Studying soil microbial diversity and their ecological interactions via Soil Chips

Soil microbial biodiversity studies commonly rely on molecular datasets from microbial communities extracted from their natural contexts. While immensely important for many research questions, this can lead to artefacts such as falsely interpreting interactions where organisms were strongly spatially separated in the soil habitat, and difficulties in differentiating active from passive or dormant organisms.

We developed a way to overcome some of the problems of the extraction steps: Microfluidic soil chips, transparent micromodels of the soil pore space, can be incubated in, or inoculated with, soil, from which the microorganisms move into, grow into, or are transported into it by water streaming. This allows for direct microscopic examination of bacteria, fungi, and protist communities under closer-to natural conditions. AI-aided image analysis helps to quantify population sizes and gives information on the community’s morphodiversity: Changes in cellular size and shapes, and the spatial distribution of the cells including group formation up to simple biofilms. Direct observations can be made on the growth and interactions of the organisms, with each other and with their immediate environment.

We found differences in microbial communities over large geographical patterns (Arctic via temperate to tropical soil bacteria) in bacterial cell sizes and their microspatial distribution. Morphodiversity of the bacterial community were also found to change across microscale soil pore space characteristics, where cells were larger in more connected microhabitats compared to less connected and more tortuous ones. Comparing the molecular microbial biodiversity in chips to the microbial biodiversity of the adjacent soil via metabarcoding, we found in chips an amplicon sequence variant richness of around 30% of the adjacent soil, indicating a reduced but still relevantly diverse microbial community. Also, fungal and protist communities can be studied in soil chips, especially valuable for research questions of interactions such as interactions with the pore space, predation, behavior, and direct reactions to experimental factors such as a pollutant.

We argue that soil chips are an intriguing complement to molecular techniques to study soil microbial diversity, and will help us to better understand soil microbial activity and interactions with each other and their environment.