201
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Balech B, Sandionigi A, Manzari C, Trucchi E, Tullo A, Licciulli F, Grillo G, Sbisà E, De Felici S, Saccone C, D'Erchia AM, Cesaroni D, Casiraghi M, Vicario S. Tackling critical parameters in metazoan meta-barcoding experiments: a preliminary study based on coxI DNA barcode. PeerJ 2018; 6:e4845. [PMID: 29915686 PMCID: PMC6004112 DOI: 10.7717/peerj.4845] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 05/04/2018] [Indexed: 11/21/2022] Open
Abstract
Nowadays DNA meta-barcoding is a powerful instrument capable of quickly discovering the biodiversity of an environmental sample by integrating the DNA barcoding approach with High Throughput Sequencing technologies. It mainly consists of the parallel reading of informative genomic fragment/s able to discriminate living entities. Although this approach has been widely studied, it still needs optimization in some necessary steps requested in its advanced accomplishment. A fundamental element concerns the standardization of bioinformatic analyses pipelines. The aim of the present study was to underline a number of critical parameters of laboratory material preparation and taxonomic assignment pipelines in DNA meta-barcoding experiments using the cytochrome oxidase subunit-I (coxI) barcode region, known as a suitable molecular marker for animal species identification. We compared nine taxonomic assignment pipelines, including a custom in-house method, based on Hidden Markov Models. Moreover, we evaluated the potential influence of universal primers amplification bias in qPCR, as well as the correlation between GC content with taxonomic assignment results. The pipelines were tested on a community of known terrestrial invertebrates collected by pitfall traps from a chestnut forest in Italy. Although the present analysis was not exhaustive and needs additional investigation, our results suggest some potential improvements in laboratory material preparation and the introduction of additional parameters in taxonomic assignment pipelines. These include the correct setup of OTU clustering threshold, the calibration of GC content affecting sequencing quality and taxonomic classification, as well as the evaluation of PCR primers amplification bias on the final biodiversity pattern. Thus, careful attention and further validation/optimization of the above-mentioned variables would be required in a DNA meta-barcoding experimental routine.
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Affiliation(s)
- Bachir Balech
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari-Consiglio Nazionale delle Ricerche, Bari, Italy.,Dipartimento di Biologia, Università degli studi di Bari 'Aldo Moro', Bari, Italy
| | - Anna Sandionigi
- Dipartimento di Biotecnologie e Bioscienze-Zooplantlab, Università degli studi di Milano Bicocca, Milan, Italy
| | - Caterina Manzari
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari-Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Emiliano Trucchi
- Dipartimento di Biologia, Università di Roma Tor Vergata, Rome, Italy
| | - Apollonia Tullo
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari-Consiglio Nazionale delle Ricerche, Bari, Italy.,Istituto di Tecnologie Biomediche-Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Flavio Licciulli
- Istituto di Tecnologie Biomediche-Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Giorgio Grillo
- Istituto di Tecnologie Biomediche-Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Elisabetta Sbisà
- Istituto di Tecnologie Biomediche-Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Stefano De Felici
- Dipartimento di Biologia, Università di Roma Tor Vergata, Rome, Italy.,Istituto di Biologia Agroambientale e Forestale-Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Cecilia Saccone
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari 'Aldo Moro', Bari, Italy
| | - Anna Maria D'Erchia
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari 'Aldo Moro', Bari, Italy
| | | | - Maurizio Casiraghi
- Dipartimento di Biotecnologie e Bioscienze-Zooplantlab, Università degli studi di Milano Bicocca, Milan, Italy
| | - Saverio Vicario
- Istituto sull'Inquinamento Atmosferico-Consiglio Nazionale delle Ricerche, Bari, Italy
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202
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Mosher BA, Huyvaert KP, Bailey LL. Beyond the swab: ecosystem sampling to understand the persistence of an amphibian pathogen. Oecologia 2018; 188:319-330. [PMID: 29860635 DOI: 10.1007/s00442-018-4167-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 05/12/2018] [Indexed: 10/14/2022]
Abstract
Understanding the ecosystem-level persistence of pathogens is essential for predicting and measuring host-pathogen dynamics. However, this process is often masked, in part due to a reliance on host-based pathogen detection methods. The amphibian pathogens Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal) are pathogens of global conservation concern. Despite having free-living life stages, little is known about the distribution and persistence of these pathogens outside of their amphibian hosts. We combine historic amphibian monitoring data with contemporary host- and environment-based pathogen detection data to obtain estimates of Bd occurrence independent of amphibian host distributions. We also evaluate differences in filter- and swab-based detection probability and assess inferential differences arising from using different decision criteria used to classify samples as positive or negative. Water filtration-based detection probabilities were lower than those from swabs but were > 10%, and swab-based detection probabilities varied seasonally, declining in the early fall. The decision criterion used to classify samples as positive or negative was important; using a more liberal criterion yielded higher estimates of Bd occurrence than when a conservative criterion was used. Different covariates were important when using the liberal or conservative criterion in modeling Bd detection. We found evidence of long-term Bd persistence for several years after an amphibian host species of conservation concern, the boreal toad (Anaxyrus boreas boreas), was last detected. Our work provides evidence of long-term Bd persistence in the ecosystem, and underscores the importance of environmental samples for understanding and mitigating disease-related threats to amphibian biodiversity.
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Affiliation(s)
- Brittany A Mosher
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Kathryn P Huyvaert
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Larissa L Bailey
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO, 80523, USA
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203
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Citizen warnings and post checkout molecular confirmations using eDNA as a combined strategy for updating invasive species distributions. J Nat Conserv 2018. [DOI: 10.1016/j.jnc.2018.02.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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204
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Harper LR, Lawson Handley L, Hahn C, Boonham N, Rees HC, Gough KC, Lewis E, Adams IP, Brotherton P, Phillips S, Hänfling B. Needle in a haystack? A comparison of eDNA metabarcoding and targeted qPCR for detection of the great crested newt ( Triturus cristatus). Ecol Evol 2018; 8:6330-6341. [PMID: 29988445 PMCID: PMC6024127 DOI: 10.1002/ece3.4013] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 01/25/2018] [Accepted: 02/09/2018] [Indexed: 12/20/2022] Open
Abstract
Environmental DNA (eDNA) analysis is a rapid, cost-effective, non-invasive biodiversity monitoring tool which utilises DNA left behind in the environment by organisms for species detection. The method is used as a species-specific survey tool for rare or invasive species across a broad range of ecosystems. Recently, eDNA and "metabarcoding" have been combined to describe whole communities rather than focusing on single target species. However, whether metabarcoding is as sensitive as targeted approaches for rare species detection remains to be evaluated. The great crested newt Triturus cristatus is a flagship pond species of international conservation concern and the first UK species to be routinely monitored using eDNA. We evaluate whether eDNA metabarcoding has comparable sensitivity to targeted real-time quantitative PCR (qPCR) for T. cristatus detection. Extracted eDNA samples (N = 532) were screened for T. cristatus by qPCR and analysed for all vertebrate species using high-throughput sequencing technology. With qPCR and a detection threshold of 1 of 12 positive qPCR replicates, newts were detected in 50% of ponds. Detection decreased to 32% when the threshold was increased to 4 of 12 positive qPCR replicates. With metabarcoding, newts were detected in 34% of ponds without a detection threshold, and in 28% of ponds when a threshold (0.028%) was applied. Therefore, qPCR provided greater detection than metabarcoding but metabarcoding detection with no threshold was equivalent to qPCR with a stringent detection threshold. The proportion of T. cristatus sequences in each sample was positively associated with the number of positive qPCR replicates (qPCR score) suggesting eDNA metabarcoding may be indicative of eDNA concentration. eDNA metabarcoding holds enormous potential for holistic biodiversity assessment and routine freshwater monitoring. We advocate this community approach to freshwater monitoring to guide management and conservation, whereby entire communities can be initially surveyed to best inform use of funding and time for species-specific surveys.
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Affiliation(s)
| | | | - Christoph Hahn
- School of Environmental SciencesUniversity of HullHullUK
- Institute of ZoologyUniversity of GrazGrazStyriaAustria
| | - Neil Boonham
- FeraSand HuttonYorkUK
- Newcastle UniversityNewcastle upon TyneUK
| | - Helen C. Rees
- ADASSchool of Veterinary Medicine and ScienceThe University of NottinghamLeicestershireUK
| | - Kevin C. Gough
- School of Veterinary Medicine and ScienceThe University of NottinghamLeicestershireUK
| | | | | | | | | | - Bernd Hänfling
- School of Environmental SciencesUniversity of HullHullUK
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205
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Macías-Hernández N, Athey K, Tonzo V, Wangensteen OS, Arnedo M, Harwood JD. Molecular gut content analysis of different spider body parts. PLoS One 2018; 13:e0196589. [PMID: 29847544 PMCID: PMC5976152 DOI: 10.1371/journal.pone.0196589] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 04/16/2018] [Indexed: 11/19/2022] Open
Abstract
Molecular gut-content analysis has revolutionized the study of food webs and feeding interactions, allowing the detection of prey DNA within the gut of many organisms. However, successful prey detection is a challenging procedure in which many factors affect every step, starting from the DNA extraction process. Spiders are liquid feeders with branched gut diverticula extending into their legs and throughout the prosoma, thus digestion takes places in different parts of the body and simple gut dissection is not possible. In this study, we investigated differences in prey detectability in DNA extracts from different parts of the spider´s body: legs, prosoma and opisthosoma, using prey-specific PCR and metabarcoding approaches. We performed feeding trials with the woodlouse hunter spider Dysdera verneaui Simon, 1883 (Dysderidae) to estimate the time at which prey DNA is detectable within the predator after feeding. Although we found that all parts of the spider body are suitable for gut-content analysis when using prey-specific PCR approach, results based on metabarcoding suggested the opisthosoma is optimal for detection of predation in spiders because it contained the highest concentration of prey DNA for longer post feeding periods. Other spiders may show different results compared to D. verneaui, but given similarities in the physiology and digestion in different families, it is reasonable to assume this to be common across species and this approach having broad utility across spiders.
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Affiliation(s)
- Nuria Macías-Hernández
- Department of Entomology, University of Kentucky, Lexington, Kentucky, United States of America
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Universitat de Barcelona, Barcelona, Spain
- Biodiversity Research Institute (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Kacie Athey
- Department of Entomology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Vanina Tonzo
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Universitat de Barcelona, Barcelona, Spain
- Biodiversity Research Institute (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Owen S. Wangensteen
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Miquel Arnedo
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Universitat de Barcelona, Barcelona, Spain
- Biodiversity Research Institute (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - James D. Harwood
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
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206
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Nichols RV, Vollmers C, Newsom LA, Wang Y, Heintzman PD, Leighton M, Green RE, Shapiro B. Minimizing polymerase biases in metabarcoding. Mol Ecol Resour 2018; 18:927-939. [PMID: 29797549 DOI: 10.1111/1755-0998.12895] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/12/2018] [Accepted: 03/01/2018] [Indexed: 01/24/2023]
Abstract
DNA metabarcoding is an increasingly popular method to characterize and quantify biodiversity in environmental samples. Metabarcoding approaches simultaneously amplify a short, variable genomic region, or "barcode," from a broad taxonomic group via the polymerase chain reaction (PCR), using universal primers that anneal to flanking conserved regions. Results of these experiments are reported as occurrence data, which provide a list of taxa amplified from the sample, or relative abundance data, which measure the relative contribution of each taxon to the overall composition of amplified product. The accuracy of both occurrence and relative abundance estimates can be affected by a variety of biological and technical biases. For example, taxa with larger biomass may be better represented in environmental samples than those with smaller biomass. Here, we explore how polymerase choice, a potential source of technical bias, might influence results in metabarcoding experiments. We compared potential biases of six commercially available polymerases using a combination of mixtures of amplifiable synthetic sequences and real sedimentary DNA extracts. We find that polymerase choice can affect both occurrence and relative abundance estimates and that the main source of this bias appears to be polymerase preference for sequences with specific GC contents. We further recommend an experimental approach for metabarcoding based on results of our synthetic experiments.
