Microbial mediated formation of Fe-carbonate minerals under extreme acidic conditions

A comprehensive review of recent advancements in microbial-induced mineralization: biosynthesis and mechanism, with potential implementation in various environmental, engineering, and medical sectors

Biomineralization has garnered profuse attention in multidisciplinary fields. Using this strategy, living things, including eukaryotes or prokaryotes, mediate the uptake of ions from the surrounding environment, followed by assembling and depositing them as greatly configured structures inside the organic matrix. The generated biominerals, including nanomaterials, possess outstanding hierarchical structures that exceed their chemically synthesized counterparts. Despite the significant progress achieved in microbial-mediated mineralization, several key knowledge gaps remain, including mechanisms controlling biomineralization pathways and the impact of environmental factors on mineral morphology, crystallinity, and stability. This review provides a comprehensive description of this biomineralization, which can be categorized into controlled, influenced, and induced biomineralization. Interestingly, we highlighted biologically-induced mineralization approaches, such as photosynthesis, methane oxidation, and nitrogen-based metabolic pathways, and identified various chemical interactions during mineral production following analytical chemistry. This review also extensively delineates updates on application of biominerals across all fields, commencing with the remediation of deleterious pollutants and biominerals exploited in industrial sectors, moving on to using them to reinforce soil, generate biocement for construction, and delving into their utilization in pharmaceutical applications to deliver drugs, repair teeth and bones, and combat cancer and pathogenic microorganisms. Moreover, the review outlines the drawbacks and adequate solutions for biomineralization, particularly CaCO₃-mediated processes, such as the generation of ammonium and nitrate during the CaCO₃ precipitation process and the relatively slow rate of microbial-mediated mineralization. Biomineralization inspired the fabrication of smart biomaterials, which combine biological advantages. Overall, this comprehensive review discusses updated research and highlights potential approaches to future studies.

Microbial Carbonate Mineralization: A Comprehensive Review of Mechanisms, Applications, and Recent Advancements

Microbial carbonate mineralization, the process by which microorganisms (Bacillus sp., Sporosarcina sp., Penicillium sp., Cyanobacteria, etc.) directly mediate or indirectly influence mineral formation and deposition, represents the next frontier in technology with vast potential across scientific disciplines, including construction, environmental remediation, and carbon sequestration. This review explores the fundamental aspects of microbial carbonate mineralization, focusing on key mechanisms such as photosynthesis, methane oxidation, sulfate reduction, ureolysis, denitrification, carbonic anhydrase activity, iron reduction, and EPS mediation, all of which influence carbonate saturation and mineral nucleation. Additionally, it highlights critical regulatory factors that enhance biomineralization for bio-inspired material development in heavy metal remediation, wastewater treatment, self-healing concrete, biomedical applications, nanoscale technologies, and 3D printing. A major focus is microbial-induced calcite precipitation (MICP), an emerging and cost-efficient biomineralization technique, with an in-depth analysis of its molecular mechanisms and expanding applications. Furthermore, this review discusses current challenges, including process scalability, long-term stability, and environmental and safety considerations, while identifying future research directions to improve the efficacy and sustainability of microbial carbonate mineralization in advanced technological applications.

Low molecular weight organic acids stabilise siderite against oxidation and influence the composition of iron (oxyhydr)oxide oxidation products

Siderite (FeCO3) is an important reservoir of mineral-bound ferrous iron in non-sulfidic, reducing soils and sediments. It is redox sensitive, and its oxidation may facilitate the reduction of a range of pollutants, produce reactive oxygen species, or induce the formation of oxidation products with large surface areas for contaminant sorption. However, there is currently a limited understanding of the stability of siderite in complex environments such as soils and sediments. Here, we use a series of batch experiments complemented with thorough characterisation of mineral oxidation products to investigate the oxidation of siderite in the presence and absence of the low molecular weight organic acids (LMWOAs) citrate, tiron, salicylate, and EDTA as analogues for naturally occurring compounds or functional groups of natural organic matter that ubiquitously coexist with siderite. Our results show that siderite alone at pH 7.5 was completely oxidised to form ferrihydrite, nanocrystalline lepidocrocite, and nanocrystalline goethite in less than 6 hours. However, in the presence of LMWOAs, up to 48% of the siderite was preserved for more than 500 hours and the formation of goethite was inhibited in favour of ferrihydrite and lepidocrocite. Using experimental data from electron microscopy and chemical speciation modelling, we hypothesise that the siderite may be preserved through the formation of an Fe(III)-passivation layer at the siderite surface.

