1
|
Nakai M, Masumoto T, Asaeda T, Rahman M. Improving the efficiency of adaptive management methods in multiple fishways using environmental DNA. PLoS One 2024; 19:e0301197. [PMID: 38557776 PMCID: PMC10984549 DOI: 10.1371/journal.pone.0301197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 03/12/2024] [Indexed: 04/04/2024] Open
Abstract
Dams and weirs impede the continuity of rivers and transit of migratory fish. To overcome this obstacle, fishways are installed worldwide; however, management after installation is important. The Miyanaka Intake Dam has three fish ladders with different flow velocities and discharges and has been under adaptive management since 2012. Fish catch surveys, conducted as an adaptive management strategy, place a heavy burden on fish. Furthermore, a large number of investigators must be mobilized during the 30-day investigation period. Thus, a monitoring method using environmental DNA that exerts no burden on fish and requires only a few surveyors (to obtain water samples) and an in-house analyst was devised; however, its implementation in a fishway away from the point of analysis and with limited flow space and its effective water sampling frequency have not been reported. Therefore, in 2019, we started a trial aiming to evaluate the methods and application conditions of environmental DNA surveys for the continuous and long-term monitoring of various fish fauna upstream and downstream of the Miyanaka Intake Dam. To evaluate the fish fauna, the results of an environmental DNA survey (metabarcoding method) for 2019 to 2022 were compared to those of a catch survey in the fishway from 2012 to 2022. The results confirmed the use of environmental DNA surveys in evaluating the contribution of fishways to biodiversity under certain conditions and introduced a novel method for sample collection.
Collapse
Affiliation(s)
- Masahiko Nakai
- Japan International Consultants for Transportation Co., Ltd, Tokyo, Japan
| | - Taku Masumoto
- Energy Planning Department, East Japan Railway Company, Tokyo, Japan
| | | | | |
Collapse
|
2
|
Liu Z, Kishe MA, Gabagambi NP, Shechonge AH, Ngatunga BP, Smith K, Saxon AD, Hudson AG, Linderoth T, Turner GF, Collins RA, Genner MJ. Nuclear environmental DNA resolves fine-scale population genetic structure in an aquatic habitat. iScience 2024; 27:108669. [PMID: 38226161 PMCID: PMC10788193 DOI: 10.1016/j.isci.2023.108669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/13/2023] [Accepted: 12/05/2023] [Indexed: 01/17/2024] Open
Abstract
There is considerable potential for nuclear genomic material in environmental DNA (eDNA) to inform us of population genetic structure within aquatic species. We tested if nuclear allelic composition data sourced from eDNA can resolve fine scale spatial genetic structure of the cichlid fish Astatotilapia calliptera in Lake Masoko, Tanzania. In this ∼35 m deep crater lake the species is diverging into two genetically distinguishable ecomorphs, separated by a thermo-oxycline at ∼15 m that divides biologically distinct water masses. We quantified population genetic structure along a depth transect using single nucleotide polymorphisms (SNPs) derived from genome sequencing of 530 individuals. This population genetic structure was reflected in a focal set of SNPs that were also reliably amplified from eDNA - with allele frequencies derived from eDNA reflecting those of fish within each depth zone. Thus, by targeting known genetic variation between populations within aquatic eDNA, we measured genetic structure within the focal species.
Collapse
Affiliation(s)
- Zifang Liu
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS81TQ, UK
| | - Mary A. Kishe
- Tanzania Fisheries Research Institute (TAFIRI), P.O. Box 9750, Dar es Salaam, Tanzania
| | - Nestory P. Gabagambi
- Tanzania Fisheries Research Institute (TAFIRI), P.O. Box 9750, Dar es Salaam, Tanzania
| | - Asilatu H. Shechonge
- Tanzania Fisheries Research Institute (TAFIRI), P.O. Box 9750, Dar es Salaam, Tanzania
| | - Benjamin P. Ngatunga
- Tanzania Fisheries Research Institute (TAFIRI), P.O. Box 9750, Dar es Salaam, Tanzania
| | - Katie Smith
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS81TQ, UK
| | - Andrew D. Saxon
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS81TQ, UK
| | - Alan G. Hudson
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS81TQ, UK
| | - Tyler Linderoth
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI 49060, USA
| | - George F. Turner
- School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Rupert A. Collins
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS81TQ, UK
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Martin J. Genner
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS81TQ, UK
| |
Collapse
|
3
|
Zhao D, Ali A, Zuck C, Uy L, Morris JG, Wong ACN. Vibrio cholerae Invasion Dynamics of the Chironomid Host Are Strongly Influenced by Aquatic Cell Density and Can Vary by Strain. Microbiol Spectr 2023; 11:e0265222. [PMID: 37074192 PMCID: PMC10269514 DOI: 10.1128/spectrum.02652-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 03/24/2023] [Indexed: 04/20/2023] Open
Abstract
Cholera has been a human scourge since the early 1800s and remains a global public health challenge, caused by the toxigenic strains of the bacterium Vibrio cholerae. In its aquatic reservoirs, V. cholerae has been shown to live in association with various arthropod hosts, including the chironomids, a diverse insect family commonly found in wet and semiwet habitats. The association between V. cholerae and chironomids may shield the bacterium from environmental stressors and amplify its dissemination. However, the interaction dynamics between V. cholerae and chironomids remain largely unknown. In this study, we developed freshwater microcosms with chironomid larvae to test the effects of cell density and strain on V. cholerae-chironomid interactions. Our results show that chironomid larvae can be exposed to V. cholerae up to a high inoculation dose (109 cells/mL) without observable detrimental effects. Meanwhile, interstrain variability in host invasion, including prevalence, bacterial load, and effects on host survival, was highly cell density-dependent. Microbiome analysis of the chironomid samples by 16S rRNA gene amplicon sequencing revealed a general effect of V. cholerae exposure on microbiome species evenness. Taken together, our results provide novel insights into V. cholerae invasion dynamics of the chironomid larvae with respect to various doses and strains. The findings suggest that aquatic cell density is a crucial driver of V. cholerae invasion success in chironomid larvae and pave the way for future work examining the effects of a broader dose range and environmental variables (e.g., temperature) on V. cholerae-chironomid interactions. IMPORTANCE Vibrio cholerae is the causative agent of cholera, a significant diarrheal disease affecting millions of people worldwide. Increasing evidence suggests that the environmental facets of the V. cholerae life cycle involve symbiotic associations with aquatic arthropods, which may facilitate its environmental persistence and dissemination. However, the dynamics of interactions between V. cholerae and aquatic arthropods remain unexplored. This study capitalized on using freshwater microcosms with chironomid larvae to investigate the effects of bacterial cell density and strain on V. cholerae-chironomid interactions. Our results suggest that aquatic cell density is the primary determinant of V. cholerae invasion success in chironomid larvae, while interstrain variability in invasion outcomes can be observed under specific cell density conditions. We also determined that V. cholerae exposure generally reduces species evenness of the chironomid-associated microbiome. Collectively, these findings provide novel insights into V. cholerae-arthropod interactions using a newly developed experimental host system.
