Metal reduction and iron biomineralization by a psychrotolerant Fe(III)-reducing bacterium, Shewanella sp. strain PV-4

Artificial and Biosynthetic Nanoparticles Boost Bioelectrochemical Reactions via Efficient Bidirectional Electron Transfer of Shewanella loihica

Bioelectrochemical reactions using whole-cell biocatalysts are promising carbon-neutral approaches because of their easy operation, low cost, and sustainability. Bidirectional (outward or inward) electron transfer via exoelectrogens plays the main role in driving bioelectrochemical reactions. However, the low electron transfer efficiency seriously inhibits bioelectrochemical reaction kinetics. Here, a three dimensional and artificial nanoparticles-constituent inverse opal-indium tin oxide (IO-ITO) electrode is fabricated and employed to connect with exoelectrogens (Shewanella loihica PV-4). The above electrode collected 128-fold higher cell density and exhibited a maximum current output approaching 1.5 mA cm-2 within 24 h at anode mode. By changing the IO-ITO electrode to cathode mode, the exoelectrogens exhibited the attractive ability of extracellular electron uptake to reduce fumarate and 16 times higher reverse current than the commercial carbon electrode. Notably, Fe-containing oxide nanoparticles are biologically synthesized at both sides of the outer cell membrane and probably contributed to direct electron transfer with the transmembrane c-type cytochromes. Owing to the efficient electron exchange via artificial and biosynthetic nanoparticles, bioelectrochemical CO2 reduction is also realized at the cathode. This work not only explored the possibility of augmenting bidirectional electron transfer but also provided a new strategy to boost bioelectrochemical reactions by introducing biohybrid nanoparticles.

Electrochemical Characterization of Two Gut Microbial Strains Cooperatively Promoting Multiple Sclerosis Pathogenesis

In this study, we explored the extracellular electron transfer (EET) capabilities of two bacterial strains, OTU0001 and OTU0002, which are demonstrated in biofilm formation in mouse gut and the induction of autoimmune diseases like multiple sclerosis. OTU0002 displayed significant electrogenic behaviour, producing microbial current on an indium tin-doped oxide electrode surface, particularly in the presence of glucose, with a current density of 60 nA/cm2. The presence of cell-surface redox substrate potentially mediating EET was revealed by the redox-based staining method and electrochemical voltammetry assay. However, medium swapping analyses and the addition of flavins, a model redox mediator, suggest that the current production is dominated by soluble endogenous redox substrates in OTU0002. Given redox substrates were detected at the cell surface, the secreted redox molecule may interact with the cellular surface of OTU0002. In contrast to OTU0002, OTU0001 did not exhibit notable electrochemical activity, lacking cell-surface redox molecules. Further, the mixture of the two strains did not increase the current production from OTU0001, suggesting that OTU0001 does not support the EET mechanism of OTU0002. The present work revealed the coexistence of EET and non-EET capable pathogens in multi-species biofilm.

Fe(III) (oxyhydr)oxide reduction by the thermophilic iron-reducing bacterium Desulfovulcanus ferrireducens

Some thermophilic bacteria from deep-sea hydrothermal vents grow by dissimilatory iron reduction, but our understanding of their biogenic mineral transformations is nascent. Mineral transformations catalyzed by the thermophilic iron-reducing bacterium Desulfovulcanus ferrireducens during growth at 55°C were examined using synthetic nanophase ferrihydrite, akaganeite, and lepidocrocite separately as terminal electron acceptors. Spectral analyses using visible-near infrared (VNIR), Fourier-transform infrared attenuated total reflectance (FTIR-ATR), and Mössbauer spectroscopies were complemented with x-ray diffraction (XRD) and transmission electron microscopy (TEM) using selected area electron diffraction (SAED) and energy dispersive X-ray (EDX) analyses. The most extensive biogenic mineral transformation occurred with ferrihydrite, which produced a magnetic, visibly dark mineral with spectral features matching cation-deficient magnetite. Desulfovulcanus ferrireducens also grew on akaganeite and lepidocrocite and produced non-magnetic, visibly dark minerals that were poorly soluble in the oxalate solution. Bioreduced mineral products from akaganeite and lepidocrocite reduction were almost entirely absorbed in the VNIR spectroscopy in contrast to both parent minerals and the abiotic controls. However, FTIR-ATR and Mössbauer spectra and XRD analyses of both biogenic minerals were almost identical to the parent and control minerals. The TEM of these biogenic minerals showed the presence of poorly crystalline iron nanospheres (50-200 nm in diameter) of unknown mineralogy that were likely coating the larger parent minerals and were absent from the controls. The study demonstrated that thermophilic bacteria transform different types of Fe(III) (oxyhydr)oxide minerals for growth with varying mineral products. These mineral products are likely formed through dissolution-reprecipitation reactions but are not easily predictable through chemical equilibrium reactions alone.

Spectral Detection of Nanophase Iron Minerals Produced by Fe(III)-Reducing Hyperthermophilic Crenarchaea

Mineral transformations by two hyperthermophilic Fe(III)-reducing crenarchaea, Pyrodictium delaneyi and Pyrobaculum islandicum, were examined using synthetic nanophase ferrihydrite, lepidocrocite, and akaganeite separately as terminal electron acceptors and compared with abiotic mineral transformations under similar conditions. Spectral analyses using visible-near-infrared, Fourier-transform infrared attenuated total reflectance (FTIR-ATR), Raman, and Mössbauer spectroscopies were complementary and revealed formation of various biomineral assemblages distinguishable from abiotic phases. The most extensive biogenic mineral transformation occurred with ferrihydrite, which formed primarily magnetite with spectral features similar to biomagnetite relative to a synthetic magnetite standard. The FTIR-ATR spectra of ferrihydrite bioreduced by P. delaneyi also showed possible cell-associated organics such as exopolysaccharides. Such combined detections of biomineral assemblages and organics might serve as biomarkers for hyperthermophilic Fe(III) reduction. With lepidocrocite, P. delaneyi produced primarily a ferrous carbonate phase reminiscent of siderite, and with akaganeite, magnetite and a ferrous phosphate phase similar to vivianite were formed. P. islandicum showed minor biogenic production of a ferrous phosphate similar to vivianite when grown on lepidocrocite, and a mixed valent phosphate or sulfate mineral when grown on akaganeite. These results expand the range of biogenic mineral transformations at high temperatures and identify spacecraft-relevant spectroscopies suitable for discriminating mineral biogenicity.

