Elucidating the 3D chemical and physical architecture of soil microstructures by combining spectromicroscopic techniques and developing of novel computational approaches
Final Report Abstract
Soil microstructures are heterogeneous and complex mixtures of mineral and organic components in random arrangement, with a highly complex association of mineral and organic constituents of different sizes, morphology and chemical composition. The surface structure and the composition of soil minerals plays a very important role for the long-term Organic Matter (OM) sequestration that fundamentally determines biogeochemical processes and thus their ecological functioning. While it has previously not been possible to study complex soil microenvironments at the micro- to nanometer scale, the latest development of instruments and imaging workflows has opened up new opportunities to reach the necessary spatial resolution and visualize even nanoscale structures in soils. Within the SOIL3D project, we demonstrate how the correlation of microscopic and spectroscopic techniques, can be used to spatially resolve the composition, 3D architecture and structural properties of intact soil microaggregates. This international project was carried out by the Technical University of Munich (TUM, Germany), and the Luxembourg Institute of Science and Technology (LIST, Luxembourg) with the main objective to develop correlative surface and volume reconstruction workflows to link the OM formation with the chemical composition and the structural morphology of soil microaggregates. At TUM, soils were incubated together with isotopically enriched organic matter to follow the fate of freshly added OM in newly formed soil microscale structures. At LIST, a correlative microscopy workflow combining 3D reconstructions from Secondary Electron (SE) microscopy images with Secondary Ion Mass Spectrometry (SIMS) image information was adapted to soil microaggregates and optimized based on a photogrammetric method. Furthermore, the consortium was able to take advantage of the latest instrumental developments realized at LIST, such as the SIMS add-on system specifically designed for the Helium Ion Microscope, therefore called "HIM-SIMS”, allowing to provide in a single instrument highest spatial resolution in SE (0.5 nm) and SIMS modes (< 20 nm). For the photogrammetric 3D reconstruction, sequential SE images are acquired at equal angular steps around a Region of Interest (ROI) allowing to provide a 3D model of the sample surface by implementing the acquired SE images into a photogrammetry software. A SIMS image is multiple acquired in-situ (e.g., HIM-SIMS instrument), or ex-situ (e.g., NanoSIMS instrument) on the same ROI and is then projected onto the 3D SE model to obtain a 4D surface reconstruction. Compared to conventional 3D SIMS reconstruction methods, this method allows to better visualize the ROI due to additional visibility in the third dimension (vs. raw SIMS images only in 2D), and to model the local structure of the soil microaggregate, i.e. to calculate the local surface curvature, allowing to study the architecture of the OM on the mineral phase of the microaggregate. With our work we open the way to further explore the soil microscale composition and architecture of the interfaces between soil minerals, organic matter and soil biota. Thus, our work provides the experimental, conceptual and technical basis to gain a more fundamental understanding on the functioning of soil microstructures, namely microaggregates.
Publications
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4D Surface Reconstructions to Study Microscale Structures and Functions in Soil Biogeochemistry. Environmental Science & Technology, 55(13), 9384-9393.
Ost, Alexander D.; Wu, Tianyi; Höschen, Carmen; Mueller, Carsten W.; Wirtz, Tom & Audinot, Jean-Nicolas
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Association of fresh low-molecular-weight organic compounds with clay-sized mineral fraction in soils of different organic carbon loading. Geoderma, 409, 115657.
Wu, Tianyi; Ost, Alexander D.; Audinot, Jean-Nicolas; Wiesmeier, Martin; Wirtz, Tom; Buegger, Franz; Häusler, Werner; Höschen, Carmen & Mueller, Carsten W.
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Elucidation of 3D Chemical and Physical Architecture of Soil Microstructures by Correlating Spectro-Microscopic Techniques and Developing Novel Computational Methods. Microscopy and Microanalysis, 28(S1), 912-913.
Ost, Alexander D; Wu, Tianyi; Wirtz, Tom; Höschen, Carmen; Mueller, Carsten W & Audinot, Jean-Nicolas
