Localization and Visualization of Microbial Community Structure and Activity in Soil Microhabitats

Abstract

In recent years, the localization and microvisualization of bacterial cells and their in situ activities in environmental samples have made tremendous progress. A future goal for methodological developments must be the application of these in situ techniques to the detection of fungal communities in the environment. On the one hand, the miniaturization and improvement of the sensitivity of enzymatic measurements and molecular biological techniques enabled new achievements in the synecological understanding of microbes on very small sample scales.On the other hand, the demonstration of in situ activities and the link to phylogenetically defined microbes using the FISH—MAR or TOF/SIMS techniques tshow promise in filling the gap between micrometer scale microbial ecology and the ecological understanding of processes on larger scales. These techniques provide rather robust and relatively rapid tools for the identification of the population structure and function of microbes in diverse environmental samples. However, for application to complex heterogenic samples, the spatial organization needs to be preserved in a refined way. The conservation of the three-dimensional structure in the micrometer range by the improvement of embedding techniques which still allow the fixation and hybridization procedure to occur at reliable precision would be very useful for further in depth studies in microbial ecology. In addition, the development of digital-image analysis tools to extract the three-dimensional spatial data from the investigated specimen would further support the in situ studies of organismic interactions.