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.