18S rRNA metabarcoding diet analysis of a predatory fish community across seasonal changes in prey availability

Ecology and Evolution
Justin M WaraniakKim T Scribner

Abstract

Predator-prey relationships are important ecological interactions, affecting biotic community composition and energy flow through a system, and are of interest to ecologists and managers. Morphological diet analysis has been the primary method used to quantify the diets of predators, but emerging molecular techniques using genetic data can provide more accurate estimates of relative diet composition. This study used sequences from the 18S V9 rRNA barcoding region to identify prey items in the gastrointestinal (GI) tracts of predatory fishes. Predator GI samples were taken from the Black River, Cheboygan Co., MI, USA (n = 367 samples, 12 predator species) during periods of high prey availability, including the larval stage of regionally threatened lake sturgeon (Acipenser fulvescens Rafinesque 1817) in late May/early June of 2015 and of relatively lower prey availability in early July of 2015. DNA was extracted and sequenced from 355 samples (96.7%), and prey DNA was identified in 286 of the 355 samples (80.6%). Prey were grouped into 33 ecologically significant taxonomic groups based on the lowest taxonomic level sequences that could be identified using sequences available on GenBank. Changes in the makeup of diet composition, ...Continue Reading

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Citations

May 23, 2020·Journal of Fish Biology·Michael TraugottDaniela Sint
Aug 12, 2020·PloS One·Justin G Mychek-LonderDaniel D Heath
Feb 5, 2021·Nature Communications·Leah A OwensTony L Goldberg
Nov 9, 2021·PLoS Computational Biology·Michael S RobesonNicholas A Bokulich

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Methods Mentioned

BETA
PCR
flow cell sequencing

Software Mentioned

R
mothur
vegan
Metabarcoding
PERMANOVA

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