Visualizing microbial community dynamics and metabolic activity within soil microbiomes

Understanding the basic biology that underpins soil microbiome interactions is required to predict the metaphenomic response to environmental shifts. A significant knowledge gap remains in how such changes affect microbial community dynamics and their metabolic landscape at microbially relevant spatial scale. Using a custom-built Soil Box system, here we demonstrate changes in microbial community growth and composition in different soil environments, contingent upon access to reservoirs of nutrient sources. The Soil Box, designed to press functionalized-glass slides against the soil surface at different depths from the top soil surface, emulates the probing depth of a common soil core. This enables determining both the spatial organization of the microbial communities that form on the slides and their metabolites by using confocal microscopy in combination with matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI). We found that increased adhesion of soil microbial biomass occurred on slides functionalized with chitin islands, with the seeding attachment event occurring as early as 2 h. The MALDI-MSI data showed a high abundance of bacterial-related lipid families on the chitin islands and low abundance on areas without chitin. Confocal microscopy measurements of these samples confirmed the increased growth of microbial biomass, and consumption of chitin during growth. The microbial growth and community dynamics were also sampled at different moisture regimes (i.e., 14%, 24%, and 34% of total soil weight). Fungal hyphal networks bridging different chitin islands over distances of 17 mm were observed only in the driest of conditions, indicating that such bridges may act as fungal highways during drought conditions. In all, through the use of multiple correlative imaging platforms, these results illustrate a system that provides unprecedented spatial information about interactions within soil microbial communities as a function of changing environments. We anticipate that this platform will be invaluable in probing specific intra- and inter-kingdom metabolic networks arising from a gradient of environmental stresses.