Bacterial iron biomineralisation in nature

Parameterization of a Fluctuating Charge Model for Complexes Containing 3d Transition Metals

Metalloproteins widely exist in biology, playing pivotal roles in diverse life processes. Meanwhile, molecular dynamics (MD) simulations based on classical force fields has emerged as an important tool in scientific research. Partial charges are critical parameters within classical force fields and usually derived from quantum mechanical (QM) calculations. However, QM calculations are often time-consuming and prone to basis set dependence. Alternatively, fluctuating charge (FQ) models offer another avenue for partial charge derivation, which has significant speed advantages and can be used for large-scale screening. Building upon our previous work, which introduced an FQ model for zinc-containing complexes, herein we extend this model to include additional 3d transition metals which are important to the life sciences, namely chromium, manganese, iron, cobalt, and nickel. Employing CM5 charges as target for parametrization, our FQ model accurately reproduces partial charges for 3d metal complexes featuring biologically relevant ligands. Furthermore, by using atomic charges derived by our FQ model, MD simulations have been performed. These charges showed excellent performance in simulating proteomic metal sites housing multiple metal ions, specifically, a metalloprotein containing an iron-sulfur cluster and another containing a dimanganese metal site, showcasing comparable performance to those of RESP charges. We anticipate that our study can accelerate the parametrization of atomic charges for metalloproteins featuring 3d transition metals, thereby facilitating simulations of relevant systems.

Modeling the geochemical evolution of mine waters during mixing

This study focuses on assessing the hydrogeochemical processes influencing the mobility of dissolved metal and metalloid species during mine effluent mixing. Field samples were collected to characterize effluents at an active gold mine located in the Abitibi Greenstone belt in western Québec, Canada. Controlled laboratory mixing experiments were further performed with real effluents. In situ physicochemical parameters, concentrations of major dissolved ions and trace elements were analyzed. Mineralogical analyses were also performed on precipitates from the laboratory mixtures. The data were used for statistical analyses and for modeling the geochemical evolution of effluents using PHREEQC with the wateq4f.dat database (with modifications). The results suggest that the formation of secondary minerals such as schwertmannite, Fe(OH)3, and jarosite could significantly affect the concentrations of trace elements in effluents. The precipitation of secondary minerals immobilized trace elements through coprecipitation and sorption processes. The main limitations of the modeling approach used here include the evaluation of the ion balance for low pH samples with high Fe and Al concentrations and the omission of biological processes. The approach provides insights into the geochemical evolution of mine effluents and could be adapted to several mining sites as a tool for improving water management.

Microbial consortium involved in ferromanganese and francolite biomineralization in an anchialine environment (Zinzulùsa Cave, Castro, Italy)

Tidally-influenced subterranean settings represent natural geomicrobiological laboratories, relatively unexplored, that facilitate the investigation of new biomineralization processes. The unusual water chemistry of Zinzulùsa Cave and its oligotrophic and aphotic conditions have allowed the development of a unique ecosystem in which complex bacterial activities induce rare biomineralization processes. A diversified microbial community develops on centimeter-thick crusts that form in the submerged part of the cave. The crusts are formed of Ca-phosphate minerals, mostly carbonate-fluoroapatite (francolite), covered by a black crust, few microns in thickness, composed of ferromanganiferous oxides (hematite and vernadite). Diffuse coccoidal and filamentous bacteria and amorphous organic matter are mixed with the minerals. The micromorphologies and comparative 16S rRNA gene-based metabarcoding analyses identify a "core microbiota" also common to other natural environments characterized by FeMn and Ca-phosphate mineralization. The microbiota is characterized by nitrifying, sulfide/sulfur/thiosulfate-oxidizing and sulfate/thiosulfate/sulfur-reducing bacteria. In addition, manganese-oxidizing bacteria include the recently described "Ca. Manganitrophus noduliformans" and an abundance of bacteria belonging to the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum, as well as Haliangiales (fruiting body-forming bacteria) and Hyphomicrobiales (stalked and budding bacteria) that are known to produce extracellular polymers that trap iron and manganese oxides. 16S rRNA gene metabarcoding analysis showed the presence of bacteria able to utilize many organic P substrates, including Ramlibacter, and SEM images revealed traces of fossilized microorganisms resembling "cable bacteria", which may play a role in Ca-phosphate biomineralization. Overall, the data indicate biomineralization processes induced by microbial metabolic activities for both ferromanganiferous oxide and francolite components of these crusts.

Contrasting morphology and growth habits of Frutexites in Late Devonian reef complexes of the Canning Basin, northwestern Australia

Frutexites-like microstructures are described from the exhumed Late Devonian reef complexes of the northern Canning Basin, Western Australia. Several high-resolution imaging techniques, including X-ray microcomputerised tomography, scanning electron microscopy and X-ray fluorescence microscopy, were used to investigate morphology and composition in two samples. Three types of Frutexites-like microstructures (Types I-III) have been identified. Type I, found lining an early marine cement-filled cavity in fore-reef grainstone facies, consists of dendritic structures formed primarily of coccoid bacteria with filamentous bacteria embedded in sheets of amorphous extracellular polymeric substances (EPS). These ferromanganiferous dendrites have laminated to spheroidal textures. Types II and III are from a toe-of-slope hardground. Type II grew in a crypt between two corals, is also dendritic and composed of bacilliform and filamentous bacteria embedded in an amorphous EPS sheet. The opaqueness of these ferriferous dendrites precludes more detailed description of textures. Type III grew as branching columnar microstromatolites and is composed of entwined filaments of Girvanella, Rothpletzella and Wetheredella with Fe-enriched outer walls that generate Frutexites-like microstructures. Types I and II resemble Frutexites sensu stricto as defined by Maslov (Stromatolites, Trudy Instituta geologicheskikh nauk Akademiya nauk SSR, 1960) and are the result of the consecutive growth and permineralisation of biofilms composed of mixed bacterial communities growing in cryptic habitats. Type III superficially resembles Frutexites sensu stricto based on macroscopic field observations, however, detailed microscopic analysis reveals that it is composed of Fe-enriched tubular walls surrounded by Mn-enriched calcite.

