Chaperone-assisted expression and purification of putrescine monooxygenase from Shewanella putrefaciens-95.

A putrescine monooxygenase from Shewanella putrefaciens 95 (SpPMO) is the initial enzyme catalyzing the hydroxylation of putrescine to N-hydroxyl putrescine, the precursor for the synthesis of a siderophore putrebactin was identified. This PMO clustered together with known characterized NMOs from Shewanella baltica, Bordetella pertussis, Erwinia amylovora, Streptomyces sp. Gordonia rubripertincta, Pseudomonas aeruginosa and outgrouped from Escherichia coli, Nocardia farcinica, and Rhodococcus erythropolis. The deduced SpPMO protein showed 53% and 36% sequence identity with other characterized bacterial NMOs from Erwinia amylovora and Gordonia rubripertincta respectively. In this investigation, we have cloned the complete 1518bp coding sequence of pubA from Shewanella putrefaciens 95 encoding the corresponding protein SpPMO. It comprises 505 amino acid residues in length and has approximately a molecular weight of 54 kDa. Chaperone-assisted heterologous expression of SpPMO in pET151Topo expression vector under the control of bacteriophage T7 promoter permitted a stringent IPTG dependent expression. It has been successfully cloned, overexpressed and purified as a soluble His6 -tagged enzyme using E. coli as a cloning and expression host. The expression of recombinant SpPMO was confirmed by Western blotting using anti-His6 antibody. The purified protein showed FAD and NADPH dependent N-hydroxylation activity. This study has paved a way to understand the hydroxylation step of putrebactin synthesis which can be further investigated by studying its kinetic mechanism and physiological role.

Dietary administration of the probiotic Shewanella putrefaciens Pdp11 promotes transcriptional changes of genes involved in growth and immunity in Solea senegalensis larvae.

Senegalese sole (Solea senegalensis) has been proposed as a high-potential species for aquaculture diversification in Southern Europe. It has been demonstrated that a proper feeding regimen during the first life stages influences larval growth and survival, as well as fry and juvenile quality. The bacterial strain Shewanella putrefaciens Pdp11 (SpPdp11) has shown very good probiotic properties in Senegalese sole, but information is scarce about its effect in the earliest stages of sole development. Thus, the aim of this study was to investigate the effect of SpPdp11, bioencapsulated in live diet, administered during metamorphosis (10-21 dph) or from the first exogenous feeding of Senegalese sole (2-21 dph). To evaluate the persistence of the probiotic effect, we sampled sole specimens from metamorphosis until the end of weaning (from 23 to 73 dph). This study demonstrated that probiotic administration from the first exogenous feeding produced beneficial effects on Senegalese sole larval development, given that specimens fed this diet exhibited higher and less dispersed weight, as well as increases in both total protein concentration and alkaline phosphatase activity, and in non-specific immune response. Moreover, real-time PCR documented changes in the expression of a set of genes involved in central metabolic functions including genes related to growth, genes coding for proteases (including several digestive enzymes), and genes implicated in the response to stress and in immunity. Overall, these results support the application of SpPdp11 in the first life stages of S. senegalensis as an effective tool with the clear potential to benefit sole aquaculture.

Proteomic assessment of the role of N-acyl homoserine lactone in Shewanella putrefaciens spoilage.