Interaction of Ca2+ and Fe3+ in co-precipitation process induced by Virgibacillus dokdonensis and its application

Biomineralization has garnered significant attention in the field of wastewater treatment due to its notable cost reduction compared to conventional methods. The reinjection water from oilfields containing an exceedingly high concentration of calcium and ferric ions will pose a major hazard in production. However, the utilization of biomineralization for precipitating these ions has been scarcely investigated due to limited tolerance among halophiles towards such extreme conditions. In this study, free and immobilized halophiles Virgibacillus dokdonensis were used to precipitate these ions and the effects were compared, at the same time, biomineralization mechanisms and mineral characteristics were further explored. The results show that bacterial concentration and carbonic anhydrase activity were higher when additionally adding ferric ion based on calcium ion; the content of protein, polysaccharides, deoxyribonucleic acid and humic substances in the extracellular polymers also increased compared to control. Calcium ions were biomineralized into calcite and vaterite with multiple morphology. Due to iron doping, the crystallinity and thermal stability of calcium carbonate decreased, the content of OC = O, NC = O and CO-PO3 increased, the stable carbon isotope values became much more negative, and β-sheet in minerals disappeared. Higher calcium concentrations facilitated ferric ion precipitation, while ferric ions hindered calcium precipitation. The immobilized bacteria performed better in ferric ion removal, with a precipitation ratio exceeding 90%. Free bacteria performed better in calcium removal, and the precipitation ratio reached a maximum of 56%. This research maybe provides some reference for the co-removal of calcium and ferric ions from the oilfield wastewater.

Acidophilic sulphate-reducing bacteria: Diversity, ecophysiology, and applications

Acidophilic sulphate-reducing bacteria (aSRB) are widespread anaerobic microorganisms that perform dissimilatory sulphate reduction and have key adaptations to tolerate acidic environments (pH <5.0), such as proton impermeability and Donnan potential. This diverse prokaryotic group is of interest from physiological, ecological, and applicational viewpoints. In this review, we summarize the interactions between aSRB and other microbial guilds, such as syntrophy, and their roles in the biogeochemical cycling of sulphur, iron, carbon, and other elements. We discuss the biotechnological applications of aSRB in treating acid mine drainage (AMD, pH <3), focusing on their ability to produce biogenic sulphide and precipitate metals, particularly in the context of utilizing microbial consortia instead of pure isolates. Metal sulphide nanoparticles recovered after AMD treatment have multiple potential technological uses, including in electronics and biomedicine, contributing to a cost-effective circular economy. The products of aSRB metabolisms, such as biominerals and isotopes, could also serve as biosignatures to understand ancient and extant microbial life in the universe. Overall, aSRB are active components of the sulphur and carbon cycles under acidic conditions, with potential natural and technological implications for the world around us.

Trace Elements Anomalous Concentrations in Building Materials-The Impact of Secondary Mineralisation Processes

The Pb, Cr, Cd, Ni, Zn, Cu, Co, As, Sr, Ba, and Zr content has been determined in the tested rock raw materials. The concentration of cadmium (Cd) was found to be elevated in all types of rock materials and was found on average to be: 1.39 mg/kg in limestones, 0.86 mg/kg-sandstones, 0.44 mg/kg-diatomites, 0.55 mg/kg-opoka rocks, 0.89 mg/kg-marls, 0.21 mg/kg-gaizes 0.42 mg/kg-kaolin clays, and 2.13 mg/kg-decalcified opoka rocks. Higher concentrations of arsenic (As) have also been recorded in sandstones and diatomites, as well as lead (Pb) in limestones and sandstones. The results obtained indicate that the anomalous level of elements is of natural origin and the results of identified secondary mineralisation processes that have affected the tested materials. Pyritization and sulfatization processes have been detected. Mineralogical research has shown that these processes can be associated with the activity of biochemical processes caused by the decomposition of the soft tissues of animal organisms and the organic substances of plant origin that fill the stylolites. It has been shown that the content of strontium (Sr) increases in geologically older Jurassic formations compared to younger Cretaceous formations, which can be used in the monitoring of building materials.

Morphological, Microstructural, and In Situ Chemical Characteristics of Siderite Produced by Iron-Reducing Bacteria

Dissimilatory iron-reducing bacteria (DIRB) oxidize organic matter or hydrogen and reduce ferric iron to form Fe(II)-bearing minerals, such as magnetite and siderite. However, compared with magnetite, which was extensively studied, the mineralization process and mechanisms of siderite remain unclear. Here, with the combination of advanced electron microscopy and synchrotron-based scanning transmission X-ray microscopy (STXM) approaches, we studied in detail the morphological, structural, and chemical features of biogenic siderite via a growth experiment with Shewanella oneidensis MR-4. Results showed that along with the growth of cells, Fe(II) ions were increasingly released into solution and reacted with CO32- to form micrometer-sized siderite minerals with spindle, rod, peanut, dumbbell, and sphere shapes. They are composed of many single-crystal siderite plates that are fanned out from the center of the particles. Additionally, STXM revealed Fh and organic molecules inside siderite. This suggests that the siderite crystals might assemble around a Fh-organic molecule core and then continue to grow radially. This study illustrates the biomineralization and assembly of siderite by a successive multistep growth process induced by DIRB, also provides evidences that the distinctive shapes and the presence of organic molecules inside might be morphological and chemical features for biogenic siderite.

