Academic literature on the topic 'Mineral bioweathering'

AbstractIn the Earth’s lithosphere, fungi are of fundamental importance as decomposer organisms, animal and plant pathogens and symbionts (e.g. lichens and mycorrhizas), being ubiquitous in sub-aerial and subsoil environments. The ability of fungi to interact with minerals, metals, metalloids and organic compounds through biomechanical and biochemical processes, makes them ideally suited as biological weathering agents of rock and building stone. They also play a fundamental role in biogeochemical cycling of nutrients, (e.g. C, N, P and S) and metals (e.g. Na, Mg, Ca, Mn, Fe, Cu, Zn, Co and Ni) essential for the growth of living organisms in the biosphere. In addition they play an integral role in the mobilization and immobilization of non-essential metals (e.g. Cs, Al, Cd, Hg and Pb). Most studies on mineral-microbe interactions and microbial involvement in geological processes have concentrated on bacteria and archaea (Prokaryota): fungi (Eukaryota) have, to a certain extent, been neglected. This article addresses the role of fungi in geomicrobiological processes, emphasizing their deteriorative potential on rock, building stone and mineral surfaces and involvement in the formation of secondary mycogenic minerals. Such roles of fungi are also of importance for the global carbon reservoir and have potential biotechnological applications, e.g. in the bioremediation of xenobiotic-, metal- and/or radionuclide-contaminated soils and wastes, and metal/radionuclide recovery.

AbstractThe Miocene dolomite-chert microbialites studied here offer a complete record of the geochemical cycles of silicate weathering and the subsequent formation of secondary products. The microbialites were formed in lacustrine systems during the Miocene of the Duero Basin, central Spain. Mineralogical, chemical and petrographic results provide evidence of the mediation of microbes in early weathering and by-product formation processes. Irrespective of the composition, the surfaces of the grains were subject to microbial attachment and concomitant weathering. Palaeo-weathering textures range from surface etching and pitting to extensive physical disaggregation of the minerals. Extreme silicate weathering led to the complete destruction of the silicate grains, whose prior existence is inferred from pseudomorphs exhibiting colonial textures like those recognized in the embedding matrix. Detailed petrographic and microanalytical examinations of the weathering effects in K-feldspars show that various secondary products with diverse crystallinity and chemical composition can coexist in the interior of a mineral. The coexistence of by-products is indicative of different microenvironmental conditions, likely created by microbial reactions. Thus, the presence of varied secondary products can be used as a criterion of biogenicity. Intensive alteration of P-bearing feldspars suggests that mineral weathering may have been driven by the nutrient requirements of the microbial consortium involved in the precipitation of dolomite. The rock record provides useful information on mineral weathering mediated by microbes.

Asbestos, silicate minerals present in soil and used for building constructions for many years, are highly toxic due primarily to the presence of high concentrations of the transition metal iron. Microbial weathering of asbestos occurs through various alteration mechanisms. Siderophores, complex agents specialized in metal chelation, are common mechanisms described in mineral alteration. Solubilized metals from the fiber can serve as micronutrients for telluric microorganisms. The review focuses on the bioweathering of asbestos fibers, found in soil or manufactured by humans with gypsum (asbestos flocking) or cement, by siderophore-producing Pseudomonas. A better understanding of the interactions between asbestos and bacteria will give a perspective of a detoxification process inhibiting asbestos toxicity.

This study reports on experimental observations during fungi–mineral substrate interactions. Selected mineral substrates of biotite, muscovite, bauxite, chromite, galena, malachite, manganite, and plagioclase were exposed in vitro to free fungal growth under open conditions. The interaction produced strong biochemical and biomechanical alterations to the mineral substrates. Specifically, reported here is a three-dimensional thigmotropic colonization pattern of the mineral surfaces that suggested a possible pattern of fungal metalophagus behavior. Authigenic secondary mineral biomineralization occurred: Ca- and Mg-Oxalates such as weddellite: CaC2O4·2H2O, whewellite: CaC2O4·H2O, and glushinskite: MgC2O4·2H2O; struvite: (NH4) MgPO4·6H2O; gibbsite: Al(OH)3; and gypsum: CaSO4·2H2O. The bioleached elements included Fe, Pb, S, Cu, and Al, which formed single crystals or aggregates, amorphous layers, amorphous aggregates, and linear forms influenced by the fungal filaments. The fungi bioleached Fe and Al from bauxite and Mn from manganite and deposited the metals as separate mineral species. Gypsum was deposited during the interaction with the manganite substrate, indicating a source of Ca and S either within manganite impurities or within the fungal growth environment. Other biochemical and biomechanical features such as tunneling, strong pitting, exfoliation, dissolution, perforations, and fragmentation of the mineral surfaces were also produced. The results of this study, besides emphasizing the role of fungi in bioweathering and mineral alteration, also show that, to produce these alterations, fungi employ a 3D fungal colonization pattern of mineral surfaces guided by thigmotropic and possible metalophagus behavior.

