Maximizing dietary information retrievable from carcasses of Great Cormorants <i>Phalacrocorax carbo</i> using a combined morphological and molecular analytical approach

Oehm, Johannes; Thalinger, Bettina; Mayr, Hannes; Traugott, Michael

doi:10.1111/ibi.12337

Cited by 12 publications

(10 citation statements)

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“…Secondary consumption, i.e., prey of the prey, parasites or accidental material consumed during feeding, may confound the results in DNA-based studies [ 52 – 54 ]. The magnitude of potential error due to secondary predation depends on digestion rates [ 54 ].…”

Section: Discussionmentioning

confidence: 99%

DNA metabarcoding reveals diverse diet of the three-spined stickleback in a coastal ecosystem

et al. 2017

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The three-spined stickleback (Gasterosteus aculeatus L., hereafter ‘stickleback’) is a common mesopredatory fish in marine, coastal and freshwater areas. In large parts of the Baltic Sea, stickleback densities have increased >10-fold during the last decades, and it is now one of the dominating fish species both in terms of biomass and effects on lower trophic levels. Still, relatively little is known about its diet—knowledge which is essential to understand the increasing role sticklebacks play in the ecosystem. Fish diet analyses typically rely on visual identification of stomach contents, a labour-intensive method that is made difficult by prey digestion and requires expert taxonomic knowledge. However, advances in DNA-based metabarcoding methods promise a simultaneous identification of most prey items, even from semi-digested tissue. Here, we studied the diet of stickleback from the western Baltic Sea coast using both DNA metabarcoding and visual analysis of stomach contents. Using the cytochrome oxidase (CO1) marker we identified 120 prey taxa in the diet, belonging to 15 phyla, 83 genera and 84 species. Compared to previous studies, this is an unusually high prey diversity. Chironomids, cladocerans and harpacticoids were dominating prey items. Large sticklebacks were found to feed more on benthic prey, such as amphipods, gastropods and isopods. DNA metabarcoding gave much higher taxonomic resolution (median rank genus) than visual analysis (median rank order), and many taxa identified using barcoding could not have been identified visually. However, a few taxa identified by visual inspection were not revealed by barcoding. In summary, our results suggest that the three-spined stickleback feeds on a wide variety of both pelagic and benthic organisms, indicating that the strong increase in stickleback populations may affect many parts of the Baltic Sea coastal ecosystem.

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Section: Discussionmentioning

confidence: 99%

DNA metabarcoding reveals diverse diet of the three-spined stickleback in a coastal ecosystem

et al. 2017

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“…This eDNA can potentially lead to false‐positive prey detections. However, DNA breakdown of this already‐fragmented eDNA is very fast and thus it is unlikely to survive digestion (Oehm et al., ).…”

Section: Discussionmentioning

confidence: 99%

“…Therefore, secondary predation, when a bird ingests a fish that itself recently consumed another fish, can affect the number of prey species detected. The implications of secondary predation have been discussed for molecular diet analysis (Oehm et al., ; Sheppard et al., ) as well as for morphological pellet analysis because hard parts of secondary prey may also be found in pellets (Blackwell & Sinclair, ). Vinson and Angradi () found 25% and 40% of dissected stomachs of predatory fish to be empty, which reduces the probability of secondary predation affecting diet assessment in piscivorous birds.…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, Oehm et al. (), analyzing the stomach content of cormorants, found that in only 20% of samples where remains of predatory fish were present next to remains of potential secondarily predated prey, secondary predation could have happened based on predator–prey fish size relationships.…”

