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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Mechanistic Studies of a Primitive Homolog of Nitrogenase Involved in Coenzyme F430 Biosynthesis (Final Report)

Methyl-coenzyme M reductase (MCR) is the key enzyme in the biological formation and anaerobic oxidation of methane (AOM). Methane is a potent greenhouse gas and the major component of natural gas. Given the abundance of natural gas reserves in remote areas, there is great current interest in a scalable bio-based process for the conversion of methane to liquid fuel and other high-value chemicals. MCR holds much promise for use in such a methane bioconversion strategy. However, MCR cannot currently be produced in an active form in a heterologous host, due in large part to the lack of genetic and biochemical information about the production of holo MCR. In an effort to overcome this deficiency, our laboratory recently elucidated the biosynthetic pathway of the unique nickel-containing coenzyme of MCR, F430. The key step in coenzyme F430 biosynthesis (Cfb) was found to involve an unprecedented reductive cyclization reaction. This remarkable transformation, which involves a 6-electron reduction, the formation of a γ-lactam ring, and the generation of 7 stereocenters, is catalyzed by a primitive homolog of nitrogenase (CfbCD). Nitrogenase is a two-component metalloenzyme that catalyzes the adenosine triphosphate (ATP)-dependent reduction of dinitrogen to ammonia (nitrogen fixation). Homologs of nitrogenase are also involved in the biosynthesis of the photosynthetic pigments chlorophyll and bacteriochlorophyll. Phylogenetic analysis of the CfbCD complex suggests that it is representative of a more ancient lineage of the nitrogenase superfamily, and a thorough investigation of its structure and function is likely to shed light on the mechanisms and evolution of these important metalloenzymes. Moreover, a detailed understanding of the mechanism of the CfbCD complex may aid in the development of specific inhibitors to help reduce natural greenhouse gas emissions and can be exploited for the heterologous production of MCR for methane bioconversion. Towards these goals, specific aims were pursued for the 1) identification of physiological electron donors and in vivo coenzyme F430 synthesis, 2) analysis of the iron sulfur centers, structure, and oligomerization state changes, and 3) characterization of transient intermediates and the intercomponent electron transfer.

03 NATURAL GAS↗
DOE OSTI2022

Building a Framework to Understand Transition Metals' Behavior in Euxinic Conditions (Final Technical Report)

This project focuses first and foremost on metal sulfide geochemistry and mineralogy as controlled by a complex matrix of environmental factors. The principal investigator’s group aim to illuminate the metal-sulfide reaction mechanisms, rates, and pathways through systematic experimentation and data collection and analyzing the relationships between the characteristics of the produced metal sulfide solid-phase/aqueous complexes and the environmental factors. This understanding is essential for obtaining a full picture of the complex cycling patterns of single or multi metal species in sulfidic environments ranging from deep-see basins, hydrothermal vents, inland seas, terrestrial water bodies, to engineered remediation systems. The specific goal of this past project was to illuminate the reaction mechanisms and kinetics of metal anions and sulfide in mixed metal cation-metal anion-sulfide systems under various aqueous conditions (which resembled a range of naturally occurring euxinic settings). For the period of this contract, we investigated the molybdenum-iron-sulfide system, with an emphasis on the conditions that caused solid phase formation. We focused on quantifying the mobility/sequestration of molybdenum under each experimental condition and identified the changes of valence states for each involved element (i.e., Mo, Fe, and S) in the precipitate. We also proposed pathways for the electron transfer that occurred in aqueous chemistry. The major analytical tools used for this study include UV-visible light spectroscopy, transmission electron microscopy, X-ray photoelectron spectroscopy, and synchrotron-based X-ray absorption spectroscopy (access gained through facility proposals to the Canadian Light Source). The biggest finding of this project was that besides pH, the iron-sulfur chemistry has a dominant control of the thiolation kinetics and subsequent reduction of Mo(VI), which are likely prerequisites of molybdenum sequestration in anoxic conditions. The results have been written up as manuscript by the end of this project (see Phillips et al.). The experimental results of this project may be critical for advancing our understanding of (1) basic chemistry involving transition metals and reduced sulfur species, (2) the validity of certain geochemical proxies, and (3) the stability and evolution of euxinic geochemical environments. It is noted that the basic results obtained through this project also have implications for Mo-S cluster-based catalyst development in inorganic chemistry and materials sciences.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Investigating Abiotic and Biotic Mechanisms of Pyrite Reduction