Oxide- and Silicate-Water Interfaces and Their Roles in Technology and the Environment

Interfacial reactions drive all elemental cycling on Earth and play pivotal roles in human activities such as agriculture, water purification, energy production and storage, environmental contaminant remediation, and nuclear waste repository management. The onset of the 21st century marked the beginning of a more detailed understanding of mineral aqueous interfaces enabled by advances in techniques that use tunable high-flux focused ultrafast laser and X-ray sources to provide near-atomic measurement resolution, as well as by nanofabrication approaches that enable transmission electron microscopy in a liquid cell. This leap into atomic- and nanometer-scale measurements has uncovered scale-dependent phenomena whose reaction thermodynamics, kinetics, and pathways deviate from previous observations made on larger systems. A second key advance is new experimental evidence for what scientists hypothesized but could not test previously, namely, interfacial chemical reactions are frequently driven by "anomalies" or "non-idealities" such as defects, nanoconfinement, and other nontypical chemical structures. Third, progress in computational chemistry has yielded new insights that allow a move beyond simple schematics, leading to a molecular model of these complex interfaces. In combination with surface-sensitive measurements, we have gained knowledge of the interfacial structure and dynamics, including the underlying solid surface and the immediately adjacent water and aqueous ions, enabling a better definition of what constitutes the oxide- and silicate-water interfaces. This critical review discusses how science progresses from understanding ideal solid-water interfaces to more realistic systems, focusing on accomplishments in the last 20 years and identifying challenges and future opportunities for the community to address. We anticipate that the next 20 years will focus on understanding and predicting dynamic transient and reactive structures over greater spatial and temporal ranges as well as systems of greater structural and chemical complexity. Closer collaborations of theoretical and experimental experts across disciplines will continue to be critical to achieving this great aspiration.

Fungal-induced CaCO3 and SrCO3 precipitation: a potential strategy for bioprotection of concrete

Biomineralization of CaCO₃ by microorganisms is a well-documented process considered applicable to concrete self-healing and metal bioremediation. Urea hydrolysis is the most widely explored and efficient pathway regarding concrete bioprotection. However, the potential of fungi has received relatively little attention compared to bacteria. In this work, we show that Fusarium cerealis, Phoma herbarum and Mucor hiemalis, isolated from concrete, could produce 828.6-941.3 mg L^-1 ammonium‑nitrogen in liquid media through urea hydrolysis indicating significant urease activity, and could grow in moderate (pH 8.3) or even extremely alkaline (pH 10.6) conditions. After culture in media containing 50 mM CaCl₂, at least 48.8% Ca²⁺ was removed from solution by the selected fungi as calcite. The accumulation of Ca by the biomass was around 83.64-114.21 mg g^-1. In addition, all fungi could mediate strontium carbonate formation with F. cerealis processing the highest ability for Sr removal, with ~61% added Sr being removed from solution. Scanning electron microscopy showed carbonate biominerals were encrusted on hyphae or aggregated in fungal pellets. When equivalent concentrations of Ca²⁺ and Sr²⁺ were supplemented to the media, CaCO₃ with incorporated Sr formed with F. cerealis and M. hiemalis, and Sr(Sr, Ca)(CO₃)₂ with P. herbarum. Our results demonstrate the potential of fungi in providing carbonate coatings for concrete surfaces and simultaneous immobilization of Sr. We anticipate our work will promote further practical field research on porous cementitious materials protection by fungi and immobilization of potentially toxic metals from metal-laden ingredients, such as fly ash and granulated ground blast furnace slag.

Identifying chemolithotrophic and pathogenic-related gene expression within suspended sediment flocs in freshwater environments: A metatranscriptomic assessment

The introduction and proliferation of pathogenic organisms in aquatic systems is a serious global issue that consequently leads to economic, financial, and health concerns. Health and safety related to recreational water use is typically monitored through water quality assessments that are outdated and can be misleading. These traditional methods focus on broad taxa groups, provide no insight into the active community or source of contamination, and the sediment compartments (bed and suspended) are often overlooked. To bridge this knowledge gap, our study aimed to 1) examine the metatranscriptome of the microbial community associated with suspended sediment (SS) in freshwater systems; 2) explore the influence of SS in tributaries to the littoral zone of the receiving lake; and 3) compare the SS fraction with previously reported nearshore bed sediment data. Samples were collected seasonally from Lake St. Clair and Lake Erie. Beaches in this region are influenced by both agriculture runoff and continued urban expansion. Results show that both adjacent tributary and beach SS have similar microbial functional diversity and are strongly correlated by site and season. We identified expression of transcripts encoding sequences with similarities to genes involved in nine bacterial infectious disease pathways, including legionellosis (sdhA) and Vibrio cholerae pathogenesis. According to MG-RAST gene categories, lake samples typically showed higher overall expression (p < 0.05) of transcripts with similarities to genes involved in infectious disease pathways compared to the tributaries, with summer upregulated (p < 0.05) compared to fall. Our data suggests SS acts as a strong vector for pathogen transport, making this facet an important area for further research as it pertains to human health regarding recreational water use. To our knowledge, this work is the first to investigate SS in aquatic microbial communities using metatranscriptomic analyses and has significant potential to help address growing issues of microbial contamination impacting freshwater security.

Magnetic Properties of Bacterial Magnetosomes Produced by Magnetospirillum caucaseum SO-1

In this study, the magnetic properties of magnetosomes isolated from lyophilized magnetotactic bacteria Magnetospirillum caucaseum SO-1 were assessed for the first time. The shape and size of magnetosomes and cell fragments were studied by electron microscopy and dynamic light scattering techniques. Phase and elemental composition were analyzed by X-ray and electron diffraction and Raman spectroscopy. Magnetic properties were studied using vibrating sample magnetometry and electron paramagnetic resonance spectroscopy. Theoretical analysis of the magnetic properties was carried out using the model of clusters of magnetostatically interacting two-phase particles and a modified method of moments for a system of dipole-dipole-interacting uniaxial particles. Magnetic properties were controlled mostly by random aggregates of magnetosomes, with a minor contribution from preserved magnetosome chains. Results confirmed the high chemical stability and homogeneity of bacterial magnetosomes in comparison to synthetic iron oxide magnetic nanoparticles.

