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

Microbially mediated iron redox processes for carbon and nitrogen removal from wastewater: Recent advances

Iron is the most abundant redox-active metal on Earth. The microbially mediated iron redox processes, including dissimilatory iron reduction (DIR), ammonium oxidation coupled with Fe(III) reduction (Feammox), Fe(III) dependent anaerobic oxidation of methane (Fe(III)-AOM), nitrate-reducing Fe(II) oxidation (NDFO), and Fe(II) dependent dissimilatory nitrate reduction to ammonium (Fe(II)-DNRA), play important parts in carbon and nitrogen biogeochemical cycling globally. In this review, the reaction mechanisms, electron transfer pathways, functional microorganisms, and characteristics of these processes are summarized; the prospective applications for carbon and nitrogen removal from wastewater are reviewed and discussed; and the research gaps and future directions of these processes for the treatment of wastewater are also underlined. This review is expected to give new insights into the development of economic and environmentally friendly iron-based wastewater treatment procedures.

An inconvenient impact: Unveiling the overlooked differences in crystalline forms of iron (hydro)oxides on anaerobic digestion

Iron (hydro)oxides are commonly used to enhance anaerobic digestion due to their cost-effectiveness and versatility. However, the influence of crystalline structure on digestion performance is often overlooked despite their unique characteristics. In this study, we investigated how different crystalline forms of FeOOH affect substrate utilization, sludge activity, and the microbiomes in up-flow anaerobic sludge blanket (UASB) reactors. The crystalline structure of FeOOH impacted reactor performance, with γ-FeOOH, β-FeOOH, and α-FeOOH showing decreasing effectiveness, as reflected in chemical oxygen demand (COD) removal efficiencies of 99.0 %, 98.3 % and 97.1 %, respectively. FeOOH crystals influenced the secretion of extracellular polymeric substances (EPS) and sludge activity by releasing Fe ions at varying rates, leading to Fe accumulation in EPS in the order of β-FeOOH > γ-FeOOH > α-FeOOH. Additionally, γ-FeOOH supported the most stable microbial community structure, as indicated by the highest Alpha diversity index. This stability was associated with increased levels of Mesotoga and Syntrophus, along with the highest coenzyme F420 activity, which was approximately twice as high as in other groups. These findings underscore the crucial role of the crystalline structure of iron oxides in enhancing anaerobic digestion, emphasizing that biocompatibility should be a priority when optimizing digestion performance.

Biogeochemical mechanisms of iron (Fe) and manganese (Mn) in groundwater and soil profiles in the Zhongning section of the Weining Plain (northwest China)

High levels of Iron (Fe) and manganese (Mn) in soils may contribute to secondary contamination of groundwater. However, there is limited understanding of the cycling mechanisms of Fe and Mn in groundwater and soil. This study aimed to investigate the biogeochemical processes constituting the Fe and Mn cycle by combining hydrochemistry, sequential extraction and microbiological techniques. The results indicated a similar vertical distribution pattern of Fe and Mn, with lower levels of the effective form (EFC-Fe/Mn) observed at the oxygenated surface, increasing near the groundwater table and decreasing below it. Generally, there was a tendency for accumulation above the water table, with Mn exhibiting a higher release potential compared to Fe. Iron‑manganese oxides (Ox-Fe/Mn) dominated the effective forms, with Fe and Mn in the soil entering groundwater through the reduction dissolution of Ox-Fe/Mn and the oxidative degradation of organic matter or sulfide (OM-Fe/Mn). Correlation analysis revealed that Fe and Mn tend to accumulate in media with fine particles and high organic carbon (TOC) contents. 16S rRNA sequencing analysis disclosed significant variation in the abundance of microorganisms associated with Fe and Mn transformations among unsaturated zone soils, saturated zone media and groundwater, with Fe/Mn content exerting an influence on microbial communities. Furthermore, functional bacterial identification results from the FAPROTAX database show a higher abundance of iron-oxidizing bacteria (9.3 %) in groundwater, while iron and manganese-reducing bacteria are scarce in both groundwater and soil environments. Finally, a conceptual model of Fe and Mn cycling was constructed, elucidating the biogeochemical processes in groundwater and soil environments. This study provides a new perspective for a deeper understanding of the environmental fate of Fe and Mn, which is crucial for mitigating Fe and Mn pollution in groundwater.

The role of iron materials in the abiotic transformation and biotransformation of polybrominated diphenyl ethers (PBDEs): A review

Polybrominated diphenyl ethers (PBDEs), widely used as flame retardants, easily enter the environment, thus posing environmental and health risks. Iron materials play a key role during the migration and transformation of PBDEs. This article reviews the processes and mechanisms of adsorption, degradation, and biological uptake and transformation of PBDEs affected by iron materials in the environment. Iron materials can effectively adsorb PBDEs through hydrophobic interactions, π-π interactions, hydrogen/halogen bonds, electrostatic interactions, coordination interactions, and pore filling interactions. In addition, they are beneficial for the photodegradation, reduction debromination, and advanced oxidation degradation and debromination of PBDEs. The iron material-microorganism coupling technology affects the uptake and transformation of PBDEs. In addition, iron materials can reduce the uptake of PBDEs in plants, affecting their bioavailability. The species, concentration, and size of iron materials affect plant physiology. Overall, iron materials play a bidirectional role in the biological uptake and transformation of PBDEs. It is necessary to strengthen the positive role of iron materials in reducing the environmental and health risks caused by PBDEs. This article provides innovative ideas for the rational use of iron materials in controlling the migration and transformation of PBDEs in the environment.

Effects of environmental metal and metalloid pollutants on plants and human health: exploring nano-remediation approach

Metal and metalloid pollutants severely threatens environmental ecosystems and human health, necessitating effective remediation strategies. Nanoparticle (NPs)-based approaches have gained significant attention as promising solutions for efficient removing heavy metals from various environmental matrices. The present review is focused on green synthesized NPs-mediated remediation such as the implementation of iron, carbon-based nanomaterials, metal oxides, and bio-based NPs. The review also explores the mechanisms of NPs interactions with heavy metals, including adsorption, precipitation, and redox reactions. Critical factors influencing the remediation efficiency, such as NPs size, surface charge, and composition, are systematically examined. Furthermore, the environmental fate, transport, and potential risks associated with the application of NPs are critically evaluated. The review also highlights various sources of metal and metalloid pollutants and their impact on human health and translocation in plant tissues. Prospects and challenges in translating NPs-based remediation from laboratory research to real-world applications are proposed. The current work will be helpful to direct future research endeavors and promote the sustainable implementation of metal and metalloid elimination.

Soil carbon and nitrogen cycles driven by iron redox: A review

Soil carbon and nitrogen cycles affect agricultural production, environmental quality, and global climate. Iron (Fe), regarded as the most abundant redox-active metal element in the Earth's crust, is involved in a biogeochemical cycle that includes Fe(III) reduction and Fe(II) oxidation. The redox reactions of Fe can be linked to the carbon and nitrogen cycles in soil in various ways. Investigating the transformation processes and mechanisms of soil carbon and nitrogen species driven by Fe redox can provide theoretical guidance for improving soil fertility, and addressing global environmental pollution as well as climate change. Although the widespread occurrence of these coupling processes in soils has been revealed, explorations of the effects of Fe redox on soil carbon and nitrogen cycles remain in the early stages, particularly when considering the broader context of global climate and environmental changes. The key functional microorganisms, mechanisms, and contributions of these coupling processes to soil carbon and nitrogen cycles have not been fully elucidated. Here, we present a systematic review of the research progress on soil carbon and nitrogen cycles mediated by Fe redox, including the underlying reaction processes, the key microorganisms involved, the influencing factors, and their environmental significance. Finally, some unresolved issues and future perspectives are addressed. This knowledge expands our understanding of the interconnected cycles of Fe, carbon and nitrogen in soils.

