Analysis of a coastal North Sea fish community: Comparison of aquatic environmental DNA concentrations to fish catches

Bleijswijk, Judith van; Engelmann, Julia C.; Klunder, Lise; Witte, Harry J.; Witte, Johannes Ij.; Veer, Henk W. van der

doi:10.1002/edn3.67

Cited by 25 publications

(38 citation statements)

References 63 publications

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“…Hänfling et al (2016) discerned that metabarcoding assay read abundances were positively correlated with findings of long-term concomitant capture-based surveys of fishes in three United Kingdom lakes. Van Bleijswijk et al (2020) found that fish biomass caught in fyke net surveys in a tidal inlet between the North and Wadden Seas showed weak positive correlation with metabarcoding sequence read abundances for just the eight most abundant species. Positive correlations with sequence reads at higher taxonomic levels have appeared more common in most studies (Thomsen et al 2016;Gillet et al 2018), although since different taxa in families often are not ecological equivalents (e.g., benthic invertivore darters and several piscivorous species in Percidae), those results are less useful than comparisons at the species level.…”

Section: Experiments Series A: Relative Abundances Of Species From Metabarcoding Assaysmentioning

confidence: 95%

Increasing confidence for discerning species and population compositions from metabarcoding assays of environmental samples: case studies of fishes in the Laurentian Great Lakes and Wabash River

Snyder¹,

Stepien²

2020

MBMG

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Community composition data are essential for conservation management, facilitating identification of rare native and invasive species, along with abundant ones. However, traditional capture-based morphological surveys require considerable taxonomic expertise, are time consuming and expensive, can kill rare taxa and damage habitats, and often are prone to false negatives. Alternatively, metabarcoding assays can be used to assess the genetic identity and compositions of entire communities from environmental samples, comprising a more sensitive, less damaging, and relatively time- and cost-efficient approach. However, there is a trade-off between the stringency of bioinformatic filtering needed to remove false positives and the potential for false negatives. The present investigation thus evaluated use of four mitochondrial (mt) DNA metabarcoding assays and a customized bioinformatic Bioinformatic pipeline to increase confidence in species identifications by removing false positives, while achieving high detection probability. Positive controls were used to calculate sequencing error, and results that fell below those cutoff values were removed, unless found with multiple assays. The performance of this approach was tested to discern and identify North American freshwater fishes using lab experiments (mock communities and aquarium experiments) and processing of a bulk ichthyoplankton sample. The method then was applied to field environmental (e) DNA water samples taken concomitant with electrofishing surveys and morphological identifications. This protocol detected 100% of species present in concomitant electrofishing surveys in the Wabash River and an additional 21 that were absent from traditional sampling. Using single 1 L water samples collected from just four locations, the metabarcoding assays discerned 73% of the total fish species that were discerned during four months of an extensive electrofishing river survey in the Maumee River, along with an additional nine species. In both rivers, total fish species diversity was best resolved when all four metabarcoding assays were used together, which identified 35 additional species missed by electrofishing. Ecological distinction and diversity levels among the fish communities also were better resolved with the metabarcoding assays than with morphological sampling and identifications, especially using all four assays together. At the population-level, metabarcoding analyses targeting the invasive round goby Neogobius melanostomus and the silver carp Hypophthalmichthys molitrix identified all population haplotype variants found using Sanger sequencing of morphologically sampled fish, along with additional intra-specific diversity, meriting further investigation. Overall findings demonstrated that the use of multiple metabarcoding assays and custom bioinformatics that filter potential error from true positive detections improves confidence in evaluating biodiversity.

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Section: Experiments Series A: Relative Abundances Of Species From Metabarcoding Assaysmentioning

confidence: 95%

Increasing confidence for discerning species and population compositions from metabarcoding assays of environmental samples: case studies of fishes in the Laurentian Great Lakes and Wabash River

Snyder¹,

Stepien²

2020

MBMG

View full text Add to dashboard Cite

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“…In this study, we propose a more direct method for inferring the absolute abundance of fish species from multiple sampling locations by combining eDNA metabarcoding with qPCR analysis, which assesses the total abundance of eDNA amplified by the universal marker used for metabarcoding. Fish-specific eDNA concentrations are then calculated from the ratios of fish species-specific read counts over the total read count of a sample (metabarcoding) multiplied by the total eDNA concentration estimated with qPCR (van Bleijswijk et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Quantitative monitoring of diverse fish communities on a large scale combining eDNA metabarcoding and qPCR

