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

Role of outer-membrane cytochromes MtrC and OmcA in the biomineralization of ferrihydrite by Shewanella oneidensis MR-1

In an effort to improve the understanding of electron transfer mechanisms at the microbe-mineral interface, Shewanella oneidensis MR-1 mutants with in-frame deletions of outer-membrane cytochromes (OMCs), MtrC and OmcA, were characterized for the ability to reduce ferrihydrite (FH) using a suite of microscopic, spectroscopic, and biochemical techniques. Analysis of purified recombinant proteins demonstrated that both cytochromes undergo rapid electron exchange with FH in vitro with MtrC displaying faster transfer rates than OmcA. Immunomicroscopy with cytochrome-specific antibodies revealed that MtrC co-localizes with iron solids on the cell surface while OmcA exhibits a more diffuse distribution over the cell surface. After 3-day incubation of MR-1 with FH, pronounced reductive transformation mineral products were visible by electron microscopy. Upon further incubation, the predominant phases identified were ferrous phosphates including vivianite [Fe(3)(PO(4))(2)x8H(2)O] and a switzerite-like phase [Mn(3),Fe(3)(PO(4))(2)x7H(2)O] that were heavily colonized by MR-1 cells with surface-exposed outer-membrane cytochromes. In the absence of both MtrC and OmcA, the cells ability to reduce FH was significantly hindered and no mineral transformation products were detected. Collectively, these results highlight the importance of the outer-membrane cytochromes in the reductive transformation of FH and support a role for direct electron transfer from the OMCs at the cell surface to the mineral.

Outer membrane-associated serine protease involved in adhesion of Shewanella oneidensis to Fe(III) oxides

The facultative anaerobe Shewanella oneidensis MR-1 respires a variety of anaerobic electron acceptors, including insoluble Fe(III) oxides. S. oneidensis employs a number of novel strategies for respiration of insoluble Fe(III) oxides, including localization of respiratory proteins to the cell outer membrane (OM). The molecular mechanism by which S. oneidensis adheres to and respires Fe(III) oxides, however, remains poorly understood. In the present study, whole cell fractionation and MALDI-TOF-MS/MS techniques were combined to identify a serine protease (SO3800) associated with the S. oneidensis OM. SO3800 contained predicted structural motifs similar to cell surface-associated serine proteases that function as bacterial adhesins in other gram-negative bacteria. The gene encoding SO3800 was deleted from the S. oneidensis genome, and the resulting mutant strain (DeltaSO3800) was tested for its ability to adhere to and respire Fe(III) oxides. DeltaSO3800 was severely impaired in its ability to adhere to Fe(III) oxides, yet retained wild-type Fe(III) respiratory capability. Laser Doppler velocimetry and cryoetch high-resolution SEM experiments indicated that DeltaSO3800 displayed a lower cell surface charge and higher amount of surface-associated exopolysaccharides. Results of this study indicate that S. oneidensis may respire insoluble Fe(III) oxides at a distance, negating the requirement for attachment prior to electron transfer.

The Mtr respiratory pathway is essential for reducing flavins and electrodes in Shewanella oneidensis

The Mtr respiratory pathway of Shewanella oneidensis strain MR-1 is required to effectively respire both soluble and insoluble forms of oxidized iron. Flavins (riboflavin and flavin mononucleotide) recently have been shown to be excreted by MR-1 and facilitate the reduction of insoluble substrates. Other Shewanella species tested accumulated flavins in supernatants to an extent similar to that of MR-1, suggesting that flavin secretion is a general trait of the species. External flavins have been proposed to act as both a soluble electron shuttle and a metal chelator; however, at biologically relevant concentrations, our results suggest that external flavins primarily act as electron shuttles for MR-1. Using deletion mutants lacking various Mtr-associated proteins, we demonstrate that the Mtr extracellular respiratory pathway is essential for the reduction of flavins and that decaheme cytochromes found on the outer surface of the cell (MtrC and OmcA) are required for the majority of this activity. Given the involvement of external flavins in the reduction of electrodes, we monitored current production by Mtr respiratory pathway mutants in three-electrode bioreactors under controlled flavin concentrations. While mutants lacking MtrC were able to reduce flavins at 50% of the rate of the wild type in cell suspension assays, these strains were unable to grow into productive electrode-reducing biofilms. The analysis of mutants lacking OmcA suggests a role for this protein in both electron transfer to electrodes and attachment to surfaces. The parallel phenotypes of Mtr mutants in flavin and electrode reduction blur the distinction between direct contact and the redox shuttling strategies of insoluble substrate reduction by MR-1.

