Multi-locus DNA metabarcoding of zooplankton communities and scat reveal trophic interactions of a generalist predator

E L Carroll,M A Sewell,R O’Rorke,H A Ross,R Constantine,L K Tooman,L Ranjard,R D Newcomb,J Zeldis,R Gallego

doi:10.1038/s41598-018-36478-x

Abstract

To understand the ecosystem dynamics that underpin the year-round presence of a large generalist consumer, the Bryde’s whale (Balaenoptera edeni brydei), we use a DNA metabarcoding approach and systematic zooplankton surveys to investigate seasonal and regional changes in zooplankton communities and if whale diet reflects such changes. Twenty-four zooplankton community samples were collected from three regions throughout the Hauraki Gulf, New Zealand, over two temperature regimes (warm and cool seasons), as well as 20 samples of opportunistically collected Bryde’s whale scat. Multi-locus DNA barcode libraries were constructed from 18S and COI gene fragments, representing a trade-off between identification and resolution of metazoan taxa. Zooplankton community OTU occurrence and relative read abundance showed regional and seasonal differences based on permutational analyses of variance in both DNA barcodes, with significant changes in biodiversity indices linked to season in COI only. In contrast, we did not find evidence that Bryde’s whale diet shows seasonal or regional trends, but instead indicated clear prey preferences for krill-like crustaceans, copepods, salps and ray-finned fishes independent of prey availability. The year-round presence of Bryde’s whales in the Hauraki Gulf is likely associated with the patterns of distribution and abundance of these key prey items.

Highlights

Determining trophic interactions is essential for effectively understanding and conserving both species and ecosystems in the face of anthropogenic pressures[1,2]
To gain more insight into whale diet, we examined all operational taxonomic units (OTUs) that were assigned to taxonomic Class with >60% confidence
To get an estimate of OTU occurrence we reduced the data to a binary matrix to entirely eliminate the influence of abundance on analyses and calculated the Jaccard dissimilarity index between samples[54]

Summary

Introduction

Determining trophic interactions is essential for effectively understanding and conserving both species and ecosystems in the face of anthropogenic pressures[1,2]. By keeping iron at the surface, the ‘whale pump’ of nutrients found in cetacean scat is hypothesised to enhance productivity and prey abundance, and aids in the transfer of nutrients from areas of high to low productivity[10] This is thought to increase both the abundance of krill and the Southern Ocean’s carrying capacity for baleen whales[11,12]. For the few regions with year-round resident populations of baleen whales, such seasonal effects may be less pronounced and research is lacking on the interaction between resident whales and their prey. As a generalist predator with the ability to specialise, the diet of Bryde’s whales needs to be studied on a population level and over seasons to gain a complete picture of prey preferences and trophic interactions in a given region. Many previous studies have been based on whales killed during hunting, and here we sought to take a non-invasive approach to investigate Bryde’s whale diet in a population that is listed as ‘Nationally Critical’[15]

Methods

Results

Discussion

Conclusion