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Affiliation(s)
- Ruth V Nichols
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California
| | - Lee A Newsom
- Department of Social Sciences, Flagler College, St. Augustine, Florida
| | - Yue Wang
- Department of Geography, University of Wisconsin-Madison, Madison, Wisconsin
| | - Peter D Heintzman
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California
- Tromsø University Museum, UiT - The Arctic University of Norway, Tromsø, Norway
| | - McKenna Leighton
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California
| | - Richard E Green
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California
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207
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Ficetola GF, Poulenard J, Sabatier P, Messager E, Gielly L, Leloup A, Etienne D, Bakke J, Malet E, Fanget B, Støren E, Reyss JL, Taberlet P, Arnaud F. DNA from lake sediments reveals long-term ecosystem changes after a biological invasion. SCIENCE ADVANCES 2018; 4:eaar4292. [PMID: 29750197 PMCID: PMC5942909 DOI: 10.1126/sciadv.aar4292] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/22/2018] [Indexed: 05/30/2023]
Abstract
What are the long-term consequences of invasive species? After invasion, how long do ecosystems require to reach a new equilibrium? Answering these questions requires long-term, high-resolution data that are vanishingly rare. We combined the analysis of environmental DNA extracted from a lake sediment core, coprophilous fungi, and sedimentological analyses to reconstruct 600 years of ecosystem dynamics on a sub-Antarctic island and to identify the impact of invasive rabbits. Plant communities remained stable from AD 1400 until the 1940s, when the DNA of invasive rabbits was detected in sediments. Rabbit detection corresponded to abrupt changes of plant communities, with a continuous decline of a dominant plant species. Furthermore, erosion rate abruptly increased with rabbit abundance. Rabbit impacts were very fast and were stronger than the effects of climate change during the 20th century. Lake sediments can allow an integrated temporal analysis of ecosystems, revealing the impact of invasive species over time and improving our understanding of underlying mechanisms.
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Affiliation(s)
- Gentile Francesco Ficetola
- Université Grenoble Alpes, CNRS, Laboratoire d’Écologie Alpine, F-38000 Grenoble, France
- Departement of Environmental Science and Policy, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Jérôme Poulenard
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, EDYTEM (Centre national de la recherche scientifique, Environnements, DYnamiques et TErritoires de la Montagne), 73000 Chambéry, France
| | - Pierre Sabatier
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, EDYTEM (Centre national de la recherche scientifique, Environnements, DYnamiques et TErritoires de la Montagne), 73000 Chambéry, France
| | - Erwan Messager
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, EDYTEM (Centre national de la recherche scientifique, Environnements, DYnamiques et TErritoires de la Montagne), 73000 Chambéry, France
| | - Ludovic Gielly
- Université Grenoble Alpes, CNRS, Laboratoire d’Écologie Alpine, F-38000 Grenoble, France
| | - Anouk Leloup
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, EDYTEM (Centre national de la recherche scientifique, Environnements, DYnamiques et TErritoires de la Montagne), 73000 Chambéry, France
| | - David Etienne
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, EDYTEM (Centre national de la recherche scientifique, Environnements, DYnamiques et TErritoires de la Montagne), 73000 Chambéry, France
| | - Jostein Bakke
- Department of Earth Science and Bjerknes Centre for Climate Research, University of Bergen, Allégaten 41, 5007 Bergen, Norway
| | - Emmanuel Malet
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, EDYTEM (Centre national de la recherche scientifique, Environnements, DYnamiques et TErritoires de la Montagne), 73000 Chambéry, France
| | - Bernard Fanget
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, EDYTEM (Centre national de la recherche scientifique, Environnements, DYnamiques et TErritoires de la Montagne), 73000 Chambéry, France
| | - Eivind Støren
- Department of Earth Science and Bjerknes Centre for Climate Research, University of Bergen, Allégaten 41, 5007 Bergen, Norway
| | - Jean-Louis Reyss
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, EDYTEM (Centre national de la recherche scientifique, Environnements, DYnamiques et TErritoires de la Montagne), 73000 Chambéry, France
| | - Pierre Taberlet
- Université Grenoble Alpes, CNRS, Laboratoire d’Écologie Alpine, F-38000 Grenoble, France
| | - Fabien Arnaud
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, EDYTEM (Centre national de la recherche scientifique, Environnements, DYnamiques et TErritoires de la Montagne), 73000 Chambéry, France
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208
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Alsos IG, Lammers Y, Yoccoz NG, Jørgensen T, Sjögren P, Gielly L, Edwards ME. Plant DNA metabarcoding of lake sediments: How does it represent the contemporary vegetation. PLoS One 2018; 13:e0195403. [PMID: 29664954 PMCID: PMC5903670 DOI: 10.1371/journal.pone.0195403] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/21/2018] [Indexed: 11/18/2022] Open
Abstract
Metabarcoding of lake sediments have been shown to reveal current and past biodiversity, but little is known about the degree to which taxa growing in the vegetation are represented in environmental DNA (eDNA) records. We analysed composition of lake and catchment vegetation and vascular plant eDNA at 11 lakes in northern Norway. Out of 489 records of taxa growing within 2 m from the lake shore, 17–49% (mean 31%) of the identifiable taxa recorded were detected with eDNA. Of the 217 eDNA records of 47 plant taxa in the 11 lakes, 73% and 12% matched taxa recorded in vegetation surveys within 2 m and up to about 50 m away from the lakeshore, respectively, whereas 16% were not recorded in the vegetation surveys of the same lake. The latter include taxa likely overlooked in the vegetation surveys or growing outside the survey area. The percentages detected were 61, 47, 25, and 15 for dominant, common, scattered, and rare taxa, respectively. Similar numbers for aquatic plants were 88, 88, 33 and 62%, respectively. Detection rate and taxonomic resolution varied among plant families and functional groups with good detection of e.g. Ericaceae, Roseaceae, deciduous trees, ferns, club mosses and aquatics. The representation of terrestrial taxa in eDNA depends on both their distance from the sampling site and their abundance and is sufficient for recording vegetation types. For aquatic vegetation, eDNA may be comparable with, or even superior to, in-lake vegetation surveys and may therefore be used as an tool for biomonitoring. For reconstruction of terrestrial vegetation, technical improvements and more intensive sampling is needed to detect a higher proportion of rare taxa although DNA of some taxa may never reach the lake sediments due to taphonomical constrains. Nevertheless, eDNA performs similar to conventional methods of pollen and macrofossil analyses and may therefore be an important tool for reconstruction of past vegetation.
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Affiliation(s)
- Inger Greve Alsos
- Tromsø Museum, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
- * E-mail:
| | - Youri Lammers
- Tromsø Museum, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Nigel Giles Yoccoz
- Department of Arctic and Marine Biology, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Tina Jørgensen
- Tromsø Museum, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Per Sjögren
- Tromsø Museum, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Ludovic Gielly
- University Grenoble Alpes, LECA, Grenoble, France
- CNRS, LECA, Grenoble, France
| | - Mary E. Edwards
- Tromsø Museum, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
- Geography and Environment, University of Southampton, Highfield, Southampton, United Kingdom
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209
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Borrell YJ, Miralles L, Mártinez-Marqués A, Semeraro A, Arias A, Carleos CE, García-Vázquez E. Metabarcoding and post-sampling strategies to discover non-indigenous species: A case study in the estuaries of the central south Bay of Biscay. J Nat Conserv 2018. [DOI: 10.1016/j.jnc.2017.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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210
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Environmental DNA filtration techniques affect recovered biodiversity. Sci Rep 2018; 8:4682. [PMID: 29549344 PMCID: PMC5856736 DOI: 10.1038/s41598-018-23052-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 03/06/2018] [Indexed: 01/01/2023] Open
Abstract
Freshwater metazoan biodiversity assessment using environmental DNA (eDNA) captured on filters offers new opportunities for water quality management. Filtering of water in the field is a logistical advantage compared to transport of water to the nearest lab, and thus, appropriate filter preservation becomes crucial for maximum DNA recovery. Here, the effect of four different filter preservation strategies, two filter types, and pre-filtration were evaluated by measuring metazoan diversity and community composition, using eDNA collected from a river and a lake ecosystem. The filters were preserved cold on ice, in ethanol, in lysis buffer and dry in silica gel. Our results show that filters preserved either dry or in lysis buffer give the most consistent community composition. In addition, mixed cellulose ester filters yield more consistent community composition than polyethersulfone filters, while the effect of pre-filtration remained ambiguous. Our study facilitates development of guidelines for aquatic community-level eDNA biomonitoring, and we advocate filtering in the field, using mixed cellulose ester filters and preserving the filters either dry or in lysis buffer.
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211
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Divoll TJ, Brown VA, Kinne J, McCracken GF, O'Keefe JM. Disparities in second-generation DNA metabarcoding results exposed with accessible and repeatable workflows. Mol Ecol Resour 2018; 18:590-601. [DOI: 10.1111/1755-0998.12770] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 01/26/2018] [Accepted: 01/30/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Timothy J. Divoll
- Department of Biology; Center for Bat Research; Outreach, and Conservation; Indiana State University; Terre Haute IN USA
| | - Veronica A. Brown
- Department of Ecology and Evolutionary Biology; University of Tennessee; Knoxville TN USA
- Genomics Core; University of Tennessee; Knoxville TN USA
| | - Jeff Kinne
- Department of Mathematics and Computer Science; Indiana State University; Terre Haute IN USA
| | - Gary F. McCracken
- Department of Ecology and Evolutionary Biology; University of Tennessee; Knoxville TN USA
| | - Joy M. O'Keefe
- Department of Biology; Center for Bat Research; Outreach, and Conservation; Indiana State University; Terre Haute IN USA
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212
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Harbert RS. Algorithms and strategies in short-read shotgun metagenomic reconstruction of plant communities. APPLICATIONS IN PLANT SCIENCES 2018; 6:e1034. [PMID: 29732264 PMCID: PMC5895191 DOI: 10.1002/aps3.1034] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 12/22/2017] [Indexed: 05/09/2023]
Abstract
PREMISE OF THE STUDY DNA may be preserved for thousands of years in very cold or dry environments, and plant tissue fragments and pollen trapped in soils and shallow aquatic sediments are well suited for the molecular characterization of past floras. However, one obstacle in this area of study is the limiting bias in the bioinformatic classification of short fragments of degraded DNA from the large, complex genomes of plants. METHODS To establish one possible baseline protocol for the rapid classification of short-read shotgun metagenomic data for reconstructing plant communities, the read classification programs Kraken, Centrifuge, and MegaBLAST were tested on simulated and ancient data with classification against a reference database targeting plants. RESULTS Performance tests on simulated data suggest that Kraken and Centrifuge outperform MegaBLAST. Kraken tends to be the most conservative approach with high precision, whereas Centrifuge has higher sensitivity. Reanalysis of 13,000 years of ancient sedimentary DNA from North America characterizes potential post-glacial vegetation succession. DISCUSSION Classification method choice has an impact on performance and any downstream interpretation of results. The reanalysis of ancient DNA from glacial lake sediments yielded vegetation histories that varied depending on method, potentially changing paleoecological conclusions drawn from molecular evidence.
