Environmental DNA for biomonitoring

Pawłowski, Jan; Bonin, Aurélie; Boyer, Frédéric; Cordier, Tristan; Taberlet, Pierre

doi:10.1111/mec.16023

Cited by 59 publications

(42 citation statements)

References 60 publications

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“…These findings support the need for a proper DNA barcode reference library for all organisms. Such misidentifications may result in avoidable consequences, as more countries and stakeholders include metabarcoding as a standard biomonitoring protocol [ 62 , 63 , 64 ].…”

Section: Discussionmentioning

confidence: 99%

Mitochondrial Genomes, Phylogenetic Associations, and SNP Recovery for the Key Invasive Ponto-Caspian Amphipods in Europe

Mamos

Grabowski

Rewicz

et al. 2021

IJMS

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The Ponto-Caspian region is the main donor of invasive amphipods to freshwater ecosystems, with at least 13 species successfully established in European inland waters. Dikerogammarus spp. and Pontogammarus robustoides are among the most successful, due to their strong invasive impact on local biota. However, genomic knowledge about these invaders is scarce, while phylogeography and population genetics have been based on short fragments of mitochondrial markers or nuclear microsatellites. In this study, we provide: (i) a reconstruction of six mitogenomes for four invasive gammarids (D. villosus, D. haemobaphes, D. bispinosus, and P. robustoides); (ii) a comparison between the structure of the newly obtained mitogenomes and those from the literature; (iii) SNP calling rates for individual D. villosus and D. haemobaphes from different invasion sites across Europe; and (iv) the first time-calibrated full mitogenome phylogeny reconstruction of several Ponto-Caspian taxa. We found that, in comparison to other gammarids, the mitogenomes of Ponto-Caspian species show a translocation between the tRNA-E and tRNA-R positions. Phylogenetic reconstruction using the mitogenomes identified that Ponto-Caspian gammarids form a well-supported group that originated in the Miocene. Our study supports paraphyly in the family Gammaridae. These provided mitogenomes will serve as vital genetic resources for the development of new markers for PCR-based identification methods and demographic studies.

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Section: Discussionmentioning

confidence: 99%

Mitochondrial Genomes, Phylogenetic Associations, and SNP Recovery for the Key Invasive Ponto-Caspian Amphipods in Europe

Mamos

Grabowski

Rewicz

et al. 2021

IJMS

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“…However, morphological identification is timeconsuming and expertise-demanding, making it costly and unpractical, particularly for largescale surveys. Recently, the metabarcoding of environmental DNA (eDNA) samples have provided new insights into biodiversity and ecological distribution of numerous taxonomic groups and offer an alternative to the traditional morphology-based approach [28][29][30] .…”

Section: Introductionmentioning

confidence: 99%

Metabarcoding Reveals High Diversity of Benthic Foraminifera Driven by Atlantification of Coastal Svalbard

Nguyen

Pawłowska

Angeles

et al. 2021

Preprint

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Arctic marine biodiversity is undergoing rapid changes due to global warming and modifications of oceanic water masses circulation. These changes have been demonstrated in the case of mega- and macrofauna, but much less is known about their impact on the biodiversity of smaller size organisms, such as foraminifera that represents a main component of meiofauna in the Arctic. Several studies analysed the distribution and diversity of Arctic foraminifera. However, all these studies are based exclusively on the morphological identification of specimens sorted from sediment samples. Here, we present the first assessment of Arctic foraminifera diversity based on metabarcoding of sediment DNA samples collected in fjords and open sea areas in Svalbard Archipelago. We obtained a total of 5,968,786 reads that represented 1,384 ASVs. More than half of the ASVs (51.7%) could not be assigned to any group in the reference database suggesting a high genetic novelty of Svalbard foraminifera. The sieved and unsieved samples resolved comparable communities, sharing 1023 ASVs, comprising over 97% of reads. Our analyses show that the foraminiferal assemblage differs between the localities, with communities distinctly separated between fjord and open sea stations. Each locality was characterized by a specific assemblage, with only a small overlap in the case of open sea areas. Our study demonstrates a clear pattern of the influence of water masses on the structure of foraminiferal communities. The stations situated on the western coast of Svalbard that is strongly influenced by warm and salty Atlantic Water (AW) are characterized by much higher diversity than stations in the northern and eastern part, where the impact of AW is less pronounced. This high diversity and specificity of Svalbard foraminifera associated with water mass distribution indicate that the foraminiferal metabarcoding data can be a very useful tool for inferring present and past environmental conditions in the Arctic.

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“…To do so, stakeholders call for guidelines and/or standards to accompany the deployment of the method for biomonitoring purposes (Blancher et al 2022). General guidelines have been recently published, providing best-practices for many applications of DNA metabarcoding (Bruce et al 2021;Pawlowski et al 2021), representing an important milestone. However, guidelines need to be even more precise to be easily and reliably handled by the operators in a variety of contexts.…”

Section: Towards a Standardised And User-friendly Methodsmentioning

confidence: 99%

Recommendations for the preservation of environmental samples in diatom metabarcoding studies

Baričević¹,

Chardon²,

Kahlert³

et al. 2022

MBMG

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Implementation of DNA metabarcoding for diatoms for environmental monitoring is now moving from a research to an operational phase, requiring rigorous guidelines and standards. In particular, the first steps of the diatom metabarcoding process, which consist of sampling and storage, have been addressed in various ways in scientific and pilot studies and now need to be rationalised. The objective of this study was to compare three currently applied preservation protocols through different storage durations (ranging from one day to one year) for phytobenthos and phytoplankton samples intended for diatom DNA metabarcoding analysis. The experimental design used samples from four freshwater and two marine sites of diverse ecological characteristics. The impact of the sample preservation and storage duration was assessed through diatom metabarcoding endpoints: DNA quality and quantity, diversity and richness, diatom assemblage composition and ecological index values (for freshwater samples). The yield and quality of extracted DNA only decreased for freshwater phytobenthos samples preserved with ethanol. Diatom diversity was not affected and their taxonomic composition predominantly reflected the site origin. Only rare taxa (< 100 reads) differed among preservation methods and storage durations. For biomonitoring purposes, freshwater ecological index values were not affected by the preservation method and storage duration tested (including ethanol preservation), all treatments returning the same ecological status for a site. This study contributes to consolidating diatom metabarcoding. Thus, accompanied by operational standards, the method will be ready to be confidently deployed and prescribed in future regulatory monitoring.

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Environmental DNA for biomonitoring

Cited by 59 publications

References 60 publications

Mitochondrial Genomes, Phylogenetic Associations, and SNP Recovery for the Key Invasive Ponto-Caspian Amphipods in Europe

Mitochondrial Genomes, Phylogenetic Associations, and SNP Recovery for the Key Invasive Ponto-Caspian Amphipods in Europe

Metabarcoding Reveals High Diversity of Benthic Foraminifera Driven by Atlantification of Coastal Svalbard

Recommendations for the preservation of environmental samples in diatom metabarcoding studies

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Environmental DNA for biomonitoring

Cited by 59 publications

References 60 publications

Mitochondrial Genomes, Phylogenetic Associations, and SNP Recovery for the Key Invasive Ponto-Caspian Amphipods in Europe

Mitochondrial Genomes, Phylogenetic Associations, and SNP Recovery for the Key Invasive Ponto-Caspian Amphipods in Europe

Metabarcoding Reveals High Diversity of Benthic Foraminifera Driven by Atlantification of Coastal Svalbard

﻿Recommendations for the preservation of environmental samples in diatom metabarcoding studies

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Recommendations for the preservation of environmental samples in diatom metabarcoding studies