DNA Metabarcoding of Amazonian Ichthyoplankton Swarms

Maggia, Marie-Eugénie; Vigouroux, Yves; Renno, Jean‐François; Duponchelle, Fabrice; Desmarais, Érick; Nunez, Jésus; García-Dávila, Carmen Rosa; Carvajal‐Vallejos, Fernando M.; Paradis, Emmanuel; Martin, Jean; Mariac, Cédric

doi:10.1371/journal.pone.0170009

Cited by 26 publications

(25 citation statements)

References 36 publications

(36 reference statements)

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“…In this study, we will compare the result from this new approach to a previous approach using four probes designed for siluriforms [ 21 ]. In the following text, we will use the term single-probe for the COI from Danio and the term siluriform probes for the four probes previously developed [ 21 ].…”

Section: Methodsmentioning

confidence: 99%

“…These two batches were randomly divided into two subsets. The first subset was used to perform individual DNA extractions and were then Sanger sequenced [ 21 ]. These individual DNAs (270 individuals from the Marañon River and 102 from the Napo River) were pooled in equimolar quantities to constitute mock samples (Mar-Mock and Nap-Mock).…”

Section: Methodsmentioning

confidence: 99%

“…We previously successfully used enrichment by capture to develop a method allowing quantification of siluriform species in Amazonian ichthyoplankton samples, using four different probes distributed in the main clades of the phylogeny of Amazonian siluriform species [ 21 ]. Yet, siluriform species represent only ~20% of the Amazonian fish diversity.…”

Section: Introductionmentioning

confidence: 99%

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Metabarcoding by capture using a single COI probe (MCSP) to identify and quantify fish species in ichthyoplankton swarms

et al. 2018

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The ability to determine the composition and relative frequencies of fish species in large ichthyoplankton swarms could have extremely important ecological applications However, this task is currently hampered by methodological limitations. We proposed a new method for Amazonian species based on hybridization capture of the COI gene DNA from a distant species (Danio rerio), absent from our study area (the Amazon basin). The COI sequence of this species is approximately equidistant from all COI of Amazonian species available. By using this sequence as probe we successfully facilitated the simultaneous identification of fish larvae belonging to the order Siluriformes and to the Characiformes represented in our ichthyoplankton samples. Species relative frequencies, estimated by the number of reads, showed almost perfect correlations with true frequencies estimated by a Sanger approach, allowing the development of a quantitative approach. We also proposed a further improvement to a previous protocol, which enables lowering the sequencing effort by 40 times. This new Metabarcoding by Capture using a Single Probe (MCSP) methodology could have important implications for ecology, fisheries management and conservation in fish biodiversity hotspots worldwide. Our approach could easily be extended to other plant and animal taxa.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Metabarcoding by capture using a single COI probe (MCSP) to identify and quantify fish species in ichthyoplankton swarms

et al. 2018

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“…This observation reinforces the idea that more sequences of fish species must be deposited in databases, especially in river basins with rich fish fauna as the Upper Paraná River. Another positive aspect is that, compared with DNA barcoding (Arroyave and Stiassny 2014, Becker et al 2015, Frantine-Silva et al 2015, our method can trigger significant advances in the quality of ecological studies in fish, as observed in some recent studies with metabarcoding (Guillerault et al 2017, Maggia et al 2017, Mariac et al 2018, Barbato et al 2019 and, mainly, to ensure significant reduction in labor time and cost per specimen reaching 80% of reduction (Shokralla et al 2015). Despite some differences in obtaining DNA samples, both environmental DNA (eDNA) and DNA metabarcoding from bulk samples are subject to false negatives and false positives (Ficetola Gentile et al 2015Gentile et al , 2016Divoll et al 2018).…”

