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

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, dietary overlap, and predator preference were analyzed comparing the periods of high and low prey abundance. Some predator species exhibited significant seasonal changes in diet composition. Dietary overlap was slightly but significantly higher during the period of high prey abundance; however, there was little change in predator preference. This suggests that change in prey availability was the driving factor in changing predator diet composition and dietary overlap. This study demonstrates the utility of molecular diet analysis and how temporal variability in community composition adds complexity to predator–prey interactions.

Rainbow Darter (Etheostoma caeruleum, Storer, 1845) predation on early ontogenetic stages of Lake Sturgeon (Acipenser fulvescens, Rafinesque, 1817)

“…In conclusion, our study increased understanding of predation risks to pre‐drift lake sturgeon. We confirmed rainbow darter predation on early ontogenetic stages of lake sturgeon, as was suggested by the genetic data presented in Waraniak, Blumstein, et al (), Waraniak, Marsh, and Scribner (). These findings are important, because they emphasize that even small‐bodied and gape‐limited species benefit from ephemeral resources such as lake sturgeon eggs deposited during the spawning season.…”

“…Results from this experiment corroborated genetic diet analyses by Waraniak, Blumstein, et al (), Waraniak, Marsh, and Scribner () in the Upper Black River by demonstrating that rainbow darters prey on early lake sturgeon ontogenetic stages. Lake sturgeon eggs were equally vulnerable to rainbow darter predation on small and large substrates.…”

“…An especially interesting result in Waraniak, Blumstein, et al () was the discovery of lake sturgeon DNA in the gastrointestinal tracts of presumably gape‐limited (<55 mm TL) species such as blackchin shiner ( Notropis heterodon , Cope, 1865), Johnny darter ( Etheostoma nigrum , Rafinesque, 1820), and rainbow darter ( Etheostoma caeruleum , Storer, 1845). As these species were likely unable to consume exogenously feeding larval lake sturgeon (18–24 mm TL; Smith & King, ), the findings in Waraniak, Blumstein, et al (), Waraniak et al () suggest smaller, riverine species feed on eggs and/or free embryo stages of lake sturgeon in the Upper Black River, MI.…”

“…As with many fishes, lake sturgeon exhibit a type III survivorship curve (Deevey Jr., 1947) characterized by high mortality in the early life stages (Caroffino, Sutton, Elliott, & Donofrio, 2011;Forsythe, Scribner, Crossman, Ragavendran, & Baker, 2013;Nichols et al, 2003). Lake sturgeon are prey for many river-resident and adfluvial fish species before and during the larval drift life stage (Caroffino et al, 2011;Duong et al, 2011;Forsythe et al, 2013;Smith & King, 2005;Waraniak, Blumstein, et al, 2017;Waraniak, Marsh, & Scribner, 2019). Lake sturgeon eggs adhere to substrate for approximately 8-14 days before hatching into free embryos, which rely on endogenous yolk reserves (Peterson et al, 2007).…”

“…The magnitude of predation risk facing lake sturgeon varies according to the timing of spawning and larval drift, availability of co-distributed prey, and taxonomic composition of piscine predators (Waraniak, Valentine, et al, 2017). Quantifying these relationships in complex riverine systems is critical to the management of threatened and endangered species (e.g., Crossman et al, 2017;Waraniak, Blumstein, et al, 2017;Waraniak et al, 2019).…”