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Abstract
The method employed for environmental DNA (eDNA) surveillance for detection and monitoring of rare species in aquatic systems has evolved dramatically since its first large-scale applications. Both active (targeted) and passive (total diversity) surveillance methods provide helpful information for management groups, but each has a suite of techniques that necessitate proper equipment training and use. The protocols described in this chapter represent some of the latest iterations in eDNA surveillance being applied in aquatic and marine systems.
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Affiliation(s)
- Andrew R Mahon
- Department of Biology, Institute for Great Lakes Research, Central Michigan University, Brooks Hall 188, Mount Pleasant, MI, 48859, USA.
| | - Christopher L Jerde
- Department of Biology, Aquatic Ecosystems Analysis Laboratory, University of Nevada, Reno, NV, 89557, USA
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102
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103
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Secondi J, Dejean T, Valentini A, Audebaud B, Miaud C. Detection of a global aquatic invasive amphibian, Xenopus laevis, using environmental DNA. AMPHIBIA-REPTILIA 2016. [DOI: 10.1163/15685381-00003036] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Detection is crucial in the study and control of invasive species but it may be limited by methodological issues. In amphibians, classical survey techniques exhibit variable detection probability depending on species and are often constrained by climatic conditions often requiring several site visits. Furthermore, detection may be reduced at low density because probability capture (passive traps), or activity (acoustic surveys) drop. Such limits may impair the study of invasive species because low density is typical of the onset of colonisation on a site. In the last few years, environmental DNA (eDNA) methods have proved their ability to detect the presence of aquatic species. We developed here an eDNA method to detectXenopus laevisin ponds. This austral African species is now present worldwide because of its use in biology and as a pet. Populations have settled and expanded on several continents so that it is now considered as one of the major invasive amphibians in the World. We detected the presence ofX. laevisat density as low as 1 ind/100 m2and found a positive relationship between density in ponds and rate of DNA amplification. Results show that eDNA can be successfully applied to survey invasive populations ofX. laeviseven at low density in order to confirm suspected cases of introduction, delimit the expansion of a colonized range, or monitor the efficiency of a control program.
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Affiliation(s)
- Jean Secondi
- GECCO, Université d’Angers, Angers, France
- UMR CNRS 6554 LETG – LEESA, Université d’Angers, Angers, France
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104
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Furlan EM, Gleeson D, Hardy CM, Duncan RP. A framework for estimating the sensitivity of eDNA surveys. Mol Ecol Resour 2015; 16:641-54. [PMID: 26536842 DOI: 10.1111/1755-0998.12483] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 10/25/2015] [Accepted: 10/29/2015] [Indexed: 01/03/2023]
Abstract
Imperfect sensitivity, or imperfect detection, is a feature of all survey methods that needs to be accounted for when interpreting survey results. Detection of environmental DNA (eDNA) is increasingly being used to infer species distributions, yet the sensitivity of the technique has not been fully evaluated. Sensitivity, or the probability of detecting target DNA given it is present at a site, will depend on both the survey method and the concentration and dispersion of target DNA molecules at a site. We present a model to estimate target DNA concentration and dispersion at survey sites and to estimate the sensitivity of an eDNA survey method. We fitted this model to data from a species-specific eDNA survey for Oriental weatherloach, Misgurnus anguillicaudatus, at three sites sampled in both autumn and spring. The concentration of target DNA molecules was similar at all three sites in autumn but much higher at two sites in spring. Our analysis showed the survey method had ≥95% sensitivity at sites where target DNA concentrations were ≥11 molecules per litre. We show how these data can be used to compare sampling schemes that differ in the number of field samples collected per site and number of PCR replicates per sample to achieve ≥95% sensitivity at a given target DNA concentration. These models allow researchers to quantify the sensitivity of eDNA survey methods to optimize the probability of detecting target species, and to compare DNA concentrations spatially and temporarily.
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Affiliation(s)
- Elise M Furlan
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2617, Australia
| | - Dianne Gleeson
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2617, Australia
| | - Christopher M Hardy
- CSIRO Land & Water, GPO Box 1700, Canberra, ACT, 2601, Australia.,Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2617, Australia
| | - Richard P Duncan
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2617, Australia
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105
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Bass D, Stentiford GD, Littlewood D, Hartikainen H. Diverse Applications of Environmental DNA Methods in Parasitology. Trends Parasitol 2015; 31:499-513. [DOI: 10.1016/j.pt.2015.06.013] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 06/16/2015] [Accepted: 06/24/2015] [Indexed: 01/05/2023]
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106
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107
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Boyer S, Cruickshank RH, Wratten SD. Faeces of generalist predators as ‘biodiversity capsules’: A new tool for biodiversity assessment in remote and inaccessible habitats. FOOD WEBS 2015. [DOI: 10.1016/j.fooweb.2015.02.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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108
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Huver JR, Koprivnikar J, Johnson PTJ, Whyard S. Development and application of an eDNA method to detect and quantify a pathogenic parasite in aquatic ecosystems. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2015; 25:991-1002. [PMID: 26380540 PMCID: PMC4570504 DOI: 10.1890/14-1530.1] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Approaches based on organismal DNA found in the environment (eDNA) have become increasingly utilized for ecological studies and biodiversity inventories as an alternative to traditional field survey methods. Such DNA-based techniques have largely been used to establish the presence of free-living organisms, but have much potential for detecting and quantifying infectious agents in the environment, which is necessary to evaluate disease risk. We developed an eDNA method to examine the distribution and abundance of the trematode Ribeiroia ondatrae, a pathogenic parasite known to cause malformations in North American amphibians. In addition to comparing this eDNA approach to classical host necropsy, we examined the detectability of R. ondatrae in water samples subject to different degradation conditions (time and temperature). Our test exhibited high specificity and sensitivity to R. ondatrae, capable of detecting as little as 14 fg (femtograms) of this parasite's DNA (1/2500th of a single infectious stage) from field water samples. Compared to our results from amphibian host necropsy, quantitative PCR was -90% concordant with respect to R. ondatrae detection from 15 field sites and was also a significant predictor of host infection abundance. DNA was still detectable in lab samples after 21 days at 25°C, indicating that our method is robust to field conditions. By comparing the advantages and disadvantages of eDNA vs. traditional survey methods for determining pathogen presence and abundance in the field, we found that the lower cost and effort associated with eDNA approaches provide many advantages. The development of alternative tools is critical for disease ecology, as wildlife management and conservation efforts require reliable establishment and monitoring of pathogens.
