Power and limitations of environmental DNA metabarcoding for surveying leaf litter eukaryotic communities

Autores
Martins Lopes, Carla; Baêta, Délio; Sasso, Thais; Vanzetti, Agustín Iván; Raquel Zamudio, Kelly; Taberlet, Pierre; Baptista Haddad, Célio Fernando
Año de publicación
2020
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Leaf litter habitats shelter a great variety of organisms, which play an important rolein ecosystem dynamics. However, monitoring species in leaf litter is challenging, especiallyin highly diverse environments such as tropical forests, because individualsmay easily camouflage themselves or hide in the litter layer. Identifying species basedon environmental DNA (eDNA) would allow us to assess biodiversity in this microhabitat,without the need for direct observation of individuals. We applied eDNAmetabarcoding to analyze large amounts of leaf litter (1 kg per sample) collected inthe Brazilian Atlantic forest. We compared two DNA extraction methods, one totaland one extracellular, and amplified a fragment of the mitochondrial 18S rRNA genecommon to all eukaryotes, to assess the performance of eDNA from leaf litter samplesin identifying different eukaryotic taxonomic groups. We also amplified twofragments of the mitochondrial 12S rRNA gene to specifically test the power of thisapproach for monitoring vertebrate species, with a focus on anurans. Most of theeukaryote sequence reads obtained were classified as Fungi, followed by Metazoa,and Viridiplantae. Most vertebrate sequences were assigned to Homo sapiens; onlytwo sequences assigned to the genus Phyllomedusa and the species Euparkerella brasiliensiscan be considered true detections of anurans in our eDNA samples. The detectionof taxa varied depending on the DNA extraction method applied. Our resultsdemonstrate that the analysis of eDNA from leaf litter samples has low power formonitoring vertebrate species and should be preferentially applied to describe activeand abundant taxa in terrestrial communities, such as Fungi and invertebrates.
Fil: Martins Lopes, Carla. Universidade Estadual Paulista Julio de Mesquita Filho; Brasil
Fil: Baêta, Délio. Universidade Estadual Paulista Julio de Mesquita Filho; Brasil
Fil: Sasso, Thais. Griffith University; Australia
Fil: Vanzetti, Agustín Iván. Universidad Nacional del Litoral. Facultad de Humanidades y Ciencias. Departamento de Ciencias Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe; Argentina
Fil: Raquel Zamudio, Kelly. Department Of Ecology And Evolutionary Biology ; Cornell University;
Fil: Taberlet, Pierre. Universite Grenoble Alpes; Francia
Fil: Baptista Haddad, Célio Fernando. Universidade Estadual Paulista Julio de Mesquita Filho; Brasil
Materia
anura
beta diversity
DNA extraction
eukaryotes
sequencing
vertebrates
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/245602
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/245602
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Power and limitations of environmental DNA metabarcoding for surveying leaf litter eukaryotic communitiesMartins Lopes, CarlaBaêta, DélioSasso, ThaisVanzetti, Agustín IvánRaquel Zamudio, KellyTaberlet, PierreBaptista Haddad, Célio Fernandoanurabeta diversityDNA extractioneukaryotessequencingvertebrateshttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Leaf litter habitats shelter a great variety of organisms, which play an important rolein ecosystem dynamics. However, monitoring species in leaf litter is challenging, especiallyin highly diverse environments such as tropical forests, because individualsmay easily camouflage themselves or hide in the litter layer. Identifying species basedon environmental DNA (eDNA) would allow us to assess biodiversity in this microhabitat,without the need for direct observation of individuals. We applied eDNAmetabarcoding to analyze large amounts of leaf litter (1 kg per sample) collected inthe Brazilian Atlantic forest. We compared two DNA extraction methods, one totaland one extracellular, and amplified a fragment of the mitochondrial 18S rRNA genecommon to all eukaryotes, to assess the performance of eDNA from leaf litter samplesin identifying different eukaryotic taxonomic groups. We also amplified twofragments of the mitochondrial 12S rRNA gene to specifically test the power of thisapproach for monitoring vertebrate species, with a focus on anurans. Most of theeukaryote sequence reads obtained were classified as Fungi, followed by Metazoa,and Viridiplantae. Most vertebrate sequences were assigned to Homo sapiens; onlytwo sequences assigned to the genus Phyllomedusa and the species Euparkerella brasiliensiscan be considered true detections of anurans in our eDNA samples. The detectionof taxa varied depending on the DNA extraction method applied. Our resultsdemonstrate that the analysis of eDNA from leaf litter samples has low power formonitoring vertebrate species and should be preferentially applied to describe activeand abundant taxa in terrestrial communities, such as Fungi and invertebrates.Fil: Martins Lopes, Carla. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: Baêta, Délio. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: Sasso, Thais. Griffith University; AustraliaFil: Vanzetti, Agustín Iván. Universidad Nacional del Litoral. Facultad de Humanidades y Ciencias. Departamento de Ciencias Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe; ArgentinaFil: Raquel Zamudio, Kelly. Department Of Ecology And Evolutionary Biology ; Cornell University;Fil: Taberlet, Pierre. Universite Grenoble Alpes; FranciaFil: Baptista Haddad, Célio Fernando. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilWiley2020-10info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/vnd.openxmlformats-officedocument.wordprocessingml.documentapplication/pdfhttp://hdl.handle.net/11336/245602Martins Lopes, Carla; Baêta, Délio; Sasso, Thais; Vanzetti, Agustín Iván; Raquel Zamudio, Kelly; et al.; Power and limitations of environmental DNA metabarcoding for surveying leaf litter eukaryotic communities; Wiley; Environmental DNA; 3; 3; 10-2020; 528-5402637-49432637-4943CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/10.1002/edn3.142info:eu-repo/semantics/altIdentifier/doi/10.1002/edn3.142info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-nd/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-15T15:23:57Zoai:ri.conicet.gov.ar:11336/245602instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-10-15 15:23:57.427CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Power and limitations of environmental DNA metabarcoding for surveying leaf litter eukaryotic communities
title Power and limitations of environmental DNA metabarcoding for surveying leaf litter eukaryotic communities
spellingShingle Power and limitations of environmental DNA metabarcoding for surveying leaf litter eukaryotic communities
Martins Lopes, Carla
anura
beta diversity
DNA extraction
eukaryotes
sequencing
vertebrates
title_short Power and limitations of environmental DNA metabarcoding for surveying leaf litter eukaryotic communities
title_full Power and limitations of environmental DNA metabarcoding for surveying leaf litter eukaryotic communities
title_fullStr Power and limitations of environmental DNA metabarcoding for surveying leaf litter eukaryotic communities
title_full_unstemmed Power and limitations of environmental DNA metabarcoding for surveying leaf litter eukaryotic communities
title_sort Power and limitations of environmental DNA metabarcoding for surveying leaf litter eukaryotic communities
dc.creator.none.fl_str_mv Martins Lopes, Carla
Baêta, Délio
Sasso, Thais
Vanzetti, Agustín Iván
Raquel Zamudio, Kelly
Taberlet, Pierre
Baptista Haddad, Célio Fernando
author Martins Lopes, Carla
author_facet Martins Lopes, Carla
Baêta, Délio
Sasso, Thais
Vanzetti, Agustín Iván
Raquel Zamudio, Kelly
Taberlet, Pierre
Baptista Haddad, Célio Fernando
author_role author
author2 Baêta, Délio
Sasso, Thais
Vanzetti, Agustín Iván
Raquel Zamudio, Kelly
Taberlet, Pierre
Baptista Haddad, Célio Fernando
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv anura
beta diversity
DNA extraction
eukaryotes
sequencing
vertebrates
topic anura
beta diversity
DNA extraction
eukaryotes
sequencing
vertebrates
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Leaf litter habitats shelter a great variety of organisms, which play an important rolein ecosystem dynamics. However, monitoring species in leaf litter is challenging, especiallyin highly diverse environments such as tropical forests, because individualsmay easily camouflage themselves or hide in the litter layer. Identifying species basedon environmental DNA (eDNA) would allow us to assess biodiversity in this microhabitat,without the need for direct observation of individuals. We applied eDNAmetabarcoding to analyze large amounts of leaf litter (1 kg per sample) collected inthe Brazilian Atlantic forest. We compared two DNA extraction methods, one totaland one extracellular, and amplified a fragment of the mitochondrial 18S rRNA genecommon to all eukaryotes, to assess the performance of eDNA from leaf litter samplesin identifying different eukaryotic taxonomic groups. We also amplified twofragments of the mitochondrial 12S rRNA gene to specifically test the power of thisapproach for monitoring vertebrate species, with a focus on anurans. Most of theeukaryote sequence reads obtained were classified as Fungi, followed by Metazoa,and Viridiplantae. Most vertebrate sequences were assigned to Homo sapiens; onlytwo sequences assigned to the genus Phyllomedusa and the species Euparkerella brasiliensiscan be considered true detections of anurans in our eDNA samples. The detectionof taxa varied depending on the DNA extraction method applied. Our resultsdemonstrate that the analysis of eDNA from leaf litter samples has low power formonitoring vertebrate species and should be preferentially applied to describe activeand abundant taxa in terrestrial communities, such as Fungi and invertebrates.