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Affiliation(s)
- Robert S. Harbert
- Sackler Institute for Comparative GenomicsAmerican Museum of Natural HistoryNew YorkNew York10024USA
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213
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Leonardi M, Librado P, Der Sarkissian C, Schubert M, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Gamba C, Willerslev E, Orlando L. Evolutionary Patterns and Processes: Lessons from Ancient DNA. Syst Biol 2018; 66:e1-e29. [PMID: 28173586 PMCID: PMC5410953 DOI: 10.1093/sysbio/syw059] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 06/04/2016] [Accepted: 06/06/2016] [Indexed: 12/02/2022] Open
Abstract
Ever since its emergence in 1984, the field of ancient DNA has struggled to overcome the challenges related to the decay of DNA molecules in the fossil record. With the recent development of high-throughput DNA sequencing technologies and molecular techniques tailored to ultra-damaged templates, it has now come of age, merging together approaches in phylogenomics, population genomics, epigenomics, and metagenomics. Leveraging on complete temporal sample series, ancient DNA provides direct access to the most important dimension in evolution—time, allowing a wealth of fundamental evolutionary processes to be addressed at unprecedented resolution. This review taps into the most recent findings in ancient DNA research to present analyses of ancient genomic and metagenomic data.
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Affiliation(s)
- Michela Leonardi
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Pablo Librado
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Ahmed H Alfarhan
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saleh A Alquraishi
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Cristina Gamba
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark.,Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark.,Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, Toulouse, France
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214
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de Boer HJ, Ghorbani A, Manzanilla V, Raclariu AC, Kreziou A, Ounjai S, Osathanunkul M, Gravendeel B. DNA metabarcoding of orchid-derived products reveals widespread illegal orchid trade. Proc Biol Sci 2018; 284:rspb.2017.1182. [PMID: 28931735 DOI: 10.1098/rspb.2017.1182] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/10/2017] [Indexed: 11/12/2022] Open
Abstract
In eastern Mediterranean countries orchids continue to be collected from the wild for the production of salep, a beverage made of dried orchid tubers. In this study we used nrITS1 and nrITS2 DNA metabarcoding to identify orchid and other plant species present in 55 commercial salep products purchased in Iran, Turkey, Greece and Germany. Thirty samples yielded a total of 161 plant taxa, and 13 products (43%) contained orchid species and these belonged to 10 terrestrial species with tuberous roots. Another 70% contained the substitute ingredient Cyamopsis tetraganoloba (Guar). DNA metabarcoding using the barcoding markers nrITS1 and nrITS2 shows the potential of these markers and approach for identification of species used in salep products. The analysis of interspecific genetic distances between sequences of these markers for the most common salep orchid genera shows that species level identifications can be made with a high level of confidence. Understanding the species diversity and provenance of salep orchid tubers will enable the chain of commercialization of endangered species to be traced back to the harvesters and their natural habitats, and thus allow for targeted efforts to protect or sustainably use wild populations of these orchids.
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Affiliation(s)
- Hugo J de Boer
- Natural History Museum, University of Oslo, Oslo, Norway .,Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Naturalis Biodiversity Center, Leiden, The Netherlands
| | | | | | - Ancuta-Cristina Raclariu
- Natural History Museum, University of Oslo, Oslo, Norway.,Stejarul Research Centre for Biological Sciences, NIRDBIS, Piatra Neamt, Romania
| | | | - Sarawut Ounjai
- Department of Biology, Chiang Mai University, Chiang Mai, Thailand
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215
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Laroche O, Wood SA, Tremblay LA, Ellis JI, Lear G, Pochon X. A cross-taxa study using environmental DNA/RNA metabarcoding to measure biological impacts of offshore oil and gas drilling and production operations. MARINE POLLUTION BULLETIN 2018; 127:97-107. [PMID: 29475721 DOI: 10.1016/j.marpolbul.2017.11.042] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 11/16/2017] [Accepted: 11/20/2017] [Indexed: 06/08/2023]
Abstract
Standardized ecosystem-based monitoring surveys are critical for providing information on marine ecosystem health. Environmental DNA/RNA (eDNA/eRNA) metabarcoding may facilitate such surveys by quickly and effectively characterizing multi-trophic levels. In this study, we assessed the suitability of eDNA/eRNA metabarcoding to evaluate changes in benthic assemblages of bacteria, Foraminifera and other eukaryotes along transects at three offshore oil and gas (O&G) drilling and production sites, and compared these to morphologically characterized macro-faunal assemblages. Bacterial communities were the most responsive to O&G activities, followed by Foraminifera, and macro-fauna (the latter assessed by morphology). The molecular approach enabled detection of hydrocarbon degrading taxa such as the bacteria Alcanivorax and Microbulbifer at petroleum impacted stations. Most identified indicator taxa, notably among macro-fauna, were highly specific to site conditions. Based on our results we suggest that eDNA/eRNA metabarcoding can be used as a stand-alone method for biodiversity assessment or as a complement to morphology-based monitoring approaches.
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Affiliation(s)
- Olivier Laroche
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; School of Biological Sciences, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand.
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Environmental Research Institute, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Louis A Tremblay
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; School of Biological Sciences, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand
| | - Joanne I Ellis
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Centre, Thuwal 23955-6900, Saudi Arabia
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand
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216
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Raemy M, Ursenbacher S. Detection of the European pond turtle (Emys orbicularis) by environmental DNA: is eDNA adequate for reptiles? AMPHIBIA-REPTILIA 2018. [DOI: 10.1163/15685381-17000025] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Recent studies have demonstrated the potential of combining molecular technologies with environmental sampling to detect various vertebrate species in aquatic ecosystems. The European pond turtle (Emys orbicularis) is a threatened and elusive aquatic reptile with shy behaviour. We aimed to develop and evaluate a methodology to detect the presence of this secretive aquatic reptile in ponds from environmental water samples. First, we determined that reptilian DNA can be isolated and amplified from water samples in artificial and natural ponds with known turtle density. Then we compared the potential of two water sampling methods (through filtration or precipitation) and found no significant differences between these approaches. Finally, we demonstrated that the eDNA concentration detected is not correlated with the number of E. orbicularis individuals or biomass. Detection of eDNA was higher in artificial ponds with small volumes of water or in the shallow waters of natural ponds. The eDNA-based methodology aims to detect the presence of specific species, even at low density, with better accuracy than visual observation. However, our study indicates that this method of population monitoring should be applied with caution to aquatic reptiles.
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Affiliation(s)
- Matthieu Raemy
- Department of Environmental Sciences, Section of Conservation Biology, University of Basel, St. Johanns-Vorstadt 10, CH-4056 Basel, Switzerland
| | - Sylvain Ursenbacher
- Department of Environmental Sciences, Section of Conservation Biology, University of Basel, St. Johanns-Vorstadt 10, CH-4056 Basel, Switzerland
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217
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Dorazio RM, Erickson RA. ednaoccupancy: An r package for multiscale occupancy modelling of environmental DNA data. Mol Ecol Resour 2017; 18:368-380. [PMID: 29120090 DOI: 10.1111/1755-0998.12735] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 10/20/2017] [Accepted: 11/01/2017] [Indexed: 12/20/2022]
Abstract
In this article, we describe ednaoccupancy, an r package for fitting Bayesian, multiscale occupancy models. These models are appropriate for occupancy surveys that include three nested levels of sampling: primary sample units within a study area, secondary sample units collected from each primary unit and replicates of each secondary sample unit. This design is commonly used in occupancy surveys of environmental DNA (eDNA). ednaoccupancy allows users to specify and fit multiscale occupancy models with or without covariates, to estimate posterior summaries of occurrence and detection probabilities, and to compare different models using Bayesian model-selection criteria. We illustrate these features by analysing two published data sets: eDNA surveys of a fungal pathogen of amphibians and eDNA surveys of an endangered fish species.
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Affiliation(s)
- Robert M Dorazio
- Wetland and Aquatic Research Center, U.S. Geological Survey, Gainesville, FL, USA
| | - Richard A Erickson
- Upper Midwest Environmental Sciences Center, U.S. Geological Survey, La Crosse, WI, USA
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218
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Clusa L, Miralles L, Basanta A, Escot C, García-Vázquez E. eDNA for detection of five highly invasive molluscs. A case study in urban rivers from the Iberian Peninsula. PLoS One 2017; 12:e0188126. [PMID: 29141037 PMCID: PMC5687721 DOI: 10.1371/journal.pone.0188126] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/01/2017] [Indexed: 11/19/2022] Open
Abstract
Biological invasions are an important threat to biodiversity especially in aquatic ecosystems, and their frequency is generally higher near urban areas. Potentially invasive non-indigenous molluscs were deliberately introduced into European waters for food (Corbicula fluminea) and biocontrol (Melanoides tuberculata), and unintentionally introduced by ballast water (Mytilopsis leucophaeata, Corbicula fluminea), stock contamination (Sinanodonta woodiana), accidental escapes from aquaculture (Sinanodonta woodiana), aquarium trade releases (Melanoides tuberculata) and even attached to aquatic birds (Corbicula fluminea). Three rivers from the Iberian Peninsula were monitored near the three most populated inland cities to evaluate the presence of these invasive molluscs through PCR amplification using taxon-specific primers from eDNA. New primers were designed within 16S rRNA and cytochrome oxidase subunit I genes, tested in silico from BLAST methodology and experimentally in vitro before application in the field. C. fluminea was found in Ebro River (near Zaragoza); M. leucophaeata in Guadalquivir River (near Sevilla). M. tuberculata and S. woodiana were found from enclosed areas (lake and reservoir respectively) upstream, respectively, Zaragoza and Madrid. The new tools are ready to be used in other regions where these species are also invasive.
