Microfluidic chips provide visual access to in situ soil ecology

Mafla-Endara et al. incubate a microfluidic chip with and directly in soil in order to examine interactions between microbial communities and the pore space microstructures. This work shows the spatiotemporal changes of soil microhabitats and demonstrates that fungal hyphae increase the dispersal range and abundance of water-dwelling organisms across air pockets.Microbes govern most soil functions, but investigation of these processes at the scale of their cells has been difficult to accomplish. Here we incubate microfabricated, transparent 'soil chips' with soil, or bury them directly in the field. Both soil microbes and minerals enter the chips, which enables us to investigate diverse community interdependences, such as inter-kingdom and food-web interactions, and feedbacks between microbes and the pore space microstructures. The presence of hyphae ('fungal highways') strongly and frequently increases the dispersal range and abundance of water-dwelling organisms such as bacteria and protists across air pockets. Physical forces such as water movements, but also organisms and especially fungi form new microhabitats by altering the pore space architecture and distribution of soil minerals in the chip. We show that soil chips hold a large potential for studying in-situ microbial interactions and soil functions, and to interconnect field microbial ecology with laboratory experiments.