High-throughput sequencing reveals unexpected phytoplankton prey of an estuarine copepod

Selective feeding by copepods has important ecological implications such as food web length, nutrient limitation, and control of algal blooms. Traditional methods for investigating copepod feeding in natural waters (e.g. stable isotope and fatty acid tracers or microdissection) have low taxonomic specificity or significant biases. We used highthroughput genetic sequencing (HTS) to identify in situ the phytoplankton prey of Pseudodiaptomus forbesi (Copepoda: Calanoida) in the San Francisco Estuary. Amplicons of the 16s rRNA gene were sequenced on an Illumina MiSeq. Cyanobacteria were the most frequently detected prey taxon, a result not predicted due to expected low nutritional value. In contrast, prey taxa expected to have high nutritional value for copepods (diatoms and cryptophytes) were not detected as frequently as anticipated based on the expectations generated using traditional approaches. Although our data is unable to resolve this unexpected result, the apparent feeding outcome could reflect unexpected feeding patterns, trophic upgrading, or poorly understood artifacts of the method. HTS analysis of copepod predation will become an increasingly valuable method as it is further developed and integrated with traditional approaches.