Involvement of Bacterial and Fungal Extracellular Products in Transformation of Manganese-Bearing Minerals and Its Environmental Impact

Manganese oxides are considered an essential component of natural geochemical barriers due to their redox and sorptive reactivity towards essential and potentially toxic trace elements. Despite the perception that they are in a relatively stable phase, microorganisms can actively alter the prevailing conditions in their microenvironment and initiate the dissolution of minerals, a process that is governed by various direct (enzymatic) or indirect mechanisms. Microorganisms are also capable of precipitating the bioavailable manganese ions via redox transformations into biogenic minerals, including manganese oxides (e.g., low-crystalline birnessite) or oxalates. Microbially mediated transformation influences the (bio)geochemistry of manganese and also the environmental chemistry of elements intimately associated with its oxides. Therefore, the biodeterioration of manganese-bearing phases and the subsequent biologically induced precipitation of new biogenic minerals may inevitably and severely impact the environment. This review highlights and discusses the role of microbially induced or catalyzed processes that affect the transformation of manganese oxides in the environment as relevant to the function of geochemical barriers.

Iron Availability and Homeostasis in Plants: A Review of Responses, Adaptive Mechanisms, and Signaling

Iron is an essential element for all living organisms, playing a major role in plant biochemistry as a redox catalyst based on iron redox properties. Iron is the fourth most abundant element of the Earth's crust, but its uptake by plants is complex because it is often in insoluble forms that are not easily accessible for plants to use. The physical and chemical speciation of iron, as well as rhizosphere activity, are key factors controlling the bioavailability of Fe. Iron can be under reduced (Fe²⁺) or oxidized (Fe³⁺) ionic forms, adsorbed onto mineral surfaces, forming complexes with organic molecules, precipitated to form poorly crystalline hydroxides to highly crystalline iron oxides, or included in crystalline Fe-rich mineral phases. Plants must thus adapt to a complex and changing iron environment, and their response is finely regulated by multiple signaling pathways initiated by a diversity of stimulus perceptions. Higher plants possess two separate strategies to uptake iron from rhizosphere soil: the chelation strategy and the reduction strategy in grass and non-grass plants, respectively. Molecular actors involved in iron uptake and mobilization through the plant have been characterized for both strategies. All these processes that contribute to iron homeostasis in plants are highly regulated in response to iron availability by downstream signaling responses, some of which are characteristic signaling signatures of iron dynamics, while others are shared with other environmental stimuli. Recent research has thus revealed key transcription factors, cis-acting elements, post-translational regulators, and other molecular mechanisms controlling these genes or their encoded proteins in response to iron availability. In addition, the most recent research is increasingly highlighting the crosstalk between iron homeostasis and nutrient response regulation. These regulatory processes help to avoid plant iron concentrations building up to potential cell functioning disruptions that could adversely affect plant fitness. Indeed, when iron is in excess in the plant, it can lead to the production and accumulation of dangerous reactive oxygen species and free radicals (H₂O₂, HO^•, O₂^•-, HO^•₂) that can cause considerable damages to most cellular components. To cope with iron oxidative stress, plants have developed defense systems involving the complementary action of antioxidant enzymes and molecular antioxidants, safe iron-storage mechanisms, and appropriate morphological adaptations.

Influence of Organic Ligands on the Redox Properties of Fe(II) as Determined by Mediated Electrochemical Oxidation

Fe(II) has been extensively studied due to its importance as a reductant in biogeochemical processes and contaminant attenuation. Previous studies have shown that ligands can alter aqueous Fe(II) redox reactivity but their data interpretation is constrained by the use of probe compounds. Here, we employed mediated electrochemical oxidation (MEO) as an approach to directly quantify the extent of Fe(II) oxidation in the absence and presence of three model organic ligands (citrate, nitrilotriacetic acid, and ferrozine) across a range of potentials (E_H) and pH, thereby manipulating oxidation over a broad range of fixed thermodynamic conditions. Fe(III)-stabilizing ligands enhanced Fe(II) reactivity in thermodynamically unfavorable regions (i.e., low pH and E_H) while an Fe(II) stabilizing ligand (ferrozine) prevented oxidation across all thermodynamic regions. We experimentally derived apparent standard redox potentials, E_H^ϕ, for these and other (oxalate, oxalate₂, NTA₂, EDTA, and OH₂) Fe-ligand redox couples via oxidative current integration. Preferential stabilization of Fe(III) over Fe(II) decreased E_H^ϕ values, and a Nernstian correlation between E_H^ϕ and log(K_Fe(III)/K_Fe(II)) exists across a wide range of potentials and stability constants. We used this correlation to estimate log(K_Fe(III)/K_Fe(II)) for a natural organic matter isolate, demonstrating that MEO can be used to measure iron stability constant ratios for unknown ligands.

Iodate Reduction by Shewanella oneidensis Requires Genes Encoding an Extracellular Dimethylsulfoxide Reductase

Microbial iodate (IO3 -) reduction is a major component of the iodine biogeochemical reaction network in anaerobic marine basins and radioactive iodine-contaminated subsurface environments. Alternative iodine remediation technologies include microbial reduction of IO3 - to iodide (I-) and microbial methylation of I- to volatile gases. The metal reduction pathway is required for anaerobic IO3 - respiration by the gammaproteobacterium Shewanella oneidensis. However, the terminal IO3 - reductase and additional enzymes involved in the S. oneidensis IO3 - electron transport chain have not yet been identified. In this study, gene deletion mutants deficient in four extracellular electron conduits (EECs; ΔmtrA, ΔmtrA-ΔmtrDEF, ΔmtrA-ΔdmsEF, ΔmtrA-ΔSO4360) and DMSO reductase (ΔdmsB) of S. oneidensis were constructed and examined for anaerobic IO3 - reduction activity with either 20 mM lactate or formate as an electron donor. IO3 - reduction rate experiments were conducted under anaerobic conditions in defined minimal medium amended with 250 μM IO3 - as anaerobic electron acceptor. Only the ΔmtrA mutant displayed a severe deficiency in IO3 - reduction activity with lactate as the electron donor, which suggested that the EEC-associated decaheme cytochrome was required for lactate-dependent IO3 - reduction. The ΔmtrA-ΔdmsEF triple mutant displayed a severe deficiency in IO3 - reduction activity with formate as the electron donor, whereas ΔmtrA-ΔmtrDEF and ΔmtrA-ΔSO4360 retained moderate IO3 - reduction activity, which suggested that the EEC-associated dimethylsulfoxide (DMSO) reductase membrane-spanning protein DmsE, but not MtrA, was required for formate-dependent IO3 - reduction. Furthermore, gene deletion mutant ΔdmsB (deficient in the extracellular terminal DMSO reductase protein DmsB) and wild-type cells grown with tungsten replacing molybdenum (a required co-factor for DmsA catalytic activity) in defined growth medium were unable to reduce IO3 - with either lactate or formate as the electron donor, which indicated that the DmsAB complex functions as an extracellular IO3 - terminal reductase for both electron donors. Results of this study provide complementary genetic and phenotypic evidence that the extracellular DMSO reductase complex DmsAB of S. oneidensis displays broad substrate specificity and reduces IO3 - as an alternate terminal electron acceptor.