Magnetotactic Bacteria and Magnetosomes: Basic Properties and Applications

Magnetotactic bacteria (MTB) belong to several phyla. This class of microorganisms exhibits the ability of magneto-aerotaxis. MTB synthesize biominerals in organelle-like structures called magnetosomes, which contain single-domain crystals of magnetite (Fe3O4) or greigite (Fe3S4) characterized by a high degree of structural and compositional perfection. Magnetosomes from dead MTB could be preserved in sediments (called fossil magnetosomes or magnetofossils). Under certain conditions, magnetofossils are capable of retaining their remanence for millions of years. This accounts for the growing interest in MTB and magnetofossils in paleo- and rock magnetism and in a wider field of biogeoscience. At the same time, high biocompatibility of magnetosomes makes possible their potential use in biomedical applications, including magnetic resonance imaging, hyperthermia, magnetically guided drug delivery, and immunomagnetic analysis. In this review, we attempt to summarize the current state of the art in the field of MTB research and applications.

Desulfovibrio Bacteria Are Associated With Parkinson's Disease

Parkinson's disease (PD) is the most prevalent movement disorder known and predominantly affects the elderly. It is a progressive neurodegenerative disease wherein α-synuclein, a neuronal protein, aggregates to form toxic structures in nerve cells. The cause of Parkinson's disease (PD) remains unknown. Intestinal dysfunction and changes in the gut microbiota, common symptoms of PD, are evidently linked to the pathogenesis of PD. Although a multitude of studies have investigated microbial etiologies of PD, the microbial role in disease progression remains unclear. Here, we show that Gram-negative sulfate-reducing bacteria of the genus Desulfovibrio may play a potential role in the development of PD. Conventional and quantitative real-time PCR analysis of feces from twenty PD patients and twenty healthy controls revealed that all PD patients harbored Desulfovibrio bacteria in their gut microbiota and these bacteria were present at higher levels in PD patients than in healthy controls. Additionally, the concentration of Desulfovibrio species correlated with the severity of PD. Desulfovibrio bacteria produce hydrogen sulfide and lipopolysaccharide, and several strains synthesize magnetite, all of which likely induce the oligomerization and aggregation of α-synuclein protein. The substances originating from Desulfovibrio bacteria likely take part in pathogenesis of PD. These findings may open new avenues for the treatment of PD and the identification of people at risk for developing PD.

Biomineralization of Uranium-Phosphates Fueled by Microbial Degradation of Isosaccharinic Acid (ISA)

Geological disposal is the globally preferred long-term solution for higher activity radioactive wastes (HAW) including intermediate level waste (ILW). In a cementitious disposal system, cellulosic waste items present in ILW may undergo alkaline hydrolysis, producing significant quantities of isosaccharinic acid (ISA), a chelating agent for radionuclides. Although microbial degradation of ISA has been demonstrated, its impact upon the fate of radionuclides in a geological disposal facility (GDF) is a topic of ongoing research. This study investigates the fate of U(VI) in pH-neutral, anoxic, microbial enrichment cultures, approaching conditions similar to the far field of a GDF, containing ISA as the sole carbon source, and elevated phosphate concentrations, incubated both (i) under fermentation and (ii) Fe(III)-reducing conditions. In the ISA-fermentation experiment, U(VI) was precipitated as insoluble U(VI)-phosphates, whereas under Fe(III)-reducing conditions, the majority of the uranium was precipitated as reduced U(IV)-phosphates, presumably formed via enzymatic reduction mediated by metal-reducing bacteria, including Geobacter species. Overall, this suggests the establishment of a microbially mediated "bio-barrier" extending into the far field geosphere surrounding a GDF is possible and this biobarrier has the potential to evolve in response to GDF evolution and can have a controlling impact on the fate of radionuclides.

Bacteria-induced mineral precipitation: a mechanistic review

Micro-organisms contribute to Earth's mineral deposits through a process known as bacteria-induced mineral precipitation (BIMP). It is a complex phenomenon that can occur as a result of a variety of physiological activities that influence the supersaturation state and nucleation catalysis of mineral precipitation in the environment. There is a good understanding of BIMP induced by bacterial metabolism through the control of metal redox states and enzyme-mediated reactions such as ureolysis. However, other forms of BIMP often cannot be attributed to a single pathway but rather appear to be a passive result of bacterial activity, where minerals form as a result of metabolic by-products and surface interactions within the surrounding environment. BIMP from such processes has formed the basis of many new innovative biotechnologies, such as soil consolidation, heavy metal remediation, restoration of historic buildings and even self-healing concrete. However, these applications to date have primarily incorporated BIMP-capable bacteria sampled from the environment, while detailed investigations of the underpinning mechanisms have been lagging behind. This review covers our current mechanistic understanding of bacterial activities that indirectly influence BIMP and highlights the complexity and connectivity between the different cellular and metabolic processes involved. Ultimately, detailed insights will facilitate the rational design of application-specific BIMP technologies and deepen our understanding of how bacteria are shaping our world.

Mechanistic insight into biopolymer induced iron oxide mineralization through quantification of molecular bonding

Microbial production of iron (oxyhydr)oxides on polysaccharide rich biopolymers occurs on such a vast scale that it impacts the global iron cycle and has been responsible for major biogeochemical events. Yet the physiochemical controls these biopolymers exert on iron (oxyhydr)oxide formation are poorly understood. Here we used dynamic force spectroscopy to directly probe binding between complex, model and natural microbial polysaccharides and common iron (oxyhydr)oxides. Applying nucleation theory to our results demonstrates that if there is a strong attractive interaction between biopolymers and iron (oxyhydr)oxides, the biopolymers decrease the nucleation barriers, thus promoting mineral nucleation. These results are also supported by nucleation studies and density functional theory. Spectroscopic and thermogravimetric data provide insight into the subsequent growth dynamics and show that the degree and strength of water association with the polymers can explain the influence on iron (oxyhydr)oxide transformation rates. Combined, our results provide a mechanistic basis for understanding how polymer-mineral-water interactions alter iron (oxyhydr)oxides nucleation and growth dynamics and pave the way for an improved understanding of the consequences of polymer induced mineralization in natural systems.