Fil: Martins Lopes, Carla. Universidade Estadual Paulista Julio de Mesquita Filho; Brasil
Fil: Baêta, Délio. Universidade Estadual Paulista Julio de Mesquita Filho; Brasil
Fil: Sasso, Thais. Griffith University; Australia
Fil: Vanzetti, Agustín Iván. Universidad Nacional del Litoral. Facultad de Humanidades y Ciencias. Departamento de Ciencias Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe; Argentina
Fil: Raquel Zamudio, Kelly. Department Of Ecology And Evolutionary Biology ; Cornell University;
Fil: Taberlet, Pierre. Universite Grenoble Alpes; Francia
Fil: Baptista Haddad, Célio Fernando. Universidade Estadual Paulista Julio de Mesquita Filho; Brasil
description Leaf litter habitats shelter a great variety of organisms, which play an important rolein ecosystem dynamics. However, monitoring species in leaf litter is challenging, especiallyin highly diverse environments such as tropical forests, because individualsmay easily camouflage themselves or hide in the litter layer. Identifying species basedon environmental DNA (eDNA) would allow us to assess biodiversity in this microhabitat,without the need for direct observation of individuals. We applied eDNAmetabarcoding to analyze large amounts of leaf litter (1 kg per sample) collected inthe Brazilian Atlantic forest. We compared two DNA extraction methods, one totaland one extracellular, and amplified a fragment of the mitochondrial 18S rRNA genecommon to all eukaryotes, to assess the performance of eDNA from leaf litter samplesin identifying different eukaryotic taxonomic groups. We also amplified twofragments of the mitochondrial 12S rRNA gene to specifically test the power of thisapproach for monitoring vertebrate species, with a focus on anurans. Most of theeukaryote sequence reads obtained were classified as Fungi, followed by Metazoa,and Viridiplantae. Most vertebrate sequences were assigned to Homo sapiens; onlytwo sequences assigned to the genus Phyllomedusa and the species Euparkerella brasiliensiscan be considered true detections of anurans in our eDNA samples. The detectionof taxa varied depending on the DNA extraction method applied. Our resultsdemonstrate that the analysis of eDNA from leaf litter samples has low power formonitoring vertebrate species and should be preferentially applied to describe activeand abundant taxa in terrestrial communities, such as Fungi and invertebrates.
publishDate 2020
dc.date.none.fl_str_mv 2020-10
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/245602
Martins Lopes, Carla; Baêta, Délio; Sasso, Thais; Vanzetti, Agustín Iván; Raquel Zamudio, Kelly; et al.; Power and limitations of environmental DNA metabarcoding for surveying leaf litter eukaryotic communities; Wiley; Environmental DNA; 3; 3; 10-2020; 528-540
2637-4943
2637-4943
CONICET Digital
CONICET
url http://hdl.handle.net/11336/245602
identifier_str_mv Martins Lopes, Carla; Baêta, Délio; Sasso, Thais; Vanzetti, Agustín Iván; Raquel Zamudio, Kelly; et al.; Power and limitations of environmental DNA metabarcoding for surveying leaf litter eukaryotic communities; Wiley; Environmental DNA; 3; 3; 10-2020; 528-540
2637-4943
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/10.1002/edn3.142
info:eu-repo/semantics/altIdentifier/doi/10.1002/edn3.142
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/vnd.openxmlformats-officedocument.wordprocessingml.document
application/pdf
dc.publisher.none.fl_str_mv Wiley
publisher.none.fl_str_mv Wiley
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.22299

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