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Affiliation(s)
- Laura Clusa
- Department of Functional Biology, University of Oviedo, Oviedo, Asturias, Spain
| | - Laura Miralles
- Department of Functional Biology, University of Oviedo, Oviedo, Asturias, Spain
| | - Ana Basanta
- Metropolitan Water Supply and Sanitation Company of Sevilla, EMASESA., Sevilla, Spain
| | - Carmelo Escot
- Metropolitan Water Supply and Sanitation Company of Sevilla, EMASESA., Sevilla, Spain
| | - Eva García-Vázquez
- Department of Functional Biology, University of Oviedo, Oviedo, Asturias, Spain
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219
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Identifying a breeding habitat of a critically endangered fish, Acheilognathus typus, in a natural river in Japan. Naturwissenschaften 2017; 104:100. [DOI: 10.1007/s00114-017-1521-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 10/20/2017] [Accepted: 10/23/2017] [Indexed: 01/02/2023]
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220
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Pochon X, Zaiko A, Fletcher LM, Laroche O, Wood SA. Wanted dead or alive? Using metabarcoding of environmental DNA and RNA to distinguish living assemblages for biosecurity applications. PLoS One 2017; 12:e0187636. [PMID: 29095959 PMCID: PMC5667844 DOI: 10.1371/journal.pone.0187636] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 10/23/2017] [Indexed: 11/19/2022] Open
Abstract
High-throughput sequencing metabarcoding studies in marine biosecurity have largely focused on targeting environmental DNA (eDNA). DNA can persist extracellularly in the environment, making discrimination of living organisms difficult. In this study, bilge water samples (i.e., water accumulating on-board a vessel during transit) were collected from 15 small recreational and commercial vessels. eDNA and eRNA molecules were co-extracted and the V4 region of the 18S ribosomal RNA gene targeted for metabarcoding. In total, 62.7% of the Operational Taxonomic Units (OTUs) were identified at least once in the corresponding eDNA and eRNA reads, with 19.5% unique to eDNA and 17.7% to eRNA. There were substantial differences in diversity between molecular compartments; 57% of sequences from eDNA-only OTUs belonged to fungi, likely originating from legacy DNA. In contrast, there was a higher percentage of metazoan (50.2%) and ciliate (31.7%) sequences in the eRNA-only OTUs. Our data suggest that the presence of eRNA-only OTUs could be due to increased cellular activities of some rare taxa that were not identified in the eDNA datasets, unusually high numbers of rRNA transcripts in ciliates, and/or artefacts produced during the reverse transcriptase, PCR and sequencing steps. The proportions of eDNA/eRNA shared and unshared OTUs were highly heterogeneous within individual bilge water samples. Multiple factors including boat type and the activities performed on-board, such as washing of scientific equipment, may play a major role in contributing to this variability. For some marine biosecurity applications analysis, eDNA-only data may be sufficient, however there are an increasing number of instances where distinguishing the living portion of a community is essential. For these circumstances, we suggest only including OTUs that are present in both eDNA and eRNA data. OTUs found only in the eRNA data need to be interpreted with caution until further research provides conclusive evidence for their origin.
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Affiliation(s)
- Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
- * E-mail:
| | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
- Marine Science and Technology Centre, Klaipeda University, Klaipeda, Lithuania
| | | | - Olivier Laroche
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Susanna A. Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Environmental Research Institute, University of Waikato, Hamilton, New Zealand
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221
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Usefulness and limitations of sample pooling for environmental DNA metabarcoding of freshwater fish communities. Sci Rep 2017; 7:14860. [PMID: 29093520 PMCID: PMC5665893 DOI: 10.1038/s41598-017-14978-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 10/18/2017] [Indexed: 11/24/2022] Open
Abstract
Environmental DNA (eDNA) metabarcoding has been used increasingly to assess biodiversity of aquatic vertebrates. However, there still remains to be developed a sampling design of eDNA metabarcoding that can ensure high detection rates of species with minimum total survey effort, especially for large-scale surveys of aquatic organisms. We here tested whether pooling of eDNA samples can be used to evaluate biodiversity of freshwater fishes in four satellite lakes of Lake Biwa, Japan. Fish communities detected by eDNA metabarcoding of the mitochondrial 12S region were compared between the individual and pooled samples. In the individual samples, 31, 22, 33, and 31 fish lineages (proxies for species) were observed at the respective sites, within which moderate spatial autocorrelation existed. In the pooled samples, 30, 20, 29, and 27, lineages were detected, respectively, even after 15 PCR replicates. Lineages accounting for < 0.05% of the total read count of each site’s individual samples were mostly undetectable in the pooled samples. Moreover, fish communities detected were similar among PCR replicates in the pooled samples. Because of the decreased detection rates, the pooling strategy is unsuitable for estimating fish species richness. However, this procedure is useful potentially for among-site comparison of representative fish communities.
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222
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Deiner K, Bik HM, Mächler E, Seymour M, Lacoursière-Roussel A, Altermatt F, Creer S, Bista I, Lodge DM, de Vere N, Pfrender ME, Bernatchez L. Environmental DNA metabarcoding: Transforming how we survey animal and plant communities. Mol Ecol 2017; 26:5872-5895. [PMID: 28921802 DOI: 10.1111/mec.14350] [Citation(s) in RCA: 614] [Impact Index Per Article: 87.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 08/31/2017] [Accepted: 09/05/2017] [Indexed: 12/14/2022]
Abstract
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.
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Affiliation(s)
- Kristy Deiner
- Atkinson Center for a Sustainable Future, Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Holly M Bik
- Department of Nematology, University of California, Riverside, CA, USA
| | - Elvira Mächler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Mathew Seymour
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales Building, Bangor University, Bangor, Gwynedd, UK
| | | | - Florian Altermatt
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales Building, Bangor University, Bangor, Gwynedd, UK
| | - Iliana Bista
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales Building, Bangor University, Bangor, Gwynedd, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - David M Lodge
- Atkinson Center for a Sustainable Future, Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Natasha de Vere
- Conservation and Research Department, National Botanic Garden of Wales, Llanarthne, Carmarthenshire, UK.,Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Michael E Pfrender
- Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame, Notre Dame, IN, USA
| | - Louis Bernatchez
- IBIS (Institut de Biologie Intégrative et des Systèmes), Université Laval, Québec, QC, Canada
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223
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Ficetola GF, Taberlet P, Coissac E. How to limit false positives in environmental DNA and metabarcoding? Mol Ecol Resour 2017; 16:604-7. [PMID: 27062589 DOI: 10.1111/1755-0998.12508] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 01/28/2016] [Indexed: 12/18/2022]
Abstract
Environmental DNA (eDNA) and metabarcoding are boosting our ability to acquire data on species distribution in a variety of ecosystems. Nevertheless, as most of sampling approaches, eDNA is not perfect. It can fail to detect species that are actually present, and even false positives are possible: a species may be apparently detected in areas where it is actually absent. Controlling false positives remains a main challenge for eDNA analyses: in this issue of Molecular Ecology Resources, Lahoz-Monfort et al. () test the performance of multiple statistical modelling approaches to estimate the rate of detection and false positives from eDNA data. Here, we discuss the importance of controlling for false detection from early steps of eDNA analyses (laboratory, bioinformatics), to improve the quality of results and allow an efficient use of the site occupancy-detection modelling (SODM) framework for limiting false presences in eDNA analysis.
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Affiliation(s)
- Gentile Francesco Ficetola
- Universite Grenoble-Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000, Grenoble, France.,Centre National de la Recherche Scientifique, Laboratoire d'Ecologie Alpine (LECA), F-38000, Grenoble, France
| | - Pierre Taberlet
- Universite Grenoble-Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000, Grenoble, France.,Centre National de la Recherche Scientifique, Laboratoire d'Ecologie Alpine (LECA), F-38000, Grenoble, France
| | - Eric Coissac
- Universite Grenoble-Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000, Grenoble, France.,Centre National de la Recherche Scientifique, Laboratoire d'Ecologie Alpine (LECA), F-38000, Grenoble, France
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224
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Shogren AJ, Tank JL, Andruszkiewicz EA, Olds B, Jerde C, Bolster D. Modelling the transport of environmental DNA through a porous substrate using continuous flow-through column experiments. J R Soc Interface 2017; 13:rsif.2016.0290. [PMID: 27251680 DOI: 10.1098/rsif.2016.0290] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 05/09/2016] [Indexed: 01/20/2023] Open
Abstract
Detecting environmental DNA (eDNA) in water samples is a powerful tool in determining the presence of rare aquatic species. However, many open questions remain as to how biological and physical conditions in flowing waters influence eDNA. Motivated by what one might find in a stream/river benthos we conducted experiments in continuous flow columns packed with porous substrates to explore eDNA transport and ask whether substrate type and the presence of colonized biofilms plays an important role for eDNA retention. To interpret our data, and for modelling purposes, we began with the assumption that eDNA could be treated as a classical tracer. Comparing our experimental data with traditional transport models, we found that eDNA behaves anomalously, displaying characteristics of a heterogeneous, polydisperse substance with particle-like behaviour that can be filtered by the substrate. Columns were quickly flushed of suspended eDNA particles while a significant amount of particles never made it through and were retained in the column, as calculated from a mass balance. Suspended eDNA was exported through the column, regardless of biofilm colonization. Our results indicate that the variable particle size of eDNA results in stochastic retention, release and transport, which may influence the interpretation eDNA detection in biological systems.
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Affiliation(s)
- Arial J Shogren
- Department of Biological Sciences, Environmental Change Initiative, University of Notre Dame, Notre Dame, IN, USA
| | - Jennifer L Tank
- Department of Biological Sciences, Environmental Change Initiative, University of Notre Dame, Notre Dame, IN, USA
| | - Elizabeth A Andruszkiewicz
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Brett Olds
- Department of Biological Sciences, Environmental Change Initiative, University of Notre Dame, Notre Dame, IN, USA Oceanic Institute of Hawai'i Pacific University, Waimanalo, HI, USA
| | - Christopher Jerde
- Department of Biological Sciences, Environmental Change Initiative, University of Notre Dame, Notre Dame, IN, USA Biology Department, Aquatic Ecosystems Analysis Laboratory, University of Nevada, Reno, NV, USA
| | - Diogo Bolster
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA
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225
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Pärtel M, Öpik M, Moora M, Tedersoo L, Szava-Kovats R, Rosendahl S, Rillig MC, Lekberg Y, Kreft H, Helgason T, Eriksson O, Davison J, de Bello F, Caruso T, Zobel M. Historical biome distribution and recent human disturbance shape the diversity of arbuscular mycorrhizal fungi. THE NEW PHYTOLOGIST 2017; 216:227-238. [PMID: 28722181 DOI: 10.1111/nph.14695] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 06/06/2017] [Indexed: 05/24/2023]
Abstract
The availability of global microbial diversity data, collected using standardized metabarcoding techniques, makes microorganisms promising models for investigating the role of regional and local factors in driving biodiversity. Here we modelled the global diversity of symbiotic arbuscular mycorrhizal (AM) fungi using currently available data on AM fungal molecular diversity (small subunit (SSU) ribosomal RNA (rRNA) gene sequences) in field samples. To differentiate between regional and local effects, we estimated species pools (sets of potentially suitable taxa) for each site, which are expected to reflect regional processes. We then calculated community completeness, an index showing the fraction of the species pool present, which is expected to reflect local processes. We found significant spatial variation, globally in species pool size, as well as in local and dark diversity (absent members of the species pool). Species pool size was larger close to areas containing tropical grasslands during the last glacial maximum, which are possible centres of diversification. Community completeness was greater in regions of high wilderness (remoteness from human disturbance). Local diversity was correlated with wilderness and current connectivity to mountain grasslands. Applying the species pool concept to symbiotic fungi facilitated a better understanding of how biodiversity can be jointly shaped by large-scale historical processes and recent human disturbance.
