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Blackman R, Couton M, Keck F, Kirschner D, Carraro L, Cereghetti E, Perrelet K, Bossart R, Brantschen J, Zhang Y, Altermatt F. Environmental DNA: The next chapter. Mol Ecol 2024; 33:e17355. [PMID: 38624076 DOI: 10.1111/mec.17355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024]
Abstract
Molecular tools are an indispensable part of ecology and biodiversity sciences and implemented across all biomes. About a decade ago, the use and implementation of environmental DNA (eDNA) to detect biodiversity signals extracted from environmental samples opened new avenues of research. Initial eDNA research focused on understanding population dynamics of target species. Its scope thereafter broadened, uncovering previously unrecorded biodiversity via metabarcoding in both well-studied and understudied ecosystems across all taxonomic groups. The application of eDNA rapidly became an established part of biodiversity research, and a research field by its own. Here, we revisit key expectations made in a land-mark special issue on eDNA in Molecular Ecology in 2012 to frame the development in six key areas: (1) sample collection, (2) primer development, (3) biomonitoring, (4) quantification, (5) behaviour of DNA in the environment and (6) reference database development. We pinpoint the success of eDNA, yet also discuss shortfalls and expectations not met, highlighting areas of research priority and identify the unexpected developments. In parallel, our retrospective couples a screening of the peer-reviewed literature with a survey of eDNA users including academics, end-users and commercial providers, in which we address the priority areas to focus research efforts to advance the field of eDNA. With the rapid and ever-increasing pace of new technical advances, the future of eDNA looks bright, yet successful applications and best practices must become more interdisciplinary to reach its full potential. Our retrospect gives the tools and expectations towards concretely moving the field forward.
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Affiliation(s)
- Rosetta Blackman
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Marjorie Couton
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - François Keck
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Dominik Kirschner
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, Ecosystems and Landscape Evolution, ETH Zürich, Zürich, Switzerland
- Department of Landscape Dynamics & Ecology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Luca Carraro
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Eva Cereghetti
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Kilian Perrelet
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
- Department of Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Urban Water Management, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Raphael Bossart
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Jeanine Brantschen
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Yan Zhang
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, China
| | - Florian Altermatt
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
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Dan ME, Portner EJ, Bowman JS, Semmens BX, Owens SM, Greenwald SM, Choy CA. Using low volume eDNA methods to sample pelagic marine animal assemblages. PLoS One 2024; 19:e0303263. [PMID: 38748719 PMCID: PMC11095688 DOI: 10.1371/journal.pone.0303263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/23/2024] [Indexed: 05/19/2024] Open
Abstract
Environmental DNA (eDNA) is an increasingly useful method for detecting pelagic animals in the ocean but typically requires large water volumes to sample diverse assemblages. Ship-based pelagic sampling programs that could implement eDNA methods generally have restrictive water budgets. Studies that quantify how eDNA methods perform on low water volumes in the ocean are limited, especially in deep-sea habitats with low animal biomass and poorly described species assemblages. Using 12S rRNA and COI gene primers, we quantified assemblages comprised of micronekton, coastal forage fishes, and zooplankton from low volume eDNA seawater samples (n = 436, 380-1800 mL) collected at depths of 0-2200 m in the southern California Current. We compared diversity in eDNA samples to concurrently collected pelagic trawl samples (n = 27), detecting a higher diversity of vertebrate and invertebrate groups in the eDNA samples. Differences in assemblage composition could be explained by variability in size-selectivity among methods and DNA primer suitability across taxonomic groups. The number of reads and amplicon sequences variants (ASVs) did not vary substantially among shallow (<200 m) and deep samples (>600 m), but the proportion of invertebrate ASVs that could be assigned a species-level identification decreased with sampling depth. Using hierarchical clustering, we resolved horizontal and vertical variability in marine animal assemblages from samples characterized by a relatively low diversity of ecologically important species. Low volume eDNA samples will quantify greater taxonomic diversity as reference libraries, especially for deep-dwelling invertebrate species, continue to expand.
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Affiliation(s)
- Michelle E. Dan
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Elan J. Portner
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Jeff S. Bowman
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Brice X. Semmens
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Sarah M. Owens
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, United States of America
| | - Stephanie M. Greenwald
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, United States of America
| | - C. Anela Choy
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
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Taylor BA, Tembrock LR, Sankovitz M, Wilson TM, Looney C, Takahashi J, Gilligan TM, Smith-Pardo AH, Harpur BA. Population genomics of the invasive Northern Giant Hornet Vespa mandarinia in North America and across its native range. Sci Rep 2024; 14:10803. [PMID: 38734771 PMCID: PMC11088652 DOI: 10.1038/s41598-024-61534-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/07/2024] [Indexed: 05/13/2024] Open
Abstract
The northern giant hornet Vespa mandarinia (NGH) is a voracious predator of other insect species, including honey bees. NGH's native range spans subtropical and temperate regions across much of east and southeast Asia and, in 2019, exotic populations of the species were discovered in North America. Despite this broad range and invasive potential, investigation of the population genomic structure of NGH across its native and introduced ranges has thus far been limited to a small number of mitochondrial samples. Here, we present analyses of genomic data from NGH individuals collected across the species' native range and from exotic individuals collected in North America. We provide the first survey of whole-genome population variation for any hornet species, covering this species' native and invasive ranges, and in doing so confirm likely origins in Japan and South Korea for the two introductions. We additionally show that, while this introduced population exhibited strongly elevated levels of inbreeding, these signatures of inbreeding are also present in some long-standing native populations, which may indicate that inbreeding depression alone is insufficient to prevent the persistence of NGH populations. As well as highlighting the importance of ongoing monitoring and eradication efforts to limit the spread of this species outside of its natural range, our data will serve as a foundational database for future genomic studies into introduced hornet populations.