Section: Species Identificationmentioning

confidence: 99%

“…To solve this problem, DNA metabarcoding, based on next generation sequencing (NGS) could offer an alternative approach, allowing a reduction of labor time as well as costs. Although Neotropical ichthyofauna metabarcoding studies are scarce (Maggia et al 2017, Mariac et al 2018, Sales et al 2019, this technique has been utilized in several ecological studies on ichthyoplankton and also to identify gut contents (Cruaud et al 2017, Guillerault et al 2017, Maggia et al 2017, Divoll et al 2018, Barbato et al 2019).…”

Section: Introductionmentioning

confidence: 99%

DNA metabarcoding of Neotropical ichthyoplankton: Enabling high accuracy with lower cost

Nobile¹,

Freitas‐Souza²,

Ruiz‐Ruano³

et al. 2019

MBMG

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Knowledge of ichthyoplankton dynamics is extremely important for conservation management as it can provide information about preferential spawning sites, reproductive period, migratory routes and recruitment success, which can be used to guide management and conservation efforts. However, identification of the eggs and larvae of Neotropical freshwater fish is a difficult task. DNA barcodes have emerged as an alternative and highly accurate approach for species identification, but DNA barcoding can be time-consuming and costly. To solve this problem, we aimed to develop a simple protocol based on DNA metabarcoding, to investigate whether it is possible to detect and quantify all species present in a pool of organisms. To do this, 230 larvae were cut in half, one half was sequenced by the Sanger technique and the other half was used to compose six arrays with a pool of larvae that were sequenced using a next-generation technique (NGS). The results of the Sanger sequencing allowed the identification of almost all larvae at species level, and the results from NGS showed high accuracy in species detection, ranging from 83% to 100%, with an average of 95% in all samples. No false positives were detected. The frequency of organisms in the two methods was positively correlated (Pearson), with low variation among species. In conclusion, this protocol represents a considerable advance in ichthyoplankton studies, allowing a rapid, cost-effective, quali-quantitative approach that improves the accuracy of identification.

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A drop in the ocean: Monitoring fish communities in spawning areas using environmental DNA

et al. 2020

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Early life stages of aquatic organisms are particularly vulnerable to climatic stressors; however, they are difficult to monitor due to challenges in sampling and morphological identification. Environmental DNA (eDNA) from water samples represents an opportunity for rapid, nondestructive monitoring of aquatic community composition as well as single species monitoring. eDNA can also detect spawning events, although has not been yet tested in offshore spawning grounds. Here, we used metabarcoding of water samples to detect the presence of key fish taxa in spawning areas that are difficult to monitor using traditional means. We analyzed DNA from water samples and fish larvae samples at 14 offshore sites, using 12S mitochondrial metabarcoding and compared taxa detections, diversity, and community structure estimated by both sample types. Species richness and diversity did not differ between water and larvae samples. Both sample types detected a core of 12 taxa across the survey, with an average agreement in detections of 75% at sampling site level. Water samples detected two of the three most abundant taxa, the sandeel, Ammodytes marinus, and clupeids, Clupea harengus/Sprattus sprattus, at 31% and 38% more sites than larvae samples respectively, while Callionymus sp. was more prevalent in larvae samples. Mackerel (Scomber scombrus) and blue whiting (Micromestius poutassou) were only detected in water samples despite sampling taking place at peak spawning times for these species. Our results demonstrate that eDNA metabarcoding provides a rapid and feasible monitoring method for the management of key taxa, such as sandeel, that cannot be easily monitored using traditional capture surveys.

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DNA Metabarcoding of Amazonian Ichthyoplankton Swarms

Cited by 26 publications

References 36 publications

Metabarcoding by capture using a single COI probe (MCSP) to identify and quantify fish species in ichthyoplankton swarms

Metabarcoding by capture using a single COI probe (MCSP) to identify and quantify fish species in ichthyoplankton swarms

DNA metabarcoding of Neotropical ichthyoplankton: Enabling high accuracy with lower cost

A drop in the ocean: Monitoring fish communities in spawning areas using environmental DNA

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