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Affiliation(s)
- Meelis Pärtel
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Maarja Öpik
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Mari Moora
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Leho Tedersoo
- Natural History Museum, University of Tartu, Vanemuise 46, Tartu, 51014, Estonia
| | - Robert Szava-Kovats
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Søren Rosendahl
- Department of Biology, Sect. Ecology & Evolution, University of Copenhagen, Universitetsparken 15, Building 3, DK-2100, Copenhagen, Denmark
| | - Matthias C Rillig
- Freie Universität Berlin, Institute of Biology, Altensteinstr. 6, D-14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195, Berlin, Germany
| | - Ylva Lekberg
- MPG Ranch, 1001 S. Higgins Ave, Missoula, MT, 59801, USA
- Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Holger Kreft
- Department of Biodiversity, Macroecology and Biogeography, Georg-August-University Göttingen, Büsgenweg 1, 37077, Göttingen, Germany
| | - Thorunn Helgason
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Ove Eriksson
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 10691, Stockholm, Sweden
| | - John Davison
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Francesco de Bello
- Department of Botany, Faculty of Sciences, University of South Bohemia, Na Zlate Stoce 1, CZ-370 05, České Budějovice, Czech Republic
- Institute of Botany, Czech Academy of Sciences, Dukelská 135, CZ-379 82, Třeboň, Czech Republic
| | - Tancredi Caruso
- School of Biological Sciences, Queen's University of Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland
| | - Martin Zobel
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
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226
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Olajos F, Bokma F, Bartels P, Myrstener E, Rydberg J, Öhlund G, Bindler R, Wang X, Zale R, Englund G. Estimating species colonization dates using
DNA
in lake sediment. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12890] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fredrik Olajos
- Department of Ecology & Environmental ScienceUmeå University Umeå Sweden
| | - Folmer Bokma
- Department of Ecology & Environmental ScienceUmeå University Umeå Sweden
| | - Pia Bartels
- Department of Ecology & Environmental ScienceUmeå University Umeå Sweden
| | - Erik Myrstener
- Department of Ecology & Environmental ScienceUmeå University Umeå Sweden
| | - Johan Rydberg
- Department of Ecology & Environmental ScienceUmeå University Umeå Sweden
| | - Gunnar Öhlund
- Department of Ecology & Environmental ScienceUmeå University Umeå Sweden
| | - Richard Bindler
- Department of Ecology & Environmental ScienceUmeå University Umeå Sweden
| | - Xiao‐Ru Wang
- Department of Ecology & Environmental ScienceUmeå University Umeå Sweden
| | - Rolf Zale
- Department of Ecology & Environmental ScienceUmeå University Umeå Sweden
| | - Göran Englund
- Department of Ecology & Environmental ScienceUmeå University Umeå Sweden
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227
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Borrell YJ, Miralles L, Do Huu H, Mohammed-Geba K, Garcia-Vazquez E. DNA in a bottle-Rapid metabarcoding survey for early alerts of invasive species in ports. PLoS One 2017; 12:e0183347. [PMID: 28873426 PMCID: PMC5584753 DOI: 10.1371/journal.pone.0183347] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 08/02/2017] [Indexed: 11/18/2022] Open
Abstract
Biota monitoring in ports is increasingly needed for biosecurity reasons and safeguarding marine biodiversity from biological invasion. Present and future international biosecurity directives can be accomplished only if the biota acquired by maritime traffic in ports is controlled. Methodologies for biota inventory are diverse and now rely principally on extensive and labor-intensive sampling along with taxonomic identification by experts. In this study, we employed an extremely simplified environmental DNA (eDNA) sampling methodology from only three 1-L bottles of water per port, followed by metabarcoding (high-throughput sequencing and DNA-based species identification) using 18S rDNA and Cytochrome oxidase I as genetic barcodes. Eight Bay of Biscay ports with available inventory of fouling invertebrates were employed as a case study. Despite minimal sampling efforts, three invasive invertebrates were detected: the barnacle Austrominius modestus, the tubeworm Ficopomatus enigmaticus and the polychaete Polydora triglanda. The same species have been previously found from visual and DNA barcoding (genetic identification of individuals) surveys in the same ports. The current costs of visual surveys, conventional DNA barcoding and this simplified metabarcoding protocol were compared. The results encourage the use of metabarcoding for early biosecurity alerts.
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Affiliation(s)
- Yaisel J. Borrell
- Department of Functional Biology, University of Oviedo, Oviedo, Spain
| | - Laura Miralles
- Department of Functional Biology, University of Oviedo, Oviedo, Spain
| | - Hoang Do Huu
- Department of Aquaculture Biotechnology, Institute of Oceanography, Vietnam Academy of Science and Technology, Nha Trang, Vietnam
| | - Khaled Mohammed-Geba
- Genetic Engineering and Molecular Biology Division, Faculty of Science, Menoufia University, Egypt
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228
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Buxton AS, Groombridge JJ, Griffiths RA. Is the detection of aquatic environmental DNA influenced by substrate type? PLoS One 2017; 12:e0183371. [PMID: 28813525 PMCID: PMC5558973 DOI: 10.1371/journal.pone.0183371] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 08/02/2017] [Indexed: 12/26/2022] Open
Abstract
The use of environmental DNA (eDNA) to assess the presence-absence of rare, cryptic or invasive species is hindered by a poor understanding of the factors that can remove DNA from the system. In aquatic systems, eDNA can be transported out either horizontally in water flows or vertically by incorporation into the sediment. Equally, eDNA may be broken down by various biotic and abiotic processes if the target organism leaves the system. We use occupancy modelling and a replicated mesocosm experiment to examine how detection probability of eDNA changes once the target species is no longer present. We hypothesise that detection probability falls faster with a sediment which has a large number of DNA binding sites such as topsoil or clay, over lower DNA binding capacity substrates such as sand. Water removed from ponds containing the target species (the great crested newt) initially showed high detection probabilities, but these fell to between 40% and 60% over the first 10 days and to between 10% and 22% by day 15: eDNA remained detectable at very low levels until day 22. Very little difference in detection was observed between the control group (no substrate) and the sand substrate. A small reduction in detection probability was observed between the control and clay substrates, but this was not significant. However, a highly significant reduction in detection probability was observed with a topsoil substrate. This result is likely to have stemmed from increased levels of PCR inhibition, suggesting that incorporation of DNA into the sentiment is of only limited importance. Surveys of aquatic species using eDNA clearly need to take account of substrate type as well as other environmental factors when collecting samples, analysing data and interpreting the results.
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Affiliation(s)
- Andrew S. Buxton
- Durrell Institute for Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Marlowe Building, Canterbury, Kent, United Kingdom
- * E-mail:
| | - Jim J. Groombridge
- Durrell Institute for Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Marlowe Building, Canterbury, Kent, United Kingdom
| | - Richard A. Griffiths
- Durrell Institute for Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Marlowe Building, Canterbury, Kent, United Kingdom
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229
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Serrao NR, Reid SM, Wilson CC. Establishing detection thresholds for environmental DNA using receiver operator characteristic (ROC) curves. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0817-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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230
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Niemeyer B, Epp LS, Stoof-Leichsenring KR, Pestryakova LA, Herzschuh U. A comparison of sedimentary DNA and pollen from lake sediments in recording vegetation composition at the Siberian treeline. Mol Ecol Resour 2017; 17:e46-e62. [DOI: 10.1111/1755-0998.12689] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 04/13/2017] [Accepted: 04/25/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Bastian Niemeyer
- Periglacial Research Section; Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research; Potsdam Germany
- Institute of Earth and Environmental Science; University of Potsdam; Potsdam-Golm Germany
| | - Laura S. Epp
- Periglacial Research Section; Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research; Potsdam Germany
| | | | - Luidmila A. Pestryakova
- Department for Geography and Biology; North-Eastern Federal University of Yakutsk; Yakutsk Russia
| | - Ulrike Herzschuh
- Periglacial Research Section; Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research; Potsdam Germany
- Institute of Earth and Environmental Science; University of Potsdam; Potsdam-Golm Germany
- Institute of Biochemistry and Biology; University of Potsdam; Potsdam-Golm Germany
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231
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Fletcher LM, Zaiko A, Atalah J, Richter I, Dufour CM, Pochon X, Wood SA, Hopkins GA. Bilge water as a vector for the spread of marine pests: a morphological, metabarcoding and experimental assessment. Biol Invasions 2017. [DOI: 10.1007/s10530-017-1489-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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232
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Lanzén A, Lekang K, Jonassen I, Thompson EM, Troedsson C. DNA extraction replicates improve diversity and compositional dissimilarity in metabarcoding of eukaryotes in marine sediments. PLoS One 2017. [PMID: 28622351 PMCID: PMC5473592 DOI: 10.1371/journal.pone.0179443] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Human impact on marine benthic communities has traditionally been assessed using visible morphological traits and has focused on the macrobenthos, whereas the ecologically important organisms of the meio- and microbenthos have received less attention. DNA metabarcoding offers an alternative to this approach and enables a larger fraction of the biodiversity in marine sediments to be monitored in a cost-efficient manner. Although this methodology remains poorly standardised and challenged by biases inherent to rRNA copy number variation, DNA extraction, PCR, and limitations related to taxonomic identification, it has been shown to be semi-quantitative and useful for comparing taxon abundances between samples. Here, we evaluate the effect of replicating genomic DNA extraction in order to counteract small scale spatial heterogeneity and improve diversity and community structure estimates in metabarcoding-based monitoring. For this purpose, we used ten technical replicates from three different marine sediment samples. The effect of sequence depth was also assessed, and in silico pooling of DNA extraction replicates carried out in order to maintain the number of reads constant. Our analyses demonstrated that both sequencing depth and DNA extraction replicates could improve diversity estimates as well as the ability to separate samples with different characteristics. We could not identify a “sufficient” replicate number or sequence depth, where further improvements had a less significant effect. Based on these results, we consider replication an attractive alternative to directly increasing the amount of sample used for DNA extraction and strongly recommend it for future metabarcoding studies and routine assessments of sediment biodiversity.
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Affiliation(s)
- Anders Lanzén
- NEIKER-Tecnalia, Department of Conservation of Natural Resources, Bizkaia Technology Park, Derio, Spain
- * E-mail:
| | - Katrine Lekang
- Department of Biology, University of Bergen, Bergen, Norway
| | - Inge Jonassen
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Eric M. Thompson
- Department of Biology, University of Bergen, Bergen, Norway
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
- Uni Research Environment, Uni Research AS, Bergen, Norway
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233
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Ushio M, Fukuda H, Inoue T, Makoto K, Kishida O, Sato K, Murata K, Nikaido M, Sado T, Sato Y, Takeshita M, Iwasaki W, Yamanaka H, Kondoh M, Miya M. Environmental DNA enables detection of terrestrial mammals from forest pond water. Mol Ecol Resour 2017; 17:e63-e75. [PMID: 28603873 DOI: 10.1111/1755-0998.12690] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 04/25/2017] [Accepted: 05/02/2017] [Indexed: 11/27/2022]
Abstract
Terrestrial animals must have frequent contact with water to survive, implying that environmental DNA (eDNA) originating from those animals should be detectable from places containing water in terrestrial ecosystems. Aiming to detect the presence of terrestrial mammals using forest water samples, we applied a set of universal PCR primers (MiMammal, a modified version of fish universal primers) for metabarcoding mammalian eDNA. The versatility of MiMammal primers was tested in silico and by amplifying DNAs extracted from tissues. The results suggested that MiMammal primers are capable of amplifying and distinguishing a diverse group of mammalian species. In addition, analyses of water samples from zoo cages of mammals with known species composition suggested that MiMammal primers could successfully detect mammalian species from water samples in the field. Then, we performed an experiment to detect mammals from natural ecosystems by collecting five 500-ml water samples from ponds in two cool-temperate forests in Hokkaido, northern Japan. MiMammal amplicon libraries were constructed using eDNA extracted from water samples, and sequences generated by Illumina MiSeq were subjected to data processing and taxonomic assignment. We thereby detected multiple species of mammals common to the sampling areas, including deer (Cervus nippon), mouse (Mus musculus), vole (Myodes rufocanus), raccoon (Procyon lotor), rat (Rattus norvegicus) and shrew (Sorex unguiculatus). Many previous applications of the eDNA metabarcoding approach have been limited to aquatic/semiaquatic systems, but the results presented here show that the approach is also promising even for forest mammal biodiversity surveys.
