Feeding Habits and Novel Prey of Larval Fishes in the San Francisco Estuary as Revealed by Gut DNA Metabarcoding

Food limitation is a likely constraint on the abundance of several species of fish in the San Francisco Estuary, California, and is particularly important for survival through early development. Here, we used gut DNA metabarcoding analysis on the guts of 228 threatened native longfin smelt (Spirinchus thaleichthys) and abundant co-occurring native Pacific herring (Clupea palasii) to describe the diversity and relative abundance of prey important to these species in greater detail and greater taxonomic resolution than was previously possible. Larval fishes and zooplankton were collected in shoals, tidal marshes, and channels during February through June 2017. We found differences in the overall DNA-prey assemblages between smelt and herring as indicated by NMDS analysis. Additional DNA barcoding of potential prey not yet in public databases revealed that herring commonly consumed the introduced cyclopoid copepod Limnoithona tetraspina in shoal and tidal marsh habitats while the smelt did not seem to consume this species despite its relatively high abundance. Results also suggest the consumption of herring eggs by smelt larvae was common in parts of San Pablo Bay and there was occasional consumption of smelt eggs by herring larvae. Finally, there were many genetic groups in the diet that could not be classified to a reliable level based on existing databases, which highlights the need for more work to be done generating DNA barcode databases for local species as eDNA and community metabarcoding continues to be used for biomonitoring and management. Ultimately, our work will identify DNA of prey in the diet that may be indicative of feeding in different areas of the Estuary and inform management actions intended to improve the availability of important food items.