Section: Discussionmentioning

confidence: 99%

“…DNA‐based methods have already been successfully applied to identify prey from pellets, feces, and stomach contents of avian piscivores such as penguins (Deagle, Chiaradia, McInnes, & Jarman, ; Deagle et al., ; Jarman et al., ), puffins (Bowser, Diamond, & Addison, ), shearwaters (Alonso et al., ), cormorants (Oehm, Thalinger, Mayr, & Traugott, ; Thalinger et al., ), and kingfishers (Thalinger et al., ). Furthermore, morphological and molecular methods of prey identification have been compared in previous studies: while molecular approaches usually were found to allow detecting a wider spectrum of prey species compared to morphological analysis (Casper, Jarman, Gales, & Hindell, ; Deagle et al., ; Thalinger et al., ), morphological identification of prey remains provides data on prey number and size (Emmrich & Düttmann, ; Zijlstra & Vaneerden, ) which is hard to get using DNA‐based techniques.…”

Section: Introductionmentioning

confidence: 99%

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Diet analysis in piscivorous birds: What can the addition of molecular tools offer?

Oehm

Thalinger

Eisenkölbl

et al. 2017

Ecology and Evolution

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In trophic studies on piscivorous birds, it is vital to know which kind of dietary sample provides the information of interest and how the prey can be identified reliably and efficiently. Often, noninvasively obtained dietary samples such as regurgitated pellets, feces, and regurgitated fish samples are the preferred source of information. Fish prey has usually been identified via morphological analysis of undigested hard parts, but molecular approaches are being increasingly used for this purpose. What remains unknown, however, is which dietary sample type is best suited for molecular diet analysis and how the molecular results compare to those obtained by morphological analysis. Pellets, feces, and regurgitated fish samples of Great Cormorants (Phalacrocorax carbo sinensis) were examined for prey using both morphological hard part analysis and molecular prey identification. The sample types and methods were compared regarding number of species detected (overall and per sample) as well as the prey species composition and its variability among individual samples. Via molecular analysis, significantly higher numbers of prey species were detected in pellets, feces, and fish samples. Of the three sample types, pellets contained the most comprehensive trophic information and could be obtained with the lowest sampling effort. Contrastingly, dietary information obtained from feces was least informative and most variable. For all sample types, the molecular approach outperformed morphological hard part identification regarding the detectable prey spectrum and prey species composition. We recommend the use of pellets in combination with molecular prey identification to study the diet of piscivorous birds.

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Evaluation of an automated protocol for efficient and reliable DNA extraction of dietary samples

Wallinger

Staudacher

Sint

et al. 2017

Ecology and Evolution

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Molecular techniques have become an important tool to empirically assess feeding interactions. The increased usage of next‐generation sequencing approaches has stressed the need of fast DNA extraction that does not compromise DNA quality. Dietary samples here pose a particular challenge, as these demand high‐quality DNA extraction procedures for obtaining the minute quantities of short‐fragmented food DNA. Automatic high‐throughput procedures significantly decrease time and costs and allow for standardization of extracting total DNA. However, these approaches have not yet been evaluated for dietary samples. We tested the efficiency of an automatic DNA extraction platform and a traditional CTAB protocol, employing a variety of dietary samples including invertebrate whole‐body extracts as well as invertebrate and vertebrate gut content samples and feces. Extraction efficacy was quantified using the proportions of successful PCR amplifications of both total and prey DNA, and cost was estimated in terms of time and material expense. For extraction of total DNA, the automated platform performed better for both invertebrate and vertebrate samples. This was also true for prey detection in vertebrate samples. For the dietary analysis in invertebrates, there is still room for improvement when using the high‐throughput system for optimal DNA yields. Overall, the automated DNA extraction system turned out as a promising alternative to labor‐intensive, low‐throughput manual extraction methods such as CTAB. It is opening up the opportunity for an extensive use of this cost‐efficient and innovative methodology at low contamination risk also in trophic ecology.

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Maximizing dietary information retrievable from carcasses of Great Cormorants Phalacrocorax carbo using a combined morphological and molecular analytical approach

Cited by 12 publications

References 41 publications

DNA metabarcoding reveals diverse diet of the three-spined stickleback in a coastal ecosystem

DNA metabarcoding reveals diverse diet of the three-spined stickleback in a coastal ecosystem

Diet analysis in piscivorous birds: What can the addition of molecular tools offer?

Evaluation of an automated protocol for efficient and reliable DNA extraction of dietary samples

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