A Novel Ag@AgCl Nanoparticle Synthesized by Arctic Marine Bacterium: Characterization, Activity and Mechanism

An additive- and pollution-free method for the preparation of biogenic silver and silver chloride nanoparticles (Ag@AgCl NPs) was developed from the bacteria Shewanella sp. Arc9-LZ, which was isolated from the deep sea of the Arctic Ocean. The optimal synthesizing conditions were explored, including light, pH, Ag⁺ concentration and time. The nanoparticles were studied by means of ultraviolet-visible (UV-Vis) spectrophotometry, energy dispersive spectrometry (EDS), X-ray diffraction (XRD) and inductively coupled plasma optical emission spectrometers (ICP-OES). The transmission electron microscope (TEM) showed that the nanoparticles were spherical and well dispersed, with particle sizes less than 20.00 nm. With Ag@AgCl nanoparticles, the kinetic rate constants for congo red (CR) and rhodamine B (RhB) dye degradation were 2.74 × 10^-1 min^-1 and 7.78 × 10^-1 min^-1, respectively. The maximum decolourization efficiencies of CR and RhB were 93.36% and 99.52%, respectively. Ag@AgCl nanoparticles also showed high antibacterial activities against the Gram-positive and Gram-negative bacteria. The Fourier transform infrared spectroscopy (FTIR) spectrum indicated that the O-H, N-H and -COO- groups in the supernatant of Arc9-LZ might participate in the reduction, stabilization and capping of nanoparticles. We mapped the schematic diagram on possible mechanisms for synthesizing Ag@AgCl NPs.

Growth and genome-based insights of Fe(III) reduction of the high-temperature and NaCl-tolerant Shewanella xiamenensis from Changqing oilfield of China

Introduction

A facultative anaerobe bacterium Shewanella xiamenensis CQ-Y1 was isolated from the wastewater of Changqing oilfield in Shaanxi Province of China. Shewanella is the important dissimilatory metal-reducing bacteria. It exhibited a well potential application in biodegradation and bioremediation.

Methods

Genome sequencing, assembling and functional annotation were conducted to explore the genome information of CQ-Y1. The effect of temperatures and NaCl concentrations on the CQ-Y1 growth and Fe(III) reduction were investigated by UV visible spectrophotometry, SEM and XRD.

Results

Genomic analysis revealed its complete genome was a circular chromosome of 4,710,887 bp with a GC content of 46.50% and 4,110 CDSs genes, 86 tRNAs and 26 rRNAs. It contains genes encoding for Na⁺/H⁺ antiporter, K⁺/Cl^- transporter, heat shock protein associated with NaCl and high-temperature resistance. The presence of genes related to flavin, Cytochrome c, siderophore, and other related proteins supported Fe(III) reduction. In addition, CQ-Y1 could survive at 10% NaCl (w/v) and 45°C, and temperature showed more pronounced effects than NaCl concentration on the bacterial growth. The maximum Fe(III) reduction ratio of CQ-Y1 reached 70.1% at 30°C without NaCl, and the reduction reaction remained active at 40°C with 3% NaCl (w/v). NaCl concentration was more effective than temperature on microbial Fe(III) reduction. And the reduction products under high temperature and high NaCl conditions were characterized as Fe₃(PO₄)₂, FeCl₂ and Fe(OH)₂.

Discussion

Accordingly, a Fe(III) reduction mechanism of CQ-Y1 mediated by Cytochrome c and flavin was hypothesised. These findings could provide information for a better understanding of the origin and evolution of genomic and metabolic diversity of S. xiamenensis.

Dielectric constants of organic pollutants determine their strength for enhancing microbial iron reduction

Physicochemical properties are essential characteristics of organic compounds, which not only impact the fate of organic pollutants but also determine their application in biological processes. Here, we first found that the dielectric constants (ɛ) of organic pollutants negatively correlated to their strength for enhancing microbial Fe(III) reduction. Those with lower ɛ values than 2.61 potentially promoted the above process following the sequence carbon tetrachloride (CT) > benzene > toluene > tetrachloroethylene (PCE) due to their different ability to deprotonate the phosphorus-related groups on the outer cell membrane of iron-reducing bacteria Shewanella oneidensis MR-1 (MR-1). The stronger deprotonation of phosphorus-related groups induced more negative charge of cell surface and more strongly increased cell membrane permeability and consequently stimulated faster release of flavin mononucleotide (FMN) as an electron shuttle/cofactor for Fe(III) reduction. These findings are significant for understanding the biogeochemistry in multi-organic contaminated subsurface and providing knowledge for remediation strategies and current production.

Insights into the Biosynthesis of Nanoparticles by the Genus Shewanella

The exploitation of microorganisms for the fabrication of nanoparticles (NPs) has garnered considerable research interest globally. The microbiological transformation of metals and metal salts into respective NPs can be achieved under environmentally benign conditions, offering a more sustainable alternative to chemical synthesis methods. Species of the metal-reducing bacterial genus Shewanella are able to couple the oxidation of various electron donors, including lactate, pyruvate, and hydrogen, to the reduction of a wide range of metal species, resulting in biomineralization of a multitude of metal NPs. Single-metal-based NPs as well as composite materials with properties equivalent or even superior to physically and chemically produced NPs have been synthesized by a number of Shewanella species. A mechanistic understanding of electron transfer-mediated bioreduction of metals into respective NPs by Shewanella is crucial in maximizing NP yields and directing the synthesis to produce fine-tuned NPs with tailored properties. In addition, thorough investigations into the influence of process parameters controlling the biosynthesis is another focal point for optimizing the process of NP generation. Synthesis of metal-based NPs using Shewanella species offers a low-cost, eco-friendly alternative to current physiochemical methods. This article aims to shed light on the contribution of Shewanella as a model organism in the biosynthesis of a variety of NPs and critically reviews the current state of knowledge on factors controlling their synthesis, characterization, potential applications in different sectors, and future prospects.

