Freshwater vertebrate metabarcoding on Illumina platforms using double-indexed primers of the mitochondrial 16S rRNA gene

Vences, Miguel; Lyra, Mariana L.; Perl, R. G. Bina; Bletz, Molly C.; Stanković, D; Lopes, Carla Martins; Jarek, Michael; Bhuju, Sabin; Geffers, Robert; Haddad, Célio F. B.; Steinfartz, Sebastian

doi:10.1007/s12686-016-0550-y

Cited by 45 publications

(41 citation statements)

References 76 publications

(101 reference statements)

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“…Most prior eDNA studies have examined vertebrates in temperate freshwater streams [66], lakes [67] or sea water [68,69]. However, Lopes et al [30] recently demonstrated that eDNA surveys were effective in revealing anurans in streams in the Brazilian Atlantic forest, while Robson et al [32] developed eDNA protocols that employ qPCR to detect invasive fish in tropical environments.…”

Section: Discussionmentioning

confidence: 99%

Using eDNA to biomonitor the fish community in a tropical oligotrophic lake

et al. 2019

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Environmental DNA (eDNA) is an effective approach for detecting vertebrates and plants, especially in aquatic ecosystems, but prior studies have largely examined eDNA in cool temperate settings. By contrast, this study employs eDNA to survey the fish fauna in tropical Lake Bacalar (Mexico) with the additional goal of assessing the possible presence of invasive fishes, such as Amazon sailfin catfish and tilapia. Sediment and water samples were collected from eight stations in Lake Bacalar on three occasions over a 4-month interval. Each sample was stored in the presence or absence of lysis buffer to compare eDNA recovery. Short fragments (184–187 bp) of the cytochrome c oxidase I (COI) gene were amplified using fusion primers and then sequenced on Ion Torrent PGM or S5 before their source species were determined using a custom reference sequence database constructed on BOLD. In total, eDNA sequences were recovered from 75 species of vertebrates including 47 fishes, 15 birds, 7 mammals, 5 reptiles, and 1 amphibian. Although all species are known from this region, six fish species represent new records for the study area, while two require verification. Sequences for five species (2 birds, 2 mammals, 1 reptile) were only detected from sediments, while sequences from 52 species were only recovered from water. Because DNA from the Amazon sailfin catfish was not detected, we used a mock eDNA experiment to confirm our methods would enable its detection. In summary, we developed protocols that recovered eDNA from tropical oligotrophic aquatic ecosystems and confirmed their effectiveness in detecting fishes and diverse species of vertebrates.

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Section: Discussionmentioning

confidence: 99%

Using eDNA to biomonitor the fish community in a tropical oligotrophic lake

et al. 2019

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“…Most prior eDNA studies have examined vertebrates in temperate freshwater streams [63], lakes [64] or sea water [65,66]. However, Lopes et al [30] recently demonstrated that eDNA surveys were effective in revealing anurans in streams in the Brazilian Atlantic forest, while Robson et al [32] developed eDNA protocols that employ qPCR to detect invasive fish in tropical environments.…”

Section: Discussionmentioning

confidence: 99%

“…There are three major approaches for of eDNA detection: the use of qPCR to detect one or a small number of target species [67,68], shotgun sequencing of aquatic metagenomes [69] and PCR-based metabarcoding [28,29,63–66]. Metabarcoding studies cannot deliver information on species composition without a reliable reference database, such as that available for Mexican freshwater fishes which includes records for 93% of the 70 species known from Lake Bacalar and associated wetlands [48,51–54,70].…”

Section: Discussionmentioning

confidence: 99%

Using eDNA to biomonitor the fish community in a tropical oligotrophic lake

Valdéz-Moreno

Ivanova

Elías‐Gutiérrez

et al. 2018

Preprint

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Environmental DNA (eDNA) is an effective approach for detecting vertebrates and plants, especially in aquatic ecosystems, but prior studies have largely examined eDNA in cool temperate settings. By contrast, this study employs eDNA to survey the fish fauna in tropical Lake Bacalar (Mexico) with the additional goal of assessing the possible presence of invasive fishes, such as Amazon sailfin catfish. Sediment and water samples were collected from eight stations in Lake Bacalar on three occasions over a 4-month interval. Each sample was stored in the presence or absence of lysis buffer to compare eDNA recovery. Short fragments (184-187 bp) of the cytochrome c oxidase I (COI) gene were amplified using fusion primers and then sequenced on Ion Torrent PGM and S5 before their source species were determined using a custom reference sequence database constructed on BOLD. In total, eDNA sequences were recovered from 75 species of vertebrates including 47 fishes, 15 birds, 7 mammals, 5 reptiles, and 1 amphibian. Although all species are known from this region, 6 fish species represent new records for the study area, while 2 require verification. Sequences for five species (2 birds, 2 mammals, 1 reptile) were only detected from sediments, while sequences from 52 species were only recovered from water. Because DNA from the Amazon sailfin catfish was not detected, we used a mock eDNA experiment to confirm our methods were appropriate for its detection. We developed protocols that enabled the recovery of eDNA from tropical oligotrophic aquatic ecosystems, and confirmed their effectiveness in detecting diverse species of vertebrates including an invasive species of Amazon catfish.

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“…16S rRNA is a mitochondrial gene, present in higher copy number than nuclear genes in eDNA samples (Thomsen & Willerslev, ). It does not show great variation within species, but it shows high variation between closely related species, especially in fishes (Maretto, Reffo, Dalvit, Barcaccia, & Mantovani, ; Vences et al, ). The number of sequences for fishes in databases is similar to other mitochondrial genes such as cytochrome c oxidase subunit 1 ( COI ) or cytochrome b (Machida, Leray, Ho, & Knowlton, ).…”

Section: Methodsmentioning

confidence: 99%

A simple, rapid method for detecting seven common invasive fish species in Europe from environmental DNA

Clusa

García‐Vázquez

2018

Aquatic Conservation

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1. Biological invasions are a global threat to biodiversity, and many arise from deliberate introductions.2. The American freshwater fish Micropterus salmoides and Ameiurus spp. (Ameiurus melas and Ameiurus nebulosus) were introduced to Europe for recreational fishing, Gambusia holbrooki and Gambusia affinis were introduced for mosquito population control, and Lepomis gibbosus was introduced as an ornamental species. The Asiatic Pseudorasbora parva was acquired inadvertently as an accompanying species in fish consignments.3. This article presents a novel approach for detecting these species directly from water samples based on a panel of five taxon-specific primers within 16S rDNA. 4. The primers were validated from tissue, in aquarium experiments, and from Ebro River water samples (Spain). With a simple polymerase chain reaction (PCR) protocol, followed by visualization in agarose gel or capillary electrophoresis, it was possible to detect these species from environmental DNA concentrations as low as 0.89-100 pg mL -1 . 5. This sensitive and economical tool can be used to control European invasions of these species and to preserve native biodiversity.

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Freshwater vertebrate metabarcoding on Illumina platforms using double-indexed primers of the mitochondrial 16S rRNA gene

Cited by 45 publications

References 76 publications

Using eDNA to biomonitor the fish community in a tropical oligotrophic lake

Using eDNA to biomonitor the fish community in a tropical oligotrophic lake

Using eDNA to biomonitor the fish community in a tropical oligotrophic lake

A simple, rapid method for detecting seven common invasive fish species in Europe from environmental DNA

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