Environmental DNA metabarcoding:Transforming how we survey animal and plant communities

The genomic revolution has fundamentally changed how we survey biodiversity on earth. High-throughput sequencing (?HTS?) platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed ?environmental DNA? or ?eDNA?). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called ?eDNA metabarcoding? and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance. We highlight eDNA applications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of different eDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the eDNA metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of eDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how eDNA metabarcoding can empower citizen science and biodiversity educationpublishersversionPeer reviewe

Trade-Offs Between Reducing Complex Terminology and Producing Accurate Interpretations from Environmental DNA: Comment on “Environmental DNA: What\u27s behind the term?” by Pawlowski et al., (2020)

In a recent paper, “Environmental DNA: What\u27s behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring,” Pawlowski et al. argue that the term eDNA should be used to refer to the pool of DNA isolated from environmental samples, as opposed to only extra-organismal DNA from macro-organisms. We agree with this view. However, we are concerned that their proposed two-level terminology specifying sampling environment and targeted taxa is overly simplistic and might hinder rather than improve clear communication about environmental DNA and its use in biomonitoring. This terminology is based on categories that are often difficult to assign and uninformative, and it overlooks a fundamental distinction within eDNA: the type of DNA (organismal or extra-organismal) from which ecological interpretations are derived

Testing propagule pressure theory: maritime transport & invasion by fouling species

Introductions of exotic fouling species have severely disrupted marine ecosystems. Theory suggests that high propagule pressure increases the probability of successful establishment. Likewise, empirical studies have shown the importance of ships and boats for transporting exotic species. However, few empirical studies have demonstrated the effect of propagule pressure on invasion success. For marine fouling species, uncertainty about vectors and pathways further impedes our ability to calculate propagule pressure and to understand establishment success. My goal was to better understand the links between propagule pressure from maritime activities and the spatial distribution of exotic fouling species. Using empirical data, I (1) determined the importance of boat characteristics and propagule exposure on boat fouling, (2) demonstrated the roles of commercial shipping and recreational boating in the invasion process, and (3) tested the effect of propagule pressure on population and community diversity. Although boats on the east coast of Canada were less fouled than New Zealand boats, boat-mediated spread may be facilitated in Canada by greater movement of boats among marinas than in New Zealand. Propagule exposure better predicted boat fouling than did boat characteristics. The spatial genetic structure of the colonial tunicate, Botryllus schlosseri, suggests that ships have frequently introduced it to the east coast of Canada and that secondary spread occurs gradually around individual ports, facilitated by recreational boating. The diversity of invasive species within commercial ports is positively related to propagule pressure and invasion success at both community (i.e. inter-specific richness) and population levels (i.e. genetic diversity). Diversity was significantly correlated to the numbers of ship arrivals but not to ballast water discharge events or the volume of ballast water discharged. This suggests that hull biofouling is a more important pathway than ballast water for exotic fouling species. Both boats and ships have influenced the invasion process of fouling species in Canadian coastal areas. The research also underlines the point that predictive models for the spread of biofouling species should be based on regional boating patterns, boating characteristics, and local propagule exposure. Defining relationships between propagule pressure and invasion success is one of the great challenges to understanding the rapid changes occurring in marine ecosystems.L'introduction des salissures biologiques exotiques a sévèrement perturbé les écosystèmes marins. La théorie suggère qu'un apport de propagules élevé augmente le risque d'envahissement. C'est ainsi que les recherches se sont concentrées à évaluer la probabilité que les navires commerciaux et les petites embarcations transportent des espèces exotiques. Malgré son importance, peu d'études empiriques supportent l'effet de l'apport de propagules sur le succès d'envahissement. Pour les salissures biologiques marines, l'incertitude entre les vecteurs et les voies de transports entrave particulièrement notre capacité à calculer l'apport de propagules entrant par les voies maritimes, limitant ainsi notre compréhension du succès d'envahissement. L'objectif de ma thèse est d'apporter une meilleure compréhension de la relation entre l'apport de propagules provenant du transport maritime et la distribution spatiale des salissures exotiques. À partir de données empiriques, (1) j'ai déterminé l'importance relative des caractéristiques des bateaux de plaisance et l'exposition des propagules environnantes sur la probabilité de la colonisation des coques, (2) j'ai démontré le rôle respectif des navires et des plaisanciers dans le processus d'invasion et (3) j'ai décrit la relation entre l'apport de propagules et la diversité des populations et des communautés. Bien que les bateaux de la côte est du Canada sont moins colonisés que les bateaux de la Nouvelle-Zélande, la propagation des salissures exotiques pourrait être facilitée au Canada par un plus grand trafic entre les marinas. L'exposition aux propagules environnantes prédit davantage l'encrassement biologique des coques que les caractéristiques des bateaux. La génétique des populations de l'ascidie Botryllus schlosseri suggère qu'il y a eu plusieurs introductions dans les ports de la côte est du Canada. Facilité par les plaisanciers, le tunicier s'est ensuite dispersé progressivement autour de ceux-ci. Les indices de diversité soutiennent la relation positive entre l'apport de propagules et le succès d'envahissement et cela autant au niveau des communautés (c.-à-d. la richesse inter-spécifique) qu'au niveau des populations (c.-à-d. diversité génétique). La diversité est significativement corrélée au nombre d'arrivées des navires, mais n'est pas corrélée au nombre de déchargements et au volume de l'eau de lest. Ces relations suggèrent une plus grande importance de l'encrassement des navires que l'eau de lest comme voie d'introduction des salissures exotiques. Cette thèse démontre que les petits bateaux et les navires influencent grandement les processus d'invasions des salissures biologiques des régions côtières du Canada. Cette recherche souligne également que les modèles de propagation des salissures exotiques devraient fonder leurs prémisses sur l'exposition des propagules locales, les caractéristiques des bateaux et l'activité nautique régionale. La nécessité de décrire avec précision les relations entre l'apport de propagules et le succès d'envahissement est l'un des grands défis écologiques afin d'améliorer notre compréhension sur les changements rapides actuellement observés dans nos écosystèmes marins

