Abstract
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.
Highlights
Correlative Microscopy (CM) has become of major importance nowadays in various domains such as nanotechnology, life, and even soil sciences
When Secondary Ion Mass Spectrometry (SIMS) is combined with scanning or transmission electron microscopy techniques (SEM and TEM)[5] and, more recently, Helium Ion Microscopy (HIM),[6−8] CM offers high sensitivity chemical information correlated with morphology
We demonstrate that correlative imaging, by a qualitative description and a deeper topographic analysis, offers the great opportunity to merge topographic and physical information with the distribution of elements and chemical data to better understand the link between soil microaggregate architecture and biogeochemical function
Summary
Correlative Microscopy (CM) has become of major importance nowadays in various domains such as nanotechnology, life, and even soil sciences. SIMS has been widely used for 3D SIMS reconstruction.[12] Sequential 2D SIMS images are obtained while eroding the surface progressively under the energetic primary ion bombardment and are assembled into a 3D stack This method does not take into account the original surface topography and its evolution during the sputtering process, since different materials and features exposed to the ion beam at different angles are sputtering at different rates.[13] The outcome is a three-dimensional block representing the ROI without any morphological information and prone to artifacts. We demonstrate that correlative imaging, by a qualitative description and a deeper topographic analysis, offers the great opportunity to merge topographic and physical information with the distribution of elements and chemical data to better understand the link between soil microaggregate architecture and biogeochemical function. We compare two sample preparation procedures for the microscale analysis of soil microaggregates (wet and powder deposition), and make use of isotopic enrichment (13C glucose) to trace the fate of freshly added OM during the formation of mineral-associated OM on the surface of microaggregates
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