Adapting metabarcoding-based benthic biomonitoring into routine marine ecological status assessment networks

Aylagas, Eva; Borja, Ángel; Muxika, Iñigo; Rodríguez-Ezpeleta, Naiara

doi:10.1016/j.ecolind.2018.07.044

Cited by 122 publications

(132 citation statements)

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“…The use of metabarcoding bulk samples for calculating water quality indices based on diatoms has been described (Apothéloz- Perret-Gentil et al, 2017), and also for calculating indices based on benthic macroinvertebrates as a key group for river water quality monitoring worldwide (Aylagas et al, 2018;Bista et al, 2017;Pawlowski et al, 2018). Molecular techniques (DNA barcoding and metabarcoding) have been compared with the morphological identification of benthic macroinvertebrates (i.e., identification based Conclusion: The usefulness of eDNA metabarcoding to assess rivers water quality based on macroinvertebrates assessment has been demonstrated in a dammed river basin.…”

Section: For Example the River Invertebrate Prediction And Classificmentioning

confidence: 99%

How can eDNA contribute in riverine macroinvertebrate assessment? A metabarcoding approach in the Nalón River (Asturias, Northern Spain)

et al. 2019

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Background: Bioassessment of rivers is a fundamental method to determine surface water quality. One of the groups most commonly employed as bioindicators of aquatic ecosystems are benthic macroinvertebrates. Their conventional assessment is based on morphological identification and entails several limitations, such as being time-consuming and requires trained experts for taxonomic identification. The use of genetic tools to solve these limitations offers an alternative way to evaluate rivers status. The use of environmental DNA (eDNA) metabarcoding has increased in recent years for different purposes, but its use in water quality evaluation is yet to be tested. Here, morphological and eDNA based inventories of macroinvertebrates were compared from the same seven sampling sites in the Upper Nalón River Basin (Asturias, Spain). Materials & Methods:High-Throughput Sequencing (HTS) of the cytochrome oxidase subunit 1 (COI) gene was carried out on DNA from water samples using an Ion Torrent platform. Biotic water quality indices were calculated from morphological and molecular data and compared with independent physico-chemical habitat assessment to validate eDNA based approach.Results: Highly positive and significant correlation was found between eDNA metabarcoding and morphological methods (Morphological and eDNA indices, r = 0.798, 5 degrees of freedom d.f., P = 0.031;) and a highly significant negative correlation was found between molecular and habitat quality indices (Stress score & eDNA, ρ = -0.878 and P = 0.009; Stress score & Visual, ρ = -0.949 and P = 0.0002). Discussion:The similarity of results from the two approaches and the correlation of eDNA metabarcoding data with the habitat quality indices, suggest that eDNA performs as well as conventional methods for calculating biotic indices in this system, positioning eDNA metabarcoding of macroinvertebrate communities to transform how river bioassessment can be achieved.

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Section: For Example the River Invertebrate Prediction And Classificmentioning

confidence: 99%

How can eDNA contribute in riverine macroinvertebrate assessment? A metabarcoding approach in the Nalón River (Asturias, Northern Spain)

et al. 2019

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“…Metabarcoding has been extensively explored and validated as an alternative tool to morphological identification (Aylagas, Borja, Irigoien, & Rodríguez‐Ezpeleta, ; Aylagas, Borja, Muxika, & Rodríguez‐Ezpeleta, ) and described as a promising tool for NIS monitoring (Comtet, Sandionigi, Viard, & Casiraghi, ). Recent studies have highlighted the potential of metabarcoding applied to eDNA to perform port biodiversity surveys (Borrell, Miralles, Huu, Mohammed‐Geba, & Garcia‐Vazquez, ; Grey et al, ; Lacoursière‐Roussel et al, ).…”

Section: Introductionmentioning

confidence: 99%

Considerations for metabarcoding‐based port biological baseline surveys aimed at marine nonindigenous species monitoring and risk assessments