Searching for microbial contribution to micritization of shallow marine sediments

Micritization is an early diagenetic process that gradually alters primary carbonate sediment grains through cycles of dissolution and reprecipitation of microcrystalline calcite (micrite). Typically observed in modern shallow marine environments, micritic textures have been recognized as a vital component of storage and flow in hydrocarbon reservoirs, attracting scientific and economic interests. Due to their endolithic activity and the ability to promote nucleation and reprecipitation of carbonate crystals, microorganisms have progressively been shown to be key players in micritization, placing this process at the boundary between the geological and biological realms. However, published research is mainly based on geological and geochemical perspectives, overlooking the biological and ecological complexity of microbial communities of micritized sediments. In this paper, we summarize the state-of-the-art and research gaps in micritization from a microbial ecology perspective. Since a growing body of literature successfully applies in vitro and in situ 'fishing' strategies to unveil elusive microorganisms and expand our knowledge of microbial diversity, we encourage their application to the study of micritization. By employing these strategies in micritization research, we advocate promoting an interdisciplinary approach/perspective to identify and understand the overlooked/neglected microbial players and key pathways governing this phenomenon and their ecology/dynamics, reshaping our comprehension of this process.

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).

Biogeochemical Niches of Fe-Cycling Communities Influencing Heavy Metal Transport along the Rio Tinto, Spain

In the mining-impacted Rio Tinto, Spain, Fe-cycling microorganisms influence the transport of heavy metals (HMs) into the Atlantic Ocean. However, it remains largely unknown how spatial and temporal hydrogeochemical gradients along the Rio Tinto shape the composition of Fe-cycling microbial communities and how this in turn affects HM mobility. Using a combination of DNA- and RNA-based 16S rRNA (gene) amplicon sequencing and hydrogeochemical analyses, we explored the impact of pH, Fe(III), Fe(II), and Cl- on Fe-cycling microorganisms. We showed that the water column at the acidic (pH 2.2) middle course of the river was colonized by Fe(II) oxidizers affiliated with Acidithiobacillus and Leptospirillum. At the upper estuary, daily fluctuations of pH (2.7 to 3.7) and Cl- (6.9 to 16.6 g/L) contributed to the establishment of a unique microbial community, including Fe(II) oxidizers belonging to Acidihalobacter, Marinobacter, and Mariprofundus, identified at this site. Furthermore, DNA- and RNA-based profiles of the benthic community suggested that acidophilic and neutrophilic Fe(II) oxidizers (e.g., Acidihalobacter, Marinobacter, and Mariprofundus), Fe(III) reducers (e.g., Thermoanaerobaculum), and sulfate-reducing bacteria drive the Fe cycle in the estuarine sediments. RNA-based relative abundances of Leptospirillum at the middle course as well as abundances of Acidihalobacter and Mariprofundus at the upper estuary were higher than DNA-based results, suggesting a potentially higher level of activity of these taxa. Based on our findings, we propose a model of how tidal water affects the composition and activity of the Fe-cycling taxa, playing an important role in the transport of HMs (e.g., As, Cd, Cr, and Pb) along the Rio Tinto. IMPORTANCE The estuary of the Rio Tinto is a unique environment in which extremely acidic, heavy metal-rich, and especially iron-rich river water is mixed with seawater. Due to the mixing events, the estuarine water is characterized by a low pH, almost seawater salinity, and high concentrations of bioavailable iron. The unusual hydrogeochemistry maintains unique microbial communities in the estuarine water and in the sediment. These communities include halotolerant iron-oxidizing microorganisms which typically inhabit acidic saline environments and marine iron-oxidizing microorganisms which, in contrast, are not typically found in acidic environments. Furthermore, highly saline estuarine water favored the prosperity of acidophilic heterotrophs, typically inhabiting brackish and saline environments. The Rio Tinto estuarine sediment harbors a diverse microbial community with both acidophilic and neutrophilic members that can mediate the iron cycle and, in turn, can directly impact the mobility and transport of heavy metals in the Rio Tinto estuary.

