A coupled microscopy approach to assess the nano-landscape of weathering

Lybrand, Rebecca A.; Austin, Jason C.; Fedenko, Jennifer; Gallery, Rachel E.; Rooney, Erin; Schroeder, Paul A.; Zaharescu, Dragos G.; Qafoku, Odeta

doi:10.1038/s41598-019-41357-0

Cited by 29 publications

(23 citation statements)

References 68 publications

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“…Previous studies on microbial induced mineral weathering have focused on investigating microbial metabolites and secondary minerals that are products of mineral weathering in the bulk soil. However, only a few studies have attempted to decipher weathering mechanisms by exploring the fungi-mineral interface 35 . This is in part due to the spatial heterogeneity of soil and the complexity of mineral weathering processes, which present challenges and necessitate innovative sampling and experimental platforms to study biotic driven mineral weathering.…”

Section: Discussionmentioning

confidence: 99%

Fungal Mineral Weathering Mechanisms Revealed Through Direct Molecular Visualization

Bhattacharjee

Qafoku

et al. 2021

Preprint

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Soil fungi facilitate the translocation of inorganic nutrients from soil minerals to other microorganisms and plants. This ability is particularly advantageous in impoverished soils, because fungal mycelial networks can bridge otherwise spatially disconnected and inaccessible nutrient hotspots. However, the molecular mechanisms underlying fungal mineral weathering and transport through soil remains poorly understood. Here, we addressed this knowledge gap by directly visualizing nutrient acquisition and transport through fungal hyphae in a mineral doped soil micromodel using a multimodal imaging approach. We observed that Fusarium sp. DS 682, a representative of common saprotrophic soil fungi, exhibited a mechanosensory response (thigmotropism) around obstacles and through pore spaces (~12 μm) in the presence of minerals. The fungus incorporated and translocated potassium (K) from K-rich mineral interfaces, as evidenced by visualization of mineral derived nutrient transport and unique K chemical moieties following fungal induced mineral weathering. Specific membrane transport proteins were expressed in the presence of minerals, including those involved in oxidative phosphorylation pathways and transmembrane transport of small molecular weight organic acids. This study establishes the significance of fungal biology and nutrient translocation mechanisms in maintaining fungal growth under water and nutrient limitations in a soil-like microenvironment.

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Section: Discussionmentioning

confidence: 99%

Fungal Mineral Weathering Mechanisms Revealed Through Direct Molecular Visualization

Bhattacharjee

Qafoku

et al. 2021

Preprint

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“…Through correlative approaches with TEM, SEM, HIM, and X-ray tomography, they were able to gain insight into microbially driven weathering processes under nutrient-rich conditions. Mineral weathering was also assessed by [96] and [97], who developed methods to analyse biological and geochemical drivers of weathering in natural settings. HIM was used to image subnanometre mineral-organic interactions, whereas SEM (EDX) was used for elemental quantification.…”

Section: Geomicrobiologymentioning

confidence: 99%

Bio-imaging with the helium-ion microscope: A review

Schmidt¹,

Byrne²,

Maasilta³

2021

Beilstein J. Nanotechnol.

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Scanning helium-ion microscopy (HIM) is an imaging technique with sub-nanometre resolution and is a powerful tool to resolve some of the tiniest structures in biology. In many aspects, the HIM resembles a field-emission scanning electron microscope (FE-SEM), but the use of helium ions rather than electrons provides several advantages, including higher surface sensitivity, larger depth of field, and a straightforward charge-compensating electron flood gun, which enables imaging of non-conductive samples, rendering HIM a promising high-resolution imaging technique for biological samples. Starting with studies focused on medical research, the last decade has seen some particularly spectacular high-resolution images in studies focused on plants, microbiology, virology, and geomicrobiology. However, HIM is not just an imaging technique. The ability to use the instrument for milling biological objects as small as viruses offers unique opportunities which are not possible with more conventional focused ion beams, such as gallium. Several pioneering technical developments, such as methods to couple secondary ion mass spectrometry (SIMS) or ionoluminescence with the HIM, also offer the possibility for new and exciting research on biological materials. In this review, we present a comprehensive overview of almost all currently published literature which has demonstrated the application of HIM for imaging of biological specimens. We also discuss some technical features of this unique type of instrument and highlight some of the new advances which will likely become more widely used in the years to come.

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“…This includes intra-and inter-granular micro-cracks generated during the formation of the granite but most importantly fracturation due to weathering (Gilkes et al 1980;Štyriaková et al 2012;Lybrand et al 2019). The Brézouard granite in the area is composed of ca.…”

Section: Full Waveform Acoustic Logging In the Strengbach Catchmentmentioning

confidence: 99%

Application of the differential effective medium theory to determine fluid saturation and crack density from measured P- and S-wave velocities

Zillmer

Kashtan

Doukoure

et al. 2021

Geophysical Journal International

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Summary The differential effective medium (DEM) theory studied in this article describes elastic moduli of a fractured medium with help of differential equations, where crack density is the independent variable and fluid saturation is a parameter. The effective medium is isotropic for randomly oriented flat ellipsoidal cracks and thus fully characterized by two elastic constants. In this article we derive an analytical solution of the equation for Poisson’s ratio and we transform the differential equation for Young’s modulus into a non-linear algebraic equation. Fluid saturation and crack density can then be determined from measured wave propagation velocities by a simple algorithm. We also derive approximate solutions for elastic moduli as a function of crack density and saturation, which allows to quantify the uncertainty of the result due to measurement errors. The DEM theory leads to higher crack densities than the self-consistent (SC) method and to lower crack densities than the non-interacting (NI) theory for measured elastic moduli, while all three methods give similar fluid saturation fractions. As an example of application of our theoretical results, we study weathered granite in the Strengbach water catchment in the Vosges mountains in France. We have performed full waveform sonic logging measurements in an 86 m deep borehole located at an altitude of 1130 m above sea level, which is used for hydro-geophysical and geochemical studies of a granitic aquifer. The logging data allows us to investigate P and S waves in the depth range between 40 and 80 m. The P and S wave propagation velocities take average values of 5.0 km/s and 2.7 km/s, respectively, with the highest values of 5.8 km/s and 3.2 km/s at 75–80 m depth. From these velocities we obtain a water saturation of 75 ± 25 per cent. The crack density describes the degree of weathering of the granite, which generally decreases with depth, but takes high values near layers of strongly weathered granite. Crack density is on average 0.5, with the highest value of 1.0 at 65 m and the lowest value of 0.2 at 75 m depth. The analysis of the full waveform logging data by the DEM method supports results from previous geochemical and hydrological studies in the Strengbach catchment which concluded that water is stored in deeper layers of the granitic aquifer.

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A coupled microscopy approach to assess the nano-landscape of weathering

Cited by 29 publications

References 68 publications

Fungal Mineral Weathering Mechanisms Revealed Through Direct Molecular Visualization

Fungal Mineral Weathering Mechanisms Revealed Through Direct Molecular Visualization

Bio-imaging with the helium-ion microscope: A review

Application of the differential effective medium theory to determine fluid saturation and crack density from measured P- and S-wave velocities

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