Pyrite (FeS 2 ) has a very low solubility and therefore has historically been considered a sink for iron (Fe) and sulfur (S) and unavailable to biology in the absence of oxygen and oxidative weathering. Anaerobic methanogens were recently shown to reduce FeS 2 and assimilate Fe and S reduction products to meet nutrient demands. However, the mechanism of FeS 2 mineral reduction and the forms of Fe and S assimilated by methanogens remained unclear. Thermodynamic calculations described herein indicate that H 2 at aqueous concentrations as low as 10 –10 M favors the reduction of FeS 2 , with sulfide (HS – ) and pyrrhotite (Fe 1–x S) as products; abiotic laboratory experiments confirmed the reduction of FeS 2 with dissolved H 2 concentrations greater than 1.98 × 10 –4 M H 2 . Growth studies of Methanosarcina barkeri provided with FeS 2 as the sole source of Fe and S resulted in H 2 production but at concentrations too low to drive abiotic FeS 2 reduction, based on abiotic laboratory experimental data. A strain of M. barkeri with deletions in all [NiFe]-hydrogenases maintained the ability to reduce FeS 2 during growth, providing further evidence that extracellular electron transport (EET) to FeS 2 does not involve H 2 or [NiFe]-hydrogenases. Physical contact between cells and FeS 2 was required for mineral reduction but was not required to obtain Fe and S from dissolution products. The addition of a synthetic electron shuttle, anthraquinone-2,6-disulfonate, allowed for biological reduction of FeS 2 when physical contact between cells and FeS 2 was prohibited, indicating that exogenous electron shuttles can mediate FeS 2 reduction. Here, transcriptomics experiments revealed upregulation of several cytoplasmic oxidoreductases during growth of M. barkeri on FeS 2 , which may indicate involvement in provisioning low potential electrons for EET to FeS 2 . Collectively, the data presented herein indicate that reduction of insoluble FeS 2 by M. barkeri occurred via electron transfer from the cell surface to the mineral surface resulting in the generation of soluble HS – and mineral-associated Fe 1–x S. Solubilized Fe(II), but not HS – , from mineral-associated Fe 1–x S reacts with aqueous HS – yielding aqueous iron sulfur clusters (FeS aq ) that likely serve as the Fe and S source for methanogen growth and activity. FeS aq nucleation and subsequent precipitation on the surface of cells may result in accelerated EET to FeS 2 , resulting in positive feedback between cell activity and FeS 2 reduction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

High-Spin and Reactive Fe 13 Cluster with Exposed Metal Sites

We report atomically defined large metal clusters have applications in new reaction development and preparation of materials with tailored properties. Expanding the synthetic toolbox for reactive high nuclearity metal complexes, we report a new class of Fe clusters, Tp* 4 W 4 Fe 13 S 12 , displaying a Fe 13 core with M-M bonds that has precedent only in main group and late metal chemistry. M 13 clusters with closed shell electron configurations can show significant stability and have been classified as superatoms. In contrast, Tp* 4 W 4 Fe 13 S 12 displays a large spin ground state of S=13. This compound performs small molecule activations involving the transfer of up to 12 electrons resulting in significant cluster rearrangements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Classifying metal‐binding sites with neural networks