Shewanella spp. are the common spoilage organisms found in aquatic food products stored at low temperature and their spoilage mechanism has been reported to be mediated by quorum sensing (QS). However, the specifically expressed proteins responding to N-acyl homoserine-lactone (AHLs) were seldom reported. This study aims to evaluate the effects of different AHL signal molecules on Shewanella putrefaciens Z4 isolated from refrigerated turbot (Scophthalmus maximus) at the proteome level. The results revealed that exogenous AHLs were utilized as QS signal molecules by S. putrefaciens Z4, and AHLs were not degraded by intracellular or extracellular enzymes secreted by S. putrefaciens Z4. Twenty-three differently expressed spots upon the addition of AHLs were selected and identified by liquid chromatography-mass spectrometry (LC-MS). The results indicated that proteins involving in growth and metabolism (i.e. citrate synthase, succinate semialdehyde dehydrogenase), environment adaptation and regulators (i.e. polysaccharide deacetylases, transaldolase) were down-regulated upon three kinds of AHLs (C4-HSL, C6-HSL and O-C6-HSL), whereas the abundance of stress response protein and DNA ligase were elevated by the addition of exogenous AHLs. Moreover, the effects of exogenous C6-HSL and O-C6-HSLwere prominent. These results provide evidence that AHL-based QS signal molecules affected some important metabolic properties of S. putrefaciens. SIGNIFICANCE AND IMPACT OF THE STUDY: N-acyl homoserine lactone (AHLs)-based quorum sensing signal molecules involving in the behavior regulation in most of the Gram-negative bacteria have widely been reported. This study aims to evaluate the effect of AHLs on Shewanella putrefaciens Z4 at the proteome level. It provides the theoretic basis for elucidating the spoilage mechanism of Shewanella spp., the common spoilage micro-organism in refrigerated marine aquatic food products.

The role of FlhF and HubP as polar landmark proteins in Shewanella putrefaciens†CN-32.

Spatiotemporal regulation of cell polarity plays a role in many fundamental processes in bacteria and often relies on 'landmark' proteins which recruit the corresponding clients to their designated position. Here, we explored the localization of two multi-protein complexes, the polar flagellar motor and the chemotaxis array, in Shewanella putrefaciens CN-32. We demonstrate that polar positioning of the flagellar system, but not of the chemotaxis system, depends on the GTPase FlhF. In contrast, the chemotaxis array is recruited by a transmembrane protein which we identified as the functional ortholog of Vibrio cholerae HubP. Mediated by its periplasmic N-terminal LysM domain, SpHubP exhibits an FlhF-independent localization pattern during cell cycle similar to its Vibrio counterpart and also has a role in proper chromosome segregation. In addition, while not affecting flagellar positioning, SpHubP is crucial for normal flagellar function and is involved in type IV pili-mediated twitching motility. We hypothesize that a group of HubP/FimV homologs, characterized by a rather conserved N-terminal periplasmic section required for polar targeting and a highly variable acidic cytoplasmic part, primarily mediating recruitment of client proteins, serves as polar markers in various bacterial species with respect to different cellular functions.

Enrichment of gilthead seabream (Sparus aurata L.) diet with palm fruit extracts and probiotics: Effects on skin mucosal immunity.

Fish skin mucus contains numerous immune substances still poorly studied. To date, there are no studies regarding the possible influence of dietary supplements on such important substances. In the present work, a commercial diet used as control diet was enriched with: 1) probiotic Shewanella putrefaciens (Pdp11 diet, 10(9) cfu g(-1)); 2) probiotic Bacillus sp. (Bacillus diet, 10(9) ufc g(-1)); 3) aqueous date palm fruits extracts (DPE diet, 4%), and 4) a combination of Pdp11 + Bacillus sp + aqueous DPE (Mix diet). After 2 and 4 weeks of the feeding trial, enzymatic activities (proteases, antiproteases and peroxidases), IgM levels and terminal carbohydrates abundance were determined in skin mucus. In addition, the expression of certain immune related genes was evaluated in the skin. Our results demonstrated the significant alteration of the terminal carbohydrate abundance in skin mucus. Carbohydrates more affected by experimental diets were N-acetyl-galactosamine, N-acetyl-glucosamine, galactose, mannose, glucose and fucose. IgM, peroxidase activity and protease were also significantly higher in fish fed enriched diets. For last, an important up-regulation on the immune related gene studied on the skin was also detected. Present findings provide robust evidence that fish skin mucosal immunity can be improved by the diet.

In vitro cytokine profile revealed differences from dorsal and ventral skin susceptibility to pathogen-probiotic interaction in gilthead seabream.

