration coupled with electron transport to insoluble minerals (referred to as extracellular electron transport [EET]) is thought to be critical for microbial energy production and persistence in many subsurface environments, especially those lacking soluble terminal electron acceptors. While EET-capable microbes have been successfully isolated from various environments, the diversity of bacteria capable of EET is still poorly understood, especially in difficult-to-sample, low energy or extreme environments, such as many subsurface ecosystems. Here, we describe an on-site electrochemical system to enrich EET-capable bacteria using an anode as a respiratory terminal electron acceptor. This anode is connected to a cathode capable of catalyzing abiotic oxygen reduction. Comparing this approach with electrocultivation methods that use a potentiostat for poising the electrode potential, the two-electrode system does not require an external power source. We present an example of our on-site enrichment utilized in an alkaline pond at the Cedars, a terrestrial serpentinization site in Northern California. Prior attempts to cultivate mineral reducing bacteria were unsuccessful, which is likely due to the low-biomass nature of this site and/or the low relative abundance of metal reducing microbes. Prior to implementing our two-electrode enrichment, we measured the vertical profile of dissolved oxygen concentration. This allowed us to place the carbon felt anode and platinum-electroplated carbon felt cathode at depths that would support anaerobic and aerobic processes, respectively. Following on-site incubation, we further enriched the anodic electrode in the laboratory and confirmed a distinct microbial community compared to the surface-attached or biofilm communities normally observed at the Cedars. This enrichment subsequently led to the isolation of the first electrogenic microbe from the Cedars. This method of on-site microbial enrichment has the potential to greatly enhance the isolation of EET-capable bacteria from low biomass or difficult to sample habitats.

Orenia metallireducens sp. nov. Strain Z6, a Novel Metal-Reducing Member of the Phylum Firmicutes from the Deep Subsurface

A novel halophilic and metal-reducing bacterium, Orenia metallireducens strain Z6, was isolated from briny groundwater extracted from a 2.02 km-deep borehole in the Illinois Basin, IL. This organism shared 96% 16S rRNA gene similarity with Orenia marismortui but demonstrated physiological properties previously unknown for this genus. In addition to exhibiting a fermentative metabolism typical of the genus Orenia, strain Z6 reduces various metal oxides [Fe(III), Mn(IV), Co(III), and Cr(VI)], using H₂ as the electron donor. Strain Z6 actively reduced ferrihydrite over broad ranges of pH (6 to 9.6), salinity (0.4 to 3.5 M NaCl), and temperature (20 to 60°C). At pH 6.5, strain Z6 also reduced more crystalline iron oxides, such as lepidocrocite (γ-FeOOH), goethite (α-FeOOH), and hematite (α-Fe₂O₃). Analysis of X-ray absorption fine structure (XAFS) following Fe(III) reduction by strain Z6 revealed spectra from ferrous secondary mineral phases consistent with the precipitation of vivianite [Fe₃(PO₄)₂] and siderite (FeCO₃). The draft genome assembled for strain Z6 is 3.47 Mb in size and contains 3,269 protein-coding genes. Unlike the well-understood iron-reducing Shewanella and Geobacter species, this organism lacks the c-type cytochromes for typical Fe(III) reduction. Strain Z6 represents the first bacterial species in the genus Orenia (order Halanaerobiales) reported to reduce ferric iron minerals and other metal oxides. This microbe expands both the phylogenetic and physiological scopes of iron-reducing microorganisms known to inhabit the deep subsurface and suggests new mechanisms for microbial iron reduction. These distinctions from other Orenia spp. support the designation of strain Z6 as a new species, Orenia metallireducens sp. nov.

IMPORTANCE

A novel iron-reducing species, Orenia metallireducens sp. nov., strain Z6, was isolated from groundwater collected from a geological formation located 2.02 km below land surface in the Illinois Basin, USA. Phylogenetic, physiologic, and genomic analyses of strain Z6 found it to have unique properties for iron reducers, including (i) active microbial iron-reducing capacity under broad ranges of temperatures (20 to 60°C), pHs (6 to 9.6), and salinities (0.4 to 3.5 M NaCl), (ii) lack of c-type cytochromes typically affiliated with iron reduction in Geobacter and Shewanella species, and (iii) being the only member of the Halanaerobiales capable of reducing crystalline goethite and hematite. This study expands the scope of phylogenetic affiliations, metabolic capacities, and catalytic mechanisms for iron-reducing microbes.

Impact of different environmental conditions on the aggregation of biogenic U(IV) nanoparticles synthesized by Desulfovibrio alaskensis G20

This study investigates the impact of specific environmental conditions on the formation of colloidal U(IV) nanoparticles by the sulfate reducing bacteria (SRB, Desulfovibrio alaskensis G20). The reduction of soluble U(VI) to less soluble U(IV) was quantitatively investigated under growth and non-growth conditions in bicarbonate or 1,4-piperazinediethanesulfonic acid (PIPES) buffered environments. The results showed that under non-growth conditions, the majority of the reduced U nanoparticles aggregated and precipitated out of solution. High resolution transmission electron microscopy revealed that only a very small fraction of cells had reduced U precipitates in the periplasmic spaces in the presence of PIPES buffer, whereas in the presence of bicarbonate buffer, reduced U was also observed in the cytoplasm with greater aggregation of biogenic U(IV) particles at higher initial U(VI) concentrations. The same experiments were repeated under growth conditions using two different electron donors (lactate and pyruvate) and three electron acceptors (sulfate, fumarate, and thiosulfate). In contrast to the results of the non-growth experiments, even after 0.2 μm filtration, the majority of biogenic U(IV) remained in the aqueous phase resulting in potentially mobile biogenic U(IV) nanoparticles. Size fractionation results showed that U(IV) aggregates were between 18 and 200 nm in diameter, and thus could be very mobile. The findings of this study are helpful to assess the size and potential mobility of reduced U nanoparticles under different environmental conditions, and would provide insights on their potential impact affecting U(VI) bioremediation efforts at subsurface contaminated sites.