Collapse
Affiliation(s)
- Dianshu Zhao
- Entomology and Nematology Department, University of Florida, Gainesville, Florida, USA
| | - Afsar Ali
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, USA
| | - Cameron Zuck
- Entomology and Nematology Department, University of Florida, Gainesville, Florida, USA
| | - Laurice Uy
- Entomology and Nematology Department, University of Florida, Gainesville, Florida, USA
| | - J. Glenn Morris
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Adam Chun-Nin Wong
- Entomology and Nematology Department, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| |
Collapse
|
4
|
Hintikka S, Carlsson JE, Carlsson J. The bacterial hitchhiker’s guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.80416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Environmental DNA (eDNA) metabarcoding from water samples has, in recent years, shown great promise for biodiversity monitoring. However, universal primers targeting the cytochrome oxidase I (COI) marker gene popular in metazoan studies have displayed high levels of nontarget amplification. To date, enrichment methods bypassing amplification have not been able to match the detection levels of conventional metabarcoding. This study evaluated the use of universal metabarcoding primers as capture probes to either isolate target DNA or to remove nontarget DNA, prior to amplification, by using biotinylated versions of universal metazoan and bacterial barcoding primers, namely metazoan COI (mlCOIintF) and bacterial 16S (515F). Additionally, each step of the protocol was assessed by amplifying for both metazoan COI (mlCOIintF/jgHCO2198) and bacterial 16S (515F/806R) to investigate the effect on the metazoan and bacterial communities. Bacterial read abundance increased significantly in response to the captures (COI library), while the quality of the captured DNA was also improved. The metazoan-oriented probe captured bacterial DNA in a range that was also amplifiable with the 16S primers, demonstrating the ability of capture probes to isolate fragments of DNA spanning over a longer distance than perhaps expected, from eDNA. Although the use of the tested COI probe cannot be recommended for metazoan enrichment, based on the experimental results, the concept of capturing these longer fragments could be applied to metazoan metabarcoding. By using a truly conserved site without a high-level taxonomic resolution as a target for capture, it may be possible to isolate DNA fragments large enough to span over a nearby barcoding region (e.g., COI), which can then be processed through a conventional metabarcoding-by-amplification protocol.
Collapse
|
5
|
Piper AM, Cunningham JP, Cogan NOI, Blacket MJ. DNA Metabarcoding Enables High-Throughput Detection of Spotted Wing Drosophila (Drosophila suzukii) Within Unsorted Trap Catches. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.822648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The spotted wing drosophila (Drosophila suzukii, Matsumara) is a rapidly spreading global pest of soft and stone fruit production. Due to the similarity of many of its life stages to other cosmopolitan drosophilids, surveillance for this pest is currently bottlenecked by the laborious sorting and morphological identification of large mixed trap catches. DNA metabarcoding presents an alternative high-throughput sequencing (HTS) approach for multi-species identification, which may lend itself ideally to rapid and scalable diagnostics of D. suzukii within unsorted trap samples. In this study, we compared the qualitative (identification accuracy) and quantitative (bias toward each species) performance of four metabarcoding primer pairs on D. suzukii and its close relatives. We then determined the sensitivity of a non-destructive metabarcoding assay (i.e., which retains intact specimens) by spiking whole specimens of target species into mock communities of increasing specimen number, as well as 29 field-sampled communities from a cherry and a stone fruit orchard. Metabarcoding successfully detected D. suzukii and its close relatives Drosophila subpulchrella and Drosophila biarmipes in the spiked communities with an accuracy of 96, 100, and 100% respectively, and identified a further 57 non-target arthropods collected as bycatch by D. suzukii surveillance methods in a field scenario. While the non-destructive DNA extraction retained intact voucher specimens, dropouts of single species and entire technical replicates suggests that these protocols behave more similarly to environmental DNA than homogenized tissue metabarcoding and may require increased technical replication to reliably detect low-abundance taxa. Adoption of high-throughput metabarcoding assays for screening bulk trap samples could enable a substantial increase in the geographic scale and intensity of D. suzukii surveillance, and thus likelihood of detecting a new introduction. Trap designs and surveillance protocols will, however, need to be optimized to adequately preserve specimen DNA for molecular identification.