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Affiliation(s)
- J. R. Huver
- Department of Biological Sciences, University of Manitoba
| | | | - P. T. J. Johnson
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder
| | - S. Whyard
- Department of Biological Sciences, University of Manitoba
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109
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Eichmiller JJ, Miller LM, Sorensen PW. Optimizing techniques to capture and extract environmental DNA for detection and quantification of fish. Mol Ecol Resour 2015; 16:56-68. [DOI: 10.1111/1755-0998.12421] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 04/21/2015] [Accepted: 04/23/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Jessica J. Eichmiller
- Department of Fisheries Wildlife and Conservation Biology; Minnesota Aquatic Invasive Species Research Center; University of Minnesota; Twin Cities Saint Paul MN 55108 USA
| | - Loren M. Miller
- Department of Fisheries Wildlife and Conservation Biology; Minnesota Aquatic Invasive Species Research Center; University of Minnesota; Twin Cities Saint Paul MN 55108 USA
- Minnesota Department of Natural Resources; Saint Paul MN 55155 USA
| | - Peter W. Sorensen
- Department of Fisheries Wildlife and Conservation Biology; Minnesota Aquatic Invasive Species Research Center; University of Minnesota; Twin Cities Saint Paul MN 55108 USA
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110
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Environmental DNA particle size distribution from Brook Trout (Salvelinus fontinalis). CONSERV GENET RESOUR 2015. [DOI: 10.1007/s12686-015-0465-z] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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111
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Egan SP, Grey E, Olds B, Feder JL, Ruggiero ST, Tanner CE, Lodge DM. Rapid molecular detection of invasive species in ballast and harbor water by integrating environmental DNA and light transmission spectroscopy. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:4113-4121. [PMID: 25686279 DOI: 10.1021/es5058659] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Invasive species introduced via the ballast water of commercial ships cause enormous environmental and economic damage worldwide. Accurate monitoring for these often microscopic and morphologically indistinguishable species is challenging but critical for mitigating damages. We apply eDNA sampling, which involves the filtering and subsequent DNA extraction of microscopic bits of tissue suspended in water, to ballast and harbor water sampled during a commercial ship's 1400 km voyage through the North American Great Lakes. Using a lab-based gel electrophoresis assay and a rapid, field-ready light transmission spectroscopy (LTS) assay, we test for the presence of two invasive species: quagga (Dreissena bugensis) and zebra (D. polymorpha) mussels. Furthermore, we spiked a set of uninfested ballast and harbor samples with zebra mussel tissue to further test each assay's detection capabilities. In unmanipulated samples, zebra mussel was not detected, while quagga mussel was detected in all samples at a rate of 85% for the gel assay and 100% for the LTS assay. In the spiked experimental samples, both assays detected zebra mussel in 94% of spiked samples and 0% of negative controls. Overall, these results demonstrate that eDNA sampling is effective for monitoring ballast-mediated invasions and that LTS has the potential for rapid, field-based detection.
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Affiliation(s)
- Scott P Egan
- †Department of BioSciences, Rice University, Houston, Texas 77005, United States
- ‡Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
- §Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Erin Grey
- §Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
- ∥College of Science, Governors State University, University Park, Illinois 60484, United States
| | - Brett Olds
- §Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jeffery L Feder
- ‡Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
- §Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Steven T Ruggiero
- §Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
- ⊥Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Carol E Tanner
- §Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
- ⊥Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - David M Lodge
- ‡Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
- §Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
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112
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Cristescu ME. Genetic reconstructions of invasion history. Mol Ecol 2015; 24:2212-25. [DOI: 10.1111/mec.13117] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Revised: 02/11/2015] [Accepted: 02/12/2015] [Indexed: 12/14/2022]
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113
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Renshaw MA, Olds BP, Jerde CL, McVeigh MM, Lodge DM. The room temperature preservation of filtered environmental DNA samples and assimilation into a phenol-chloroform-isoamyl alcohol DNA extraction. Mol Ecol Resour 2015; 15:168-76. [PMID: 24834966 PMCID: PMC4312482 DOI: 10.1111/1755-0998.12281] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 05/09/2014] [Accepted: 05/12/2014] [Indexed: 11/28/2022]
Abstract
Current research targeting filtered macrobial environmental DNA (eDNA) often relies upon cold ambient temperatures at various stages, including the transport of water samples from the field to the laboratory and the storage of water and/or filtered samples in the laboratory. This poses practical limitations for field collections in locations where refrigeration and frozen storage is difficult or where samples must be transported long distances for further processing and screening. This study demonstrates the successful preservation of eDNA at room temperature (20 °C) in two lysis buffers, CTAB and Longmire's, over a 2-week period of time. Moreover, the preserved eDNA samples were seamlessly integrated into a phenol-chloroform-isoamyl alcohol (PCI) DNA extraction protocol. The successful application of the eDNA extraction to multiple filter membrane types suggests the methods evaluated here may be broadly applied in future eDNA research. Our results also suggest that for many kinds of studies recently reported on macrobial eDNA, detection probabilities could have been increased, and at a lower cost, by utilizing the Longmire's preservation buffer with a PCI DNA extraction.
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Affiliation(s)
- Mark A Renshaw
- Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Sciences Center, Notre Dame, IN, 46556, USA
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114
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Turner CR, Miller DJ, Coyne KJ, Corush J. Improved methods for capture, extraction, and quantitative assay of environmental DNA from Asian bigheaded carp (Hypophthalmichthys spp.). PLoS One 2014; 9:e114329. [PMID: 25474207 PMCID: PMC4256254 DOI: 10.1371/journal.pone.0114329] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 11/06/2014] [Indexed: 02/04/2023] Open
Abstract
Indirect, non-invasive detection of rare aquatic macrofauna using aqueous environmental DNA (eDNA) is a relatively new approach to population and biodiversity monitoring. As such, the sensitivity of monitoring results to different methods of eDNA capture, extraction, and detection is being investigated in many ecosystems and species. One of the first and largest conservation programs with eDNA-based monitoring as a central instrument focuses on Asian bigheaded carp (Hypophthalmichthys spp.), an invasive fish spreading toward the Laurentian Great Lakes. However, the standard eDNA methods of this program have not advanced since their development in 2010. We developed new, quantitative, and more cost-effective methods and tested them against the standard protocols. In laboratory testing, our new quantitative PCR (qPCR) assay for bigheaded carp eDNA was one to two orders of magnitude more sensitive than the existing endpoint PCR assays. When applied to eDNA samples from an experimental pond containing bigheaded carp, the qPCR assay produced a detection probability of 94.8% compared to 4.2% for the endpoint PCR assays. Also, the eDNA capture and extraction method we adapted from aquatic microbiology yielded five times more bigheaded carp eDNA from the experimental pond than the standard method, at a per sample cost over forty times lower. Our new, more sensitive assay provides a quantitative tool for eDNA-based monitoring of bigheaded carp, and the higher-yielding eDNA capture and extraction method we describe can be used for eDNA-based monitoring of any aquatic species.