Release of trace elements during bioreductive dissolution of magnetite from metal mine tailings: Potential impact on marine environments

Adverse impacts of mine tailings on water and sediments quality are major worldwide environmental problems. Due to the environmental issues associated with the deposition of mine tailings on land, a controversial discussed alternative is submarine tailings disposal (STD). However, Fe(III) bioreduction of iron oxides (e.g., magnetite) in the tailings disposed might cause toxic effects on coastal environments due to the release of different trace elements (TEs) contained in the oxides. To study the extent and kinetics of magnetite bioreduction under marine conditions and the potential release of TEs, a number of batch experiments with artificial seawater (pH 8.2) and a marine microbial strain (Shewanella loihica) were performed using several magnetite ore samples from different mines and a mine tailings sample. The elemental composition of the magnetite determined in the tailings showed relatively high amounts of TEs (e.g., Mn, Zn, Co) compared with those of the magnetite ore samples (LA-ICP-MS and EMPA analyses). The experiments were conducted at 10 °C in the dark for up to 113 days. Based on the consumption of lactate and production of acetate and aqueous Fe(II) over time, the magnitude of Fe(III) bioreduction was calculated using a geochemical model including Monod kinetics. Model simulations reproduced the release of iron and TEs observed throughout the experiments, e.g., Mn (up to 203 μg L^-1), V (up to 79 μg L^-1), As (up to 17 μg L^-1) and Cu (up to 328 μg L^-1), suggesting a potential contamination of pore water by STD. Therefore, the results of this study can help to better evaluate the potential impacts of STD.

Identification of a pathway for electron uptake in Shewanella oneidensis

Extracellular electron transfer (EET) could enable electron uptake into microbial metabolism for the synthesis of complex, energy dense organic molecules from CO2 and renewable electricity1-6. Theoretically EET could do this with an efficiency comparable to H2-oxidation7,8 but without the need for a volatile intermediate and the problems it causes for scale up9. However, significant gaps remain in understanding the mechanism and genetics of electron uptake. For example, studies of electron uptake in electroactive microbes have shown a role for the Mtr EET complex in the electroactive microbe Shewanella oneidensis MR-110-14, though there is substantial variation in the magnitude of effect deletion of these genes has depending on the terminal electron acceptor used. This speaks to the potential for previously uncharacterized and/or differentially utilized genes involved in electron uptake. To address this, we screened gene disruption mutants for 3667 genes, representing ≈99% of all nonessential genes, from the S. oneidensis whole genome knockout collection using a redox dye oxidation assay. Confirmation of electron uptake using electrochemical testing allowed us to identify five genes from S. oneidensis that are indispensable for electron uptake from a cathode. Knockout of each gene eliminates extracellular electron uptake, yet in four of the five cases produces no significant defect in electron donation to an anode. This result highlights both distinct electron uptake components and an electronic connection between aerobic and anaerobic electron transport chains that allow electrons from the reversible EET machinery to be coupled to different respiratory processes in S. oneidensis. Homologs to these genes across many different genera suggesting that electron uptake by EET coupled to respiration could be widespread. These gene discoveries provide a foundation for: studying this phenotype in exotic metal-oxidizing microbes, genetic optimization of electron uptake in S. oneidensis; and genetically engineering electron uptake into a highly tractable host like E. coli to complement recent advances in synthetic CO2 fixation15.

Microbiologically influenced corrosion inhibition mechanisms in corrosion protection: A review

Microbial activities can change the properties of biofilm/metal interfaces to accelerate or decelerate the corrosion of metals in a given environment. Microbiologically influenced corrosion inhibition (MICI) is the inhibition of corrosion that is directly or indirectly induced by microbial action. Compared with conventional methods for protection from corrosion, MICI is environmentally friendly and an emerging approach for the prevention and treatment of (bio)corrosion. However, due to the diversity of microorganisms and the fact that their metabolic processes are greatly complicated by environmental factors, MICI is still facing challenges for practical application. This review provides a comprehensive overview of the mechanisms of MICI under different conditions and their advantages and disadvantages for potential applications in corrosion protection.

Towards Bioleaching of a Vanadium Containing Magnetite for Metal Recovery

Vanadium - a transition metal - is found in the ferrous-ferric mineral, magnetite. Vanadium has many industrial applications, such as in the production of high-strength low-alloy steels, and its increasing global industrial consumption requires new primary sources. Bioleaching is a biotechnological process for microbially catalyzed dissolution of minerals and wastes for metal recovery such as biogenic organic acid dissolution of bauxite residues. In this study, 16S rRNA gene amplicon sequencing was used to identify microorganisms in Nordic mining environments influenced by vanadium containing sources. These data identified gene sequences that aligned to the Gluconobacter genus that produce gluconic acid. Several strategies for magnetite dissolution were tested including oxidative and reductive bioleaching by acidophilic microbes along with dissimilatory reduction by Shewanella spp. that did not yield significant metal release. In addition, abiotic dissolution of the magnetite was tested with gluconic and oxalic acids, and yielded 3.99 and 81.31% iron release as a proxy for vanadium release, respectively. As a proof of principle, leaching via gluconic acid production by Gluconobacter oxydans resulted in a maximum yield of 9.8% of the available iron and 3.3% of the vanadium. Addition of an increased concentration of glucose as electron donor for gluconic acid production alone, or in combination with calcium carbonate to buffer the pH, increased the rate of iron dissolution and final vanadium recoveries. These data suggest a strategy of biogenic organic acid mediated vanadium recovery from magnetite and point the way to testing additional microbial species to optimize the recovery.

