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

Effective monitoring of freshwater fish

Freshwater ecosystems constitute only a small fraction of the planet’s water resources, yet support much of its diversity, with freshwater fish accounting for more species than birds, mammals, amphibians, or reptiles. Fresh waters are, however, particularly vulnerable to anthropogenic impacts, including habitat loss, climate and land use change, nutrient enrichment, and biological invasions. This environmental degradation, combined with unprecedented rates of biodiversity change, highlights the importance of robust and replicable programmes to monitor freshwater fish assemblages. Such monitoring programmes can have diverse aims, including confirming the presence of a single species (e.g. early detection of alien species), tracking changes in the abundance of threatened species, or documenting long-term temporal changes in entire communities. Irrespective of their motivation, monitoring programmes are only fit for purpose if they have clearly articulated aims and collect data that can meet those aims. This review, therefore, highlights the importance of identifying the key aims in monitoring programmes, and outlines the different methods of sampling freshwater fish that can be used to meet these aims. We emphasise that investigators must address issues around sampling design, statistical power, species’ detectability, taxonomy, and ethics in their monitoring programmes. Additionally, programmes must ensure that high-quality monitoring data are properly curated and deposited in repositories that will endure. Through fostering improved practice in freshwater fish monitoring, this review aims to help programmes improve understanding of the processes that shape the Earth's freshwater ecosystems, and help protect these systems in face of rapid environmental change

Hull fouling as an invasion vector: Can simple models explain a complex problem?

1. The most effective way to manage nonindigenous species and their impacts is to prevent their introduction via vector regulation. While ships' ballast water is very well studied and this vector is actively managed, hull fouling has received far less attention and regulations are only now being considered despite its importance for introductions to coastal, marine systems. 2. We conducted comprehensive in situ sampling and video recording of hulls of 40 transoceanic vessels to assess propagule and colonization pressure in Vancouver and Halifax, dominant coastal ports in Canada. Concomitant sampling was conducted of harbour fouling communities to compare hull and port communities as part of a vector risk assessment. 3. Although this vector has been operational for a long time, hull and harbour communities were highly divergent, with mean Sørensen's similarity values of 0·03 in Halifax and 0·01 in Vancouver, suggesting invasion risk is high. Propagule pressure (up to 600 000 ind. ship-1) and colonization pressure (up to 156 species ship-1) were high and varied significantly between ports, with Vancouver receiving much higher abundances and diversity of potential invaders. The higher risk of fouling introductions in Vancouver is consistent with historical patterns of successful hull fouling invasions. 4. The extent of hull fouling was modelled using ship history predictors. Propagule pressure increased with time spent in previous ports-of-call and time since last application of antifouling paint, whereas colonization pressure increased with time since last painting and with the number of regions visited by the ship. Both propagule and colonization pressure were negatively related to the time spent at sea and the latitude of ports visited. 5. Synthesis and applications. A major challenge for applied invasion ecology is the effective management of introduction vectors. We found that hull fouling has a strong potential for introduction of many species to coastal marine habitats and that management should be considered. Simple variables related to the vessels' hull husbandry, voyage, and sailing patterns may be used to predict and manage hull fouling intensity. The results presented here should interest policy makers and environmental managers who seek to reduce invasion risk, and ship owners seeking to optimize fuel efficiency.Fil: Sylvester, Francisco. University of Windsor. Great Lakes Institute for Enviromental Research; Canadá. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Ecología, Genética y Evolución; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Kalaci, Odion. University of Windsor. Great Lakes Institute for Enviromental Research; CanadáFil: Leung, Brian. McGill University; CanadáFil: Lacoursière Roussel, Anaïs. McGill University; CanadáFil: Murray, Cathryn Clarke. University of British Columbia; CanadáFil: Choi, Francis M.. University of British Columbia; CanadáFil: Bravo, Monica A.. Fisheries and Oceans Canada; CanadáFil: Therriault, Thomas W.. Fisheries and Oceans Canada; CanadáFil: MacIsaac, Hugh J.. University of Windsor. Great Lakes Institute for Enviromental Research; Canad