Microbes play key geoactive roles in the biosphere, particularly in the areas of element biotransformations and biogeochemical cycling, metal and mineral transformations, decomposition, bioweathering, and soil and sediment formation. All kinds of microbes, including prokaryotes and eukaryotes and their symbiotic associations with each other and ‘higher organisms’, can contribute actively to geological phenomena, and central to many such geomicrobial processes are transformations of metals and minerals. Microbes have a variety of properties that can effect changes in metal speciation, toxicity and mobility, as well as mineral formation or mineral dissolution or deterioration. Such mechanisms are important components of natural biogeochemical cycles for metals as well as associated elements in biomass, soil, rocks and minerals, e.g. sulfur and phosphorus, and metalloids, actinides and metal radionuclides. Apart from being important in natural biosphere processes, metal and mineral transformations can have beneficial or detrimental consequences in a human context. Bioremediation is the application of biological systems to the clean-up of organic and inorganic pollution, with bacteria and fungi being the most important organisms for reclamation, immobilization or detoxification of metallic and radionuclide pollutants. Some biominerals or metallic elements deposited by microbes have catalytic and other properties in nanoparticle, crystalline or colloidal forms, and these are relevant to the development of novel biomaterials for technological and antimicrobial purposes. On the negative side, metal and mineral transformations by microbes may result in spoilage and destruction of natural and synthetic materials, rock and mineral-based building materials (e.g. concrete), acid mine drainage and associated metal pollution, biocorrosion of metals, alloys and related substances, and adverse effects on radionuclide speciation, mobility and containment, all with immense social and economic consequences. The ubiquity and importance of microbes in biosphere processes make geomicrobiology one of the most important concepts within microbiology, and one requiring an interdisciplinary approach to define environmental and applied significance and underpin exploitation in biotechnology.

ABSTRACTFungi play important roles in biogeochemical processes such as organic matter decomposition, bioweathering of minerals and rocks, and metal transformations and therefore influence elemental cycles for essential and potentially toxic elements, e.g., P, S, Pb, and As. Arsenic is a potentially toxic metalloid for most organisms and naturally occurs in trace quantities in soil, rocks, water, air, and living organisms. Among more than 300 arsenic minerals occurring in nature, mimetite [Pb5(AsO4)3Cl] is the most stable lead arsenate and holds considerable promise in metal stabilization forin situandex situsequestration and remediation through precipitation, as do other insoluble lead apatites, such as pyromorphite [Pb5(PO4)3Cl] and vanadinite [Pb5(VO4)3Cl]. Despite the insolubility of mimetite, the organic acid-producing soil fungusAspergillus nigerwas able to solubilize mimetite with simultaneous precipitation of lead oxalate as a new mycogenic biomineral. Since fungal biotransformation of both pyromorphite and vanadinite has been previously documented, a new biogeochemical model for the biogenic transformation of lead apatites (mimetite, pyromorphite, and vanadinite) by fungi is hypothesized in this study by application of geochemical modeling together with experimental data. The models closely agreed with experimental data and provided accurate simulation of As and Pb complexation and biomineral formation dependent on, e.g., pH, cation-anion composition, and concentration. A general pattern for fungal biotransformation of lead apatite minerals is proposed, proving new understanding of ecological implications of the biogeochemical cycling of component elements as well as industrial applications in metal stabilization, bioremediation, and biorecovery.

Rare earth element (REE) fluorocarbonate mineralization occurs in lacustrine shales in the Lower Devonian Rhynie chert, Aberdeenshire, UK, preserved by hot spring silicification. Mineralization follows a combination of first-cycle erosion of granite to yield detrital monazite grains, bioweathering of the monazite to liberate REEs, and interaction with fluorine-rich hot spring fluids in an alkaline sedimentary environment. The mineral composition of most of the fluorocarbonates is referable to synchysite. Mineralization occurs at the surface, and the host shales subsequently experience maximum temperatures of about 110 ℃. Most fluorocarbonate mineralization originates at much higher temperatures, but the Rhynie occurrence emphasizes that low-temperature deposits are possible when both fluorine and REEs are available from granite into the sedimentary environment.

