eDNA extraction protocol for metagenomic studies in tropical soils
Fabián Echeverría-Beirute,
Ingrid Varela-Benavides,
Jose P Jiménez-Madrigal,
Milagro Carvajal-Chacon,
Tomás Guzmán-Hernández
Affiliations
Fabián Echeverría-Beirute
1Instituto Tecnológico de Costa Rica, Campus Tecnológico Local San Carlos, DOCINADE, Apartado 223-21001, Alajuela, San Carlos, Ciudad Quesada, Costa Rica
Ingrid Varela-Benavides
1Instituto Tecnológico de Costa Rica, Campus Tecnológico Local San Carlos, DOCINADE, Apartado 223-21001, Alajuela, San Carlos, Ciudad Quesada, Costa Rica
Jose P Jiménez-Madrigal
1Instituto Tecnológico de Costa Rica, Campus Tecnológico Local San Carlos, DOCINADE, Apartado 223-21001, Alajuela, San Carlos, Ciudad Quesada, Costa Rica
Milagro Carvajal-Chacon
2Instituto Tecnológico de Costa Rica, Campus Tecnológico Local San Carlos, Escuela de Agronomía, Apartado 223-21001, Alajuela, San Carlos, Ciudad Quesada, Costa Rica
Tomás Guzmán-Hernández
1Instituto Tecnológico de Costa Rica, Campus Tecnológico Local San Carlos, DOCINADE, Apartado 223-21001, Alajuela, San Carlos, Ciudad Quesada, Costa Rica
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.