Alice Dohnalkova

Secondary mineralization pathways induced by dissimilatory iron reduction of ferrihydrite under advective flow

Iron (hydr)oxides not only serve as potent sorbents and repositories for nutrients and contaminants but also provide a terminal electron acceptor for microbial respiration. The microbial reduction of Fe (hydr)oxides and the subsequent secondary solid-phase transformations will, therefore, have a profound influence on the biogeochemical cycling of Fe as well as associated metals. Here we elucidate the pathways and mechanisms of secondary mineralization during dissimilatory iron reduction by a common iron-reducing bacterium, Shewanella putrefaciens (strain CN32), of 2-line ferrihydrite under advective flow conditions. Secondary mineralization of ferrihydrite occurs via a coupled, biotic-abiotic pathway primarily resulting in the production of magnetite and goethite with minor amounts of green rust. Operating mineralization pathways are driven by competing abiotic reactions of bacterially generated ferrous iron with the ferrihydrite surface. Subsequent to the initial sorption of ferrous iron on ferrihydrite, goethite (via dissolution/reprecipitation) and/or magnetite (via solid-state conversion) precipitation ensues resulting in the spatial coupling of both goethite and magnetite with the ferrihydrite surface. The distribution of goethite and magnetite within the column is dictated, in large part, by flow-induced ferrous Fe profiles. While goethite precipitation occurs over a large Fe(II) concentration range, magnetite accumulation is only observed at concentrations exceeding 0.3 mmol/L (equivalent to 0.5 mmol Fe[II]/g ferrihydrite) following 16 d of reaction. Consequently, transport-regulated ferrous Fe profiles result in a progression of magnetite levels downgradient within the column. Declining microbial reduction over time results in lower Fe(II) concentrations and a subsequent shift in magnetite precipitation mechanisms from nucleation to crystal growth. While the initial precipitation rate of goethite exceeds that of magnetite, continued growth is inhibited by magnetite formation, potentially a result of lower Fe(III) activity. Conversely, the presence of lower initial Fe(II) concentrations followed by higher concentrations promotes goethite accumulation and inhibits magnetite precipitation even when Fe(II) concentrations later increase, thus revealing the importance of both the rate of Fe(II) generation and flow-induced Fe(II) profiles. As such, the operating secondary mineralization pathways following reductive dissolution of ferrihydrite at a given pH are governed principally by flow-regulated Fe(II) concentration, which drives mineral precipitation kinetics and selection of competing mineral pathways.

In vitro cell culture infectivity assay for human noroviruses

A 3-dimensional organoid human small intestinal epithelium model was used.

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.

Steam reforming of methanol over highly active Pd/ZnO catalyst

Abstract Pd/ZnO catalysts were investigated for steam reforming of methanol. Unlike precious metal-based catalysts, Pd/ZnO catalysts not only exhibited high activity, but more importantly very low selectivity to CO for methanol steam reforming. Under the conditions examined, the decomposition activity is minimal. The novel function is attributed to the formation of highly structured Pd–Zn alloy at moderate temperatures under mild reducing environments. The current catalytic system was characterized by TPR, transmission electron microscopy (TEM), H 2 chemisorption, and X-ray diffraction (XRD).

Synthesis and properties of nano zeolitic imidazolate frameworks

Nanosized zeolitic imidazolate frameworks [nZIF-8] with excellent chemical and thermal stability have been synthesized at room temperature by simple mixing of 2-methylimidazole and zinc nitrate hexahydrate in methanol/1% high molecular weight poly(diallyldimethylammonium chloride) solution for 24 h.

Influence of Mn oxides on the reduction of uranium(VI) by the metal-reducing bacterium Shewanella putrefaciens

Abstract The potential for Mn oxides to modify the biogeochemical behavior of U during reduction by the subsurface bacterium Shewanella putrefaciens strain CN32 was investigated using synthetic Mn(III/IV) oxides (pyrolusite [β-MnO2], bixbyite [Mn2O3] and K+-birnessite [K4Mn14O27 · 8H2O]). In the absence of bacteria, pyrolusite and bixbyite oxidized biogenic uraninite (UO2[s]) to soluble U(VI) species, with bixbyite being the most rapid oxidant. The Mn(III/IV) oxides lowered the bioreduction rate of U(VI) relative to rates in their absence or in the presence of gibbsite (Al[OH]3) added as a non-redox-reactive surface. Evolved Mn(II) increased with increasing initial U(VI) concentration in the biotic experiments, indicating that valence cycling of U facilitated the reduction of Mn(III/IV). Despite an excess of the Mn oxide, 43 to 100% of the initial U was bioreduced after extended incubation. Analysis of thin sections of bacterial Mn oxide suspensions revealed that the reduced U resided in the periplasmic space of the bacterial cells. However, in the absence of Mn(III/IV) oxides, UO2(s) accumulated as copious fine-grained particles external to the cell. These results indicate that the presence of Mn(III/IV) oxides may impede the biological reduction of U(VI) in subsoils and sediments. However, the accumulation of U(IV) in the cell periplasm may physically protect reduced U from oxidation, promoting at least a temporal state of redox disequilibria.