Preservation of Underground Microbial Diversity in Ancient Subsurface Deposits (>6 Ma) of the Rio Tinto Basement

The drilling of the Rio Tinto basement has provided evidence of an underground microbial community primarily sustained by the Fe and S metabolism through the biooxidation of pyrite orebodies. Although the gossan is the microbial activity product, which dates back to the Oligocene (25 Ma), no molecular evidence of such activity in the past has been reported yet. A Time of Flight Secondary Ion Mass Spectrometry (ToF-SIMS) molecular analysis of a subsurface sample in the Peña de Hierro basement has provided novel data of the ancient underground microbial community. It shows that the microbial remains are preserved in a mineral matrix composed of laminated Fe-oxysulfates and K- and Na-bearing sulfates alternating with secondary silica. In such a mineral substrate, the biomolecule traces are found in five different microstructure associations, (1) <15 micron-sized nodular microstructures composed of POn(2≤n≤4)-, (2) <30 micron-size micronodules containing fatty acids, acylglycerides, and alkanol chains, (3) <20 micro-sized nodules containing NOn-(2≤n≤3) ions, (4) 40-micron size nodules with NH4+ and traces of peptides, and (5) >200-micron thick layer with N-bearing adducts, and sphingolipid and/or peptide traces. It suggests the mineralization of at least five microbial preserved entities with different metabolic capabilities, including: (1) Acidiphilium/Tessaracoccus-like phosphate mineralizers, (2) microbial patches preserving phosphate-free acylglycerides bacteria, (3) nitrogen oxidizing bacteria (e.g., Acidovorax sp.), (4) traces of heterotrophic ammonifying bacteria, and (5) sphingolipid bearing bacteria (e.g., Sphingomonadales, and δ-Proteobacteria) and/or mineralized biofilms. The primary biooxidation process acted as a preservation mechanism to release the inorganic ions that ultimately mineralized the microbial structures.

Forced Biomineralization: A Review

Biologically induced and controlled mineralization of metals promotes the development of protective structures to shield cells from thermal, chemical, and ultraviolet stresses. Metal biomineralization is widely considered to have been relevant for the survival of life in the environmental conditions of ancient terrestrial oceans. Similar behavior is seen among extremophilic biomineralizers today, which have evolved to inhabit a variety of industrial aqueous environments with elevated metal concentrations. As an example of extreme biomineralization, we introduce the category of "forced biomineralization", which we use to refer to the biologically mediated sequestration of dissolved metals and metalloids into minerals. We discuss forced mineralization as it is known to be carried out by a variety of organisms, including polyextremophiles in a range of psychrophilic, thermophilic, anaerobic, alkaliphilic, acidophilic, and halophilic conditions, as well as in environments with very high or toxic metal ion concentrations. While much additional work lies ahead to characterize the various pathways by which these biominerals form, forced biomineralization has been shown to provide insights for the progression of extreme biomimetics, allowing for promising new forays into creating the next generation of composites using organic-templating approaches under biologically extreme laboratory conditions relevant to a wide range of industrial conditions.

Iron Elution from Iron and Steel Slag Using Bacterial Complex Identified from the Seawater

Iron and steel slag (ISS) is a byproduct of iron refining processes. The lack of iron in seawater can cause barren grounds where algae cannot grow. To improve the barren grounds of the sea, a supply of iron to the seawater is necessary. This study focused on bacteria interacting with ISS and promoting iron elution in seawater. Sulfitobacter sp. (TO1A) and Pseudomonas sp. (TO1B) were isolated from Tokyo Bay and Sagami Bay. The co-culture of both bacteria promoted more iron elution than individual cultures. After the incubation of both bacteria with ISS, quartz and vaterite appeared on the surface of the ISS. To maintain continuous iron elution from the ISS in the seawater, we also isolated Pseudoalteromonas sp. (TO7) that formed a yellow biofilm on the ISS. Iron was eluted by TO1A and TO1B, and biofilm was synthesized by TO7 continuously in the seawater. The present research is expected to contribute to the improvement of ISS usage as a material for the construction of seaweed forests.

Interplay of microbial communities with mineral environments in coralline algae

Coralline algae are worldwide carbonate builders, considered to be foundational species and biodiversity hotspots. Coralline habitats face increasing pressure from human activities and effects related to Global Change, yet their ecological properties and adaptive responses remain poorly understood. The relationships of the algal microbiota with the mineral bioconstructions, as well as plasticity and resilience of coralline holobionts in a changing environment, are of particular interest. In the Gulf of California, Neogoniolithon trichotomum (Rhodophyta) is the main carbonate builder in tidal pools. We performed a multi-disciplinary assessment of the N. trichotomum microstructure using XRD, SEM microscopy and SR-FTIR spectromicroscopy. In the algal perithallus, magnesium-calcite and aragonite were spatially segregated and embedded in a polysaccharide matrix (rich in sulfated polysaccharides). Mg-calcites (18-19 mol% Mg) were the main mineral components of the thallus overall, followed by iron carbonates related to dolomite (ankerite) and siderite. Minerals of late evaporitic sequences (sylvite and bischofite) were also present, suggesting potential halophilic microenvironments within the algal thalli. The diverse set of abundant halophilic, halotolerant and oligotrophic taxa, whose abundance increase in the summer, further suggests this condition. We created an integrated model, based on environmental parameters and the microbiota distribution, that identified temperature and nutrient availability (particularly nitrate and silicate) as the main parameters related to specific taxa patterns. Among these, Hahella, Granulossicoccus, Ferrimonas, Spongiibacteraceae and cyanobacterial Xenococcaceae and Nostocaceae change significantly between seasons. These bacterial components might play relevant roles in algal plasticity and adaptive responses to a changing environment. This study contributes to the understanding of the interplay of the prokaryotic microbiota with the mineral microenvironments of coralline algae. Because of their carbonates with potential resistance to dissolution in a higher pCO₂ world and their seasonally dynamic bacteria, coralline algae are relevant targets to study coastal resilience and carbonated systems responses to changing environments.