Spatial distribution and biogeochemistry of redox active species in arctic sedimentary porewaters and seeps

Redox active species in Arctic lacustrine sediments play an important, regulatory role in the carbon cycle, yet there is little information on their spatial distribution, abundance, and oxidation states. Here, we use voltammetric microelectrodes to quantify the in situ concentrations of redox-active species at high vertical resolution (mm to cm) in the benthic porewaters of an oligotrophic Arctic lake (Toolik Lake, AK, USA). Mn(II), Fe(II), O₂, and Fe(III)-organic complexes were detected as the major redox-active species in these porewaters, indicating both Fe(II) oxidation and reductive dissolution of Fe(III) and Mn(IV) minerals. We observed significant spatial heterogeneity in their abundance and distribution as a function of both location within the lake and depth. Microbiological analyses and solid phase Fe(III) measurements were performed in one of the Toolik Lake cores to determine the relationship between biogeochemical redox gradients and microbial communities. Our data reveal iron cycling involving both oxidizing (FeOB) and reducing (FeRB) bacteria. Additionally, we profiled a large microbial iron mat in a tundra seep adjacent to an Arctic stream (Oksrukuyik Creek) where we observed Fe(II) and soluble Fe(III) in a highly reducing environment. The variable distribution of redox-active substances at all the sites yields insights into the nature and distribution of the important terminal electron acceptors in both lacustrine and tundra environments capable of exerting significant influences on the carbon cycle.

Recent Advances in the Siderophore Biology of Shewanella

Despite the abundance of iron in nature, iron acquisition is a challenge for life in general because the element mostly exists in the extremely insoluble ferric (Fe³⁺) form in oxic environments. To overcome this, microbes have evolved multiple iron uptake strategies, a common one of which is through the secretion of siderophores, which are iron-chelating metabolites generated endogenously. Siderophore-mediated iron transport, a standby when default iron transport routes are abolished under iron rich conditions, is essential under iron starvation conditions. While there has been a wealth of knowledge about the molecular basis of siderophore synthesis, uptake and regulation in model bacteria, we still know surprisingly little about siderophore biology in diverse environmental microbes. Shewanella represent a group of γ-proteobacteria capable of respiring a variety of organic and inorganic substrates, including iron ores. This respiratory process relies on a large number of iron proteins, c-type cytochromes in particular. Thus, iron plays an essential and special role in physiology of Shewanella. In addition, these bacteria use a single siderophore biosynthetic system to produce an array of macrocyclic dihydroxamate siderophores, some of which show particular biological activities. In this review, we first outline current understanding of siderophore synthesis, uptake and regulation in model bacteria, and subsequently discuss the siderophore biology in Shewanella.

Tuning Microbial Activity via Programmatic Alteration of Cell/Substrate Interfaces

A wide portfolio of advanced programmable materials and structures has been developed for biological applications in the last two decades. Particularly, due to their unique properties, semiconducting materials have been utilized in areas of biocomputing, implantable electronics, and healthcare. As a new concept of such programmable material design, biointerfaces based on inorganic semiconducting materials as substrates introduce unconventional paths for bioinformatics and biosensing. In particular, understanding how the properties of a substrate can alter microbial biofilm behavior enables researchers to better characterize and thus create programmable biointerfaces with necessary characteristics on demand. Herein, the current status of advanced microorganism-inorganic biointerfaces is summarized along with types of responses that can be observed in such hybrid systems. This work identifies promising inorganic material types along with target microorganisms that will be critical for future research on programmable biointerfacial structures.

Electromicrobiology: the ecophysiology of phylogenetically diverse electroactive microorganisms

Electroactive microorganisms markedly affect many environments in which they establish outer-surface electrical contacts with other cells and minerals or reduce soluble extracellular redox-active molecules such as flavins and humic substances. A growing body of research emphasizes their broad phylogenetic diversity and shows that these microorganisms have key roles in multiple biogeochemical cycles, as well as the microbiome of the gut, anaerobic waste digesters and metal corrosion. Diverse bacteria and archaea have independently evolved cytochrome-based strategies for electron exchange between the outer cell surface and the cell interior, but cytochrome-free mechanisms are also prevalent. Electrically conductive protein filaments, soluble electron shuttles and non-biological conductive materials can substantially extend the electronic reach of microorganisms beyond the surface of the cell. The growing appreciation of the diversity of electroactive microorganisms and their unique electronic capabilities is leading to a broad range of applications.

Biogeochemical dynamics and microbial community development under sulfate- and iron-reducing conditions based on electron shuttle amendment

Iron reduction and sulfate reduction are two of the major biogeochemical processes that occur in anoxic sediments. Microbes that catalyze these reactions are therefore some of the most abundant organisms in the subsurface, and some of the most important. Due to the variety of mechanisms that microbes employ to derive energy from these reactions, including the use of soluble electron shuttles, the dynamics between iron- and sulfate-reducing populations under changing biogeochemical conditions still elude complete characterization. Here, we amended experimental bioreactors comprised of freshwater aquifer sediment with ferric iron, sulfate, acetate, and the model electron shuttle AQDS (9,10-anthraquinone-2,6-disulfonate) and monitored both the changing redox conditions as well as changes in the microbial community over time. The addition of the electron shuttle AQDS did increase the initial rate of Fe^III reduction; however, it had little effect on the composition of the microbial community. Our results show that in both AQDS- and AQDS+ systems there was an initial dominance of organisms classified as Geobacter (a genus of dissimilatory Fe^III-reducing bacteria), after which sequences classified as Desulfosporosinus (a genus of dissimilatory sulfate-reducing bacteria) came to dominate both experimental systems. Furthermore, most of the ferric iron reduction occurred under this later, ostensibly “sulfate-reducing” phase of the experiment. This calls into question the usefulness of classifying subsurface sediments by the dominant microbial process alone because of their interrelated biogeochemical consequences. To better inform models of microbially-catalyzed subsurface processes, such interactions must be more thoroughly understood under a broad range of conditions.

Link between characteristics of Fe(III) oxides and critical role in enhancing anaerobic methanogenic degradation of complex organic compounds

Fe(III) oxides have been investigated to accelerate anaerobic methanogenic degradation of complex organic compounds. However, the critical role linked to the characteristics of different types of Fe(III) oxides is still unclear. Study presented here performed a side-by-side comparison of four types of Fe(III) oxides including Fe(III)-citrate, ferrihydrite, hematite and magnetite to evaluate their effectiveness in methanogenic degradation of phenol. Results showed that, amorphous Fe(III)-citrate group showed the fastest phenol degradation and Fe²⁺ release among all the groups, followed by poorly crystalline ferrihydrite. Although Fe(III)-citrate group also showed the fastest methane production rate, the efficiency of electron recovery in methane production was only 58-78%, which was evidently lower than that in both crystalline hematite (86-89%) and magnetite (93-97%) groups. Methane production rate with non-conductive ferrihydrite was nearly same as that with conductive magnetite, both of which were significantly higher than that with semi-conductive hematite. X-ray Diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) analysis showed that sludge collected from hematite and magnetite group still respectively presented a relatively intact characteristic spectra involved in hematite and magnetite. Differently, the characteristic spectra involved in ferrihydrite was not evident in sludge collected from ferrihydrite group, whereas the characteristic spectra involved in magnetite was detected. Microbial community analysis showed that, both Fe(III)-citrate and ferrihydrite specially enriched Fe(III)-reducing bacteria capable of degrading phenol into fatty acids (Trichococcus and Caloramator) via dissimilatory Fe(III) reduction. Fe(III)-citrate also stimulated the growth of Syntrophus capable of degrading phenol/benzoate into acetate and proceeding direct interspecies electron transfer (DIET). In magnetite and hematite group, the abundance of Enterococcus species evidently increased, and they might proceed DIET with Methanothrix species in syntrophic conversion of fatty acids into methane.

