DNA-Based Faecal Dietary Analysis: A Comparison of qPCR and High Throughput Sequencing Approaches

Murray, Dáithí C.; Bunce, Michael; Cannell, Belinda; Oliver, Rebecca; Houston, Jayne; White, Nicole E.; Barrero, Roberto A.; Bellgard, M.; Haile, James

doi:10.1371/journal.pone.0025776

Cited by 124 publications

(122 citation statements)

References 46 publications

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“…An increasing number of studies using next-generation sequencing (including DNA metabarcoding) has offered particular insights into the broad range of taxa consumed by aquatic organisms (e.g., Deagle et al 2009Deagle et al , 2010Murray et al 2011;O'Rorke et al 2012bO'Rorke et al , 2013O'Rorke et al , 2014Leray et al 2013; Barcoding a coral reef food web). However, their main focus has been on the dietary analysis of larger taxa such as seals, penguins, and fish and in marine over freshwater systems.…”

Section: Clarifying the Links Of Aquatic Food Websmentioning

confidence: 99%

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

Roslin

Majaneva

2016

Genome

105

103

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By depicting who eats whom, food webs offer descriptions of how groupings in nature (typically species or populations) are linked to each other. For asking questions on how food webs are built and work, we need descriptions of food webs at different levels of resolution. DNA techniques provide opportunities for highly resolved webs. In this paper, we offer an exposé of how DNA-based techniques, and DNA barcodes in particular, have recently been used to construct food web structure in both terrestrial and aquatic systems. We highlight how such techniques can be applied to simultaneously improve the taxonomic resolution of the nodes of the web (i.e., the species), and the links between them (i.e., who eats whom). We end by proposing how DNA barcodes and DNA information may allow new approaches to the construction of larger interaction webs, and overcome some hurdles to achieving adequate sample size. Most importantly, we propose that the joint adoption and development of these techniques may serve to unite approaches to food web studies in aquatic and terrestrial systems-revealing the extent to which food webs in these environments are structured similarly to or differently from each other, and how they are linked by dispersal.Key words: DNA barcodes, food webs, species delimitation, species identification, trophic links, ecological networks.Résumé : En brossant le tableau de qui mange qui, les réseaux trophiques livrent une description des liens qui unissent des groupes d'espèces ou de populations. Afin de déterminer comment ces réseaux sont constitués et comment ils fonctionnent, il nous faut une description de ces réseaux à différents niveaux de résolution. Les techniques de l'ADN permettent de produire des réseaux trophiques de grande résolution. Dans ce travail, les auteurs décrivent comment les techniques fondées sur l'ADN, en particulier les codes à barres de l'ADN, ont récemment été employées pour étudier la structure des réseaux trophiques chez des systèmes tant terrestres qu'aquatiques. Les auteurs soulignent comment ces techniques peuvent servir à simultanément améliorer la résolution taxonomique des noeuds d'un réseau (i.e. les espèces) ainsi que les relations entre eux (qui mange qui). Les auteurs terminent en proposant des moyens via lesquels les codes à barres et l'information tirée de l'ADN rendent possible de nouvelles approches en vue de la construction de plus grands réseaux d'interaction et permettent de surmonter des difficultés rencontrées dans l'acquisition d'échantillons de taille suffisante. Surtout, les auteurs proposent que l'adoption et le développement conjoints de ces techniques peut contribuer à unifier les approches employées dans l'étude des réseaux trophiques au sein des systèmes aquatiques et terrestres. Cela permettra de révéler l'étendue de la similarité ou de la dissimilarité dans la façon dont sont structurés les réseaux dans ces différents environnements et comment ils sont liés par la dispersion. [Traduit par la Rédaction]

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Section: Clarifying the Links Of Aquatic Food Websmentioning

confidence: 99%

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

Roslin

Majaneva

2016

Genome

105

103

View full text Add to dashboard Cite

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“…Indeed, only dietary studies allow the comprehension of the trophic interactions and of the dynamics of food webs specific for fishes in aquatic systems (Winemiller and Polis, 1996;CarreonMartinez and Heath, 2010;Murray et al, 2011). For these purposes, food items are traditionally identified through visual analysis of stomach, gut, or fecal contents under microscope (Hyslop, 1980;Taguchi et al, 2014) and through stable isotope analysis Epstein, 1978, 1981;Post, 2002;MercadoSilva et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