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

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

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.

The microbially driven formation of siderite in salt marsh sediments

We employ complementary field and laboratory-based incubation techniques to explore the geochemical environment where siderite concretions are actively forming and growing, including solid-phase analysis of the sediment, concretion, and associated pore fluid chemistry. These recently formed siderite concretions allow us to explore the geochemical processes that lead to the formation of this less common carbonate mineral. We conclude that there are two phases of siderite concretion growth within the sediment, as there are distinct changes in the carbon isotopic composition and mineralogy across the concretions. Incubated sediment samples allow us to explore the stability of siderite over a range of geochemical conditions. Our incubation results suggest that the formation of siderite can be very rapid (about two weeks or within 400 hr) when there is a substantial source of iron, either from microbial iron reduction or from steel material; however, a source of dissolved iron is not enough to induce siderite precipitation. We suggest that sufficient alkalinity is the limiting factor for siderite precipitation during microbial iron reduction while the lack of dissolved iron is the limiting factor for siderite formation if microbial sulfate reduction is the dominant microbial metabolism. We show that siderite can form via heated transformation (at temperature 100°C for 48 hr) of calcite and monohydrocalcite seeds in the presence of dissolved iron. Our transformation experiments suggest that the formation of siderite is promoted when carbonate seeds are present.

Deciphering Biosignatures in Planetary Contexts

Microbial life permeates Earth's critical zone and has likely inhabited nearly all our planet's surface and near subsurface since before the beginning of the sedimentary rock record. Given the vast time that Earth has been teeming with life, do astrobiologists truly understand what geological features untouched by biological processes would look like? In the search for extraterrestrial life in the Universe, it is critical to determine what constitutes a biosignature across multiple scales, and how this compares with "abiosignatures" formed by nonliving processes. Developing standards for abiotic and biotic characteristics would provide quantitative metrics for comparison across different data types and observational time frames. The evidence for life detection falls into three categories of biosignatures: (1) substances, such as elemental abundances, isotopes, molecules, allotropes, enantiomers, minerals, and their associated properties; (2) objects that are physical features such as mats, fossils including trace-fossils and microbialites (stromatolites), and concretions; and (3) patterns, such as physical three-dimensional or conceptual n-dimensional relationships of physical or chemical phenomena, including patterns of intermolecular abundances of organic homologues, and patterns of stable isotopic abundances between and within compounds. Five key challenges that warrant future exploration by the astrobiology community include the following: (1) examining phenomena at the "right" spatial scales because biosignatures may elude us if not examined with the appropriate instrumentation or modeling approach at that specific scale; (2) identifying the precise context across multiple spatial and temporal scales to understand how tangible biosignatures may or may not be preserved; (3) increasing capability to mine big data sets to reveal relationships, for example, how Earth's mineral diversity may have evolved in conjunction with life; (4) leveraging cyberinfrastructure for data management of biosignature types, characteristics, and classifications; and (5) using three-dimensional to n-D representations of biotic and abiotic models overlain on multiple overlapping spatial and temporal relationships to provide new insights.

Mechanistic Morphogenesis of Organo-Sedimentary Structures Growing Under Geochemically Stressed Conditions: Keystone to Proving the Biogenicity of Some Archaean Stromatolites?