Abstract To advance our ability to predict impacts of the protein scaffold on catalysis, robust classification schemes to define features of proteins that will influence reactivity are needed. One of these features is a protein's metal‐binding ability, as metals are critical to catalytic conversion by metalloenzymes. As a step toward realizing this goal, we used convolutional neural networks (CNNs) to enable the classification of a metal cofactor binding pocket within a protein scaffold. CNNs enable images to be classified based on multiple levels of detail in the image, from edges and corners to entire objects, and can provide rapid classification. First, six CNN models were fine‐tuned to classify the 20 standard amino acids to choose a performant model for amino acid classification. This model was then trained in two parallel efforts: to classify a 2D image of the environment within a given radius of the central metal binding site, either an Fe ion or a [2Fe‐2S] cofactor, with the metal visible (effort 1) or the metal hidden (effort 2). We further used two sub‐classifications of the [2Fe‐2S] cofactor: (1) a standard [2Fe‐2S] cofactor and (2) a Rieske [2Fe‐2S] cofactor. The accuracy for the model correctly identifying all three defined features was >95%, despite our perception of the increased challenge of the metalloenzyme identification. This demonstrates that machine learning methodology to classify and distinguish similar metal‐binding sites, even in the absence of a visible cofactor, is indeed possible and offers an additional tool for metal‐binding site identification in proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

An alcove at the acetyl-CoA synthase nickel active site is required for productive substrate CO binding and anaerobic carbon fixation

One of the seven natural CO 2 fixation pathways, the anaerobic Wood-Ljungdahl pathway (WLP) is unique in generating CO as a metabolic intermediate, operating through organometallic intermediates, and in conserving (versus utilizing) net ATP. The key enzyme in the WLP is acetyl-CoA synthase (ACS), which uses an active site [2Ni-4Fe-4S] cluster (A-cluster), a CO tunnel, and an organometallic (Ni-CO, Ni-methyl, and Ni-acetyl) reaction sequence to generate acetyl-CoA. Here, we reveal that an alcove, which interfaces the tunnel and the A-cluster, is essential for CO 2 fixation and autotrophic growth by the WLP. In vitro spectroscopy, kinetics, binding, and in vivo growth experiments reveal that a Phe229A substitution at one wall of the alcove decreases CO affinity thirty-fold and abolishes autotrophic growth; however, a F229W substitution enhances CO binding 80-fold. Our results indicate that the structure of the alcove is exquisitely tuned to concentrate CO near the A-cluster; protect ACS from CO loss during catalysis, provide a haven for inhibitory CO, and stabilize the tetrahedral coordination at the Nip site where CO binds. The directing, concentrating, and protective effects of the alcove explain the inability of F209A to grow autotrophically. The alcove also could help explain current controversies over whether ACS binds CO and methyl through a random or ordered mechanism. Our work redefines what we historically refer to as the metallocenter "active site". The alcove is so crucial for enzymatic function that we propose it is part of the active site. The community should now look for such alcoves in all "gas handling" metalloenzymes.

bacterial metabolism↗
DOE OSTI2025

Insight Into the High-Potential Branch of the Alternate Nad+-Dependent NADPH:Ferredoxin Oxidoreductase II (NfnII) from Pyrococcus Furiosus. Evidence for the Gating Step in Electron Bifurcation

We have investigated the rapid-reaction kinetics of the NAD+-dependent NADPH:ferredoxin oxidoreductase II (NfnII) from Pyrococcus furiosus, permitting a comparison with recent work done with the paralog NfnI from the same organism. The half-potentials of the electron-bifurcating L-FAD are highly crossed in both NfnI, meaning the potential for the quinone/semiquinone couple is significantly lower than that for the semiquinone/hydroquinone couple so that the semiquinone oxidation state is thermodynamically unstable. The same appears to be the case with NfnII on the basis of its similar behavior in transient absorption spectroscopy experiments and the absence of any evidence for FAD*- accumulation in the course of reductive titrations (which would be manifested as a transient increase in absorbance at ~380 nm)1. Reductive titrations with both the one-electron donor sodium dithionite and the obligate two-electron donor NADPH demonstrate that, in contrast to NfnI, little FADH* accumulates in the high-potential pathway of NfnII in the course of reduction, as reflected in the absence of a transient increase in absorbance in the 500-600 nm region. This indicates that the half-potentials of the S-FAD are crossed in NfnII by a minimum of 120 mV. Rapid-reaction experiments mixing oxidized NfnII with NADPH also show no evidence of S-FADH* accumulation. Furthermore, the enzyme is only partially reduced at the end of the reaction with NADPH, indicating that there is little electron transfer into the high-potential pathway of NfnII. When the reaction is carried out in the presence of the one-electron carrier ferredoxin, only approximately one equivalent of ferredoxin becomes reduced, in contrast to the maximum of three equivalents seen with NfnI. This is consistent with only a single electron bifurcation event taking place under these conditions with NfnII, with only a single high-potential electron passing into the [2Fe-2S] cluster of the high-potential pathway of NfnII but not progressing further to the S-FAD. This accounts for the observation that NfnII has greatly reduced bifurcating activity compared to NfnI. The lack of electron transfer into the S-FAD of NfnII due to its crossed half-potentials prevents successive bifurcation activity and indicates that electron transfer within the high-potential branch gates bifurcation activity in NfnI.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