Collapse
|
6
|
Suchan T, Kusliy MA, Khan N, Chauvey L, Tonasso-Calvière L, Schiavinato S, Southon J, Keller M, Kitagawa K, Krause J, Bessudnov AN, Bessudnov AA, Graphodatsky AS, Valenzuela-Lamas S, Wilczyński J, Pospuła S, Tunia K, Nowak M, Moskal-delHoyo M, Tishkin AA, Pryor AJE, Outram AK, Orlando L. Performance and automation of ancient DNA capture with RNA hyRAD probes. Mol Ecol Resour 2021; 22:891-907. [PMID: 34582623 PMCID: PMC9291508 DOI: 10.1111/1755-0998.13518] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 09/10/2021] [Accepted: 09/15/2021] [Indexed: 01/23/2023]
Abstract
DNA hybridization-capture techniques allow researchers to focus their sequencing efforts on preselected genomic regions. This feature is especially useful when analysing ancient DNA (aDNA) extracts, which are often dominated by exogenous environmental sources. Here, we assessed, for the first time, the performance of hyRAD as an inexpensive and design-free alternative to commercial capture protocols to obtain authentic aDNA data from osseous remains. HyRAD relies on double enzymatic restriction of fresh DNA extracts to produce RNA probes that cover only a fraction of the genome and can serve as baits for capturing homologous fragments from aDNA libraries. We found that this approach could retrieve sequence data from horse remains coming from a range of preservation environments, including beyond radiocarbon range, yielding up to 146.5-fold on-target enrichment for aDNA extracts showing extremely low endogenous content (<1%). Performance was, however, more limited for those samples already characterized by good DNA preservation (>20%-30%), while the fraction of endogenous reads mapping on- and off-target was relatively insensitive to the original endogenous DNA content. Procedures based on two instead of a single round of capture increased on-target coverage up to 3.6-fold. Additionally, we used methylation-sensitive restriction enzymes to produce probes targeting hypomethylated regions, which improved data quality by reducing post-mortem DNA damage and mapping within multicopy regions. Finally, we developed a fully automated hyRAD protocol utilizing inexpensive robotic platforms to facilitate capture processing. Overall, our work establishes hyRAD as a cost-effective strategy to recover a set of shared orthologous variants across multiple ancient samples.
Collapse
Affiliation(s)
- Tomasz Suchan
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Mariya A Kusliy
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France.,Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Naveed Khan
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France.,Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan
| | - Loreleï Chauvey
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Laure Tonasso-Calvière
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Stéphanie Schiavinato
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - John Southon
- Earth System Science Department, University of California, Irvine, Irvine, California, USA
| | - Marcel Keller
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Keiko Kitagawa
- SFB 1070 ResourceCultures, University of Tübingen, Tübingen, Germany.,Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Tübingen, Germany
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.,Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Alexander A Bessudnov
- Institute for the History of Material Culture, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Alexander S Graphodatsky
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Silvia Valenzuela-Lamas
- Institución Milà i Fontanals de Humanidades, Consejo Superior de Investigaciones Científicas (IMF-CSIC), Barcelona, Spain
| | - Jarosław Wilczyński
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | - Sylwia Pospuła
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | - Krzysztof Tunia
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, Kraków, Poland
| | - Marek Nowak
- Institute of Archaeology, Jagiellonian University, Kraków, Poland
| | | | - Alexey A Tishkin
- Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | | | - Alan K Outram
- Department of Archaeology, University of Exeter, Exeter, UK
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| |
Collapse
|
7
|
Günther B, Marre S, Defois C, Merzi T, Blanc P, Peyret P, Arnaud-Haond S. Capture by hybridization for full-length barcode-based eukaryotic and prokaryotic biodiversity inventories of deep sea ecosystems. Mol Ecol Resour 2021; 22:623-637. [PMID: 34486815 DOI: 10.1111/1755-0998.13500] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 08/04/2021] [Accepted: 09/01/2021] [Indexed: 01/04/2023]
Abstract
Biodiversity inventory of marine systems remains limited due to unbalanced access to the three ocean dimensions. The use of environmental DNA (eDNA) for metabarcoding allows fast and effective biodiversity inventory and is forecast as a future biodiversity research and biomonitoring tool. However, in poorly understood ecosystems, eDNA results remain difficult to interpret due to large gaps in reference databases and PCR bias limiting the detection of some major phyla. Here, we aimed to circumvent these limitations by avoiding PCR and recollecting larger DNA fragments to improve assignment of detected taxa through phylogenetic reconstruction. We applied capture by hybridization (CBH) to enrich DNA from deep-sea sediment samples and compared the results with those obtained through an up-to-date metabarcoding PCR-based approach (MTB). Originally developed for bacterial communities and targeting 16S rDNA, the CBH approach was applied to 18S rDNA to improve the detection of species forming benthic communities of eukaryotes, with a particular focus on metazoans. The results confirmed the possibility of extending CBH to metazoans with two major advantages: (i) CBH revealed a broader spectrum of prokaryotic, eukaryotic, and particularly metazoan diversity, and (ii) CBH allowed much more robust phylogenetic reconstructions of full-length barcodes with up to 1900 base pairs. This is particularly important for taxa whose assignment is hampered by gaps in reference databases. This study provides a database and probes to apply 18S CBH to diverse marine systems, confirming this promising new tool to improve biodiversity assessments in data-poor ecosystems such as those in the deep sea.
Collapse
Affiliation(s)
- Babett Günther
- MARBEC, Universite of Montpellier, CNRS, Ifremer, IRD, Sète, France
| | - Sophie Marre
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - Clémence Defois
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - Thomas Merzi
- Total SE, Centre Scientifique et Technique Jean Feger, Pau, France
| | - Philippe Blanc
- Total SE, Centre Scientifique et Technique Jean Feger, Pau, France
| | - Pierre Peyret
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | | |
Collapse
|
8
|
Mariac C, Renno JF, Carmen Garcia-Davila, Vigouroux Y, Mejia E, Angulo C, Castro Ruiz D, Estivals G, Nolorbe C, García Vasquez A, Nuñez J, Cochonneau G, Flores M, Alvarado J, Vertiz J, Chota-Macuyama W, Sánchez H, Miranda G, Duponchelle F. Species-level ichthyoplankton dynamics for 97 fishes in two major river basins of the Amazon using quantitative metabarcoding. Mol Ecol 2021; 31:1627-1648. [PMID: 33949023 DOI: 10.1111/mec.15944] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 02/20/2021] [Accepted: 04/23/2021] [Indexed: 12/01/2022]
Abstract
The Amazon basin holds the world's largest freshwater fish diversity. Information on the intensity and timing of reproductive ecology of Amazonian fish is scant. We use a metabarcoding method by capture using a single probe to quantify species-level ichthyoplankton dynamics. We sampled the Marañón and the Ucayali rivers in Peru monthly for 2 years. We identified 97 species that spawned mainly during the flood start, the flood end or the receding periods, although some species had spawning activity in more than one period. This information was new for 40 of the species in the Amazon basin and 80 species in Peru. Most species ceased spawning for a month during a strong hydrological anomaly in January 2016, demonstrating the rapidity with which they react to environmental modifications during the breeding season. We also document another unreported event in the Amazon basin, the inverse phenology of species belonging to one genus (Triportheus). Overall larval flow in the Marañón was more than twice that of the Ucayali, including for most commercial species (between two and 20 times higher), whereas the Ucayali accounts for ~80% of the fisheries landings in the region. Our results are discussed in the light of the main anthropogenic threats to fishes, hydropower dam construction and the Hidrovía Amazónica, and should serve as a pre-impact baseline.
