Comparison of morphological and DNA metabarcoding analyses of diets in exploited marine fishes

Berry, Oliver; Bulman, CM; Bunce, Michael; Coghlan, Megan L.; Murray, Dáithí C.; Ward, Robert

doi:10.3354/meps11524

Cited by 100 publications

(101 citation statements)

References 59 publications

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“…For metabarcoding, errors can occur due to technical artefacts specific to DNA amplification and sequencing (Barnes & Turner, ; Pompanon et al., ), and biological limitations such as species‐specific digestion and DNA degradation rates (Deagle, Chiaradia, McInnes, & Jarman, ; Murray et al., ; Pinol et al., ; Sakaguchi et al., ). Furthermore, some of the DNA detected might come from secondary predation (taxa present in the stomach of preyed organisms; Berry et al., ; Kartzinel & Pringle, ). Cannibalism also imposes a specific problem in trophic molecular studies since it cannot be identified by means of metabarcoding (Berry et al., ; Ray et al., ).…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, some of the DNA detected might come from secondary predation (taxa present in the stomach of preyed organisms; Berry et al., ; Kartzinel & Pringle, ). Cannibalism also imposes a specific problem in trophic molecular studies since it cannot be identified by means of metabarcoding (Berry et al., ; Ray et al., ). Large brown shrimps are known to be cannibalistic (Evans, ; Pihl & Rosenberg, ) but the removal of C. crangon sequence reads from our data set makes it impossible to gauge insights into the extent of cannibalism in this species.…”

Section: Discussionmentioning

confidence: 99%

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DNA metabarcoding unveils multiscale trophic variation in a widespread coastal opportunist

et al. 2018

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A thorough understanding of ecological networks relies on comprehensive information on trophic relationships among species. Since unpicking the diet of many organisms is unattainable using traditional morphology‐based approaches, the application of high‐throughput sequencing methods represents a rapid and powerful way forward. Here, we assessed the application of DNA metabarcoding with nearly universal primers for the mitochondrial marker cytochrome c oxidase I in defining the trophic ecology of adult brown shrimp, Crangon crangon, in six European estuaries. The exact trophic role of this abundant and widespread coastal benthic species is somewhat controversial, while information on geographical variation remains scant. Results revealed a highly opportunistic behaviour. Shrimp stomach contents contained hundreds of taxa (>1,000 molecular operational taxonomic units), of which 291 were identified as distinct species, belonging to 35 phyla. Only twenty ascertained species had a mean relative abundance of more than 0.5%. Predominant species included other abundant coastal and estuarine taxa, including the shore crab Carcinus maenas and the amphipod Corophium volutator. Jacobs’ selectivity index estimates based on DNA extracted from both shrimp stomachs and sediment samples were used to assess the shrimp's trophic niche indicating a generalist diet, dominated by crustaceans, polychaetes and fish. Spatial variation in diet composition, at regional and local scales, confirmed the highly flexible nature of this trophic opportunist. Furthermore, the detection of a prevalent, possibly endoparasitic fungus (Purpureocillium lilacinum) in the shrimp's stomach demonstrates the wide range of questions that can be addressed using metabarcoding, towards a more robust reconstruction of ecological networks.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

DNA metabarcoding unveils multiscale trophic variation in a widespread coastal opportunist

et al. 2018

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“…18S has been the molecule of choice in metabarcoding studies of eukaryotes so far, but attempts have been made recently to incorporate COI data in these studies (e.g, Leray and Knowlton, 2015;Berry et al, 2015;Aylagas et al, 2016;. Being COI the standard molecule in the Barcode of Life initiative for many groups, it seems highly desirable to be able to use the wealth of information that is being presently generated.…”

Section: Discussionmentioning

confidence: 99%

Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding

Wangensteen

Cebrián

Palacín

et al. 2018

Marine Pollution Bulletin

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Running title: community-wide effects of invasive algae in MPAs Highlights  Hard-bottom communities dominated by invasive algae were studied with metabarcoding  A size-fractionation method is developed for the metabarcoding of complex samples  A modified primer set is used for the amplification of a COI fragment  A semiquantitave abundance index is proposed for statistical analyses  Results show effects of canopy-forming invasive algae on the underlying communities AbstractWe analysed with multigene (18S and COI) metabarcoding the effects of the proliferation of invasive seaweeds on rocky littoral communities in two Spanish Marine Protected Areas. The invasive algae studied were Caulerpa cylindracea, Lophocladia lallemandii and Asparagopsis armata. They are canopy-forming, landscape-dominant seaweeds, and we were interested in their effects on the underlying communities of meiobenthos and macrobenthos, separated in two size fractions through sieving. A new semiquantitative treatment of metabarcoding data is introduced. The results for both markers showed that the presence of the invasive seaweed had a significant effect on the understory communities for Lophocladia lallemandii and Asparagopsis armata but not for Caulerpa cylindracea. Likewise, changes in MOTU richness and diversity with invasion status varied in magnitude and direction depending on the alga considered. Our results showed that metabarcoding allows monitoring of the less conspicuous, but not least important, effects of the presence of dominant invasive seaweeds.

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“…This so‐called metabarcoding approach (Taberlet, Coissac, Hajibabaei, & Rieseberg, ) has proved to be an effective tool for characterizing the diet of predators (Deagle, Chiaradia, McInnes, & Jarman, ; Deagle, Kirkwood, & Jarman, ; Murray et al., ; Shehzad et al., ) and herbivores (Soininen et al., ; Valentini et al., ) through analysis of their feces or gut content. However, at present, metabarcoding applications in marine food webs are still limited (Albaina, Aguirre, Abad, Santos, & Estonba, ; Berry et al., ; Leray, Meyer, & Mills, ; Leray et al., ).…”

Section: Introductionmentioning

confidence: 99%

A metabarcoding approach for the feeding habits of European hake in the Adriatic Sea

Riccioni

Stagioni

Piccinetti

et al. 2018

Ecology and Evolution

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European hake (Merluccius merluccius) is one of the most economically important fish for the Mediterranean Sea. It is an important predator of deep upper shelf slope communities currently characterized by growth overexploitation: the understanding of hake's diet might support next generation management tools. However, all current European hake diet studies depend on the morphological identification of prey remains in stomach content, with consequent limitations. In this study, we set up a metabarcoding approach based on cytochrome oxidase I PCR amplification and Miseq Illumina paired‐end sequencing of M. merluccius stomach content remains and compared the results to classic morphological analyses. A total of 95 stomach contents of M. merluccius sampled in the North‐Central Adriatic Sea were analyzed with both the metabarcoding and morphological approaches. Metabarcoding clearly outperformed the morphological method in the taxonomic identification of prey describing more complex trophic relationships even when considering the morphological identification of 200 stomach contents. Statistical analysis of diet composition revealed a weak differentiation among the hake's size classes, confirming an opportunistic feeding behavior. All the analyses performed showed the presence of a core of shared prey among the size classes and a cloud of size‐specific prey. Our study highlights the exceptional potential of metabarcoding as an approach to provide unprecedented taxonomic resolution in the diet of M. merluccius and potentially of other marine predators, due to the broad‐spectrum of detection of the primers used. A thorough description of these complex trophic relationships is fundamental for the implementation of an ecosystem approach to fisheries.

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Comparison of morphological and DNA metabarcoding analyses of diets in exploited marine fishes

Cited by 100 publications

References 59 publications

DNA metabarcoding unveils multiscale trophic variation in a widespread coastal opportunist

DNA metabarcoding unveils multiscale trophic variation in a widespread coastal opportunist

Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding

A metabarcoding approach for the feeding habits of European hake in the Adriatic Sea

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