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Poster for Interpore2025, describing the use of biomineralization to seal shale fractures under in situ conditions, examined with micro-CT and magnetic resonance.
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. In this study, 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.
Uranium contamination of soils and groundwater in the United States represents a significant health risk and will require multiple remediation approaches. Microbial phosphatase activity coupled to the addition of an organic P source has recently been studied as a remediation strategy that provides an extended release of inorganic P (Pi) into U-contaminated sites, resulting in the precipitation of meta-autunite minerals. Previous laboratory- and field-based biomineralization studies have investigated environments with relatively high U concentrations (>20 μM). However, most contaminated sites have much lower U concentrations (<2 μM). The Environmental Protection Agency (EPA) limit for U in drinking water is 0.126 μM. Reaching this regulatory limit becomes challenging as U concentrations approach autunite solubility. Furthermore, we studied the precipitation of U(VI)-phosphate minerals by an environmental isolate of Caulobacter sp. (strain OR37) from an Oak Ridge, Tennessee, U-contaminated site. Abiotic U(VI) solubility experiments reveal that U(VI)-phosphate minerals do not form in the presence of excess Pi (500 μM) when U(VI) concentrations are <1 μM and pH is <5. When OR37 cells are reacted under the same conditions with Pi or glycerol-2-phosphate, U(VI)-phosphate mineral formation was observed, along with the formation of intracellular polyphosphate granules. These results show that bacteria provide supersaturated microenvironments needed for U(VI)-phosphate mineralization while hydrolyzing organic P sources. This provides a pathway to lower U concentrations to below EPA limits for drinking water.
The global manganese cycle relies on microbes to oxidize soluble Mn(II) to insoluble Mn(IV) oxides. Some microbes require peroxide or superoxide as oxidants, but others can use O 2 directly, via multicopper oxidase (MCO) enzymes. One of these, MnxG from Bacillus sp. strain PL-12, was isolated in tight association with small accessory proteins, MnxE and MnxF. The protein complex, called Mnx, has eluded crystallization efforts, but we now report the 3D structure of a point mutant using cryo-EM single particle analysis, cross-linking mass spectrometry, and AlphaFold Multimer prediction. The ß-sheet–rich complex features MnxG enzyme, capped by a heterohexameric ring of alternating MnxE and MnxF subunits, and a tunnel that runs through MnxG and its MnxE 3 F 3 cap. The tunnel dimensions and charges can accommodate the mechanistically inferred binuclear manganese intermediates. Furthermore, comparison with the Fe(II)-oxidizing MCO, ceruloplasmin, identifies likely coordinating groups for the Mn(II) substrate, at the entrance to the tunnel. Thus, the 3D structure provides a rationale for the established manganese oxidase mechanism, and a platform for further experiments to elucidate mechanistic details of manganese biomineralization.
Scleractinian corals typically form a robust calcium carbonate skeleton beneath their living tissue. This skeleton, through its trace element composition and isotope ratios, may record environmental conditions of water surrounding the coral animal. While bulk unrecrystallized aragonite coral skeletons can be used to reconstruct past ocean conditions, corals that have undergone significant diagenesis have altered geochemical signatures and are typically assumed to retain insufficient meaningful information for bulk or macrostructural analysis. However, partially recrystallized skeletons may retain organic molecular components of the skeletal organic matrix (SOM), which is secreted by the animal and directs aspects of the biomineralization process. Some SOM proteins can be retained in fossil corals and can potentially provide past oceanographic, ecological, and indirect genetic information. Here, we describe a dataset of scleractinian coral skeletons, aged from modern to Cretaceous plus a Carboniferous rugosan, characterized for their crystallography, trace element composition, and amino acid compositions. We show that some specimens that are partially recrystallized to calcite yield potentially useful biochemical information whereas complete recrystalization or silicification leads to significant alteration or loss of the SOM fraction. Our analysis is informative to biochemical-paleoceanographers as it suggests that previously discounted partially recrystallized coral skeletons may indeed still be useful at the microstructural level.
As part of a long term study of biological markers (biomarkers), we are documenting a variety of features which reflect the previous presence of living organisms. As we study meteorites and samples returned from Mars, our main clue to recognizing possible microbial material may be the presence of biomarkers rather than the organisms themselves. One class of biomarkers consists of biominerals which have either been precipitated directly by microorganisms, or whose precipitation has been influenced by the organisms. Such microbe-mediated mineral formation may include important clues to the size, shape, and environment of the microorganisms. The process of fossilization or mineralization can cause major changes in morphologies and textures of the original organisms. The study of fossilized terrestrial organisms can help provide insight into the interpretation of mineral biomarkers. This paper describes the results of investigations of microfossils in Cambrian phosphate-rich rocks (phosphorites) that were found in Khubsugul, Northern Mongolia.