An evolving view on biogeochemical cycling of iron

Biogeochemical cycling of iron is crucial to many environmental processes, such as ocean productivity, carbon storage, greenhouse gas emissions and the fate of nutrients, toxic metals and metalloids. Knowledge of the underlying processes involved in iron cycling has accelerated in recent years along with appreciation of the complex network of biotic and abiotic reactions dictating the speciation, mobility and reactivity of iron in the environment. Recent studies have provided insights into novel processes in the biogeochemical iron cycle such as microbial ammonium oxidation and methane oxidation coupled to Fe(III) reduction. They have also revealed that processes in the biogeochemical iron cycle spatially overlap and may compete with each other, and that oxidation and reduction of iron occur cyclically or simultaneously in many environments. This Review discusses these advances with particular focus on their environmental consequences, including the formation of greenhouse gases and the fate of nutrients and contaminants.

Microbial Fe(II) oxidation by Sideroxydans lithotrophicus ES-1 in the presence of Schlöppnerbrunnen fen-derived humic acids

Controlled laboratory experiments were combined with field measurements to better understand the interactions between dissolved organic matter (DOM) and reduced iron in organic-rich peatlands. Addition of peat-derived humic acid extract (HA) to Sideroxydans lithotrophicus ES-1 liquid cultures led to higher cell numbers and up to 1.4 times higher Fe(II) oxidation rates compared to chemical controls. This effect was positively correlated with increasing HA concentrations. Similar Fe(III) (oxyhydr)oxide mineralogies were formed both abiotically and biotically irrespective of HA amendment, but minerals formed in the presence of ES-1 and HA were smaller. ES-1 growth with HA promoted aggregation of Fe(III) products in agarose-stabilized gradient tubes as shown by voltammetric profiling. In situ voltammetry in an acidic, iron-rich peatland revealed a gap between oxygen penetration and iron reduction that may reflect active Fe(II)-oxidizing microorganisms. The highest abundance of Fe(II) oxidizers Sideroxydans (4.9 × 107 gene copies gww-1) and Gallionella (1.5 × 107 gene copies gww-1) in the upper peat layer coincided with small-sized minerals resembling nanoparticulate ferrihydrite or goethite. Our results suggest that microbially mediated Fe(II) oxidation dominates in the presence of DOM leading to the formation of nano-sized biogenic Fe(III) (oxyhydr)oxides that might be readily bioavailable and likely important to iron and carbon cycling.

Microbial iron reduction enhances in-situ control of biogenic hydrogen sulfide by FeOOH granules in sediments of polluted urban waters

This paper discusses the abiotic and biotic processes in the in-situ control of biogenic hydrogen sulfide generated from microbial sulfate reduction by ferric (Fe^III) (hydr)oxides (FeOOH) granules in the sediments of polluted urban waters. Granular ferric hydroxide (GFH, β-FeOOH) and granular ferric oxide (GFO, α-FeOOH) dosed in the organic- and sulfate-rich sediments had 180% and 19% higher sulfide removal capacities than those used for the purely abiotic removal of dissolved sulfide, respectively. The enhancement was attributable to the involvement of the biotic pathways, besides the abiotic pathways (mainly sulfide oxidation). The FeOOH granules stimulated the microbial reduction of surface Fe^III by iron-reducing bacteria (e.g., Desulfovibrio and Carnobacterium), and increased the microbial sulfate reduction by 24%-30% under an organic-rich condition, likely due to the enhanced organic fermentation. The microbial iron reduction significantly enhanced the removal of the formed biogenic hydrogen sulfide through increasing sulfide precipitation because it remarkably promoted the release of Fe²⁺ ions from the granule surface, likely due to the involvement of siderophores as ligands. This biotic pathway led to the formation of amorphous FeS_(s) as a major sulfur product (56%-81%), instead of elemental sulfur. The enhancement in the sulfide control performance was much more pronounced when the poorly ordered GFH was used, because of the faster Fe²⁺ release, compared to the highly ordered GFO. The abiotic and biotic mechanisms elucidated in this study provide insights into the iron-sulfur chemistry in the sediments of various polluted waters (e.g., storm drains, urban rivers, and estuary), where the manually-dosed and naturally-occurring Fe^III (hydr)oxides control biogenic hydrogen sulfide.

Enhancing anaerobic degradation of phenol to methane via solubilizing Fe(III) oxides for dissimilatory iron reduction with organic chelates

The improved performances during anaerobic degradation of phenol to methane with Fe(OH)₃ were usually inapparent, due to its lower solubility (unaccessible to dissimilatory iron reduction) and more positive reduction potential of Fe(III)/Fe(II) (unfavorable for enriching Fe(III)-reducing bacteria [IRBs]). In this study, citrate, the organic chelates, were used to solubilize Fe(III) with the aim of improving the phenol degradation and declining the reduction potential of Fe(III)/Fe(II). Results showed that, in the co-occurrence of citrate and Fe(OH)₃, the degradation rates of phenol were about 1.3-fold rapider than that with sole Fe(OH)₃. Analysis of cyclic voltammetry demonstrated that the reduction potential of Fe(III)/Fe(II) in the form of Fe(OH)₃ (-0.41 to -0.28 V vs Ag/AgCl) declined to -0.61 to -0.41 V. As a result, the Fe(III)-reducing genera, such as Petrimonas and Shewanella, which held a great potential of proceeding syntrophic metabolism via direct interspecies electron transfer (DIET), were significantly enriched.

Phosphorus mobility in dam reservoir affected by redox oscillations: An experimental study

The internal sedimentary phosphorus (P) load of aquatic systems is able to support eutrophication, especially in dam-reservoir systems where sedimentary P stock is high and where temporary anaerobic conditions occur. The aim of this study therefore is to examine the response of sedimentary P exposed to redox oscillations. Surface sediments collected in the Champsanglard dam-reservoir (on the Creuse River, France) were subjected to two aerobic phases (10 and 12 days) alternated with two anaerobic periods (21 and 27 days) through batch incubations. The studied sediment contained 77 ± 3 μmol/g DW of P, mainly associated with the ascorbate fraction (amorphous Fe/Mn oxyhydroxides). The used sediment was rich in organic matter (OM) (21% ± 1%) with primarily allochthone signature. Our results showed that redox oscillations enhance dissolved inorganic phosphorus release at sediment/water interface. During the first anaerobic stage, the P release was mainly controlled by the dissolution/precipitation of iron minerals. The more pronounced increase of P release during the second anaerobic stage (44%) was due to various mechanisms related to the change in quality of dissolved organic matter (DOM), namely a higher SUVA₂₅₄ and humification indices. The release of more refractory DOM (rDOM) served to lower the microbial metabolism activity, possibly favored iron oxyhydroxide aggregation and thus limiting iron reduction. In addition, rDOM is able to compete for mineral P sorption sites, leading to a greater P release. In reservoir with predominant allochthone OM input, the release of more aromatic DOM therefore plays an important role in P mobility.