Experimental determination of nonequilibrium transport parameters reflecting the competitive sorption between Cu and Pb in slag-sand column

Competitive sorption and resulting nonequilibrium transport of Cu and Pb were investigated using slag as a primary sorbent. A series of estimation models were applied based on the equilibrium, and nonequilibrium sorption respectively, and finally calibrated by incorporating the experimentally determined batch kinetic data. When applied individually, the behavior of metals in slag-sand column were well predicted by both equilibrium and nonequilibrium models in CXTFIT code. However, coexisting Cu and Pb exhibited competition for sorption sites, generating an irregular breakthrough curves such as overshoot (higher concentration in effluent than the feed concentration) of Cu and corresponding earlier peak of Pb followed by gradual re-rising. Although two-site nonequilibrium model further considers coupled hydrochemical process, desorption of the Cu from competition made the model prediction inaccurate. However, the parameter estimation could be improved by incorporating the experimentally determined mass transfer rate, ωexp from batch kinetics. Based on the calibrated model, the fraction of instantaneous retardation, βexp of Pb decreased from 0.41 in the single system to 0.30 in the binary system, indicating the shift from equilibrium to nonequilibrium state, where which of Cu increased from 0.39 to 0.94, representing the shift towards equilibrium. The modified results were also compared with five-step sequential extraction data, confirming that the shift of particular metal fractions from the competition triggered the nonequilibrium transport.

Cleaning of titanium substrates after application in a bioreactor

Plain and microstructured cp-titanium samples were studied as possible biofilm reactor substrates. The biofilms were grown by exposition of the titanium samples to bacteria in a flow cell. As bacteria the rod shaped gram negative Pseudomonas fluorescens and the spherical gram negative Paracoccus seriniphilus were chosen. Afterward, the samples were cleaned in subsequent steps: First, with a standard solvent based cleaning procedure with acetone, isopropanol, and ultrapure water and second by oxygen plasma sputtering. It will be demonstrated by means of x-ray photoelectron spectroscopy, fluorescence microscopy, and confocal laser scanning microscopy that oxygen plasma cleaning is a necessary and reliant tool to fully clean and restore titanium surfaces contaminated with a biofilm. The microstructured surfaces act beneficial to biofilm growth, while still being fully restorable after biofilm contamination. Scanning electron microscopy images additionally show, that the plasma process does not affect the microstructures. The presented data show the importance of the cleaning procedure. Just using solvents does not remove the biofilm and all its components reliably while a cleaning process by oxygen plasma regenerates the surfaces.

Electron transport and protein secretion pathways involved in Mn(III) reduction by Shewanella oneidensis

Soluble Mn(III) represents an important yet overlooked oxidant in marine and freshwater systems. The molecular mechanism of microbial Mn(III) reduction, however, has yet to be elucidated. Extracellular reduction of insoluble Mn(IV) and Fe(III) oxides by the metal-reducing γ-proteobacterium Shewanella oneidensis involves inner (CymA) and outer (OmcA) membrane-associated c-type cytochromes, the extracellular electron conduit MtrCAB, and GspD, the secretin of type II protein secretion. CymA, MtrCAB and GspD mutants were unable to reduce Mn(III) and Mn(IV) with lactate, H2, or formate as electron donor. The OmcA mutant reduced Mn(III) and Mn(IV) at near wild-type rates with lactate and formate as electron donor. With H2 as electron donor, however, the OmcA mutant was unable to reduce Mn(III) but reduced Mn(IV) at wild-type rates. Analogous Fe(III) reduction rate analyses indicated that other electron carriers compensated for the absence of OmcA, CymA, MtrCAB and GspD during Fe(III) reduction in an electron donor-dependent fashion. Results of the present study demonstrate that the S. oneidensis electron transport and protein secretion components involved in extracellular electron transfer to external Mn(IV) and Fe(III) oxides are also required for electron transfer to Mn(III) and that OmcA may function as a dedicated component of an H2 oxidation-linked Mn(III) reduction system.

Nitrite reduction by biogenic hydroxycarbonate green rusts: evidence for hydroxy-nitrite green rust formation as an intermediate reaction product

The present study investigates for the first time the reduction of nitrite by biogenic hydroxycarbonate green rusts, bio-GR(CO3), produced from the bioreduction of ferric oxyhydroxycarbonate (Fohc), a poorly crystalline solid phase, and of lepidocrocite, a well-crystallized Fe(III)-oxyhydroxide mineral. Results show a fast Fe(II) production from Fohc, which leads to the precipitation of bio-GR(CO3) particles that were roughly 2-fold smaller (2.3 ± 0.4 μm) than those obtained from the bioreduction of lepidocrocite (5.0 ± 0.4 μm). The study reveals that both bio-GR(CO3) are capable of reducing nitrite ions into gaseous nitrogen species such as NO, N2O, or N2 without ammonium production at neutral initial pH and that nitrite reduction proceeded to a larger extent with smaller particles than with larger ones. On the basis of the identification of intermediates and end-reaction products using X-ray diffraction and X-ray absorption fine structure (XAFS) spectroscopy at the Fe K-edge, our study shows the formation of hydroxy-nitrite green rust, GR(NO2), a new type of green rust 1, and suggests that the reduction of nitrite by biogenic GR(CO3) involves both external and internal reaction sites and that such a mechanism could explain the higher reactivity of green rust with respect to nitrite, compared to other mineral substrates possessing only external reactive sites.

Analysis of protein thermostability enhancing factors in industrially important thermus bacteria species

Elucidation of evolutionary factors that enhance protein thermostability is a critical problem and was the focus of this work on Thermus species. Pairs of orthologous sequences of T. scotoductus SA-01 and T. thermophilus HB27, with the largest negative minimum folding energy (MFE) as predicted by the UNAFold algorithm, were statistically analyzed. Favored substitutions of amino acids residues and their properties were determined. Substitutions were analyzed in modeled protein structures to determine their locations and contribution to energy differences using PyMOL and FoldX programs respectively. Dominant trends in amino acid substitutions consistent with differences in thermostability between orthologous sequences were observed. T. thermophilus thermophilic proteins showed an increase in non-polar, tiny, and charged amino acids. An abundance of alanine substituted by serine and threonine, as well as arginine substituted by glutamine and lysine was observed in T. thermophilus HB27. Structural comparison showed that stabilizing mutations occurred on surfaces and loops in protein structures.