Collapse
Affiliation(s)
- Cédric Mariac
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France.,Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France
| | - Jean-François Renno
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France.,Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France
| | - Carmen Garcia-Davila
- Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France.,Laboratorio de Biología y Genética Molecular (LBGM), Instituto de Investigaciones de la Amazonía Peruana (IIAP), Iquitos, Perú
| | - Yves Vigouroux
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France.,Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France
| | - Eduardo Mejia
- Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France.,Laboratorio de Biología y Genética Molecular (LBGM), Instituto de Investigaciones de la Amazonía Peruana (IIAP), Iquitos, Perú
| | - Carlos Angulo
- Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France.,Laboratorio de Biología y Genética Molecular (LBGM), Instituto de Investigaciones de la Amazonía Peruana (IIAP), Iquitos, Perú
| | - Diana Castro Ruiz
- Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France.,Laboratorio de Biología y Genética Molecular (LBGM), Instituto de Investigaciones de la Amazonía Peruana (IIAP), Iquitos, Perú
| | - Guillain Estivals
- Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France.,Laboratorio de Biología y Genética Molecular (LBGM), Instituto de Investigaciones de la Amazonía Peruana (IIAP), Iquitos, Perú
| | - Christian Nolorbe
- Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France.,Laboratorio de Biología y Genética Molecular (LBGM), Instituto de Investigaciones de la Amazonía Peruana (IIAP), Iquitos, Perú
| | - Aurea García Vasquez
- Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France.,Laboratorio de Biología y Genética Molecular (LBGM), Instituto de Investigaciones de la Amazonía Peruana (IIAP), Iquitos, Perú
| | - Jesus Nuñez
- Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France.,BOREA, MNHN, SU, UA, CNRS, IRD, Université de Caen-Normandie, France
| | | | - Mayra Flores
- Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France.,Laboratorio de Biología y Genética Molecular (LBGM), Instituto de Investigaciones de la Amazonía Peruana (IIAP), Iquitos, Perú
| | - Jhon Alvarado
- Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France.,Laboratorio de Biología y Genética Molecular (LBGM), Instituto de Investigaciones de la Amazonía Peruana (IIAP), Iquitos, Perú
| | - José Vertiz
- Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France.,Laboratorio de Biología y Genética Molecular (LBGM), Instituto de Investigaciones de la Amazonía Peruana (IIAP), Iquitos, Perú
| | - Werner Chota-Macuyama
- Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France.,Laboratorio de Biología y Genética Molecular (LBGM), Instituto de Investigaciones de la Amazonía Peruana (IIAP), Iquitos, Perú
| | - Homero Sánchez
- Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France.,Laboratorio de Biología y Genética Molecular (LBGM), Instituto de Investigaciones de la Amazonía Peruana (IIAP), Iquitos, Perú
| | - Guido Miranda
- Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France.,Wildlife Conservation Society, Bolivia Program, La Paz, Bolivia.,Unidad de Limnología, Instituto de Ecología, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - Fabrice Duponchelle
- Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France.,MARBEC, CNRS, Ifremer, IRD, Univ Montpellier, Montpellier, France
| |
Collapse
|
9
|
Batovska J, Piper AM, Valenzuela I, Cunningham JP, Blacket MJ. Developing a non-destructive metabarcoding protocol for detection of pest insects in bulk trap catches. Sci Rep 2021; 11:7946. [PMID: 33846382 PMCID: PMC8041782 DOI: 10.1038/s41598-021-85855-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/02/2021] [Indexed: 01/04/2023] Open
Abstract
Metabarcoding has the potential to revolutionise insect surveillance by providing high-throughput and cost-effective species identification of all specimens within mixed trap catches. Nevertheless, incorporation of metabarcoding into insect diagnostic laboratories will first require the development and evaluation of protocols that adhere to the specialised regulatory requirements of invasive species surveillance. In this study, we develop a multi-locus non-destructive metabarcoding protocol that allows sensitive detection of agricultural pests, and subsequent confirmation using traditional diagnostic techniques. We validate this protocol for the detection of tomato potato psyllid (Bactericera cockerelli) and Russian wheat aphid (Diuraphis noxia) within mock communities and field survey traps. We find that metabarcoding can reliably detect target insects within mixed community samples, including specimens that morphological identification did not initially detect, but sensitivity appears inversely related to community size and is impacted by primer biases, target loci, and sample indexing strategy. While our multi-locus approach allowed independent validation of target detection, lack of reference sequences for 18S and 12S restricted its usefulness for estimating diversity in field samples. The non-destructive DNA extraction proved invaluable for resolving inconsistencies between morphological and metabarcoding identification results, and post-extraction specimens were suitable for both morphological re-examination and DNA re-extraction for confirmatory barcoding.
Collapse
Affiliation(s)
- Jana Batovska
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia. .,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia.