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

2018

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Fish diets have been traditionally studied through the direct visual identification of food items found in their stomachs. Stomach contents of Vandeliinae and Stegophilinae (family Trichomycteridae) parasite catfishes, however, cannot be identified by usual optical methods due to their mucophagic, lepidophagic, or hematophagic diets, in such a way that the trophic interactions and the dynamics of food webs in aquatic systems involving these catfishes are mostly unknown. The knowledge about trophic interactions, including difficult relation between parasites and hosts, are crucial to understand the whole working of food webs. In this way, molecular markers can be useful to determine the truly hosts of these catfishes, proving a preference in their feeding behavior for specific organisms and not a generalist. Sequences of cytochrome oxidase subunit 1 (COI) were successfully extracted and amplified from mucus or scales found in the stomach contents of two species of stegophilines, Homodiaetus anisitsi, and Pseudostegophilus maculatus, to identify the host species. The two species were found to be obligatory mucus-feeders and occasionally lepidophagic. Selection of host species is associated to host behavior, being constituted mainly by substrate-sifting benthivores. Characiformes are preferred hosts, but host choice depends on what characiform species are available in their environments, usually corresponding to the most abundant species. This is the first time that host species of parasitic fishes bearing mucophagous habits are identified, and demonstrates the effectiveness of the extraction and amplification of mitochondrial DNA from the ingested mucus in gut contents. The molecular markers effectively allowed determine parasite preferences and helps in better understanding the food web and trophic interaction on which fish species are involved. Despite, the methodology applied here can be used for an infinitive of organisms improving ecological trophic studies.

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“…There are known constraints on metabarcoding, including the inability to quantify the species information obtained (Deagle et al 2010, 2013, Bowles et al 2011, Murray et al 2011. Results are limited or biased to the frequency of occurrence, which still provides useful information when seeking to understand localized effects of an invasive predator.…”

Section: Introductionmentioning

confidence: 99%

Use of DNA metabarcoding for stomach content analysis in the invasive lionfish Pterois volitans in Puerto Rico

Harms-Tuohy¹,

Schizas²,

Appeldoorn³

2016

Mar. Ecol. Prog. Ser.

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Studies of lionfish feeding ecology seek to document the ecological impact of this invasive predatory species and determine which native prey species are at greatest risk. There are 2 common approaches to feeding ecology through gut content analysis: morphological identification to the lowest possible taxonomic rank and/or DNA barcoding of individual prey components in the stomach. The major disadvantage of both techniques is their inability to use advanced digested material. This study introduces next-generation sequencing to lionfish feeding ecology, employing DNA metabarcoding to analyze all components of the gut contents, including the previously unidentifiable portion. Sixty-three lionfish were caught from the inshore and offshore reefs of La Parguera, Puerto Rico. Stomach contents were separated into 2 sample componentsa liquid (i.e. digested) and undigested tissue. A 313 bp region of the cytochrome oxidase subunit I (COI) gene was amplified from extracted DNA using specific primers for Caribbean reef fish. Samples were sequenced with an Illumina MiSeq platform, and the resulting 950+ sequences were compared against GenBank and the Barcode of Life Database to identify specimens at the lowest taxonomic level. Thirty-nine fish species from 16 families were identified (35 each in the digested and tissue fractions), including members of Pomacentridae, Acanthuridae, Gobiidae, Apogonidae, and Scaridae. Using the digested liquiform material proved efficient in detecting prey species, especially those that would have been missed with traditional methods.

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DNA-Based Faecal Dietary Analysis: A Comparison of qPCR and High Throughput Sequencing Approaches

Cited by 124 publications

References 46 publications

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

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

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

Use of DNA metabarcoding for stomach content analysis in the invasive lionfish Pterois volitans in Puerto Rico

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