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

Redox signaling-driven modulation of microbial biosynthesis and biocatalysis

Microbial communication can drive coordinated functions through sensing, analyzing and processing signal information, playing critical roles in biomanufacturing and life evolution. However, it is still a great challenge to develop effective methods to construct a microbial communication system with coordinated behaviors. Here, we report an electron transfer triggered redox communication network consisting of three building blocks including signal router, optical verifier and bio-actuator for microbial metabolism regulation and coordination. In the redox communication network, the Fe3+/Fe2+ redox signal can be dynamically and reversibly transduced, channeling electrons directly and specifically into bio-actuator cells through iron oxidation pathway. The redox communication network drives gene expression of electron transfer proteins and simultaneously facilitates the critical reducing power regeneration in the bio-actuator, thus enabling regulation of microbial metabolism. In this way, the redox communication system efficiently promotes the biomanufacturing yield and CO2 fixation rate of bio-actuator. Furthermore, the results demonstrate that this redox communication strategy is applicable both in co-culture and microbial consortia. The proposed electron transfer triggered redox communication strategy in this work could provide an approach for reducing power regeneration and metabolic optimization and could offer insights into improving biomanufacturing efficiency.

Bioenergetics of aerobic and anaerobic growth of Shewanella putrefaciens CN32

Shewanella putrefaciens is a model dissimilatory iron-reducing bacterium that can use Fe(III) and O2 as terminal electron acceptors. Consequently, it has the ability to influence both aerobic and anaerobic groundwater systems, making it an ideal microorganism for improving our understanding of facultative anaerobes with iron-based metabolism. In this work, we examine the bioenergetics of O2 and Fe(III) reduction coupled to lactate oxidation in Shewanella putrefaciens CN32. Bioenergetics were measured directly via isothermal calorimetry and by changes to the chemically defined growth medium. We performed these measurements from 25 to 36°C. Modeling metabolism with macrochemical equations allowed us to define a theoretical growth stoichiometry for the catabolic reaction of 1.00 O2:lactate and 1.33 Fe(III):lactate that was consistent with the observed ratios of O2:lactate (1.20 ± 0.23) and Fe(III):lactate (1.46 ± 0.15) consumption. Aerobic growth showed minimal variation with temperature and minimal variation in thermodynamic potentials of incubation. Fe(III)-based growth showed a strong temperature dependence. The Gibbs energy and enthalpy of incubation was minimized at ≥30°C. Energy partitioning modeling of Fe(III)-based calorimetric incubation data predicted that energy consumption for non-growth associate maintenance increases substantially above 30°C. This prediction agrees with the data at 33 and 35°C. These results suggest that the effects of temperature on Shewanella putrefaciens CN32 are metabolism dependent. Gibbs energy of incubation above 30°C was 3-5 times more exergonic with Fe(III)-based growth than with aerobic growth. We compared data gathered in this study with predictions of microbial growth based on standard-state conditions and based on the thermodynamic efficiency of microbial growth. Quantifying the growth requirements of Shewanella putrefaciens CN32 has advanced our understanding of the thermodynamic constraints of this dissimilatory iron-reducing bacterium.

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.

Carbonate Minerals and Dissimilatory Iron-Reducing Organisms Trigger Synergistic Abiotic and Biotic Chain Reactions under Elevated CO2 Concentration

Increasing CO₂ emission has resulted in pressing climate and environmental issues. While abiotic and biotic processes mediating the fate of CO₂ have been studied separately, their interactions and combined effects have been poorly understood. To explore this knowledge gap, an iron-reducing organism, Orenia metallireducens, was cultured under 18 conditions that systematically varied in headspace CO₂ concentrations, ferric oxide loading, and dolomite (CaMg(CO₃)₂) availability. The results showed that abiotic and biotic processes interactively mediate CO₂ acidification and sequestration through "chain reactions", with pH being the dominant variable. Specifically, dolomite alleviated CO₂ stress on microbial activity, possibly via pH control that transforms the inhibitory CO₂ to the more benign bicarbonate species. The microbial iron reduction further impacted pH via the competition between proton (H⁺) consumption during iron reduction and H⁺ generation from oxidization of the organic substrate. Under Fe(III)-rich conditions, microbial iron reduction increased pH, driving dissolved CO₂ to form bicarbonate. Spectroscopic and microscopic analyses showed enhanced formation of siderite (FeCO₃) under elevated CO₂, supporting its incorporation into solids. The results of these CO₂-microbe-mineral experiments provide insights into the synergistic abiotic and biotic processes that alleviate CO₂ acidification and favor its sequestration, which can be instructive for practical applications (e.g., acidification remediation, CO₂ sequestration, and modeling of carbon flux).

