Roles of soil pores in determining water retention and microbial dynamics

Soil pore provides an essential habitat for microbial communities to participate in various biogeochemical processes. The complex pore spaces, which are defined by the arrangement of particles of varying sizes, govern the distribution of water for microbial dispersal and movement and microbial interaction with one another, such as bacterial cell-to-cell and bacterium-virus interactions. This research focused on exploring how soil pores influence soil water retention and bacterial interactions and quantify the spatial distribution of bacteria and viruses in fine-scale of soil pores. Using a mathematical model, this study simulated a soil water retention curve based on the relationship between soil pores and water retention characteristics. A fractional bulk density (FBD) concept was proposed in the model to estimate pore water content under varying matric potential. Comparing the estimated results of the water retention curve with the measured data, the model behaved overall well. The proposed model provides an easy way to evaluate the impacts of soil pores on water conservation in soils. Based on the concept in the FBD model, sand media with different pore sizes coupled with different surface properties were used to evaluate conjugation-based bacterial cell-to-cell interactions. The presence of sand increased conjugation frequency compared to sand-free controls. The frequencies were a function of pore size and bacterial adhesion on sand surfaces with smaller pores and more adhesion lowering bacterial conjugation frequency. Collision of bacteria in pore spaces promoted their interactions, while limited motility of bacteria trapped in smaller pores or adhered to sand surfaces reduced the interactions. To further investigate microbial activity in fine-scale pores, the spatial distribution of bacteria and viruses in soil was characterized by using advanced small-angle X-ray/neutron scattering techniques. Bacteria and viruses have their optimal strategies for survival in soil pores in response to soil harsh environments. Bacteria preferred to colonize in the pores greatly close to their sizes and viruses aggregated to prevent penetrating into nanopores. These observations highlighted soil pore-associated water and microbial dynamics and advance the understanding of the functions of soil pores in soil ecosystems.