Skin is the first barrier of defense on fish, which is crucial to protection against different stressors, including pathogens. Skin samples obtained from dorsal and ventral part of Sparus aurata specimens were incubated with Photobacterium damselae subsp. piscicida (a pathogen for this fish species), with Shewanella putrefaciens Pdp11 (a probiotic bacteria isolated from healthy gilthead seabream skin) or with both bacteria. The gene expression profile of nine cytokines (il1b, tnfa, il6, il7, il8, il15, il18, il10 and tgfb) was studied by qPCR in all the skin samples. The present findings revealed different patterns of cytokine profile in dorsal and ventral skin of gilthead seabream, which could be related to the influence and susceptibility to a possible infection.

Effects of Shewanella putrefaciens on innate immunity and cytokine expression profile upon high stocking density of gilthead seabream specimens.

High stocking density increases the number of emerging diseases triggering economic losses worldwide. Probiotics provide an effective and natural solution for preventing some diseases through an improvement of innate immune system among others. In the present work dietary administration of the probiotic Shewanella putrefaciens (known as Pdp11) was evaluated under stress by high stocking density after 2 and 4 weeks of administration to gilthead seabream (Sparus aurata) specimens. Results showed an increase in cellular peroxidase and respiratory burst activity as well as a modulation of cytokine profile when Pdp11 was administered to fish reared at high stocking density. Overall, our results showed how Pdp11 is not only able to improve to some extent the cellular and humoral immunity but also to increase the gene expression profile of pro-inflammatory cytokines such as il1b or il6 in response to high stocking density in gilthead seabream. These findings may support the potential use of this probiotic as functional feed against stress in fish farms.

Dietary administration of ß-1,3/1,6-glucan and probiotic strain Shewanella putrefaciens, single or combined, on gilthead seabream growth, immune responses and gene expression.

It is widely known that ß-glucans and probiotic bacteria are good immunostimulants for fish. In the present work we have evaluated the dietary effect of ß-1,3/1,6-glucan (isolated from Laminarina digitata) and Pdp 11 (Shewanella putrefaciens, probiotic isolated from gilthead seabream skin), single or combined, on growth, humoural (seric level of total IgM antibodies and peroxidase and antiprotease activities) and cellular innate immune response (peroxidase and phagocytic activities of head-kidney leucocytes), as well as the expression of immune-related genes in gilthead seabream (Sparus aurata). Four treatment groups were established: control (non-supplemented diet), Pdp 11 (10(9) cfu g(-1)), ß-1,3/1,6-glucan (0.1%) and ß-1,3/1,6-glucan + Pdp 11 (0.1% and 10(9) cfu g(-1), respectively). Fish were sampled after 1, 2 and 4 weeks of feeding. Interestingly, all supplemented diets produced increments in the seabream growth rates, mainly the Pdp 11-suplemented diet. Overall, Pdp 11 dietary administration resulted in decreased serum IgM levels and peroxidase activity. However, the seric antiprotease activity was increased in fish fed with both supplements together. Furthermore, ß-1,3/1,6-glucan and combined diet increased phagocytic activity after 2 or 4 weeks. At gene level, IL-1ß and INFγ transcripts were always up-regulated in HK but only the interleukin reached significance after 4 weeks in the group fed with ß-glucan. On the contrary, IgM gene expression tended to be down-regulated being significant after 1 week in seabream specimens fed with ß-glucan or ß-glucan plus Pdp 11. These results suggest that ß-1,3/1,6-glucan and Pdp 11 modulate the immune response and stimulates growth of the gilthead seabream, one of the species with the highest rate of production in Mediterranean aquaculture.

Abiotic reductive immobilization of U(VI) by biogenic mackinawite.