Exploring the secondary mineral products generated by microbial iron respiration in Archean ocean simulations

Marine chemical sedimentary deposits known as Banded Iron Formations (BIFs) archive Archean ocean chemistry and, potentially, signs of ancient microbial life. BIFs contain a diversity of iron- and silica-rich minerals in disequilibrium, and thus many interpretations of these phases suggest they formed secondarily during early diagenetic processes. One such hypothesis posits that the early diagenetic microbial respiration of primary iron(III) oxides in BIFs resulted in the formation of other iron phases, including the iron-rich silicates, carbonates, and magnetite common in BIF assemblages. Here, we simulated this proposed pathway in laboratory incubations combining a model dissimilatory iron-reducing (DIR) bacterium, Shewanella putrefaciens CN32, and the ferric oxyhydroxide mineral ferrihydrite under conditions mimicking the predicted Archean seawater geochemistry. We assessed the impact of dissolved silica, calcium, and magnesium on the bioreduced precipitates. After harvesting the solid products from these experiments, we analyzed the reduced mineral phases using Raman spectroscopy, electron microscopy, powder x-ray diffraction, and spectrophotometric techniques to identify mineral precipitates and track the bulk distributions of Fe(II) and Fe(III). These techniques detected a diverse range of calcium carbonate morphologies and polymorphism in incubations with calcium, as well as secondary ferric oxide phases like goethite in silica-free experiments. We also identified aggregates of curling, iron- and silica-rich amorphous precipitates in all incubations amended with silica. Although ferric oxides persist even in our electron acceptor-limited incubations, our observations indicate that microbial iron reduction of ferrihydrite is a viable pathway for the formation of early iron silicate phases. This finding allows us to draw parallels between our experimental proto-silicates and the recently characterized iron silicate nanoinclusions in BIF chert deposits, suggesting that early iron silicates could possibly be signatures of iron-reducing metabolisms on early Earth.

Understanding the Importance of Labile Fe(III) during Fe(II)-Catalyzed Transformation of Metastable Iron Oxyhydroxides

Transformation of metastable Fe(III) oxyhydroxides is a prominent process in natural environments and can be significantly accelerated by the coexisting aqueous Fe(II) (Fe(II)_aq). Recent evidence points to the solution mass transfer of labile Fe(III) (Fe(III)_labile) as the primary intermediate species of general importance. However, a mechanistic aspect that remains unclear is the dependence of phase outcomes on the identity of the metastable Fe(III) oxyhydroxide precursor. Here, we compared the coupled evolution of Fe(II) species, solid phases, and Fe(III)_labile throughout the Fe(II)-catalyzed transformation of lepidocrocite (Lp) versus ferrihydrite (Fh) at equal Fe(III) mass loadings with 0.2-1.0 mM Fe(II)_aq at pH = 7.0. Similar to Fh, the conversion of Lp to product phases occurs by a dissolution-reprecipitation mechanism mediated by Fe(III)_labile that seeds the nucleation of products. Though for Fh we observed a transformation to goethite (Gt), accompanied by the transient emergence and decline of Lp, for initial Lp we observed magnetite (Mt) as the main product. A linear correlation between the formation rate of Mt and the effective supersaturation in terms of Fe(III)_labile concentration shows that Fe(II)-induced transformation of Lp into Mt is governed by the classical nucleation theory. When Lp is replaced by equimolar Gt, Mt formation is suppressed by opening a lower barrier pathway to Gt by heterogeneous nucleation and growth on the added Gt seeds. The collective findings add to the mechanistic understanding of factors governing phase selections that impact iron bioavailability, system redox potential, and the fate and transport of coupled elements.