Morphologically diverse organo-sedimentary structures (including microbial mats and stromatolites) provide a palaeobiological record through more than three billion years of Earth history. Since understanding much of the Archaean fossil record is contingent upon proving the biogenicity of such structures, mechanistic interpretations of well-preserved fossil microbialites can reinforce our understanding of their biogeochemistry and distinguish unambiguous biological characteristics in these structures, which represent some of the earliest records of life. Mechanistic morphogenetic understanding relies upon the analysis of geomicrobiological experiments. Herein, we report morphological-biogeochemical comparisons between micromorphologies observed in growth experiments using photosynthetic mats built by the cyanobacterium Coleofasciculus chthonoplastes (formerly Microcoleus) and green anoxygenic phototrophic Chloroflexus spp. (i.e., Coleofasciculus–Chloroflexus mats), and Precambrian organo-sedimentary structures, demonstrating parallels between them. In elevated ambient concentrations of Cu (toxic to Coleofasciculus), Coleofasciculus–Chloroflexus mats respond by forming centimetre-scale pinnacle-like structures (supra-lamina complexities) associated with large quantities of EPS at their surfaces. µPIXE mapping shows that Cu and other metals become concentrated within surficial sheath-EPS-Chloroflexus-rich layers, producing density-differential micromorphologies with distinct fabric orientations that are detectable using X-ray computed micro-tomography (X-ray µCT). Similar micromorphologies are also detectable in stromatolites from the 3.481 Ga Dresser Formation (Pilbara, Western Australia). The cause and response link between the presence of toxic elements (geochemical stress) and the development of multi-layered topographical complexities in organo-sedimentary structures may thus be considered an indicator of biogenicity, being an indisputably biological and predictable morphogenetic response reflecting, in this case, the differential responses of Coleofasciculus and Chloroflexus to Cu. Growth models for microbialite morphogenesis rely upon linking morphology to intrinsic (biological) and extrinsic (environmental) influences. Since the pinnacles of Coleofasciculus–Chloroflexus mats have an unambiguously biological origin linked to extrinsic geochemistry, we suggest that similar micromorphologies observed in ancient organo-sedimentary structures are indicative of biogenesis. An identical Coleofasciculus–Chloroflexus community subjected to salinity stress also produced supra-lamina complexities (tufts) but did not produce identifiable micromorphologies in three dimensions since salinity seems not to negatively impact either organism, and therefore cannot be used as a morphogenetic tool for the interpretation of density-homogeneous micro-tufted mats—for example, those of the 3.472 Ga Middle Marker horizon. Thus, although correlative microscopy is the keystone to confirming the biogenicity of certain Precambrian stromatolites, it remains crucial to separately interrogate each putative trace of ancient life, ideally using three-dimensional analyses, to determine, where possible, palaeoenvironmental influences on morphologies. Widespread volcanism and hydrothermal effusion into the early oceans likely concentrated toxic elements in early biomes. Morphological diversity in fossil microbialites could, therefore, reflect either (or both of) differential exposure to ambient fluids enriched in toxic elements and/or changing ecosystem structure and tolerance to elements through evolutionary time—for example, after incorporation into enzymes. Proof of biogenicity by deducing morphogenesis (i.e., a process preserved in the fossil record) overcomes many of the shortcomings inherent to the proof of biogenicity by descriptions of morphology alone.

Can Primary Ferroan Dolomite and Ankerite Be Precipitated? Its Implications for Formation of Submarine Methane-Derived Authigenic Carbonate (MDAC) Chimney

Microbes can mediate the precipitation of primary dolomite under surface conditions. Meanwhile, primary dolomite mediated by microbes often contains more Fe2+ than standard dolomite in modern microbial culture experiments. Ferroan dolomite and ankerite have been regarded as secondary products. This paper reviews the process and possible mechanisms of microbial mediated precipitation of primary ferroan dolomite and/or ankerite. In the microbial geochemical Fe cycle, many dissimilatory iron-reducing bacteria (DIRB), sulfate-reducing bacteria (SRB), and methanogens can reduce Fe3+ to Fe2+, while SRB and methanogens can also promote the precipitation of primary dolomite. There are an oxygen respiration zone (ORZ), an iron reduction zone (IRZ), a sulfate reduction zone (SRZ), and a methanogenesis zone (MZ) from top to bottom in the muddy sediment diagenesis zone. DIRB in IRZ provide the lower section with Fe2+, which composes many enzymes and proteins to participate in metabolic processes of SRB and methanogens. Lastly, heterogeneous nucleation of ferroan dolomite on extracellular polymeric substances (EPS) and cell surfaces is mediated by SRB and methanogens. Exploring the origin of microbial ferroan dolomite may help to solve the “dolomite problem”.

Sol-Gel Processes in Micro-Environments of Black Shale: Learning from the Industrial Production of Nanometer-Sized TiO2 Polymorphs

Micro-environments in black shale are reactors for geochemical reactions that differ from the bulk scale. They occur in small isolated pores of several 10 s to 100 s of nanometers without or with limited ionic exchange by diffusion to the surrounding matrix. The example of the formation of titania polymorphs brookite (and anatase) in black shale demonstrates that pH < 4 of the pore waters or lower must prevail to enable dissolution of Ti-bearing precursors followed by the precipitation of these metastable solids. Comparably low pH is applied during the industrial production of nanometer-sized brookite or anatase by sol-gel methods. The process parameters during industrial production such as low pH, negative Eh, or low ionic strength (to promote agglomeration) allow a comparison with parameters during geochemical processes leading to titania formation in black shale. Sol-gel processes are suggested herein as key geochemical processes in micro-environments of black shale in order to understand the formation of single brookite crystals or agglomerates on a nanometer scale.