Microorganisms from deep-sea hydrothermal vents

With a rich variety of chemical energy sources and steep physical and chemical gradients, hydrothermal vent systems offer a range of habitats to support microbial life. Cultivation-dependent and independent studies have led to an emerging view that diverse microorganisms in deep-sea hydrothermal vents live their chemolithoautotrophic, heterotrophic, or mixotrophic life with versatile metabolic strategies. Biogeochemical processes are mediated by microorganisms, and notably, processes involving or coupling the carbon, sulfur, hydrogen, nitrogen, and metal cycles in these unique ecosystems. Here, we review the taxonomic and physiological diversity of microbial prokaryotic life from cosmopolitan to endemic taxa and emphasize their significant roles in the biogeochemical processes in deep-sea hydrothermal vents. According to the physiology of the targeted taxa and their needs inferred from meta-omics data, the media for selective cultivation can be designed with a wide range of physicochemical conditions such as temperature, pH, hydrostatic pressure, electron donors and acceptors, carbon sources, nitrogen sources, and growth factors. The application of novel cultivation techniques with real-time monitoring of microbial diversity and metabolic substrates and products are also recommended.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-020-00086-4.

Microbial-based magnetic nanoparticles production: a mini-review

The ever-increasing biomedical application of magnetic nanoparticles (MNPs) implies increasing demand in their scalable and high-throughput production, with finely tuned and well-controlled characteristics. One of the options to meet the demand is microbial production by nanoparticles-synthesizing bacteria. This approach has several benefits over the standard chemical synthesis methods, including improved homogeneity of synthesis, cost-effectiveness, safety and eco-friendliness. There are, however, specific challenges emanating from the nature of the approach that are to be accounted and resolved in each manufacturing instance. Most of the challenges can be resolved by proper selection of the producing organism and optimizing cell culture and nanoparticles extraction conditions. Other issues require development of proper continuous production equipment, medium usage optimization and precursor ions recycling. This mini-review focuses on the related topics in microbial synthesis of MNPs: producing organisms, culturing methods, nanoparticles characteristics tuning, nanoparticles yield and synthesis timeframe considerations, nanoparticles isolation as well as on the respective challenges and possible solutions.

Siderite-based anaerobic iron cycle driven by autotrophic thermophilic microbial consortium

Using a sample from a terrestrial hot spring (pH 6.8, 60 °C), we enriched a thermophilic microbial consortium performing anaerobic autotrophic oxidation of hydrothermal siderite (FeCO₃), with CO₂/bicarbonate as the electron acceptor and the only carbon source, producing green rust and acetate. In order to reproduce Proterozoic environmental conditions during the deposition of banded iron formation (BIF), we incubated the microbial consortium in a bioreactor that contained an unmixed anoxic layer of siderite, perfectly mixed N₂/CO₂-saturated liquid medium and microoxic (2% O₂) headspace. Long-term incubation (56 days) led to the formation of magnetite (Fe₃O₄) instead of green rust as the main product of Fe(II) oxidation, the precipitation of newly formed metabolically induced siderite in the anoxic zone, and the deposition of hematite (Fe₂O₃) on bioreactor walls over the oxycline boundary. Acetate was the only metabolic product of CO₂/bicarbonate reduction. Thus, we have demonstrated the ability of autotrophic thermophilic microbial consortium to perform a short cycle of iron minerals transformation: siderite–magnetite–siderite, accompanied by magnetite and hematite accumulation. This cycle is believed to have driven the evolution of the early biosphere, leading to primary biomass production and deposition of the main iron mineral association of BIF.

Geochemical and isotopic study of abiotic nitrite reduction coupled to biologically produced Fe(II) oxidation in marine environments

Estuarine sediments are often characterized by abundant iron oxides, organic matter, and anthropogenic nitrogen compounds (e.g., nitrate and nitrite). Anoxic dissimilatory iron reducing bacteria (e.g., Shewanella loihica) are ubiquitous in these environments where they can catalyze the reduction of Fe(III) (oxyhydr)oxides, thereby releasing aqueous Fe(II). The biologically produced Fe(II) can later reduce nitrite to form nitrous oxide. The effect on nitrite reduction by both biologically produced and artificially amended Fe(II) was examined experimentally. Ferrihydrite was reduced by Shewanella loihica in a batch reaction with an anoxic synthetic sea water medium. Some of the Fe(II) released by S. loihica adsorbed onto ferrihydrite, which was involved in the transformation of ferrihydrite to magnetite. In a second set of experiments with identical medium, no microorganism was present, instead, Fe(II) was amended. The amount of solid-bound Fe(II) in the experiments with bioproduced Fe(II) increased the rate of abiotic NO₂^- reduction with respect to that with synthetic Fe(II), yielding half-lives of 0.07 and 0.47 d, respectively. The δ¹⁸O and δ¹⁵N of NO₂^- was measured through time for both the abiotic and innoculated experiments. The ratio of ε¹⁸O/ε¹⁵N was 0.6 for the abiotic experiments and 3.1 when NO₂^- was reduced by S. loihica, thus indicating two different mechanisms for the NO₂^- reduction. Notably, there is a wide range of the ε¹⁸O/ε¹⁵N values in the literature for abiotic and biotic NO₂^- reduction, as such, the use of this ratio to distinguish between reduction mechanisms in natural systems should be taken with caution. Therefore, we suggest an additional constraint to identify the mechanisms (i.e. abiotic/biotic) controlling NO₂^- reduction in natural settings through the correlation of δ¹⁵N-NO₂^- and the aqueous Fe(II) concentration.