In-situ formation and self-immobilization of biogenic Fe oxides in anaerobic granular sludge for enhanced performance of acidogenesis and methanogenesis

Addition of ferric oxides into flocculent anaerobic sludge was reported to enhance methanogenesis due to accelerated direct interspecies electron transfer (DIET) between syntrophic microbial communities. However, it is generally hard to incorporate Fe oxides into already matured anaerobic granular sludge (AGS) due to its special aggregated structure. In this study, a novel method was attempted to fast incorporate Fe oxides into AGS through in-situ microbial formation and immobilization of biogenic Fe oxides. Factors influencing the formation of Fe oxides were investigated and effects of Fe oxides on the acidogenic and methanogenic performance of AGS were assessed. Results showed that AGS could form Fe oxides mainly in the form of magnetite and hematite through biological reduction of Fe(III) oxyhydroxide. A maximum loading amount of 83.9 mg Fe/g MLVSS was obtained at pH 7 after contacting with 60 mM Fe(III) oxyhydroxide. The efficiency of electron donors which supported Fe(III) reduction followed the order of pyruvate > propionate > glucose > acetate > lactate > formate. Addition of electron transfer mediators (ETMs) promoted the formation of Fe oxides and their performance followed the order of AQDS > AQC > humics > FMN > riboflavin. Presence of Fe oxides in AGS (134.6 Fe/g VSS) increased the production of volatile fatty acids (VFAs) and methane by 16.28% and 41.94% respectively, comparing to the control. The enhancement may be attributed to increased conductivity and stimulated growth of exoelectrogens (Clostridium and Anaerolinea) and methanogenic endoelectrogens Methanosaeta in granular sludge which may strengthen direct interspecies electron transfer between syntrophic microbial communities. Overall, this study provides an alternative strategy to improve the digestion performance of AGS through in-situ formation and immobilization of biogenic Fe oxides.

Assessment of geochemical modeling applications and research hot spots-a year in review

Geochemical modeling has been employed in several fields of science and engineering in recent years. This review seeks to provide an overview of case studies that applied geochemical modeling in the 2019 year, which includes over 250 articles. This review is intended to inform new users on the possibilities that geochemical modeling brings, while also informing existing and past users on its latest developments. The survey of studies was conducted with an emphasis on the modeling techniques, the objective of studies, the prevalent simulated variables and the use of specific software packages. The analysis showed that geochemical modeling is still predominantly employed in experimental projects and in the form of equilibrium modeling. PHREEQC and Visual MINTEQ were recognized as the most popular software packages for simulating a wide range of processes, using equilibrium or other geochemical modeling forms. The study of fluid-rock interactions and pollution and remediation processes can be regarded as the principal geochemical modeling objectives, constituting 37% and 36% of the reviewed studies, respectively. Focusing on fluid-rock interactions, hydrogeochemical processes, carbon capture and storage and enhanced oil recovery have been the main topics examined with geochemical modeling. Assessments of the toxicity of metals in terms of leachate and mobilization, as well as their removal from soil and water systems, have been major topics investigated with the aid of geochemical modeling in terms of pollution and remediation research. It was found that the scholars benefit from geochemical modeling in their research both as a main technique and as an accessory tool. Saturation index, elemental concentration and speciation, mineral mass and composition and pH were among the most common variables modeled in reviewed studies. Geochemical modeling has gained a wider user base in recent years, and many research groups have used it in consecutive studies to deepen knowledge. However, much potential for further dissemination still remains.

Combined Effects of Fe(III)-Bearing Clay Minerals and Organic Ligands on U(VI) Bioreduction and U(IV) Speciation

Reduction of U(VI) to U(IV) drastically reduces its solubility and has been proposed as a method for remediation of uranium contamination. However, much is still unknown about the kinetics, mechanisms, and products of U(VI) bioreduction in complex systems. In this study, U(VI) bioreduction experiments were conducted with Shewanella putrefaciens strain CN32 in the presence of clay minerals and two organic ligands: citrate and EDTA. In reactors with U and Fe(III)-clay minerals, the rate of U(VI) bioreduction was enhanced due to the presence of ligands, likely because soluble Fe³⁺- and Fe²⁺-ligand complexes served as electron shuttles. In the presence of citrate, bioreduced U(IV) formed a soluble U(IV)-citrate complex in experiments with either Fe-rich or Fe-poor clay mineral. In the presence of EDTA, U(IV) occurred as a soluble U(IV)-EDTA complex in Fe-poor montmorillonite experiments. However, U(IV) remained associated with the solid phase in Fe-rich nontronite experiments through the formation of a ternary U(IV)-EDTA-surface complex, as suggested by the EXAFS analysis. Our study indicates that organic ligands and Fe(III)-bearing clays can significantly affect the microbial reduction of U(VI) and the stability of the resulting U(IV) phase.

