DNA metabarcoding in diet studies: Unveiling ecological aspects in aquatic and terrestrial ecosystems

Abstract

Effective conservation of species and ecosystems requires the understanding of important ecological traits, such as dietary habits, food webs, and trophic niches. In diet studies, the visual identification of partially digested prey has been enhanced with the recent more powerful and accurate technique, DNA barcoding. Here, we summarize the contribution of this recent methodology to the investigation of both terrestrial and aquatic taxa diet, and compare the level of novelty uncovered through the use of this technique regarding species' ecology. From a total of 150 studies analyzed, focusing on more than 250 vertebrate wild species, seven domesticated taxa, and humans, we suggest that barcoding has led to more significant findings for aquatic taxa and ecosystems, where direct observations of feeding events and consequent trophic niche understanding are typically limited. Finally, we introduce the term dietary DNA (dDNA) to describe environmental approaches that use DNA extracted from gut, stomach, or fecal contents, aiming to assess both species dietary habits and describe local biodiversity. Particularly, we highlight the complementarity of environmental DNA (eDNA) and dDNA as a new tool for biodiversity assessments in remote areas, including most of the aquatic realm.

Partitioning of diet between species and life history stages of sympatric and cryptic snappers (Lutjanidae) based on DNA metabarcoding

“…Species-level identification of prey items is now possible through the use of DNA metabarcoding [26][27][28] . DNA metabarcoding simultaneously generates millions of copies of DNA sequences of digested prey from predators' gut contents or faeces, and matches them against barcode sequences in databases to reveal the taxa of consumed species 6,29 . This method lends itself to more comprehensive evaluation of dietary partitioning of sympatric, cryptic species at a much finer-scale 30,31 .…”

Feeding habits and novel prey of larval fishes in the northern San Francisco Estuary

“…Like any single method, this type of analysis has several limitations: identification of prey depends on the skill of the analyst, guts may contain unidentifiable material or appear empty but still contain prey remains (e.g., Slater & Baxter 2014), and variable digestion time of the prey can bias results toward hard-bodied prey (Hyslop 1980). All of these limitations can lead to an incomplete understanding of aquatic food webs (Pompanon et al, 2012;Sousa et al, 2019). Although arthropods are important prey for larval fishes (Llopiz 2013), many soft-bodied plankton can provide important nutrition to larval fishes.…”

Molecular Assays of Pollen Use Consistently Reflect Pollinator Visitation Patterns in a System of Flowering Plants

“…These approaches rely on single-locus PCR amplicons, leveraging the power of high-throughput DNA sequencing to compare reads to a database of putative DNA sources. The applications of metabarcoding are manifold, including analyses of microbiomes and diets (Sousa et al 2019), as well as environmental DNA analysis to quantify community composition (Deiner et al 2017, Sousa et al 2019). Such molecular approaches have also recently been applied to plant identification from the pollen found on bees to determine which species of flowers they have visited (Wilson et al 2010; Galimberti et al 2014; Sickel et al 2015; Bell et al 2016, Bell et al 2017).…”