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Fine-grained soils containing diatom microfossils of biological origin are found worldwide. However, although these soils are acknowledged to have unique physical and mechanical properties, the exact role of diatoms in determining their compression and hydraulic behaviours remains unclear, especially when high effective stress is involved, and the underlying micromechanism is yet to be revealed. This study investigated the compression and permeability of diatomaceous soils prepared by mixing pure diatom and kaolin powders through one-dimensional constant rate of strain compression tests with a maximum vertical stress of 10 MPa. The microstructure of the soils studied was observed by atomic force microscopy, scanning electron microscopy and mercury intrusion porosimetry, and the microstructural evolution during compression was traced. The results indicate that the special hollow structure of diatom particles with internal pores contributes significantly to the high void ratio, compressibility and permeability of diatomaceous soils, and increasing the diatom content improves the pore distribution non-uniformity of the diatom–kaolin mixtures. In addition, the diatom particles have high brittleness and breakage potential, leading to microstructural rearrangement during compression, especially pore-structure adjustment. Lower compressive stress deforms the inter- and intra-aggregate pores, but higher vertical stress damages the diatoms’ hollow structure, which changes the compression and hydraulic parameters in a different manner from the case of conventional clay. This paper enriches the knowledge concerning the multilevel behaviour of fine-grained soils containing diatom microfossils and provides a fundamental dataset.

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