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Affiliation(s)
- Masayuki Ushio
- Center for Ecological Research, Kyoto University, Otsu, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan.,Joint Research Center for Science and Technology, Ryukoku University, Otsu, Japan
| | - Hisato Fukuda
- Department of Environmental Solution Technology, Ryukoku University, Otsu, Japan
| | - Toshiki Inoue
- Department of Environmental Solution Technology, Ryukoku University, Otsu, Japan
| | - Kobayashi Makoto
- Teshio Experimental Forest, Field Science Center for Northern Biosphere, Hokkaido University, Hokkaido, Japan
| | - Osamu Kishida
- Teshio Experimental Forest, Field Science Center for Northern Biosphere, Hokkaido University, Hokkaido, Japan.,Tomakomai Experimental Forest, Field Science Center for Northern Biosphere, Hokkaido University, Hokkaido, Japan
| | - Keiichi Sato
- Okinawa Churashima Research Center, Okinawa, Japan
| | - Koichi Murata
- College of Bioresource Sciences, Nihon University, Kanagawa, Japan.,Yokohama Zoological Gardens ZOORASIA, Kanagawa, Japan
| | - Masato Nikaido
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Tetsuya Sado
- Natural History Museum and Institute, Chiba, Japan
| | - Yukuto Sato
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | | | - Wataru Iwasaki
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroki Yamanaka
- Department of Environmental Solution Technology, Ryukoku University, Otsu, Japan.,The Research Center for Satoyama Studies, Ryukoku University, Shiga, Japan
| | - Michio Kondoh
- Department of Environmental Solution Technology, Ryukoku University, Otsu, Japan
| | - Masaki Miya
- Natural History Museum and Institute, Chiba, Japan
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234
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Opportunities and challenges in metabarcoding approaches for helminth community identification in wild mammals. Parasitology 2017; 145:608-621. [PMID: 28534454 DOI: 10.1017/s0031182017000610] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Despite metabarcoding being widely used to analyse bacterial community composition, its application in parasitological research remains limited. What interest there has been has focused on previously intractable research settings where traditional methods are inappropriate, for example, in longitudinal studies and studies involving endangered species. In settings such as these, non-invasive sampling combined with metabarcoding can provide a fast and accurate assessment of component communities. In this paper we review the use of metabarcoding in the study of helminth communities in wild mammals, outlining the necessary procedures from sample collection to statistical analysis. We highlight the limitations of the metabarcoding approach and speculate on what type of parasitological study would benefit from such methods in the future.
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235
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Laroche O, Wood SA, Tremblay LA, Lear G, Ellis JI, Pochon X. Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities. PeerJ 2017; 5:e3347. [PMID: 28533985 PMCID: PMC5437860 DOI: 10.7717/peerj.3347] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/22/2017] [Indexed: 11/20/2022] Open
Abstract
Sequencing environmental DNA (eDNA) is increasingly being used as an alternative to traditional morphological-based identification to characterize biological assemblages and monitor anthropogenic impacts in marine environments. Most studies only assess eDNA which, compared to eRNA, can persist longer in the environment after cell death. Therefore, eRNA may provide a more immediate census of the environment due to its relatively weaker stability, leading some researchers to advocate for the use of eRNA as an additional, or perhaps superior proxy for portraying ecological changes. A variety of pre-treatment techniques for screening eDNA and eRNA derived operational taxonomic units (OTUs) have been employed prior to statistical analyses, including removing singleton taxa (i.e., OTUs found only once) and discarding those not present in both eDNA and eRNA datasets. In this study, we used bacterial (16S ribosomal RNA gene) and eukaryotic (18S ribosomal RNA gene) eDNA- and eRNA-derived data from benthic communities collected at increasing distances along a transect from an oil production platform (Taranaki, New Zealand). Macro-infauna (visual classification of benthic invertebrates) and physico-chemical data were analyzed in parallel. We tested the effect of removing singleton taxa, and removing taxa not present in the eDNA and eRNA libraries from the same environmental sample (trimmed by shared OTUs), by comparing the impact of the oil production platform on alpha- and beta-diversity of the eDNA/eRNA-based biological assemblages, and by correlating these to the morphologically identified macro-faunal communities and the physico-chemical data. When trimmed by singletons, presence/absence information from eRNA data represented the best proxy to detect changes on species diversity for both bacteria and eukaryotes. However, assessment of quantitative beta-diversity from read abundance information of bacteria eRNA did not, contrary to eDNA, reveal any impact from the oil production activity. Overall, the data appeared more robust when trimmed by shared OTUs, showing a greater effect of the platform on alpha- and beta-diversity. Trimming by shared OTUs likely removes taxa derived from legacy DNA and technical artefacts introduced through reverse transcriptase, polymerase-chain-reaction and sequencing. Findings from our scoping study suggest that metabarcoding-based biomonitoring surveys should, if funds, time and expertise allow, be assessed using both eDNA and eRNA products.
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Affiliation(s)
- Olivier Laroche
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Susanna A Wood
- Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,Environmental Research Institute, University of Waikato, Hamilton, New Zealand
| | - Louis A Tremblay
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Joanne I Ellis
- Red Sea Research Centre, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Xavier Pochon
- Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,Institute of Marine Science, University of Auckland, Auckland, New Zealand
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236
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Parducci L, Bennett KD, Ficetola GF, Alsos IG, Suyama Y, Wood JR, Pedersen MW. Ancient plant DNA in lake sediments. THE NEW PHYTOLOGIST 2017; 214:924-942. [PMID: 28370025 DOI: 10.1111/nph.14470] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 12/07/2016] [Indexed: 05/14/2023]
Abstract
Contents 924 I. 925 II. 925 III. 927 IV. 929 V. 930 VI. 930 VII. 931 VIII. 933 IX. 935 X. 936 XI. 938 938 References 938 SUMMARY: Recent advances in sequencing technologies now permit the analyses of plant DNA from fossil samples (ancient plant DNA, plant aDNA), and thus enable the molecular reconstruction of palaeofloras. Hitherto, ancient frozen soils have proved excellent in preserving DNA molecules, and have thus been the most commonly used source of plant aDNA. However, DNA from soil mainly represents taxa growing a few metres from the sampling point. Lakes have larger catchment areas and recent studies have suggested that plant aDNA from lake sediments is a more powerful tool for palaeofloristic reconstruction. Furthermore, lakes can be found globally in nearly all environments, and are therefore not limited to perennially frozen areas. Here, we review the latest approaches and methods for the study of plant aDNA from lake sediments and discuss the progress made up to the present. We argue that aDNA analyses add new and additional perspectives for the study of ancient plant populations and, in time, will provide higher taxonomic resolution and more precise estimation of abundance. Despite this, key questions and challenges remain for such plant aDNA studies. Finally, we provide guidelines on technical issues, including lake selection, and we suggest directions for future research on plant aDNA studies in lake sediments.
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Affiliation(s)
- Laura Parducci
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
| | - Keith D Bennett
- Department of Geography & Sustainable Development, School of Geography & Geosciences, University of St Andrews, St Andrews, Fife, KY16 9AL, UK
- Marine Laboratory, Queen's University Belfast, Portaferry, BT22 1LS, UK
| | - Gentile Francesco Ficetola
- CNRS, Université Grenoble-Alpes, Laboratoire d'Ecologie Alpine (LECA), Grenoble, F-38000, France
- Department of Biosciences, Università degli Studi di Milano, Milan, 20133, Italy
| | - Inger Greve Alsos
- Tromsø Museum, UiT - The Arctic University of Norway, Tromsø, NO-9037, Norway
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi, 989-6711, Japan
| | - Jamie R Wood
- Long-term Ecology Lab, Landcare Research, PO Box 69040, Lincoln Canterbury, 7640, New Zealand
| | - Mikkel Winther Pedersen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, 1350, Denmark
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237
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Andruszkiewicz EA, Starks HA, Chavez FP, Sassoubre LM, Block BA, Boehm AB. Biomonitoring of marine vertebrates in Monterey Bay using eDNA metabarcoding. PLoS One 2017; 12:e0176343. [PMID: 28441466 PMCID: PMC5404852 DOI: 10.1371/journal.pone.0176343] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 04/10/2017] [Indexed: 02/03/2023] Open
Abstract
Molecular analysis of environmental DNA (eDNA) can be used to assess vertebrate biodiversity in aquatic systems, but limited work has applied eDNA technologies to marine waters. Further, there is limited understanding of the spatial distribution of vertebrate eDNA in marine waters. Here, we use an eDNA metabarcoding approach to target and amplify a hypervariable region of the mitochondrial 12S rRNA gene to characterize vertebrate communities at 10 oceanographic stations spanning 45 km within the Monterey Bay National Marine Sanctuary (MBNMS). In this study, we collected three biological replicates of small volume water samples (1 L) at 2 depths at each of the 10 stations. We amplified fish mitochondrial DNA using a universal primer set. We obtained 5,644,299 high quality Illumina sequence reads from the environmental samples. The sequence reads were annotated to the lowest taxonomic assignment using a bioinformatics pipeline. The eDNA survey identified, to the lowest taxonomic rank, 7 families, 3 subfamilies, 10 genera, and 72 species of vertebrates at the study sites. These 92 distinct taxa come from 33 unique marine vertebrate families. We observed significantly different vertebrate community composition between sampling depths (0 m and 20/40 m deep) across all stations and significantly different communities at stations located on the continental shelf (<200 m bottom depth) versus in the deeper waters of the canyons of Monterey Bay (>200 m bottom depth). All but 1 family identified using eDNA metabarcoding is known to occur in MBNMS. The study informs the implementation of eDNA metabarcoding for vertebrate biomonitoring.
