Using environmental DNA (eDNA) metabarcoding to assess aquatic plant communities

Description

Environmental DNA (eDNA) metabarcoding targets sequences with interspecific
variation that can be amplified using universal primers allowing simultaneous detection
of multiple species from environmental samples. I developed novel primers for three
barcodes commonly used to identify plant species, and compared amplification success
for aquatic plant DNA against pre-existing primers. Control eDNA samples of 45 plant
species showed that species-level identification was highest for novel matK and preexisting
ITS2 primers (42% each); remaining primers each identified between 24% and
33% of species. Novel matK, rbcL, and pre-existing ITS2 primers combined identified
88% of aquatic species. The novel matK primers identified the largest number of species
from eDNA collected from the Black River, Ontario; 21 aquatic plant species were
identified using all primers. This study showed that eDNA metabarcoding allows for
simultaneous detection of aquatic plants including invasive species and species-at-risk,
thereby providing a biodiversity assessment tool with a variety of applications.
Author Keywords: aquatic plants, biodiversity, bioinformatics, environmental DNA (eDNA), high-throughput sequencing, metabarcoding