Dietary specialisation in a Critically Endangered pipefish revealed by faecal eDNA metabarcoding

The estuarine pipefish, Syngnathus watermeyeri, is one of the rarest animals in Africa and occurs in only two South African estuaries. The species was declared provisionally extinct in 1994, but was later rediscovered and is currently listed by the IUCN as Critically Endangered. A conservation programme was launched in 2017, with the re-introduction of captive-bred individuals into estuaries where this species was recorded historically was the main aims. Successful captive breeding requires knowledge of the species9 dietary requirements. In the present study, we used metabarcoding of faecal DNA to identify prey species consumed by wild-captured S. watermeyeri from one of the two surviving populations. We compared the diet of the estuarine pipefish with that of the longsnout pipefish, S. temminckii, in the same estuary, to determine whether these two species compete for the same prey items. Both species occupy similar estuarine habitats, but S. temminckii has a much wider distribution and also occurs in the marine environment. Our results show that even though both pipefish species prey on three major invertebrate classes (Gastropoda, Malacostraca and Maxillopoda), the relative proportions differ. Syngnathus watermeyeri primarily targets Maxillopoda, with a single species of calanoid copepod constituting >95% of the Amplicon Sequence Variants (ASVs) identified from its faecal DNA, whereas the diet of S. temminckii mostly comprises snail and decapod crustacean larvae. Our finding supports the hypothesis that population declines and localised extirpations of S. watermeyeri during previous decades may have been the result of reductions in the abundance of calanoid copepods. Calanoids rely on freshwater pulses to thrive, but such events have become rare in the two estuaries inhabited by S. watermeyeri due to excessive freshwater abstraction for urban and agricultural use.