Imaging and Analytical Approaches for Characterization of Soil Mineral Weathering (original) (raw)
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Mineral weathering by bacteria: ecology, actors and mechanisms
Trends in Microbiology, 2009
Acidic forest: forest with a soil characterized by low pH (<4.5) and poorly weatherable minerals. Acidolysis: mineral dissolution owing to acidification of the medium. Apatite: a calcium phosphate mineral. Biotite: a mica-type mineral containing potassium, iron and magnesium. Complexolysis: mineral dissolution owing to chelation of ions. Endolithic: an organism growing inside a rock or in the pores between the mineral grains of a rock. Epilithic: an organism living on rocks or other mineral surfaces. Goethite: iron-bearing oxide mineral found in soil and other low-temperature environments [FeO(OH)]. Hematite: mineral form of iron (III) oxide (Fe 2 O 3). Mineral weathering: dissolution and transformation of a mineral. Mycorrhizal fungi: fungi growing in symbiosis with a plant, forming mycorrhizae. Mycorrhizosphere: volume of soil under the influence of mycorrhizae. Phyllosilicate: a type of mineral containing SiO 4 tetrahedral crystals. Rhizoplane: surface of plant roots. Rhizosphere: the volume of soil under the root influence.
Microscopy Today
Microbial-induced calcite precipitation (MICP) has gained much attention in soil improvement studies, where it can enhance the physical properties of sandy soil. Small-scale sand cylinder tests were conducted to investigate the formation and failure of calcium carbonate precipitation bonding between individual sand particles. Bonding formation by precipitation was examined by scanning electron microscopy. Energy-dispersive X-ray spectroscopy analysis verified the existence of calcium, carbon, and oxygen, which could form CaCO 3 after MICP-treatment. Focused-ion-beam milling was applied to study the interior structure of calcium carbonate precipitation during the MICP process.
A coupled microscopy approach to assess the nano-landscape of weathering
Scientific Reports
Mineral weathering is a balanced interplay among physical, chemical, and biological processes. Fundamental knowledge gaps exist in characterizing the biogeochemical mechanisms that transform microbe-mineral interfaces at submicron scales, particularly in complex field systems. Our objective was to develop methods targeting the nanoscale by using high-resolution microscopy to assess biological and geochemical drivers of weathering in natural settings. Basalt, granite, and quartz (53-250 µm) were deployed in surface soils (10 cm) of three ecosystems (semiarid, subhumid, humid) for one year. We successfully developed a reference grid method to analyze individual grains using: (1) helium ion microscopy to capture micron to sub-nanometer imagery of mineral-organic interactions; and (2) scanning electron microscopy to quantify elemental distribution on the same surfaces via element mapping and point analyses. We detected locations of biomechanical weathering, secondary mineral precipitation, biofilm formation, and grain coatings across the three contrasting climates. To our knowledge, this is the first time these coupled microscopy techniques were applied in the earth and ecosystem sciences to assess microbe-mineral interfaces and in situ biological contributors to incipient weathering.
Mineralogical footprints of microbial life
American Journal of Science, 2005
This paper is dedicated to Dr. Terry J. Beveridge, mentor and friend, on the occasion of his 60th birthday. ABSTRACT. Earth's geosphere is intimately tied to its biosphere. A major link between the two lies in the microbial realm; microorganisms grow in and upon rocks and minerals, often relying on their substratum for critical compounds needed in order to produce cellular energy. The presence of a metabolizing cell on a mineral substrate has a significant effect on the mineral texture and on the geochemistry of the surrounding microenvironment. In nature, microorganisms exist in microbial communities as mats or biofilms growing upon a solid substrate. As such they cover a vast surface area both within and below the surface of Earth's land and sea. The following review will provide a glimpse into the latest findings in the field of geomicrobiology and is intended to convey a sense of the profound influence microorganisms can have upon the geological environment they inhabit.