AbstractThe weathering phenomena resulting from the growth of six foliose and crustose lichens (Parmelia subrudecta, Xanthoria ectaneoides, Parmelia conspersa, Aspicilia radiosa, Caloplaca sp. and Ochrolechia parella) on three mafic rocks have been studied. The bioweathering results in more or less extensive fragmentation and corrosion of the mineral surfaces immediately beneath the lichen thalli and in the formation, in the thallus or at the rock-lichen interface, of secondary products. The significant amounts of whewellite found in all interfaces, and the bipiramids of weddellite detected at the serpentine rock-Ochrolechia parella interface, suggest that the oxalic acid secreted by the mycobiont is the chemical substance principally involved. The capacity of the lichens to alter their rock substrata does not appear to be related to their thallus morphology.

L’altération des roches silicatées constitue le dénominateur commun d’une multitude de problématiques environnementales et sociétales. Du fait de la difficulté d’extrapoler au milieu naturel les cinétiques de dissolution des minéraux mesurées in vitro, cette thèse propose de réviser en profondeur l’approche actuelle de la réactivité minérale du laboratoire au terrain. Ce travail démontre que l’évolution intrinsèque des propriétés texturales et structurales de l’interface réactive au cours de la dissolution induit des variations de vitesse qui ne peuvent être expliquées dans le cadre des théories thermocinétiques classiques. Nous proposons une nouvelle méthode permettant de sonder la réactivité biogéochimique des minéraux sur le terrain et de révéler les interactions réciproques entre le minéral et le monde microbien au sein de la minéralosphère. Nous démontrons la pertinence des phénomènes de passivation pour l’altération de surface et l’incapacité des microorganismes à les surmonter
Chemical weathering of silicate minerals is central to numerous environmental and societal challenges. This study addresses the long-standing question of the inconsistency between field and laboratory estimates of dissolution kinetics, by revisiting current approaches of mineral reactivity. It is demonstrated that evolution of feldspar reaction rates are inaccurately describedby current kinetics rate laws, due to textural and structural changes occurring at the fluid-mineral interface over the course of the dissolution process. A novel method is developed to enable probing biogeochemical weathering rates in the field. Bacterial and fungal metagenomic data reveal that subtle reciprocal relationships are established between microorganisms and mineral substrates within the mineralosphere. This thesis emphasizes the impact of passivation phenomena on dissolution rates, under field-relevant reacting conditions and the incapacity of microorganisms to overcome the passivation barrier

