DNA Barcoding of San Francisco Estuary Zooplankton

The base of aquatic food webs is rife with complex, microscopic predator-prey relationships. The San Francisco Estuary, which has been heavily impacted by human activities, provides critical habitats to many native and declining species. Ongoing research in the Estuary has utilized high-throughput DNA sequencing to investigate the diet of the threatened longfin smelt (Spirinchus thaleichthyes) to better inform habitat restoration efforts that aim to benefit this native species. Results from this ongoing research found many DNA sequences in the guts of the fishes that could not be identified due to gaps in the NCBI Genbank database. This project aimed to contribute relevant new sequences to the database, targeting cyclopoid copepods, harpacticoid copepods, insect larvae, and annelid worms. Organisms were identified morphologically from zooplankton samples collected concurrently with the fish. Their DNA was extracted and sequenced, targeting the mitochondrial cytochrome c oxidase subunit I gene (mtCOI). Of the cyclopoid copepods not yet in the genetic database, the mtCOI gene was successfully sequenced for Limnoithona tetraspina. New sequences were also obtained for two species of cyclopoid copepod and two species of harpacticoid copepod, which will require further morphological evaluation to confirm their identities. Morphological identification was confirmed with DNA for two cyclopoids present in the database: Mesocyclops pehpeiensis and Acanthocyclops americanus. Additional DNA sequences and voucher photos were obtained for six putative species of annelid worms and one insect. These new species contribute to global efforts in DNA barcoding aquatic species and will be used in the San Francisco Estuary to inform longfin smelt conservation efforts.