Abstract
The estuarine pipefish, Syngnathus watermeyeri, is a rare and elusive species facing a
population decline, with only two remaining populations located in the Bushmans and Kariega
estuaries located in the Eastern Cape, South Africa. To conserve this species, thorough
knowledge of its feeding ecology is required to simulate natural feeding in captive breeding.
This study aimed to assess the effectiveness of two DNA sequencing methods, metabarcoding
and metagenomics, in the dietary analysis of S. watermeyeri and a closely related congener S.
temminckii; the diets of these two pipefish were also compared to determine if there is any
indication of resource competition which may be a contributor to the decline of the estuarine
pipefish populations. Metabarcoding, using the cytochrome oxidase I gene region, and
metagenomics were assessed on their effectiveness as dietary assessment tools. It was found
that both pipefish species consume different prey items with a few instances of overlap but
there were not enough similarities to justify resource competition. Calanoid crustaceans make
up most of the estuarine pipefish diet with some mollusc veliger larvae and insects, whereas
caridean shrimp make up most of the S. temminckii diet. The effectiveness of both methods
could not conclusively be determined as both performed similarly and produced similar results
based on the identified prey classes; however, an incomplete reference database likely
contributed to the poor performance in some instances, where no matches were found and
some matches could only be identified to class level.