Fungi play a critical role in rock weathering and nutrient cycling, yet their spatial interactions with minerals remain poorly understood. This study employs high-resolution micro-computed tomography (micro-CT) to visualize fungal colonization within basaltic rocks, offering a non-destructive 3D perspective on microbe-mineral interactions. Observation from SEM scans suggest preferential fungal hyphae directionality towards certain features in the rock, versus other. To verify and quantify these patterns, we scanned 13 basalt samples from three locations at a resolution of 3–4 µm, enabling clear visualization of fungal structures (5–10 µm in diameter) and their association with different rock features.
We employed advanced image processing techniques using Dragonfly, Fiji/ImageJ software, and statistical tools for image analysis, for segmentation and quantitative assessment. In addition, we used polarized-light microscopy for petrographic analysis. These combined approaches allowed us to track hyphal growth pathways, determine fungal selectivity for different features, and assess the extent of mineral weathering.
Our findings demonstrate that micro-CT enables unprecedented 3D visualization of fungal hyphae within rocks substrates, providing a deeper understanding of fungal-mediated bioweathering. By integrating multiple imaging techniques with computational analysis, this study advances our ability to quantify fungal-mineral interactions and their role in geochemical processes.