Feeding habits and novel prey of larval fishes in the northern San Francisco Estuary

Food limitation can dampen survival and growth of fish during early development. To investigate prey diversity important to the planktivorous larval longfin smelt (Spirinchus thaleichthys) and Pacific herring (Clupea pallasii) from the San Francisco Estuary, we used DNA metabarcoding analysis of the cytochrome oxidase I gene on the guts of these fishes and on environmental zooplankton samples. Differential abundance analysis suggested that both species consumed the most abundant zooplankton at a lower rate than their availability in the environment. Both fish consumed the prey that were commonly available and relatively abundant. Prey taxa substantially overlapped between the two species (Schoeners index = 0.66), and alpha diversity analysis suggested high variability in the content of individual guts. Abundant prey taxa in both fish species included the copepods Eurytemora carolleeae, Acanthocyclops americanus, and A. robustus; the Acanthocyclops spp. are difficult to identify morphologically. A few uncommon prey in the diets hint at variable feeding strategies, such as herring (presumably egg) DNA in the longfin smelt diets, which suggests feeding near substrates. Herring consumed the small (<0.5 mm) copepod Limnoithona tetraspina more frequently (30%) than did smelt (2%), possibly indicating differences in foraging behavior or sensory abilities. Among the unexpected prey found in the diets was the cnidarian Hydra oligactis, the polychaete Dasybranchus sp., and a newly identified species Mesocyclops pehpeiensis. "Unknown" DNA was in 56% of longfin smelt diets and 57% of herring diets, and made up 17% and 21% of the relative read abundance in the two species, respectively. Our results suggest that these two fishes, which overlap in nursery habitat, also largely overlap in food resources necessary for larval survival.