From feces to data: A metabarcoding method for analyzing consumed and available prey in a bird-insect food web.
Identifieur interne : 000493 ( Main/Exploration ); précédent : 000492; suivant : 000494From feces to data: A metabarcoding method for analyzing consumed and available prey in a bird-insect food web.
Auteurs : Seppo Rytkönen ; Eero J. Vesterinen ; Coen Westerduin ; Tiina Levi Kangas ; Emma Vatka ; Marko Mutanen ; Panu V Lim Ki ; Markku Hukkanen ; Marko Suokas ; Markku OrellSource :
- Ecology and evolution [ 2045-7758 ] ; 2019.
Abstract
Diets play a key role in understanding trophic interactions. Knowing the actual structure of food webs contributes greatly to our understanding of biodiversity and ecosystem functioning. The research of prey preferences of different predators requires knowledge not only of the prey consumed, but also of what is available. In this study, we applied DNA metabarcoding to analyze the diet of 4 bird species (willow tits Poecile montanus, Siberian tits Poecile cinctus, great tits Parus major and blue tits Cyanistes caeruleus) by using the feces of nestlings. The availability of their assumed prey (Lepidoptera) was determined from feces of larvae (frass) collected from the main foraging habitat, birch (Betula spp.) canopy. We identified 53 prey species from the nestling feces, of which 11 (21%) were also detected from the frass samples (eight lepidopterans). Approximately 80% of identified prey species in the nestling feces represented lepidopterans, which is in line with the earlier studies on the parids' diet. A subsequent laboratory experiment showed a threshold for fecal sample size and the barcoding success, suggesting that the smallest frass samples do not contain enough larval DNA to be detected by high-throughput sequencing. To summarize, we apply metabarcoding for the first time in a combined approach to identify available prey (through frass) and consumed prey (via nestling feces), expanding the scope and precision for future dietary studies on insectivorous birds.
DOI: 10.1002/ece3.4787
PubMed: 30680143
PubMed Central: PMC6342092
Affiliations:
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Vesterinen</name><affiliation><nlm:affiliation>Biodiversity Unit University of Turku Turku Finland.</nlm:affiliation><wicri:noCountry code="no comma">Biodiversity Unit University of Turku Turku Finland.</wicri:noCountry></affiliation><affiliation><nlm:affiliation>Spatial Foodweb Ecology Group University of Helsinki Helsinki Finland.</nlm:affiliation><wicri:noCountry code="no comma">Spatial Foodweb Ecology Group University of Helsinki Helsinki Finland.</wicri:noCountry></affiliation></author><author><name sortKey="Westerduin, Coen" sort="Westerduin, Coen" uniqKey="Westerduin C" first="Coen" last="Westerduin">Coen Westerduin</name><affiliation><nlm:affiliation>Department of Ecology and Genetics University of Oulu Oulu Finland.</nlm:affiliation><wicri:noCountry code="no comma">Department of Ecology and Genetics University of Oulu Oulu Finland.</wicri:noCountry></affiliation></author><author><name sortKey="Levi Kangas, Tiina" sort="Levi Kangas, Tiina" uniqKey="Levi Kangas T" first="Tiina" 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University of Oulu Oulu Finland.</wicri:noCountry></affiliation></author><author><name sortKey="Vesterinen, Eero J" sort="Vesterinen, Eero J" uniqKey="Vesterinen E" first="Eero J" last="Vesterinen">Eero J. Vesterinen</name><affiliation><nlm:affiliation>Biodiversity Unit University of Turku Turku Finland.</nlm:affiliation><wicri:noCountry code="no comma">Biodiversity Unit University of Turku Turku Finland.</wicri:noCountry></affiliation><affiliation><nlm:affiliation>Spatial Foodweb Ecology Group University of Helsinki Helsinki Finland.</nlm:affiliation><wicri:noCountry code="no comma">Spatial Foodweb Ecology Group University of Helsinki Helsinki Finland.</wicri:noCountry></affiliation></author><author><name sortKey="Westerduin, Coen" sort="Westerduin, Coen" uniqKey="Westerduin C" first="Coen" last="Westerduin">Coen Westerduin</name><affiliation><nlm:affiliation>Department of Ecology and Genetics University of Oulu Oulu Finland.</nlm:affiliation><wicri:noCountry code="no comma">Department of Ecology and Genetics University of Oulu Oulu Finland.</wicri:noCountry></affiliation></author><author><name sortKey="Levi Kangas, Tiina" sort="Levi Kangas, Tiina" uniqKey="Levi Kangas T" first="Tiina" last="Levi Kangas">Tiina Levi Kangas</name><affiliation><nlm:affiliation>Department of Ecology and Genetics University of Oulu Oulu Finland.</nlm:affiliation><wicri:noCountry code="no comma">Department of Ecology and Genetics University of Oulu Oulu Finland.</wicri:noCountry></affiliation></author><author><name sortKey="Vatka, Emma" sort="Vatka, Emma" uniqKey="Vatka E" first="Emma" last="Vatka">Emma Vatka</name><affiliation><nlm:affiliation>Department of Ecology and Genetics University of Oulu Oulu Finland.