Physical processes affecting microbial habitats and activity in unsaturated agricultural soils

experimental methods for quantifying effects of water content and other dynamic environmental factors on bacterial growth in partially-saturated soils. Towards this end we reviewed critically the relevant scientific literature and performed theoretical and experimental studies of bacterial growth and activity in modeled, idealized and real unsaturated soils. The natural wetting-drying cycles common to agricultural soils affect water content and liquid organization resulting in fragmentation of aquatic habitats and limit hydraulic connections. Consequently, substrate diffusion pathways to soil microbial communities become limiting and reduce nutrient fluxes, microbial growth, and mobility. Key elements that govern the extent and manifestation of such ubiquitous interactions include characteristics of diffusion pathways and pore space, the timing, duration, and extent of environmental perturbations, the nature of microbiological adjustments (short-term and longterm), and spatial distribution and properties of EPS clusters (microcolonies). Of these key elements we have chosen to focus on a manageable subset namely on modeling microbial growth and coexistence on simple rough surfaces, and experiments on bacterial growth in variably saturated sand samples and columns. Our extensive review paper providing a definitive “snap-shot” of present scientific understanding of microbial behavior in unsaturated soils revealed a lack of modeling tools that are essential for enhanced predictability of microbial processes in soils. We therefore embarked on two pronged approach of development of simple microbial growth models based on diffusion-reaction principles to incorporate key controls for microbial activity in soils such as diffusion coefficients and temporal variations in soil water content (and related substrate diffusion rates), and development of new methodologies in support of experiments on microbial growth in simple and observable porous media under controlled water status conditions. Experimental efforts led to a series of microbial growth experiments in granular media under variable saturation and ambient conditions, and introduction of atomic force microscopy (AFM) and confocal scanning laser microscopy (CSLM) to study cell size, morphology and multi-cell arrangement at a high resolution from growth experiments in various porous media. The modeling efforts elucidated important links between unsaturated conditions and microbial coexistence which is believed to support the unparallel diversity found in soils. We examined the role of spatial and temporal variation in hydration conditions (such as exist in agricultural soils) on local growth rates and on interactions between two competing microbial species. Interestingly, the complexity of soil spaces and aquatic niches are necessary for supporting a rich microbial diversity and the wide array of microbial functions in unsaturated soils. This project supported collaboration between soil physicists and soil microbiologist that is absolutely essential for making progress in both disciplines. It provided a few basic tools (models, parameterization) for guiding future experiments and for gathering key information necessary for prediction of biological processes in agricultural soils. The project sparked a series of ongoing studies (at DTU and EPFL and in the ARO) into effects of soil hydration dynamics on microbial survival strategy under short term and prolonged desiccation (important for general scientific and agricultural applications).