Electrochemical measurement of electron transfer kinetics by Shewanella oneidensis MR-1

Shewanella oneidensis strain MR-1 can respire using carbon electrodes and metal oxyhydroxides as electron acceptors, requiring mechanisms for transferring electrons from the cell interior to surfaces located beyond the cell. Although purified outer membrane cytochromes will reduce both electrodes and metals, S. oneidensis also secretes flavins, which accelerate electron transfer to metals and electrodes. We developed techniques for detecting direct electron transfer by intact cells, using turnover and single turnover voltammetry. Metabolically active cells attached to graphite electrodes produced thin (submonolayer) films that demonstrated both catalytic and reversible electron transfer in the presence and absence of flavins. In the absence of soluble flavins, electron transfer occurred in a broad potential window centered at approximately 0 V (versus standard hydrogen electrode), and was altered in single (DeltaomcA, DeltamtrC) and double deletion (DeltaomcA/DeltamtrC) mutants of outer membrane cytochromes. The addition of soluble flavins at physiological concentrations significantly accelerated electron transfer and allowed catalytic electron transfer to occur at lower applied potentials (-0.2 V). Scan rate analysis indicated that rate constants for direct electron transfer were slower than those reported for pure cytochromes (approximately 1 s(-1)). These observations indicated that anodic current in the higher (>0 V) window is due to activation of a direct transfer mechanism, whereas electron transfer at lower potentials is enabled by flavins. The electrochemical dissection of these activities in living cells into two systems with characteristic midpoint potentials and kinetic behaviors explains prior observations and demonstrates the complementary nature of S. oneidensis electron transfer strategies.

Effects of humic substances and quinones at low concentrations on ferrihydrite reduction by Geobacter metallireducens

Humic substances (HS) and quinones can accelerate dissimilatory Fe(III) reduction by electron shuttling between microorganisms and poorly soluble iron(III) (hydr)oxides. The mechanism of electron shuttling for HS is not fully understood, but it is suggested that the most important redox-active components in HS are also quinones. Here we studied the influence of HS and different quinones at low concentrations on ferrihydrite reduction by Geobacter metallireducens. The aquatic HS used were humic and fulvic acids (HA and FA) isolated from groundwater of a deep aquifer in Gorleben (Niedersachsen, Germany). HA stimulated iron reduction stronger than FA down to total HA concentrations as low as 1 mg/L. The quinones studied showed large differences: some had strong accelerating effects, whereas others showed only small effects, no effects, or even inhibitory effects on the kinetics of iron reduction. We found that the redox potentials of the most active quinones fall in a narrow range of -137 to -225 mV vs NHE at pH 7. These results give evidence that the kinetic of microbial iron reduction mediated by electron shuttles is mainly controlled by thermodynamic parameters, i.e., by the redox potential of the shuttle compound, rather than by the proportion of dissolved vs adsorbed compound.

The roles of outer membrane cytochromes of Shewanella and Geobacter in extracellular electron transfer

As key components of the electron transfer (ET) pathways used for dissimilatory reduction of solid iron [Fe(III)] (hydr)oxides, outer membrane multihaem c-type cytochromes MtrC and OmcA of Shewanella oneidensis MR-1 and OmcE and OmcS of Geobacter sulfurreducens mediate ET reactions extracellularly. Both MtrC and OmcA are at least partially exposed to the extracellular side of the outer membrane and their translocation across the outer membrane is mediated by bacterial type II secretion system. Purified MtrC and OmcA can bind Fe(III) oxides, such as haematite (α-Fe2 O3 ), and directly transfer electrons to the haematite surface. Bindings of MtrC and OmcA to haematite are probably facilitated by their putative haematite-binding motifs whose conserved sequence is Thr-Pro-Ser/Thr. Purified MtrC and OmcA also exhibit broad operating potential ranges that make it thermodynamically feasible to transfer electrons directly not only to Fe(III) oxides but also to other extracellular substrates with different redox potentials. OmcE and OmcS are proposed to be located on the Geobacter cell surface where they are believed to function as intermediates to relay electrons to type IV pili, which are hypothesized to transfer electrons directly to the metal oxides. Cell surface-localized cytochromes thus are key components mediating extracellular ET reactions in both Shewanella and Geobacter for extracellular reduction of Fe(III) oxides.