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Affiliation(s)
- Elizabeth A. Andruszkiewicz
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States of America
| | - Hilary A. Starks
- Center for Ocean Solutions, Stanford University, Stanford, CA, United States of America
| | - Francisco P. Chavez
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States of America
| | - Lauren M. Sassoubre
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States of America
| | - Barbara A. Block
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA, United States of America
| | - Alexandria B. Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States of America
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238
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Stoeckle MY, Soboleva L, Charlop-Powers Z. Aquatic environmental DNA detects seasonal fish abundance and habitat preference in an urban estuary. PLoS One 2017; 12:e0175186. [PMID: 28403183 PMCID: PMC5389620 DOI: 10.1371/journal.pone.0175186] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/21/2017] [Indexed: 11/28/2022] Open
Abstract
The difficulty of censusing marine animal populations hampers effective ocean management. Analyzing water for DNA traces shed by organisms may aid assessment. Here we tested aquatic environmental DNA (eDNA) as an indicator of fish presence in the lower Hudson River estuary. A checklist of local marine fish and their relative abundance was prepared by compiling 12 traditional surveys conducted between 1988–2015. To improve eDNA identification success, 31 specimens representing 18 marine fish species were sequenced for two mitochondrial gene regions, boosting coverage of the 12S eDNA target sequence to 80% of local taxa. We collected 76 one-liter shoreline surface water samples at two contrasting estuary locations over six months beginning in January 2016. eDNA was amplified with vertebrate-specific 12S primers. Bioinformatic analysis of amplified DNA, using a reference library of GenBank and our newly generated 12S sequences, detected most (81%) locally abundant or common species and relatively few (23%) uncommon taxa, and corresponded to seasonal presence and habitat preference as determined by traditional surveys. Approximately 2% of fish reads were commonly consumed species that are rare or absent in local waters, consistent with wastewater input. Freshwater species were rarely detected despite Hudson River inflow. These results support further exploration and suggest eDNA will facilitate fine-scale geographic and temporal mapping of marine fish populations at relatively low cost.
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Affiliation(s)
- Mark Y. Stoeckle
- Program for the Human Environment, The Rockefeller University, New York, New York, United States of America
- * E-mail:
| | - Lyubov Soboleva
- Program for the Human Environment, The Rockefeller University, New York, New York, United States of America
| | - Zachary Charlop-Powers
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, New York, United States of America
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239
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De la Cadena G, Papadopoulou A, Maes JM, Gómez-Zurita J. Evaluation of bias on the assessment of diet breadth of herbivorous insects using molecular methods. INSECT SCIENCE 2017; 24:194-209. [PMID: 26663763 DOI: 10.1111/1744-7917.12303] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/29/2015] [Indexed: 06/05/2023]
Abstract
The interactions between herbivores and their host plants play a key role in ecological processes. Understanding the width and nature of these interactions is fundamental to ecology and conservation. Recent research on DNA-based inference of trophic associations suggests that the host range of phytophagous insects in the tropics may be wider than previously thought based on traditional observation. However, the reliability of molecular inference of ecological associations, still strongly dependent on PCR and thus exposed to the risk of contamination with environmental DNA, is under debate. Here, we explored alternative procedures to reduce the chance of amplification of external, nondiet DNA, including surface decontamination and analysis of mid/hind guts, comparing the results with those obtained using the standard protocol. We studied 261 specimens in eight species of Neotropical Chrysomelidae that yielded 316 psbA-trnH intergenic spacer sequences (cpDNA marker of putative diets) from unique and multiple-band PCR results. The taxonomic identity of these sequences was inferred using the automated pipeline BAGpipe, yielding results consistent with 31 plant families. Regardless of the protocol used, a wide taxonomic spectrum of food was inferred for all chrysomelid species. Canonical Correspondence Analysis using these data revealed significant differences attributed mainly to species (expectedly, since they represent different ecologies), but also to treatment (untreated vs. cleaned/gut samples) and PCR results (single vs. multiple bands). Molecular identification of diets is not straightforward and, regardless of the species' niche breadth, combining approaches that reduce external contamination and studying multiple individuals per species may help increasing confidence in results.
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Affiliation(s)
- Gissela De la Cadena
- Animal Biodiversity and Evolution, Institut de Biologia Evolutiva (CSIC-Univ. Pompeu Fabra), Barcelona, Spain
| | - Anna Papadopoulou
- Animal Biodiversity and Evolution, Institut de Biologia Evolutiva (CSIC-Univ. Pompeu Fabra), Barcelona, Spain
- Department of Integrative Ecology, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | | | - Jesús Gómez-Zurita
- Animal Biodiversity and Evolution, Institut de Biologia Evolutiva (CSIC-Univ. Pompeu Fabra), Barcelona, Spain
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240
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Pereira RPA, Peplies J, Brettar I, Höfle MG. Development of a genus-specific next generation sequencing approach for sensitive and quantitative determination of the Legionella microbiome in freshwater systems. BMC Microbiol 2017; 17:79. [PMID: 28359254 PMCID: PMC5374610 DOI: 10.1186/s12866-017-0987-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 03/21/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Next Generation Sequencing (NGS) has revolutionized the analysis of natural and man-made microbial communities by using universal primers for bacteria in a PCR based approach targeting the 16S rRNA gene. In our study we narrowed primer specificity to a single, monophyletic genus because for many questions in microbiology only a specific part of the whole microbiome is of interest. We have chosen the genus Legionella, comprising more than 20 pathogenic species, due to its high relevance for water-based respiratory infections. METHODS A new NGS-based approach was designed by sequencing 16S rRNA gene amplicons specific for the genus Legionella using the Illumina MiSeq technology. This approach was validated and applied to a set of representative freshwater samples. RESULTS Our results revealed that the generated libraries presented a low average raw error rate per base (<0.5%); and substantiated the use of high-fidelity enzymes, such as KAPA HiFi, for increased sequence accuracy and quality. The approach also showed high in situ specificity (>95%) and very good repeatability. Only in samples in which the gammabacterial clade SAR86 was present more than 1% non-Legionella sequences were observed. Next-generation sequencing read counts did not reveal considerable amplification/sequencing biases and showed a sensitive as well as precise quantification of L. pneumophila along a dilution range using a spiked-in, certified genome standard. The genome standard and a mock community consisting of six different Legionella species demonstrated that the developed NGS approach was quantitative and specific at the level of individual species, including L. pneumophila. The sensitivity of our genus-specific approach was at least one order of magnitude higher compared to the universal NGS approach. Comparison of quantification by real-time PCR showed consistency with the NGS data. Overall, our NGS approach can determine the quantitative abundances of Legionella species, i. e. the complete Legionella microbiome, without the need for species-specific primers. CONCLUSIONS The developed NGS approach provides a new molecular surveillance tool to monitor all Legionella species in qualitative and quantitative terms if a spiked-in genome standard is used to calibrate the method. Overall, the genus-specific NGS approach opens up a new avenue to massive parallel diagnostics in a quantitative, specific and sensitive way.
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Affiliation(s)
- Rui P A Pereira
- Department of Vaccinology and Applied Microbiology, RG Microbial Diagnostics, Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, 38124, Braunschweig, Germany.,Present address: School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Jörg Peplies
- Ribocon GmbH, Fahrenheitstraße 1, 28359, Bremen, Germany
| | - Ingrid Brettar
- Department of Vaccinology and Applied Microbiology, RG Microbial Diagnostics, Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Manfred G Höfle
- Department of Vaccinology and Applied Microbiology, RG Microbial Diagnostics, Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, 38124, Braunschweig, Germany.
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241
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Guillera‐Arroita G, Lahoz‐Monfort JJ, Rooyen AR, Weeks AR, Tingley R. Dealing with false‐positive and false‐negative errors about species occurrence at multiple levels. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12743] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
| | | | | | - Andrew R. Weeks
- School of BioSciences University of Melbourne Parkville Vic. 3010 Australia
- Cesar Pty Ltd 293 Royal Pde Parkville Vic. 3052 Australia
| | - Reid Tingley
- School of BioSciences University of Melbourne Parkville Vic. 3010 Australia
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242
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Sollmann R, Mohamed A, Niedballa J, Bender J, Ambu L, Lagan P, Mannan S, Ong RC, Langner A, Gardner B, Wilting A. Quantifying mammal biodiversity co-benefits in certified tropical forests. DIVERS DISTRIB 2017. [DOI: 10.1111/ddi.12530] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Rahel Sollmann
- Department of Forestry and Environmental Resources; North Carolina State University; Raleigh NC USA
- Leibniz Institute for Zoo and Wildlife Research; Alfred-Kowalke-Str. 17 10315 Berlin Germany
| | - Azlan Mohamed
- Leibniz Institute for Zoo and Wildlife Research; Alfred-Kowalke-Str. 17 10315 Berlin Germany
| | - Jürgen Niedballa
- Leibniz Institute for Zoo and Wildlife Research; Alfred-Kowalke-Str. 17 10315 Berlin Germany
| | - Johannes Bender
- Leibniz Institute for Zoo and Wildlife Research; Alfred-Kowalke-Str. 17 10315 Berlin Germany
| | - Laurentius Ambu
- Sabah Wildlife Department; 5th Floor, B Block, Wisma MUIS 88100 Kota Kinabalu Sabah Malaysia
| | - Peter Lagan
- Sabah Forestry Department; Locked Bag 68 90009 Sandakan Sabah Malaysia
| | - Sam Mannan
- Sabah Forestry Department; Locked Bag 68 90009 Sandakan Sabah Malaysia
| | - Robert C. Ong
- Forest Research Centre; Sabah Forestry Department; P.O. Box 1407 90715 Sandakan Sabah Malaysia
| | - Andreas Langner
- European Commission; Joint Research Centre; Institute for Environment and Sustainability; Via Enrico Fermi 2749 I - 21027 Ispra Italy
| | - Beth Gardner
- Department of Forestry and Environmental Resources; North Carolina State University; Raleigh NC USA
| | - Andreas Wilting
- Leibniz Institute for Zoo and Wildlife Research; Alfred-Kowalke-Str. 17 10315 Berlin Germany
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243
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Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea. Sci Rep 2017; 7:40368. [PMID: 28079122 PMCID: PMC5227697 DOI: 10.1038/srep40368] [Citation(s) in RCA: 248] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 12/06/2016] [Indexed: 01/09/2023] Open
Abstract
Environmental DNA (eDNA) metabarcoding has emerged as a potentially powerful tool to assess aquatic community structures. However, the method has hitherto lacked field tests that evaluate its effectiveness and practical properties as a biodiversity monitoring tool. Here, we evaluated the ability of eDNA metabarcoding to reveal fish community structures in species-rich coastal waters. High-performance fish-universal primers and systematic spatial water sampling at 47 stations covering ~11 km2 revealed the fish community structure at a species resolution. The eDNA metabarcoding based on a 6-h collection of water samples detected 128 fish species, of which 62.5% (40 species) were also observed by underwater visual censuses conducted over a 14-year period. This method also detected other local fishes (≥23 species) that were not observed by the visual censuses. These eDNA metabarcoding features will enhance marine ecosystem-related research, and the method will potentially become a standard tool for surveying fish communities.
