Revealing the invisible contributors to the diets of larval longfin smelt and striped bass in the San Francisco Estuary

Start/End: April, 2017 to March, 2019

Pelagic fish throughout the San Francisco estuary appear to be facing a food shortage in recent decades. Understanding the essential diets and food web interactions of threatened, native longfin smelt and a co-occurring abundant species can help managers develop more effective plans for the restoration of food webs and to better support fish populations.

The conventional method of identifying prey relies on morphological analysis of partially digested organisms extracted from the guts of fish. To supplement, expand, and improve upon existing research, the researcher will use molecular techniques to identify the species composition of the fish diets in greater detail, greater taxonomic resolution, and perhaps identify zooplankton prey not previously identified using traditional methods. Additionally, this research will allow for a direct comparison of morphological diet studies to DNA-based methods.

The goal of this study is to generate information about the zooplankton prey important to larval and juvenile longfin smelt and an abundant co-occurring species such as the pacific herring, and inform habitat restoration efforts in the San Francisco Estuary. Specific objectives include:

  1. characterizing the species composition of the potential fish-larval zooplankton prey community using high-throughput DNA-based analysis, and
  2. measuring the difference in composition and frequency of different prey across habitats.

This information will help inform actions to develop and implement more effective plans for the restoration of food webs throughout the Delta. Furthermore, understanding vital prey can be used to understand how shifts in species abundance, new organism introduction, and habitat shifts associated with climate change would affect survival of the fishes.