</nlm:affiliation><wicri:noCountry code="no comma">Department of Ecology and Genetics University of Oulu Oulu Finland.</wicri:noCountry></affiliation><affiliation><nlm:affiliation>Ecological Genetics Research Unit University of Helsinki Helsinki Finland.</nlm:affiliation><wicri:noCountry code="no comma">Ecological Genetics Research Unit University of Helsinki Helsinki Finland.</wicri:noCountry></affiliation></author><author><name sortKey="Mutanen, Marko" sort="Mutanen, Marko" uniqKey="Mutanen M" first="Marko" last="Mutanen">Marko Mutanen</name><affiliation><nlm:affiliation>Department of Ecology and Genetics University of Oulu Oulu Finland.</nlm:affiliation><wicri:noCountry code="no comma">Department of Ecology and Genetics University of Oulu Oulu Finland.</wicri:noCountry></affiliation></author><author><name sortKey="V Lim Ki, Panu" sort="V Lim Ki, Panu" uniqKey="V Lim Ki P" first="Panu" last="V Lim Ki">Panu V Lim Ki</name><affiliation><nlm:affiliation>Department of Ecology and Genetics University of Oulu Oulu Finland.</nlm:affiliation><wicri:noCountry code="no comma">Department of Ecology and Genetics University of Oulu Oulu Finland.</wicri:noCountry></affiliation></author><author><name sortKey="Hukkanen, Markku" sort="Hukkanen, Markku" uniqKey="Hukkanen M" first="Markku" last="Hukkanen">Markku Hukkanen</name><affiliation><nlm:affiliation>Department of Ecology and Genetics University of Oulu Oulu Finland.</nlm:affiliation><wicri:noCountry code="no comma">Department of Ecology and Genetics University of Oulu Oulu Finland.</wicri:noCountry></affiliation></author><author><name sortKey="Suokas, Marko" sort="Suokas, Marko" uniqKey="Suokas M" first="Marko" last="Suokas">Marko Suokas</name><affiliation><nlm:affiliation>Department of Ecology and Genetics University of Oulu Oulu Finland.</nlm:affiliation><wicri:noCountry code="no comma">Department of Ecology and Genetics University of Oulu Oulu Finland.</wicri:noCountry></affiliation></author><author><name sortKey="Orell, Markku" sort="Orell, Markku" uniqKey="Orell M" first="Markku" last="Orell">Markku Orell</name><affiliation><nlm:affiliation>Department of Ecology and Genetics University of Oulu Oulu Finland.</nlm:affiliation><wicri:noCountry code="no comma">Department of Ecology and Genetics University of Oulu Oulu Finland.</wicri:noCountry></affiliation></author></analytic><series><title level="j">Ecology and evolution</title><idno type="ISSN">2045-7758</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Diets play a key role in understanding trophic interactions. Knowing the actual structure of food webs contributes greatly to our understanding of biodiversity and ecosystem functioning. The research of prey preferences of different predators requires knowledge not only of the prey consumed, but also of what is available. In this study, we applied DNA metabarcoding to analyze the diet of 4 bird species (willow tits <i>Poecile montanus</i>, Siberian tits <i>Poecile cinctus</i>, great tits <i>Parus major</i> and blue tits <i>Cyanistes caeruleus</i>) by using the feces of nestlings. The availability of their assumed prey (Lepidoptera) was determined from feces of larvae (frass) collected from the main foraging habitat, birch (<i>Betula</i> spp.) canopy. We identified 53 prey species from the nestling feces, of which 11 (21%) were also detected from the frass samples (eight lepidopterans). Approximately 80% of identified prey species in the nestling feces represented lepidopterans, which is in line with the earlier studies on the parids' diet. A subsequent laboratory experiment showed a threshold for fecal sample size and the barcoding success, suggesting that the smallest frass samples do not contain enough larval DNA to be detected by high-throughput sequencing. To summarize, we apply metabarcoding for the first time in a combined approach to identify available prey (through frass) and consumed prey (via nestling feces), expanding the scope and precision for future dietary studies on insectivorous birds.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">30680143</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">2045-7758</ISSN><JournalIssue CitedMedium="Print"><Volume>9</Volume><Issue>1</Issue><PubDate><Year>2019</Year><Month>Jan</Month></PubDate></JournalIssue><Title>Ecology and evolution</Title><ISOAbbreviation>Ecol Evol</ISOAbbreviation></Journal><ArticleTitle>From feces to data: A metabarcoding method for analyzing consumed and available prey in a bird-insect food web.