ATR-FTIR spectroscopy study of the influence of pH and contact time on the adhesion of Shewanella putrefaciens bacterial cells to the surface of hematite

Attachment of live cells of Shewanella putrefaciens strain CN-32 to the surface of hematite (α-Fe(2)O(3)) was studied with in situ ATR-FTIR spectroscopy at variable pH (4.5-7.7) and contact times up to 24 h. The IR spectra indicate that phosphate based functional groups on the cell wall play an important role in mediating adhesion through formation of inner-sphere coordinative bonds to hematite surface sites. The inner-sphere attachment mode of microbial P groups varies with pH, involving either a change in protonation or in coordination to hematite surface sites as pH is modified. At all pH values, spectra collected during the early stages of adhesion show intense IR bands associated with reactive P-groups, suggestive of preferential coordination of P-moieties at the hematite surface. Spectra collected after longer sorption times show distinct frequencies from cell wall protein and carboxyl groups, indicating that bacterial adhesion occurring over longer time scales is to a lesser degree associated with preferential attachment of P-based bacterial functional groups to the hematite surface. The results of this study demonstrate that pH and reaction time influence cell-mineral interactions, implying that these parameters play an important role in determining cell mobility and biofilm formation in aqueous geochemical environments.

Bio-reduction of Fe(III) ores using three pure strains of Aeromonas hydrophila, Serratia fonticola and Clostridium celerecrescens and a natural consortium

The present work describes a research approach to the anaerobic bioleaching of Fe(III) ores. Three strains (Serratia fonticola, Aeromonas hydrophila and Clostridium celerecrescens) isolated from an acidic abandoned mine were selected to test their ability to reduce dissimilatory Fe(III). Total iron bio-reduction was achieved after 48 h using either the consortium or the Aeromonas cultures. In the latter case, there was no evidence of precipitates and Fe(II) remained in solution at neutral pH through complex formation with citrate. None of the other cultures tested (mixed culture and the two isolates) exhibited this behaviour. Biotechnologically, this is a very promising result since it obviates the problem associated with undesirable precipitation of iron compounds in Fe(III)-reducing bacterial cultures. The performance of the Aeromonas culture was improved progressively by adaptation to moderately acidic pH values (up to 4.5) and to three different Fe(III)-oxyhydroxides as the sole source of iron: ferrihydrite, hematite and jarosite, commonly found as weathering compounds at mine sites. Dissimilatory Fe(III)-reducers for iron extraction from ores is therefore especially attractive in that acidification of the surrounding area can be minimized.

Roles of siderophores, oxalate, and ascorbate in mobilization of iron from hematite by the aerobic bacterium Pseudomonas mendocina

In aerobic, circumneutral environments, the essential element Fe occurs primarily in scarcely soluble mineral forms. We examined the independent and combined effects of a siderophore, a reductant (ascorbate), and a low-molecular-weight carboxylic acid (oxalate) on acquisition of Fe from the mineral hematite (alpha-Fe(2)O(3)) by the obligate aerobe Pseudomonas mendocina ymp. A site-directed DeltapmhA mutant that was not capable of producing functional siderophores (i.e., siderophore(-) phenotype) did not grow on hematite as the only Fe source. The concentration of an added exogenous siderophore (1 microM desferrioxamine B [DFO-B]) needed to restore wild-type (WT)-like growth kinetics to the siderophore(-) strain was approximately 50-fold less than the concentration of the siderophore secreted by the WT organism grown under the same conditions. The roles of a reductant (ascorbate) and a simple carboxylic acid (oxalate) in the Fe acquisition process were examined in the presence and absence of the siderophore. Addition of ascorbate (50 microM) alone restored the growth of the siderophore(-) culture to the WT levels. A higher concentration of oxalate (100 microM) had little effect on the growth of a siderophore(-) culture; however, addition of 0.1 muM DFO-B and 100 muM oxalate restored the growth of the mutant to WT levels when the oxalate was prereacted with the hematite, demonstrating that a metabolizing culture benefits from a synergistic effect of DFO-B and oxalate.

Mineralogical and geochemical controls of arsenic speciation and mobility under different redox conditions in soil, sediment and water at the Mokrsko-West gold deposit, Czech Republic

Naturally contaminated soil, sediment and water at the Mokrsko-West gold deposit, Central Bohemia, have been studied in order to determine the processes that lead to release of As into water and to control its speciation under various redox conditions. In soils, As is bonded mainly to secondary arseniosiderite, pharmacosiderite and Fe oxyhydroxides and, rarely, to scorodite; in sediments, As is bonded mainly to Fe oxyhydroxides and rarely to arsenate minerals. The highest concentrations of dissolved As were found in groundwater (up to 1141 microg L(-1)), which mostly represented a redox transition zone where neither sulphide minerals nor Fe oxyhydroxide are stable. The main processes releasing dissolved As in this zone are attributed to the reductive dissolution of Fe oxyhydroxides and arsenate minerals, resulting in a substantial decrease in their amounts below the groundwater level. Some shallow subsurface environments with high organic matter contents were characterized by reducing conditions that indicated a relatively high amount of S(-2,0) in the solid phase and a lower dissolved As concentration (70-80 microg L(-1)) in the pore water. These findings are attributed to the formation of Fe(II) sulphides with the sorbed As. Under oxidizing conditions, surface waters were undersaturated with respect to arsenate minerals and this promoted the dissolution of secondary arsenates and increased the As concentrations in the water to characteristic values from 300 to 450 microg L(-1) in the stream and fishpond waters. The levels of dissolved As(III) often predominate over As(V) levels, both in groundwaters and in surface waters. The As(III)/As(V) ratio is closely related to the DOC concentration and this could support the assumption of a key role of microbial processes in transformations of aqueous As species as well as in the mobility of As.