Anaerobic respiration of elemental sulfur and thiosulfate by Shewanella oneidensis MR-1 requires psrA, a homolog of the phsA gene of Salmonella enterica serovar typhimurium LT2

Shewanella oneidensis MR-1, a facultatively anaerobic gammaproteobacterium, respires a variety of anaerobic terminal electron acceptors, including the inorganic sulfur compounds sulfite (SO3(2-)), thiosulfate (S2O3(2-)), tetrathionate (S4O6(2-)), and elemental sulfur (S(0)). The molecular mechanism of anaerobic respiration of inorganic sulfur compounds by S. oneidensis, however, is poorly understood. In the present study, we identified a three-gene cluster in the S. oneidensis genome whose translated products displayed 59 to 73% amino acid similarity to the products of phsABC, a gene cluster required for S(0) and S2O3(2-) respiration by Salmonella enterica serovar Typhimurium LT2. Homologs of phsA (annotated as psrA) were identified in the genomes of Shewanella strains that reduce S(0) and S2O3(2-) yet were missing from the genomes of Shewanella strains unable to reduce these electron acceptors. A new suicide vector was constructed and used to generate a markerless, in-frame deletion of psrA, the gene encoding the putative thiosulfate reductase. The psrA deletion mutant (PSRA1) retained expression of downstream genes psrB and psrC but was unable to respire S(0) or S2O3(2-) as the terminal electron acceptor. Based on these results, we postulate that PsrA functions as the main subunit of the S. oneidensis S2O3(2-) terminal reductase whose end products (sulfide [HS-] or SO3(2-)) participate in an intraspecies sulfur cycle that drives S(0) respiration.

Kinetic characterization of OmcA and MtrC, terminal reductases involved in respiratory electron transfer for dissimilatory iron reduction in Shewanella oneidensis MR-1

We have used scaling kinetics and the concept of kinetic competence to elucidate the role of hemeproteins OmcA and MtrC in iron reduction by Shewanella oneidensis MR-1. Second-order rate constants for OmcA and MtrC were determined by single-turnover experiments. For soluble iron species, a stopped-flow apparatus was used, and for the less reactive iron oxide goethite, a conventional spectrophotometer was used to measure rates. Steady-state experiments were performed to obtain molecular rate constants by quantifying the OmcA and MtrC contents of membrane fractions and whole cells by Western blot analysis. For reduction of soluble iron, rates determined from transient-state experiments were able to account for rates obtained from steady-state experiments. However, this was not true with goethite; rate constants determined from transient-state experiments were 100 to 1,000 times slower than those calculated from steady-state experiments with membrane fractions and whole cells. In contrast, addition of flavins to the goethite experiments resulted in rates that were consistent with both transient- and steady-state experiments. Kinetic simulations of steady-state results with kinetic constants obtained from transient-state experiments supported flavin involvement. Therefore, we show for the first time that OmcA and MtrC are kinetically competent to account for catalysis of soluble iron reduction in whole Shewanella cells but are not responsible for electron transfer via direct contact alone with insoluble iron-containing minerals. This work supports the hypothesis that electron shuttles are important participants in the reduction of solid Fe phases by this organism.

Iron-binding characterization and polysaccharide production by Klebsiella oxytoca strain isolated from mine acid drainage

AIMS

To investigate Klebsiella oxytoca strain BAS-10 growth on ferric citrate under anaerobic conditions for exopolysaccharide (EPS) production and localization on cell followed by the purification and the EPS determination of the iron-binding stability constant to EPS or biotechnological applications.

METHODS AND RESULTS

Klebsiella oxytoca ferments ferric citrate under anaerobic conditions and produces a ferric hydrogel, whereas ferrous ions were formed in solution. During growth, cells precipitate and a hydrogel formation was observed: the organic material was constituted of an EPS bound to Fe(III) ions, this was found by chemical analyses of the iron species and transmission electron microscopy of the cell cultures. Iron binding to EPS was studied by cyclic voltammetric measurements, either directly on the hydrogel or in an aqueous solutions containing Fe(III)-citrate and purified Fe(III)-EPS. From the voltammetric data, the stability constant for the Fe(III)-EPS complex can be assumed to have values of approx. 10(12)-10(13). It was estimated that this is higher than for the Fe(III)-citrate complex.

CONCLUSIONS

The production of Fe(III)-EPS under anaerobic conditions is a strategy for the strain to survive in mine drainages and other acidic conditions. This physiological feature can be used to produce large amounts of valuable Fe(III)-EPS, starting from a low cost substrate such as Fe(III)-citrate.

