Detecting aquatic and terrestrial biodiversity in a tropical estuary using environmental DNA

Estuaries are characterized by a tidal regime and are strongly influenced by hydrodynamics and host diverse and highly dynamic habitats, from fresh, brackish, or saltwater to terrestrial, whose biodiversity is especially difficult to monitor. Here, we investigated the potential of environmental DNA...

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Published inBiotropica Vol. 53; no. 6; pp. 1606 - 1619
Main Authors Polanco F., Andrea, Mutis Martinezguerra, Maria, Marques, Virginie, Villa‐Navarro, Francisco, Borrero Pérez, Giomar Helena, Cheutin, Marie‐Charlotte, Dejean, Tony, Hocdé, Régis, Juhel, Jean‐Baptiste, Maire, Eva, Manel, Stéphanie, Spescha, Manuel, Valentini, Alice, Mouillot, David, Albouy, Camille, Pellissier, Loïc
Format Journal Article
LanguageEnglish
Published Hoboken Wiley Subscription Services, Inc 01.11.2021
Wiley
Subjects
Amphibians
Aquatic organisms
Aquatic reptiles
Biodiversity
Biodiversity and Ecology
biomonitoring
Caribbean Sea
Colombia
Deoxyribonucleic acid
DNA
DNA barcoding
Don Diego River
ecosystems
Environmental DNA
Environmental Engineering
Environmental Sciences
Estuaries
Estuarine dynamics
Flight
Freshwater
Freshwater fish
genes
Hydrodynamics
Inland water environment
Marine fish
Mitochondrial DNA
Reptiles
ribosomal RNA
River mouth
River mouths
Rivers
rRNA 12S
Saline water
Seawater
Sierra Nevada de Santa Marta
Terrestrial environments
Tropical climate
tropical ecosystem
vertebrate
Vertebrates
Colombia
Colombia
biodiversity
biomonitoring
Sierra Nevada de Santa Marta
environmental DNA
Don Diego River
vertebrate
tropical ecosystem
Caribbean Sea
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Abstract Estuaries are characterized by a tidal regime and are strongly influenced by hydrodynamics and host diverse and highly dynamic habitats, from fresh, brackish, or saltwater to terrestrial, whose biodiversity is especially difficult to monitor. Here, we investigated the potential of environmental DNA (eDNA) metabarcoding, with three primer sets targeting different regions of the mitochondrial DNA 12S ribosomal RNA gene, to detect vertebrate diversity in the estuary of the Don Diego River in Colombia. With eDNA, we detected not only aquatic organisms, including fishes, amphibians, and reptiles, but also a large diversity of terrestrial, arboreal, and flying vertebrates, including mammals and birds, living in the estuary surroundings. Further, the eDNA signal remained relatively localized along the watercourse. A transect from the deep outer section of the estuary, across the river mouth toward the inner section of the river, showed marked taxonomic turnover from typical marine to freshwater fishes, while eDNA of terrestrial and arboreal species was mainly found in the inner section of the estuary. Our results indicate that eDNA enables the detection of a large diversity of vertebrates and could become an important tool for biodiversity monitoring in estuaries, where water integrates information across the ecosystem. in Spanish is available with online material. Resumen Los estuarios se caracterizan por un régimen de mareas y están fuertemente influenciados por la hidrodinámica, albergando hábitats diversos y muy dinámicos, desde agua dulce, salobre o salada hasta terrestre, cuya biodiversidad es especialmente difícil de monitorear. Aquí investigamos el potencial del metabarcoding del ADN ambiental (eDNA), con tres pares de marcadores dirigidos a diferentes regiones del gen 12S del ADN mitocondrial en el ARN ribosomal, para detectar la diversidad de vertebrados en el estuario del río Don Diego en Colombia. Con el eDNA, detectamos no sólo organismos acuáticos, incluyendo peces, anfibios y reptiles, sino también una gran diversidad de vertebrados terrestres, arborícolas y voladores, incluyendo mamíferos y aves, que viven en los alrededores del estuario. Además, la señal de eDNA se mantuvo relativamente localizada a lo largo del curso de agua. Un transecto desde la sección exterior profunda del estuario, a través de la desembocadura del río hacia la sección interior del mismo, mostró un marcado cambio taxonómico desde los típicos peces marinos a los de agua dulce, mientras que el eDNA de las especies terrestres y arborícolas se encontró principalmente en la sección interior del estuario. Nuestros resultados indican que el eDNA permite detectar una gran diversidad de vertebrados y podría convertirse en una herramienta importante para el seguimiento de la biodiversidad en los estuarios, donde el agua integra la información de todo el ecosistema. eDNA enables the detection of a large diversity of vertebrates and could become an important tool for biodiversity monitoring in estuaries, where water integrates information across the ecosystem.