Towards environmental systems biology of Shewanella

Bacteria of the genus Shewanella are known for their versatile electron-accepting capacities, which allow them to couple the decomposition of organic matter to the reduction of the various terminal electron acceptors that they encounter in their stratified environments. Owing to their diverse metabolic capabilities, shewanellae are important for carbon cycling and have considerable potential for the remediation of contaminated environments and use in microbial fuel cells. Systems-level analysis of the model species Shewanella oneidensis MR-1 and other members of this genus has provided new insights into the signal-transduction proteins, regulators, and metabolic and respiratory subsystems that govern the remarkable versatility of the shewanellae.

The surface physicochemistry and adhesiveness of Shewanella are affected by their surface polysaccharides

Shewanella strains have previously been studied with regard to their cell surface ultrastructure and LPS composition. They have now been further characterized with respect to their surface physicochemistry and ability to adhere to haematite. The surfaces of the Shewanella strains were found to be electronegative and hydrophilic, and these properties could be correlated with LPS composition or the presence of capsular polysaccharides. Strains expressing rough LPS with no capsule were more hydrophobic and electronegative than those possessing smooth LPS or capsules. By combining different approaches, such as contact-angle measurement, hydrophilic/hydrophobic chromatography, microelectrophoresis, adhesion assays and calculation of interaction energies, it was shown that electrostatic interactions predominate over hydrophobic interactions at the cell-iron oxide interface. Bacterial adhesion to haematite was significantly reduced in strains expressing smooth LPS or a capsule. These findings remained true for Shewanella strains grown under either aerobic or anaerobic conditions, although the surfaces of anaerobic cells appeared to be less electronegative and more hydrophilic than those of aerobic cells.

Kinetic Monte Carlo model of charge transport in hematite (α-Fe2O3)

The mobility of electrons injected into iron oxide minerals via abiotic and biotic electron transfer processes is one of the key factors that control the reductive dissolution of such minerals. Building upon our previous work on the computational modeling of elementary electron transfer reactions in iron oxide minerals using ab initio electronic structure calculations and parametrized molecular dynamics simulations, we have developed and implemented a kinetic Monte Carlo model of charge transport in hematite that integrates previous findings. The model aims to simulate the interplay between electron transfer processes for extended periods of time in lattices of increasing complexity. The electron transfer reactions considered here involve the IIIII valence interchange between nearest-neighbor iron atoms via a small polaron hopping mechanism. The temperature dependence and anisotropic behavior of the electrical conductivity as predicted by our model are in good agreement with experimental data on hematite single crystals. In addition, we characterize the effect of electron polaron concentration and that of a range of defects on the electron mobility. Interaction potentials between electron polarons and fixed defects (iron substitution by divalent, tetravalent, and isovalent ions and iron and oxygen vacancies) are determined from atomistic simulations, based on the same model used to derive the electron transfer parameters, and show little deviation from the Coulombic interaction energy. Integration of the interaction potentials in the kinetic Monte Carlo simulations allows the electron polaron diffusion coefficient and density and residence time around defect sites to be determined as a function of polaron concentration in the presence of repulsive and attractive defects. The decrease in diffusion coefficient with polaron concentration follows a logarithmic function up to the highest concentration considered, i.e., approximately 2% of iron(III) sites, whereas the presence of repulsive defects has a linear effect on the electron polaron diffusion. Attractive defects are found to significantly affect electron polaron diffusion at low polaron to defect ratios due to trapping on nanosecond to microsecond time scales. This work indicates that electrons can diffuse away from the initial site of interfacial electron transfer at a rate that is consistent with measured electrical conductivities, but that the presence of certain kinds of defects will severely limit the mobility of donated electrons.

Shewanella putrefaciens produces an Fe(III)-solubilizing organic ligand during anaerobic respiration on insoluble Fe(III) oxides

The mechanism of Fe(III) reduction was investigated using voltammetric techniques in anaerobic incubations of Shewanella putrefaciens strain 200 supplemented with Fe(III) citrate or a suite of Fe(III) oxides as terminal electron acceptor. Results indicate that organic complexes of Fe(III) are produced during the reduction of Fe(III) at rates that correlate with the reactivity of the Fe(III) phase and bacterial cell density. Anaerobic Fe(III) solubilization activity is detected with either Fe(III) oxides or Fe(III) citrate, suggesting that the organic ligand produced is strong enough to destabilize Fe(III) from soluble or solid Fe(III) substrates. Results also demonstrate that Fe(III) oxide dissolution is not controlled by the intrinsic chemical reactivity of the Fe(III) oxides. Instead, the chemical reaction between the endogenous organic ligand is only affected by the number of reactive surface sites available to S. putrefaciens. This report describes the first application of voltammetric techniques to demonstrate production of soluble organic-Fe(III) complexes by any Fe(III)-reducing microorganism and is the first report of a Fe(III)-solubilizing ligand generated by a metal-reducing member of the genus Shewanella.

Specific bonds between an iron oxide surface and outer membrane cytochromes MtrC and OmcA from Shewanella oneidensis MR-1

Shewanella oneidensis MR-1 is purported to express outer membrane cytochromes (e.g., MtrC and OmcA) that transfer electrons directly to Fe(III) in a mineral during anaerobic respiration. A prerequisite for this type of reaction would be the formation of a stable bond between a cytochrome and an iron oxide surface. Atomic force microscopy (AFM) was used to detect whether a specific bond forms between a hematite (Fe(2)O(3)) thin film, created with oxygen plasma-assisted molecular beam epitaxy, and recombinant MtrC or OmcA molecules coupled to gold substrates. Force spectra displayed a unique force signature indicative of a specific bond between each cytochrome and the hematite surface. The strength of the OmcA-hematite bond was approximately twice that of the MtrC-hematite bond, but direct binding to hematite was twice as favorable for MtrC. Reversible folding/unfolding reactions were observed for mechanically denatured MtrC molecules bound to hematite. The force measurements for the hematite-cytochrome pairs were compared to spectra collected for an iron oxide and S. oneidensis under anaerobic conditions. There is a strong correlation between the whole-cell and pure-protein force spectra, suggesting that the unique binding attributes of each cytochrome complement one another and allow both MtrC and OmcA to play a prominent role in the transfer of electrons to Fe(III) in minerals. Finally, by comparing the magnitudes of binding force for the whole-cell versus pure-protein data, we were able to estimate that a single bacterium of S. oneidensis (2 by 0.5 microm) expresses approximately 10(4) cytochromes on its outer surface.