Microbial Mg-rich Carbonates in an Extreme Alkaline Lake (Las Eras, Central Spain)

This paper provides strong evidence for the contribution of the phylum Firmicutes in mediating the primary precipitation of Mg-rich carbonates (hydromagnesite, dolomite, magnesite, and nesquehonite) in recent microbialites from a highly alkaline and ephemeral inland lake (Las Eras, Central Spain). The carbonate mineral precipitation occurs sequentially as the microbial mats decay. Scanning electron microscopy (SEM) provided solid proof that hydromagnesite nucleation is initiated on the exopolymeric substances (EPS) and the microbial cells associated to the microbial mat degradation areas. The progressive mineralization of the EPS and bacterial cells by hydromagnesite plate-like crystals on their surface, results in the entombment of the bacteria and formation of radiating aggregates of hydromagnesite crystals. The hydrous phases, mostly hydromagnesite, were produced at a high percentage in the first stages of the microbial degradation of organic matter. When the availability of organic substrates declines, the heterotrophs tend to reduce their number and metabolic activity, remain dormant. At this stage, the anhydrous phases, dolomite and magnesite, nucleate on bacterial nanoglobules and/or collapsed cells. Evidence for the sequential formation of the Mg-rich carbonates trough the decay of organic matter by a fermentative EPS-forming bacterium isolated from the microbialites, Desemzia incerta, is drawn through a comparative analysis of carbonate formation in both natural and experimental settings. This study will help to constrain potential mechanisms of carbonate formation in natural systems, which are of fundamental importance not only for understanding modern environments but also as a window into the geologic past of Earth and potentially Mars.

Geochemical Anomalies of Frozen Ground due to Hydrocarbon Migration in West Siberian Cryolithozone

According to the study of frozen deposits in the territory south of the Taz Peninsula, geochemical processes are considered under the hydrocarbon migration from the lower productive complex. An analysis of the cryolithological structure of the frozen stratum was performed, and the composition of the gas and authigenic associations was studied. It was shown that the migration of gases is caused by shear deformations with the formation of cryogenic textures with the presence of gas-bearing ice crystallites on slip surfaces. It was found that the migration of hydrocarbons causes significant local changes in pH/Eh parameters in the frozen stratum and determines the micromosaic distribution of sulfate and iron reduction processes that lead to the formation (including microbiological processes) of various forms of iron: sulphides, carbonates and oxides.

Complex patterns in fossilized stromatolites revealed by hyperspectral imaging (400-2496 nm)

Hyperspectral imaging (400-2496 nm) was used to quantitatively map surface textures and compositional variations in stromatolites to determine whether complexity of textures could be used as evidence to support biogenicity in the absence of preserved biomarkers. Four samples of 2.72-2.4 Ga stromatolites from a variety of settings, encompassing marine and lacustrine environments, were selected for hyperspectral imaging. Images of the sawn surfaces of samples were processed to identify reflectance and mineral absorption features and quantify their intensity (as an index of mineral abundance) using automated feature extraction. Amounts of ferrous iron were quantified using a ratio of reflectance at 1650 and 1299 nm. Visible near infrared imagery (400-970 nm) did not reveal additional textural patterns to those obtained from visual inspection. Shortwave infrared imagery (1000-2496 nm), however, revealed complex laminar and convoluted patterns, including a distinctive texture of sharp peaks and broad, low troughs in one sample, similar to living tufted microbial mats. Spectral analysis revealed another sample to be composed of dolomite. Two other samples were dominated by calcite or chlorite ± illite. Large variations in amounts of ferrous iron were found, but ferric iron was exclusively located in the oxidation crust. Hyperspectral imaging revealed large differences between parts of a sample of biogenic and non-biogenic origin. The former was characterized by calcite with varying amounts of ferrous iron, distributed in lenticular, convoluted patterns; the latter by Mg-Fe chlorite with large amounts of aluminium silicate, distributed as fine laminar layers. All minerals identified by hyperspectral imaging were confirmed by thin section petrography and XRD analyses. Spatial statistics generated from quantitative minerals maps showed different patterns between these different parts of the sample. Thus, hyperspectral imaging was shown to be a powerful tool for detecting structures in stromatolites that could be used, together with other lines of evidence, to support biogenicity.

