MetaBARFcoding: DNA‐barcoding of regurgitated prey yields insights into Christmas shearwater (Puffinus nativitatis) foraging ecology at Hōlanikū (Kure Atoll), Hawaiʻi

Abstract

Morphological identification of digested prey remains from a generalist predator can be challenging, especially when attempting to match degraded remains to taxonomic keys. DNA techniques, whereby prey is sequenced and matched to large public nucleotide sequence databases, are increasingly being used to augment morphological identification. We used “metaBARFcoding” (DNA metabarcoding) to target a region of the cytochrome c oxidase subunit I (COI) mitochondrial gene to identify prey in highly digested regurgitations from Christmas shearwaters Puffinus nativitatis at Hōlanikū (Kure Atoll). Metabarcoding was used to bulk‐process 92 water samples from regurgitations collected from 2009 to 2017, providing an overview of the seabird's diet. We additionally Sanger‐sequenced 100 prey items from 50 randomly chosen regurgitations to verify that metabarcoding characterized key components of the diet. The metabarcoding technique identified 87 unique taxa from 29 families of fish and squid, spanning diverse taxa, including reef‐associated, pelagic–oceanic, and mesopelagic species. Rare prey (frequency of occurrence ≤5% of samples) constituted 66% of the species richness, demonstrating the highly diverse diet of this generalist predator. Overall, 81% of the families detected in the contemporary diet were previously documented in Christmas shearwater diets from the Northwestern Hawaiian Islands. Our results indicate that metabarcoding the COI region is useful in identifying a wide range of taxa from highly digested regurgitations, thus facilitating this approach to study seabird diets.

Metabarcoding the marine environment: from single species to biogeographic patterns

“…Other common prey included fish generally living at depths ranging from 200 to 5000 m (mesopelagic zone) during the day, which is well beyond the maximum diving depth of these seabirds. Thus, these seabirds likely consumed mesopelagic fish when they migrated to the surface at night, a feeding behavior that has not been observed for birds in this colony (Nimz et al, 2021). Wells et al (2020) identified an unsuspected coupling between terrestrial and marine food webs using DNA metabarcoding of the gut contents of the giant plumose anemone (Metridium farcimen).…”

“…Tropical seabirds redistribute nutrients from vast oligotrophic marine seas to terrestrial ecosystems, but the exact pathways remain poorly known because prey digested while at sea quickly become unidentifiable. Nimz et al (2021) conduct metabarcoding sequencing of the regurgitations of the Christmas Shearwater (Puffinus nativitatis). Nocturnal reef fish likely captured at the larval stage in the pelagic environment were among the most abundant prey.…”

Using low volume eDNA methods to sample pelagic marine animal assemblages

“…To maximize broad detection of animals while minimizing the number of primers applied, we selected mitochondrial 12S ribosomal RNA (12S) and cytochrome oxidase subunit I (COI) genes as barcode regions. Both barcode regions have large reference libraries and effectively identify a broad diversity of invertebrates and vertebrates, respectively [ 23 , 32 , 37 – 39 ]. We applied 12S-V5 primers amplifying a 73–110 bp fragment of the 12S gene [ 40 ] and the mlCOIintF and jgHCO2198 primers amplifying a 313 bp fragment of the animal COI gene [ 41 ].…”

Metabarcoding fecal samples to investigate spatiotemporal variation in the diet of the endangered Westland Petrel ( Procellaria westlandica )

“…In recent years, dietary DNA (dDNA) has been a useful tool for studying seabirds' diet and food webs (Deagle et al 2007, McInnes et al 2017b, Kleinschmidt et al 2019, Carreiro et al 2020, Young et al 2020, Nimz et al 2022. Dietary DNA approaches using feces have helped, for instance, to unravel the dietary spectrum of Macaroni Penguins (Eudypes chrysolophus; Deagle et al 2007) and it also shed light onto the diet of the Black-browed Albatross (Thalassarche melanophris) and Campbell Albatross (Thalassarche impavida) in the Falkland Islands (McInnes et al 2017b).…”