4D Surface Reconstructions to Study Microscale Structures and Functions in Soil Biogeochemistry

The development of high-resolution microscopy and spectroscopy techniques has allowed the analysis of microscopic 3D objects in fields like nanotechnology and life and soil sciences. Soils have the ability to incorporate and store large amounts of organic carbon. To study this organic matter (OM) sequestration, it is essential to analyze its association with soil minerals at the relevant microaggregate scale. This has been previously studied in 2D. However, 3D surface representations would allow a variable angle and magnification analysis, providing detailed insight on their architecture. Here we illustrate a 4D surface reconstruction workflow able to locate preferential sites for OM deposition with respect to microaggregate topography. We used Helium Ion Microscopy to acquire overlapping Secondary Electron (SE) images to reconstruct the soil topography in 3D. Then we used nanoscale Secondary Ion Mass Spectrometry imaging to chemically differentiate between the OM and mineral constituents forming the microaggregates. This image was projected onto the 3D SE model to create a 4D surface reconstruction. Our results show that organo-mineral associations mainly form at medium curvatures while flat and highly curved surfaces are avoided. This method presents an important step forward to survey the 3D physical structure and chemical composition of microscale biogeochemical systems correlatively.高分辨率显微与光谱技术的发展，使得纳米技术、生命科学及土壤科学等领域中微观三维物体的分析成为可能。土壤可固存并储存大量有机碳。为探究此类有机质（organic matter, OM）固存过程，在对应微团聚体尺度下分析其与土壤矿物的缔合机制至关重要。此前此类研究多基于二维层面展开。而三维表面表征技术可支持可变角度与放大倍数下的分析，为解析其微观结构提供更为细致的认知。本文展示了一套四维表面重建流程，可基于微团聚体形貌定位有机质沉积的优先位点。本研究采用氦离子显微镜（Helium Ion Microscopy）采集重叠的二次电子（Secondary Electron, SE）图像，以重建土壤的三维形貌；随后利用纳米级二次离子质谱成像（Secondary Ion Mass Spectrometry）技术，对构成微团聚体的有机质与矿物组分实现化学区分。将该成像结果投影至三维二次电子模型中，即可构建四维表面重建结果。研究结果显示，有机-矿物缔合主要形成于中等曲率表面，而平坦及高曲率表面则鲜有此类缔合形成。该方法为同步表征微观尺度生物地球化学系统的三维物理结构与化学组成提供了重要的技术进展。