Data from: Estimating fish abundance and biomass from eDNA concentrations: variability among capture methods and environmental conditions

Environmental DNA (eDNA) promises to ease non-invasive quantification of fish biomass or abundance, but its integration within conservation and fisheries management is currently limited by a lack of understanding of the influence of eDNA collection method and environmental conditions on eDNA concentrations in water samples. Water temperature is known to influence the metabolism of fish and consequently could strongly affect eDNA release rate. As water temperature varies in temperate regions (both seasonally and geographically), the unknown effect of water temperature on eDNA concentrations poses practical limitations on quantifying fish populations using eDNA from water samples. This study aims to clarify how water temperature and the eDNA capture method alter the relationships between eDNA concentration and fish abundance/biomass. Water samples (1 L) were collected from 30 aquaria including triplicate of 0, 5, 10, 15 and 20 Brook Charr specimens at two different temperatures. Water samples were filtered with five different types of filters. The eDNA concentration obtained by quantitative PCR (qPCR) varied significantly with fish abundance and biomass and type of filters (Mixed-design ANOVA, P < 0.001). Results also show that fish released more eDNA in warm water than cold water and that eDNA concentration better reflects fish abundance/biomass at high temperature. From a technical standpoint, higher levels of eDNA were captured with glass fiber (GF) than mixed cellulose ester (MCE) filters and support the importance of adequate filters to quantify fish abundance based on the eDNA method. This study supports the importance of including water temperature in fish abundance/biomass prediction models based on eDNA

Improving herpetological surveys in eastern North America using the environmental DNA method

Among vertebrates, herpetofauna has the highest proportion of declining species. Detection of eDNA is a promising method towards significantly increasing large-scale herpetological conservation efforts. However, the integration of eDNA results within a management framework requires an evaluation of the efficiency of the method in large natural environments and the calibration of eDNA surveys with the quantitative monitoring tools currently used by conservation biologists. Towards this end, we first developed species-specific primers to detect the Wood turtle (Glyptemys insculpta) a species at risk in Canada, by quantitative PCR (qPCR). The rate of eDNA detection obtained by qPCR was also compared to the relative abundance of this species in nine rivers obtained by standardized visual surveys in the Province of QuĂŠbec (Canada). Secondly, we developed multi-species primers to detect North American amphibian and reptile species using eDNA metabarcoding analysis. An occurrence index based on the distribution range and habitat type was compared with the eDNA metabarcoding dataset from samples collected in seven lakes and five rivers. Our results empirically support the effectiveness of eDNA metabarcoding to characterize herpetological species distributions. Moreover, detection rates provided similar results to standardized visual surveys currently used to develop conservation strategies for the Wood turtle. We conclude that eDNA detection rates may provide an effective semi-quantitative survey tool, provided that assay calibration and standardization is performed.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Data from: Quantifying relative fish abundance with eDNA: a promising tool for fisheries management

Assessment and monitoring of exploited fish populations are challenged by costs, logistics and negative impacts on target populations. These factors therefore limit large-scale effective management strategies. Evidence is growing that the quantity of eDNA may be related not only to species presence/absence, but also to species abundance. In this study, the concentrations of environmental DNA (eDNA) from a highly prized sport fish species, Lake Trout Salvelinus namaycush (Walbaum 1792), were estimated in water samples from 12 natural lakes and compared to abundance and biomass data obtained from standardized gillnet catches as performed routinely for fisheries management purposes. To reduce environmental variability among lakes, all lakes were sampled in spring, between ice melt and water stratification. The eDNA concentration did not vary significantly with water temperature, dissolved oxygen, pH and turbidity, but was significantly positively correlated with relative fish abundance estimated as catch per unit effort (CPUE), whereas the relationship with biomass per unit effort (BPUE) was less pronounced. The value of eDNA to inform about local aquatic species distribution was further supported by the similarity between the spatial heterogeneity of eDNA distribution and spatial variation in CPUE measured by the gillnet method. Synthesis and applications. Large-scale empirical evidence of the relationship between the eDNA concentration and species abundance allows for the assessment of the potential to integrate eDNA within fisheries management plans. As such, the eDNA quantitative method represents a promising population abundance assessment tool that could significantly reduce the costs associated with sampling and increase the power of detection, the spatial coverage and the frequency of sampling, without any negative impacts on fish populations

ALR et al._Mol Ecol Res_DRYAD_22Feb2016

The eDNA concentration (ng/L) per amplification including water temperature, fish abundance, fish biomass, number of the sampled aquarium, types of filters

eDNA DATA_ALR et al. JAppEcol2015

The environmental DNA (eDNA) concentration (pg/L) of each sample is provided, including replicate measurements. For each site, the latitude, longitude and site depth (m) are also provided