L'étude de la surface des minéraux altérés et, en particulier, leur topographie, joue un rôle fondamental dans la reconstitution des conditions environnementales passées et dans la détection de traces de vie dans l’enregistrement géologique, sur Terre et au-delà. En effet, on sait que la microtopographie de surface des minéraux altérés peut conserver des signatures caractéristiques des conditions dans lesquelles ont pu se dérouler leurs interactions avec des solutions aqueuses. Par exemple, les puits de corrosion figurent parmi les signatures admises des interactions entre un fluide aqueux fortement sous-saturé et une surface minérale. Toutefois, d'autres empreintes d'interactions fluides-minéraux restent à définir. Dans le même ordre d'idées, des empreintes microtopographiques spécifiques ont déjà interprétées comme résultant de l’interaction entre micro-organismes et surfaces minérales : en particulier, il a été suggéré que les puits et microcanaux ressemblant à des micro-organismes en termes de ‘taille, forme et distribution’ pouvaient constituer des biosignatures. Cependant, il a été démontré que des caractéristiques de surface qualitativement similaires peuvent également être reproduites par des processus purement abiotiques. Il apparait donc crucial de développer des critères plus univoques pour différencier les caractéristiques d'altération abiotiques et microbiennes. Dans le cadre de cette thèse, ces questions ont été abordées en combinant des approches expérimentales et de modélisation. Des expériences de dissolution de calcite ont été réalisées à divers états de saturation du fluide, à la fois dans des conditions abiotiques et avec un biofilm de cyanobactéries couvrant la surface de la calcite. Des analyses statistiques de la topographie de surface résultante, déterminée au cours du temps à l'aide d’un interféromètre à balayage vertical, ont ensuite été effectuées. Les résultats suggèrent que la rugosité de surface à l'état stationnaire résultant de la dissolution peut être utilisée comme un traceur caractéristique de l'état de saturation du fluide. Dans ce contexte, une modélisation stochastique de la dissolution de la calcite a permis de définir le temps de relaxation nécessaire pour que la microtopographie de surface passe d'une configuration d'équilibre à une autre, en réponse à un changement de composition de la solution. Les résultats suggèrent que la microtopographie des minéraux altérés dans le milieu naturel peut être représentative de la composition du dernier fluide en contact avec le minéral. En outre, les résultats expérimentaux ont montré que les caractérisations statistiques de la microtopographie de surface des minéraux altérés peuvent être utilisées pour détecter quantitativement – et donc de manière moins ambiguë - les empreintes de bio-altération. Plus précisément, dans des conditions loin de l'équilibre, la dissolution sous biofilm a conduit à la formation de régions surélevées de la surface de la calcite, mises en évidence par l’utilisation d’outils statistiques d’analyse de la rugosité tels que des variogrammes. Des simulations stochastiques à l'échelle atomique du processus de dissolution suggèrent que ces caractéristiques d’altération biotique résultaient d'une augmentation locale de l'état de saturation du fluide au contact du biofilm avec le minéral, entraînant une réduction localisée de la vitesse de dissolution. Dans l'ensemble, ce travail introduit des critères quantitatifs et mécanistes novateurs pour reconstituer les conditions environnementales passées et pour identifier des biosignatures dans l’enregistrement géologique, sur Terre et au-delà, de manière plus univoque et à l’aide d’outils non-destructifs
Studying the topography of altered rock surfaces represents a cornerstone for reconstructing past environmental conditions and for the identification of traces of life in the geological record, on Earth and beyond. Indeed, the surface microtopography of altered minerals has proven effective in retaining signatures of fluid-mineral interactions. For example, etch pits are among the commonly accepted signatures of interactions between a highly undersaturated aqueous fluid and a mineral surface. However, additional imprints of water-mineral interactions remain to be defined. On a similar note, weathering imprints supposedly left by microorganisms have been proposed as potential biosignatures. These include etching features and microchannels resembling microbes in ‘size, shape and distribution’. Neverthless, it has been shown that qualitatively similar surface features can also be reproduced through purely abiotic processes. Therefore, it becomes crucial to develop less ambiguous criteria to differentiate between abiotic and biotic weathering features. In this PhD thesis, these questions were addressed through a combination of experimental and modeling approaches. Calcite dissolution experiments were carried out at various saturation states, both under abiotic conditions and with a cyanobacteria biofilm covering the calcite surface. Time-resolved statistical analyses of the resulting surface topography acquired using vertical scanning interferometry were then conducted. The results suggested that the steady-state surface roughness resulting from dissolution can be used as a proxy to back-estimate the saturation state of the fluid. In this context, stochastic modeling of crystal dissolution helped defining the relaxation time that is required for the surface microtopography to switch from a given steady-state configuration to another, as a result of a change in the solution composition. This suggested that the microtopography of naturally weathered minerals may be representative of the fluid composition most recently visited. Furthermore, the experimental results showed that statistical characterizations of the surface microtopography of altered minerals can be used to quantitatively -thus less ambiguously- detect bio-weathering imprints. Specifically, at far-from-equilibrium conditions, biofilm-mediated dissolution led to the formation of high-elevation regions across the calcite surface, which could be quantitatively detected by semi-variogram analyses. Atomic-scale stochastic simulations of the dissolution process suggested that these bio-weathering features resulted from a local increase in fluid saturation state at the biofilm-mineral contact, leading to a localized reduction in dissolution rate. Altogether, this work provides novel, mechanistically-supported quantitative criteria that may help reconstruct past weathering conditions and identify mineral bio-weathering signatures in natural settings in a non-destructive and less ambiguous way

Fungi play important geoactive roles in the biosphere, particularly element biotransformations and biogeochemical cycling, metal and mineral transformations, decomposition, bioweathering, and soil and sediment formation. Fungi can apply various mechanisms to effect changes in metal speciation, toxicity and mobility, mineral formation and/or mineral dissolution. This research has examined fungal roles in bioweathering and bioleaching of zinc sulfide ore, together with an investigation of the role of fungal phosphatases in the bioprecipitation of uranium and lead when utilising an organic phosphorus-containing substrate as the sole phosphorus source. The results obtained revealed that test fungal species showed bioweathering effects on zinc sulfide ore, and clear evidence of biotransformation and bioleaching of zinc sulfide was obtained after growth of A. niger. The formation of zinc oxalate dihydrate resulted from oxalic acid excretion. The formation of uranium- and lead-containing biominerals after growth of yeasts and filamentous fungi with organic phosphorus sources have also been demonstrated and characterized. Test fungi were capable of precipitating uranium phosphate and pyromorphite, and also produced mycogenic lead oxalate during this process. This work is the first demonstration that filamentous fungi are capable of precipitating a variety of uranium- and lead-containing phosphate biominerals when grown with an organic phosphorus source. The role of fungal processes in the bioweathing and bioleaching of mineral ores, and the significance of phosphatases in the formation of uranium and lead secondary minerals has thrown further light on potential fungal roles in metal and mineral biogeochemistry as well as the possible significance of these mechanisms for element biorecovery or bioremediation.