Simultaneous cobalt(III)-histidine reduction and aerobic denitrification by Paracoccus versutus LYM

Cobalt(II)-histidine [Co(II)His] is potentially a better alternative to ferrous complexes in the chemical absorption-biological reduction (CABR) flue gas denitrification process in view of its higher oxygenation reversibility. Though with excellent O₂-resistant ability, Co(II)His was still gradually oxidized into Co(III)His, losing NO binding capacity. Thus, Co(III)His biological reduction is an indispensable step in CABR process. Co(III)His reduction by Paracoccus versutus LYM under aerobic condition in the presence of nitrate or nitrite was investigated. Results indicated that simultaneous Co(III)His reduction and aerobic denitrification were achieved by strain LYM. Co(III)His reduction was significantly promoted by denitrification process, but dramatically inhibited by 5-15 mM sulfite. Co(II)His absorbent regeneration could be facilitated by adjusting O₂ supply properly or adding nitrogen and carbon source regularly. These findings provide a basis for the application of Co(II)His as the absorbent in the CABR process and qualify P. versutus LYM as an applicable and competitive strain for this process.

Formation of Zerovalent Iron in Iron-Reducing Cultures of Methanosarcina barkeri

Methanogenic archaea have been shown to reduce iron from ferric [Fe(III)] to ferrous [Fe(II)] state, but minerals that form during iron reduction by different methanogens remain to be characterized. Here, we show that zerovalent iron (ZVI) minerals, ferrite [α-Fe(0)] and austenite [γ-Fe(0)], appear in the X-ray diffraction spectra minutes after the addition of ferrihydrite to the cultures of a methanogenic archaeon, Methanosarcina barkeri (M. barkeri). M. barkeri cells and redox-active, nonenzymatic soluble organic compounds in organic-rich spent culture supernatants can promote the formation of ZVI; the latter compounds also likely stabilize ZVI. Methanogenic microbes that inhabit organic- and Fe(III)-rich anaerobic environments may similarly reduce Fe(III) to Fe(II) and ZVI, with implications for the preservation of paleomagnetic signals during sediment diagenesis and potential applications in the protection of iron metals against corrosion and in the green synthesis of ZVI.

Selective metal removal from chromium-containing synthetic effluents using Shewanella xiamenensis biofilm supported on zeolite

A scheme of selective removal of metal ions from chromium-containing synthetic solutions with the following chemical composition, Cr (VI)-Fe (III), Cr (VI)-Fe (III)-Ni (II), Cr (VI)-Fe (III)-Ni (II)-Zn (II), and Cr (VI)-Fe (III)-Ni (II)-Zn (II)-Cu (II)) by Shewanella xiamenensis biofilm immobilized on a zeolite support, was proposed. Three biological processes, biosorption, bioaccumulation, and longtime bioreduction, were applied for metal removal. The process of Zn (II), Ni (II), and Cu (II) showed to be pH dependent. The maximum removal of Ni (II) was achieved during a 1-hour biosorption process at pH 5.0-6.0, of Zn (II) at pH 5.0, and of Cu (II) at pH 3.0. Chromium (VI) and Fe (III) ions were more efficiently removed by bioaccumulation. Chromium (VI) removal in the studied systems varied from 16.4% to 34.8 and of iron from 55.8 to 94.6%. In a long-term bioreduction experiment, it was possible to achieve complete reduction of Cr (VI) to Cr (III) ions by Shewanella xiamenensis in 42 days and by Shewanella xiamenensis biofilm on zeolite in 35 days. Shewanella oneidensis can be effectively used to remove metal ions from chemically complex effluents.

Dissimilatory bioreduction of iron(III) oxides by Shewanella loihica under marine sediment conditions

Shewanella is a genus of marine bacteria capable of dissimilatory iron reduction (DIR). In the context of deep-sea mining activities or submarine mine tailings disposal, dissimilatory iron reducing bacteria may play an important role in biogeochemical reactions concerning iron oxides placed on the sea bed. In this study, batch experiments were performed to evaluate the capacity of Shewanella loihica PV-4 to bioreduce different iron oxides (ferrihydrite, magnetite, goethite and hematite) under conditions similar to those in anaerobic sea sediments. Results showed that bioreduction of structural Fe(III) via oxidation of labile organic matter occurred in all these iron oxides. Based on the aqueous Fe (II) released, derived Fe(II)/acetate ratios and bioreduction coefficients seem to be only up to about 4% of the theoretical ones, considering the ideal stoichiometry of the reaction. A loss of aqueous Fe (II) was caused by adsorption and mineral transformation processes. Scanning electron microscope images showed that Shewanella lohica was attached to the Fe(III)-oxide surfaces during bioreduction. Our findings suggest that DIR of Fe(III) oxides from mine waste placed in marine environments could result in adverse ecological impacts such as liberation of trace metals in the environment.

Electron Donor Utilization and Secondary Mineral Formation during the Bioreduction of Lepidocrocite by Shewanella putrefaciens CN32

The bioreduction of Fe(III) oxides by dissimilatory iron reducing bacteria (DIRB) may result in the production of a suite of Fe(II)-bearing secondary minerals, including magnetite, siderite, vivianite, green rusts, and chukanovite; the formation of specific phases controlled by the interaction of various physiological and geochemical factors. In an effort to better understand the effects of individual electron donors on the formation of specific Fe(II)-bearing secondary minerals, we examined the effects of a series of potential electron donors on the bioreduction of lepidocrocite (γ-FeOOH) by Shewanella putrefaciens CN32. Biomineralization products were identified by X-ray diffraction, Mössbauer spectroscopy, and scanning electron microscopy. Acetate, citrate, ethanol, glucose, glutamate, glycerol, malate, and succinate were not effectively utilized for the bioreduction of lepidocrocite by S. putrefaciens CN32; however, substantial Fe(II) production was observed when formate, lactate, H2, pyruvate, serine, or N acetylglucosamine (NAG) was provided as an electron donor. Carbonate or sulfate green rust was the dominant Fe(II)-bearing secondary mineral when formate, H2, lactate, or NAG was provided, however, siderite formed with pyruvate or serine. Geochemical modeling indicated that pH and carbonate concentration are the key factors determining the prevalence of carbonate green rust verses siderite.