Metal Reduction and Protein Secretion Genes Required for Iodate Reduction by Shewanella oneidensis

The metal-reducing gammaproteobacterium Shewanella oneidensis reduces iodate (IO₃ ^-) as an anaerobic terminal electron acceptor. Microbial IO₃ ^- electron transport pathways are postulated to terminate with nitrate (NO₃ ^-) reductase, which reduces IO₃ ^- as an alternative electron acceptor. Recent studies with S. oneidensis, however, have demonstrated that NO₃ ^- reductase is not involved in IO₃ ^- reduction. The main objective of the present study was to determine the metal reduction and protein secretion genes required for IO₃ ^- reduction by Shewanella oneidensis with lactate, formate, or H₂ as the electron donor. With all electron donors, the type I and type V protein secretion mutants retained wild-type IO₃ ^- reduction activity, while the type II protein secretion mutant lacking the outer membrane secretin GspD was impaired in IO₃ ^- reduction. Deletion mutants lacking the cyclic AMP receptor protein (CRP), cytochrome maturation permease CcmB, and inner membrane-tethered c-type cytochrome CymA were impaired in IO₃ ^- reduction with all electron donors, while deletion mutants lacking c-type cytochrome MtrA and outer membrane β-barrel protein MtrB of the outer membrane MtrAB module were impaired in IO₃ ^- reduction with only lactate as an electron donor. With all electron donors, mutants lacking the c-type cytochromes OmcA and MtrC of the metal-reducing extracellular electron conduit MtrCAB retained wild-type IO₃ ^- reduction activity. These findings indicate that IO₃ ^- reduction by S. oneidensis involves electron donor-dependent metal reduction and protein secretion pathway components, including the outer membrane MtrAB module and type II protein secretion of an unidentified IO₃ ^- reductase to the S. oneidensis outer membrane.IMPORTANCE Microbial iodate (IO₃ ^-) reduction is a major component in the biogeochemical cycling of iodine and the bioremediation of iodine-contaminated environments; however, the molecular mechanism of microbial IO₃ ^- reduction is poorly understood. Results of the present study indicate that outer membrane (type II) protein secretion and metal reduction genes encoding the outer membrane MtrAB module of the extracellular electron conduit MtrCAB are required for IO₃ ^- reduction by S. oneidensis On the other hand, the metal-reducing c-type cytochrome MtrC of the extracellular electron conduit is not required for IO₃ ^- reduction by S. oneidensis These findings indicate that the IO₃ ^- electron transport pathway terminates with an as yet unidentified IO₃ ^- reductase that associates with the outer membrane MtrAB module to deliver electrons extracellularly to IO₃^.

Impact of Fe(II) oxidation in the presence of iron-reducing bacteria on subsequent Fe(III) bio-reduction

The interplay of Fe(II) oxidation and Fe(III) bio-reduction occurs widely in both natural and engineered redox-dynamic systems. This study aimed to unravel the impact of Fe(II) oxidation by O₂ in the presence of iron-reducing bacteria on subsequent Fe(III) bio-reduction. Mixed solutions of Fe²⁺ (0.1-0.5 mM) and Shewanella oneidensis strain MR-1 (MR-1, 2.0 × 10⁷ CFU/mL) at neutral pH were first exposed to laboratory air for Fe(II) oxidation and bacterial inactivation, and then the resultant Fe(III) suspensions were switched to anoxic conditions for bio-reduction by the surviving bacteria. In the oxidation step, the coexisting MR-1 was inactivated by 0.8-1.71 orders of magnitude within 60 min. In the subsequent bio-reduction step, the resultant Fe(III) was bio-reduced by the surviving MR-1. Bio-reduction of the resultant Fe(III) by the surviving MR-1 was 1.8-2.5 times faster than that of the Fe(III) that was produced from Fe²⁺ oxidation without MR-1 by fresh MR-1 cells at 2.0 × 10⁷ CFU/mL. Although MR-1 inactivation during Fe(II) oxidation may inhibit Fe(III) bio-reduction, the increase in bio-availability of the resultant Fe(III) and the residual reactivity of dead cells led to net enhancement of bio-reduction under the tested conditions. Lepidocrocite was the sole Fe(III) mineral that was produced from Fe²⁺ oxidation without MR-1, while 19% ferrihydrite was produced from Fe²⁺ oxidation in the presence of MR-1. The formation of low-crystallinity ferrihydrite accounts for the increase in bio-availability of the Fe(III) minerals. The findings of this study highlight an important but overlooked impact underlying the interplay of Fe(II) oxidation and Fe(III) bio-reduction.

The chemical biology and coordination chemistry of putrebactin, avaroferrin, bisucaberin, and alcaligin

Dihydroxamic acid macrocyclic siderophores comprise four members: putrebactin (putH₂), avaroferrin (avaH₂), bisucaberin (bisH₂), and alcaligin (alcH₂). This mini-review collates studies of the chemical biology and coordination chemistry of these macrocycles, with an emphasis on putH₂. These Fe(III)-binding macrocycles are produced by selected bacteria to acquire insoluble Fe(III) from the local environment. The macrocycles are optimally pre-configured for Fe(III) binding, as established from the X-ray crystal structure of dinuclear [Fe₂(alc)₃] at neutral pH. The dimeric macrocycles are biosynthetic products of two endo-hydroxamic acid ligands flanked by one amine group and one carboxylic acid group, which are assembled from 1,4-diaminobutane and/or 1,5-diaminopentane as initial substrates. The biosynthesis of alcH₂ includes an additional diamine C-hydroxylation step. Knowledge of putH₂ biosynthesis supported the use of precursor-directed biosynthesis to generate unsaturated putH₂ analogues by culturing Shewanella putrefaciens in medium supplemented with unsaturated diamine substrates. The X-ray crystal structures of putH₂, avaH₂ and alcH₂ show differences in the relative orientations of the amide and hydroxamic acid functional groups that could prescribe differences in solvation and other biological properties. Functional differences have been borne out in biological studies. Although evolved for Fe(III) acquisition, solution coordination complexes have been characterised between putH₂ and oxido-V(IV/V), Mo(VI), or Cr(V). Retrosynthetic analysis of 1:1 complexes of [Fe(put)]⁺, [Fe(ava)]⁺, and [Fe(bis)]⁺ that dominate at pH < 5 led to a forward metal-templated synthesis approach to generate the Fe(III)-loaded macrocycles, with apo-macrocycles furnished upon incubation with EDTA. This mini-review aims to capture the rich chemistry and chemical biology of these seemingly simple compounds.

EDDS enhanced Shewanella putrefaciens CN32 and α-FeOOH reductive dechlorination of carbon tetrachloride

S,S-ethylenediamine-N,N-disuccinic acid (EDDS) enhanced reductive dissolution of α-FeOOH by Shewanella putrefaciens CN32 (CN32), resulting in formation of surface-bound Fe(II) species (Fe^IIEDDS) to improve reductive dechlorination of carbon tetrachloride (CT). The pseudo-first-order rate constants for bio-reduction extents of α-FeOOH by CN32 in the presence of 1.36 mM EDDS was 0.023 ± 0.0003 d^-1 which was higher than without EDDS. The enhancement mechanism of bio-reduction was attributed to the strong complexation ability of EDDS to formed Fe^IIIEDDS, which could be better utilized by CN32. The dechlorination kinetic of CT by Fe^IIEDDS (2.016 h^-1) in the presence of 1.36 mM EDDS was 24 times faster than without EDDS. Chloroform were detected as main products for the degradation of CT. The chemical analyses and morphological observation showed that combination between EDDS and Fe²⁺ produced Fe^IIEDDS complex, which had a reductive potential of -0.375 V and significantly enhanced CT dechlorination. The results showed that EDDS played an important role in enhancing the bio-reduction of α-FeOOH to accelerate reductive dechlorination of CT.

