Expanding toolbox for Microfluidic Soil Chips to study biophysicochemical interactions and microbial community dynamics

Soil is arguably the most complicated biomaterial on the planet. It is the largest terrestrial carbon sink, and the most species rich habitat on Earth. Microorganisms driving biogeochemical cycles live and interact in the soil’s intricate pore space labyrinth, but they are difficult to study in their realistic settings because of the soil’s opaqueness. Microfluidic Soil Chips allow us to study the impact of soil physical microstructures on microbes and vice versa, realistic microbial interactions, and microbial impact on biogeochemical cycles live and at the scale of their cells.

 

Chips can be tailored according to each research question, designing labyrinths or realistic image-based pore spaces, and also microchemical conditions can be varied in a controlled manner. We found that pore space geometry impacted the growth and degradation activity of the two microbial groups - bacteria and fungi - in synthetic communities in opposing ways: fungi were inhibited by increasing spatial complexity of the pore space, while bacteria and their enzymatic activity were enhanced in increasingly intricate pore spaces.

 

We can study bio-physical interactions throughout processes such as drying, freezing and soil aggregation, and can trace biochemical changes of cells and their environment, including metabolic rates of single fungal hyphae, via Raman microspectroscopy. Inoculating the chips with soil brings a large proportion of the natural microbial community into their inner microstructures, allowing us to study and manipulate interactions among species embedded in their complex food webs. We developed AI-based image analyses for soil bacteria, fungi and protists that aid counting, movement tracking and morphotyping biodiversity, which can complement molecular biodiversity measurements. The soil chips enable us to conduct complex ecological studies, such as testing the effect of predator removal on community composition and bacterial and fungal population and necromass dynamics.

 

Beyond the scientific potential, the image footage from soil chips can also bring soil ecosystems closer to people,aiming to increase appreciation of their beauty, and engagement in soil health conservation.