How a Formate Dehydrogenase Responds to Oxygen: Unexpected O 2 Insensitivity of an Enzyme Harboring Tungstopterin, Selenocysteine, and [4Fe–4S] Clusters

The reversible two-electron interconversion of formate and CO 2 is catalyzed by both nonmetallo- and metallo-formate dehydrogenases (FDHs). The latter group comprises molybdenum- or tungsten-containing enzymes with the metal coordinated by two equivalents of a pyranopterin cofactor, a cysteinyl or selenocysteinyl (Sec) ligand supplied by the polypeptide, and a catalytically essential terminal sulfido ligand. In addition, these biocatalysts incorporate one or more [4Fe–4S] clusters for facilitating long-distance electron transfer. However, an interesting dichotomy arises when attempting to understand how the metallo-FDHs react with O 2 . Whereas existing scholarship portrays these enzymes as being unable to perform in air due to extreme O 2 lability of their metal centers, studies dating as far back as the 1930s emphasize that some of these systems exhibit formate oxidase (FOX) activity, coupling formate oxidation to O 2 reduction. Therefore, to reconcile these conflicting views, we explored context-dependent functional linkages between metallo-FDHs and their cognate electron acceptors within the same organism vis-à-vis catalysis under atmospheric O 2 . Here, we report the discovery and characterization of an O 2 -insensitive FDH2 from the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough (DvH) that ligates tungsten, Sec, and four [4Fe–4S] clusters. By advancing a robust expression platform for its recombinant production, we eliminate both the requirement of nitrate or azide during purification and reductive activation with thiols and/or formate prior to catalysis. Because the distinctive spectral signatures of formate-reduced DvH-FDH2 remain invariant under anaerobic and aerobic conditions, we benchmarked the enzyme activity in air, identifying CO 2 as the catalytic product. Full reaction progress curve analysis discloses a high catalytic efficiency when probed with a high-potential artificial electron acceptor. Furthermore, we show that DvH-FDH2 enables near-stoichiometric hydrogen peroxide production without superoxide release to achieve O 2 insensitivity. Notably, simultaneous electron transfer to cytochrome c and O 2 reveals that metal-based electron bifurcation is operational in this system. Taken together, our work proves the co-occurrence of redox bifurcated FDH and FOX activities within a metalloenzyme scaffold. These findings set the stage for uncovering previously unknown O 2 -insensitive flavin-based electron bifurcation mechanisms, as well as for developing authentic formate/air biofuel cells, engineering O 2 -stable FDHs and biohybrid metallocatalysts, and discerning formate bioenergetics of gut microbiota.