Pont

Meulenbroek

Bammer

et al. 2022

Preprint

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eDNA metabarcoding is an effective method for studying fish communities but allows only an estimation of relative species abundance (density / biomass). Here, we combine metabarcoding with an estimation of the total abundance of eDNA amplified by our universal marker (teleo) using a qPCR approach to infer the absolute abundance of fish species. We carried out a 2850 km eDNA survey within the Danube catchment using a spatial integrative sampling protocol coupled with traditional electrofishing for fish biomass and density estimation. Total fish eDNA concentrations and total fish abundance were highly correlated. The correlation between eDNA concentrations per taxon and absolute specific abundance was of comparable strength when all sites were pooled and remained significant when the sites were considered separately. Furthermore, a non-linear mixed model showed that species richness was underestimated when the amount of teleo-DNA extracted from a sample was below a threshold of 0.65.106 copies of eDNA. This result, combined with the decrease in teleo-DNA concentration by several orders of magnitude with river size, highlights the need to increase sampling effort in large rivers. Our results show a comprehensive description of longitudinal changes in fish communities and underline our combined metabarcoding/qPCR approach for biomonitoring and bioassessment surveys when a rough estimate of absolute species abundance is sufficient.

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“…This is because beta diversity is more complicated to record and synthesize from multiple sources, as it is often reported using different metrics, also calling for more standardized reporting of data enabling future assessments and meta-analyses. Nonetheless, beta diversity remains an important component of diversity and can give different results if analysed through DNA or traditional methods (Bleijswijk et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

Meta-analysis shows both congruence and complementarity of DNA metabarcoding to traditional methods for biological community assessment

Keck

Blackman

Bossart

et al. 2021

Preprint

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Assessment of the diversity and composition of biological communities is central to studies in ecology as well as for ecological monitoring. Historically, individual taxonomic groups have been assessed separately, while for an understanding of the state and change of biodiversity under ongoing global change an integrated assessment would be necessary. DNA metabarcoding has been proposed to be a highly promising approach especially for the assessment of aquatic communities, and numerous studies have investigated the consistency of this new technique with traditional morpho-taxonomic approaches. These individual studies have used DNA metabarcoding to assess diversity and community structure of aquatic organisms both in marine and freshwater systems globally over the last decade. However, a systematic analysis of the comparability and effectiveness of DNA-based community assessment across all of these studies has hitherto been lacking. Here we performed the first meta-analysis of all available studies comparing traditional methods and DNA metabarcoding to measure and assess biological diversity of key aquatic groups, including microorganisms, macroinvertebrates, and fish. Across 215 datasets, we found that DNA metabarcoding provides diversity estimates (richness) that are globally consistent to those obtained using traditional methods. DNA metabarcoding also generates species inventories that are highly congruent with traditional methods for fish. Contrastingly, however, species inventories of microorganisms and macroinvertebrates obtained by DNA metabarcoding showed pronounced differences to traditional methods, missing some taxa but at the same time detecting otherwise overseen diversity. Our results indicate that DNA metabarcoding is efficient to estimate local and regional richness. The method is generally sufficiently advanced to study the composition of fish communities and replace more invasive traditional methods. For smaller organisms, like macroinvertebrates and microorganisms, DNA metabarcoding may continue to give complementary rather than identical estimates compared to traditional approaches. Systematic and comparable data collection will increase the understanding of different aspects of this complementarity, and increase the effectiveness of the method and adequate interpretation of the results.

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Analysis of a coastal North Sea fish community: Comparison of aquatic environmental DNA concentrations to fish catches

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 25 publications

References 63 publications

Increasing confidence for discerning species and population compositions from metabarcoding assays of environmental samples: case studies of fishes in the Laurentian Great Lakes and Wabash River

Increasing confidence for discerning species and population compositions from metabarcoding assays of environmental samples: case studies of fishes in the Laurentian Great Lakes and Wabash River

Quantitative monitoring of diverse fish communities on a large scale combining eDNA metabarcoding and qPCR

Meta-analysis shows both congruence and complementarity of DNA metabarcoding to traditional methods for biological community assessment

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