During subsurface bioremediation of uranium-contaminated sites, indigenous metal and sulfate-reducing bacteria may utilize a variety of electron acceptors, including ferric iron and sulfate that could lead to the formation of various biogenic minerals in situ. Sulfides, as well as structural and adsorbed Fe(II) associated with biogenic Fe(II)-sulfide phases, can potentially catalyze abiotic U(VI) reduction via direct electron transfer processes. In the present work, the propensity of biogenic mackinawite (Fe 1+x S, x = 0 to 0.11) to reduce U(VI) abiotically was investigated. The biogenic mackinawite produced by Shewanella putrefaciens strain CN32 was characterized by employing a suite of analytical techniques including TEM, SEM, XAS, and Mössbauer analyses. Nanoscale and bulk analyses (microscopic and spectroscopic techniques, respectively) of biogenic mackinawite after exposure to U(VI) indicate the formation of nanoparticulate UO2. This study suggests the relevance of sulfide-bearing biogenic minerals in mediating abiotic U(VI) reduction, an alternative pathway in addition to direct enzymatic U(VI) reduction.

Coupling a detergent lysis/cleanup methodology with intact protein fractionation for enhanced proteome characterization.

The expanding use of surfactants for proteome sample preparations has prompted the need to systematically optimize the application and removal of these MS-deleterious agents prior to proteome measurements. Here we compare four detergent cleanup methods (trichloroacetic acid (TCA) precipitation, chloroform/methanol/water (CMW) extraction, a commercial detergent removal spin column method (DRS) and filter-aided sample preparation (FASP)) to provide efficiency benchmarks with respect to protein, peptide, and spectral identifications in each case. Our results show that for protein-limited samples, FASP outperforms the other three cleanup methods, while at high protein amounts, all the methods are comparable. This information was used to investigate and contrast molecular weight-based fractionated with unfractionated lysates from three increasingly complex samples ( Escherichia coli K-12, a five microbial isolate mixture, and a natural microbial community groundwater sample), all of which were prepared with an SDS-FASP approach. The additional fractionation step enhanced the number of protein identifications by 8% to 25% over the unfractionated approach across the three samples.

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.

Impacts of Shewanella putrefaciens strain CN-32 cells and extracellular polymeric substances on the sorption of As(V) and As(III) on Fe(III)-(hydr)oxides.

We investigated the effects of Shewanella putrefaciens cells and extracellular polymeric substances on the sorption of As(III) and As(V) to goethite, ferrihydrite, and hematite at pH 7.0. Adsorption of As(III) and As(V) at solution concentrations between 0.001 and 20 µM decreased by 10 to 45% in the presence of 0.3 g L(-1) EPS, with As(III) being affected more strongly than As(V). Also, inactivated Shewanella cells induced desorption of As(V) from the Fe(III)-(hydr)oxide mineral surfaces. ATR-FTIR studies of ternary As(V)-Shewanella-hematite systems indicated As(V) desorption concurrent with attachment of bacterial cells at the hematite surface, and showed evidence of inner-sphere coordination of bacterial phosphate and carboxylate groups at hematite surface sites. Competition between As(V) and bacterial phosphate and carboxylate groups for Fe(III)-(oxyhydr)oxide surface sites is proposed as an important factor leading to increased solubility of As(V). The results from this study have implications for the solubility of As(V) in the soil rhizosphere and in geochemical systems undergoing microbially mediated reduction and indicate that the presence of sorbed oxyanions may affect Fe-reduction and biofilm development at mineral surfaces.

Spatially resolved force spectroscopy of bacterial surfaces using force-volume imaging.

Force spectroscopy using the atomic force microscope (AFM) is a powerful technique for measuring physical properties and interaction forces at microbial cell surfaces. Typically for such a study, the point at which a force measurement will be made is located by first imaging the cell using AFM in contact mode. In this study, we image the bacterial cell Shewanella putrefaciens for subsequent force measurements using AFM in force-volume mode and compare this to contact-mode images. It is known that contact-mode imaging does not accurately locate the apical surface and periphery of the cell since, in contact mode, a component of the applied load laterally deforms the cell during the raster scan. Here, we illustrate that contact-mode imaging does not accurately locate the apical surface and periphery of the cell since, in contact mode, a component of the applied load laterally deforms the cell during the raster scan. This is an artifact due to the deformability and high degree of curvature of bacterial cells. We further show that force-volume mode imaging avoids the artifacts associated with contact-mode imaging due to surface deformation since it involves the measurement of a grid of individual force profiles. The topographic image is subsequently reconstructed from the zero-force height (the contact distance between the AFM tip and the surface) at each point on the cell surface. We also show how force-volume measurements yield applied load versus indentation data from which mechanical properties of the cell such as Young's modulus, cell turgor pressure and elastic and plastic energies can be extracted.

pH-dependent microbial reduction of uranium(VI) in carbonate-free solutions: UV-vis, XPS, TEM, and thermodynamic studies.