Reduction of soluble and insoluble iron forms by membrane fractions of Shewanella oneidensis grown under aerobic and anaerobic conditions

The effect of iron substrates and growth conditions on in vitro dissimilatory iron reduction by membrane fractions of Shewanella oneidensis MR-1 was characterized. Membrane fractions were separated by sucrose density gradients from cultures grown with O(2), fumarate, and aqueous ferric citrate as the terminal electron acceptor. Marker enzyme assays and two-dimensional gel electrophoresis demonstrated the high degree of separation between the outer and cytosolic membrane. Protein expression pattern was similar between chelated iron- and fumarate-grown cultures, but dissimilar for oxygen-grown cultures. Formate-dependent ferric reductase activity was assayed with citrate-Fe(3+), ferrozine-Fe(3+), and insoluble goethite as electron acceptors. No activity was detected in aerobic cultures. For fumarate and chelated iron-grown cells, the specific activity for the reduction of soluble iron was highest in the cytosolic membrane. The reduction of ferrozine-Fe(3+) was greater than the reduction of citrate-Fe(3+). With goethite, the specific activity was highest in the total membrane fraction (containing both cytosolic and outer membrane), indicating participation of the outer membrane components in electron flow. Heme protein content and specific activity for iron reduction was highest with chelated iron-grown cultures with no heme proteins in aerobically grown membrane fractions. Western blots showed that CymA, a heme protein involved in iron reduction, expression was also higher in iron-grown cultures compared to fumarate- or aerobic-grown cultures. To study these processes, it is important to use cultures grown with chelated Fe(3+) as the electron acceptor and to assay ferric reductase activity using goethite as the substrate.

Enhancement of PAH biomineralization rates by cyclodextrins under Fe(III)-reducing conditions

Amendment of a soil slurry with low concentrations of a cyclodextrin, hydroxypropyl-beta-cyclodextrin (HPCD), (0.05-0.5 g l(-1)) increased the phenanthrene mineralization rate of a microbial consortium by 25% under Fe(III)-reducing conditions. Although a higher concentration (5.0 g l(-1)) resulted in a faster initial rate of mineralization, mineralization ceased after 25 days with maximum mineralization 17% lower than the control (no HPCD). At lower HPCD concentrations, mineralization was still taking place at day 76. Although pH should affect Fe(III) solubility, mineralization rates at pH 6.0 and 8.0 were comparable. Decreasing the temperature reduced the extent and rate of mineralization, but mineralization rates at 10 degrees C were still 60% of that obtained at 30 degrees C.

Inhibition of NO3- and NO2- reduction by microbial Fe(III) reduction: evidence of a reaction between NO2- and cell surface-bound Fe2+

A recent study (D. C. Cooper, F. W. Picardal, A. Schimmelmann, and A. J. Coby, Appl. Environ. Microbiol. 69:3517-3525, 2003) has shown that NO(3)(-) and NO(2)(-) (NO(x)(-)) reduction by Shewanella putrefaciens 200 is inhibited in the presence of goethite. The hypothetical mechanism offered to explain this finding involved the formation of a Fe(III) (hydr)oxide coating on the cell via the surface-catalyzed, abiotic reaction between Fe(2+) and NO(2)(-). This coating could then inhibit reduction of NO(x)(-) by physically blocking transport into the cell. Although the data in the previous study were consistent with such an explanation, the hypothesis was largely speculative. In the current work, this hypothesis was tested and its environmental significance explored through a number of experiments. The inhibition of approximately 3 mM NO(3)(-) reduction was observed during reduction of a variety of Fe(III) (hydr)oxides, including goethite, hematite, and an iron-bearing, natural sediment. Inhibition of oxygen and fumarate reduction was observed following treatment of cells with Fe(2+) and NO(2)(-), demonstrating that utilization of other soluble electron acceptors could also be inhibited. Previous adsorption of Fe(2+) onto Paracoccus denitrificans inhibited NO(x)(-) reduction, showing that Fe(II) can reduce rates of soluble electron acceptor utilization by non-iron-reducing bacteria. NO(2)(-) was chemically reduced to N(2)O by goethite or cell-sorbed Fe(2+), but not at appreciable rates by aqueous Fe(2+). Transmission and scanning electron microscopy showed an electron-dense, Fe-enriched coating on cells treated with Fe(2+) and NO(2)(-). The formation and effects of such coatings underscore the complexity of the biogeochemical reactions that occur in the subsurface.

Cell adhesion of Shewanella oneidensis to iron oxide minerals: Effect of different single crystal faces

The results of experiments designed to test the hypothesis that near-surface molecular structure of iron oxide minerals influences adhesion of dissimilatory iron reducing bacteria are presented. These experiments involved the measurement, using atomic force microscopy, of interaction forces generated between Shewanella oneidensis MR-1 cells and single crystal growth faces of iron oxide minerals. Significantly different adhesive force was measured between cells and the (001) face of hematite, and the (100) and (111) faces of magnetite. A role for electrostatic interactions is apparent. The trend in relative forces of adhesion generated at the mineral surfaces is in agreement with predicted ferric site densities published previously. These results suggest that near-surface structure does indeed influence initial cell attachment to iron oxide surfaces; whether this is mediated via specific cell surface-mineral surface interactions or by more general interfacial phenomena remains untested.

pH dependence of ferrous sorption onto two smectite clays

This work examines the abilities of two smectite minerals (SWa-1 and Wyoming montmorillonite) to adsorb ferrous iron at concentrations from 0.037 mM (2 ppm) to 2.5 mM (240 ppm) over a range of pHs from 4.0 to 8.0. Both sorption isotherm and sorption edge data are presented. Ferrous sorption (Fe(aq)2+ = 0.1 mM) to both SWa-1 and Wyoming montmorillonite over the pH range 4.0-6.75 is relatively constant at approximately 1000 l kg(-1) for both minerals. Sorption in this pH range is attributed to the cation exchange capacity of the clay along the basal surfaces. At pH values above 6.75 the amount of ferrous iron sorbed increases dramatically. At pH 8, sorption (Fe(aq)+ = 0.1 mM) reaches 6600 l kg(-1) and 8000 l kg(-1) for Swa-1 and Wyoming montmorillonite respectively. This is attributed to the specific interaction between ferrous ions and surface sites along mineral edges. The overriding geochemical implication is that in reduced sediments containing more than a few percent clay, the pool of sorbed ferrous iron is vast. This pool of reduced iron is both redox labile and bio-available and is not readily indicated by simple measurement of dissolved Fe2+.

