Application ofDNAbarcoding for identification of freshwater carnivorous fish diets: Is number of prey items dependent on size class forMicropterus salmoides?

Abstract

Understanding predator–prey interactions is a major challenge in ecological studies. In particular, the accurate identification of prey is a fundamental requirement in elucidating food-web structure. This study took a molecular approach in determining the species identity of consumed prey items of a freshwater carnivorous fish (largemouth bass, Micropterus salmoides), according to their size class. Thirty randomly selected gut samples were categorized into three size classes, based on the total length of the bass. Using the universal primer for the mtDNA cytochrome oxidase I (COI) region, polymerase chain reaction (PCR) amplification was performed on unidentified gut contents and then sequenced after cloning. Two gut samples were completely empty, and DNA materials from 27 of 28 gut samples were successfully amplified by PCR (success rate: 96.4%). Sequence database navigation yielded a total of 308 clones, containing DNA from 26 prey items. They comprised four phyla, including seven classes, 12 orders, and 12 families based on BLAST and BOLD database searches. The results indicate that largemouth bass show selective preferences in prey item consumption as they mature. These results corroborate a hypothesis, presence of ontogenetic diet shift, derived through other methodological approaches. Despite the practical limitations inherent in DNA barcoding analysis, high-resolution (i.e., species level) identification was possible, and the predation patterns of predators of different sizes were identifiable. The utilization of this method is strongly recommended for determining specific predator–prey relationships in complex freshwater ecosystems.

The use of DNA barcodes in food web construction—terrestrial and aquatic ecologists unite!

“…A few studies to date have sampled specific aquatic predator taxa more deeply, and demonstrated the occurrence of trophic segregation between different life stages (e.g., age, breeding status, and sex; Alonso et al 2014;Jo et al 2014). Thus, they suggest that different population segments choose different diets.…”

Unrevealing Parasitic Trophic Interactions—A Molecular Approach for Fluid-Feeding Fishes

“…None of these methods, however, allow the identification of items that are easily digested or of specific parasitic-host (or predator-prey) interactions, which may cause a bias in data interpretation (Sheppard and Harwood, 2005;Paquin et al, 2014). This may be especially problematic when dealing with small species (Sheppard and Harwood, 2005;Jo et al, 2014;Paquin et al, 2014).…”

“…In most animal groups, the cytochrome oxidase subunit 1 (COI) is the reference for the DNA barcoding system (Hebert et al, 2003). COI sequences libraries are available through on-line systems (such as GenBank, Bold), enabling its use in the identifications of host or prey species (Valentini et al, 2009;Corse et al, 2010;Leray et al, 2013a;Jo et al, 2014). DNA barcode techniques have been used to determine host-parasitoids webs in arthropods (Hrček and Godfray, 2014), as in Lepidoptera (Janzen et al, 2009) and Hemiptera (Gordon and Weirauch, 2015).…”

Discovering hidden biodiversity: the use of complementary monitoring of fish diet based on DNA barcoding in freshwater ecosystems

“…(2014) ensure accurate species identification. The first criterion was acceptance of a species name if the given OTU had ≥98% compliance with a known species.…”

“…In freshwater habitats, Jo et al. (2014) showed that DNA‐based approaches permit species level identification and revelation of hidden biodiversity as exemplified by analysis of chironomids in the guts of the generalist predator fish Micropterus salmoides .…”