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Affiliation(s)
- Cameron R. Turner
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Derryl J. Miller
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Kathryn J. Coyne
- College of Earth, Ocean, and Environment, University of Delaware, Lewes, Delaware, United States of America
| | - Joel Corush
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
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115
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Merkes CM, McCalla SG, Jensen NR, Gaikowski MP, Amberg JJ. Persistence of DNA in carcasses, slime and avian feces may affect interpretation of environmental DNA data. PLoS One 2014; 9:e113346. [PMID: 25402206 PMCID: PMC4234652 DOI: 10.1371/journal.pone.0113346] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 10/22/2014] [Indexed: 01/10/2023] Open
Abstract
The prevention of non-indigenous aquatic invasive species spreading into new areas is a goal of many resource managers. New techniques have been developed to survey for species that are difficult to capture with conventional gears that involve the detection of their DNA in water samples (eDNA). This technique is currently used to track the invasion of bigheaded carps (silver carp and bighead carp; Hypophthalmichthys molitrix and H. nobilis) in the Chicago Area Waterway System and Upper Mississippi River. In both systems DNA has been detected from silver carp without the capture of a live fish, which has led to some uncertainty about the source of the DNA. The potential contribution to eDNA by vectors and fomites has not been explored. Because barges move from areas with a high abundance of bigheaded carps to areas monitored for the potential presence of silver carp, we used juvenile silver carp to simulate the barge transport of dead bigheaded carp carcasses, slime residue, and predator feces to determine the potential of these sources to supply DNA to uninhabited waters where it could be detected and misinterpreted as indicative of the presence of live bigheaded carp. Our results indicate that all three vectors are feasible sources of detectable eDNA for at least one month after their deposition. This suggests that current monitoring programs must consider alternative vectors of DNA in the environment and consider alternative strategies to minimize the detection of DNA not directly released from live bigheaded carps.
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Affiliation(s)
- Christopher M Merkes
- IAP Worldwide Services Inc., Upper Midwest Environmental Sciences Center, La Crosse, Wisconsin, United States of America; United States Geological Survey, Upper Midwest Environmental Sciences Center, La Crosse, Wisconsin, United States of America
| | - S Grace McCalla
- United States Geological Survey, Upper Midwest Environmental Sciences Center, La Crosse, Wisconsin, United States of America
| | - Nathan R Jensen
- United States Geological Survey, Upper Midwest Environmental Sciences Center, La Crosse, Wisconsin, United States of America
| | - Mark P Gaikowski
- United States Geological Survey, Upper Midwest Environmental Sciences Center, La Crosse, Wisconsin, United States of America
| | - Jon J Amberg
- United States Geological Survey, Upper Midwest Environmental Sciences Center, La Crosse, Wisconsin, United States of America
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116
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Eichmiller JJ, Bajer PG, Sorensen PW. The relationship between the distribution of common carp and their environmental DNA in a small lake. PLoS One 2014; 9:e112611. [PMID: 25383965 PMCID: PMC4226586 DOI: 10.1371/journal.pone.0112611] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 10/19/2014] [Indexed: 01/18/2023] Open
Abstract
Although environmental DNA (eDNA) has been used to infer the presence of rare aquatic species, many facets of this technique remain unresolved. In particular, the relationship between eDNA and fish distribution is not known. We examined the relationship between the distribution of fish and their eDNA (detection rate and concentration) in a lake. A quantitative PCR (qPCR) assay for a region within the cytochrome b gene of the common carp (Cyprinus carpio or ‘carp’), an ubiquitous invasive fish, was developed and used to measure eDNA in Lake Staring (MN, USA), in which both the density of carp and their distribution have been closely monitored for several years. Surface water, sub-surface water, and sediment were sampled from 22 locations in the lake, including areas frequently used by carp. In water, areas of high carp use had a higher rate of detection and concentration of eDNA, but there was no effect of fish use on sediment eDNA. The detection rate and concentration of eDNA in surface and sub-surface water were not significantly different (p≥0.5), indicating that eDNA did not accumulate in surface water. The detection rate followed the trend: high-use water > low-use water > sediment. The concentration of eDNA in sediment samples that were above the limit of detection were several orders of magnitude greater than water on a per mass basis, but a poor limit of detection led to low detection rates. The patchy distribution of eDNA in the water of our study lake suggests that the mechanisms that remove eDNA from the water column, such as decay and sedimentation, are rapid. Taken together, these results indicate that effective eDNA sampling methods should be informed by fish distribution, as eDNA concentration was shown to vary dramatically between samples taken less than 100 m apart.
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Affiliation(s)
- Jessica J Eichmiller
- Department of Fisheries, Wildlife, and Conservation Biology, Minnesota Aquatic Invasive Species Research Center, University of Minnesota, Twin Cities, St. Paul, Minnesota, United States of America
| | - Przemyslaw G Bajer
- Department of Fisheries, Wildlife, and Conservation Biology, Minnesota Aquatic Invasive Species Research Center, University of Minnesota, Twin Cities, St. Paul, Minnesota, United States of America
| | - Peter W Sorensen
- Department of Fisheries, Wildlife, and Conservation Biology, Minnesota Aquatic Invasive Species Research Center, University of Minnesota, Twin Cities, St. Paul, Minnesota, United States of America
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117
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Nathan LM, Simmons M, Wegleitner BJ, Jerde CL, Mahon AR. Quantifying environmental DNA signals for aquatic invasive species across multiple detection platforms. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:12800-12806. [PMID: 25299381 DOI: 10.1021/es5034052] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The use of molecular surveillance techniques has become popular among aquatic researchers and managers due to the improved sensitivity and efficiency compared to traditional sampling methods. Rapid expansion in the use of environmental DNA (eDNA), paired with the advancement of molecular technologies, has resulted in new detection platforms and techniques. In this study we present a comparison of three eDNA surveillance platforms: traditional polymerase chain reaction (PCR), quantitative PCR (qPCR), and digital droplet PCR (ddPCR) in which water samples were collected over a 24 h time period from mesocosm experiments containing a population gradient of invasive species densities. All platforms reliably detected the presence of DNA, even at low target organism densities within the first hour. The two quantitative platforms (qPCR and ddPCR) produced similar estimates of DNA concentrations. The analyses completed with ddPCR was faster from sample collection through analyses and cost approximately half the expenditure of qPCR. Although a new platform for eDNA surveillance of aquatic species, ddPCR was consistent with more commonly used qPCR and a cost-effective means of estimating DNA concentrations. Use of ddPCR by researchers and managers should be considered in future eDNA surveillance applications.