Alkaliphilus transvaalensis gen. nov., sp. nov., an extremely alkaliphilic bacterium isolated from a deep South African gold mine.

A novel extreme alkaliphile was isolated from a mine water containment dam at 3.2 km below land surface in an ultra-deep gold mine near Carletonville, South Africa. The cells of this bacterium were straight to slightly curved rods, motile by flagella and formed endospores. Growth was observed over the temperature range 20-50 degrees C (optimum 40 degrees C; 45 min doubling time) and pH range 8.5-12.5 (optimum pH 10.0). The novel isolate, one of the most alkaliphilic micro-organisms yet described, was a strictly anaerobic chemo-organotroph capable of utilizing proteinaceous substrates such as yeast extract, peptone, tryptone and casein. Elemental sulfur, thiosulfate or fumarate, when included as accessory electron acceptors, improved growth. The G+C content of genomic DNA was 36.4 mol %. Phylogenetic analysis based on the 16S rDNA sequence indicated that the isolate is a member of cluster XI within the low G+C gram-positive bacteria, but only distantly related to previously described members. On the basis of physiological and molecular properties, the isolate represents a novel species, for which the name Alkaliphilus transvaalensis gen. nov., sp. nov. is proposed (type strain SAGM1T = JCM 10712T = ATCC 700919T). The mechanism of generation of the highly alkaline microbial habitat and the possible source of the alkaliphile are discussed.

Imaging Hydrated Microbial Extracellular Polymers: Comparative Analysis by Electron Microscopy

ABSTRACT Microbe-mineral and -metal interactions represent a major intersection between the biosphere and geosphere but require high-resolution imaging and analytical tools for investigation of microscale associations. Electron microscopy has been used extensively for geomicrobial investigations, and although used bona fide, the traditional methods of sample preparation do not preserve the native morphology of microbiological components, especially extracellular polymers. Herein, we present a direct comparative analysis of microbial interactions by conventional electron microscopy approaches with imaging at room temperature and a suite of cryogenic electron microscopy methods providing imaging in the close-to-natural hydrated state. In situ, we observed an irreversible transformation of the hydrated bacterial extracellular polymers during the traditional dehydration-based sample preparation that resulted in their collapse into filamentous structures. Dehydration-induced polymer collapse can lead to inaccurate spatial relationships and hence could subsequently affect conclusions regarding the nature of interactions between microbial extracellular polymers and their environment.

Direct Involvement of Type II Secretion System in Extracellular Translocation of Shewanella oneidensis Outer Membrane Cytochromes MtrC and OmcA

MtrC and OmcA are cell surface-exposed lipoproteins important for reducing solid metal oxides. Deletions of type II secretion system (T2SS) genes reduced their extracellular release and their accessibility to the proteinase K treatment, demonstrating the direct involvement of T2SS in translocation of MtrC and OmcA to the bacterial cell surface.

Rapid electron exchange between surface-exposed bacterial cytochromes and Fe(III) minerals

The mineral-respiring bacterium Shewanella oneidensis uses a protein complex, MtrCAB, composed of two decaheme cytochromes, MtrC and MtrA, brought together inside a transmembrane porin, MtrB, to transport electrons across the outer membrane to a variety of mineral-based electron acceptors. A proteoliposome system containing a pool of internalized electron carriers was used to investigate how the topology of the MtrCAB complex relates to its ability to transport electrons across a lipid bilayer to externally located Fe(III) oxides. With MtrA facing the interior and MtrC exposed on the outer surface of the phospholipid bilayer, the established in vivo orientation, electron transfer from the interior electron carrier pool through MtrCAB to solid-phase Fe(III) oxides was demonstrated. The rates were 103 times higher than those reported for reduction of goethite, hematite, and lepidocrocite by S. oneidensis, and the order of the reaction rates was consistent with those observed in S. oneidensis cultures. In contrast, established rates for single turnover reactions between purified MtrC and Fe(III) oxides were 103 times lower. By providing a continuous flow of electrons, the proteoliposome experiments demonstrate that conduction through MtrCAB directly to Fe(III) oxides is sufficient to support in vivo, anaerobic, solid-phase iron respiration.