Discussion

The pragmatic approach applied here facilitated prey studies of small-sized copepods despite an overabundance of non-informative consumer DNA. By scaling up the sequencing to offset losses in consumer reads, we avoided using expensive and potentially biased blocking primers. While the pilot sequencing resulted in approximating the full diversity of our samples, deeper sequencing reduced the zOTU discovery rate from 10.3 in the pilot to 3.6 and 4.5 new prey zOTUs per 1000 reads in the full pilot and full datasets, respectively. Our results from small-sized marine copepods, which are known to consume a wide diversity of prey, thus suggest that upscaled brute force sequencing is a suitable general method for determining the prey of small consumers, regardless of a priori access to the consumer sequence or possibility of dissection.