Genotypic diversity among Shewanella spp. collected from freshwater fish

Different Shewanella species are isolated both from healthy and from diseased fish. To date, contemporary methods do not provide sufficient insight to determine species and detail differentiation between tested strains. Bacteria isolated from cultured (n = 33), wild (n = 12) and ornamental (n = 6) fish, as well as several reference strains, were tested by 16S rRNA gene sequencing, ERIC-PCR and pulsed-field gel electrophoresis (PFGE) assays. Our study indicates that isolates collected from freshwater fish were genetically diverse. Based on 16S rRNA gene sequences, bacteria were clustered into groups S. putrefaciens, S. xiamenensis and S. oneidensis. Some isolates were classified only to genus Shewanella; thus, 16S rRNA gene analyses were not enough to determine the species. ERIC-PCR revealed 49 different genotype profiles indicating that the method might be useful for differentiation of Shewanella isolates irrespectively to species identification, contrary to PFGE which is not suitable for Shewanella typing.

Temperature Controls Crystalline Iron Oxide Utilization by Microbial Communities in Methanic Ferruginous Marine Sediment Incubations

Microorganisms can use crystalline iron minerals for iron reduction linked to organic matter degradation or as conduits for direct interspecies electron transfer (mDIET) to syntrophic partners, e.g., methanogens. The environmental conditions that lead either to reduction or conduit use are so far unknown. We investigated microbial community shifts and interactions with crystalline iron minerals (hematite and magnetite) in methanic ferruginous marine sediment incubations during organic matter (glucose) degradation at varying temperatures. Iron reduction rates increased with decreasing temperature from 30°C to 4°C. Both hematite and magnetite facilitated iron reduction at 4°C, demonstrating that microorganisms in the methanic zone of marine sediments can reduce crystalline iron oxides under psychrophilic conditions. Methanogenesis occurred, however, at higher rates with increasing temperature. At 30°C, both hematite and magnetite accelerated methanogenesis onset and maximum process rates. At lower temperatures (10°C and 4°C), hematite could still facilitate methanogenesis but magnetite served more as an electron acceptor for iron reduction than as a conduit. Different temperatures selected for different key microorganisms: at 30°C, members of genus Orenia, Halobacteroidaceae, at 10°C, Photobacterium and the order Clostridiales, and at 4°C Photobacterium and Psychromonas were enriched. Members of the order Desulfuromonadales harboring known dissimilatory iron reducers were also enriched at all temperatures. Our results show that crystalline iron oxides predominant in some natural environments can facilitate electron transfer between microbial communities at psychrophilic temperatures. Furthermore, temperature has a critical role in determining the pathway of crystalline iron oxide utilization in marine sediment shifting from conduction at 30°C to predominantly iron reduction at lower temperatures.

IN SILICO GENOME-SCALE RECONSTRUCTION AND ANALYSIS OF THE SHEWANELLA LOIHICA PV-4 METABOLIC NETWORK

Microbial Fuel Cells (MFCs) are devices that generate electricity directly from organic compounds with microbes (electricigens) serving as anodic catalysts. As a novel environment-friendly energy source, MFCs have extensive practical value. Since the biological features and metabolic mechanism of electricigens have a great effect on the electricity production of MFCs, it is a big deal to screen strains with high electricity productivity for improving the power output of MFC. Reconstructions and simulations of metabolic networks are of significant help in studying the metabolism of microorganisms so as to guide gene engineering and metabolic engineering to improve their power-generating efficiency. Herein, we reconstructed a genome-scale constraint-based metabolic network model of Shewanella loihica PV-4, an important electricigen, based on its genomic functional annotations, reaction databases and published metabolic network models of seven microorganisms. The resulting network model iGX790 consists of 902 reactions (including 71 exchange reactions), 798 metabolites and 790 genes, covering the main pathways such as carbon metabolism, energy metabolism, amino acid metabolism, nucleic acid metabolism and lipid metabolism. Using the model, we simulated the growth rate, the maximal synthetic rate of ATP, the flux variability analysis of metabolic network, gene deletion and so on to examine the metabolism of S. loihica PV-4.

Reduction and Morphological Transformation of Synthetic Nanophase Iron Oxide Minerals by Hyperthermophilic Archaea

Fe(III) (oxyhydr)oxides are electron acceptors for some hyperthermophilic archaea in mildly reducing geothermal environments. However, the kinds of iron oxides that can be used, growth rates, extent of iron reduction, and the morphological changes that occur to minerals are poorly understood. The hyperthermophilic iron-reducing crenarchaea Pyrodictium delaneyi and Pyrobaculum islandicum were grown separately on six different synthetic nanophase Fe(III) (oxyhydr)oxides. For both organisms, growth on ferrihydrite produced the highest growth rates and the largest amounts of Fe(II), although P. delaneyi produced four times more Fe(II) (25 mM) than P. islandicum (6 mM). Both organisms grew on lepidocrocite and akaganéite and produced 2 and 3 mM Fe(II). Modest growth occurred for both organisms on goethite, hematite, and maghemite where ≤1 mM Fe(II) was produced. The diameters of the spherical mineral end-products following P. delaneyi growth increased by 30 nm for ferrihydrite and 50–150 nm for lepidocrocite relative to heated abiotic controls. For akaganéite, spherical particle sizes were the same for P. delaneyi-reacted samples and heated abiotic controls, but the spherical particles were more numerous in the P. delaneyi samples. For P. islandicum, there was no increase in grain size for the mineral end-products following growth on ferrihydrite, lepidocrocite, or akaganéite relative to the heated abiotic controls. High-resolution transmission electron microscopy of lattice fringes and selected-area electron diffraction of the minerals produced by both organisms when grown on ferrihydrite showed that magnetite and/or possibly maghemite were the end-products while the heated abiotic controls only contained ferrihydrite. These results expand the current view of bioavailable Fe(III) (oxyhydr)oxides for reduction by hyperthermophilic archaea when presented as synthetic nanophase minerals. They show that growth and reduction rates are inversely correlated with the iron (oxyhydr)oxide crystallinity and that iron (oxyhydr)oxide mineral transformation takes different forms for these two organisms.