Rapid Iron Reduction Rates Are Stimulated by High-Amplitude Redox Fluctuations in a Tropical Forest Soil

Iron oxides are important structural and biogeochemical components of soils that can be strongly altered by redox-driven processes. This study examined the influence of temporal oxygen variations on Fe speciation in soils from the Luquillo Critical Zone Observatory (Puerto Rico). We incubated soils under cycles of oxic-anoxic conditions (τ_oxic:τ_anoxic = 1:6) at three frequencies with and without phosphate addition. Fe(II) production, P availability, and Fe mineral composition were monitored using batch analytical and spectroscopic techniques. The rate of soil Fe(II) production increased from ∼3 to >45 mmol Fe(II) kg^-1 d^-1 over the experiment with a concomitant increase of an Fe(II) concentration plateau within each anoxic period. The apparent maximum in Fe(II) produced is similar in all treatments, but was hastened by P-amendment. Numerical modeling suggests the Fe(II) dynamics can be explained by the formation of a rapidly reducible Fe(III) phases derived from the progressive dissolution and re-oxidation of native Fe(III) oxides accompanied by minor increases in Fe reducer populations. The shift in Fe(III) reactivity is evident from Fe-reducibility assays using Shewanella sp., however was undetectable by chemical extractions, Mössbauer or X-ray Absorption spectroscopies. More broadly, our findings suggest Fe reduction rates are strongly coupled to redox dynamics of the recent past, and that frequent shifts in redox conditions can prime a soil for rapid Fe-reduction.

The interactions between nanoscale zero-valent iron and microbes in the subsurface environment: A review

Nanoscale zero-valent iron (NZVI) particles, applied for in-situ subsurface remediation, are inevitable to interact with various microbes in the remediation sites directly or indirectly. This review summarizes their interactions, including the effects of NZVI on microbial activity and growth, the synergistic effect of NZVI and microbes on the contaminant removal, and the effects of microbes on the aging of NZVI. NZVI could exert either inhibitive or stimulative effects on the growth of microbes. The mechanisms of NZVI cytotoxicity (i.e., the inhibitive effect) include physical damage and biochemical destruction. The stimulative effects of NZVI on certain bacteria are associated with the creation of appropriate living environment, either through providing electron donor (e.g., H₂) or carbon sources (e.g., the engineered organic surface modifiers), or through eliminating the noxious substances that can cause bactericidal consequence. As a result of the positive interaction, the combination of NZVI and some microbes shows synergistic effect on contaminant removal. Additionally, the aged NZVI can be utilized by some iron-reducing bacteria, resulting in the transformation of Fe(III) to Fe(II), which can further contribute to the contaminant reduction. However, the Fe(III)-reduction process can probably induce environmental risks, such as environmental methylation and remobilization of the previously entrapped heavy metals.

Manganese in Marine Microbiology

The importance of manganese in the physiology of marine microbes, the biogeochemistry of the ocean and the health of microbial communities of past and present is emerging. Manganese is distributed widely throughout the global ocean, taking the form of an essential antioxidant (Mn²⁺), a potent oxidant (Mn³⁺) and strong adsorbent (Mn oxides) sequestering disproportionately high levels of trace metals and nutrients in comparison to the surrounding seawater. Manganese is, in fact, linked to nearly all other elemental cycles and intricately involved in the health, metabolism and function of the ocean's microbiome. Here, we briefly review the diversity of microbes and pathways responsible for the transformation of Mn within the three Mn pools and their distribution within the marine environment. Despite decades of interrogation, we still have much to learn about the players, mechanisms and consequences of the Mn cycle, and new and exciting discoveries are being made at a rapid rate. What is clear is the dynamic and ever-inspiring complexity of reactions involving Mn, and the acknowledgement that microorganisms are the catalytic engine driving the Mn cycle.

In Situ Analysis of a Silver Nanoparticle-Precipitating Shewanella Biofilm by Surface Enhanced Confocal Raman Microscopy

Shewanella oneidensis MR-1 is an electroactive bacterium, capable of reducing extracellular insoluble electron acceptors, making it important for both nutrient cycling in nature and microbial electrochemical technologies, such as microbial fuel cells and microbial electrosynthesis. When allowed to anaerobically colonize an Ag/AgCl solid interface, S. oneidensis has precipitated silver nanoparticles (AgNp), thus providing the means for a surface enhanced confocal Raman microscopy (SECRaM) investigation of its biofilm. The result is the in-situ chemical mapping of the biofilm as it developed over time, where the distribution of cytochromes, reduced and oxidized flavins, polysaccharides and phosphate in the undisturbed biofilm is monitored. Utilizing AgNp bio-produced by the bacteria colonizing the Ag/AgCl interface, we could perform SECRaM while avoiding the use of a patterned or roughened support or the introduction of noble metal salts and reducing agents. This new method will allow a spatially and temporally resolved chemical investigation not only of Shewanella biofilms at an insoluble electron acceptor, but also of other noble metal nanoparticle-precipitating bacteria in laboratory cultures or in complex microbial communities in their natural habitats.

Immobilization of Shewanella oneidensis MR-1 in diffusive gradients in thin films for determining metal bioavailability

Assessing metal bioavailability in soil is important in modeling the effects of metal toxicity on the surrounding ecosystem. Current methods based on diffusive gradient thin films (DGTs) and Gel-Integrated Microelectrode are limited in their availability and sensitivity. To address this, Shewanella oneidensis, an anaerobic iron reducing bacterium, was incorporated into a thin layer of agarose to replace the polyacrylamide gel that is normally present in DGT to form biologically mobilizing DGT (BMDGT). Viability analysis revealed that 16-35% of the cells remained viable within the BMDGTs depending on the culturing conditions over a 20 h period with/without metals. Deployment of BMDGTs in standardized metal solutions showed significant differences to cell-free BMDGTs when cells grown in Luria Broth (LB) were incorporated into BMDGTs and deployed under anaerobic conditions. Deployment of these BMDGTs in hematite revealed no significant differences between BMDGTs and BMDGTs containing heat killed cells. Whether heat killed cells retain the ability to affect bioavailability is uncertain. This is the first study to investigate how a microorganism that was incorporated into a DGT device such as the metal reducing bacteria, S. oneidensis, may affect the mobility of metals.

Microbially driven Fenton reaction for degradation of the widespread environmental contaminant 1,4-dioxane

The carcinogenic cyclic ether compound 1,4-dioxane is employed as a stabilizer of chlorinated industrial solvents and is a widespread environmental contaminant in surface water and groundwater. In the present study, a microbially driven Fenton reaction was designed to autocatalytically generate hydroxyl (HO•) radicals that degrade 1,4-dioxane. In comparison to conventional (purely abiotic) Fenton reactions, the microbially driven Fenton reaction operated at circumneutral pH and did not the require addition of exogenous H2O2 or UV irradiation to regenerate Fe(II) as Fenton reagents. The 1,4-dioxane degradation process was driven by pure cultures of the Fe(III)-reducing facultative anaerobe Shewanella oneidensis manipulated under controlled laboratory conditions. S. oneidensis batch cultures were provided with lactate, Fe(III), and 1,4-dioxane and were exposed to alternating aerobic and anaerobic conditions. The microbially driven Fenton reaction completely degraded 1,4-dioxane (10 mM initial concentration) in 53 h with an optimal aerobic-anaerobic cycling period of 3 h. Acetate and oxalate were detected as transient intermediates during the microbially driven Fenton degradation of 1,4-dioxane, an indication that conventional and microbially driven Fenton degradation processes follow similar reaction pathways. The microbially driven Fenton reaction provides the foundation for development of alternative in situ remediation technologies to degrade environmental contaminants susceptible to attack by HO• radicals generated by the Fenton reaction.

