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      DNA barcoding reveals seasonal shifts in diet and consumption of deep-sea fishes in wedge-tailed shearwaters

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          Abstract

          The foraging ecology of pelagic seabirds is difficult to characterize because of their large foraging areas. In the face of this difficulty, DNA metabarcoding may be a useful approach to analyze diet compositions and foraging behaviors. Using this approach, we investigated the diet composition and its seasonal variation of a common seabird species on the Ogasawara Islands, Japan: the wedge-tailed shearwater Ardenna pacifica. We collected fecal samples during the prebreeding ( N = 73) and rearing ( N = 96) periods. The diet composition of wedge-tailed shearwater was analyzed by Ion Torrent sequencing using two universal polymerase chain reaction primers for the 12S and 16S mitochondrial DNA regions that targeted vertebrates and mollusks, respectively. The results of a BLAST search of obtained sequences detected 31 and 1 vertebrate and mollusk taxa, respectively. The results of the diet composition analysis showed that wedge-tailed shearwaters frequently consumed deep-sea fishes throughout the sampling season, indicating the importance of these fishes as a stable food resource. However, there was a marked seasonal shift in diet, which may reflect seasonal changes in food resource availability and wedge-tailed shearwater foraging behavior. The collected data regarding the shearwater diet may be useful for in situ conservation efforts. Future research that combines DNA metabarcoding with other tools, such as data logging, may provide further insight into the foraging ecology of pelagic seabirds.

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          Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex.

          Micah Hamady, Jeffrey Walker, J Kirk Harris … (2008)
          We constructed error-correcting DNA barcodes that allow one run of a massively parallel pyrosequencer to process up to 1,544 samples simultaneously. Using these barcodes we processed bacterial 16S rRNA gene sequences representing microbial communities in 286 environmental samples, corrected 92% of sample assignment errors, and thus characterized nearly as many 16S rRNA genes as have been sequenced to date by Sanger sequencing.
          Article 0 comments Cited 459 times – based on 0 reviews     Review now
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            DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet.

            M De Barba, C Miquel, F Boyer … (2014)
            Ecological understanding of the role of consumer-resource interactions in natural food webs is limited by the difficulty of accurately and efficiently determining the complex variety of food types animals have eaten in the field. We developed a method based on DNA metabarcoding multiplexing and next-generation sequencing to uncover different taxonomic groups of organisms from complex diet samples. We validated this approach on 91 faeces of a large omnivorous mammal, the brown bear, using DNA metabarcoding markers targeting the plant, vertebrate and invertebrate components of the diet. We included internal controls in the experiments and performed PCR replication for accuracy validation in postsequencing data analysis. Using our multiplexing strategy, we significantly simplified the experimental procedure and accurately and concurrently identified different prey DNA corresponding to the targeted taxonomic groups, with ≥ 60% of taxa of all diet components identified to genus/species level. The systematic application of internal controls and replication was a useful and simple way to evaluate the performance of our experimental procedure, standardize the selection of sequence filtering parameters for each marker data and validate the accuracy of the results. Our general approach can be adapted to the analysis of dietary samples of various predator species in different ecosystems, for a number of conservation and ecological applications entailing large-scale population level diet assessment through cost-effective screening of multiple DNA metabarcodes, and the detection of fine dietary variation among samples or individuals and of rare food items.
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              Ocean's least productive waters are expanding