AORA - Atlantic Ocean Research Alliance - Marine Microbiome Roadmap

“The Science We Need For The Ocean We Want.” We are on the threshold of a new and exciting era of discovery in the oceans that will shape the development of human endeavours for decades to come. New insights on the significance of the microscopic scale of ocean life has shown this level affects almost every aspect of our lives (health, food, industry, ecosystems). For society’s future, we need to investigate the science of marine microbiomes, integrate the novel technologies discovered and initiate policies that foster truly sustainable marine development. The United Nations will dedicate the next decade to Ocean Science for Sustainable Development. The Decade’s vision and mission are consistent with the objective of the Atlantic Ocean Research Alliance (AORA) between the European Union, Canada and the United States, that is to “advance the shared vision of an Atlantic Ocean that is healthy, resilient, safe, productive, understood and treasured, to promote the well-being, prosperity and security of the Atlantic for present and future generations”. Relevant to the missions of both AORA and the Decade, here, we outline how the marine microbiome is at the heart of the ocean as a living system, driving its nutrient and biogeochemical cycles, forming the basis of its food webs, performing essential and yet unknown functions in climate regulation, including buffering the effects of global change. Furthermore, the oceans are a largely untapped resource for biodiscovery and the bioeconomy, with a high potential for the development of new products and processes. To ensure early coordination and interoperability guided by a shared vision, we need to bring together science, industry and policy makers to advance the “Next Great Exploration of the Oceans”. The following Roadmap is the result of an international cooperative effort between the United States, Canada, and the European Union produced within the AORA framework and consistent with the Galway Statement on Atlantic Ocean Cooperation. Within the marine microbiome Roadmap, three thematic pillars have been identified by AORA scientists and policy makers, all supported with underlying cross-cutting elements: Environment and Climate, Food Value Chain and Biodiscovery

Author Correction: Effects of sampling effort on biodiversity patterns estimated from environmental DNA metabarcoding surveys (Scientific Reports, (2018), 8, 1, (8843), 10.1038/s41598-018-27048-2)

10.1038/s41598-019-43804-4Scientific Reports911589

Data from: Effects of sampling effort on biodiversity patterns estimated from environmental DNA metabarcoding surveys

Environmental DNA (eDNA) metabarcoding can greatly enhance our understanding of global biodiversity and our ability to detect rare or cryptic species. However, sampling effort must be considered when interpreting results from these surveys. We explored how sampling effort influenced biodiversity patterns and nonindigenous species (NIS) detection in an eDNA metabarcoding survey of four commercial ports. Overall, we captured sequences from 18 metazoan phyla with minimal differences in taxonomic coverage between 18 S and COI primer sets. While community dissimilarity patterns were consistent across primers and sampling effort, richness patterns were not, suggesting that richness estimates are extremely sensitive to primer choice and sampling effort. The survey detected 64 potential NIS, with COI identifying more known NIS from port checklists but 18 S identifying more operational taxonomic units shared between three or more ports that represent un-recorded potential NIS. Overall, we conclude that eDNA metabarcoding surveys can reveal global similarity patterns among ports across a broad array of taxa and can also detect potential NIS in these key habitats. However, richness estimates and species assignments require caution. Based on results of this study, we make several recommendations for port eDNA sampling design and suggest several areas for future research

Effects of sampling effort on biodiversity patterns estimated from environmental DNA metabarcoding surveys

Environmental DNA (eDNA) metabarcoding can greatly enhance our understanding of global biodiversity and our ability to detect rare or cryptic species. However, sampling effort must be considered when interpreting results from these surveys. We explored how sampling effort influenced biodiversity patterns and nonindigenous species (NIS) detection in an eDNA metabarcoding survey of four commercial ports. Overall, we captured sequences from 18 metazoan phyla with minimal differences in taxonomic coverage between 18 S and COI primer sets. While community dissimilarity patterns were consistent across primers and sampling effort, richness patterns were not, suggesting that richness estimates are extremely sensitive to primer choice and sampling effort. The survey detected 64 potential NIS, with COI identifying more known NIS from port checklists but 18 S identifying more operational taxonomic units shared between three or more ports that represent un-recorded potential NIS. Overall, we conclude that eDNA metabarcoding surveys can reveal global similarity patterns among ports across a broad array of taxa and can also detect potential NIS in these key habitats. However, richness estimates and species assignments require caution. Based on results of this study, we make several recommendations for port eDNA sampling design and suggest several areas for future research.ISSN:2045-232