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Affiliation(s)
- Lucas M Nathan
- Department of Biology, Institute for Great Lakes Research, Central Michigan University , Mount Pleasant, Michigan 48859 United States
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118
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Xiao X, Sogge H, Lagesen K, Tooming-Klunderud A, Jakobsen KS, Rohrlack T. Use of high throughput sequencing and light microscopy show contrasting results in a study of phytoplankton occurrence in a freshwater environment. PLoS One 2014; 9:e106510. [PMID: 25171164 PMCID: PMC4149573 DOI: 10.1371/journal.pone.0106510] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 07/19/2014] [Indexed: 11/25/2022] Open
Abstract
Assessing phytoplankton diversity is of primary importance for both basic and applied ecological studies. Following the advances in molecular methods, phytoplankton studies are switching from using classical microscopy to high throughput sequencing approaches. However, methodological comparisons of these approaches have rarely been reported. In this study, we compared the two methods, using a unique dataset of multiple water samples taken from a natural freshwater environment. Environmental DNA was extracted from 300 water samples collected weekly during 20 years, followed by high throughput sequencing of amplicons from the 16S and 18S rRNA hypervariable regions. For each water sample, phytoplankton diversity was also estimated using light microscopy. Our study indicates that species compositions detected by light microscopy and 454 high throughput sequencing do not always match. High throughput sequencing detected more rare species and picoplankton than light microscopy, and thus gave a better assessment of phytoplankton diversity. However, when compared to light microscopy, high throughput sequencing of 16S and 18S rRNA amplicons did not adequately identify phytoplankton at the species level. In summary, our study recommends a combined strategy using both morphological and molecular techniques.
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Affiliation(s)
- Xi Xiao
- University of Oslo, Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, Oslo, Norway
- Zhejiang University, Ocean College, Hangzhou, China
| | - Hanne Sogge
- University of Oslo, Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, Oslo, Norway
| | - Karin Lagesen
- University of Oslo, Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, Oslo, Norway
- Norwegian Sequencing Centre, Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Ave Tooming-Klunderud
- University of Oslo, Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, Oslo, Norway
| | - Kjetill S. Jakobsen
- University of Oslo, Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, Oslo, Norway
| | - Thomas Rohrlack
- Norwegian University of Life Sciences, Department of Plant and Environmental Sciences, Ås, Norway
- Norwegian Institute for Water Research (NIVA), Oslo, Norway
- * E-mail:
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119
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Moyer GR, Díaz-Ferguson E, Hill JE, Shea C. Assessing environmental DNA detection in controlled lentic systems. PLoS One 2014; 9:e103767. [PMID: 25079969 PMCID: PMC4117544 DOI: 10.1371/journal.pone.0103767] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 07/07/2014] [Indexed: 12/17/2022] Open
Abstract
Little consideration has been given to environmental DNA (eDNA) sampling strategies for rare species. The certainty of species detection relies on understanding false positive and false negative error rates. We used artificial ponds together with logistic regression models to assess the detection of African jewelfish eDNA at varying fish densities (0, 0.32, 1.75, and 5.25 fish/m3). Our objectives were to determine the most effective water stratum for eDNA detection, estimate true and false positive eDNA detection rates, and assess the number of water samples necessary to minimize the risk of false negatives. There were 28 eDNA detections in 324, 1-L, water samples collected from four experimental ponds. The best-approximating model indicated that the per-L-sample probability of eDNA detection was 4.86 times more likely for every 2.53 fish/m3 (1 SD) increase in fish density and 1.67 times less likely for every 1.02 C (1 SD) increase in water temperature. The best section of the water column to detect eDNA was the surface and to a lesser extent the bottom. Although no false positives were detected, the estimated likely number of false positives in samples from ponds that contained fish averaged 3.62. At high densities of African jewelfish, 3–5 L of water provided a >95% probability for the presence/absence of its eDNA. Conversely, at moderate and low densities, the number of water samples necessary to achieve a >95% probability of eDNA detection approximated 42–73 and >100 L, respectively. Potential biases associated with incomplete detection of eDNA could be alleviated via formal estimation of eDNA detection probabilities under an occupancy modeling framework; alternatively, the filtration of hundreds of liters of water may be required to achieve a high (e.g., 95%) level of certainty that African jewelfish eDNA will be detected at low densities (i.e., <0.32 fish/m3 or 1.75 g/m3).
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Affiliation(s)
- Gregory R Moyer
- United States Fish and Wildlife Service, Conservation Genetics Laboratory, Warm Springs, Georgia, United States of America
| | - Edgardo Díaz-Ferguson
- United States Fish and Wildlife Service, Conservation Genetics Laboratory, Warm Springs, Georgia, United States of America; Department of Fisheries and Allied Aquacultures, Auburn University, Auburn, Alabama, United States of America
| | - Jeffrey E Hill
- Program in Fisheries and Aquatic Sciences Tropical Aquaculture Laboratory, University of Florida, Ruskin, Florida, United States of America
| | - Colin Shea
- Department of Biology, Tennessee Technological University, Cookeville, Tennessee, United States of America
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120
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Turner CR, Barnes MA, Xu CCY, Jones SE, Jerde CL, Lodge DM. Particle size distribution and optimal capture of aqueous macrobial
eDNA. Methods Ecol Evol 2014. [DOI: 10.1111/2041-210x.12206] [Citation(s) in RCA: 281] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Cameron R. Turner
- Department of Biological Sciences University of Notre Dame Notre Dame IN 46556 USA
| | - Matthew A. Barnes
- Department of Biological Sciences University of Notre Dame Notre Dame IN 46556 USA
- Environmental Change Initiative University of Notre Dame Notre Dame IN 46556 USA
| | - Charles C. Y. Xu
- Department of Biological Sciences University of Notre Dame Notre Dame IN 46556 USA
| | - Stuart E. Jones
- Department of Biological Sciences University of Notre Dame Notre Dame IN 46556 USA
| | - Christopher L. Jerde
- Department of Biological Sciences University of Notre Dame Notre Dame IN 46556 USA
- Environmental Change Initiative University of Notre Dame Notre Dame IN 46556 USA