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244
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Clarke LJ, Beard JM, Swadling KM, Deagle BE. Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies. Ecol Evol 2017; 7:873-883. [PMID: 28168024 PMCID: PMC5288259 DOI: 10.1002/ece3.2667] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 11/02/2016] [Accepted: 11/08/2016] [Indexed: 02/06/2023] Open
Abstract
DNA metabarcoding is a promising approach for rapidly surveying biodiversity and is likely to become an important tool for measuring ecosystem responses to environmental change. Metabarcoding markers need sufficient taxonomic coverage to detect groups of interest, sufficient sequence divergence to resolve species, and will ideally indicate relative abundance of taxa present. We characterized zooplankton assemblages with three different metabarcoding markers (nuclear 18S rDNA, mitochondrial COI, and mitochondrial 16S rDNA) to compare their performance in terms of taxonomic coverage, taxonomic resolution, and correspondence between morphology‐ and DNA‐based identification. COI amplicons sequenced on separate runs showed that operational taxonomic units representing >0.1% of reads per sample were highly reproducible, although slightly more taxa were detected using a lower annealing temperature. Mitochondrial COI and nuclear 18S showed similar taxonomic coverage across zooplankton phyla. However, mitochondrial COI resolved up to threefold more taxa to species compared to 18S. All markers revealed similar patterns of beta‐diversity, although different taxa were identified as the greatest contributors to these patterns for 18S. For calanoid copepod families, all markers displayed a positive relationship between biomass and sequence reads, although the relationship was typically strongest for 18S. The use of COI for metabarcoding has been questioned due to lack of conserved primer‐binding sites. However, our results show the taxonomic coverage and resolution provided by degenerate COI primers, combined with a comparatively well‐developed reference sequence database, make them valuable metabarcoding markers for biodiversity assessment.
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Affiliation(s)
- Laurence J Clarke
- Antarctic Climate & Ecosystems Cooperative Research Centre University of Tasmania Hobart Tas. Australia; Australian Antarctic Division Kingston Tas. Australia
| | - Jason M Beard
- Institute for Marine and Antarctic Studies University of Tasmania Hobart Tas. Australia
| | - Kerrie M Swadling
- Antarctic Climate & Ecosystems Cooperative Research Centre University of Tasmania Hobart Tas. Australia; Institute for Marine and Antarctic Studies University of Tasmania Hobart Tas. Australia
| | - Bruce E Deagle
- Antarctic Climate & Ecosystems Cooperative Research Centre University of Tasmania Hobart Tas. Australia; Australian Antarctic Division Kingston Tas. Australia
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245
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Sjögren P, Edwards ME, Gielly L, Langdon CT, Croudace IW, Merkel MKF, Fonville T, Alsos IG. Lake sedimentary DNA accurately records 20 th Century introductions of exotic conifers in Scotland. THE NEW PHYTOLOGIST 2017; 213:929-941. [PMID: 27678125 PMCID: PMC5215665 DOI: 10.1111/nph.14199] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 08/08/2016] [Indexed: 05/08/2023]
Abstract
Sedimentary DNA (sedDNA) has recently emerged as a new proxy for reconstructing past vegetation, but its taphonomy, source area and representation biases need better assessment. We investigated how sedDNA in recent sediments of two small Scottish lakes reflects a major vegetation change, using well-documented 20th Century plantations of exotic conifers as an experimental system. We used next-generation sequencing to barcode sedDNA retrieved from subrecent lake sediments. For comparison, pollen was analysed from the same samples. The sedDNA record contains 73 taxa (mainly genus or species), all but one of which are present in the study area. Pollen and sedDNA shared 35% of taxa, which partly reflects a difference in source area. More aquatic taxa were recorded in sedDNA, whereas taxa assumed to be of regional rather than local origin were recorded only as pollen. The chronology of the sediments and planting records are well aligned, and sedDNA of exotic conifers appears in high quantities with the establishment of plantations around the lakes. SedDNA recorded other changes in local vegetation that accompanied afforestation. There were no signs of DNA leaching in the sediments or DNA originating from pollen.
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Affiliation(s)
- Per Sjögren
- Tromsø University MuseumUiT – The Arctic University of NorwayLars Thøringsvei 10N‐9037TromsøNorway
| | - Mary E. Edwards
- Tromsø University MuseumUiT – The Arctic University of NorwayLars Thøringsvei 10N‐9037TromsøNorway
- Department of Geography and EnvironmentUniversity of SouthamptonSouthamptonSO17 1BJUK
| | - Ludovic Gielly
- Laboratoire d'Ecologie AlpineUniversité Grenoble AlpesF‐38000GrenobleFrance
- Laboratoire d'Ecologie AlpineCNRSF‐38000GrenobleFrance
| | - Catherine T. Langdon
- Department of Geography and EnvironmentUniversity of SouthamptonSouthamptonSO17 1BJUK
| | - Ian W. Croudace
- Ocean and Earth ScienceUniversity of SouthamptonNational Oceanography CentreSouthamptonSO14 3ZHUK
| | | | - Thierry Fonville
- Department of Geography and EnvironmentUniversity of SouthamptonSouthamptonSO17 1BJUK
| | - Inger Greve Alsos
- Tromsø University MuseumUiT – The Arctic University of NorwayLars Thøringsvei 10N‐9037TromsøNorway
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246
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Kamenova S, Bartley T, Bohan D, Boutain J, Colautti R, Domaizon I, Fontaine C, Lemainque A, Le Viol I, Mollot G, Perga ME, Ravigné V, Massol F. Invasions Toolkit. ADV ECOL RES 2017. [DOI: 10.1016/bs.aecr.2016.10.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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247
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Freeland JR. The importance of molecular markers and primer design when characterizing biodiversity from environmental DNA. Genome 2016; 60:358-374. [PMID: 28177833 DOI: 10.1139/gen-2016-0100] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Environmental DNA (eDNA) comprises DNA fragments that have been shed into the environment by organisms, and which can be extracted from environmental samples such as water or soil. Characterization of eDNA can allow researchers to infer the presence or absence of species from a particular site without the need to locate and identify individuals, and therefore may provide an extremely valuable tool for quantifying biodiversity. However, as is often the case with relatively new protocols, methodological challenges remain. A number of earlier reviews have discussed these challenges, but none have provided extensive treatment of the critical decisions surrounding molecular markers and primer development for use in eDNA assays. This review discusses a number of options and approaches that can be used when determining which primers and gene regions are most appropriate for either targeted species detection or metabarcoding macro-organisms from eDNA. The latter represents a new field that is growing rapidly, and which has the potential to revolutionize future assessments of community and ecosystem diversity.
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Affiliation(s)
- Joanna R Freeland
- Department of Biology, Trent University, Peterborough, ON K9J 7B8, Canada.,Department of Biology, Trent University, Peterborough, ON K9J 7B8, Canada
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248
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Khanam S, Howitt R, Mushtaq M, Russell JC. Diet analysis of small mammal pests: A comparison of molecular and microhistological methods. Integr Zool 2016; 11:98-110. [PMID: 27001489 DOI: 10.1111/1749-4877.12172] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Knowledge of what pest species are eating is important to determine their impact on stored food products and to plan management strategies accordingly. In this study, we investigated the food habits of 2 rodents, Rattus rattus (ship rat) and Mus musculus castaneus (house mouse) as well as an insectivore, Suncus murinus (shrew), present in human dwellings. Both a microhistological approach and a DNA barcoding approach were used in the present study. Following DNA extraction, amplification was performed using group-specific primers targeting birds, plants and invertebrates. Resulting polymerase chain reaction products were sequenced and analyzed to identify the different prey species present in the gut contents. The findings from the application of both techniques were in agreement, but the detection of prey type with each technique was different. The DNA barcoding approach gave greater species-level identification when compared to the microhistological method, especially for the invertebrate and avian prey. Overall, with both techniques, 23 prey taxa were identified in the gut contents of the 3 species, including 15 plants, 7 insects and a single bird species. We conclude that with a selection of suitable "barcode genes" and optimization of polymerase chain reaction protocols, DNA barcoding can provide more accurate and faster results. Prey detection from either technique alone can bias the dietary information. Hence, combining prey information of both microhistological analysis and DNA barcoding is recommended to study pest diet, especially if the pest is an omnivore or insectivore species.
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Affiliation(s)
- Surrya Khanam
- Department of Zoology, PMAS Arid Agriculture University Rawalpindi, Pakistan
| | - Robyn Howitt
- EcoGene®, Landcare Research, Auckland, New Zealand
| | - Muhammad Mushtaq
- Department of Zoology, PMAS Arid Agriculture University Rawalpindi, Pakistan
| | - James C Russell
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Department of Statistics, University of Auckland, Auckland, New Zealand.,Allan Wilson Centre, University of Auckland, Auckland, New Zealand
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249
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Hunter ME, Dorazio RM, Butterfield JSS, Meigs‐Friend G, Nico LG, Ferrante JA. Detection limits of quantitative and digital
PCR
assays and their influence in presence–absence surveys of environmental
DNA. Mol Ecol Resour 2016; 17:221-229. [DOI: 10.1111/1755-0998.12619] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 08/31/2016] [Accepted: 09/19/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Margaret E. Hunter
- U.S. Geological Survey Wetland and Aquatic Research Center 7920 NW 71st Street Gainesville FL 32653 USA
| | - Robert M. Dorazio
- U.S. Geological Survey Wetland and Aquatic Research Center 7920 NW 71st Street Gainesville FL 32653 USA
| | - John S. S. Butterfield
- U.S. Geological Survey Wetland and Aquatic Research Center 7920 NW 71st Street Gainesville FL 32653 USA
| | - Gaia Meigs‐Friend
- U.S. Geological Survey Wetland and Aquatic Research Center 7920 NW 71st Street Gainesville FL 32653 USA
| | - Leo G. Nico
- U.S. Geological Survey Wetland and Aquatic Research Center 7920 NW 71st Street Gainesville FL 32653 USA
| | - Jason A. Ferrante
- U.S. Geological Survey Wetland and Aquatic Research Center 7920 NW 71st Street Gainesville FL 32653 USA
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250
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MacDonald AJ, Sarre SD. A framework for developing and validating taxon-specific primers for specimen identification from environmental DNA. Mol Ecol Resour 2016; 17:708-720. [PMID: 27768246 DOI: 10.1111/1755-0998.12618] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 09/16/2016] [Accepted: 09/26/2016] [Indexed: 01/07/2023]
Abstract
Taxon-specific DNA tests are applied to many ecological and management questions, increasingly using environmental DNA (eDNA). eDNA facilitates noninvasive ecological studies but introduces additional risks of bias and error. For effective application, PCR primers must be developed for each taxon and validated in each system. We outline a nine step framework for the development and validation of taxon-specific primers for eDNA analysis in ecological studies, involving reference database construction, phylogenetic evaluation of the target gene, primer design, primer evaluation in silico, and laboratory evaluation of primer specificity, sensitivity and utility. Our framework makes possible a rigorous evaluation of likely sources of error. The first five steps can be conducted relatively rapidly and (where reference DNA sequences are available) require minimal laboratory resources, enabling assessment of primer suitability before investing in further work. Steps six to eight require more costly laboratory analyses but are essential to evaluate risks of false-positive and false-negative results, while step 9 relates to field implementation. As an example, we have developed and evaluated primers to specifically amplify part of the mitochondrial ND2 gene from Australian bandicoots. If adopted during the early stages of primer development, our framework will facilitate large-scale implementation of well-designed DNA tests to detect specific wildlife from eDNA samples. This will provide researchers and managers with an understanding of the strengths and limitations of their data and the conclusions that can be drawn from them.
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Affiliation(s)
- Anna J MacDonald
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| | - Stephen D Sarre
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
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