eDNA extraction protocol for metagenomic studies in tropical soils

The lack of knowledge about biological communities residing in soils, especially those in tropical regions, represents a constraint to management practices to take advantage of the ecological services provided by soil microbiota to agroecosystems. One of the complexities derived from describing biological diversity in such tropical conditions comes from the methods used to isolate microorganisms without altering the composition of the sample. The goal of this study was to establish a protocol for adequate soil sampling and environmental DNA extraction from a tropical region in Costa Rica. We present an up-to-date protocol optimized for tropical soils which improves sevenfold the amount of DNA extracted without significantly affecting the 260/280 and 260/230 ratios compared with commercially available kits and standard protocols. METHOD SUMMARY Soils from cultivated pineapple fields and adjacent forests were sampled and stored in cold and 96% alcohol to study and optimize an eDNA extraction protocol. Three protocols were used and one later modified based on higher DNA quantity and quality.