eDNA metabarcoding vs metagenomics: an assessment of dietary competition in two estuarine pipefishes

Abstract

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 species’ 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.

Distribution and density of the Critically Endangered estuarine pipefish across its range – implications for conservation

“…Different hypotheses have been developed in the past to explain the reason for the threatened status of the estuarine pipefish. These include adverse impacts from a loss of freshwater inflow into its estuarine habitats (Vorwerk, Froneman & Paterson, 2007; Whitfield et al, 2017) combined with increased vulnerability owing to prey specificity (Ntshudisane et al, 2021). Data generated by this study provide new insights into the status of the estuarine pipefish and pertinent threats to its survival, which will be discussed in relation to these existing hypotheses.…”

“…It has been suggested that S. watermeyeri is a specialist feeder that depends on specific prey, in particular the copepod Pseudodiaptomus hessei , for its survival (Whitfield et al, 2017; Ntshudisane et al, 2021). Based on the assumption that S. watermeyeri is a specialist feeder, the lack of freshwater inflow into the Kariega and Bushmans estuaries has been identified as one of the leading causes for the rarity of this species (Whitfield & Ter Morshuizen, 1992; Whitfield & Bruton, 1996; Whitfield et al, 2017) owing to the adverse effects on invertebrate communities caused by a decrease in freshwater pulses (Froneman & Vorwerk, 2013).…”

Life cycles and challenges for fish species that breed in South African estuaries

“…The early juveniles are released into littoral macrophyte beds (Figure 1) and some may be lost to the sea during ebb tides. The estuarine pipefish feeds mainly on zooplankton (Serite et al, 2023), especially the copepod Pseudodiaptomus hessei .…”

Environmental DNA: Enhancing Species Detection and Study Comparability with Synthetic DNA Tracers

“…Although individual high-diversity genes or genomic regions may differ between studies, 2 metabarcoding is now being applied to detect and analyze diverse species across a wide range of ecological contexts 17 . By contrast with micro-organismal studies where it is the norm, direct "shotgun" sequencing of eDNA samples for macro-organismal analysis is still at an exploratory stage 21 .…”