Electron transport and protein secretion pathways involved in Mn(III) reduction by Shewanella oneidensis

Soluble Mn(III) represents an important yet overlooked oxidant in marine and freshwater systems. The molecular mechanism of microbial Mn(III) reduction, however, has yet to be elucidated. Extracellular reduction of insoluble Mn(IV) and Fe(III) oxides by the metal-reducing γ-proteobacterium Shewanella oneidensis involves inner (CymA) and outer (OmcA) membrane-associated c-type cytochromes, the extracellular electron conduit MtrCAB, and GspD, the secretin of type II protein secretion. CymA, MtrCAB and GspD mutants were unable to reduce Mn(III) and Mn(IV) with lactate, H2, or formate as electron donor. The OmcA mutant reduced Mn(III) and Mn(IV) at near wild-type rates with lactate and formate as electron donor. With H2 as electron donor, however, the OmcA mutant was unable to reduce Mn(III) but reduced Mn(IV) at wild-type rates. Analogous Fe(III) reduction rate analyses indicated that other electron carriers compensated for the absence of OmcA, CymA, MtrCAB and GspD during Fe(III) reduction in an electron donor-dependent fashion. Results of the present study demonstrate that the S. oneidensis electron transport and protein secretion components involved in extracellular electron transfer to external Mn(IV) and Fe(III) oxides are also required for electron transfer to Mn(III) and that OmcA may function as a dedicated component of an H2 oxidation-linked Mn(III) reduction system.

Physiological and electrochemical effects of different electron acceptors on bacterial anode respiration in bioelectrochemical systems

To understand the interactions between bacterial electrode respiration and the other ambient bacterial electron acceptor reductions, alternative electron acceptors (nitrate, Fe2O3, fumarate, azo dye MB17) were added singly or multiply into Shewanella decolorationis microbial fuel cells (MFCs). All the added electron acceptors were reduced simultaneously with current generation. Adding nitrate or MB17 resulted in more rapid cell growth, higher flavin concentration and higher biofilm metabolic viability, but lower columbic efficiency (CE) and normalized energy recovery (NER) while the CE and NER were enhanced by Fe2O3 or fumarate. The added electron acceptors also significantly influenced the cyclic voltammetry profile of anode biofilm probably via altering the cytochrome c expression. The highest power density was observed in MFCs added with MB17 due to the electron shuttle role of the naphthols from MB17 reduction. The results provided important information for MFCs applied in practical environments where contains various electron acceptors.

Bioreduction of hydrogen uranyl phosphate: mechanisms and U(IV) products

The mobility of uranium (U) in subsurface environments is controlled by interrelated adsorption, redox, and precipitation reactions. Previous work demonstrated the formation of nanometer-sized hydrogen uranyl phosphate (abbreviated as HUP) crystals on the cell walls of Bacillus subtilis, a non-U(VI)-reducing, Gram-positive bacterium. The current study examined the reduction of this biogenic, cell-associated HUP mineral by three dissimilatory metal-reducing bacteria, Anaeromyxobacter dehalogenans strain K, Geobacter sulfurreducens strain PCA, and Shewanella putrefaciens strain CN-32, and compared it to the bioreduction of abiotically formed and freely suspended HUP of larger particle size. Uranium speciation in the solid phase was followed over a 10- to 20-day reaction period by X-ray absorption fine structure spectroscopy (XANES and EXAFS) and showed varying extents of U(VI) reduction to U(IV). The reduction extent of the same mass of HUP to U(IV) was consistently greater with the biogenic than with the abiotic material under the same experimental conditions. A greater extent of HUP reduction was observed in the presence of bicarbonate in solution, whereas a decreased extent of HUP reduction was observed with the addition of dissolved phosphate. These results indicate that the extent of U(VI) reduction is controlled by dissolution of the HUP phase, suggesting that the metal-reducing bacteria transfer electrons to the dissolved or bacterially adsorbed U(VI) species formed after HUP dissolution, rather than to solid-phase U(VI) in the HUP mineral. Interestingly, the bioreduced U(IV) atoms were not immediately coordinated to other U(IV) atoms (as in uraninite, UO2) but were similar in structure to the phosphate-complexed U(IV) species found in ningyoite [CaU(PO4)2·H2O]. This indicates a strong control by phosphate on the speciation of bioreduced U(IV), expressed as inhibition of the typical formation of uraninite under phosphate-free conditions.

Anaerobic sulfur metabolism coupled to dissimilatory iron reduction in the extremophile Acidithiobacillus ferrooxidans

Gene transcription (microarrays) and protein levels (proteomics) were compared in cultures of the acidophilic chemolithotroph Acidithiobacillus ferrooxidans grown on elemental sulfur as the electron donor under aerobic and anaerobic conditions, using either molecular oxygen or ferric iron as the electron acceptor, respectively. No evidence supporting the role of either tetrathionate hydrolase or arsenic reductase in mediating the transfer of electrons to ferric iron (as suggested by previous studies) was obtained. In addition, no novel ferric iron reductase was identified. However, data suggested that sulfur was disproportionated under anaerobic conditions, forming hydrogen sulfide via sulfur reductase and sulfate via heterodisulfide reductase and ATP sulfurylase. Supporting physiological evidence for H2S production came from the observation that soluble Cu(2+) included in anaerobically incubated cultures was precipitated (seemingly as CuS). Since H(2)S reduces ferric iron to ferrous in acidic medium, its production under anaerobic conditions indicates that anaerobic iron reduction is mediated, at least in part, by an indirect mechanism. Evidence was obtained for an alternative model implicating the transfer of electrons from S(0) to Fe(3+) via a respiratory chain that includes a bc(1) complex and a cytochrome c. Central carbon pathways were upregulated under aerobic conditions, correlating with higher growth rates, while many Calvin-Benson-Bassham cycle components were upregulated during anaerobic growth, probably as a result of more limited access to carbon dioxide. These results are important for understanding the role of A. ferrooxidans in environmental biogeochemical metal cycling and in industrial bioleaching operations.

Characterisation of the dissimilatory reduction of Fe(III)-oxyhydroxide at the microbe-mineral interface: the application of STXM-XMCD

A combination of scanning transmission X-ray microscopy and X-ray magnetic circular dichroism was used to spatially resolve the distribution of different carbon and iron species associated with Shewanella oneidensis MR-1 cells. S. oneidensis MR-1 couples the reduction of Fe(III)-oxyhydroxides to the oxidation of organic matter in order to conserve energy for growth. Several potential mechanisms may be used by S. oneidensis MR-1 to facilitate Fe(III)-reduction. These include direct contact between the cell and mineral surface, secretion of either exogenous electron shuttles or Fe-chelating agents and the production of conductive 'nanowires'. In this study, the protein/lipid signature of the bacterial cells was associated with areas of magnetite (Fe₃O₄), the product of dissimilatory Fe(III) reduction, which was oversaturated with Fe(II) (compared to stoichiometric magnetite). However, areas of the sample rich in polysaccharides, most likely associated with extracellular polymeric matrix and not in direct contact with the cell surface, were undersaturated with Fe(II), forming maghemite-like (γ-Fe₂O₃) phases compared to stoichiometric magnetite. The reduced form of magnetite will be much more effective in environmental remediation such as the immobilisation of toxic metals. These findings suggest a dominant role for surface contact-mediated electron transfer in this study and also the inhomogeneity of magnetite species on the submicron scale present in microbial reactions. This study also illustrates the applicability of this new synchrotron-based technique for high-resolution characterisation of the microbe-mineral interface, which is pivotal in controlling the chemistry of the Earth's critical zone.

