Speaker
Description
Nematodes are abundant and diverse in soil, and they can influence microbial community composition, plant performance, and nutrient cycling, serving as vital bioindicators for soil ecology and health. While metabarcoding techniques have become highly standardized in the identification of microbial (i.e., bacterial and fungal) communities, similar techniques are still under development for soil animals. As metabarcoding techniques become increasingly popular for characterizing soil animals, establishing protocols that are adapted to larger organisms is necessary. To improve the quality of nematode metabarcoding data, we explored the effect of various DNA extraction procedures adapted to larger soil samples on soil nematode biodiversity estimates.
We extracted total DNA from soil samples and sequenced a nematode-specific 18S rRNA primer set (Nemf/18Sr2b; N1F/18Sr2b), and a general 18S rRNA primer set as reference (1391f/EukBr) with an Illumina MiSeq. We tested different DNA extraction methods for large soil samples (10 g), focusing on the effectiveness of different lysis buffers, bead beating durations, and enzymatic digestion applications. Sequencing data obtained from different protocols were filtered, trimmed, merged using the DADA2 pipeline, followed by taxonomy assignment using the PR2 reference database.
Our results highlight varying extraction efficiencies from each technique, and their effects on soil nematode alpha and beta diversity assessments. Protocols employing 1% SDS lysis buffer with longer bead beating times yielded the highest concentration of DNA extracts. This study serves as a guide for the selection of DNA extraction methods for DNA-based studies of soil fauna.
| Status Group | Doctoral Researcher |
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