| | - Alexander M Piper
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Isabel Valenzuela
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia
| | - John Paul Cunningham
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Mark J Blacket
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia
| |
Collapse
|
10
|
Valdivia-Carrillo T, Rocha-Olivares A, Reyes-Bonilla H, Domínguez-Contreras JF, Munguia-Vega A. Integrating eDNA metabarcoding and simultaneous underwater visual surveys to describe complex fish communities in a marine biodiversity hotspot. Mol Ecol Resour 2021; 21:1558-1574. [PMID: 33683812 DOI: 10.1111/1755-0998.13375] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/13/2021] [Accepted: 03/02/2021] [Indexed: 12/01/2022]
Abstract
Marine biodiversity can be surveyed using underwater visual censuses and recently with eDNA metabarcoding. Although a promising tool, eDNA studies have shown contrasting results related to its detection scale and the number of species identified compared to other survey methods. Also, its accuracy relies on complete reference databases used for taxonomic assignment and, as other survey methods, species detection may show false-negative and false-positive errors. Here, we compared results from underwater visual censuses and simultaneous eDNA metabarcoding fish surveys in terms of observed species and community composition. We also assess the effect of a custom reference database in the taxonomic assignment, and evaluate occupancy, capture and detection probabilities, as well as error rates of eDNA survey data. We amplified a 12S rRNA fish barcode from 24 sampling sites in the gulf of California. More species were detected with eDNA metabarcoding than with UVC. Because each survey method largely detected different sets of species, the combined approach doubled the number of species registered. Both survey methods recovered a known biodiversity gradient and a biogeographic break, but eDNA captured diversity over a broader geographic and bathymetric scale. Furthermore, the use of a modest-sized custom reference database significantly increased taxonomic assignment. In a subset of species, occupancy models revealed eDNA surveys provided similar or higher detection probabilities compared to UVC. The occupancy value of each species had a large influence on eDNA detectability, and in the false positive and negative error. Overall, these results highlight the potential of eDNA metabarcoding in complementing other established ecological methods for studies of marine fishes.
Collapse
Affiliation(s)
- Tania Valdivia-Carrillo
- Laboratorio de Ecología Molecular, Departamento de Oceanografía Biológica, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Baja California Sur, México.,Lab Applied Genomics, La Paz, Baja California Sur, México
| | - Axayácatl Rocha-Olivares
- Laboratorio de Ecología Molecular, Departamento de Oceanografía Biológica, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Baja California Sur, México
| | - Héctor Reyes-Bonilla
- Laboratorio de Sistemas Arrecifales, Universidad Autónoma de Baja California Sur (UABCS), La Paz, Baja California Sur, México
| | | | - Adrian Munguia-Vega
- Conservation Genetics Laboratory & Desert Laboratory on Tumamoc Hill, The University of Arizona, Tucson, AZ, USA.,Lab Applied Genomics, La Paz, Baja California Sur, México
| |
Collapse
|
11
|
Gorden EM, Sturk-Andreaggi K, Marshall C. Capture enrichment and massively parallel sequencing for human identification. Forensic Sci Int Genet 2021; 53:102496. [PMID: 33770700 DOI: 10.1016/j.fsigen.2021.102496] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 01/07/2023]
Abstract
In the past decade, hybridization capture has gained attention within the forensic field for its possible use in human identification. One of the primary benefits to capture enrichment is its applicability to degraded DNA fragments that, due to their reduced size, are not amenable to traditional PCR enrichment techniques. Hybridization capture is typically introduced after genomic library preparation of extracted DNA templates for the subsequent enrichment of mitochondrial DNA or single nucleotide polymorphisms within the nuclear genome. The enriched molecules are then subjected to massively parallel sequencing (MPS) for sensitive and high-throughput DNA sequence generation. Bioinformatic analysis of capture product removes PCR duplicates that were introduced during the laboratory workflow in order to characterize the original DNA template molecules. In the case of aged and degraded skeletal remains, the fraction of endogenous human DNA may be very low; therefore low-coverage sequence analysis may be required. This review contains an overview of current capture methodologies and the primary literature on hybridization capture as evaluated for forensic applications.
Collapse
Affiliation(s)
- Erin M Gorden
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE, USA; SNA International LLC, Alexandria, VA, USA
| | - Kimberly Sturk-Andreaggi
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE, USA; SNA International LLC, Alexandria, VA, USA; Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Charla Marshall
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE, USA; SNA International LLC, Alexandria, VA, USA; Forensic Science Program, The Pennsylvania State University, State College, PA, USA.
| |
Collapse
|
12
|
Jensen MR, Sigsgaard EE, Liu S, Manica A, Bach SS, Hansen MM, Møller PR, Thomsen PF. Genome-scale target capture of mitochondrial and nuclear environmental DNA from water samples. Mol Ecol Resour 2020; 21:690-702. [PMID: 33179423 PMCID: PMC7983877 DOI: 10.1111/1755-0998.13293] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 10/23/2020] [Accepted: 11/02/2020] [Indexed: 02/06/2023]
Abstract
Environmental DNA (eDNA) provides a promising supplement to traditional sampling methods for population genetic inferences, but current studies have almost entirely focused on short mitochondrial markers. Here, we develop one mitochondrial and one nuclear set of target capture probes for the whale shark (Rhincodon typus) and test them on seawater samples collected in Qatar to investigate the potential of target capture for eDNA‐based population studies. The mitochondrial target capture successfully retrieved ~235× (90× − 352× per base position) coverage of the whale shark mitogenome. Using a minor allele frequency of 5%, we find 29 variable sites throughout the mitogenome, indicative of at least five contributing individuals. We also retrieved numerous mitochondrial reads from an abundant nontarget species, mackerel tuna (Euthynnus affinis), showing a clear relationship between sequence similarity to the capture probes and the number of captured reads. The nuclear target capture probes retrieved only a few reads and polymorphic variants from the whale shark, but we successfully obtained millions of reads and thousands of polymorphic variants with different allele frequencies from E. affinis. We demonstrate that target capture of complete mitochondrial genomes and thousands of nuclear loci is possible from aquatic eDNA samples. Our results highlight that careful probe design, taking into account the range of divergence between target and nontarget sequences as well as presence of nontarget species at the sampling site, is crucial to consider. eDNA sampling coupled with target capture approaches provide an efficient means with which to retrieve population genomic data from aggregating and spawning aquatic species.
