eDNA in a bottleneck: Obstacles to fish metabarcoding studies in megadiverse freshwater systems

Jackman, Jake M.; Benvenuto, Chiara; Coscia, Ilaria; Carvalho, Cintia Oliveira; Ready, Jonathan Stuart; Boubli, Jean P.; Magnusson, William E.; McDevitt, Allan D.; Sales, Naiara Guimarães

doi:10.1002/edn3.191

Cited by 45 publications

(36 citation statements)

References 59 publications

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“…Likewise 37 , detected and correctly assigned all 67 species with 12S previously designed primers and reference library in the São Francisco River, Brazil. In contrast 32 , assigned only 4 of 84 MOTUs to species, demonstrating problems of taxonomic resolution in the target gene and general threshold used for species assignment.…”

Section: Discussionmentioning

confidence: 95%

“…In addition to the two aforementioned factors, other specific issues such as low sampling effort in the stream (i.e., restricted to a 50-m stretch), difficulty to sample cryptobiotic habits, hidden species diversity, and lack of www.nature.com/scientificreports/ an appropriate threshold for taxonomic assignments 32 in Amazonian fishes could have contributed to the low overlap between CBS and MBS in our study. Examples of these problems are discussed in the section below.…”

Section: Discussionmentioning

confidence: 97%

“…Thus, it is likely that, in the near future, DNA barcoding and eDNA metabarcoding methods will converge to use large portions of the mitochondrial genome. Regardless of the fragment or the threshold used to delimit species (e.g., 32 ), it is essential that studies involving eDNA for assessing fish diversity move towards building robust mitochondrial DNA reference libraries based on vouchered specimens.…”

Section: Discussionmentioning

confidence: 99%

“…Any thresholds for taxonomic assignments (e.g., 98.5% as used here) are arbitrary and should reflect both over-and underestimation of species diversity, considering that there are several morphologically cryptic species with large molecular divergence and morphologically distinct species with small genetic divergence. The dereplicated reads were denoised by removing all putatively chimeric and erroneous detections to keep only true sequences, yet overestimations in the number of species may still be the result of ASVs (e.g., 32 ). For example, our recognition of the nine species of Leporinus (Leporinus apollo, Leporinus sp.…”

Section: Discussionmentioning

confidence: 99%

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The critical role of natural history museums in advancing eDNA for biodiversity studies: a case study with Amazonian fishes

Santana

Parenti

Dillman

et al. 2021

Sci Rep

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Ichthyological surveys have traditionally been conducted using whole-specimen, capture-based sampling with varied but conventional fishing gear. Recently, environmental DNA (eDNA) metabarcoding has emerged as a complementary, and possible alternative, approach to whole-specimen methodologies. In the tropics, where much of the diversity remains undescribed, vast reaches continue unexplored, and anthropogenic activities are constant threats; there have been few eDNA attempts for ichthyological inventories. We tested the discriminatory power of eDNA using MiFish primers with existing public reference libraries and compared this with capture-based methods in two distinct ecosystems in the megadiverse Amazon basin. In our study, eDNA provided an accurate snapshot of the fishes at higher taxonomic levels and corroborated its effectiveness to detect specialized fish assemblages. Some flaws in fish metabarcoding studies are routine issues addressed in natural history museums. Thus, by expanding their archives and adopting a series of initiatives linking collection-based research, training and outreach, natural history museums can enable the effective use of eDNA to survey Earth’s hotspots of biodiversity before taxa go extinct. Our project surveying poorly explored rivers and using DNA vouchered archives to build metabarcoding libraries for Neotropical fishes can serve as a model of this protocol.

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Section: Discussionmentioning

confidence: 95%

Section: Discussionmentioning

confidence: 97%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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The critical role of natural history museums in advancing eDNA for biodiversity studies: a case study with Amazonian fishes

Santana

Parenti

Dillman

et al. 2021

Sci Rep

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“…Although eDNA metabarcoding is a powerful tool for biodiversity, as it has been widely used for different purposes and different taxonomic groups, including identification and quantification of Neotropical ichthyofauna 16,76,77 , many issues can hamper the metabarcoding results 7,10,78,79 . Shaw et al 10 drew attention to methodological considerations related to the eDNA sampling process for freshwater fishes.…”

Section: Discussionmentioning

confidence: 99%

Monitoring fish communities through environmental DNA metabarcoding in the fish pass system of the second largest hydropower plant in the world

Pont

Ritter

Agostinis³

et al. 2021

Preprint

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The Itaipu Hydroelectric Power Plant is the second largest in the world in power generation. The artificial barrier created by its dam imposes an obstacle for fish migration. Thus, in 2002, a fish pass system, named Piracema Channel, was built to allow fish to access areas upstream of the reservoir. We tested the potential of metabarcoding to monitor the impact of both the dam and associated fish pass system in the Parana River fish communities and to compare it with traditional monitoring methods. Using a fragment of the 12S gene, we characterized richness and community composition based on amplicon sequence variants, operational taxonomic units, and zero-radius OTUs. We combined GenBank and in-house data for taxonomic assignment. We found that different bioinformatics approaches showed similar results. Also, we found a decrease in fish diversity from 2019 to 2020 probably due to the recent extreme drought experienced in southeastern Brazil. The highest alpha diversity was recorded in the mouth of the fish pass system, located in a protected valley with the highest environmental heterogeneity. Despite the clear indication that the reference databases need to be continuously improved, our results demonstrate the analytical efficiency of the metabarcoding to monitor fish species.

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Comparing the performance of 12S mitochondrial primers for fish environmental DNA across ecosystems

Richards

Flück

et al. 2021

Environmental DNA

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Through the development of environmental DNA (eDNA) metabarcoding, in situ monitoring of organisms is becoming easier and promises a revolution in our approaches to detect changes in biodiversity over space and time. A cornerstone of eDNA approach is the development of primer pairs that allow amplifying the DNA of specific taxonomic groups, which is then used to link the DNA sequence to taxonomic identification. Here, we propose a framework for comparing primer pairs regarding (a) their capacity to bind and amplify a broad coverage of species within the target clade using in silico PCR, (b) their capacity to not only discriminate between species but also genera or families, and (c) their in situ specificity and efficiency across a variety of environments. As a case study, we focus on two mitochondrial 12S primer pairs, MiFish‐U and teleo, which were designed to amplify fishes. We found that the performance of in silico PCRs were high for both primer pairs, but teleo amplified more genera across Actinopterygii, Chondrichthyes, and Petromyzontomorphi than MiFish‐U. In contrast, the discriminatory power for species, genera, and families were higher for MiFish‐U than teleo, likely associated with the greater length of the amplified DNA fragments. The evaluation of their in situ efficiency showed a higher recovered species richness of teleo compared to MiFish‐U in tropical and temperate freshwater environments, but that generally both teleo and MiFish‐U primers pairs perform well to monitor fish species. Since more species were detected when used together, those primer pairs are best used in combination to increase the ability of species detection.

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eDNA in a bottleneck: Obstacles to fish metabarcoding studies in megadiverse freshwater systems

Abstract: This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

Cited by 45 publications

References 59 publications

The critical role of natural history museums in advancing eDNA for biodiversity studies: a case study with Amazonian fishes

The critical role of natural history museums in advancing eDNA for biodiversity studies: a case study with Amazonian fishes

Monitoring fish communities through environmental DNA metabarcoding in the fish pass system of the second largest hydropower plant in the world

Comparing the performance of 12S mitochondrial primers for fish environmental DNA across ecosystems

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