AbstractList Estuaries are characterized by a tidal regime and are strongly influenced by hydrodynamics and host diverse and highly dynamic habitats, from fresh, brackish, or saltwater to terrestrial, whose biodiversity is especially difficult to monitor. Here, we investigated the potential of environmental DNA (eDNA) metabarcoding, with three primer sets targeting different regions of the mitochondrial DNA 12S ribosomal RNA gene, to detect vertebrate diversity in the estuary of the Don Diego River in Colombia. With eDNA, we detected not only aquatic organisms, including fishes, amphibians, and reptiles, but also a large diversity of terrestrial, arboreal, and flying vertebrates, including mammals and birds, living in the estuary surroundings. Further, the eDNA signal remained relatively localized along the watercourse. A transect from the deep outer section of the estuary, across the river mouth toward the inner section of the river, showed marked taxonomic turnover from typical marine to freshwater fishes, while eDNA of terrestrial and arboreal species was mainly found in the inner section of the estuary. Our results indicate that eDNA enables the detection of a large diversity of vertebrates and could become an important tool for biodiversity monitoring in estuaries, where water integrates information across the ecosystem. in Spanish is available with online material. Resumen Los estuarios se caracterizan por un régimen de mareas y están fuertemente influenciados por la hidrodinámica, albergando hábitats diversos y muy dinámicos, desde agua dulce, salobre o salada hasta terrestre, cuya biodiversidad es especialmente difícil de monitorear. Aquí investigamos el potencial del metabarcoding del ADN ambiental (eDNA), con tres pares de marcadores dirigidos a diferentes regiones del gen 12S del ADN mitocondrial en el ARN ribosomal, para detectar la diversidad de vertebrados en el estuario del río Don Diego en Colombia. Con el eDNA, detectamos no sólo organismos acuáticos, incluyendo peces, anfibios y reptiles, sino también una gran diversidad de vertebrados terrestres, arborícolas y voladores, incluyendo mamíferos y aves, que viven en los alrededores del estuario. Además, la señal de eDNA se mantuvo relativamente localizada a lo largo del curso de agua. Un transecto desde la sección exterior profunda del estuario, a través de la desembocadura del río hacia la sección interior del mismo, mostró un marcado cambio taxonómico desde los típicos peces marinos a los de agua dulce, mientras que el eDNA de las especies terrestres y arborícolas se encontró principalmente en la sección interior del estuario. Nuestros resultados indican que el eDNA permite detectar una gran diversidad de vertebrados y podría convertirse en una herramienta importante para el seguimiento de la biodiversidad en los estuarios, donde el agua integra la información de todo el ecosistema. eDNA enables the detection of a large diversity of vertebrates and could become an important tool for biodiversity monitoring in estuaries, where water integrates information across the ecosystem.
Estuaries are characterized by a tidal regime and are strongly influenced by hydrodynamics and host diverse and highly dynamic habitats, from fresh, brackish, or saltwater to terrestrial, whose biodiversity is especially difficult to monitor. Here, we investigated the potential of environmental DNA (eDNA) metabarcoding, with three primer sets targeting different regions of the mitochondrial DNA 12S ribosomal RNA gene, to detect vertebrate diversity in the estuary of the Don Diego River in Colombia. With eDNA, we detected not only aquatic organisms, including fishes, amphibians, and reptiles, but also a large diversity of terrestrial, arboreal, and flying vertebrates, including mammals and birds, living in the estuary surroundings. Further, the eDNA signal remained relatively localized along the watercourse. A transect from the deep outer section of the estuary, across the river mouth toward the inner section of the river, showed marked taxonomic turnover from typical marine to freshwater fishes, while eDNA of terrestrial and arboreal species was mainly found in the inner section of the estuary. Our results indicate that eDNA enables the detection of a large diversity of vertebrates and could become an important tool for biodiversity monitoring in estuaries, where water integrates information across the ecosystem.
Estuaries are characterized by a tidal regime and are strongly influenced by hydrodynamics and host diverse and highly dynamic habitats, from fresh, brackish, or saltwater to terrestrial, whose biodiversity is especially difficult to monitor. Here, we investigated the potential of environmental DNA (eDNA) metabarcoding, with three primer sets targeting different regions of the mitochondrial DNA 12S ribosomal RNA gene, to detect vertebrate diversity in the estuary of the Don Diego River in Colombia. With eDNA, we detected not only aquatic organisms, including fishes, amphibians, and reptiles, but also a large diversity of terrestrial, arboreal, and flying vertebrates, including mammals and birds, living in the estuary surroundings. Further, the eDNA signal remained relatively localized along the watercourse. A transect from the deep outer section of the estuary, across the river mouth toward the inner section of the river, showed marked taxonomic turnover from typical marine to freshwater fishes, while eDNA of terrestrial and arboreal species was mainly found in the inner section of the estuary. Our results indicate that eDNA enables the detection of a large diversity of vertebrates and could become an important tool for biodiversity monitoring in estuaries, where water integrates information across the ecosystem. Abstract in Spanish is available with online material. Los estuarios se caracterizan por un régimen de mareas y están fuertemente influenciados por la hidrodinámica, albergando hábitats diversos y muy dinámicos, desde agua dulce, salobre o salada hasta terrestre, cuya biodiversidad es especialmente difícil de monitorear. Aquí investigamos el potencial del metabarcoding del ADN ambiental (eDNA), con tres pares de marcadores dirigidos a diferentes regiones del gen 12S del ADN mitocondrial en el ARN ribosomal, para detectar la diversidad de vertebrados en el estuario del río Don Diego en Colombia. Con el eDNA, detectamos no sólo organismos acuáticos, incluyendo peces, anfibios y reptiles, sino también una gran diversidad de vertebrados terrestres, arborícolas y voladores, incluyendo mamíferos y aves, que viven en los alrededores del estuario. Además, la señal de eDNA se mantuvo relativamente localizada a lo largo del curso de agua. Un transecto desde la sección exterior profunda del estuario, a través de la desembocadura del río hacia la sección interior del mismo, mostró un marcado cambio taxonómico desde los típicos peces marinos a los de agua dulce, mientras que el eDNA de las especies terrestres y arborícolas se encontró principalmente en la sección interior del estuario. Nuestros resultados indican que el eDNA permite detectar una gran diversidad de vertebrados y podría convertirse en una herramienta importante para el seguimiento de la biodiversidad en los estuarios, donde el agua integra la información de todo el ecosistema.