Visualizing Different Crystalline States during the Infrared Imaging of Calcium Phosphates

Methods utilizing relatively simple mathematical operations during physical analyses to enable the visualization of otherwise invisible correlations and effects are of particular appeal to researchers and students in pedagogical settings. At the same time, discerning the amorphous phase from its crystalline counterpart in materials is challenging with the use of vibrational spectroscopy and is nowhere as straightforward as in phase composition analytical methods such as X-ray diffraction. A method is demonstrated for the use of first- and second-order differentiation of Fourier transform infrared spectra of calcium phosphates to distinguish their amorphous states from the crystalline ones based on the exact line positioning rather than on comparatively vaguer band broadening and splitting effects. The study utilizes a kinetic approach, focusing on the comparison of spectral features of amorphous precursors annealed in air at different temperatures and aged for different periods of time in an aqueous solution until transforming to one or a mixture of crystalline phases, including hydroxyapatite and α- and β-tricalcium phosphate. One of the findings challenges the concept of the nucleation lag time preceding the crystallization from amorphous precursors as a "dead" period and derives a finite degree of constructive changes occurring at the atomic scale in its course. The differential method for highlighting spectral differences depending on the sample crystallinity allows for monitoring in situ the process of conversion of the amorphous calcium phosphate phase to its crystalline analogue(s). One such method can be of practical significance for synthetic solid state chemists testing for the chemical stability and/or concentration of the reactive amorphous phase in these materials, but also for biologists measuring the maturity of bone and medical researchers evaluating its phase composition and, thus, the state of metabolic and mechanical stability.

Trace metal comparative analysis of sinking particles and sediments from a coastal environment of the Jiaozhou Bay, North China: Influence from sediment resuspension

To constrain the resuspension influence to the biogeochemical behavior of trace metals (TMs) in settling materials, the concentrations and chemical speciations of macro-elements (Al, Fe, Mn) and selected particulate TMs (V, Cr, Co, Cu, Zn, Ga, Sr, Cd, Ba, Tl, Pb, U) in trap-collected particles (TCPs), surface sediments (SS) and core sediment samples (CS5) of the Jiaozhou Bay were compared. Two approaches, mass conservation method and vertical two end-members mixing model, both calculated a resuspension ratio of more than 90%. Greater TM concentrations and Al-normalization levels than SS/CS5 determined the TCPs an important TM-sink, predominantly owing to grain-size effects and TCP-specific characteristics, i.e., structural capacity of organic-Fe associations for TMs' scavenging, preferential remineralization of TM than biogenic elements in autochthonous microorganisms. Comparison revealed distinct, Fe mineral controls on TM sequestration patterns: higher metal sequestration associated with amorphous Fe oxyhydroxides, while less reactive crystalline Fe oxides hold less metal. Nevertheless, turbulent hydrodynamics muted the wide TM retention divergences between TCP and SS, which should have happened based on different Fe minerals distribution for TCP/SS. The net effect of TM release by the organic carrier phase and then adsorption principally onto Mn/Fe oxyhydroxide phase for raised overall TCP-TM concentrations was also identified.

Cyanobacteria evolution: Insight from the fossil record

Cyanobacteria played an important role in the evolution of Early Earth and the biosphere. They are responsible for the oxygenation of the atmosphere and oceans since the Great Oxidation Event around 2.4 Ga, debatably earlier. They are also major primary producers in past and present oceans, and the ancestors of the chloroplast. Nevertheless, the identification of cyanobacteria in the early fossil record remains ambiguous because the morphological criteria commonly used are not always reliable for microfossil interpretation. Recently, new biosignatures specific to cyanobacteria were proposed. Here, we review the classic and new cyanobacterial biosignatures. We also assess the reliability of the previously described cyanobacteria fossil record and the challenges of molecular approaches on modern cyanobacteria. Finally, we suggest possible new calibration points for molecular clocks, and strategies to improve our understanding of the timing and pattern of the evolution of cyanobacteria and oxygenic photosynthesis.

Rare earth element and yttrium geochemistry in sinking particles and sediments of the Jiaozhou Bay, North China: Potential proxy assessment for sediment resuspension

To exploit the resolving ability of rare earth element and yttrium (REY) in resuspension binary mixing model, and discover potential new REY-related resuspension proxy, this preliminary research studied the geochemical signature of REY in different Jiaozhou Bay samples including surficial/core sediments and settling trap-collected particles. Close quantitative relation for bulk concentration in particles, sediments and fine-grained fraction of major river sediments around the Yellow Sea, approved the priority contribution of catchment detrital materials. Moreover, common characteristics occurred for compartment-specific partitioning REY signatures in six operated-defined fractions, and multiple REY normalization pattern indexes (i.e. Y/Ho divergence, and Ce/Eu anomalies). All constrain the application of REY in resuspension discrimination of marginal shallow seas. However, linearity with different slopes and intercepts were plotted for the MREE bulge index versus HREE/LREE figure in reducible amorphous Fe-oxides fraction, which could provide new discrimination perceptions.

Microbial Diversity in Actively Forming Iron Oxides from Weathered Banded Iron Formation Systems

The surface crust that caps highly weathered banded iron formations (BIFs) supports a unique ecosystem that is a post-mining restoration priority in iron ore areas. Geochemical evidence indicates that biological processes drive the dissolution of iron oxide minerals and contribute to the ongoing evolution of this duricrust. However, limited information is available on present-day biogeochemical processes in these systems, particularly those that contribute to the precipitation of iron oxides and, thus, the cementation and stabilization of duricrusts. Freshly formed iron precipitates in water bodies perched on cangas in Karijini National Park, Western Australia, were sampled for microscopic and molecular analyses to understand currently active microbial contributions to iron precipitation in these areas. Microscopy revealed sheaths and stalks associated with iron-oxidizing bacteria. The iron-oxidizing lineages Sphaerotilus, Sideroxydans, and Pedomicrobium were identified in various samples and Leptothrix was common in four out of five samples. The iron-reducing bacteria Anaeromyxobacter dehalogens and Geobacter lovleyi were identified in the same four samples, with various heterotrophs and diverse cyanobacteria. Given this arid, deeply weathered environment, the driver of contemporary iron cycling in Karijini National Park appears to be iron-reducing bacteria, which may exist in anaerobic niches through associations with aerobic heterotrophs. Overall oxidizing conditions and Leptothrix iron-oxidizers contribute to net iron oxide precipitation in our sampes, rather than a closed biogeochemical cycle, which would result in net iron oxide dissolution as has been suggested for canga caves in Brazil. Enhancements in microbial iron oxide dissolution and subsequent reprecipitation have potential as a surface-crust-ecosystem remediation strategy at mine sites.

