James K. Fredrickson

Biogenic iron mineralization accompanying the dissimilatory reduction of hydrous ferric oxide by a groundwater bacterium

Dissimilatory iron-reducing bacteria (DIRB) couple the oxidation of organic matter or H2 to the reduction of iron oxides. The factors controlling the rate and extent of these reduction reactions and the resulting solid phases are complex and poorly understood. Batch experiments were conducted with amorphous hydrous ferric oxide (HFO) and the DIRB Shewanella putrefaciens, strain CN32, in well-defined aqueous solutions to investigate the reduction of HFO and formation of biogenic Fe(II) minerals. Lactate-HFO solutions buffered with either bicarbonate or 1,4-piperazinediethanesulfonic acid (PIPES) containing various combinations of phosphate and anthraquinone-2,6-disulfonate (AQDS), were inoculated with S. putrefaciens CN32. AQDS, a humic acid analog that can be reduced to dihydroanthraquinone by CN32, was included because of its ability to function as an electron shuttle during microbial iron reduction and as an indicator of pe. Iron reduction was measured with time, and the resulting solids were analyzed by X-ray diffraction, scanning electron microscopy (SEM), and transmission electron microscopy (TEM) with energy-dispersive X-ray spectroscopy (EDS) and selected area electron diffraction (SAED). In HCO3− buffered medium with AQDS, HFO was rapidly and extensively reduced, and the resulting solids were dominated by ferrous carbonate (siderite). Ferrous phosphate (vivianite) was also present in HCO3− medium containing P, and fine-grained magnetite was present as a minor phase in HCO3− medium with or without P. In the PIPES-buffered medium, the rate and extent of reduction was strongly influenced by AQDS and P. With AQDS, HFO was rapidly converted to highly crystalline magnetite whereas in its absence, magnetite mineralization was slower and the final material less crystalline. In PIPES with both P and AQDS, a green rust type compound [Fe(6-x)IIFexIII(OH)12]x+[(A2−)x/2 · yH2O]x− was the dominant solid phase formed; in the absence of AQDS a poorly crystalline product was observed. The measured pe and nature of the solids identified were consistent with thermodynamic considerations. The composition of aqueous media in which microbial iron reduction occurred strongly impacted the rate and extent of iron reduction and the nature of the reduced solids. This, in turn, can provide a feedback control mechanism on microbial metabolism. Hence, in sediments where geochemical conditions promote magnetite formation, two-thirds of the Fe(III) will be sequestered in a form that may not be available for anaerobic bacterial respiration.

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.

Respiration of metal (hydr)oxides by Shewanella and Geobacter: a key role for multihaem c‐type cytochromes

Dissimilatory reduction of metal (e.g. Fe, Mn) (hydr)oxides represents a challenge for microorganisms, as their cell envelopes are impermeable to metal (hydr)oxides that are poorly soluble in water. To overcome this physical barrier, the Gram‐negative bacteria Shewanella oneidensis MR‐1 and Geobacter sulfurreducens have developed electron transfer (ET) strategies that require multihaem c‐type cytochromes (c‐Cyts). In S. oneidensis MR‐1, multihaem c‐Cyts CymA and MtrA are believed to transfer electrons from the inner membrane quinone/quinol pool through the periplasm to the outer membrane. The type II secretion system of S. oneidensis MR‐1 has been implicated in the reduction of metal (hydr)oxides, most likely by translocating decahaem c‐Cyts MtrC and OmcA across outer membrane to the surface of bacterial cells where they form a protein complex. The extracellular MtrC and OmcA can directly reduce solid metal (hydr)oxides. Likewise, outer membrane multihaem c‐Cyts OmcE and OmcS of G. sulfurreducens are suggested to transfer electrons from outer membrane to type IV pili that are hypothesized to relay the electrons to solid metal (hydr)oxides. Thus, multihaem c‐Cyts play critical roles in S. oneidensis MR‐1‐ and G. sulfurreducens‐mediated dissimilatory reduction of solid metal (hydr)oxides by facilitating ET across the bacterial cell envelope.

Archaeal Diversity in Waters from Deep South African Gold Mines

ABSTRACT A culture-independent molecular analysis of archaeal communities in waters collected from deep South African gold mines was performed by performing a PCR-mediated terminal restriction fragment length polymorphism (T-RFLP) analysis of rRNA genes (rDNA) in conjunction with a sequencing analysis of archaeal rDNA clone libraries. The water samples used represented various environments, including deep fissure water, mine service water, and water from an overlying dolomite aquifer. T-RFLP analysis revealed that the ribotype distribution of archaea varied with the source of water. The archaeal communities in the deep gold mine environments exhibited great phylogenetic diversity; the majority of the members were most closely related to uncultivated species. Some archaeal rDNA clones obtained from mine service water and dolomite aquifer water samples were most closely related to environmental rDNA clones from surface soil (soil clones) and marine environments (marine group I [MGI]). Other clones exhibited intermediate phylogenetic affiliation between soil clones and MGI in the Crenarchaeota. Fissure water samples, derived from active or dormant geothermal environments, yielded archaeal sequences that exhibited novel phylogeny, including a novel lineage ofEuryarchaeota. These results suggest that deep South African gold mines harbor novel archaeal communities distinct from those observed in other environments. Based on the phylogenetic analysis of archaeal strains and rDNA clones, including the newly discovered archaeal rDNA clones, the evolutionary relationship and the phylogenetic organization of the domain Archaea are reevaluated.