13C NMR↗
DOE OSTI2022

Templating Bicarbonate in the Second Coordination Sphere Enhances Electrochemical CO 2 Reduction Catalyzed by Iron Porphyrins

Bicarbonate-based electrolytes are ubiquitous in aqueous electrochemical CO 2 reduction, particularly in heterogenous catalysis, where they demonstrate improved catalytic performance relative to other buffers. In contrast, the presence of bicarbonate in organic electrolytes and its roles in homogeneous electrocatalysis remain underexplored. Here, we investigate the influence of bicarbonate on iron porphyrin-catalyzed electrochemical CO 2 reduction. In this work, we show that bicarbonate is a viable proton donor in organic electrolyte (p K a = 20.8 in dimethyl sulfoxide) and that urea pendants in the second coordination sphere can be used to template bicarbonate in the vicinity of a molecular iron porphyrin catalyst. The templated binding of bicarbonate increases its acidity, resulting in a 1500-fold enhancement in catalytic rates relative to unmodified parent iron porphyrin. This work emphasizes the importance of bicarbonate speciation in wet organic electrolytes and establishes second-sphere bicarbonate templating as a design strategy to harness this adventitious acid and enhance CO 2 reduction catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Temperature-dependent iron motion in extremophile rubredoxins – no need for ‘corresponding states’

Extremophile organisms are known that can metabolize at temperatures down to – 25 °C (psychrophiles) and up to 122 °C (hyperthermophiles). Understanding viability under extreme conditions is relevant for human health, biotechnological applications, and our search for life elsewhere in the universe. Information about the stability and dynamics of proteins under environmental extremes is an important factor in this regard. Here we compare the dynamics of small Fe-S proteins – rubredoxins – from psychrophilic and hyperthermophilic microorganisms, using three different nuclear techniques as well as molecular dynamics calculations to quantify motion at the Fe site. The theory of ‘corresponding states’ posits that homologous proteins from different extremophiles have comparable flexibilities at the optimum growth temperatures of their respective organisms. Although ‘corresponding states’ would predict greater flexibility for rubredoxins that operate at low temperatures, we find that from 4 to 300 K, the dynamics of the Fe sites in these homologous proteins are essentially equivalent.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The pathway for coenzyme M biosynthesis in bacteria

Mercaptoethane sulfonate or coenzyme M (CoM) is the smallest known organic cofactor and is most commonly associated with the methane-forming step in all methanogenic archaea but is also associated with the anaerobic oxidation of methane to CO 2 in anaerobic methanotrophic archaea and the oxidation of short-chain alkanes in Syntrophoarchaeum species. It has also been found in a small number of bacteria capable of the metabolism of small organics. Although many of the steps for CoM biosynthesis in methanogenic archaea have been elucidated, a complete pathway for the biosynthesis of CoM in archaea or bacteria has not been reported. Here, we present the complete CoM biosynthesis pathway in bacteria, revealing distinct chemical steps relative to CoM biosynthesis in methanogenic archaea. The existence of different pathways represents a profound instance of convergent evolution. The five-step pathway involves the addition of sulfite, the elimination of phosphate, decarboxylation, thiolation, and the reduction to affect the sequential conversion of phosphoenolpyruvate to CoM. The salient features of the pathway demonstrate reactivities for members of large aspartase/fumarase and pyridoxal 5'-phosphate–dependent enzyme families.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

S-adenosyl-L-methionine is the unexpected methyl donor for the methylation of mercury by the membrane-associated HgcAB complex

Mercury (Hg) is a heavy metal that exhibits high biological toxicity. Monomethylmercury and dimethylmercury are neurotoxins and a significant environmental concern as they bioaccumulate and biomagnify within the aquatic food web. Microbial Hg methylation involves two proteins, HgcA and HgcB. Here, we show that HgcA and HgcB can be heterologously coexpressed, and the HgcAB complex can be purified. We demonstrated that HgcA is a membrane-associated cobalamin-dependent methyltransferase and HgcB is a ferredoxin-like protein containing two [4Fe-4S] clusters. Further, spectroscopic and kinetic results demonstrate that S-adenosyl-L-methionine (SAM) donates the methyl group to Hg in a two-step reaction involving a methylcob(III)alamin intermediate including Co-thiolate ligation from a conserved Cys residue. Our findings uncover a biological role for SAM in microbial Hg methylation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Evidence for autotrophic growth of purple sulfur bacteria using pyrite as electron and sulfur source