Fossilized Bacteria in Fe-Mn-Mineralization: Evidence from the Legrena Valley, W. Lavrion Mine (Greece)

The primary mineralization in the famous Lavrion mine in the Lavreotiki area, Attica (Greece), associated with a granodiorite intrusion of Upper Miocene age and composed of massive sulphide Pb-Zn-Ag ores [sphalerite, pyrite and galena (B.P.G)], has been extensively studied. The present study is focused on thin, hard, dark brown to black Fe-Mn crusts (a few mm to cm in thickness) in the Legrena valley, SW Lavreotiki, aiming to provide new insights on that type of Fe-Mn-mineralization. The scanning electron microscope (SEM)/energy dispersive spectroscopy (EDS) data presented revealed the presence of fine rounded fragments, resembling nodules (up to 200 μm) and fossilized bacteriomorphic Fe-Mn-oxides/hydroxides, within brecciated and foliated zones of carbonate rocks. They exhibit unusual features when compared to the common massive Fe-Mn mineralization with regards the following: (a) the extensive occurrence of bacteriomorphic Fe-oxides/hydroxides and their micro-textures; and (b) the minor elements (K, Na, P, S, Ca, As and Cl). The occurrence of abundant bacteriomophic Fe-Mn-oxides/hydroxides in the samples from the Legrena valley may reflect their catalytic role in the redox reactions during ore-forming processes. The characteristic features of that type of Fe-Mn mineralization seems to be the result of multistage supergene processes superimposed over initial hydrothermal stages. Such a multistage remobilization and precipitation of metals along open space surfaces on karstified carbonates during a subsequent stage of their initial precipitation may be widespread in the Attica region, Greece.

Magnetite and Green Rust: Synthesis, Properties, and Environmental Applications of Mixed-Valent Iron Minerals

Mixed-valent iron [Fe(II)-Fe(III)] minerals such as magnetite and green rust have received a significant amount of attention over recent decades, especially in the environmental sciences. These mineral phases are intrinsic and essential parts of biogeochemical cycling of metals and organic carbon and play an important role regarding the mobility, toxicity, and redox transformation of organic and inorganic pollutants. The formation pathways, mineral properties, and applications of magnetite and green rust are currently active areas of research in geochemistry, environmental mineralogy, geomicrobiology, material sciences, environmental engineering, and environmental remediation. These aspects ultimately dictate the reactivity of magnetite and green rust in the environment, which has important consequences for the application of these mineral phases, for example in remediation strategies. In this review we discuss the properties, occurrence, formation by biotic as well as abiotic pathways, characterization techniques, and environmental applications of magnetite and green rust in the environment. The aim is to present a detailed overview of the key aspects related to these mineral phases which can be used as an important resource for researchers working in a diverse range of fields dealing with mixed-valent iron minerals.

Overcoming antibiotic resistance: Is siderophore Trojan horse conjugation an answer to evolving resistance in microbial pathogens?

Comparative study of siderophore biosynthesis pathway in pathogens provides potential targets for antibiotics and host drug delivery as a part of computationally feasible microbial therapy. Iron acquisition using siderophore models is an essential and well established model in all microorganisms and microbial infections a known to cause great havoc to both plant and animal. Rapid development of antibiotic resistance in bacterial as well as fungal pathogens has drawn us at a verge where one has to get rid of the traditional way of obstructing pathogen using single or multiple antibiotic/chemical inhibitors or drugs. 'Trojan horse' strategy is an answer to this imperative call where antibiotic are by far sneaked into the pathogenic cell via the siderophore receptors at cell and outer membrane. This antibiotic once gets inside, generates a 'black hole' scenario within the opportunistic pathogens via iron scarcity. For pathogens whose siderophore are not compatible to smuggle drug due to their complex conformation and stiff valence bonds, there is another approach. By means of the siderophore biosynthesis pathways, potential targets for inhibition of these siderophores in pathogenic bacteria could be achieved and thus control pathogenic virulence. Method to design artificial exogenous siderophores for pathogens that would compete and succeed the battle of intake is also covered with this review. These manipulated siderophore would enter pathogenic cell like any other siderophore but will not disperse iron due to which iron inadequacy and hence pathogens control be accomplished. The aim of this review is to offer strategies to overcome the microbial infections/pathogens using siderophore.

Experimental fossilization of mat-forming cyanobacteria in coarse-grained siliciclastic sediments

Microbial fossils and textures are commonly preserved in Ediacaran and early Cambrian coarse-grained siliciclastic sediments that were deposited in tidal and intertidal marine settings. In contrast, the fossilization of micro-organisms in similar marine environments of post-Cambrian age is less frequently reported. Thus, temporal discrepancies in microbial preservation may have resulted from the opening and closing of a unique taphonomic window during the terminal Proterozoic and early Phanerozoic, respectively. Here, we expand upon previous work to identify environmental factors which may have facilitated the preservation of cyanobacteria growing on siliciclastic sand, by experimentally determining the ability of microbial mats to trap small, suspended mineral grains, and precipitate minerals from ions in solution. We show that (i) fine grains coat the sheaths of filamentous cyanobacteria (e.g., Nodosilinea sp.) residing within the mat, after less than 1 week of cell growth under aerobic conditions, (ii) clay minerals do not coat sterile cellulose fibers and rarely coat unsheathed cyanobacterial cells (e.g., Nostoc sp.), (iii) stronger disturbances (where culture jars were agitated at 170 rpm; 3 mm orbital diameter) produce the smoothest and most extensive mineral veneers around cells, compared with those agitated at slower rotational speeds (150 and 0 rpm), and (iv) mineral veneers coating cyanobacterial cells are ~1 μm in width. These new findings suggest that sheathed filamentous cyanobacteria may be preferentially preserved under conditions of high fluid energy. We integrate these results into a mechanistic model that explains the preservation of microbial fossils and textures in Ediacaran sandstones and siltstones, and in fine-grained siliciclastic deposits that contain exceptionally preserved microbial mats.