Biomineralization of Poorly Crystalline Fe(III) Oxides by Dissimilatory Metal Reducing Bacteria (DMRB)

Dissimilatory metal reducing bacteria (DMRB) catalyze the reduction of Fe(III) to Fe(II) in anoxic soils, sediments, and groundwater. Two-line ferrihydrite is a bioavailable Fe(III) oxide form that is exploited by DMRB as a terminal electron acceptor. A wide variety of biomineralization products result from the interaction of DMRB with 2-line ferrihydrite. Here we describe the state of knowledge on the biotransformation of synthetic 2-line ferrihydrite by laboratory cultures of DMRB using select published data and new experimental results. A facultative DMRB is emphasized ( Shewanella putrefaciens ) upon which most of this work has been performed. Key factors controlling the identity of the secondary mineral suite are evaluated including medium composition, electron donor and acceptor concentrations, ferrihydrite aging/recrystallization status, sorbed ions, and co-associated crystalline Fe(III) oxides. It is shown that crystalline ferric (goethite, hematite, lepidocrocite), ferrous (siderite, vivianite), and mixed valence (magnetite, green rust) iron solids are formed in anoxic, circumneutral DMRB incubations. Some products are well rationalized based on thermodynamic considerations, but others appear to result from kinetic pathways driven by ions that inhibit interfacial electron transfer or the precipitation of select phases. The primary factor controlling the nature of the secondary mineral suite appears to be the Fe(II) supply rate and magnitude, and its surface reaction with the residual oxide and other sorbed ions. The common observation of end-product mineral mixtures that are not at global equilibrium indicates that microenvironments surrounding respiring DMRB cells or the reaction-path trajectory (over Eh-pH space) may influence the identity of the final biomineralization suite.

Reduction of U(VI) in goethite (α-FeOOH) suspensions by a dissimilatory metal-reducing bacterium

Abstract Dissimilatory metal-reducing bacteria (DMRB) can utilize Fe(III) associated with aqueous complexes or solid phases, such as oxide and oxyhydroxide minerals, as a terminal electron acceptor coupled to the oxidation of H2 or organic substrates. These bacteria are also capable of reducing other metal ions including Mn(IV), Cr(VI), and U(VI), a process that has a pronounced effect on their solubility and overall geochemical behavior. In spite of considerable study on an individual basis, the biogeochemical behavior of multiple metals subject to microbial reduction is poorly understood. To probe these complex processes, the reduction of U(VI) by the subsurface bacterium, Shewanella putrefaciens CN32, was investigated in the presence of goethite under conditions where the aqueous composition was controlled to vary U speciation and solubility. Uranium(VI), as the carbonate complexes UO2(CO3)3(aq)4− and UO2(CO3)2(aq)2−, was reduced by the bacteria to U(IV) with or without goethite [α-FeOOH(s)] present. Uranium(VI) in 1,4-piperazinediethhanesulfonic acid (PIPES) buffer that was estimated to be present predominantly as the U(VI) mineral metaschoepite [UO3 · 2H2O(s)], was also reduced by the bacteria with or without goethite. In contrast, only ∼30% of the U(VI) associated with a synthetic metaschoepite was reduced by the organism in the presence of goethite with 1 mM lactate as the electron donor. This may have been due to the formation of a layer of UO2(s) or Fe(OH)3(s) on the surface of the metaschoepite that physically obstructed further bioreduction. Increasing the lactate to a non-limiting concentration (10 mM) increased the reduction of U(VI) from metaschoepite to greater than 80% indicating that the hypothesized surface-veneering effect was electron donor dependent. Uranium(VI) was also reduced by bacterially reduced anthraquinone-2,6-disulfonate (AQDS) in the absence of cells, and by Fe(II) sorbed to goethite in abiotic control experiments. In the absence of goethite, uraninite was a major product of direct microbial reduction and reduction by AH2DS. These results indicate that DMRB, via a combination of direct enzymatic or indirect mechanisms, can reduce U(VI) to insoluble U(IV) in the presence of solid Fe oxides.

c-Type cytochrome-dependent formation of U(IV) nanoparticles by Shewanella oneidensis.