| | - David M. Lodge
- Department of Biological Sciences University of Notre Dame Notre Dame IN 46556 USA
- Environmental Change Initiative University of Notre Dame Notre Dame IN 46556 USA
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121
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Darling JA. Genetic studies of aquatic biological invasions: closing the gap between research and management. Biol Invasions 2014. [DOI: 10.1007/s10530-014-0726-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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122
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Bohmann K, Evans A, Gilbert MTP, Carvalho GR, Creer S, Knapp M, Yu DW, de Bruyn M. Environmental DNA for wildlife biology and biodiversity monitoring. Trends Ecol Evol 2014; 29:358-67. [DOI: 10.1016/j.tree.2014.04.003] [Citation(s) in RCA: 515] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 04/08/2014] [Accepted: 04/09/2014] [Indexed: 01/07/2023]
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123
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Mahon AR, Nathan LR, Jerde CL. Meta-genomic surveillance of invasive species in the bait trade. CONSERV GENET RESOUR 2014. [DOI: 10.1007/s12686-014-0213-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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124
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Zhan A, Bailey SA, Heath DD, Macisaac HJ. Performance comparison of genetic markers for high-throughput sequencing-based biodiversity assessment in complex communities. Mol Ecol Resour 2014; 14:1049-59. [PMID: 24655333 DOI: 10.1111/1755-0998.12254] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/27/2014] [Accepted: 03/10/2014] [Indexed: 11/29/2022]
Abstract
Metabarcode surveys of DNA extracted from environmental samples are increasingly popular for biodiversity assessment in natural communities. Such surveys rely heavily on robust genetic markers. Therefore, analysis of PCR efficiency and subsequent biodiversity estimation for different types of genetic markers and their corresponding primers is important. Here, we test the PCR efficiency and biodiversity recovery potential of three commonly used genetic markers - nuclear small subunit ribosomal DNA (18S), mitochondrial cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (mt16S) - using 454 pyrosequencing of a zooplankton community collected from Hamilton Harbour, Ontario. We found that biodiversity detection power and PCR efficiency varied widely among these markers. All tested primers for COI failed to provide high-quality PCR products for pyrosequencing, but newly designed primers for 18S and 16S passed all tests. Furthermore, multiple analyses based on large-scale pyrosequencing (i.e. 1/2 PicoTiter plate for each marker) showed that primers for 18S recover more (38 orders) groups than 16S (10 orders) across all taxa, and four vs. two orders and nine vs. six families for Crustacea. Our results showed that 18S, using newly designed primers, is an efficient and powerful tool for profiling biodiversity in largely unexplored communities, especially when amplification difficulties exist for mitochondrial markers such as COI. Universal primers for higher resolution markers such as COI are still needed to address the possible low resolution of 18S for species-level identification.
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Affiliation(s)
- Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China; Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Avenue, Windsor, Ontario, Canada, N9B 3P4
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125
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Strand DA, Jussila J, Johnsen SI, Viljamaa-Dirks S, Edsman L, Wiik-Nielsen J, Viljugrein H, Engdahl F, Vrålstad T. Detection of crayfish plague spores in large freshwater systems. J Appl Ecol 2014. [DOI: 10.1111/1365-2664.12218] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- David A. Strand
- Norwegian Veterinary Institute; P.O. Box 750 Sentrum NO-0106 Oslo Norway
- Department of Biosciences; Microbial Evolution Research Group (MERG); University of Oslo; P.O. Box 1066 Blindern 0316 Oslo Norway
| | - Japo Jussila
- Kuopio Campus; University of Eastern Finland; P.O. Box 1627 FI-70211 Kuopio Finland
| | - Stein I. Johnsen
- Norwegian Institute for Nature Research; Fakkelgården 2624 Lillehammer Norway
| | | | - Lennart Edsman
- Department of Aquatic Resources; Institute of Freshwater Research; Swedish University of Agricultural Sciences; SE-178 93 Drottningholm Sweden
| | | | | | - Frederik Engdahl
- Department of Aquatic Resources; Institute of Freshwater Research; Swedish University of Agricultural Sciences; SE-178 93 Drottningholm Sweden
| | - Trude Vrålstad
- Norwegian Veterinary Institute; P.O. Box 750 Sentrum NO-0106 Oslo Norway
- Department of Biosciences; Microbial Evolution Research Group (MERG); University of Oslo; P.O. Box 1066 Blindern 0316 Oslo Norway
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126
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Kelly RP, Port JA, Yamahara KM, Crowder LB. Using environmental DNA to census marine fishes in a large mesocosm. PLoS One 2014; 9:e86175. [PMID: 24454960 PMCID: PMC3893283 DOI: 10.1371/journal.pone.0086175] [Citation(s) in RCA: 192] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 12/05/2013] [Indexed: 11/21/2022] Open
Abstract
The ocean is a soup of its resident species' genetic material, cast off in the forms of metabolic waste, shed skin cells, or damaged tissue. Sampling this environmental DNA (eDNA) is a potentially powerful means of assessing whole biological communities, a significant advance over the manual methods of environmental sampling that have historically dominated marine ecology and related fields. Here, we estimate the vertebrate fauna in a 4.5-million-liter mesocosm aquarium tank at the Monterey Bay Aquarium of known species composition by sequencing the eDNA from its constituent seawater. We find that it is generally possible to detect mitochondrial DNA of bony fishes sufficient to identify organisms to taxonomic family- or genus-level using a 106 bp fragment of the 12S ribosomal gene. Within bony fishes, we observe a low false-negative detection rate, although we did not detect the cartilaginous fishes or sea turtles present with this fragment. We find that the rank abundance of recovered eDNA sequences correlates with the abundance of corresponding species' biomass in the mesocosm, but the data in hand do not allow us to develop a quantitative relationship between biomass and eDNA abundance. Finally, we find a low false-positive rate for detection of exogenous eDNA, and we were able to diagnose non-native species' tissue in the food used to maintain the mesocosm, underscoring the sensitivity of eDNA as a technique for community-level ecological surveys. We conclude that eDNA has substantial potential to become a core tool for environmental monitoring, but that a variety of challenges remain before reliable quantitative assessments of ecological communities in the field become possible.
