Embracing the structural framework of soil in microbiological and ecological research

Soil is a complex system with a high degree of physical, chemical, and biological heterogeneity. Soil structure is organized into entangled pore networks that provide an immense surface area and are partially filled with gases and aqueous solutions. This heterogeneous landscape houses a multitude of active and inactive organisms of which soil bacteria and fungi are considered the driving forces of nutrient cycling and biogeochemical processes. Standard analyses such as soil respiration are meaningful measures to estimate processes on a meso- and macroscale while the biological agents whose actions we measure are mainly to be found on the microscale. Yet, our understanding of microbial living conditions in soil and their consequences for activity, growth, and turnover is severely limited. In this presentation I will focus on a microbial perspective and present data from various experiments where soil microbial identity and/or activity were investigated while acknowledging spatial aspects of their microenvironments. I will provide an updated view on spatial distribution of microbial communities within soils, including evidence that suggests that the density of bacteria in soils has likely been underestimated by orders of magnitudes for decades. Microbial density arguably is a major determinant of cell-to-cell interactions, and thus many processes involved in microbial nutrient cycling that we measure on a larger scale. I will further argue to embrace soil heterogeneity rather than minimizing it, for example by using intact soil cores instead of sieved soils for stable isotope labelling experiments. I will present data on in situ bacterial and fungal growth which suggests that preserving soil physical architecture while investigating microbial parameters could bring experimental measurements significantly closer to field conditions, while also opening new avenues to improve our understanding of spatial aspects of soil microbiology.