Dissimilatory Fe(III) and Mn(IV) reduction

Dissimilatory Fe(III) and Mn(IV) reduction has an important influence on the geochemistry of modern environments, and Fe(III)-reducing microorganisms, most notably those in the Geobacteraceae family, can play an important role in the bioremediation of subsurface environments contaminated with organic or metal contaminants. Microorganisms with the capacity to conserve energy from Fe(III) and Mn(IV) reduction are phylogenetically dispersed throughout the Bacteria and Archaea. The ability to oxidize hydrogen with the reduction of Fe(III) is a highly conserved characteristic of hyperthermophilic microorganisms and one Fe(III)-reducing Archaea grows at the highest temperature yet recorded for any organism. Fe(III)- and Mn(IV)-reducing microorganisms have the ability to oxidize a wide variety of organic compounds, often completely to carbon dioxide. Typical alternative electron acceptors for Fe(III) reducers include oxygen, nitrate, U(VI) and electrodes. Unlike other commonly considered electron acceptors, Fe(III) and Mn(IV) oxides, the most prevalent form of Fe(III) and Mn(IV) in most environments, are insoluble. Thus, Fe(III)- and Mn(IV)-reducing microorganisms face the dilemma of how to transfer electrons derived from central metabolism onto an insoluble, extracellular electron acceptor. Although microbiological and geochemical evidence suggests that Fe(III) reduction may have been the first form of microbial respiration, the capacity for Fe(III) reduction appears to have evolved several times as phylogenetically distinct Fe(III) reducers have different mechanisms for Fe(III) reduction. Geobacter species, which are representative of the family of Fe(III) reducers that predominate in a wide diversity of sedimentary environments, require direct contact with Fe(III) oxides in order to reduce them. In contrast, Shewanella and Geothrix species produce chelators that solubilize Fe(III) and release electron-shuttling compounds that transfer electrons from the cell surface to the surface of Fe(III) oxides not in direct contact with the cells. Electron transfer from the inner membrane to the outer membrane in Geobacter and Shewanella species appears to involve an electron transport chain of inner-membrane, periplasmic, and outer-membrane c-type cytochromes, but the cytochromes involved in these processes in the two organisms are different. In addition, Geobacter species specifically express flagella and pili during growth on Fe(III) and Mn(IV) oxides and are chemotactic to Fe(II) and Mn(II), which may lead Geobacter species to the oxides under anoxic conditions. The physiological characteristics of Geobacter species appear to explain why they have consistently been found to be the predominant Fe(III)- and Mn(IV)-reducing microorganisms in a variety of sedimentary environments. In comparison with other respiratory processes, the study of Fe(III) and Mn(IV) reduction is in its infancy, but genome-enabled approaches are rapidly advancing our understanding of this environmentally significant physiology.

Intracellular manganese granules formed by a subsurface bacterium

The demonstrated ability of prokaryotes to form internal metal oxide particles during active metabolism has been restricted to Fe. Mineral-bound Mn(IV) is a known electron acceptor during dissimilatory metal reduction by Shewanella putrefaciens, yet no internal deposits of Mn have been reported to form during anaerobic respiration. We observed distinct nanometre-sized Mn-rich granules in the cytoplasm when either birnessite or pyrolusite (beta-MnO(2)) served as the electron acceptor during growth. During rapid Mn reduction, additional precipitates of Mn were also observed in the periplasm together with the cytoplasmic granules. The bacteria did not accumulate detectable Mn in the outer membrane during formation of the internal precipitates. This is the first report of an intracellular Mn solid produced by bacteria and coupled anaerobically to DR.

Combining in situ reverse transcriptase polymerase chain reaction, optical microscopy, and X-ray photoelectron spectroscopy to investigate mineral surface-associated microbial activities

A study was undertaken to investigate expression of a gene encoding a c-type cytochrome in cells of the dissimilatory metal reducing bacterium (DMRB) Geobacter sulfurreducens during association with poorly crystalline and crystalline solid-phase Fe(III)-oxides. The gene encoding OmcC (outer membrane c-type cytochrome) was used as a target for PCR-based molecular detection and visualization of omcC gene expression by individual cells and aggregates of cells of G. sulfurreducens associated with ferrihydrite and hematite mineral particles. Expression of omcC was demonstrated in individual bacterial cells associated with these Fe-oxide surfaces by in situ RT-PCR (IS-RT PCR) and epifluorescence microscopy. Epifluorescence microscopy also permitted visualization of total DAPI-stained cells in the same field of view to assess the fraction of the cell population expressing omcC. By combining reflected differential interference contrast (DIC) microscopy and epifluorescence microscopy, it was possible to determine the spatial relationship between cells expressing omcC and the mineral surface. Introduction of the fluorescently labeled lectin concanavalin A revealed extracellular polymeric substances (EPS) extending between aggregations of bacterial cells and the mineral surface. The results indicate that EPS mediates an association between cells of G. sulfurreducens and ferrihydrite particles, but that direct cell contact with the mineral surface is not required for expression of omcC. XPS analysis revealed forms of reduced Fe associated with areas of the mineral surface where EPS-mediated bacterial associations occurred. The results demonstrate that by combining molecular biology, reflectance microscopy, and XPS, chemical transformations at a mineral surface can be related to the expression of specific genes by individual bacterial cells and cell aggregates associated with the mineral surface. The approach should be useful in establishing involvement of specific gene products in a wide variety of surface chemical processes.

