Effectiveness of DNA barcoding for identifying piscine prey items in stomach contents of piscivorous catfishes

Moran, Zach; Orth, Donald J.; Schmitt, Joseph D.; Hallerman, Eric M.; Aguilar, Robert

doi:10.1007/s10641-015-0448-7

Cited by 41 publications

(35 citation statements)

References 28 publications

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“…Sequencing analysis revealed that many of the riverine fish predators analyzed in this study had diverse diets, with nine or more prey taxa identified at least to the class level contributing at least 1% of the prey sequences within the diet samples of each predator species. This high diversity observed in this study can largely be attributed to the ability of metabarcoding to detect quickly digested soft‐bodied prey that are often difficult to identify in morphological analyses of diet samples (Albaina et al, ; Alonso et al, ; Moran, Orth, Schitt, Hallerman, & Aguilar, ; Sakaguchi et al, ).…”

Section: Discussionmentioning

confidence: 69%

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

Waraniak

Marsh

Scribner

2019

Ecology and Evolution

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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.

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Section: Discussionmentioning

confidence: 69%

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

Waraniak

Marsh

Scribner

2019

Ecology and Evolution

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“…above). Another example derives from a study of the gut contents of North American catfishes: here, Moran et al (2016) were able to match 86% of lightly or moderately digested stomach contents and 66% of heavily digested prey fish sequences to reference sequences in GenBank. With global databases being increasingly populated, more and more taxa will reach similar levels-but this can only be achieved by joint efforts, aided by standardization of marker choices among research groups.…”

Section: Clarifying the Links Of Aquatic Food Websmentioning

confidence: 99%

“…In most cases, these studies build on one of two techniques: specific PCR primers designed to reveal predation on one or a few specific prey taxa, or the amplification of DNA using universal or group-specific primers as followed by sequencing of the amplicon. Diet studies of these types have been applied extensively to marine taxa ranging from higher trophic levels (e.g., Deagle et al 2005;Dunn et al 2010;Méheust et al 2015) through marine birds (e.g., Deagle et al 2007;Bowser et al 2013) and fish (e.g., Moran et al 2016) to different invertebrates and lower trophic levels (e.g., Jarman et al 2002;Nejstgaard et al 2003;Blankenship and Yayanos 2005;Leal et al 2014b;Olsen et al 2014;Hu et al 2015;reviewed in Calado and Leal 2015). DNA-based approaches have also yielded breakthrough dietary analyses in complex freshwater systems (e.g., Corse et al 2010;Carreon-Martinez et al 2011;Bartley et al 2015).…”

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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“…DNA‐based techniques have been used to identify prey to the species level for predatory mammals (Gillet et al ., ) and birds (Wong et al ., ). For fishes, DNA‐based techniques have been used to study diet using stomach or gut contents (Smith et al ., ; Jo et al ., , ; Moran et al ., ) and faeces (Corse et al ., ; Taguchi et al ., ) and often provide better resolution than conventional stomach‐content analysis.…”

Section: Number Of Silurus Glanis Individuals In Which Prey Were Founmentioning

confidence: 99%

Application of DNA metabarcoding on faeces to identify European catfish Silurus glanis diet

Guillerault

Boulêtreau

Iribar

et al. 2017

Journal of Fish Biology

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In this study, the results of conventional stomach-content analysis are compared with the recent DNA metabarcoding approach on faeces to identify fish species consumed by non-native European catfish Silurus glanis in the Garonne River (south-western France), with a special emphasis on anadromous prey. Fourteen prey species were identified in the stomach contents or faeces, including four anadromous fish species. Despite higher intestine than stomach emptiness, more species were identified through faecal analysis (11 of 14) than through stomach-content analysis (five of 14) suggesting that DNA metabarcoding on faeces is an efficient, non-intrusive technique to study the diet of predatory fishes.

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Effectiveness of DNA barcoding for identifying piscine prey items in stomach contents of piscivorous catfishes

Cited by 41 publications

References 28 publications

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

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

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

Application of DNA metabarcoding on faeces to identify European catfish Silurus glanis diet

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