Biological organisms naturally synthesize complex, hierarchical, multifunctional materials through mineralization processes at ambient conditions and under physiological pH. One such example is the ultrahard and wear-resistant radular teeth found in mollusks, which are used to scape against the rock to feed on algae. Herein, the biologically controlled structural development of the hard, outer magnetite-containing shell of the chitin teeth is revealed. Specifically, the formation of a series of mesocrystalline iron oxide phases, templated by chitin-binding proteins, is identified. The initial domains, consisting of ferrihydrite mesocrystals with a spherulite-like morphology, undergo a solid-state phase transformation to form magnetite while maintaining mesocrystallinity, likely via a shear-induced solid-state reaction, without any noticeable architectural changes. Subsequent growth via Ostwald ripening leads to nearly single-crystalline rod-like elements. In addition, an interpenetrating organic matrix is identified that, at early stages of tooth development, potentially contains iron-binding proteins that guide the self-assembly of the mesocrystalline mineral and influence the preferred orientation of the later-formed magnetite nanorods, which ultimately determines the mechanical behavior of the mature chiton teeth.
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Magnetotactic bacteria (MTB) are a group of bacteria that can form nano-sized crystals of magnetic minerals. MTB are likely an important part of their ecosystems, because they can account for up to a third of the microbial biomass in an aquatic habitat and consume large amounts of iron, potentially impacting the iron cycle.
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Ameloblasts are specialized cells derived from the dental epithelium that produce enamel, a hierarchically structured tissue comprised of highly elongated hydroxylapatite (OHAp) crystallites. The unique function of the epithelial cells synthesizing crystallites and assembling them in a mechanically robust structure is not fully elucidated yet, partly due to limitations with in vitro experimental models. Herein, we demonstrate the ability to generate mineralizing dental epithelial organoids (DEOs) from adult dental epithelial stem cells (aDESCs) isolated from mouse incisor tissues. DEOs expressed ameloblast markers, could be maintained for more than five months (11 passages) in vitro in media containing modulators of Wnt, Egf, Bmp, Fgf and Notch signaling pathways, and were amenable to cryostorage. When transplanted underneath murine kidney capsules, organoids produced OHAp crystallites similar in composition, size, and shape to mineralized dental tissues, including some enamel-like elongated crystals. DEOs are thus a powerful in vitro model to study mineralization process by dental epithelium, which can pave the way to understanding amelogenesis and developing regenerative therapy of enamel.
Summary In this manuscript, we describe the second of two field demonstrations of microbially induced calcium carbonate precipitation (MICP) performed in a failed waterflood injection well in Indiana. In 2012, fracture-related flow pathways developed in the wellbore cement, causing injection water to bypass the oil-bearing formation and enter a high-permeability sandstone thief zone, thereby substantially decreasing injection pressure. In the first field demonstration, our study team characterized the well's mode of failure and successfully applied MICP to decrease flow through the defective cement. However, because the MICP treatment was conducted using a bailer delivery system, the degree of permeability reduction achievable was not adequate to fully restore the historic injection pressure of 1,400 psi at 1 gal/min. For the second field demonstration (reported herein), a direct injection system was developed that substantially increased the injection volume of MICP-promoting fluids. Two strategies were implemented to produce more ureolytic microbes: resuspending concentrated frozen cells immediately before injection and scaling up the bioreactor growth capacity. Multiple pulses of microbes and urea-calcium media were pumped into a string of 1-in.-diameter tubing separated by brine spacers and injected continuously at a flow rate of 3.4 to 1.4 gal/min. During the third day of injection, an injection pressure of 1,384 psi at a flow rate of 1.4 gal/min was achieved, and the experiment was terminated. This study demonstrates that MICP can be successfully used in large-volume applications where the time frame for the delivery of reactants is limited. This finding has significant relevance for commercialization of the MICP biotechnology in the oil and gas industry.
Extremophilic methylotrophs, such as Methylotuvimicrobium alcaliphilum 20ZR are known for their natural ability to carry out REE capture and uptake. It has been predicted that proteins associated with surface layers facilitate transport and homeostasis of essential metals. Indeed, electron microscopic analysis coupled with antibody staining revealed that cell envelop of metal-grown M. alcaliphilum 20ZR contains metal-binding proteins in the base of the cup-shaped structures of S-layers. While less explored, the proteins associated with S-layers are also predicted to contribute to scavenging of other minerals essential for core metabolism. Here, we employed bottom-up proteomic study to compare the protein content of S-layer fractions of M. alcaliphilum 20ZR cultures grown in the presence and absence trace metals to identify putative components REE-scavenging machinery.