Frontiers in Environmental Science
Research over the last few decades has shown that the characterization of microaggregates at the micrometer scale using Transmission Electron Microscopy (TEM) provides useful information on the influence of microorganisms on soil functioning. By taking soil heterogeneity into account, TEM provides qualitative information about the state of bacteria and fungi (e.g., intact state of living organisms, spores, residues) at the sampling date within organo-mineral associations, from the soil-root interface to the bulk soil, and in biogenic structures such as casts. The degree of degradation of organic matter can be related to the visualized enzymatic potential of microorganisms that degrade them, thus indicating organic matter dynamics within soil aggregates. In addition, analytical TEM characterization of microaggregates by EELS (Electron Energy Loss Spectroscopy) or EDX (Energy Dispersive X-rays spectroscopy) provides in situ identification of microbial involvement in the biogeochemical cycles of elements. Furthermore, micrometer characterization associated with other methodologies such as Nanoscale Secondary Ion Mass Spectrometry (NanoSIMS) or soil fractionation, enables monitoring both incorporation of biodegraded litter within soil aggregates and impacts of microbial dynamics on soil aggregation, particularly due to production of extracellular polymeric substances. The present focused review suggests that such an approach using micrometer characterization of soil microhabitats provides relevant qualitative and quantitative information when monitoring and modeling microbial processes in dynamics of organo-mineral associations.
Geochimica Et Cosmochimica Acta, 2011
In soils, mycorrhiza (microscopic fungal hypha) living in symbiosis with plant roots are the biological interface by which plants obtain, from rocks and organic matter, the nutrients necessary for their growth and maintenance. Despite their central role in soils, the mechanism and kinetics of mineral alteration by mycorrhiza are poorly constrained quantitatively. Here, we report in situ quantification of weathering rates from a mineral substrate, (0 0 1) basal plane of biotite, by a surface-bound hypha of Paxillus involutus, grown in association with the root system of a Scots pine, Pinus sylvestris. Four thin-sections were extracted by focused ion beam (FIB) milling along a single hypha grown over the biotite surface. Depth-profile of Si, O, K, Mg, Fe and Al concentrations were performed at the hypha-biotite interface by scanning transmission electron microscopyenergy dispersive X-ray spectroscopy (STEM-EDX). Large removals of K (50-65%), Mg (55-75%), Fe (80-85%) and Al (75-85%) were observed in the topmost 40 nm of biotite underneath the hypha while Si and O are preserved throughout the depth-profile. A quantitative model of alteration at the hypha-scale was developed based on solid-state diffusion fluxes of elements into the hypha and the break-down/mineralogical re-arrangement of biotite. A strong acidification was also observed with hypha bound to the biotite surface reaching pH < 4.6. When consistently compared with the abiotic biotite dissolution, we conclude that the surface-bound mycorrhiza accelerate the biotite alteration kinetics between pH 3.5 and 5.8 to $0.04 lmol biotite m À2 h À1 . Our current work reaffirms that fungal mineral alteration is a process that combines our previously documented bio-mechanical forcing with the lm-scale acidification mediated by surface-bound hypha and a subsequent chemical element removal due to the fungal action. As such, our study presents a first kinetic framework for mycorrhizal alteration at the hypha-scale under close-to-natural experimental conditions.
Microbial Colonization of Bare Rocks: Laboratory Biofilm Enhances Mineral Weathering
Procedia Earth and Planetary Science, 2014
A laboratory biofilm consisting of the phototrophic cyanobacterium Nostoc punctiforme ATCC 29133 and the rock-inhabiting ascomycete Knufia petricola CBS 726.95 was tested for its mineral weathering potential. Minerals with different grain sizes and mineralogy were incubated with and without biofilm in batch and in flow-through column experiments. After incubation, the mineral dissolution was quantified analysing (i) leachate chemistry via ICP-OES/MS (inductively coupled plasma optical emission spectrometry/mass spectrometry) and (ii) the residual grains as thin polished sections via SEM/TEM-EDX (scanning electron microscopy/transmission electron microscopy-energy dispersive X-ray spectrometry). Mineral dissolution was enhanced in biotic experiments as compared to abiotic ones, for both batch culture and flow-through approaches. Analyses of thin polished sections confirmed the leaching of these elements near the surface of the mineral grains. These results clearly indicate a biotic effect on the weathering of minerals produced by the laboratory biofilm.