Investigating the effects of soil microstructures on bacterial growth via microfluidic channels and an agent-based model.

Soil is a suitable habitat for various microorganisms. These soil microorganisms establish complex social relationships and build biogeochemical cycles, such as carbon or nitrogen cycles, which synthesize plant nutrients and greenhouse gases. Clarifying microbial activities inside the soil is essential for agricultural and environmental fields. One of critical factors influencing bacterial activity in soil is the physical structure of the soil built by soil aggregates. The size distribution of soil aggregates widely ranges from µm to mm and creates pores with various sizes that act as pathways for air, water, and nutrients and affect microbial activities. Although it is known that pore size in soil is important for bacterial activity, how the pore size distribution affects bacterial activity remains unclear. The pore size distribution is considered to affect the movement of bacteria within the soil as well as that of air, water, and nutrients. Therefore, further investigation into the relationship between the size distribution of micrometer-sized pores in soil and the bacterial movement in micrometer space is required to understand bacterial activity in soil. In this study, we investigated the dependence of fractally distributed pore size distributions (from micrometers to millimeters) on bacterial activity, especially bacterial growth, using a polydimethylsiloxane culture device and numerical simulations. We fabricated a culture device with 2 μm depth with the pillars arranged fractally or periodically to represent soil particles and pore size distributions. Escherichia coli was cultured for 20 h in a culture device, and the results showed that final amount of E. coli was significantly higher in the device with the pillars arranged fractally than in the one with pillars arranged in an array. Bacterial growth was simulated in a two-dimensional space with pillars. The results also showed clear relationships among bacterial growth, movement, and pillar arrangement. Our findings provide insights into microbial activity inside complex physical structures such as soils.