ABSTRACT Purple sulfur bacteria (PSB) are capable of anoxygenic photosynthesis via oxidizing reduced sulfur compounds and are considered key drivers of the sulfur cycle in a range of anoxic environments. In this study, we show that Allochromatium vinosum (a PSB species) is capable of autotrophic growth using pyrite as the electron and sulfur source. Comparative growth profile, substrate characterization, and transcriptomic sequencing data provided valuable insight into the molecular mechanisms underlying the bacterial utilization of pyrite and autotrophic growth. Specifically, the pyrite-supported cell cultures (“py”’) demonstrated robust but much slower growth rates and distinct patterns from their sodium sulfide-amended positive controls. Up to ~200-fold upregulation of genes encoding various c - and b -type cytochromes was observed in “py,” pointing to the high relevance of these molecules in scavenging and relaying electrons from pyrite to cytoplasmic metabolisms. Conversely, extensive downregulation of genes related to LH and RC complex components indicates that the electron source may have direct control over the bacterial cells’ photosynthetic activity. In terms of sulfur metabolism, genes encoding periplasmic or membrane-bound proteins (e.g., FccAB and SoxYZ) were largely upregulated, whereas those encoding cytoplasmic proteins (e.g., Dsr and Apr groups) are extensively suppressed. Other notable differentially expressed genes are related to flagella/fimbriae/pilin(+), metal efflux(+), ferrienterochelin(−), and [NiFe] hydrogenases(+). Characterization of the biologically reacted pyrite indicates the presence of polymeric sulfur. These results have, for the first time, put the interplay of PSB and transition metal sulfide chemistry under the spotlight, with the potential to advance multiple fields, including metal and sulfur biogeochemistry, bacterial extracellular electron transfer, and artificial photosynthesis. IMPORTANCE Microbial utilization of solid-phase substrates constitutes a critical area of focus in environmental microbiology, offering valuable insights into microbial metabolic processes and adaptability. Recent advancements in this field have profoundly deepened our knowledge of microbial physiology pertinent to these scenarios and spurred innovations in biosynthesis and energy production. Furthermore, research into interactions between microbes and solid-phase substrates has directly linked microbial activities to the surrounding mineralogical environments, thereby enhancing our understanding of the relevant biogeochemical cycles. Our study represents a significant step forward in this field by demonstrating, for the first time, the autotrophic growth of purple sulfur bacteria using insoluble pyrite (FeS2) as both the electron and sulfur source. The presented comparative growth profiles, substrate characterizations, and transcriptomic sequencing data shed light on the relationships between electron donor types, photosynthetic reaction center activities, and potential extracellular electron transfer in these organisms capable of anoxygenic photosynthesis. Furthermore, the findings of our study may provide new insights into early-Earth biogeochemical evolutions, offering valuable constraints for understanding the environmental conditions and microbial processes that shaped our planet’s history.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A Reduced F 420 -Dependent Nitrite Reductase in an Anaerobic Methanotrophic Archaeon

Coenzyme F 420 -dependent sulfite reductase (Fsr) protects methanogenic archaea inhabiting deep-sea hydrothermal vents from the inactivation of methyl coenzyme M reductase (Mcr), one of their essential energy production enzymes. Anaerobic methanotrophic archaea (ANME) that oxidize methane and rely on Mcr, carry Fsr homologs that form a distinct clade.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A shift between mineral and nonmineral sources of iron and sulfur causes proteome-wide changes in Methanosarcina barkeri