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Affiliation(s)
- Ryan P. Kelly
- Center for Ocean Solutions, Woods Institute for the Environment, Stanford University, Palo Alto, California, United States of America
- School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| | - Jesse A. Port
- Center for Ocean Solutions, Woods Institute for the Environment, Stanford University, Palo Alto, California, United States of America
| | - Kevan M. Yamahara
- Center for Ocean Solutions, Woods Institute for the Environment, Stanford University, Palo Alto, California, United States of America
| | - Larry B. Crowder
- Center for Ocean Solutions, Woods Institute for the Environment, Stanford University, Palo Alto, California, United States of America
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127
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Barnes MA, Turner CR, Jerde CL, Renshaw MA, Chadderton WL, Lodge DM. Environmental conditions influence eDNA persistence in aquatic systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:1819-27. [PMID: 24422450 DOI: 10.1021/es404734p] [Citation(s) in RCA: 336] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Environmental DNA (eDNA) surveillance holds great promise for improving species conservation and management. However, few studies have investigated eDNA dynamics under natural conditions, and interpretations of eDNA surveillance results are clouded by uncertainties about eDNA degradation. We conducted a literature review to assess current understanding of eDNA degradation in aquatic systems and an experiment exploring how environmental conditions can influence eDNA degradation. Previous studies have reported macrobial eDNA persistence ranging from less than 1 day to over 2 weeks, with no attempts to quantify factors affecting degradation. Using a SYBR Green quantitative PCR assay to observe Common Carp ( Cyprinus carpio ) eDNA degradation in laboratory mesocosms, our rate of Common Carp eDNA detection decreased over time. Common Carp eDNA concentration followed a pattern of exponential decay, and observed decay rates exceeded previously published values for aquatic macrobial eDNA. Contrary to our expectations, eDNA degradation rate declined as biochemical oxygen demand, chlorophyll, and total eDNA (i.e., from any organism) concentration increased. Our results help explain the widely divergent, previously published estimates for eDNA degradation. Measurements of local environmental conditions, consideration of environmental influence on eDNA detection, and quantification of local eDNA degradation rates will help interpret future eDNA surveillance results.
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Affiliation(s)
- Matthew A Barnes
- Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame , Notre Dame, Indiana 46556, United States
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128
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Count your eggs before they invade: identifying and quantifying egg clutches of two invasive apple snail species (Pomacea). PLoS One 2013; 8:e77736. [PMID: 24147069 PMCID: PMC3797708 DOI: 10.1371/journal.pone.0077736] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 09/11/2013] [Indexed: 11/19/2022] Open
Abstract
Winning the war against invasive species requires early detection of invasions. Compared to terrestrial invaders, aquatic species often thrive undetected under water and do not garner notice until too late for early action. However, fortunately for managers, apple snails (Family Ampullariidae, Genus Pomacea) provide their own conspicuous sign of invasion in the form of vibrantly colored egg clutches. Managers can potentially use egg clutches laid in the riparian zone as a means of early detection and species identification. To facilitate such efforts, we quantified differences in characteristics (length, width, depth, mass, egg number) of field-laid clutches for the two most common invasive species of apple snail, P. canaliculata and P. maculata, in native and non-native populations. Pomacea canaliculata native and non-native populations differed noticeably only in width. Native P. maculata clutches possessed significantly greater width, mass and eggs numbers compared with native P. canaliculata. Non-native P. maculata clutches significantly exceeded all other populations in all measured characteristics. Consequently, these traits may successfully distinguish between species. Fecundity data also allowed us to develop models that accurately estimated the number of eggs per clutch for each species based on clutch dimensions. We tested one, two and three dimensional models of clutches, including rendering a clutch as either a complete ellipsoid or an ellipsoid intersected by a cylinder to represent the oviposition site. Model comparisons found the product of length and depth, with a different function for each population, best predicted egg number for both species. Comparisons of egg number to clutch volume and mass implied non-native P. canaliculata may be food limited, while non-native P. maculata appeared to produce such enormous clutches by having access to greater nutrients than the native population. With these new tools, researchers and managers can quickly identify, quantify and begin eradication of new non-native apple snail populations.
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129
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Pilliod DS, Goldberg CS, Arkle RS, Waits LP. Factors influencing detection of eDNA from a stream-dwelling amphibian. Mol Ecol Resour 2013; 14:109-16. [PMID: 24034561 DOI: 10.1111/1755-0998.12159] [Citation(s) in RCA: 210] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 07/29/2013] [Accepted: 07/31/2013] [Indexed: 11/28/2022]
Abstract
Environmental DNA (eDNA) methods for detecting and estimating abundance of aquatic species are emerging rapidly, but little is known about how processes such as secretion rate, environmental degradation, and time since colonization or extirpation from a given site affect eDNA measurements. Using stream-dwelling salamanders and quantitative PCR (qPCR) analysis, we conducted three experiments to assess eDNA: (i) production rate; (ii) persistence time under different temperature and light conditions; and (iii) detectability and concentration through time following experimental introduction and removal of salamanders into previously unoccupied streams. We found that 44-50 g individuals held in aquaria produced 77 ng eDNA/h for 2 h, after which production either slowed considerably or began to equilibrate with degradation. eDNA in both full-sun and shaded treatments degraded exponentially to <1% of the original concentration after 3 days. eDNA was no longer detectable in full-sun samples after 8 days, whereas eDNA was detected in 20% of shaded samples after 11 days and 100% of refrigerated control samples after 18 days. When translocated into unoccupied streams, salamanders were detectable after 6 h, but only when densities were relatively high (0.2481 individuals/m(2) ) and when samples were collected within 5 m of the animals. Concentrations of eDNA detected were very low and increased steadily from 6-24 h after introduction, reaching 0.0022 ng/L. Within 1 h of removing salamanders from the stream, eDNA was no longer detectable. These results suggest that eDNA detectability and concentration depend on production rates of individuals, environmental conditions, density of animals, and their residence time.