Modern approaches for bioremediation of radionuclide contaminated environments are based on the ability of microorganisms to effectively catalyze changes in the oxidation states of metals that in turn influence their solubility. Although microbial metal reduction has been identified as an effective means for immobilizing highly-soluble uranium(VI) complexes in situ, the biomolecular mechanisms of U(VI) reduction are not well understood. Here, we show that c-type cytochromes of a dissimilatory metal-reducing bacterium, Shewanella oneidensis MR-1, are essential for the reduction of U(VI) and formation of extracelluar UO 2 nanoparticles. In particular, the outer membrane (OM) decaheme cytochrome MtrC (metal reduction), previously implicated in Mn(IV) and Fe(III) reduction, directly transferred electrons to U(VI). Additionally, deletions of mtrC and/or omcA significantly affected the in vivo U(VI) reduction rate relative to wild-type MR-1. Similar to the wild-type, the mutants accumulated UO 2 nanoparticles extracellularly to high densities in association with an extracellular polymeric substance (EPS). In wild-type cells, this UO 2-EPS matrix exhibited glycocalyx-like properties and contained multiple elements of the OM, polysaccharide, and heme-containing proteins. Using a novel combination of methods including synchrotron-based X-ray fluorescence microscopy and high-resolution immune-electron microscopy, we demonstrate a close association of the extracellular UO 2 nanoparticles with MtrC and OmcA (outer membrane cytochrome). This is the first study to our knowledge to directly localize the OM-associated cytochromes with EPS, which contains biogenic UO 2 nanoparticles. In the environment, such association of UO 2 nanoparticles with biopolymers may exert a strong influence on subsequent behavior including susceptibility to oxidation by O 2 or transport in soils and sediments.

Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments

We have developed a radiation resistant bacterium for the treatment of mixed radioactive wastes containing ionic mercury. The high cost of remediating radioactive waste sites from nuclear weapons production has stimulated the development of bioremediation strategies using Deinococcus radiodurans, the most radiation resistant organism known. As a frequent constituent of these sites is the highly toxic ionic mercury (Hg) (II), we have generated several D. radiodurans strains expressing the cloned Hg (II) resistance gene (merA) from Escherichia coli strain BL308. We designed four different expression vectors for this purpose, and compared the relative advantages of each. The strains were shown to grow in the presence of both radiation and ionic mercury at concentrations well above those found in radioactive waste sites, and to effectively reduce Hg (II) to the less toxic volatile elemental mercury. We also demonstrated that different gene clusters could be used to engineer D. radiodurans for treatment of mixed radioactive wastes by developing a strain to detoxify both mercury and toluene. These expression systems could provide models to guide future D. radiodurans engineering efforts aimed at integrating several remediation functions into a single host.

Stochastic and deterministic assembly processes in subsurface microbial communities

A major goal of microbial community ecology is to understand the forces that structure community composition. Deterministic selection by specific environmental factors is sometimes important, but in other cases stochastic or ecologically neutral processes dominate. Lacking is a unified conceptual framework aiming to understand why deterministic processes dominate in some contexts but not others. Here we work toward such a framework. By testing predictions derived from general ecological theory we aim to uncover factors that govern the relative influences of deterministic and stochastic processes. We couple spatiotemporal data on subsurface microbial communities and environmental parameters with metrics and null models of within and between community phylogenetic composition. Testing for phylogenetic signal in organismal niches showed that more closely related taxa have more similar habitat associations. Community phylogenetic analyses further showed that ecologically similar taxa coexist to a greater degree than expected by chance. Environmental filtering thus deterministically governs subsurface microbial community composition. More importantly, the influence of deterministic environmental filtering relative to stochastic factors was maximized at both ends of an environmental variation gradient. A stronger role of stochastic factors was, however, supported through analyses of phylogenetic temporal turnover. Although phylogenetic turnover was on average faster than expected, most pairwise comparisons were not themselves significantly non-random. The relative influence of deterministic environmental filtering over community dynamics was elevated, however, in the most temporally and spatially variable environments. Our results point to general rules governing the relative influences of stochastic and deterministic processes across micro- and macro-organisms.

Structure of a bacterial cell surface decaheme electron conduit

Some bacterial species are able to utilize extracellular mineral forms of iron and manganese as respiratory electron acceptors. In Shewanella oneidensis this involves decaheme cytochromes that are located on the bacterial cell surface at the termini of trans-outer-membrane electron transfer conduits. The cell surface cytochromes can potentially play multiple roles in mediating electron transfer directly to insoluble electron sinks, catalyzing electron exchange with flavin electron shuttles or participating in extracellular intercytochrome electron exchange along “nanowire” appendages. We present a 3.2-Å crystal structure of one of these decaheme cytochromes, MtrF, that allows the spatial organization of the 10 hemes to be visualized for the first time. The hemes are organized across four domains in a unique crossed conformation, in which a staggered 65-Å octaheme chain transects the length of the protein and is bisected by a planar 45-Å tetraheme chain that connects two extended Greek key split β-barrel domains. The structure provides molecular insight into how reduction of insoluble substrate (e.g., minerals), soluble substrates (e.g., flavins), and cytochrome redox partners might be possible in tandem at different termini of a trifurcated electron transport chain on the cell surface.