Reduction of Vanadium(V) by Iron(II)-Bearing Minerals

Fe(II)-bearing minerals (magnetite, siderite, green rust, etc.) are common products of microbial Fe(III) reduction, and they provide a reservoir of reducing capacity in many subsurface environments that may contribute to the reduction of redox active elements such as vanadium; which can exist as V(V), V(IV), and V(III) under conditions typical of near-surface aquatic and terrestrial environments. To better understand the redox behavior of V under ferrugenic/sulfidogenic conditions, we examined the interactions of V(V) (1 mM) in aqueous suspensions containing 50 mM Fe(II) as magnetite, siderite, vivianite, green rust, or mackinawite, using X-ray absorption spectroscopy at the V K-edge to determine the valence state of V. Two additional systems of increased complexity were also examined, containing either 60 mM Fe(II) as biogenic green rust (BioGR) or 40 mM Fe(II) as a mixture of biogenic siderite, mackinawite, and magnetite (BioSMM). Within 48 h, total solution-phase V concentrations decreased to <20 µM in all but the vivianite and the biogenic BiSMM systems; however, >99.5% of V was removed from solution in the BioSMM and vivianite systems within 7 and 20 months, respectively. The most rapid reduction was observed in the mackinawite system, where V(V) was reduced to V(III) within 48 h. Complete reduction of V(V) to V(III) occurred within 4 months in the green rust system, 7 months in the siderite system, and 20 months in the BioGR system. Vanadium(V) was only partially reduced in the magnetite, vivianite, and BioSMM systems, where within 7 months the average V valence state stabilized at 3.7, 3.7, and 3.4, respectively. The reduction of V(V) in soils and sediments has been largely attributed to microbial activity, presumably involving direct enzymatic reduction of V(V); however the reduction of V(V) by Fe(II)-bearing minerals suggests that abiotic or coupled biotic–abiotic processes may also play a critical role in V redox chemistry, and thus need to be considered in modeling the global biogeochemical cycling of V.

Effects of Fe(III) Oxide Mineralogy and Phosphate on Fe(II) Secondary Mineral Formation during Microbial Iron Reduction

The bioreduction of Fe(III) oxides by dissimilatory iron-reducing bacteria may result in the formation of a suite of Fe(II)-bearing secondary minerals, including magnetite (a mixed Fe(II)/Fe(III) oxide), siderite (Fe(II) carbonate), vivianite (Fe(II) phosphate), chukanovite (ferrous hydroxy carbonate), and green rusts (mixed Fe(II)/Fe(III) hydroxides). In an effort to better understand the factors controlling the formation of specific Fe(II)-bearing secondary minerals, we examined the effects of Fe(III) oxide mineralogy, phosphate concentration, and the availability of an electron shuttle (9,10-anthraquinone-2,6-disulfonate, AQDS) on the bioreduction of a series of Fe(III) oxides (akaganeite, feroxyhyte, ferric green rust, ferrihydrite, goethite, hematite, and lepidocrocite) by Shewanella putrefaciens CN32, and the resulting formation of secondary minerals, as determined by X-ray diffraction, Mössbauer spectroscopy, and scanning electron microscopy. The overall extent of Fe(II) production was highly dependent on the type of Fe(III) oxide provided. With the exception of hematite, AQDS enhanced the rate of Fe(II) production; however, the presence of AQDS did not always lead to an increase in the overall extent of Fe(II) production and did not affect the types of Fe(II)-bearing secondary minerals that formed. The effects of the presence of phosphate on the rate and extent of Fe(II) production were variable among the Fe(III) oxides, but in general, the highest loadings of phosphate resulted in decreased rates of Fe(II) production, but ultimately higher levels of Fe(II) than in the absence of phosphate. In addition, phosphate concentration had a pronounced effect on the types of secondary minerals that formed; magnetite and chukanovite formed at phosphate concentrations of ≤1 mM (ferrihydrite), <~100 µM (lepidocrocite), 500 µM (feroxyhyte and ferric green rust), while green rust, or green rust and vivianite, formed at phosphate concentrations of 10 mM (ferrihydrite), ≥100 µM (lepidocrocite), and 5 mM (feroxyhyte and ferric green rust). These results further demonstrate that the bioreduction of Fe(III) oxides, and accompanying Fe(II)-bearing secondary mineral formation, is controlled by a complex interplay of mineralogical, geochemical, and microbiological factors.