SIGNIFICANT AND IMPACT OF THE STUDY

The data herein demonstrates that an interesting metal-binding molecule can be produced as a novel catalyst for a variety of potential applications and the EPS itself is a valuable source for rhamnose purification.

Microbial colonization of an in situ sediment cap and correlation to stratified redox zones

In situ capping is a management technique for contaminated sediments involving the placement of clean material at the sediment-water interface. This work combined porewater geochemical profiling with quantitative microbial data to investigate the intrinsic microbial colonization of a sand cap. Geochemical characterization using voltammetric microelectrodes indicated vertical stratification of biogeochemical processes within a capped sediment column. Following dissection of the column, quantitative real-time PCR (qPCR) enumerated microbial populations within each discrete redoxzone and was accompanied by terminal-restriction fragment length polymorphism (T-RFLP) to elucidate general community shifts. Bacteria and Archaea were present within the cap according to qPCR, with higher concentrations generally observed in the underlying sediment. Iron-reducing populations were detected and quantified using newly designed qPCR primer pairs for Anaeromyxobacter spp. and Shewanella spp. and published primer sets for delta-Proteobacteria and Geobacteracea. Results confirmed geochemical measurements indicating that microbial Fe(III) reduction was a major process in the overlying cap. Genes encoding microbial sulfate reduction (dsrA) and methanogenesis (mcrA) were also present within the cap but were more prevalent in the sediment. Canonical correspondence analysis of terminal-restriction fragment length polymorphism (T-RFLP) patterns verified that spatial changes in bacterial community composition were significantly correlated to depth and Fe2+ and Mn2+ concentration gradients. Cumulatively, results demonstrate that microorganisms indigenous to aquatic sediments colonized the overlying cap to form complex communities mirroring redox stratification. Implications of capping for biogeochemical cycling, contaminant fate and transport, and remedial design are discussed.

Microbial biofilm voltammetry: direct electrochemical characterization of catalytic electrode-attached biofilms

While electrochemical characterization of enzymes immobilized on electrodes has become common, there is still a need for reliable quantitative methods for study of electron transfer between living cells and conductive surfaces. This work describes growth of thin (<20 microm) Geobacter sulfurreducens biofilms on polished glassy carbon electrodes, using stirred three-electrode anaerobic bioreactors controlled by potentiostats and nondestructive voltammetry techniques for characterization of viable biofilms. Routine in vivo analysis of electron transfer between bacterial cells and electrodes was performed, providing insight into the main redox-active species participating in electron transfer to electrodes. At low scan rates, cyclic voltammetry revealed catalytic electron transfer between cells and the electrode, similar to what has been observed for pure enzymes attached to electrodes under continuous turnover conditions. Differential pulse voltammetry and electrochemical impedance spectroscopy also revealed features that were consistent with electron transfer being mediated by an adsorbed catalyst. Multiple redox-active species were detected, revealing complexity at the outer surfaces of this bacterium. These techniques provide the basis for cataloging quantifiable, defined electron transfer phenotypes as a function of potential, electrode material, growth phase, and culture conditions and provide a framework for comparisons with other species or communities.

Effects of electron transfer mediators on the bioreduction of lepidocrocite (gamma-FeOOH) by Shewanella putrefaciens CN32

Electron transfer mediators (ETMs) such as low-molecular-mass quinones (e.g., juglone and lawsone) and humic substances are believed to play a role in many redox reactions involved in contaminant transformations and the biogeochemical cycling of many redox-active elements (e.g., Fe and Mn) in aquatic and terrestrial environments. This study examines the effects of a series of compounds representing major classes of natural and synthetic organic ETMs, including low-molecular-mass quinones, humic substances, phenazines, phenoxazines, phenothiazines, and indigo derivatives, on the bioreduction of lepidocrocite (gamma-FeOOH) by the dissimilatory Fe(III)-reducing bacterium Shewanella putrefaciens CN32. Although S. putrefaciens CN32 was able to reduce lepidocrocite in the absence of exogenous ETMs, the addition of exogenous ETMs enhanced the bioreduction of lepidocrocite. In general, the rate of Fe(II) production correlated well with the reduction potentials of the ETMs. The addition of humic acids or unfractionated natural organic matter at concentrations of 10 mg organic CL(-1) resulted in, at best, a minimal enhancement of lepidocrocite bioreduction. This observation suggests that electron shuttling by humic substances is not likely to play a major role in Fe(lll) bioreduction in oligotrophic environments such as subsurface sediments with low organic C contents.

