David M. Lodge

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 education.

eDNA metabarcoding as a new surveillance approach for coastal Arctic biodiversity

Abstract Because significant global changes are currently underway in the Arctic, creating a large‐scale standardized database for Arctic marine biodiversity is particularly pressing. This study evaluates the potential of aquatic environmental DNA (eDNA) metabarcoding to detect Arctic coastal biodiversity changes and characterizes the local spatio‐temporal distribution of eDNA in two locations. We extracted and amplified eDNA using two COI primer pairs from ~80 water samples that were collected across two Canadian Arctic ports, Churchill and Iqaluit, based on optimized sampling and preservation methods for remote regions surveys. Results demonstrate that aquatic eDNA surveys have the potential to document large‐scale Arctic biodiversity change by providing a rapid overview of coastal metazoan biodiversity, detecting nonindigenous species, and allowing sampling in both open water and under the ice cover by local northern‐based communities. We show that DNA sequences of ~50% of known Canadian Arctic species and potential invaders are currently present in public databases. A similar proportion of operational taxonomic units was identified at the species level with eDNA metabarcoding, for a total of 181 species identified at both sites. Despite the cold and well‐mixed coastal environment, species composition was vertically heterogeneous, in part due to river inflow in the estuarine ecosystem, and differed between the water column and tide pools. Thus, COI‐based eDNA metabarcoding may quickly improve large‐scale Arctic biomonitoring using eDNA, but we caution that aquatic eDNA sampling needs to be standardized over space and time to accurately evaluate community structure changes.

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.

National Academies report has broad support

VOLUME 35 NUMBER 4 APRIL 2017 NATURE BIOTECHNOLOGY Giddings and Henry Miller2 published in your December issue. After reading their Correspondence, we wish to share our assessment of the NAS report with your readers. We represent a subset of Forum participants. Although our views have not been formally endorsed by all of our respective scientific societies, we represent a wealth of diverse scientific expertise and experience. As a whole, our professional assessment is that the NAS report offers an extensive and authoritative review of peer-reviewed scientific literature on a wide range of topics related to the agronomic performance of GE crops, the social, economic, political, health, safety, and regulatory context that guides the trajectory of GE technological innovation, and the costs and benefits of these technologies. We broadly agree with key conclusions of the NAS report that: • “...no differences have been found that implicate a higher risk to human health safety from these GE foods than from their non-GE counterparts” (p. 19); • GE crops “have generally had favorable economic outcomes for producers who have adopted these crops, but there is high heterogeneity in outcomes” (p. 20); • the ability of GE crops “to benefit intended stakeholders will depend on the social and economic contexts in which the technology is developed and diffused” (p. 22); and finally, • the scientific evidence suggests that “it is the product, not the process, that should be regulated” (p. 26). The NAS report notes that most of the extant peer-reviewed scientific research is focused on resistance to herbicides (mainly glyphosate) and resistance to insect pests (via Bacillus-thuringiensis-derived Cry proteins). We concur with the committee’s conclusion that GE crops have been adopted on millions of hectares without the emergence of scientific evidence of serious health and environmental problems that were expected by early critics of the technology. At the same time, we applaud the report for not overstating what is known about potential shortand long-term health, environmental, and socioeconomic implications of emerging GE traits. Giddings and Miller criticize the qualified language of the report because they were hoping for the NAS to “overtly back GE crops.” But in our view, the more nuanced phrasing in the NAS report represents a balanced and objective reading of the peer-reviewed evidence. The NAS committee reported that, on a national scale, rates of yield increases in maize, cotton, and soybean were the same before the advent of GE crops as afterward, concluding Science and Policy, Jaharis Family Center for Biomedical and Nutrition Sciences, Boston, Massachusetts, USA. 11Purdue University, Dept. of Food Science, West Lafayette, Indiana, USA. 12University of California, Los Angeles, Institute of the Environment and Sustainability, Los Angeles, California, USA. 13Johns Hopkins University School of Advanced International Studies, Washington, DC, USA. 14Oregon State University, Dept. of Crop and Soil Science, Corvallis, Oregon, USA. 15CIMMYT (Centro Internacional de Mejoramiento de Maíz y Trigo), Texcoco CP, Edo. de México, Mexico. 16University of Richmond, Dept. of Sociology and Anthropology, University of Richmond, Virginia, USA. 17University of Virginia, Dept. of Engineering and Society, Charlottesville, Charlottesville, Virginia, USA. 18Texas A&M University, Dept. of Soil and Crop Sciences, College Station, Texas, USA. 19University of Tennessee, Dept. of Plant Sciences, Knoxville, Tennessee, USA. 20Produce Marketing Association (PMA), Newark, Delaware, USA. e-mail: fred_gould@ncsu.edu