Soluble electron shuttles can mediate energy taxis toward insoluble electron acceptors

Shewanella species grow in widely disparate environments and play key roles in elemental cycling, especially in environments with varied redox conditions. To obtain a system-level understanding of Shewanella's robustness and versatility, the complex interplay of cellular growth, metabolism, and transport under conditions of limiting carbon sources, energy sources, and electron acceptors must be elucidated. In this paper, population-level taxis of Shewanella oneidensis MR-1 cells in the presence of a rate-limiting, insoluble electron acceptor was investigated. A novel mechanism, mediated energy taxis, is proposed by which Shewanella use riboflavin as both an electron shuttle and an attractant to direct cell movement toward local sources of insoluble electron acceptors. The cells secrete reduced riboflavin, which diffuses to a nearby particle containing an insoluble electron acceptor and is oxidized. The oxidized riboflavin then diffuses away from the particle, establishing a spatial gradient that draws cells toward the particle. Experimental and modeling results are presented to support this mechanism. S. oneidensis MR-1 cells inoculated into a uniform dispersion of MnO(2) particles in dilute agar exhibited taxis outward, creating a clear zone within which riboflavin was detected by mass spectrometry. Cells inoculated into dilute agar containing oxidized riboflavin similarly exhibited taxis, rapidly forming an expanding zone of reduced riboflavin. A mathematical model based on the proposed mechanism was able to predict experimental trends, including how concentrations of riboflavin and insoluble electron acceptors (e.g., MnO(2)) affected tactic cell migration.

Influence of arsenate adsorption to ferrihydrite, goethite, and boehmite on the kinetics of arsenate reduction by Shewanella putrefaciens strain CN-32

The kinetics of As(V) reduction by Shewanella putrefaciens strain CN-32 was investigated in suspensions of 0.2, 2, or 20 g L(-1) ferrihydrite, goethite, or boehmite at low As (10 μM) and lactate (25 μM) concentrations. Experimental data were compared with model predictions based on independently determined sorption isotherms and rates of As(V) desorption, As(III) adsorption, and microbial reduction of dissolved As(V), respectively. The low lactate concentration was chosen to prevent significant Fe(III) reduction, but still allowing complete As(V) reduction. Reduction of dissolved As(V) followed first-order kinetics with a 3 h half-life of As(V). Addition of mineral sorbents resulted in pronounced decreases in reduction rates (32-1540 h As(V) half-life). The magnitude of this effect increased with increasing sorbent concentration and sorption capacity (goethite < boehmite < ferrihydrite). The model consistently underestimated the concentrations of dissolved As(V) and the rates of microbial As(V) reduction after addition of S. putrefaciens (∼5 × 10(9) cells mL(-1)), suggesting that attachment of S. putrefaciens cells to oxide mineral surfaces promoted As(V) desorption and thereby facilitated As(V) reduction. The interplay between As(V) sorption to mineral surfaces and bacterially induced desorption may thus be critical in controlling the kinetics of As reduction and release in reducing soils and sediments.

SO2907, a putative TonB-dependent receptor, is involved in dissimilatory iron reduction by Shewanella oneidensis strain MR-1

Shewanella oneidensis strain MR-1 utilizes soluble and insoluble ferric ions as terminal electron acceptors during anaerobic respiration. The components of respiratory metabolism are localized in the membrane fractions which include the outer membrane and cytoplasmic membrane. Many of the biological components that interact with the various iron forms are proposed to be localized in these membrane fractions. To identify the iron-binding proteins acting either as an iron transporter or as a terminal iron reductase, we used metal-catalyzed oxidation reactions. This system catalyzed the oxidation of amino acids in close proximity to the iron binding site. The carbonyl groups formed from this oxidation can then be labeled with fluoresceinamine (FLNH(2)). The peptide harboring the FLNH(2) can then be proteolytically digested, purified by HPLC and then identified by MALDI-TOF tandem MS. A predominant peptide was identified to be part of SO2907 that encodes a putative TonB-dependent receptor. Compared with wild type (wt), the so2907 gene deletion (ΔSO2907) mutant has impaired ability to reduce soluble Fe(III), but retains the same ability to respire oxygen or fumarate as the wt. The ΔSO2907 mutant was also impacted in reduction of insoluble iron. Iron binding assays using isothermal titration calorimetry and fluorescence tryptophan quenching demonstrated that a truncated form of heterologous-expressed SO2907 that contains the Fe(III) binding site, is capable of binding soluble Fe(III) forms with K(d) of approximate 50 μm. To the best of our knowledge, this is the first report of the physiological role of SO2907 in Fe(III) reduction by MR-1.

Mutational and gene expression analysis of mtrDEF, omcA and mtrCAB during arsenate and iron reduction in Shewanella sp. ANA-3

Arsenate respiration and Fe(III) reduction are important processes that influence the fate and transport of arsenic in the environment. The goal of this study was to investigate the impact of arsenate on Fe(III) reduction using arsenate and Fe(III) reduction deficient mutants of Shewanella sp. strain ANA-3. Ferrihydrite reduction in the absence of arsenate was similar for an arsenate reduction mutant (arrA and arsC deletion strain of ANA-3) compared with wild-type ANA-3. However, the presence of arsenate adsorbed onto ferrihydrite impeded Fe(III) reduction for the arsenate reduction mutant but not in the wild-type. In an Fe(III) reduction mutant (mtrDEF, omcA, mtrCAB null mutant of ANA-3), arsenate was reduced similarly to wild-type ANA-3 indicating the Fe(III) reduction pathway is not required for ferrihydrite-associated arsenate reduction. Expression analysis of the mtr/omc gene cluster of ANA-3 showed that omcA and mtrCAB were expressed under soluble Fe(III), ferrihydrite and arsenate growth conditions and not in aerobically grown cells. Expression of arrA was greater with ferrihydrite pre-adsorbed with arsenate relative to ferrihydrite only. Lastly, arrA and mtrA were simultaneously induced in cells shifted to anaerobic conditions and exposed to soluble Fe(III) and arsenate. These observations suggest that, unlike Fe(III), arsenate can co-induce operons (arr and mtr) implicated in arsenic mobilization.

Siderophores are not involved in Fe(III) solubilization during anaerobic Fe(III) respiration by Shewanella oneidensis MR-1

Shewanella oneidensis MR-1 respires a wide range of anaerobic electron acceptors, including sparingly soluble Fe(III) oxides. In the present study, S. oneidensis was found to produce Fe(III)-solubilizing organic ligands during anaerobic Fe(III) oxide respiration, a respiratory strategy postulated to destabilize Fe(III) and produce more readily reducible soluble organic Fe(III). In-frame gene deletion mutagenesis, siderophore detection assays, and voltammetric techniques were combined to determine (i) if the Fe(III)-solubilizing organic ligands produced by S. oneidensis during anaerobic Fe(III) oxide respiration were synthesized via siderophore biosynthesis systems and (ii) if the Fe(III)-siderophore reductase was required for respiration of soluble organic Fe(III) as an anaerobic electron acceptor. Genes predicted to encode the siderophore (hydroxamate) biosynthesis system (SO3030 to SO3032), the Fe(III)-hydroxamate receptor (SO3033), and the Fe(III)-hydroxamate reductase (SO3034) were identified in the S. oneidensis genome, and corresponding in-frame gene deletion mutants were constructed. DeltaSO3031 was unable to synthesize siderophores or produce soluble organic Fe(III) during aerobic respiration yet retained the ability to solubilize and respire Fe(III) at wild-type rates during anaerobic Fe(III) oxide respiration. DeltaSO3034 retained the ability to synthesize siderophores during aerobic respiration and to solubilize and respire Fe(III) at wild-type rates during anaerobic Fe(III) oxide respiration. These findings indicate that the Fe(III)-solubilizing organic ligands produced by S. oneidensis during anaerobic Fe(III) oxide respiration are not synthesized via the hydroxamate biosynthesis system and that the Fe(III)-hydroxamate reductase is not essential for respiration of Fe(III)-citrate or Fe(III)-nitrilotriacetic acid (NTA) as an anaerobic electron acceptor.