Interpore 2023 presentation showing the use of microbially induced calcium carbonate precipitation to heal fractured shales using nuclear magnetic resonance and computed tomography scanning
Synthetic iron oxides (goethite, alpha-FeO.OH; hematite, Fe2O3; and ferrihydrite, Fe(OH)3) were used as model compounds to simulate the mineralogy of surface films on carbon steel. Dissolution of these oxides exposed to pure cultures of the metal-reducing bacterium, Shewanella putrefaciens, was followed by direct atomic absorption spectroscopy measurement of ferrous iron coupled with microscopic analyses using confocal laser scanning and environmental scanning electron microscopies. During an 8-day exposure the organism colonized mineral surfaces and reduced solid ferric oxides to soluble ferrous ions. Elemental composition, as monitored by energy dispersive x-ray spectroscopy, indicated mineral replacement reactions with both ferrihydrite and goethite as iron reduction occurred. When carbon steel electrodes were exposed to S. putrefaciens, microbiologically influenced corrosion was demonstrated electrochemically and microscopically.
Investigation of the nucleation and growth of crystals in both abiotic and biotic systems is critical to seemingly diverse disciplines of geology, biology, environmental science, and astrobiology. While there are abundant studies devoted to the determination of the structure and composition of inorganic crystals, as well as to the development of thermodynamic and kinetic models, it is only recently that research efforts have been directed towards understanding mineralization in biological systems (i.e., biomineralization). Biomineralization refers to the processes by which living organisms form inorganic solids. Studies of the processes of biomineralization under low temperature aqueous conditions have focused primarily on magnetite forming bacteria and shell forming marine organisms. Many of the biological building materials consist of inorganic minerals (calcium carbonate, calcium phosphate, silica or iron oxide) intricately combined with organic polymers (like proteins). More recently, efforts have been undertaken to explore the nature of biological activities in ancient rocks. In the absence of well-preserved microorganisms or genetic material required for the polmerase chain reaction (PCR) method in molecular phylogenetic studies, using biominerals as biomarkers offers an alternative approach for the recognition of biogenic activity in both terrestrial and extraterrestrial environments. The primary driving force in biomineralization is the interaction between organic and inorganic phases. Thus, the investigation of the ultrastructure and the nature of reactions at the molecular level occurring at the interface between inorganic and organic phases is essential to understanding the processes leading to the nucleation and growth of crystals. It is recognized that crystal surfaces can serve as the substrate for the organization of organic molecules that lead to the formation of polymers and other complex organic molecules, and in discussions of the origins of life, is referred to as organic synthesis on mineral surfaces. Furthermore, it is suggested that the interaction between mineral surfaces and simple organic molecules resulted in the formation of amino acids, RNA, and perhaps other more complex molecules such as proteins. On the other hand, in natural systems, it is recognized that functional groups on cell walls or membranes of microorganisms serve as sites of nucleation and crystallization. The precise replication of biominerals with controlled structure, morphology, size and texture is not confined to higher organisms as it also occurs in primitive prokaryotic cells such as magnetotactic bacteria and cyanobacteria. This suggests that the principal strategies of biomineralization were established early on in the evolutionary history of organisms. It is critical, therefore, to search for common mechanisms within diverse biological systems. One such common factor is the capability for organization and self-assembly. Organic macromolecules such as proteins and lipids can aggregate and polymerize forming membranes or extracellular matrix. At the organic-inorganic interface, several factors such as lattice geometry, polarity, stereochemistry and topography may act in concert to control nucleation and growth of crystals. Although several models have been proposed that discuss the significance of these factors for biomineralization, no comprehensive experimental data are available. In contrast to crystallization in exclusively inorganic systems, the kinetics of reaction and structural relationships between organic and inorganic phases in biominerals or biomimetic material is poorly understood. For example, it is not clear if the concept of epitactic growth (geometrical matching of unit cells at the interface of a secondary crystal growing on a primary crystal) applies to organic-inorganic systems. In contrast to inorganic templates that often have a smooth and rigid surface that promotes epitactic growth, biological substrates are usually rough and result in a large degree of mismatch. It is apparent that factors controlling the reaction at the crystal-matrix interface are strongly dependent upon the nature of the substrate. Therefore, characterization of the assembled organic surface and surface structure of the inorganic phase is crucial to understanding the processes of biomineralization. The focus of our research is the investigation of the processes leading to the nucleation and growth of crystals on both natural and synthetic systems through an interdisciplinary approach that integrates molecular biology, morphology and mineralogy using advanced preparation and analytical techniques. We have studied run-products, particularly magnetite, siderite and other carbonates, that resulted from extracellular biomineralization by extremophiles isolated from a variety of extreme environments ranging from permafrost to hydrothermal vent systems. The results of this study are critical to recognizing biomarkers in terrestrial and extraterrestrial environments.