U(VI)aq bioreduction has an important effect on the fate and transport of uranium isotopes in groundwater at nuclear test sites. In this study, we focus on the pH-dependent bioreduction of U(VI)aq in carbonate-free solutions and give mechanistic insight into the removal kinetics of U(VI)aq. An enhancement in the removal of U(VI)aq with increasing pH was observed within 5 h, e.g., from 19.4% at pH 4.52 to 99.7% at pH 8.30. The removal of U(VI)aq at pH 4.52 was due to the biosorption of U(VI)aq onto the living cells of Shewanella putrefaciens, as evidenced by the almost constant UV-vis absorption intensity of U(VI)aq immediately after contact with S. putrefaciens. Instead, the removal observed at pH 5.97 to 8.30 resulted from the bioreduction of U(VI)aq. The end product of U(VI)aq bioreduction was analyzed using XPS and HRTEM and identified as nanosized UO2. An increasing trend in the biosorption of U(VI)aq onto heat-killed cells was also observed, e.g., ~ 80% at pH 8.38. Evidently, the U(VI)aq that sorbed onto the living cells at pH > 4.52 was further reduced to UO2, although biosorption made a large contribution to the initial removal of U(VI)aq. These results may reveal the removal mechanism, in which the U(VI)aq that was sorbed onto cells rather than the U(VI)aq complexed in solution was reduced. The decreases in the redox potentials of the main complex species of U(VI)aq (e.g., [Formula: see text] and [Formula: see text]) with increasing pH support the proposed removal mechanism.

Structure prediction and functional analyses of a thermostable lipase obtained from Shewanella putrefaciens.

Previous experimental studies on thermostable lipase from Shewanella putrefaciens suggested the maximum activity at higher temperatures, but with little information on its conformational profile. In this study, the three-dimensional structure of lipase was predicted and a 60 ns molecular dynamics (MD) simulation was carried out at temperatures ranging from 300 to 400 K to better understand its thermostable nature at the molecular level. MD simulations were performed in order to predict the optimal activity of thermostable lipase. The results suggested strong conformational temperature dependence. The thermostable lipase maintained its bio-active conformation at 350 K during the 60 ns MD simulations.

Multiscale dynamics of the cell envelope of Shewanella putrefaciens as a response to pH change.

The bacterial surface properties of gram-negative Shewanella putrefaciens were characterized by microbial adhesion to hydrocarbons (MATH), adhesion to polystyrene dishes, and electrophoresis at different values of pH and ionic strength. The bacterial adhesion to these two apolar substrates shows significant variations according to pH and ionic strength. Such behavior could be partly explained by electrostatic repulsions between bacteria and the solid or liquid interface. However, a similar trend was also observed at rather high ionic strength where electrostatic interactions are supposed to be screened. The nanomechanical properties at pH 4 and 10 and at high ionic strength were investigated by using atomic force microscopy (AFM). The indentation curves revealed the presence of a polymeric external layer that swells and softens up with increasing pH. This suggests a concomitant increase of the water permeability and so did of the hydrophilicity of the bacterial surface. Such evolution of the bacterial envelope in response to changes in pH brings new insight to the pH dependence in the bacterial adhesion tests. It especially demonstrates the necessity to consider the hydrophobic/hydrophilic surface properties of bacteria as not univocal for the various experimental conditions investigated.

Structure of the phenol-soluble polysaccharide from Shewanella putrefaciens strain A6.

