A novel method for characterizing the microscale 3D spatial distribution of bacteria in soil

Knowledge of the microscale spatial distribution of bacteria in soil would improve our understanding of microbial ecology and function. A specific 3D method has been developed to characterize the spatial distribution of bacterial microhabitats in soil. The method combines a specific microsampling strategy with a statistical data analysis. The sampling strategy involves several different unit volumes (minimum sample side: length of 50 μm) subsequently tested for the presence or absence of the targeted microorganisms. The statistical analysis is based on the comparison of experimental sampling data with data expected from the limited sampling of numerous theoretical spatial distributions. Since the exact spatial pattern of the zones colonized by bacteria requires the spatial coordinates of the samples, this approach only identifies possible distributions. Distributions are characterized by descriptors relevant to soil, such as the average size of colonized patches and their average number g−1 of soil. These descriptors provide the basis for comparing spatial patterns. Computer simulations confirmed the methodʹs ability to distinguish between different spatial patterns. The spatial patterns in soil of two bacterial types, NH4+ oxidizers and 2,4-D degraders, were studied independently in repacked soil columns percolated with solutions containing either NH4+ or 2,4-D. The spatial analysis method distinguished between the two microbial spatial distributions (P≤0.025). Thus, this method constitutes a useful tool for identifying factors regulating bacterial spatial distributions in soil at the microscale.