eDNA Extraction Protocol for Metagenomic Studies in Tropical Soils

Abstract

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.

Coupling remote sensing and eDNA to monitor environmental impact: A pilot to quantify the environmental benefits of sustainable agriculture in the Brazilian Amazon

“…This limited the viable approaches for sample preservation, in contrast to other studies using soil in Amazonia where either -40°C freezer storage or ethanol was available [e.g. 155 ], or samples could be analyzed hours after collection [ 156 ].…”

“…To avoid sample contamination and ensure consistency across samples, a protocol was followed during sampling that included the use of disposable sampling materials and gloves and samples were labeled and individually packed according to plots and sites to ensure no cross-contamination occurred [detail of methods see S2 File ; 83 , 84 ]. Following collection, soil samples were stored with silica desiccant bags (minimum of 25g per sample) protected from heat and sunlight to prevent DNA degradation, and later transported to the laboratory facilities for further laboratory analysis.…”

Improving the efficiency of DNA extraction from iron incrustations and oilfield-produced water

“…DNA extraction from some environmental samples can be challenging but crucial in terms of performance, sustainability, and economy. Ample studies have been performed evaluating the efficacy of DNA extraction methods from water 29 , animal guts 30 , 31 , soil 21 , 32 , 33 , rock and coral 14 , 34 , freshwater and marine sediments 35 , 36 , and found variation in microbial communities. However, to our best knowledge, no study has yet been performed on evaluating and optimising DNA extraction from iron incrustations and produced water from oilfields.…”

Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions

“…DNA extraction should also be conducted carefully to limit any impurities from the host DNA. In previous studies, specific protocols were developed for different samples such as human fecal samples, tropical soils, and plant tissues [29][30][31]. Meanwhile, commercial kits for metagenomics have also been developed such as FastDNA™Spin Kit for Soil (MP Biomedicals, Irvine, CA, USA), Favor-Prep™ Soil DNA Isolation Mini Kit (Favorgen Biotech, Taiwan, China), MagAttract Pow-erSoil DNA KF Kit (Qiagen, Redwood, CA, USA), PureLink MicrobiomeTM Purification Kit (ThermoFisher Scientific, Waltham, MA, USA), and ZymoBIOMICS 96 Magbead DNA Kit (ZymoBIOMICS, Irvine, CA, USA).…”