Comparing eDNA metabarcoding primers (12S and 18S) for assessing riparian biodiversity

This title will be presented on Friday, December 15, 2023 at 10.55-11.05 GMT+7

Abstract

This title will be presented on Friday, December 15, 2023 at 10.55-11.05 GMT+7

The use of environmental DNA metabarcoding for biodiversity evaluations in terrestrial and aquatic populations is growing. De novo primer design or the selection of a suitable primer set from the dozens of already published primer sets will determine the efficacy and result of these efforts. However, not much research has explicitly compared the effectiveness of various metabarcoding primers in riparian systems. Here, we assess two widely used primer sets for rRNA barcoding gene amplification and compare their efficacy with sediment samples taken from riparian areas in the highly biodiverse Ciliwung River. This study amplified the target region of 18S using 1391f and Eukbr primers and 12S-V5 set primers for the 12S target region. We identified a non-comparable number of species and non-similarly high Shannon's diversity values for the 12S and 18S primer sets using a conservative 99% similarity threshold for species-level designations (36 and 264 species, respectively). Furthermore, we found 29 genera, 23 families, 17 orders, 3 classes, and 1 phylum in the 12S target region. Meanwhile, 209 genera, 136 families, 86 orders, 47 classes, and 18 phyla were discovered in the 18S target region. Unfortunately, the 12S-V5 primer set only detected the classes Actinopterygii, Aves, and Mammalia (phylum Chordata). Meanwhile, 1391f and Eukbr primers (target region 18S) also found the same class and complemented the findings, especially plankton and other microorganisms that were not detected with the 12S-V5 primer set. These findings emphasize the importance of utilizing multiple primer sets and primers that target various genomic regions. Moreover, our results suggest that amplification with the target region of 18S using 1391f and Eukbr primers may be the best choice compared to the 12S-V5 primer set for detecting riparian biodiversity.