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Affiliation(s)
- Benjamin A Taylor
- Department of Entomology, Purdue University, West Lafayette, IN, 47907, USA.
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Madison Sankovitz
- Department of Ecology and Evolutionary Biology and BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303, USA
| | - Telissa M Wilson
- Washington State Department of Agriculture, Olympia, WA, 98501, USA
| | - Chris Looney
- Washington State Department of Agriculture, Olympia, WA, 98501, USA
| | - Junichi Takahashi
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8047, Japan
| | - Todd M Gilligan
- USDA Animal and Plant Health Inspection Service (APHIS), Fort Collins, CO, 80526-1825, USA
| | - Allan H Smith-Pardo
- USDA Animal and Plant Health Inspection Service (APHIS), Fort Collins, CO, 80526-1825, USA
| | - Brock A Harpur
- Department of Entomology, Purdue University, West Lafayette, IN, 47907, USA
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Curd EE, Gal L, Gallego R, Silliman K, Nielsen S, Gold Z. rCRUX: A Rapid and Versatile Tool for Generating Metabarcoding Reference libraries in R. ENVIRONMENTAL DNA (HOBOKEN, N.J.) 2024; 6:e489. [PMID: 38370872 PMCID: PMC10871694 DOI: 10.1002/edn3.489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/19/2023] [Indexed: 02/20/2024]
Abstract
The sequencing revolution requires accurate taxonomic classification of DNA sequences. Key to making accurate taxonomic assignments are curated, comprehensive reference barcode databases. However, the generation and curation of such databases has remained challenging given the large and continuously growing volumes of both DNA sequence data and novel reference barcode targets. Monitoring and research applications require a greater diversity of specialized gene regions and targeted taxa then are currently curated by professional staff. Thus there is a growing need for an easy to implement computational tool that can generate comprehensive metabarcoding reference libraries for any bespoke locus. We address this need by reimagining CRUX from the Anacapa Toolkit and present the rCRUX package in R which, like it's predecessor, relies on sequence homology and PCR primer compatibility instead of keyword-searches to avoid limitations of user-defined metadata. The typical workflow involves searching for plausible seed amplicons (get_seeds_local() or get_seeds_remote()) by simulating in silico PCR to acquire a set of sequences analogous to PCR products containing a user-defined set of primer sequences. Next, these seeds are used to iteratively blast search seed sequences against a local copy of the National Center for Biotechnology Information (NCBI) formatted nt database using a taxonomic-rank based stratified random sampling approach ( blast_seeds() ). This results in a comprehensive set of sequence matches. This database is dereplicated and cleaned (derep_and_clean_db()) by identifying identical reference sequences and collapsing the taxonomic path to the lowest taxonomic agreement across all matching reads. This results in a curated, comprehensive database of primer-specific reference barcode sequences from NCBI. Databases can then be compared (compare_db()) to determine read and taxonomic overlap. We demonstrate that rCRUX provides more comprehensive reference databases for the MiFish Universal Teleost 12S, Taberlet trnl, fungal ITS, and Leray CO1 loci than CRABS, MetaCurator, RESCRIPt, and ecoPCR reference databases. We then further demonstrate the utility of rCRUX by generating 24 reference databases for 20 metabarcoding loci, many of which lack dedicated reference database curation efforts. The rCRUX package provides a simple to use tool for the generation of curated, comprehensive reference databases for user-defined loci, facilitating accurate and effective taxonomic classification of metabarcoding and DNA sequence efforts broadly.
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Affiliation(s)
- Emily E. Curd
- Vermont Biomedical Research Network, University of Vermont, VT, USA
| | - Luna Gal
- Landmark College, VT, USA
- California Cooperative Oceanic Fisheries Investigations (CalCOFI), Scripps Institution of Oceanography, University of California San Diego (UCSD), La Jolla, CA, USA
| | - Ramon Gallego
- Departamento de Biología, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Katherine Silliman
- Northern Gulf Institute, Mississippi State University, Starkville, MS, USA
- NOAA Atlantic Oceanographic and Meteorological Laboratory, Miami, FL, USA
| | | | - Zachary Gold
- California Cooperative Oceanic Fisheries Investigations (CalCOFI), Scripps Institution of Oceanography, University of California San Diego (UCSD), La Jolla, CA, USA
- NOAA Pacific Marine Environmental Laboratory, Seattle, WA, USA
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