Newly designed primers to explore diversity of Heterolobosea by High-Throughput Sequencing

Diversity of Heterolobosea (Excavata) in environments is poorly understood despite their ecological occurrence and health-associated risk. To overcome the limits of the traditional morpho-taxonomy-based biomonitoring, we constructed a primer database listing previously completed with newly designed specific primer pairs that have been evaluated for Heterolobosea 18S rRNA metabarcoding. In silico taxonomy performance against the current SILVA SSU database allowed the selection of primer pairs that were next evaluated on reference culture amoebal strains. Two primer pairs were retained for monitoring diversity of Heterolobosea in freshwater environments.Naegleria was by far the most represented genus in freshwater and in sediments from the 4 rivers. In addition, results showed that one of the newly designed primer pair allowed an accurate identification at species level