Collapse
Affiliation(s)
| | | | - Shenglin Liu
- Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge, UK
| | | | | | - Peter Rask Møller
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen Ø, Denmark
| | | |
Collapse
|
13
|
Giebner H, Langen K, Bourlat SJ, Kukowka S, Mayer C, Astrin JJ, Misof B, Fonseca VG. Comparing diversity levels in environmental samples: DNA sequence capture and metabarcoding approaches using 18S and COI genes. Mol Ecol Resour 2020; 20:1333-1345. [PMID: 32462738 DOI: 10.1111/1755-0998.13201] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/20/2020] [Accepted: 05/15/2020] [Indexed: 12/25/2022]
Abstract
Environmental DNA studies targeting multiple taxa using metabarcoding provide remarkable insights into levels of species diversity in any habitat. The main drawbacks are the presence of primer bias and difficulty in identifying rare species. We tested a DNA sequence-capture method in parallel with the metabarcoding approach to reveal possible advantages of one method over the other. Both approaches were performed using the same eDNA samples and the same 18S and COI regions, followed by high throughput sequencing. Metabarcoded eDNA libraries were PCR amplified with one primer pair from 18S and COI genes. DNA sequence-capture libraries were enriched with 3,639 baits targeting the same gene regions. We tested amplicon sequence variants (ASVs) and operational taxonomic units (OTUs) in silico approaches for both markers and methods, using for this purpose the metabarcoding data set. ASVs methods uncovered more species for the COI gene, whereas the opposite occurred for the 18S gene, suggesting that clustering reads into OTUs could bias diversity richness especially using 18S with relaxed thresholds. Additionally, metabarcoding and DNA sequence-capture recovered 80%-90% of the control sample species. DNA sequence-capture was 8x more expensive, nonetheless it identified 1.5x more species for COI and 13x more genera for 18S than metabarcoding. Both approaches offer reliable results, sharing ca. 40% species and 72% families and retrieve more taxa when nuclear and mitochondrial markers are combined. eDNA metabarcoding is quite well established and low-cost, whereas DNA-sequence capture for biodiversity assessment is still in its infancy, is more time-consuming but provides more taxonomic assignments.
Collapse
Affiliation(s)
- Hendrik Giebner
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany
| | - Kathrin Langen
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany
| | - Sarah J Bourlat
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany
| | - Sandra Kukowka
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany
| | - Christoph Mayer
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany
| | - Jonas J Astrin
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany
| | - Bernhard Misof
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany
| | - Vera G Fonseca
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany.,Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK
| |
Collapse
|
14
|
Martin AR, Lea VJ. A mink‐free GB: perspectives on eradicating American mink
Neovison vison
from Great Britain and its islands. Mamm Rev 2020. [DOI: 10.1111/mam.12178] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Anthony R. Martin
- Centre for Remote Environments University of Dundee Dundee DD1 4HN UK
| | - Vince J. Lea
- Countryside Restoration Trust Barton Cambridge CB23 7AG UK
| |
Collapse
|
15
|
Huerlimann R, Cooper MK, Edmunds RC, Villacorta‐Rath C, Le Port A, Robson HLA, Strugnell JM, Burrows D, Jerry DR. Enhancing tropical conservation and ecology research with aquatic environmental DNA methods: an introduction for non‐environmental DNA specialists. Anim Conserv 2020. [DOI: 10.1111/acv.12583] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- R. Huerlimann
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia
- Centre for Tropical Bioinformatics and Molecular Biology James Cook University Townsville QLD Australia
| | - M. K. Cooper
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia
- Centre for Tropical Bioinformatics and Molecular Biology James Cook University Townsville QLD Australia
| | - R. C. Edmunds
- Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER) James Cook University Townsville QLD Australia
| | - C. Villacorta‐Rath
- Centre for Tropical Bioinformatics and Molecular Biology James Cook University Townsville QLD Australia
- Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER) James Cook University Townsville QLD Australia
| | - A. Le Port
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia
| | - H. L. A. Robson
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia
| | - J. M. Strugnell
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia
- Centre for Tropical Bioinformatics and Molecular Biology James Cook University Townsville QLD Australia
| | - D. Burrows
- Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER) James Cook University Townsville QLD Australia
| | - D. R. Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia
- Tropical Futures Institute James Cook University Singapore Singapore
| |
Collapse
|
16
|
Zhan SH, Shih C, Liu S. Reappraising plastid markers of the red algae for phylogenetic community ecology in the genomic era. Ecol Evol 2020; 10:1299-1310. [PMID: 32076515 PMCID: PMC7029088 DOI: 10.1002/ece3.5984] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/03/2019] [Accepted: 12/05/2019] [Indexed: 11/07/2022] Open
Abstract
Selection of appropriate genetic markers to quantify phylogenetic diversity is crucial for community ecology studies. Yet, systematic evaluation of marker genes for this purpose is scarcely done. Recently, the combined effort of phycologists has produced a rich plastid genome resource with taxonomic representation spanning all of the major lineages of the red algae (Rhodophyta). In this proof-of-concept study, we leveraged this resource by developing and applying a phylogenomic strategy to seek candidate plastid markers suitable for phylogenetic community analysis. We ranked the core genes of 107 published plastid genomes based on various sequence-derived properties and their tree distance to plastid genome phylogenies. The resulting ranking revealed that the most widely used marker, rbcL, is not necessarily the optimal marker, while other promising markers might have been overlooked. We designed and tested PCR primers for several candidate marker genes, and successfully amplified one of them, rpoC1, in a taxonomically broad set of red algal specimens. We suggest that our general marker identification methodology and the rpoC1 primers will be useful to the phycological community for investigating the biodiversity and community ecology of the red algae.
Collapse
Affiliation(s)
- Shing Hei Zhan
- Department of Zoology & Biodiversity Research Centrethe University of British ColumbiaVancouverBCCanada
| | - Chun‐Chi Shih
- Department of Life Science & Center for Ecology and EnvironmentTunghai UniversityTaichungTaiwan
| | - Shao‐Lun Liu
- Department of Life Science & Center for Ecology and EnvironmentTunghai UniversityTaichungTaiwan
| |
Collapse
|
17
|
Sigsgaard EE, Jensen MR, Winkelmann IE, Møller PR, Hansen MM, Thomsen PF. Population-level inferences from environmental DNA-Current status and future perspectives. Evol Appl 2020; 13:245-262. [PMID: 31993074 PMCID: PMC6976968 DOI: 10.1111/eva.12882] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 10/07/2019] [Indexed: 01/01/2023] Open
Abstract
Environmental DNA (eDNA) extracted from water samples has recently shown potential as a valuable source of population genetic information for aquatic macroorganisms. This approach offers several potential advantages compared with conventional tissue-based methods, including the fact that eDNA sampling is noninvasive and generally more cost-efficient. Currently, eDNA approaches have been limited to single-marker studies of mitochondrial DNA (mtDNA), and the relationship between eDNA haplotype composition and true haplotype composition still needs to be thoroughly verified. This will require testing of bioinformatic and statistical software to correct for erroneous sequences, as well as biases and random variation in relative sequence abundances. However, eDNA-based population genetic methods have far-reaching potential for both basic and applied research. In this paper, we present a brief overview of the achievements of eDNA-based population genetics to date, and outline the prospects for future developments in the field, including the estimation of nuclear DNA (nuDNA) variation and epigenetic information. We discuss the challenges associated with eDNA samples as opposed to those of individual tissue samples and assess whether eDNA might offer additional types of information unobtainable with tissue samples. Lastly, we provide recommendations for determining whether an eDNA approach would be a useful and suitable choice in different research settings. We limit our discussion largely to contemporary aquatic systems, but the advantages, challenges, and perspectives can to a large degree be generalized to eDNA studies with a different spatial and temporal focus.