Reduction of Hg(II) by Fe(II)-Bearing Smectite Clay Minerals

Aluminosilicate clay minerals are often a major component of soils and sediments and many of these clays contain structural Fe (e.g., smectites and illites). Structural Fe(III) in smectite clays is redox active and can be reduced to Fe(II) by biotic and abiotic processes. Fe(II)-bearing minerals such as magnetite and green rust can reduce Hg(II) to Hg(0); however, the ability of other environmentally relevant Fe(II) phases, such as structural Fe(II) in smectite clays, to reduce Hg(II) is largely undetermined. We conducted experiments examining the potential for reduction of Hg(II) by smectite clay minerals containing 0–25 wt% Fe. Fe(III) in the clays (SYn-1 synthetic mica-montmorillonite, SWy-2 montmorillonite, NAu-1 and NAu-2 nontronite, and a nontronite from Cheney, Washington (CWN)) was reduced to Fe(II) using the citrate-bicarbonate-dithionite method. Experiments were initiated by adding 500 µM Hg(II) to reduced clay suspensions (4 g clay L−1) buffered at pH 7.2 in 20 mM 3-morpholinopropane-1-sulfonic acid (MOPS). The potential for Hg(II) reduction in the presence of chloride (0–10 mM) and at pH 5–9 was examined in the presence of reduced NAu-1. Analysis of the samples by Hg LIII-edge X-ray absorption fine structure (XAFS) spectroscopy indicated little to no reduction of Hg(II) by SYn-1 (0% Fe), while reduction of Hg(II) to Hg(0) was observed in the presence of reduced SWy-2, NAu-1, NAu-2, and CWN (2.8–24.8% Fe). Hg(II) was reduced to Hg(0) by NAu-1 at all pH and chloride concentrations examined. These results suggest that Fe(II)-bearing smectite clays may contribute to Hg(II) reduction in suboxic/anoxic soils and sediments.

New Perspectives on Iron-Based Nanostructures

Among all minerals, iron is one of the elements identified early by human beings to take advantage of and be used. The role of iron in human life is so great that it made an era in the ages of humanity. Pure iron has a shiny grayish-silver color, but after combining with oxygen and water it can make a colorful set of materials with divergent properties. This diversity sometimes appears ambiguous but provides variety of applications. In fact, iron can come in different forms: zero-valent iron (pure iron), iron oxides, iron hydroxides, and iron oxide hydroxides. By taking these divergent materials into the nano realm, new properties are exhibited, providing us with even more applications. This review deals with iron as a magic element in the nano realm and provides comprehensive data about its structure, properties, synthesis techniques, and applications of various forms of iron-based nanostructures in the science, medicine, and technology sectors.

Controls on Iron Reduction and Biomineralization over Broad Environmental Conditions as Suggested by the Firmicutes Orenia metallireducens Strain Z6

Microbial iron reduction is a ubiquitous biogeochemical process driven by diverse microorganisms in a variety of environments. However, it is often difficult to separate the biological from the geochemical controls on bioreduction of Fe(III) oxides. Here, we investigated the primary driving factor(s) that mediate secondary iron mineral formation over a broad range of environmental conditions using a single dissimilatory iron reducer, Orenia metallireducens strain Z6. A total of 17 distinct geochemical conditions were tested with differing pH (6.5-8.5), temperature (22-50 °C), salinity (2-20% NaCl), anions (phosphate and sulfate), electron shuttle (anthraquinone-2,6-disulfonate), and Fe(III) oxide mineralogy (ferrihydrite, lepidocrocite, goethite, hematite, and magnetite). The observed rates and extent of iron reduction differed significantly with k_int between 0.186 and 1.702 mmol L^-1 day^-1 and Fe(II) production ranging from 6.3% to 83.7% of the initial Fe(III). Using X-ray absorption and scattering techniques (EXAFS and XRD), we identified and assessed the relationship between secondary minerals and the specific environmental conditions. It was inferred that the observed bifurcation of the mineralization pathways may be mediated by differing extents of Fe(II) sorption on the remaining Fe(III) minerals. These results expand our understanding of the controls on biomineralization during microbial iron reduction and aid the development of practical applications.