Metabarcoding demonstrates dietary niche partitioning in two coexisting blackfish species

Abstract

A problem for fisheries ecologists who carry out dietary analysis on their specimens is dealing with contents that are difficult to identify, particularly when the contents comprise digested prey. We used a DNA metabarcoding approach to determine the diets of two co-occurring black fish species (Gadopsis bispinosus and Gadopsis marmoratus) to circumvent any issues with trying to apply microscopic methods to identify diets. We examined the frequency of occurrence of taxa across all specimens and the proportion that taxa contributed to total diet. In this way we hoped to demonstrate that a DNA-based method could resolve dietary differences of coexisting taxa. We showed that 10 macroinvertebrate taxa dominated the diets of both species and, of these, 7 occurred in all specimens of both taxa, indicating they were an important component of the diet of both species. Twelve taxa were present only in the G. bispinosus diet and four of those were terrestrial invertebrates; six taxa were found only in G. marmoratus. Our DNA-based approach to examine the taxa in the guts of two co-existing Gadopsis species provided sufficient resolution to show a significant degree of dietary partitioning.

Characteristics and consequences of a disease outbreak in aquatic insects

“…Diet overlap varies between members of the group (Lancaster, 2020) and so the shifts in relative abundance that may arise from species‐specific infections provide opportunity for shifting competitive interactions through resource consumption or intraguild predation. Less is known about their predators, but reduced abundances could reduce food supply for in‐stream predators such as larger insect larvae and fish (Rees et al., 2020), while flying adults contribute subsidies to the diets of terrestrial predators (Clarke‐Wood, 2019).…”

Using DNA metabarcoding as a novel approach for analysis of platypus diet

“…Mostly, traditional dietary analyses rely on visual observations, morphological identification of prey components in the stomach or faeces, or stable isotope analyses 11 . More recently, DNA-based methods are used because they can identify morphologically indistinct material, allowing greater precision in diet studies with more taxa detected 12 – 14 . Specifically, DNA metabarcoding can determine species’ composition by sequencing DNA from soft-bodied and hard-bodied taxa 15 , 16 .…”

“…Specifically, DNA metabarcoding can determine species’ composition by sequencing DNA from soft-bodied and hard-bodied taxa 15 , 16 . DNA metabarcoding has been used successfully to assess the diet of different mammal 13 , 17 – 19 and fish species 14 , 20 , 21 .…”

High‐throughput sequencing outperforms traditional morphological methods in Blue Catfish diet analysis and reveals novel insights into diet ecology

“…Recent studies have sought to address the full impact of Blue Catfish feeding ecology in its non‐native range using visual, morphometric methods (Waters et al., 2004), sometimes in combination with DNA barcoding of specific tissues (Aguilar et al., 2017; Moran et al., 2015; Schmitt et al., 2017). Such studies are difficult to use in quantifying the effect of Blue Catfish predation on ecosystems as taxonomic identification of prey items is highly dependent upon tissue degradation, thus limiting prey identification to those items only recently consumed and of sufficient mass to withstand rapid digestive processes (Rees et al., 2020; Su et al., 2018). Studies indicate that soft‐tissue prey, including larval and juvenile fishes, are unrecognizably digested within a span of twenty minutes to a few hours of consumption (Bromley, 1994; Carreon‐Martinez et al., 2011).…”

“…The use of high‐throughput sequencing (HTS) for diet studies is becoming more widely accepted (Casey et al., 2019; Rees et al., 2020; Waraniak et al., 2019). Such methods perform better than morphological observation, especially when diet items, including at‐risk or economically important species, are partially or fully digested with no assemblance of an organism for viewing, as mentioned above (Schwarz et al., 2018; Tverin et al., 2019; Waraniak et al., 2018).…”