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Affiliation(s)
- David S Pilliod
- Forest and Rangeland Ecosystem Science Center, U.S. Geological Survey, Boise, ID, 83706, USA
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130
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Andrew RL, Bernatchez L, Bonin A, Buerkle CA, Carstens BC, Emerson BC, Garant D, Giraud T, Kane NC, Rogers SM, Slate J, Smith H, Sork VL, Stone GN, Vines TH, Waits L, Widmer A, Rieseberg LH. A road map for molecular ecology. Mol Ecol 2013; 22:2605-26. [DOI: 10.1111/mec.12319] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 03/16/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Rose L. Andrew
- Department of Botany; University of British Columbia; 3529-6270 University Blvd Vancouver BC V6T 1Z4 Canada
| | - Louis Bernatchez
- DInstitut de Biologie Intégrative et des Systémes; Département de Biologie; 1030, Avenue de la Médecine Université Laval; Québec QC G1V 0A6 Canada
| | - Aurélie Bonin
- Laboratoire d'Ecologie Alpine; CNRS UMR 5553 Université Joseph Fourier; BP 53, 38041 Grenoble Cedex 9 France
| | - C. Alex. Buerkle
- Department of Botany; University of Wyoming; 1000 E. University Ave. Laramie WY 82071 USA
| | - Bryan C. Carstens
- Department of Evolution, Ecology and Organismal Biology; 318 W. 12th Ave. The Ohio State University; Columbus OH 43210 USA
| | - Brent C. Emerson
- Island Ecology and Evolution Research Group; Instituto de Productos Naturales y Agrobiología (IPNA-CSIC) C/Astrofísico Francisco Sánchez 3 La Laguna Tenerife; Canary Islands 38206 Spain
| | - Dany Garant
- Département de Biologie; Université de Sherbrooke; Sherbrooke QC J1K 2R1 Canada
| | - Tatiana Giraud
- Laboratoire Ecologie, Systématique et Evolution; UMR 8079 CNRS-UPS-AgroParisTech, Bâtiment 360 Univ. Paris Sud; 91405 Orsay cedex France
| | - Nolan C. Kane
- Department of Botany; University of British Columbia; 3529-6270 University Blvd Vancouver BC V6T 1Z4 Canada
| | - Sean M. Rogers
- Department of Biological Sciences; University of Calgary; 2500 University Drive N.W., Calgary AB T2N 1N4 Canada
| | - Jon Slate
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield S10 2TN UK
| | - Harry Smith
- 79 Melton Road Burton-on-the-Wolds Loughborough LE12 5TQ UK
| | - Victoria L. Sork
- Department of Ecology and Evolutionary Biology; University of California Los Angeles; 4139 Terasaki Life Sciences Building, 610 Charles E. Young Drive East Los Angeles CA 90095 USA
| | - Graham N. Stone
- Institute of Evolutionary Biology; University of Edinburgh; The King's Buildings, West Mains Road, Edinburgh EH9 3JT UK
| | - Timothy H. Vines
- Molecular Ecology Editorial Office; 6270 University Blvd Vancouver BC V6T 1Z4 Canada
| | - Lisette Waits
- Department of Fish and Wildlife Sciences; University of Idaho; 875 Perimeter Drive MS 1136 Moscow ID 83844 USA
| | - Alex Widmer
- ETH Zurich; Institute of Integrative Biology; Universitätstrasse 16 Zurich 8092 Switzerland
| | - Loren H. Rieseberg
- Department of Botany; University of British Columbia; 3529-6270 University Blvd Vancouver BC V6T 1Z4 Canada
- Department of Biology; Indiana University; 1001 E. 3 St., Bloomington IN 47405 USA
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131
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Wilcox TM, McKelvey KS, Young MK, Jane SF, Lowe WH, Whiteley AR, Schwartz MK. Robust detection of rare species using environmental DNA: the importance of primer specificity. PLoS One 2013; 8:e59520. [PMID: 23555689 PMCID: PMC3608683 DOI: 10.1371/journal.pone.0059520] [Citation(s) in RCA: 215] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 02/15/2013] [Indexed: 11/18/2022] Open
Abstract
Environmental DNA (eDNA) is being rapidly adopted as a tool to detect rare animals. Quantitative PCR (qPCR) using probe-based chemistries may represent a particularly powerful tool because of the method’s sensitivity, specificity, and potential to quantify target DNA. However, there has been little work understanding the performance of these assays in the presence of closely related, sympatric taxa. If related species cause any cross-amplification or interference, false positives and negatives may be generated. These errors can be disastrous if false positives lead to overestimate the abundance of an endangered species or if false negatives prevent detection of an invasive species. In this study we test factors that influence the specificity and sensitivity of TaqMan MGB assays using co-occurring, closely related brook trout (Salvelinus fontinalis) and bull trout (S. confluentus) as a case study. We found qPCR to be substantially more sensitive than traditional PCR, with a high probability of detection at concentrations as low as 0.5 target copies/µl. We also found that number and placement of base pair mismatches between the Taqman MGB assay and non-target templates was important to target specificity, and that specificity was most influenced by base pair mismatches in the primers, rather than in the probe. We found that insufficient specificity can result in both false positive and false negative results, particularly in the presence of abundant related species. Our results highlight the utility of qPCR as a highly sensitive eDNA tool, and underscore the importance of careful assay design.
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Affiliation(s)
- Taylor M Wilcox
- United States Department of Agriculture Forest Service, Rocky Mountain Research Station, Missoula, Montana, United States of America.
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132
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Egan SP, Barnes MA, Hwang CT, Mahon AR, Feder JL, Ruggiero ST, Tanner CE, Lodge DM. Rapid Invasive Species Detection by Combining Environmental DNA with Light Transmission Spectroscopy. Conserv Lett 2013. [DOI: 10.1111/conl.12017] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Scott P. Egan
- Department of Biological Sciences; University of Notre Dame; Notre Dame IN 46556 USA
- Advanced Diagnostics and Therapeutics Initiative; University of Notre Dame; Notre Dame IN 46556 USA
- Environmental Change Initiative; University of Notre Dame; Notre Dame IN 46556 USA
| | - Matthew A. Barnes
- Department of Biological Sciences; University of Notre Dame; Notre Dame IN 46556 USA
| | - Ching-Ting Hwang
- Department of Biological Sciences; University of Notre Dame; Notre Dame IN 46556 USA
- Department of Physics; University of Notre Dame; Notre Dame IN 46556 USA
| | - Andrew R. Mahon
- Department of Biological Sciences; University of Notre Dame; Notre Dame IN 46556 USA
- Department of Biology and Institute for Great Lakes Research; Central Michigan University; Mount Pleasant MI 48859 USA
| | - Jeffery L. Feder
- Department of Biological Sciences; University of Notre Dame; Notre Dame IN 46556 USA
- Advanced Diagnostics and Therapeutics Initiative; University of Notre Dame; Notre Dame IN 46556 USA
- Environmental Change Initiative; University of Notre Dame; Notre Dame IN 46556 USA
| | - Steven T. Ruggiero
- Environmental Change Initiative; University of Notre Dame; Notre Dame IN 46556 USA
- Department of Physics; University of Notre Dame; Notre Dame IN 46556 USA
| | - Carol E. Tanner
- Environmental Change Initiative; University of Notre Dame; Notre Dame IN 46556 USA
- Department of Physics; University of Notre Dame; Notre Dame IN 46556 USA
| | - David M. Lodge
- Department of Biological Sciences; University of Notre Dame; Notre Dame IN 46556 USA
- Advanced Diagnostics and Therapeutics Initiative; University of Notre Dame; Notre Dame IN 46556 USA
- Environmental Change Initiative; University of Notre Dame; Notre Dame IN 46556 USA
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133
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Mahon AR, Jerde CL, Galaska M, Bergner JL, Chadderton WL, Lodge DM, Hunter ME, Nico LG. Validation of eDNA surveillance sensitivity for detection of Asian carps in controlled and field experiments. PLoS One 2013; 8:e58316. [PMID: 23472178 PMCID: PMC3589332 DOI: 10.1371/journal.pone.0058316] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 02/01/2013] [Indexed: 11/19/2022] Open
Abstract
In many North American rivers, populations of multiple species of non-native cyprinid fishes are present, including black carp (Mylpharyngodon piceus), grass carp (Ctenopharyngodon idella), bighead carp (Hypophthalmichthys nobilis), silver carp (Hypophthalmichthys molitrix), common carp (Cyprinus carpio), and goldfish (Carassius auratus). All six of these species are found in the Mississippi River basin and tracking their invasion has proven difficult, particularly where abundance is low. Knowledge of the location of the invasion front is valuable to natural resource managers because future ecological and economic damages can be most effectively prevented when populations are low. To test the accuracy of environmental DNA (eDNA) as an early indicator of species occurrence and relative abundance, we applied eDNA technology to the six non-native cyprinid species putatively present in a 2.6 river mile stretch of the Chicago (IL, USA) canal system that was subsequently treated with piscicide. The proportion of water samples yielding positive detections increased with relative abundance of the six species, as indicated by the number of carcasses recovered after poisoning. New markers for black carp, grass carp, and a common carp/goldfish are reported and details of the marker testing to ensure specificity are provided.