Nitrilotriacetate stimulation of anaerobic Fe(III) respiration by mobilization of humic materials in soil

An enrichment culture capable of naphthalene mineralization reduced Fe(III) oxides without direct contact in anaerobic soil microcosms when the Fe(III) was placed in dialysis membranes or entrapped within alginate beads. Both techniques demonstrated that a component in soil, possibly humic materials, facilitated Fe(III) reduction when direct contact between cells and Fe(III) was not possible. The addition of the synthetic Fe(III) chelator, nitrilotriacetic acid (NTA), to soil enhanced Fe(III) reduction across the dialysis membrane and alginate beads, with the medium changing from clear to a dark brown color. An NTA-soil extract was more effective in Fe(III) reduction than the extracted soil itself. Characteristics of the NTA extract were consistent with that of humic substances. The results indicate that NTA improved Fe(III) reduction not by Fe(III) solubilization but by extraction of humic substances from soil into the aqueous medium. This is the first study in which stimulation of Fe(III) reduction through the addition of chemical chelators is shown to be due to the extraction of electron-shuttling compounds from the soil and not to solubilization of the Fe(III) and indicates that mobilization of humic materials could be an important component of anaerobic biostimulation.

Characterization of the lipopolysaccharides and capsules of Shewanella spp

Electron microscopy, sodium dodecyl sulfate-polyacrylamide gel electrophoresis with silver staining and (1)H, (13)C, and (31)P-nuclear magnetic resonance (NMR) were used to detect and characterize the lipopolysaccharides (LPSs) of several Shewanella species. Many expressed only rough LPS; however, approximately one-half produced smooth LPS (and/or capsular polysaccharides). Some LPSs were affected by growth temperature with increased chain length observed below 25 degrees C. Maximum LPS heterogeneity was found at 15 to 20 degrees C. Thin sections of freeze-substituted cells revealed that Shewanella oneidensis, S. algae, S. frigidimarina, and Shewanella sp. strain MR-4 possessed either O-side chains or capsular fringes ranging from 20 to 130 nm in thickness depending on the species. NMR detected unusual sugars in S. putrefaciens CN32 and S. algae BrY(DL). It is possible that the ability of Shewanella to adhere to solid mineral phases (such as iron oxides) could be affected by the composition and length of surface polysaccharide polymers. These same polymers in S. algae may also contribute to this opportunistic pathogen's ability to promote infection.

The structure of the carbohydrate backbone of the LPS from Shewanella putrefaciens CN32

The lipopolysaccharide (LPS) from a natural rough strain of Shewanella putrefaciens CN32 was analyzed using NMR and mass spectroscopy and chemical methods, and the following structure of its carbohydrate backbone is proposed: beta-Galf-(1-->3)-beta-Gal-(1-->4)-beta-Glc-(1-->4)-alpha-DDHep2PEtN-(1-->5)-alpha-Kdo4P-(1-->6)-beta-GlcN4P-(1-->6)-alpha-GlcN1P

Enhancement of hematite bioreduction by natural organic matter

The effects of natural organic matter (NOM), ferrozine, and AQDS (anthraquinone-2,6-disulfonate) on the reduction of hematite (alpha-Fe2O3) by Shewanella putrefaciens CN32 were studied. It has been proposed that NOM enhances the reduction of Fe(III) by means of electron shuttling or by Fe(II) complexation. Previously both mechanisms were studied separately using "functional analogues" (AQDS for electron shuttling and ferrozine for complexation) and are presently compared with seven different NOMs. AQDS enhanced hematite reduction within the first 24 h of incubation, and this had been ascribed to electron shuttling. Most of the NOMs enhanced hematite reduction after 1 day of incubation indicating that these materials could also serve as electron shuttles. The effect of ferrozine was linear with concentration, and all of the NOMs exhibited this behavior. Fe(II) complexation only enhanced hematite reduction after sufficient Fe(II) had accumulated in the system. Fe(II) complexation appeared to alleviate a suppression of the hematite reduction rate caused by accumulation of Fe(II) in the system. Addition of Fe(II) to the hematite suspension, prior to inoculation with CN32, significantly inhibited hematite reduction and greatly diminished the effects of all of the organic materials, although some enhancement was observed due to addition of anthroquinone-2,6-disulfonate. These results demonstrate that NOM can enhance iron reduction by electron shuttling and by complexation mechanisms.

Enhancement of biological reduction of hematite by electron shuttling and Fe(II) complexation

Natural organic matter (NOM) enhancement of the biological reduction of hematite (alpha-Fe2O3) by the dissimilatory iron-reducing bacterium Shewanella putrefaciens strain CN32 was investigated under nongrowth conditions designed to minimize precipitation of biogenic Fe(II). Hydrogen served as the electron donor. Anthraquinone-2,6-disulfonate (AQDS), methyl viologen, and methylene blue [quinones with an Ew0 (pH 7) of 0.011 V or less], ferrozine [a strong Fe(II) complexing agent], and characterized aquatic NOM (Georgetown NOM or Suwannee River fulvic acid) enhanced bioreduction in 5-day experiments whereas 1,4-benzoquinone (Ew0 value = 0.280 V) did not. A linear relationship existed between total Fe(II) produced and concentrations of ferrozine or NOM but not quinones, except in the case of methylene blue. Such a linear relationship between Fe(II) and methylene blue concentrations could be due to the systems being far undersaturated with respect to methylene blue or the loss of the thermodynamic driving force. A constant concentration of AQDS and variable concentrations of ferrozine produced a linear relationship between total Fe(II) produced and the concentration of ferrozine. Enhancement effects of both AQDS and ferrozine were additive. NOM may serve as both an electron shuttle and an Fe(II) complexant; however, the concentration dependence of hematite reduction with NOM was more similar to ferrozine than quinones. NOM likely enhances hematite reduction initially by electron shuttling and then further by Fe(II) complexation, which prevents Fe(II) sorption to hematite and cell surfaces.