              Jeffrey Polovina, Evan Howell, Melanie Abecassis (2008)
              Article 0 comments Cited 221 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Taketo Komura:
                ORCID: http://orcid.org/0000-0001-7491-5594
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: VisualizationRole: Writing – original draft
                Haruko Ando: Role: MethodologyRole: Writing – review & editing
                Kazuo Horikoshi: Role: ConceptualizationRole: Funding acquisitionRole: InvestigationRole: Project administration
                Hajime Suzuki: Role: Investigation
                Yuji Isagi: Role: SupervisionRole: Writing – review & editing
                Hideyuki Doi: Role: Editor
                Journal
                Journal ID (nlm-ta): PLoS One
                Journal ID (iso-abbrev): PLoS ONE
                Journal ID (publisher-id): plos
                Journal ID (pmc): plosone
                Title: PLoS ONE
                Publisher: Public Library of Science (San Francisco, CA USA )
                ISSN (Electronic): 1932-6203
                Publication date (Electronic): 9 April 2018
                Publication date Collection: 2018
                Volume: 13
                Issue: 4
                Electronic Location Identifier: e0195385
                Affiliations
                [1 ] Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
                [2 ] Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, Japan
                [3 ] Institute of Boninology, Nishi-machi, Chichijima, Ogasawara, Tokyo, Japan
                University of Hyogo, JAPAN
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0001-7491-5594
                Article
                Publisher ID: PONE-D-17-34923
                DOI: 10.1371/journal.pone.0195385
                PMC ID: 5891018
                PubMed ID: 29630670
                SO-VID: 70019eb7-bd91-453c-a62f-ce321769a730
                Copyright © © 2018 Komura et al
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                Date received : 27 September 2017
                Date accepted : 21 March 2018
                Page count
                Figures: 4, Tables: 3, Pages: 18
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100006120, Ministry of the Environment;
                Award ID: Environment Research and Technology Development Fund (4-1402)
                Award Recipient :
                This study was supported by the Environment Research and Technology Development Fund (4-1402) of the Ministry of the Environment, Japan ( http://www.env.go.jp/policy/kenkyu/suishin/gaiyou/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Subject: Research Article
                Subject: Biology and Life Sciences
                Subject: Behavior
                Subject: Animal Behavior
                Subject: Foraging
                Subject: Biology and Life Sciences
                Subject: Zoology
                Subject: Animal Behavior
                Subject: Foraging
                Subject: Biology and Life Sciences
                Subject: Ecology
                Subject: Community Ecology
                Subject: Trophic Interactions
                Subject: Ecology and Environmental Sciences
                Subject: Ecology
                Subject: Community Ecology
                Subject: Trophic Interactions
                Subject: Earth Sciences
                Subject: Geomorphology
                Subject: Topography
                Subject: Landforms
                Subject: Islands
                Subject: Research and Analysis Methods
                Subject: Database and Informatics Methods
                Subject: Biological Databases
                Subject: Sequence Databases
                Subject: Research and Analysis Methods
                Subject: Database and Informatics Methods
                Subject: Bioinformatics
                Subject: Sequence Analysis
                Subject: Sequence Databases
                Subject: Biology and Life Sciences
                Subject: Organisms
                Subject: Eukaryota
                Subject: Animals
                Subject: Vertebrates
                Subject: Amniotes
                Subject: Birds
                Subject: Seabirds
                Subject: Biology and Life Sciences
                Subject: Nutrition
                Subject: Diet
                Subject: Medicine and Health Sciences
                Subject: Nutrition
                Subject: Diet
                Subject: Biology and Life Sciences
                Subject: Ecology
                Subject: Community Ecology
                Subject: Trophic Interactions
                Subject: Predation
                Subject: Ecology and Environmental Sciences
                Subject: Ecology
                Subject: Community Ecology
                Subject: Trophic Interactions
                Subject: Predation
                Subject: Biology and Life Sciences
                Subject: Molecular Biology
                Subject: Molecular Biology Techniques
                Subject: Artificial Gene Amplification and Extension
                Subject: Polymerase Chain Reaction
                Subject: Research and Analysis Methods
                Subject: Molecular Biology Techniques
                Subject: Artificial Gene Amplification and Extension
                Subject: Polymerase Chain Reaction
                Custom metadata
                Data Availability All nucleotide sequence data files are available from the DDBJ database (accession number DRA006191).

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                ScienceOpen disciplines: Uncategorized

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