Biogenic nanosized iron oxides obtained from cultivation of iron bacteria from the genus Leptothrix

A detailed investigation of nanostructured iron oxides/(oxy)hydroxides gathered after cultivation of bacteria from the genus Leptothrix as iron (II) oxidizers is presented. A specific type of medium is selected for the cultivation of the bacteria. Results for sediment powder and bio-film on glass substrate samples from the same media are discussed. XRD, Raman spectroscopy, SEM, and TEM images and PPMS measurements are used to prove the exact composition of the biogenic products and to interpret the oxidation process. Analysis of the data collected shows that around 80 % of the iron (II) from the growth medium has been transformed into iron (III) in the form of different (oxy)hydroxides, with the rest found to be in a mixed 2,5 valence in magnetite. Our investigation shows that the bio-film sample has a phase content different from that of the powdered biomass and that lepidocrocite (γ-FeOOH) is the predominant and the initial biogenic phase in both samples. Magnetite nanoparticles are a secondary product in the bio-film, part of which possesses a defective quasi-maghemite surface layer. In the powdered biomass, the oxidation steps are not fully completed. The initial products are non-stoichiometric and due to the mixed ferric and ferrous ions present, they develop into: (i) lepidocrocite (γ-FeOOH) as a basic sediment, (ii) magnetite (Fe₃O₄) and (iii) goethite (α-FeOOH) in small quantities. The average size of all iron-bearing particles is found to be below 30 nm. The magnetic measurements performed show a superparamagnetic behavior of the material at room temperature.

Probing Synechocystis-Arsenic Interactions through Extracellular Nanowires

Microbial nanowires (MNWs) can play an important role in the transformation and mobility of toxic metals/metalloids in environment. The potential role of MNWs in cell-arsenic (As) interactions has not been reported in microorganisms and thus we explored this interaction using Synechocystis PCC 6803 as a model system. The effect of half maximal inhibitory concentration (IC50) [~300 mM As (V) and ~4 mM As (III)] and non-inhibitory [4X lower than IC50, i.e., 75 mM As (V) and 1 mM As (III)] of As was studied on Synechocystis cells in relation to its effect on Chlorophyll (Chl) a, type IV pili (TFP)-As interaction and intracellular/extracellular presence of As. In silico analysis showed that subunit PilA1 of electrically conductive TFP, i.e., microbial nanowires of Synechocystis have putative binding sites for As. In agreement with in silico analysis, transmission electron microscopy analysis showed that As was deposited on Synechocystis nanowires at all tested concentrations. The potential of Synechocystis nanowires to immobilize As can be further enhanced and evaluated on a large scale and thus can be applied for bioremediation studies.

Limited influence of Si on the preservation of Fe mineral-encrusted microbial cells during experimental diagenesis

The reconstruction of the history of microbial life since its emergence on early Earth is impaired by the difficulty to prove the biogenicity of putative microfossils in the rock record. While most of the oldest rocks on Earth have been exposed to different grades of diagenetic alterations, little is known about how the remains of micro-organisms evolve when exposed to pressure (P) and temperature (T) conditions typical of diagenesis. Using spectroscopy and microscopy, we compared morphological, mineralogical, and chemical biosignatures exhibited by Fe mineral-encrusted cells of the bacterium Acidovorax sp. BoFeN1 after long-term incubation under ambient conditions and after experimental diagenesis. We also evaluated the effects of Si on the preservation of microbial cells during the whole process. At ambient conditions, Si affected the morphology but not the identity (goethite) of Fe minerals that formed around cells. Fe-encrusted cells were morphologically well preserved after 1 week at 250 °C-140 MPa and after 16 weeks at 170 °C-120 MPa in the presence or in the absence of Si. Some goethite transformed to hematite and magnetite at 250 °C-140 MPa, but in the presence of Si more goethite was preserved. Proteins-the most abundant cellular components-were preserved over several months at ambient conditions but disappeared after incubations at high temperature and pressure conditions, both in the presence and in the absence of Si. Other organic compounds, such as lipids and extracellular polysaccharides seemed well preserved after exposure to diagenetic conditions. This study provides insights about the composition and potential preservation of microfossils that could have formed in Fe- and Si-rich Precambrian oceans.

Iron and lead ion adsorption by microbial flocculants in synthetic wastewater and their related carbonate formation

Although microbial treatments of heavy metal ions in wastewater have been studied, the removal of these metals through incorporation into carbonate minerals has rarely been reported. To investigate the removal of Fe3+ and Pb2+, two representative metals in wastewater, through the precipitation of carbonate minerals by a microbial flocculant (MBF) produced by Bacillus mucilaginosus. MBF was added to synthetic wastewater containing different Fe3+ and Pb2+ concentrations, and the extent of flocculation was analyzed. CO2 was bubbled into the mixture of MBF and Fe3+/Pb2+ to initiate the reaction. The solid substrates were analyzed via X-ray diffraction, transmission electron microscopy and energy dispersive spectroscopy. The results showed that the removal efficiency decreased and the MBF adsorption capacity for metals increased with increasing heavy metal concentration. In the system containing MBF, metals (Fe3+ and Pb2+), and CO2, the concentrated metals adsorbed onto the MBF combined with the dissolved CO2, resulting in oversaturation of metal carbonate minerals to form iron carbonate and lead carbonates. These results may be used in designing a method in which microbes can be utilized to combine CO2 with wastewater heavy metals to form carbonates, with the aim of mitigating environmental problems.

