Validating a Liquid Soil Model to Explore Soil Microbial Community Dynamics

Soil microbial communities (SMCs) play an important role in multiple ecological processes, such as plant growth and carbon cycling. However, modeling SMCs in the lab has remained a challenge, because of vast number of unculturable species in soil. Performing assays in solid soil is laborious and time-consuming. Further, solid soil sampling is not amenable to adaptation to high-throughput sequencing platforms. We developed a liquid extraction model, Solubilized Extract of Soil Organic Materia (SESOM), for direct soil metagenomic analysis. We collected DNA from solid soil and liquid-extracted samples and applied 16S rRNA amplicon sequencing to observe the variations of microbe species and abundance in soil communities until after 28 days’ extraction. Based on the bacteria taxonomy analysis, Alphaproteobacteria, Bacteroidia, Actinobacteria and Gammaproteobacteria are the dominant bacterial classes in all the samples. In addition, the solid SMCs composition was maintained in liquid extraction samples over a period of up to 28 days. SMCs composition in liquid samples represents the starting microbiome in solid samples. The dynamics of solid and liquid samples is further observed by principal coordinate analysis (PCoA) with weighted UniFrac distance analysis of SMCs. A clear separation of two different types of soil in the PCoA plot and different clusters reflect the change of SMC over time. The results promisingly implied that liquid soil extracts could be a good replacement of solid samples to explore and exploit the soil microbial communities for soil-related studies as a more convenient, efficient laboratory model.