Biodegradation of sulfonamides by Shewanella oneidensis MR-1 and Shewanella sp. strain MR-4

Because of extensive sulfonamides application in aquaculture and animal husbandry and the consequent increase in sulfonamides discharged into the environment, strategies to remediate sulfonamide-contaminated environments are essential. In this study, the resistance of Shewanella oneidensis MR-1 and Shewanella sp. strain MR-4 to the sulfonamides sulfapyridine (SPY) and sulfamethoxazole (SMX) were determined, and sulfonamides degradation by these strains was assessed. Shewanella oneidensis MR-1 and Shewanella sp. strain MR-4 were resistant to SPY and SMX concentrations as high as 60 mg/L. After incubation for 5 days, 23.91 ± 1.80 and 23.43 ± 2.98% of SPY and 59.88 ± 1.23 and 63.89 ± 3.09% of SMX contained in the medium were degraded by S. oneidensis MR-1 and Shewanella sp. strain MR-4, respectively. The effects of the initial concentration of the sulfonamides and initial pH of the medium on biodegradation, and the degradation of different sulfonamides were assessed. The products were measured by LC-MS; with SPY as a substrate, 2-AP (2-aminopyridine) was the main stable metabolite, and with SMX as a substrate, 3A5MI (3-amino-5-methyl-isoxazole) was the main stable metabolite. The co-occurrence of 2-AP or 3A5MI and 4-aminobenzenesulfonic acid suggests that the initial step in the biodegradation of the two sulfonamides is S-N bond cleavage. These results suggest that S. oneidensis MR-1 and Shewanella sp. strain MR-4 are potential bacterial resources for biodegrading sulfonamides and therefore bioremediation of sulfonamide-polluted environments.

Structures, Compositions, and Activities of Live Shewanella Biofilms Formed on Graphite Electrodes in Electrochemical Flow Cells

An electrochemical flow cell equipped with a graphite working electrode (WE) at the bottom was inoculated with Shewanella oneidensis MR-1 expressing an anaerobic fluorescent protein, and biofilm formation on the WE was observed over time during current generation at WE potentials of +0.4 and 0 V (versus standard hydrogen electrodes), under electrolyte-flow conditions. Electrochemical analyses suggested the presence of unique electron-transfer mechanisms in the +0.4-V biofilm. Microscopic analyses revealed that, in contrast to aerobic biofilms, current-generating biofilm (at +0.4 V) was thin and flat (∼10 μm in thickness), and cells were evenly and densely distributed in the biofilm. In contrast, cells were unevenly distributed in biofilm formed at 0 V. In situ fluorescence staining and biofilm recovery experiments showed that the amounts of extracellular polysaccharides (EPSs) in the +0.4-V biofilm were much smaller than those in the aerobic and 0-V biofilms, suggesting that Shewanella cells suppress the production of EPSs at +0.4 V under flow conditions. We suggest that Shewanella cells perceive electrode potentials and modulate the structure and composition of biofilms to efficiently transfer electrons to electrodes.IMPORTANCE A promising application of microbial fuel cells (MFCs) is to save energy in wastewater treatment. Since current is generated in these MFCs by biofilm microbes under horizontal flows of wastewater, it is important to understand the mechanisms for biofilm formation and current generation under water-flow conditions. Although massive work has been done to analyze the molecular mechanisms for current generation by model exoelectrogenic bacteria, such as Shewanella oneidensis, limited information is available regarding the formation of current-generating biofilms over time under water-flow conditions. The present study developed electrochemical flow cells and used them to examine the electrochemical and structural features of current-generating biofilms under water-flow conditions. We show unique features of mature biofilms actively generating current, creating opportunities to search for as-yet-undiscovered current-generating mechanisms in Shewanella biofilms. Furthermore, information provided in the present study is useful for researchers attempting to develop anode architectures suitable for wastewater treatment MFCs.

Incorporation of molybdenum(vi) in akaganéite (β-FeOOH) and the microbial reduction of Mo–akaganéite by Shewanella loihica PV-4

Among all highly-crystalline iron oxides present in the environment, akaganéite (β-FeO(OH, Cl)) possesses one of the most unconventional structural setups and is a known scavenger for large quantitates of molybdenum (Mo⁶⁺).

Sulfur-Mediated Electron Shuttling Sustains Microbial Long-Distance Extracellular Electron Transfer with the Aid of Metallic Iron Sulfides

In addition to serving as an energy source for microbial growth, iron sulfides are proposed to act as naturally occurring electrical wires that mediate long-distance extracellular electron transfer (EET) and bridge spatially discrete redox environments. These hypothetical EET reactions stand on the abilities of microbes to use the interfacial electrochemistry of metallic/semiconductive iron sulfides to maintain metabolisms; however, the mechanisms of these phenomena remain unexplored. To obtain insight into EET to iron sulfides, we monitored EET at the interface between Shewanella oneidensis MR-1 cells and biomineralized iron sulfides in an electrochemical cell. Respiratory current steeply increased with the concomitant formation of poorly crystalline mackinawite (FeS) minerals, indicating that S. oneidensis has the ability to exploit extracellularly formed metallic FeS for long-distance EET. Deletion of major proteins of the metal-reduction (Mtr) pathway (OmcA, MtrC, CymA, and PilD) caused only subtle effects on the EET efficiency, a finding that sharply contrasts the majority of studies that report that the Mtr pathway is indispensable for the reduction of metal oxides and electrodes. The gene expression analyses of polysulfide and thiosulfate reductase suggest the existence of a sulfur-mediated electron-shuttling mechanism by which HS(-) ions and water-soluble polysulfides (HS(n)(-), where n ≥ 2) generated in the periplasmic space deliver electrons from cellular metabolic processes to cell surface-associated FeS. The finding of this Mtr-independent pathway indicates that polysulfide reductases complement the function of outer-membrane cytochromes in EET reactions and, thus, significantly expand the number of microbial species potentially capable of long-distance EET in sulfur-rich anoxic environments.