Rey

Basurko

Rodríguez-Ezpeleta

2020

Ecology and Evolution

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Monitoring introduction and spread of nonindigenous species via maritime transport and performing risk assessments require port biological baseline surveys. Yet, the comprehensiveness of these surveys is often compromised by the large number of habitats present in a port, the seasonal variability, and the time‐consuming morphological approach used for taxonomic identification. Metabarcoding represents a promising alternative for rapid comprehensive port biological baseline surveys, but its application in this context requires further assessments. We applied metabarcoding (based on barcodes of the cytochrome c oxidase subunit I and of the 18S ribosomal RNA gene) to 192 port samples collected (a) from diverse habitats (water column—including environmental DNA and zooplankton, sediment, and fouling structures), (b) at different sites (from inner to outer estuary), and iii) during the four seasons of the year. By comparing the biodiversity metrics derived from each sample group, we show that each sampling method resulted in a distinct community profile and that environmental DNA alone cannot substitute for organismal sampling, and that, although sampling at different seasons and locations resulted in higher observed biodiversity, operational results can be obtained by sampling selected locations and seasons. By assessing the taxonomic composition of the samples, we show that metabarcoding data allowed the detection of previously recorded nonindigenous species as well as to reveal presence of new ones, even if in low abundance. Synthesis and application. Our comprehensive assessment of metabarcoding for port biological baseline surveys sets the basics for cost‐effective, standardized, and comprehensive monitoring of nonindigenous species and for performing risk assessments in ports. This development will contribute to the implementation of the recently entered into force International Convention for the Control and Management of Ships' Ballast Water and Sediments.

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“…Some issues still need to be solved and standard protocols to be developed before DNA 193 metabarcoding becomes the method of choice in aquatic biomonitoring. The use of both 194 organismal and environmental DNA (eDNA) in nature management decisions is already 195 being tested in some European countries (Hering et al, 2018), and the genetic water quality 196 index recently developed for marine waters (gAMBI) is performing well (Aylagas et al, 2018;197 Aylagas et al, 2014). The EU COST Action DNAqua-Net (CA15219) was initiated with the 198 many organism groups available for DNA analysis.…”

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confidence: 99%

DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work

Weigand

Beermann

Cĭampor

et al. 2019

Preprint

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100Effective identification of species using short DNA fragments (DNA barcoding and DNA 101 metabarcoding) requires reliable sequence reference libraries of known taxa. Both 102 taxonomically comprehensive coverage and content quality are important for sufficient 103 accuracy. For aquatic ecosystems in Europe, reliable barcode reference libraries are 104 particularly important if molecular identification tools are to be implemented in biomonitoring 105 and reports in the context of the EU Water Framework Directive (WFD) and the Marine 106Strategy Framework Directive (MSFD). We analysed gaps in the two most important 107 reference databases, Barcode of Life Data Systems (BOLD) and NCBI GenBank, with a 108 focus on the taxa most frequently used in WFD and MSFD. Our analyses show that 109 coverage varies strongly among taxonomic groups, and among geographic regions. In 110 general, groups that were actively targeted in barcode projects (e.g. fish, true bugs, 111 caddisflies and vascular plants) are well represented in the barcode libraries, while others 112 have fewer records (e.g. marine molluscs, ascidians, and freshwater diatoms). We also 113 found that species monitored in several countries often are represented by barcodes in 114 reference libraries, while species monitored in a single country frequently lack sequence 115 records. A large proportion of species (up to 50%) in several taxonomic groups are only 116represented by private data in BOLD. Our results have implications for the future strategy to 117 fill existing gaps in barcode libraries, especially if DNA metabarcoding is to be used in the 118 monitoring of European aquatic biota under the WFD and MSFD. For example, missing 119 species relevant to monitoring in multiple countries should be prioritized. We also discuss 120 why a strategy for quality control and quality assurance of barcode reference libraries is 121 needed and recommend future steps to ensure full utilization of metabarcoding in aquatic 122 biomonitoring. 123 124

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Adapting metabarcoding-based benthic biomonitoring into routine marine ecological status assessment networks

Abstract: Adapting metabarcoding-based benthic biomonitoring into routine marine ecological status assessment networks.

Cited by 122 publications

References 74 publications

How can eDNA contribute in riverine macroinvertebrate assessment? A metabarcoding approach in the Nalón River (Asturias, Northern Spain)

How can eDNA contribute in riverine macroinvertebrate assessment? A metabarcoding approach in the Nalón River (Asturias, Northern Spain)

Considerations for metabarcoding‐based port biological baseline surveys aimed at marine nonindigenous species monitoring and risk assessments

DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work

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