Electron transfer at the microbe-mineral interface: a grand challenge in biogeochemistry

The interplay between microorganisms and minerals is a complex and dynamic process that has sculpted the geosphere for nearly the entire history of the Earth. The work of Dr Terry Beveridge and colleagues provided some of the first insights into metal-microbe and mineral-microbe interactions and established a foundation for subsequent detailed investigations of interactions between microorganisms and minerals. Beveridge also envisioned that interdisciplinary approaches and teams would be required to explain how individual microbial cells interact with their immediate environment at nano- or microscopic scales and that through such approaches and using emerging technologies that the details of such interactions would be revealed at the molecular level. With this vision as incentive and inspiration, a multidisciplinary, collaborative team-based investigation was initiated to probe the process of electron transfer (ET) at the microbe-mineral interface. The grand challenge to this team was to address the hypothesis that multiheme c-type cytochromes of dissimilatory metal-reducing bacteria localized to the cell exterior function as the terminal reductases in ET to Fe(III) and Mn(IV) oxides. This question has been the subject of extensive investigation for years, yet the answer has remained elusive. The team involves an integrated group of experimental and computational capabilities at US Department of Energy's Environmental Molecular Sciences Laboratory, a national scientific user facility, as the collaborative focal point. The approach involves a combination of in vitro and in vivo biologic and biogeochemical experiments and computational analyses that, when integrated, provide a conceptual model of the ET process. The resulting conceptual model will be evaluated by integrating and comparing various experimental, i.e. in vitro and in vivo ET kinetics, and theoretical results. Collectively, the grand challenge will provide a detailed view of how organisms engage with mineral surfaces to exchange energy and electron density as required for life function.

Spatial and temporal evolution of biogeochemical processes following in situ capping of contaminated sediments

In situ capping has recently emerged as a remedial method for contaminated sediments and involves placing a layer of clean material at the sediment-water interface. The biogeochemical response of native sediment following capping, as well as the redoxenvironmentsthatdevelopwithinthe cap, are currently unknown. Column experiments were performed using voltammetric microelectrodes to characterize spatial and temporal distributions of biogeochemical processes in capped sediments under stagnant and upflow conditions. Oxygen penetration into sand caps extended only a few centimeters, thus maintaining underlying sediment anaerobic. Chemical species indicative of heterotrophic organic matter degradation (Mn2+, Fe2+, organic--FeIII(aq), FexSy(aq), sigmaH2S) were observed in stratified zones below the oxic layer. The majority of the overlying cap was subject to iron-reducing conditions under stagnant flow, while upflow conditions led to a compression of the redox zones toward the cap-water interface. Controls confirmed that sediment capping induced an upward, vertical shift of biogeochemical processes into the overlying cap, with redox stratification conserved. The redox conditions within the cap, specifically the predominance of iron reduction, should allow for reductive contaminant attenuation processes to extend into the overlying cap. These findings improve our understanding of the dynamics of biogeochemical processes following capping of contaminated sediments.

Shewanella secretes flavins that mediate extracellular electron transfer

Bacteria able to transfer electrons to metals are key agents in biogeochemical metal cycling, subsurface bioremediation, and corrosion processes. More recently, these bacteria have gained attention as the transfer of electrons from the cell surface to conductive materials can be used in multiple applications. In this work, we adapted electrochemical techniques to probe intact biofilms of Shewanella oneidensis MR-1 and Shewanella sp. MR-4 grown by using a poised electrode as an electron acceptor. This approach detected redox-active molecules within biofilms, which were involved in electron transfer to the electrode. A combination of methods identified a mixture of riboflavin and riboflavin-5'-phosphate in supernatants from biofilm reactors, with riboflavin representing the dominant component during sustained incubations (>72 h). Removal of riboflavin from biofilms reduced the rate of electron transfer to electrodes by >70%, consistent with a role as a soluble redox shuttle carrying electrons from the cell surface to external acceptors. Differential pulse voltammetry and cyclic voltammetry revealed a layer of flavins adsorbed to electrodes, even after soluble components were removed, especially in older biofilms. Riboflavin adsorbed quickly to other surfaces of geochemical interest, such as Fe(III) and Mn(IV) oxy(hydr)oxides. This in situ demonstration of flavin production, and sequestration at surfaces, requires the paradigm of soluble redox shuttles in geochemistry to be adjusted to include binding and modification of surfaces. Moreover, the known ability of isoalloxazine rings to act as metal chelators, along with their electron shuttling capacity, suggests that extracellular respiration of minerals by Shewanella is more complex than originally conceived.