Collapse
Affiliation(s)
| | | | | | - Peter Rask Møller
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagen ØDenmark
| | | | | |
Collapse
|
18
|
|
19
|
Harrison JB, Sunday JM, Rogers SM. Predicting the fate of eDNA in the environment and implications for studying biodiversity. Proc Biol Sci 2019; 286:20191409. [PMID: 31744434 DOI: 10.1098/rspb.2019.1409] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Environmental DNA (eDNA) applications are transforming the standard of characterizing aquatic biodiversity via the presence, location and abundance of DNA collected from environmental samples. As eDNA studies use DNA fragments as a proxy for the presence of organisms, the ecological properties of the complex and dynamic environments from which eDNA is sampled need to be considered for accurate biological interpretation. In this review, we discuss the role that differing environments play on the major processes that eDNA undergoes between organism and collection, including shedding, decay and transport. We focus on a mechanistic understanding of these processes and highlight how decay and transport models are being developed towards more accurate and robust predictions of the fate of eDNA. We conclude with five recommendations for eDNA researchers and practitioners, to advance current best practices, as well as to support a future model of eDNA spatio-temporal persistence.
Collapse
Affiliation(s)
- Jori B Harrison
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | | | - Sean M Rogers
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| |
Collapse
|
20
|
Monitoring spawning migrations of potamodromous fish species via eDNA. Sci Rep 2019; 9:15388. [PMID: 31659232 PMCID: PMC6817844 DOI: 10.1038/s41598-019-51398-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 09/17/2019] [Indexed: 11/15/2022] Open
Abstract
Potamodromous fish are considered important indicators of habitat connectivity in freshwater ecosystems, but they are globally threatened by anthropogenic impacts. Hence, non-invasive techniques are necessary for monitoring during spawning migrations. The use of environmental DNA (eDNA) potentially facilitates these efforts, albeit quantitative examinations of spawning migrations remain so far mostly uncharted. Here, we investigated spawning migrations of Danube bleak, Alburnus mento, and Vimba bream, Vimba vimba, and found a strong correlation between daily visual fish counts and downstream eDNA signals obtained from filtered water samples analysed with digital PCR and end-point PCR coupled with capillary electrophoresis. By accounting for daily discharge fluctuations, it was possible to predict eDNA signal strength from the number of migrating fish: first, the whole spawning reach was taken into account. Second, the model was validated using eDNA signals and fish counts obtained from the upper half of the examined river stretch. Consequently, fish counts and their day-to-day changes could be described via an eDNA-based time series model for the whole migration period. Our findings highlight the capability of eDNA beyond delivering simple presence/absence data towards efficient and informative monitoring of highly dynamic aquatic processes such as spawning migrations of potamodromous fish species.
Collapse
|
21
|
Collins RA, Bakker J, Wangensteen OS, Soto AZ, Corrigan L, Sims DW, Genner MJ, Mariani S. Non‐specific amplification compromises environmental DNA metabarcoding with COI. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13276] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
| | - Judith Bakker
- Department of Biological Sciences Florida International University Miami FL USA
- Ecosystems & Environment Research Centre, School of Environment & Life Sciences University of Salford Salford UK
| | - Owen S. Wangensteen
- Ecosystems & Environment Research Centre, School of Environment & Life Sciences University of Salford Salford UK
- Norwegian College of Fishery Science, UiT The Arctic University of Norway Tromsø Norway
| | - Ana Z. Soto
- Ecosystems & Environment Research Centre, School of Environment & Life Sciences University of Salford Salford UK
| | - Laura Corrigan
- Environment Agency Tyneside House Newcastle upon Tyne UK
| | - David W. Sims
- The Laboratory Marine Biological Association of the United Kingdom Plymouth UK
- Ocean and Earth Science, National Oceanography Centre Southampton University of Southampton Southampton UK
| | | | - Stefano Mariani
- Ecosystems & Environment Research Centre, School of Environment & Life Sciences University of Salford Salford UK
- School of Natural Sciences & Psychology Liverpool John Moores University Liverpool UK
| |
Collapse
|
22
|
Gauthier M, Konecny‐Dupré L, Nguyen A, Elbrecht V, Datry T, Douady C, Lefébure T. Enhancing DNA metabarcoding performance and applicability with bait capture enrichment and DNA from conservative ethanol. Mol Ecol Resour 2019; 20:79-96. [DOI: 10.1111/1755-0998.13088] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/15/2019] [Accepted: 08/19/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Mailys Gauthier
- CNRS UMR 5023 ENTPE Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés Univ Lyon Université Claude Bernard Lyon 1 Villeurbanne France
- IRSTEA UR‐RiverLy Centre de Lyon‐Villeurbanne Villeurbanne Cedex France
| | - Lara Konecny‐Dupré
- CNRS UMR 5023 ENTPE Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés Univ Lyon Université Claude Bernard Lyon 1 Villeurbanne France
| | | | - Vasco Elbrecht
- Centre for Biodiversity Genomics University of Guelph Guelph Ontario Canada
| | - Thibault Datry
- IRSTEA UR‐RiverLy Centre de Lyon‐Villeurbanne Villeurbanne Cedex France
| | - Christophe Douady
- CNRS UMR 5023 ENTPE Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés Univ Lyon Université Claude Bernard Lyon 1 Villeurbanne France
| | - Tristan Lefébure
- CNRS UMR 5023 ENTPE Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés Univ Lyon Université Claude Bernard Lyon 1 Villeurbanne France
| |
Collapse
|
23
|
Ji Y, Huotari T, Roslin T, Schmidt NM, Wang J, Yu DW, Ovaskainen O. SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes. Mol Ecol Resour 2019; 20:256-267. [PMID: 31293086 DOI: 10.1111/1755-0998.13057] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/15/2019] [Accepted: 07/03/2019] [Indexed: 11/24/2022]
Abstract
The accurate quantification of eukaryotic species abundances from bulk samples remains a key challenge for community ecology and environmental biomonitoring. We resolve this challenge by combining shotgun sequencing, mapping to reference DNA barcodes or to mitogenomes, and three correction factors: (a) a percent-coverage threshold to filter out false positives, (b) an internal-standard DNA spike-in to correct for stochasticity during sequencing, and (c) technical replicates to correct for stochasticity across sequencing runs. The SPIKEPIPE pipeline achieves a strikingly high accuracy of intraspecific abundance estimates (in terms of DNA mass) from samples of known composition (mapping to barcodes R2 = .93, mitogenomes R2 = .95) and a high repeatability across environmental-sample replicates (barcodes R2 = .94, mitogenomes R2 = .93). As proof of concept, we sequence arthropod samples from the High Arctic, systematically collected over 17 years, detecting changes in species richness, species-specific abundances, and phenology. SPIKEPIPE provides cost-efficient and reliable quantification of eukaryotic communities.
