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.