Comparing High Throughput Sequencing and Real Time qPCR for Characterizing Entomopathogenic Nematode Biogeography

Entomopathogenic nematodes (EPNs) are widely distributed in soils across all continents except Antarctica. Assessing the EPN community structure in an ecoregion can help reveal their biological control potential against important crop pests. Common methods for detecting EPNs in soil samples include baiting with sentinel insects, direct observation of extracted nematodes, or use of species-specific primer-probe combinations using qPCR. Less well studied is the use of high throughput sequencing (HTS), which has tremendous potential to characterize soil communities of EPNs and natural enemies of EPNs. Here, for the first time, we compared qPCR and HTS to characterize EPN food webs. The frequency and abundance of 10 EPN species and 13 organisms associated with EPNs from 50 orchard and natural area sites in two ecoregions of Portugal were evaluated using qPCR tools, and results were published in 2019. We applied a HTS approach to analyze frozen DNA samples from 36 sites in that study. Universal primers targeting ITS1 were used for nematode detection.