</ArticleTitle><Pagination><MedlinePgn>631-639</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1002/ece3.4787</ELocationID><Abstract><AbstractText>Diets play a key role in understanding trophic interactions. Knowing the actual structure of food webs contributes greatly to our understanding of biodiversity and ecosystem functioning. The research of prey preferences of different predators requires knowledge not only of the prey consumed, but also of what is available. In this study, we applied DNA metabarcoding to analyze the diet of 4 bird species (willow tits <i>Poecile montanus</i>, Siberian tits <i>Poecile cinctus</i>, great tits <i>Parus major</i> and blue tits <i>Cyanistes caeruleus</i>) by using the feces of nestlings. The availability of their assumed prey (Lepidoptera) was determined from feces of larvae (frass) collected from the main foraging habitat, birch (<i>Betula</i> spp.) canopy. We identified 53 prey species from the nestling feces, of which 11 (21%) were also detected from the frass samples (eight lepidopterans). Approximately 80% of identified prey species in the nestling feces represented lepidopterans, which is in line with the earlier studies on the parids' diet. A subsequent laboratory experiment showed a threshold for fecal sample size and the barcoding success, suggesting that the smallest frass samples do not contain enough larval DNA to be detected by high-throughput sequencing. To summarize, we apply metabarcoding for the first time in a combined approach to identify available prey (through frass) and consumed prey (via nestling feces), expanding the scope and precision for future dietary studies on insectivorous birds.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Rytkönen</LastName><ForeName>Seppo</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Ecology and Genetics University of Oulu Oulu Finland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vesterinen</LastName><ForeName>Eero J</ForeName><Initials>EJ</Initials><Identifier Source="ORCID">https://orcid.org/0000-0003-3665-5802</Identifier><AffiliationInfo><Affiliation>Biodiversity Unit University of Turku Turku Finland.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Spatial Foodweb Ecology Group University of Helsinki Helsinki Finland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Westerduin</LastName><ForeName>Coen</ForeName><Initials>C</Initials><Identifier Source="ORCID">https://orcid.org/0000-0002-6264-5555</Identifier><AffiliationInfo><Affiliation>Department of Ecology and Genetics University of Oulu Oulu Finland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Leviäkangas</LastName><ForeName>Tiina</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Department of Ecology and Genetics University of Oulu Oulu Finland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vatka</LastName><ForeName>Emma</ForeName><Initials>E</Initials><Identifier Source="ORCID">https://orcid.org/0000-0003-2935-8295</Identifier><AffiliationInfo><Affiliation>Department of Ecology and Genetics University of Oulu Oulu Finland.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Ecological Genetics Research Unit University of Helsinki Helsinki Finland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mutanen</LastName><ForeName>Marko</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Ecology and Genetics University of Oulu Oulu Finland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Välimäki</LastName><ForeName>Panu</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Department of Ecology and Genetics University of Oulu Oulu Finland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hukkanen</LastName><ForeName>Markku</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Ecology and Genetics University of Oulu Oulu Finland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Suokas</LastName><ForeName>Marko</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Ecology and Genetics University of Oulu Oulu Finland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Orell</LastName><ForeName>Markku</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Ecology and Genetics University of Oulu Oulu Finland.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>Dryad</DataBankName><AccessionNumberList><AccessionNumber>10.5061/dryad.4f1n785</AccessionNumber></AccessionNumberList></DataBank></DataBankList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2018</Year><Month>12</Month><Day>21</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Ecol Evol</MedlineTA><NlmUniqueID>101566408</NlmUniqueID><ISSNLinking>2045-7758</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">DNA barcoding</Keyword><Keyword MajorTopicYN="N">Lepidoptera</Keyword><Keyword MajorTopicYN="N">dietary ecology</Keyword><Keyword MajorTopicYN="N">fecal DNA</Keyword><Keyword MajorTopicYN="N">frass</Keyword><Keyword MajorTopicYN="N">insectivorous birds</Keyword><Keyword MajorTopicYN="N">metagenomics</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>04</Month><Day>03</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2018</Year><Month>10</Month><Day>24</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>1</Month><Day>26</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>1</Month><Day>27</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>1</Month><Day>27</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">30680143</ArticleId><ArticleId 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