Dissimilatory Fe(III) and Mn(IV) reduction by Shewanella putrefaciens requires ferE, a homolog of the pulE (gspE) type II protein secretion gene

Shewanella putrefaciens strain 200 respires anaerobically on a wide range of compounds as the sole terminal electron acceptor, including ferric iron [Fe(III)] and manganese oxide [Mn(IV)]. Previous studies demonstrated that a 23.3-kb S. putrefaciens wild-type DNA fragment conferred metal reduction capability to a set of respiratory mutants with impaired Fe(III) and Mn(IV) reduction activities (T. DiChristina and E. DeLong, J. Bacteriol. 176:1468-1474, 1994). In the present study, the smallest complementing fragment was found to contain one open reading frame (ORF) (ferE) whose translated product displayed 87% sequence similarity to Aeromonas hydrophila ExeE, a member of the PulE (GspE) family of proteins found in type II protein secretion systems. Insertional mutants E726 and E912, constructed by targeted replacement of wild-type ferE with an insertionally inactivated ferE construct, were unable to respire anaerobically on Fe(III) or Mn(IV) yet retained the ability to grow on all other terminal electron acceptors. Nucleotide sequence analysis of regions flanking ferE revealed the presence of one partial and two complete ORFs whose translated products displayed 55 to 70% sequence similarity to the PulD, -F, and -G homologs of type II secretion systems. A contiguous cluster of 12 type II secretion genes (pulC to -N homologs) was found in the unannotated genome sequence of Shewanella oneidensis (formerly S. putrefaciens) MR-1. A 91-kDa heme-containing protein involved in Fe(III) reduction was present in the peripheral proteins loosely attached to the outside face of the outer membrane of the wild-type and complemented (Fer+) B31 transconjugates yet was missing from this location in Fer mutants E912 and B31 and in uncomplemented (Fer-) B31 transconjugates. Membrane fractionation studies with the wild-type strain supported this finding: the 91-kDa heme-containing protein was detected with the outer membrane fraction and not with the inner membrane or soluble fraction. These findings provide the first genetic evidence linking dissimilatory metal reduction to type II protein secretion and provide additional biochemical evidence supporting outer membrane localization of S. putrefaciens proteins involved in anaerobic respiration on Fe(III) and Mn(IV).

Measurement of iron(III) bioavailability in pure iron oxide minerals and soils using anthraquinone-2,6-disulfonate oxidation

The quinol form (AHDS) of 9,10-anthraquinone-2,6-disulfonate (AQDS) was used as a titrant to determine bioavailability of Fe(III) in pure iron minerals and several soils. AHDS oxidation to AQDS was coupled to Fe(III) reduction to Fe(ll) in biological media consisting of trace salts and vitamins, providing estimates of bioavailability consistentwith the biogeochemical mechanisms and conditions that control Fe(III) availability to iron-reducing bacteria. Iron(III) oxide sources were synthetic oxides (amorphous and crystalline) and three soils separated into two size fractions each (0-500 and 500-1000 microm). This titration gave a measurement of the amount of Fe(III) available to dissimilatory iron-reducing bacteria and was compared to hydroxylamine reduction, oxalate extraction, and biological reduction by Shewanella alga BrY. The advantage of AHDS titration over existing chemical techniques is that it can be performed at normal soil pH and ionic strength, and it allows for distinction of iron(III) oxides rendered unavailable by sorption of Fe(II) or by other pH-dependent geochemical processes. This approach also allows distinction of Fe(III) present in micropores that is not directly available to bacteria but bioavailable in the presence of an electron shuttle capable of transporting electrons into the micropores.

Growth of Pseudomonas mendocina on Fe(III) (hydr)oxides

Although iron (Fe) is an essential element for almost all living organisms, little is known regarding its acquisition from the insoluble Fe(III) (hydr)oxides in aerobic environments. In this study a strict aerobe, Pseudomonas mendocina, was grown in batch culture with hematite, goethite, or ferrihydrite as a source of Fe. P. mendocina obtained Fe from these minerals in the following order: goethite > hematite > ferrihydrite. Furthermore, Fe release from each of the minerals appears to have occurred in excess, as evidenced by the growth of P. mendocina in the medium above that of the insoluble Fe(III) (hydr)oxide aggregates, and this release was independent of the mineral's surface area. These results demonstrate that an aerobic microorganism was able to obtain Fe for growth from several insoluble Fe minerals and did so with various growth rates.

Kinetic analysis of the bacterial reduction of goethite

The kinetics of dissimilatory reduction of goethite (alpha-FeOOH) was studied in batch cultures of a groundwater bacterium, Shewanella putrefaciens, strain CN32 in pH 7 bicarbonate buffer. The rate and extent of goethite reduction were measured as a function of electron acceptor (goethite) and donor (lactate) concentrations. Increasing goethite concentrations increased both the rate and extent of Fe(III) reduction when cell and lactate concentrations were held constant. However, constant initial reduction rates were observed after normalization to the Fe(II) sorption capacity of FeOOH, suggesting that the bacterial reduction rate was first orderwith respect to surface site concentration. Increasing the lactate concentration also increased the rate and extent of FeOOH reduction. Monod-type kinetic behaviorwas observed with respectto lactate concentration. Fe(II) sorption on FeOOH was well-described by the Langmuir sorption isotherm. However, the Fe(II) sorption capacities hyperbolically decreased with increasing FeOOH concentration (10-100 mM) implying aggregation, while the affinity constant between Fe(II) and goethite was constant (log K approximately equals 3). Evaluation of the end states of the variable FeOOH and lactate experiments when iron reduction ceased indicated a consistent excess in reaction free energy of -22.7 kJ/mol. This value was remarkably close to the minimum value reported for bacteria to mediate a given reaction (-20 kJ/mol). X-ray diffraction (XRD) and scanning electron microscopy (SEM) indicated that siderite (FeCO3) was the only biogenic Fe(II) solid formed upon FeOOH bioreduction. A kinetic biogeochemical model that incorporated Monod kinetics with respect to lactate concentration, first-order kinetics with respectto goethite surface concentration, a Gibbs free energy availability factor, the rates of Fe(II) sorption on goethite and siderite precipitation, and aqueous speciation reactions was applied to the experimental data. Using independently estimated parameters, the developed model successfully described bacterial goethite reduction with variable FeOOH and lactate concentrations.