Open AccesseDNA extraction protocol for metagenomic studies in tropical soils
Author(s) -
Fabián Echeverría-Beirute,
Ingrid VarelaBenavides,
Jose Pablo Jiménez-Madrigal,
Milagro Carvajal-Chacon,
Tomás de Jesús Guzmán-Hernández
Publication year - 2021
Publication title -
biotechniques/biotechniques
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.617
H-Index - 131
eISSN - 1940-9818
pISSN - 0736-6205
DOI - 10.2144/btn-2021-0057
Subject(s) - metagenomics , soil water , protocol (science) , tropics , environmental dna , agroecosystem , environmental science , dna extraction , ecology , extraction (chemistry) , microorganism , tropical climate , biodiversity , sampling (signal processing) , biology , agriculture , bacteria , computer science , polymerase chain reaction , chemistry , medicine , genetics , alternative medicine , pathology , gene , filter (signal processing) , chromatography , computer vision
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.