Environmental DNA Metabarcoding of a Seagrass Meadow in Vostok Bay (Peter the Great Bay, Sea of Japan): A COI Snapshot of Coastal Biodiversity and Its Limitations

Temperate seagrass meadows are foundation habitats, but their communities are hard to census. Here, I provide a first COI environmental DNA (eDNA) metabarcoding snapshot from seawater at a Zostera marina meadow in the Vostok Bay marine reserve (Peter the Great Bay, Sea of Japan). In September 2021, eDNA from two 900 mL replicates of water were filtered, isolated, amplified for the 313 bp COI fragment with dual-index PCR (multiple replicates), and sequenced on Illumina NovaSeq. I obtained 53,666 reads for 176 operational taxonomic units (OTUs). Eukaryota dominated (154 OTUs; 93.7% of reads), while 22 bacterial OTUs comprised 6.3%. The assemblage was largely photosynthetic microeukaryotes, especially diatoms (61 OTUs; 49% of reads), consistent with late-summer productivity. Metazoan detections included a strong signal of the phoronid Phoronopsis harmeri (7511 reads; 14%), diverse invertebrates, and few vertebrate reads (0.5%), indicating limited fish sensitivity of universal COI assays. One abundant OTU was initially assigned to the giant kelp Macrocystis pyrifera but was rejected after additional BLAST and phylogenetic checks, illustrating database-driven misassignments. COI eDNA offers rapid, low-impact screening for marine protected area monitoring, but robust use requires seasonal replication, multi-marker assays, and a curated regional reference library.