Uranium redox transition pathways in acetate-amended sediments

Redox transitions of uranium [from U(VI) to U(IV)] in low-temperature sediments govern the mobility of uranium in the environment and the accumulation of uranium in ore bodies, and inform our understanding of Earth’s geochemical history. The molecular-scale mechanistic pathways of these transitions determine the U(IV) products formed, thus influencing uranium isotope fractionation, reoxidation, and transport in sediments. Studies that improve our understanding of these pathways have the potential to substantially advance process understanding across a number of earth sciences disciplines. Detailed mechanistic information regarding uranium redox transitions in field sediments is largely nonexistent, owing to the difficulty of directly observing molecular-scale processes in the subsurface and the compositional/physical complexity of subsurface systems. Here, we present results from an in situ study of uranium redox transitions occurring in aquifer sediments under sulfate-reducing conditions. Based on molecular-scale spectroscopic, pore-scale geochemical, and macroscale aqueous evidence, we propose a biotic–abiotic transition pathway in which biomass-hosted mackinawite (FeS) is an electron source to reduce U(VI) to U(IV), which subsequently reacts with biomass to produce monomeric U(IV) species. A species resembling nanoscale uraninite is also present, implying the operation of at least two redox transition pathways. The presence of multiple pathways in low-temperature sediments unifies apparently contrasting prior observations and helps to explain sustained uranium reduction under disparate biogeochemical conditions. These findings have direct implications for our understanding of uranium bioremediation, ore formation, and global geochemical processes.

Biogenic Inspiration for the Controlled Nucleation and Growth of Inorganic Materials

The development of effective protocols for the control of crystal structure, size and morphology attracts considerable interest given the requirement for particles of modal size and shape in many areas of particle processing and the importance of crystallochemical selectivity in determining the exploitable properties of crystalline solids. In biological systems there are many examples of advanced “crystal engineering” in which materials are deposited in a highly controlled manner to produce crystal phases that are unique with respect to their structure, habit, uniformity of size and texture. A review of biomineralisation will show that while a complex array of strategies have evolved for regulating crystal growth, one feature is common to the biological paradigm. Interactions between supramolecular organic structures and the nascent inorganic solids play a fundamental role in controlling the deposition of the biominerals and ordering the assembly of these units into hierarchical structures. In order to gain a better understanding of the molecular recognition events, which take place at the organic-inorganic interface, a bio-inspired crystal chemical approach has been adopted. For this work organised organic assemblies (e.g. surfactant aggregates, peptide mimics, dendrimers) of precise molecular design (head group identity, packing conformation, primary sequence etc.) are being assayed for their effectiveness in controlling the nucleation and growth of crystals. It is evident from these studies that the chemical organisation of the polymeric microenvironment operates at the molecular level to control certain aspects of the nucleation, growth and stabilisation of inorganic particles. By systematically changing the molecular motif of the organic template we have established that the size, crystallographic orientation, growth and assembly of the mineral phase can be tailored to function. These results have relevance not only to our understanding of biomineralisation but also suggest a multiplicity of exploitable opportunities for the engineering of crystals.

Soft X-ray spectro-tomography study of cyanobacterial biomineral nucleation

Quantitative three-dimensional (3D) chemical mapping using angle-scan spectro-tomography in a scanning transmission (soft) X-ray microscope (STXM) has been used for the first time to characterize the early stages of CaCO(3) biomineral nucleation on the surface of planktonic freshwater cyanobacterial cells of the strain Synechococcus leopoliensis PCC 7942. The apparatus for STXM angle-scan tomography is described. Aspects of sample preparation, sample mounting and data acquisition and quantitative analysis and interpretation are discussed in detail. Angle-scan tomography and chemically selective 3D imaging at multiple photon energies has been combined with a complete 2D spectromicroscopic characterization of the biochemical and mineralogical composition. This has provided detailed insights into the mechanisms of mineral nucleation, leading to development of a detailed model of CaCO(3) nucleation by the cyanobacterial strain S. leopoliensis PCC 7942. It shows that Ca is absorbed by the extracellular polymeric substances (EPS) of the cyanobacteria and that CaCO(3) with aragonite-like short-range order is precipitated rather homogeneously within the EPS. The precipitation of the thermodynamically more stable calcite polymorph then starts at Ca-rich hot spots within the EPS and close to the cyanobacteria.

Degeneration of biogenic superparamagnetic magnetite

Magnetite crystals precipitated as a consequence of Fe(III) reduction by Shewanella algae BrY after 265 h incubation and 5-year anaerobic storage were investigated with transmission electron microscopy, Mössbauer spectroscopy and X-ray diffraction. The magnetite crystals were typically superparamagnetic with an approximate size of 13 nm. The lattice constants of the 265 h and 5-year crystals are 8.4164A and 8.3774A, respectively. The Mössbauer spectra indicated that the 265 h magnetite had excess Fe(II) in its crystal-chemistry (Fe(3+) (1.990)Fe(2+) (1.015)O(4)) but the 5-year magnetite was Fe(II)-deficient in stoichiometry (Fe(3+) (2.388)Fe(2+) (0.419)O(4)). Such crystal-chemical changes may be indicative of the degeneration of superparamagnetic magnetite through the aqueous oxidization of Fe(II) anaerobically, and the concomitant oxidation of the organic phases (fatty acid methyl esters) that were present during the initial formation of the magnetite. The observation of a corona structure on the aged magnetite corroborates the anaerobic oxidation of Fe(II) on the outer layers of magnetite crystals. These results suggest that there may be a possible link between the enzymatic activity of the bacteria and the stability of Fe(II)-excess magnetite, which may help explain why stable nano-magnetite grains are seldom preserved in natural environments.