Distribution of iron- and sulfate-reducing bacteria across a coastal acid sulfate soil (CASS) environment: implications for passive bioremediation by tidal inundation

Coastal acid sulfate soils (CASS) constitute a serious and global environmental problem. Oxidation of iron sulfide minerals exposed to air generates sulfuric acid with consequently negative impacts on coastal and estuarine ecosystems. Tidal inundation represents one current treatment strategy for CASS, with the aim of neutralizing acidity by triggering microbial iron- and sulfate-reduction and inducing the precipitation of iron-sulfides. Although well-known functional guilds of bacteria drive these processes, their distributions within CASS environments, as well as their relationships to tidal cycling and the availability of nutrients and electron acceptors, are poorly understood. These factors will determine the long-term efficacy of "passive" CASS remediation strategies. Here we studied microbial community structure and functional guild distribution in sediment cores obtained from 10 depths ranging from 0 to 20 cm in three sites located in the supra-, inter- and sub-tidal segments, respectively, of a CASS-affected salt marsh (East Trinity, Cairns, Australia). Whole community 16S rRNA gene diversity within each site was assessed by 454 pyrotag sequencing and bioinformatic analyses in the context of local hydrological, geochemical, and lithological factors. The results illustrate spatial overlap, or close association, of iron-, and sulfate-reducing bacteria (SRB) in an environment rich in organic matter and controlled by parameters such as acidity, redox potential, degree of water saturation, and mineralization. The observed spatial distribution implies the need for empirical understanding of the timing, relative to tidal cycling, of various terminal electron-accepting processes that control acid generation and biogeochemical iron and sulfur cycling.

Shewanella-mediated biosynthesis of manganese oxide micro-/nanocubes as efficient electrocatalysts for the oxygen reduction reaction

Developing efficient electrocatalysts for the oxygen reduction reaction (ORR) is critical for promoting the widespread application of fuel cells and metal-air batteries. Here, we develop a biological low-cost, ecofriendly method for the synthesis of Mn2 O3 micro-/nanocubes by calcination of MnCO3 precursors in an oxygen atmosphere. Microcubic MnCO3 precursors with an edge length of 2.5 μm were fabricated by dissimilatory metal-reducing Shewanella loihica PV-4 in the presence of MnO4 (-) as the sole electron acceptor under anaerobic conditions. After calcining the MnCO3 precursors at 500 and 700 °C, porous Mn2 O3 -500 and Mn2 O3 -700 also showed microcubic morphology, while their edge lengths decreased to 1.8 μm due to thermal decomposition. Moreover, the surfaces of the Mn2 O3 microcubes were covered by granular nanoparticles with average diameters in the range of 18-202 nm, depending on the calcination temperatures. Electrochemical measurements demonstrated that the porous Mn2 O3 -500 micro-/nanocubes exhibit promising catalytic activity towards the ORR in an alkaline medium, which should be due to a synergistic effect of the overlapping molecular orbitals of oxygen/manganese and the hierarchically porous structures that are favorable for oxygen absorption. Moreover, these Mn2 O3 micro-/nanocubes possess better stability than commercial Pt/C catalysts and methanol-tolerance property in alkaline solution. Thus the Shewanella-mediated biosynthesis method we provided here might be a new strategy for the preparation of various transition metal oxides as high-performance ORR electrocatalysts at low cost.

Hybrid bio-organic interfaces with matchable nanoscale topography for durable high extracellular electron transfer activity

Here, we developed a novel hybrid bio-organic interface with matchable nano-scale topography between a polypyrrole nanowire array (PPy-NA) and the bacterium Shewanella, which enabled a remarkably increased extracellular electron transfer (EET) current from genus Shewanella over a rather long period. PPy-NA thus exhibited outstanding performance in mediating bacterial EET, which was superior to normal electrodes such as carbon plates, Au and tin-doped In₂O₃. It was proposed that the combined effect of the inherent electrochemical nature of PPy and the porous structured bacterial network that was generated on the PPy-NA enabled long-term stability, while the high efficiency was attributed to the enhanced electron transfer rate between PPy-NA and microbes caused by the enhanced local topological interactions.

Iron reduction and mineralization of deep-sea iron reducing bacterium Shewanella piezotolerans WP3 at elevated hydrostatic pressures

In this study, iron reduction and concomitant biomineralization of a deep-sea iron reducing bacterium (IRB), Shewanella piezotolerans WP3, were systematically examined at different hydrostatic pressures (0.1, 5, 20, and 50 MPa). Our results indicate that bacterial iron reduction and induced biomineralization are influenced by hydrostatic pressure. Specifically, the iron reduction rate and extent consistently decreases with the increase in hydrostatic pressure. By extrapolation, the iron reduction rate should drop to zero by ~68 MPa, which suggests a possible shut-off of enzymatic iron reduction of WP3 at this pressure. Nano-sized superparamagnetic magnetite minerals are formed under all the experimental pressures; nevertheless, even as magnetite production decreases, the crystallinity and grain size of magnetite minerals increase at higher pressure. These results imply that IRB may play an important role in iron reduction, biomineralization, and biogeochemical cycling in deep-sea environments.

Rate enhancement of bacterial extracellular electron transport involves bound flavin semiquinones

Extracellular redox-active compounds, flavins and other quinones, have been hypothesized to play a major role in the delivery of electrons from cellular metabolic systems to extracellular insoluble substrates by a diffusion-based shuttling two-electron-transfer mechanism. Here we show that flavin molecules secreted by Shewanella oneidensis MR-1 enhance the ability of its outer-membrane c-type cytochromes (OM c-Cyts) to transport electrons as redox cofactors, but not free-form flavins. Whole-cell differential pulse voltammetry revealed that the redox potential of flavin was reversibly shifted more than 100 mV in a positive direction, in good agreement with increasing microbial current generation. Importantly, this flavin/OM c-Cyts interaction was found to facilitate a one-electron redox reaction via a semiquinone, resulting in a 10(3)- to 10(5)-fold faster reaction rate than that of free flavin. These results are not consistent with previously proposed redox-shuttling mechanisms but suggest that the flavin/OM c-Cyts interaction regulates the extent of extracellular electron transport coupled with intracellular metabolic activity.