ABSTRACT Iron (Fe) and sulfur (S) are required elements for life, and changes in their availability can limit the ecological distribution and function of microorganisms. In anoxic environments, soluble Fe typically exists as ferrous iron [Fe(II)] and S as sulfide (HS − ). These species exhibit a strong affinity that ultimately drives the formation of sedimentary pyrite (FeS 2 ). Recently, paradigm-shifting studies indicate that Fe and S in FeS 2 can be made bioavailable by methanogens through a reductive dissolution process. However, the impact of the utilization of FeS 2 , as opposed to canonical Fe and S sources, on the phenotype of cells is not fully understood. Here, shotgun proteomics was utilized to measure changes in the phenotype of Methanosarcina barkeri MS grown with FeS 2 , Fe(II)/HS − , or Fe(II)/cysteine. Shotgun proteomics tracked 1,019 proteins overall, with 307 observed to change between growth conditions. Functional characterization and pathway analyses revealed these changes to be systemic and largely tangential to Fe/S metabolism. As a final step, the proteomics data were viewed with respect to previously collected transcriptomics data to deepen the analysis. Presented here is evidence that M. barkeri adopts distinct phenotypes to exploit specific sources of Fe and S in its environment. This is supported by observed protein abundance changes across broad categories of cellular biology. DNA adjacent metabolism, central carbon metabolism methanogenesis, metal trafficking, quorum sensing, and porphyrin biosynthesis pathways are all features in the phenotypic differentiation. Differences in trace metal availability attributed to complexation with HS − , either as a component of the growth medium [Fe(II)/HS − ] or generated through reduction of FeS 2 , were likely a major factor underpinning these phenotypic differences. IMPORTANCE The methanogenic archaeon Methanosarcina barkeri holds great potential for industrial bio-mining and energy generation technologies. Much of the biochemistry of this microbe is poorly understood, and its characterization will provide a glimpse into biological processes that evolved close to life’s origin. The discovery of its ability to extract iron and sulfur from bulk, solid-phase minerals shifted a longstanding paradigm that these elements were inaccessible to biological systems. The full elucidation of this process has the potential to help scientists and engineers extract valuable metals from low-grade ore and mine waste generating energy in the form of methane while doing so.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Interactions between molecular-scale biogeochemical processes and hyporheic exchange for understanding coupled Fe-S-C cycling in iron-rich riparian wetlands (Final Technical Report)

Riparian wetlands are dynamic interfaces that exert strong control over water quality, contaminant mobility, and greenhouse gas emissions. These systems are characterized by hyporheic exchange between oxic surface water and anoxic groundwater, which generates steep redox gradients and promotes spatially and temporally variable microbial activity. Despite growing recognition of tightly coupled iron (Fe), sulfur (S), and carbon (C) cycling in these environments, the mechanisms governing these interactions—particularly under low-sulfate freshwater conditions—remain poorly constrained. This project developed a mechanistic understanding of how hydrologic variability and microbial processes interact to control Fe–S–C cycling in iron-rich riparian wetlands. Using a multi-scale and multi-method approach integrating field observations, geochemical and spectroscopic analyses, metagenomics, and reactive transport modeling, we demonstrate that “cryptic” sulfur cycling—rapid sulfur transformations involving intermediate-valence species—plays a dominant and previously underrecognized role in freshwater wetlands. These processes persist despite low sulfate concentrations and significantly influence iron reduction, carbon mineralization, and methane dynamics. The results show that cryptic sulfur cycling enhances dissolved Fe 2+ production, regulates methane concentrations, and is strongly controlled by climate-driven hydrologic fluxes. By linking hydroclimate, subsurface flow, and biogeochemical reactions, this work provides a predictive framework for understanding how wetland systems respond to environmental change, with direct implications for water quality and carbon cycling.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Liquid Copper and Iron Production from Chalcopyrite, in the Absence of Oxygen

Clean energy infrastructure depends on chalcopyrite: the mineral that contains 70% of the world’s copper reserves, as well as a range of precious and critical metals. Smelting is the only commercially viable route to process chalcopyrite, where the oxygen-rich environment dictates the distribution of impurities and numerous upstream and downstream unit operations to manage noxious gases and by-products. However, unique opportunities to address urgent challenges faced by the copper industry arise by excluding oxygen and processing chalcopyrite in the native sulfide regime. Through electrochemical experiments and thermodynamic analysis, gaseous sulfur and electrochemical reduction in a molten sulfide electrolyte are shown to be effective levers to selectively extract the elements in chalcopyrite for the first time. We present a new process flow to supply the increasing demand for copper and byproduct metals using electricity and an inert anode, while decoupling metal production from fugitive gas emissions and oxidized by-products.

36 MATERIALS SCIENCE↗