Better knowledge of microbial movement and interaction with plant roots is essential to understanding soil ecosystems. However, the lack of a suitable approach for observing biological activity in such environments severely impedes advances in this field of research.

Recent work suggests that such limitations could be lifted using "environmental microscope", which are defined as a live-sample imaging platforms dedicated to the observation of physical and biological interactions relevant to the understanding environmental processes. The work presented by Liu et al shows that microscopes dedicated to live environmental studies present an invaluable tool to understand life in soils. The study combined the use of transparent soil with cutting edge light sheet microscopy techniques provide a detailed analysis of the movements of Bacillus subtilis. Results revealed how the soil pore structure influences the behaviour of the bacteria, both before and during the formation of biofilms on the root surface. This work sheds light on previously unseen phenomenon, and accelerates our understanding of soil dwelling organisms which were, before now, unobserved in their native environment.

Download the code for 3D reconstruction here