Metabarcoding for rapidly identifying Phytoseiidae predatory mite species

Abstract: The identification of Phytoseiidae mites is mainly based on morphological characters. Sometimes, this identification is cumbersome because the characters that allow separating species are difficult to observe and/or their diagnostic value is not totally accepted. Recently, molecular markers were developed for a barcoding purpose. This approach successfully differentiates closely related species where morphology fails and provides support for testing the validity of morphological characters. However, barcoding implies that each specimen is sequenced individually hence, each mite from a sample should be analysed individually, with obvious consequences for cost and working time. This study aims to determine how high-throughput sequencing could be used to identify multiple species of Phytoseiidae mites in environmental samples. Several females from five species important for biological control (Kampimodromus aberrans, Typhlodromus exhilaratus, T. phialatus, Euseius gallicus, E. stipulatus) were mixed in a single tube. DNA extraction of all mites was carried out, as well as PCR using the 12S rRNA fragment. This procedure proved efficient for identifying Phytoseiidae species. Three technical replicates were carried out for a total of 1.2 millions of illumina reads. All the species initially present in the sample were retrieved using BLAST against our local taxonomy database. It is however impossible at the time being to relate the number of reads obtained to the proportion of each species in the sample analysed as multiple biases would affect the interpretation. This methodological advances open new doors for rapid identification of predators and potentially give access to food webs, identifying prey species eaten by the predators.