Evaluation of fish biodiversity in estuaries using environmental DNA metabarcoding

Ahn, Hyojin; Kume, Manabu; Terashima, Yuki; Feng, Ye; Kameyama, Shuichi; Miya, Masaki; Yamashita, Yoh; Kasai, Atsushi

doi:10.1371/journal.pone.0231127

Cited by 40 publications

(36 citation statements)

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“…In this context, a set of universal PCR primers for metabarcoding eDNA from fishes has been developed targeting a length of around 163-185 bp of the 12S rRNA gene region (MiFish; Miya et al, 2015). This widely used primer set has been pivotal in describing fish communities on a truly global scale (Miya et al, 2020) and has also provided meaningful information for species-rich rivers (Ahn et al, 2020). Despite the efforts made by global barcoding initiatives toward the development of more comprehensive reference databases, in most circumstances these databases remain far from complete, especially for the currently commonly used 12S mitochondrial gene region (Doble et al, 2020;Sales et al, 2020;Weigand et al 2019).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2021

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Section: Introductionmentioning

confidence: 99%

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

et al. 2021

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“…In contrast, the dynamic nature of riverine systems presents a suite of conditions that are thought to influence eDNA transport and persistence, and while studies have attempted to understand the abiotic factors affecting eDNA detection in lotic systems (e.g., Barnes et al, 2020; Jerde et al, 2016; Shogren et al, 2018) there remains a higher degree of uncertainty regarding inferred species detections using eDNA (Evans & Lamberti, 2018; Thalinger et al, 2020). There are relatively few studies focusing explicitly on estuaries (e.g., Ahn et al, 2020; Stoeckle et al, 2017) which face a suite of challenges including water turbidity during the eDNA collection process, clogging filters, and impeding DNA extraction (Sanches & Schreier, 2020; K. E. Williams et al, 2017), as well as inhibitors to PCR such as humic acid from vegetation decomposition, and sewage by products (Schrader et al, 2012). Due to the variable abiotic conditions of riverine habitats, there are few lotic eDNA studies spanning environmental gradients of salinity (but see Sales et al (2021) and García‐Machado et al (2021)).…”

Section: Introductionmentioning

confidence: 99%

Biodiversity assessment across a dynamic riverine system: A comparison of eDNA metabarcoding versus traditional fish surveying methods

et al. 2021

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While many studies have considered the ability of eDNA to assess animal communities in lacustrine settings, fewer have considered riverine systems, particularly those spanning the environmental gradients present in large river basins. Such dynamic systems are challenging for eDNA biomonitoring due to differing eDNA transport distances in rivers and the effects of river chemistry. To address this challenge, we focused on the Thames River system, UK, which has exceptional historical fish records providing a baseline to test the accuracy of eDNA metabarcoding in recovering fish community structure across both fresh and tidal zones. Two primer sets targeting 12S and CO1 regions were used to capture fish communities across the Thames catchment, from the upper freshwaters to the mid estuary. eDNA was collected at 35 sites, 14 of which were simultaneously paired with traditional fish surveys for direct comparison. We demonstrated that eDNA metabarcoding consistently detected more freshwater species than traditional methods, despite extensive sampling effort using the latter. In contrast, metabarcoding did not perform as well as traditional approaches in estuarine waters, although results included the novel detection of the protected sea lamprey. We further demonstrated that minor variations in the recovery of all approaches would not impact on the assessment of simple ecological models of community structure and, thus, some variability between approaches should not be viewed as a serious hindrance to uptake. Rather, our findings support a growing consensus that eDNA can reliably detect fish communities across dynamic freshwater habitats.

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“…In this context, a set of universal PCR primers for metabarcoding eDNA from fishes has been developed targeting a length of around 163-185 bp of the 12S rRNA gene region (MiFish; Miya et al, 2015). This widely used primer set has been pivotal in describing fish communities on a truly global scale (Miya, Gotoh & Sado, 2020), and has also provided meaningful information for species-rich rivers (Ahn et al, 2020). Despite the efforts made by global barcoding initiatives towards the development of more comprehensive reference databases, in most circumstances these databases remain far from complete, especially for the currently commonly used 12S mitochondrial gene region (Doble et al, 2020;Sales et al, 2020;Weigand et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

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

Jackman

Benvenuto

Coscia

et al. 2021

Preprint

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The current capacity of environmental DNA (eDNA) to provide accurate insights into the biodiversity of megadiverse regions (e.g., the Neotropics) requires further evaluation to ensure its reliability for long-term monitoring. In this study, we first evaluated the taxonomic resolution capabilities of a short fragment from the 12S rRNA gene widely used in fish eDNA metabarcoding studies, and then compared eDNA metabarcoding data from water samples with traditional sampling using nets. For the taxonomic discriminatory power analysis, we used a specifically curated reference dataset consisting of 373 sequences from 264 neotropical fish species (including 47 newly generated sequences) to perform a genetic distance-based analysis of the amplicons targeted by the MiFish primer set. We obtained an optimum delimitation threshold value of 0.5% due to lowest cumulative errors. The barcoding gap analysis revealed only a 50.38% success rate in species recovery (133/264), highlighting a poor taxonomic resolution from the targeted amplicon. To evaluate the empirical performance of this amplicon for biomonitoring, we assessed fish biodiversity using eDNA metabarcoding from water samples collected from the Amazon (Adolpho Ducke Forest Reserve and two additional locations outside the Reserve). From a total of 84 identified Molecular Operational Taxonomic Units (MOTUs), only four could be assigned to species level using a fixed threshold. Measures of α-diversity analyses within the Reserve showed similar patterns in each site between the number of MOTUs (eDNA dataset) and species (netting data) found. However, β-diversity revealed contrasting patterns between the methods. We therefore suggest that a new approach is needed, underpinned by sound taxonomic knowledge, and a more thorough evaluation of better molecular identification procedures such as multi-marker metabarcoding approaches and tailor-made (i.e., order-specific) taxonomic delimitation thresholds.

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Evaluation of fish biodiversity in estuaries using environmental DNA metabarcoding

Cited by 40 publications

References 40 publications

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

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

Biodiversity assessment across a dynamic riverine system: A comparison of eDNA metabarcoding versus traditional fish surveying methods

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

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