Collapse
Affiliation(s)
- Yinqiu Ji
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Tea Huotari
- Department of Agricultural Sciences, Spatial Foodweb Ecology Group, University of Helsinki, Helsinki, Finland
| | - Tomas Roslin
- Department of Agricultural Sciences, Spatial Foodweb Ecology Group, University of Helsinki, Helsinki, Finland.,Department of Ecology, Spatial Foodweb Ecology Group, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Niels Martin Schmidt
- Arctic Research Centre, Aarhus University, Aarhus, Denmark.,Department of Bioscience, Aarhus University, Roskilde, Denmark
| | - Jiaxin Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,School of Biological Sciences, University of East Anglia, Norfolk, UK.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Otso Ovaskainen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| |
Collapse
|
24
|
Piper AM, Batovska J, Cogan NOI, Weiss J, Cunningham JP, Rodoni BC, Blacket MJ. Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance. Gigascience 2019; 8:giz092. [PMID: 31363753 PMCID: PMC6667344 DOI: 10.1093/gigascience/giz092] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 06/25/2019] [Accepted: 07/09/2019] [Indexed: 12/21/2022] Open
Abstract
Trap-based surveillance strategies are widely used for monitoring of invasive insect species, aiming to detect newly arrived exotic taxa as well as track the population levels of established or endemic pests. Where these surveillance traps have low specificity and capture non-target endemic species in excess of the target pests, the need for extensive specimen sorting and identification creates a major diagnostic bottleneck. While the recent development of standardized molecular diagnostics has partly alleviated this requirement, the single specimen per reaction nature of these methods does not readily scale to the sheer number of insects trapped in surveillance programmes. Consequently, target lists are often restricted to a few high-priority pests, allowing unanticipated species to avoid detection and potentially establish populations. DNA metabarcoding has recently emerged as a method for conducting simultaneous, multi-species identification of complex mixed communities and may lend itself ideally to rapid diagnostics of bulk insect trap samples. Moreover, the high-throughput nature of recent sequencing platforms could enable the multiplexing of hundreds of diverse trap samples on a single flow cell, thereby providing the means to dramatically scale up insect surveillance in terms of both the quantity of traps that can be processed concurrently and number of pest species that can be targeted. In this review of the metabarcoding literature, we explore how DNA metabarcoding could be tailored to the detection of invasive insects in a surveillance context and highlight the unique technical and regulatory challenges that must be considered when implementing high-throughput sequencing technologies into sensitive diagnostic applications.
Collapse
Affiliation(s)
- Alexander M Piper
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - Jana Batovska
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - Noel O I Cogan
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - John Weiss
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
| | - John Paul Cunningham
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
| | - Brendan C Rodoni
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - Mark J Blacket
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
| |
Collapse
|
25
|
Adams CIM, Knapp M, Gemmell NJ, Jeunen GJ, Bunce M, Lamare MD, Taylor HR. Beyond Biodiversity: Can Environmental DNA (eDNA) Cut It as a Population Genetics Tool? Genes (Basel) 2019; 10:E192. [PMID: 30832286 PMCID: PMC6470983 DOI: 10.3390/genes10030192] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/19/2019] [Accepted: 02/26/2019] [Indexed: 01/23/2023] Open
Abstract
Population genetic data underpin many studies of behavioral, ecological, and evolutionary processes in wild populations and contribute to effective conservation management. However, collecting genetic samples can be challenging when working with endangered, invasive, or cryptic species. Environmental DNA (eDNA) offers a way to sample genetic material non-invasively without requiring visual observation. While eDNA has been trialed extensively as a biodiversity and biosecurity monitoring tool with a strong taxonomic focus, it has yet to be fully explored as a means for obtaining population genetic information. Here, we review current research that employs eDNA approaches for the study of populations. We outline challenges facing eDNA-based population genetic methodologies, and suggest avenues of research for future developments. We advocate that with further optimizations, this emergent field holds great potential as part of the population genetics toolkit.
Collapse
Affiliation(s)
- Clare I M Adams
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin, Otago 9016, New Zealand.
| | - Michael Knapp
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin, Otago 9016, New Zealand.
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin, Otago 9016, New Zealand.
| | - Gert-Jan Jeunen
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin, Otago 9016, New Zealand.
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, Perth, WA 6102, Australia.
| | - Miles D Lamare
- Department of Marine Science, University of Otago, 310 Castle Street, Dunedin, Otago 9016, New Zealand.
| | - Helen R Taylor
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin, Otago 9016, New Zealand.
| |
Collapse
|