Characterization of the microbial community composition and the distribution of Fe-metabolizing bacteria in a creek contaminated by acid mine drainage

A small watershed heavily contaminated by long-term acid mine drainage (AMD) from an upstream abandoned coal mine was selected to study the microbial community developed in such extreme system. The watershed consists of AMD-contaminated creek, adjacent contaminated soils, and a small cascade aeration unit constructed downstream, which provide an excellent contaminated site to study the microbial response in diverse extreme AMD-polluted environments. The results showed that the innate microbial communities were dominated by acidophilic bacteria, especially acidophilic Fe-metabolizing bacteria, suggesting that Fe and pH are the primary environmental factors in governing the indigenous microbial communities. The distribution of Fe-metabolizing bacteria showed distinct site-specific patterns. A pronounced shift from diverse communities in the upstream to Proteobacteria-dominated communities in the downstream was observed in the ecosystem. This location-specific trend was more apparent at genus level. In the upstream samples (sampling sites just below the coal mining adit), a number of Fe(II)-oxidizing bacteria such as Alicyclobacillus spp., Metallibacterium spp., and Acidithrix spp. were dominant, while Halomonas spp. were the major Fe(II)-oxidizing bacteria observed in downstream samples. Additionally, Acidiphilium, an Fe(III)-reducing bacterium, was enriched in the upstream samples, while Shewanella spp. were the dominant Fe(III)-reducing bacteria in downstream samples. Further investigation using linear discriminant analysis (LDA) effect size (LEfSe), principal coordinate analysis (PCoA), and unweighted pair group method with arithmetic mean (UPGMA) clustering confirmed the difference of microbial communities between upstream and downstream samples. Canonical correspondence analysis (CCA) and Spearman's rank correlation indicate that total organic carbon (TOC) content is the primary environmental parameter in structuring the indigenous microbial communities, suggesting that the microbial communities are shaped by three major environmental parameters (i.e., Fe, pH, and TOC). These findings were beneficial to a better understanding of natural attenuation of AMD.

Nucleation of Fe-rich phosphates and carbonates on microbial cells and exopolymeric substances

Although phosphate and carbonate are important constituents in ancient and modern environments, it is not yet clear their biogeochemical relationships and their mechanisms of formation. Microbially mediated carbonate formation has been widely studied whereas little is known about the formation of phosphate minerals. Here we report that a new bacterial strain, Tessarococcus lapidicaptus, isolated from the subsurface of Rio Tinto basin (Huelva, SW Spain), is capable of precipitating Fe-rich phosphate and carbonate minerals. We observed morphological differences between phosphate and carbonate, which may help us to recognize these minerals in terrestrial and extraterrestrial environments. Finally, considering the scarcity and the unequal distribution and preservation patterns of phosphate and carbonates, respectively, in the geological record and the biomineralization process that produces those minerals, we propose a hypothesis for the lack of Fe-phosphates in natural environments and ancient rocks.

Río tinto: a geochemical and mineralogical terrestrial analogue of Mars

The geomicrobiological characterization of the water column and sediments of Río Tinto (Huelva, Southwestern Spain) have proven the importance of the iron and the sulfur cycles, not only in generating the extreme conditions of the habitat (low pH, high concentration of toxic heavy metals), but also in maintaining the high level of microbial diversity detected in the basin. It has been proven that the extreme acidic conditions of Río Tinto basin are not the product of 5000 years of mining activity in the area, but the consequence of an active underground bioreactor that obtains its energy from the massive sulfidic minerals existing in the Iberian Pyrite Belt. Two drilling projects, MARTE (Mars Astrobiology Research and Technology Experiment) (2003–2006) and IPBSL (Iberian Pyrite Belt Subsurface Life Detection) (2011–2015), were developed and carried out to provide evidence of subsurface microbial activity and the potential resources that support these activities. The reduced substrates and the oxidants that drive the system appear to come from the rock matrix. These resources need only groundwater to launch diverse microbial metabolisms. The similarities between the vast sulfate and iron oxide deposits on Mars and the main sulfide bioleaching products found in the Tinto basin have given Río Tinto the status of a geochemical and mineralogical Mars terrestrial analogue.

Nickel-resistance determinants in Acidiphilium sp. PM identified by genome-wide functional screening

Acidiphilium spp. are conspicuous dwellers of acidic, metal-rich environments. Indeed, they are among the most metal-resistant organisms; yet little is known about the mechanisms behind the metal tolerance in this genus. Acidiphilium sp. PM is an environmental isolate from Rio Tinto, an acidic, metal-laden river located in southwestern Spain. The characterization of its metal resistance revealed a remarkable ability to tolerate high Ni concentrations. Here we report the screening of a genomic library of Acidiphilium sp. PM to identify genes involved in Ni resistance. This approach revealed seven different genes conferring Ni resistance to E. coli, two of which form an operon encoding the ATP-dependent protease HslVU (ClpQY). This protease was found to enhance resistance to both Ni and Co in E. coli, a function not previously reported. Other Ni-resistance determinants include genes involved in lipopolysaccharide biosynthesis and the synthesis of branched amino acids. The diversity of molecular functions of the genes recovered in the screening suggests that Ni resistance in Acidiphilium sp. PM probably relies on different molecular mechanisms.