Metabarcoding hyperdiverse marine communities in temperate kelp forests:
an experimental approach to inform future studies.
Classical taxonomic approaches to quantifying biodiversity can be
notoriously laborious and restrictive. Instead, molecular metabarcoding
is emerging as a rapid, high-throughput and cost-effective tool to
catalogue biodiversity. Despite the appeal of metabarcoding however,
methodological and procedural biases must be understood before robust
biodiversity inferences can be made. Here, we use CO1 metabarcoding to
characterize marine eukaryote communities associated with the holdfasts
of Ecklonia radiata, the dominant eco-engineering kelp of temperate New
Zealand and Australia. To establish a standardized and reproducible
community metabarcoding protocol, we examined the influence of different
sample preparation, laboratory and bioinformatic steps on inferences of
species richness and composition for kelp-holdfast communities.
Specifically, we examined: the effect of fractioning the community into
different size classes, the replicability of results across DNA
extractions, PCR reactions, and sequencing. Overall, our approach
identified 18 marine eukaryote Phyla in the holdfast communities. We
found that size fractioning the sample before DNA extraction enabled
detection of a greater diversity of taxa, especially smaller organisms.
When compared with traditional morphology-based inventories of
kelp-holdfast biodiversity, we found that although the taxonomic
precision of our metabarcoding approach at the species and genus level
was limited by the availability of reference sequences in public
repositories, we recovered a greater number of operational taxonomic
units, and a greater taxonomic breadth of organisms than morphological
surveys. Based on our findings, we provide methodological guidelines for
the use of metabarcoding as a tool for surveying and monitoring the
hyperdiverse species assemblages associated with kelp-holdfasts.