Estuaries are characterized by a tidal regime and are strongly influenced by hydrodynamics and host diverse and highly dynamic habitats, from fresh, brackish, or saltwater to terrestrial, whose biodiversity is especially difficult to monitor. Here, we investigated the potential of environmental DNA (eDNA) metabarcoding, with three primer sets targeting different regions of the mitochondrial DNA 12S ribosomal RNA gene, to detect vertebrate diversity in the estuary of the Don Diego River in Colombia. With eDNA, we detected not only aquatic organisms, including fishes, amphibians, and reptiles, but also a large diversity of terrestrial, arboreal, and flying vertebrates, including mammals and birds, living in the estuary surroundings. Further, the eDNA signal remained relatively localized along the watercourse. A transect from the deep outer section of the estuary, across the river mouth toward the inner section of the river, showed marked taxonomic turnover from typical marine to freshwater fishes, while eDNA of terrestrial and arboreal species was mainly found in the inner section of the estuary. Our results indicate that eDNA enables the detection of a large diversity of vertebrates and could become an important tool for biodiversity monitoring in estuaries, where water integrates information across the ecosystem. Abstract in Spanish is available with online material.
Author Valentini, Alice
Mutis Martinezguerra, Maria
Mouillot, David
Polanco F., Andrea
Spescha, Manuel
Pellissier, Loïc
Manel, Stéphanie
Maire, Eva
Albouy, Camille
Cheutin, Marie‐Charlotte
Dejean, Tony
Borrero Pérez, Giomar Helena
Hocdé, Régis
Juhel, Jean‐Baptiste
Marques, Virginie
Villa‐Navarro, Francisco
Author_xml – sequence: 1
  givenname: Andrea
  orcidid: 0000-0001-6121-5214
  surname: Polanco F.
  fullname: Polanco F., Andrea
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  organization: Museo de Historia Natural Marina de Colombia (MHNMC
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Copyright 2021 The Association for Tropical Biology and Conservation
Copyright © 2021 The Association for Tropical Biology and Conservation
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Copyright_xml – notice: 2021 The Association for Tropical Biology and Conservation
– notice: Copyright © 2021 The Association for Tropical Biology and Conservation
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Issue 6
Keywords Colombia
biodiversity
biomonitoring
Sierra Nevada de Santa Marta
environmental DNA
Don Diego River
vertebrate
tropical ecosystem
Caribbean Sea
Language English
License Distributed under a Creative Commons Attribution 4.0 International License: http://creativecommons.org/licenses/by/4.0
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Notes Camille Albouy and Loïc Pellissier shared senior authorship
Associate Editor: Jennifer Powers
Handling Editor: Gustavo Romero
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Snippet Estuaries are characterized by a tidal regime and are strongly influenced by hydrodynamics and host diverse and highly dynamic habitats, from fresh, brackish,...
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SubjectTerms Amphibians
Aquatic organisms
Aquatic reptiles
Biodiversity
Biodiversity and Ecology
biomonitoring
Caribbean Sea
Colombia
Deoxyribonucleic acid
DNA
DNA barcoding
Don Diego River
ecosystems
Environmental DNA
Environmental Engineering
Environmental Sciences
Estuaries
Estuarine dynamics
Flight
Freshwater
Freshwater fish
genes
Hydrodynamics
Inland water environment
Marine fish
Mitochondrial DNA
Reptiles
ribosomal RNA
River mouth
River mouths
Rivers
rRNA 12S
Saline water
Seawater
Sierra Nevada de Santa Marta
Terrestrial environments
Tropical climate
tropical ecosystem
vertebrate
Vertebrates
Title Detecting aquatic and terrestrial biodiversity in a tropical estuary using environmental DNA
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https://hal.science/hal-04203573
Volume 53
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