Dinosaurian soft tissues interpreted as bacterial biofilms

A scanning electron microscope survey was initiated to determine if the previously reported findings of "dinosaurian soft tissues" could be identified in situ within the bones. The results obtained allowed a reinterpretation of the formation and preservation of several types of these "tissues" and their content. Mineralized and non-mineralized coatings were found extensively in the porous trabecular bone of a variety of dinosaur and mammal species across time. They represent bacterial biofilms common throughout nature. Biofilms form endocasts and once dissolved out of the bone, mimic real blood vessels and osteocytes. Bridged trails observed in biofilms indicate that a previously viscous film was populated with swimming bacteria. Carbon dating of the film points to its relatively modern origin. A comparison of infrared spectra of modern biofilms with modern collagen and fossil bone coatings suggests that modern biofilms share a closer molecular make-up than modern collagen to the coatings from fossil bones. Blood cell size iron-oxygen spheres found in the vessels were identified as an oxidized form of formerly pyritic framboids. Our observations appeal to a more conservative explanation for the structures found preserved in fossil bone.

Control of ferrous iron oxidation within circumneutral microbial iron mats by cellular activity and autocatalysis

Ferrous iron (Fe2+) oxidation by microbial iron mat samples, dominated by helical stalks of Gallionella ferruginea or sheaths of Leptothrix ochracea, was examined. Pseudo-first-order rate constants for the microbial mat samples ranged from 0.029 +/- 0.004 to 0.249 +/- 0.042 min(-1) and correlated well with iron content (R2 = 0.929). Rate constants for Na azide-treated (1 mM) samples estimated autocatalytic oxidation by iron oxide stalks or sheaths, with values ranging from 0.016 +/- 0.008 to 0.062 +/- 0.006 min(-1). Fe2+ oxidation attributable to cellular activities was variable with respect to sampling location and sampling time, with rate constants from 0.013 +/- 0.005 to 0.187 +/- 0.037 min(-1). Rates of oxidation of the same order of magnitude for cellular processes and autocatalysis suggested that bacteria harnessing Fe2+ as an energy source compete with their own byproducts for growth, not chemical oxidation (under conditions where aqueous oxygen concentrations are less than saturating). The use of cyclic voltammetry within this study for the simultaneous measurement of Fe2+ and oxygen allowed the collection of statistically meaningful and reproducible data, two factors that have limited aerobic, circumneutral, Fe2+ -oxidation rate studies.

Interactions between the Fe(III)-reducing bacterium Geobacter sulfurreducens and arsenate, and capture of the metalloid by biogenic Fe(II)

Previous work has shown that microbial communities in As-mobilizing sediments from West Bengal were dominated by Geobacter species. Thus, the potential of Geobacter sulfurreducens to mobilize arsenic via direct enzymatic reduction and indirect mechanisms linked to Fe(III) reduction was analyzed. G. sulfurreducens was unable to conserve energy for growth via the dissimilatory reduction of As(V), although it was able to grow in medium containing fumarate as the terminal electron acceptor in the presence of 500 muM As(V). There was also no evidence of As(III) in culture supernatants, suggesting that resistance to 500 muM As(V) was not mediated by a classical arsenic resistance operon, which would rely on the intracellular reduction of As(V) and the efflux of As(III). When the cells were grown using soluble Fe(III) as an electron acceptor in the presence of As(V), the Fe(II)-bearing mineral vivianite was formed. This was accompanied by the removal of As, predominantly as As(V), from solution. Biogenic siderite (ferrous carbonate) was also able to remove As from solution. When the organism was grown using insoluble ferrihydrite as an electron acceptor, Fe(III) reduction resulted in the formation of magnetite, again accompanied by the nearly quantitative sorption of As(V). These results demonstrate that G. sulfurreducens, a model Fe(III)-reducing bacterium, did not reduce As(V) enzymatically, despite the apparent genetic potential to mediate this transformation. However, the reduction of Fe(III) led to the formation of Fe(II)-bearing phases that are able to capture arsenic species and could act as sinks for arsenic in sediments.

The mechanism of metals precipitation by biologically generated alkalinity in biofilm reactors

Microbial strains, characterized by increased tolerance and ability to grow in metal bearing wastewaters as well as by effective metal sequestering capability by both active (bioaccumulative) and passive (biosorptive) processes, were tested as inoculum for metal laden wastewater treatment systems. Their capacity to grow in metal bearing wastewater, using an easily available and inexpensive carbon source such as acetate, was studied in batch experiments. Two principal conclusions were drawn: (1). Growth was observed for all the strains examined suggesting that the strains can be acclimated to metals bearing wastewaters. (2). Solution pH increased from neutral to alkaline values during growth (pH(initial)=7, pH(final)=10). The later was observed systematically for all strains. Metal precipitation, due to the metabolically generated alkalinity is expected as a result.Supporting evidence for this hypothesis was provided during the operation of two pilot moving bed sand filters treating two different metal bearing wastewaters. Acetate was used as carbon source to support the growth and maintenance of microbial biomass on the sand grains of the filters. The characteristics of the sludge produced from the operation of the pilot plants were subsequently studied in the laboratory. Both sludges were significantly loaded with large amounts of metals.A mechanism of metal precipitation induced by the metabolically generated alkalinity, when acetate is used as carbon source, could be proposed as the main process responsible for the metals sequestering inside the moving bed sandfilter reactor.

Phototrophs in high iron microbial mats: microstructure of mats in iron-depositing hot springs

Chocolate Pots Hot Springs in Yellowstone National Park are high in ferrous iron, silica and bicarbonate. The springs are contributing to the active development of an iron formation. The microstructure of photosynthetic microbial mats in these springs was studied with conventional optical microscopy, confocal laser scanning microscopy and transmission electron microscopy. The dominant mats at the highest temperatures (48-54 degrees C) were composed of Synechococcus and Chloroflexus or Pseudanabaena and Mastigocladus. At lower temperatures (36-45 degrees C), a narrow Oscillatoria dominated olive green cyanobacterial mats covering most of the iron deposit. Vertically oriented cyanobacterial filaments were abundant in the top 0.5 mm of the mats. Mineral deposits accumulated beneath this surface layer. The filamentous microstructure and gliding motility may contribute to binding the iron minerals. These activities and heavy mineral encrustation of cyanobacteria may contribute to the growth of the iron deposit. Chocolate Pots Hot Springs provide a model for studying the potential role of photosynthetic prokaryotes in the origin of Precambrian iron formations.