Phytoplankton prey of an abundant estuarine copepod identified in situ using DNA metabarcoding

Abstract Plankton trophic interactions play a crucial role in ecosystem processes. Diet analysis using high-throughput sequencing methods such as metabarcoding can provide new insight where traditional methods have been limited. We used 16S ribosomal RNA gene metabarcoding to identify phytoplankton from the guts of the copepod Pseudodiaptomus forbesi and in seston from the Cache Slough Complex, a tidal freshwater reach of the San Francisco Estuary, California, USA. Cyanobacteria, assumed to have low nutritional value for copepods, were detected in all copepod samples and comprised the highest relative read abundance in metabarcoding results. Differential abundance analysis, used to compare representation of operational taxonomic units between copepod and seston samples, showed that two filamentous taxa (a streptophyte and a cyanobacterium) were most overrepresented in copepod samples, whereas cryptophytes and most ochropytes (diatoms and related taxa) were underrepresented in copepod samples. These findings could reflect unexpected feeding patterns or trophic upgrading. Understanding the capabilities and limitations of DNA metabarcoding is key to its use in diet analysis and integration with traditional approaches.