The structure of the phenol-soluble polysaccharide from Shewanella putrefaciens strain A6 has been elucidated. Chemical modifications of the polymer in conjunction with 1H and 13C NMR spectroscopy, including 2D techniques, were employed in the analysis. It is concluded that the repeating unit is composed of two nine-carbon sugars as follows: -->4)-alpha-NonpA-(2-->3)-beta-Sugp-(1--> where alpha-NonpA is 5-acetamido-7-acetamidino-8-O-acetyl-3,5,7,9-tetradeoxy-L-glycero-alpha-D-galacto-non-2-ulosonic acid (8eLeg) and beta-Sugp is 2-acetamido-2,6-dideoxy-4-C-(3'-carboxamide-2',2'-dihydroxypropyl)-beta-D-galactopyranose, with the proposed name Shewanellose (She).

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

Specific surface chemical interactions between hydrous ferric oxide and iron-reducing bacteria determined using pK(a) spectra.

A modified regularized least squares pK(a) spectrum approach is applied to determine disassociation constants and proton binding site concentrations on bacteria, hydrous ferric oxide (HFO), and bacteria/HFO composite surfaces. This involves fitting experimental acid-base titration data to a continuous binding site model for a chemically heterogeneous surface with a variety of reactive groups yielding a pK(a) spectrum. The modified parameter fitting method optimizes simultaneously for both smoothness of the pK(a) spectrum and goodness of fit, whereas other methods optimize for goodness of fit given a fixed smoothness factor. Uncertainty estimates in pK(a) spectra were made by taking the mean and standard deviation of the spectra from replicate titration data. Titration of Shewanella putrefaciens strain CN32, a facultative iron-reducing bacterial species, demonstrate five types of binding sites consistent with known cell surface groups on bacteria, with mean pK(a) values of 3.62, 4.97, 6.92, 8.22, and 9.97. Composite surfaces formed by precipitation of HFO onto bacteria surfaces were also titrated. These surfaces no longer yielded low pK(a) sites in pK(a) spectra, indicating that ferric iron interacts with the bacteria via carboxylic (low pK(a)) sites during precipitation. In addition, mechanically mixed HFO bacterial samples also showed removal of carboxylic binding sites, suggesting that solid phase HFO interacts directly with carboxylic sites on bacterial cells. Moreover, the pK(a) spectra for HFO bacterial composites were not dependent on how the composite was formed; the mechanically mixed or surface-precipitated samples exhibited very similar binding site distributions. The determined pK(a) spectra imply that the overall binding mechanism for bacteria interactions with HFO involve carboxylic groups on the bacteria binding to the most basic sites on the HFO surface in approximately 1:1 stoichiometry.

2-Nitrophenol reduction promoted by S. putrefaciens 200 and biogenic ferrous iron: the role of different size-fractions of dissolved organic matter.

The reduction of nitroaromatic compounds (listed as a priority pollutant) in natural subsurface environments typically coexists with dissimilatory reduction of iron oxides effected by dissolved organic matter (DOM). Investigating the impact of the DOM that influences those reduction processes is crucial for understanding and predicting the geochemical fate of these environmental species. This study investigated the impact of different molecular weight DOM fractions (DMWDs) on the 2-nitrophenol (2-NP) reduction by S. putrefaciens 200 (SP200) and α-Fe2O3 with lactate (excluding electron donor interference). Kinetic measurements demonstrated that 2-NP reduction rates were affected by the redox reactivity of active species under DMWDs (denoted as L-DOM, M-DOM, and H-DOM). The enhanced reduction rates are consistent with the negative shifts in peak oxidation potential values, the increases in HA-like/FA-like values, aromaticity index values and electron transfer capacity values. L-DOM acted mainly as ligands to complex Fe(II), whereas the significant role of H-DOM in reductive reactions should be acting as an electron shuttle, transferring electrons from SP200 to Fe(III) and 2-NP and from biogenic Fe(II) to 2-NP, further accelerating the 2-NP reductions. Those observations provide valuable insights into the role of DOM in the biogeochemical redox processes and the remediation of contaminated soil in a natural environment.