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Affiliation(s)
- Andrew R Mahon
- Department of Biology, Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, Michigan, USA.
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134
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Zhan A, Hulák M, Sylvester F, Huang X, Adebayo AA, Abbott CL, Adamowicz SJ, Heath DD, Cristescu ME, MacIsaac HJ. High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities. Methods Ecol Evol 2013. [DOI: 10.1111/2041-210x.12037] [Citation(s) in RCA: 170] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Aibin Zhan
- Great Lakes Institute for Environmental Research; University of Windsor; 401 Sunset Avenue Windsor Ontario N9B 3P4 Canada
- Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; 18 Shuangqing Road Haidian District Beijing 100085 China
| | - Martin Hulák
- Great Lakes Institute for Environmental Research; University of Windsor; 401 Sunset Avenue Windsor Ontario N9B 3P4 Canada
| | - Francisco Sylvester
- Facultad de Ciencias Exactas y Naturales; Departamento de Ecología; Genética y Evolución and Consejo Nacional de Investigaciones Científicas y Técnicas; Universidad de Buenos Aires; Buenos Aires Argentina
| | - Xiaoting Huang
- Key Laboratory of Marine Genetics and Breeding (MGB); Ministry of Education, College of Marine Life Sciences; Ocean University of China; 5 Yushan Road Qingdao 266003 China
| | - Abisola A. Adebayo
- Great Lakes Institute for Environmental Research; University of Windsor; 401 Sunset Avenue Windsor Ontario N9B 3P4 Canada
| | - Cathryn L. Abbott
- Pacific Biological Station; Fisheries and Oceans Canada; 3190 Hammond Bay Road Nanaimo British Columbia V9T 6N7 Canada
| | - Sarah J. Adamowicz
- Biodiversity Institute of Ontario and Department of Integrative Biology; University of Guelph; 50 Stone Road East Guelph Ontario N1G 2W1 Canada
| | - Daniel D. Heath
- Great Lakes Institute for Environmental Research; University of Windsor; 401 Sunset Avenue Windsor Ontario N9B 3P4 Canada
| | - Melania E. Cristescu
- Great Lakes Institute for Environmental Research; University of Windsor; 401 Sunset Avenue Windsor Ontario N9B 3P4 Canada
- Department of Biology; McGill University; 1205 Docteur Penfield Montreal Quebec H3A 1B1 Canada
| | - Hugh J. MacIsaac
- Great Lakes Institute for Environmental Research; University of Windsor; 401 Sunset Avenue Windsor Ontario N9B 3P4 Canada
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135
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Takahara T, Minamoto T, Doi H. Using environmental DNA to estimate the distribution of an invasive fish species in ponds. PLoS One 2013; 8:e56584. [PMID: 23437177 PMCID: PMC3577852 DOI: 10.1371/journal.pone.0056584] [Citation(s) in RCA: 279] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Accepted: 01/15/2013] [Indexed: 11/30/2022] Open
Abstract
Knowledge of the presence of an invasive species is critical to monitoring the sustainability of communities and ecosystems. Environmental DNA (eDNA), DNA fragments that are likely to be bound to organic matters in the water or in shed cells, has been used to monitor the presence of aquatic animals. Using an eDNA-based method, we estimated the presence of the invasive bluegill sunfish, Lepomis macrochirus, in 70 ponds located in seven locales on the Japanese mainland and on surrounding islands. We quantified the concentration of DNA copies in a 1 L water sample using quantitative real-time polymerase chain reaction (qPCR) with a primer/probe set. In addition, we visually observed the bluegill presence in the ponds from the shoreline. We detected bluegill eDNA in all the ponds where bluegills were observed visually and some where bluegills were not observed. Bluegills were also less prevalent on the islands than the mainland, likely owing to limited dispersal and introduction by humans. Our eDNA method simply and rapidly detects the presence of this invasive fish species with less disturbance to the environment during field surveys than traditional methods.
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Affiliation(s)
- Teruhiko Takahara
- Institute for Sustainable Sciences and Development, Hiroshima University, Higashi-Hiroshima, Japan.
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136
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Mahon AR, Barnes MA, Li F, Egan SP, Tanner CE, Ruggiero ST, Feder JL, Lodge DM. DNA-based species detection capabilities using laser transmission spectroscopy. J R Soc Interface 2012; 10:20120637. [PMID: 23015524 PMCID: PMC3565792 DOI: 10.1098/rsif.2012.0637] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Early detection of invasive species is critical for effective biocontrol to mitigate potential ecological and economic damage. Laser transmission spectroscopy (LTS) is a powerful solution offering real-time, DNA-based species detection in the field. LTS can measure the size, shape and number of nanoparticles in a solution and was used here to detect size shifts resulting from hybridization of the polymerase chain reaction product to nanoparticles functionalized with species-specific oligonucleotide probes or with the species-specific oligonucleotide probes alone. We carried out a series of DNA detection experiments using the invasive freshwater quagga mussel (Dreissena bugensis) to evaluate the capability of the LTS platform for invasive species detection. Specifically, we tested LTS sensitivity to (i) DNA concentrations of a single target species, (ii) the presence of a target species within a mixed sample of other closely related species, (iii) species-specific functionalized nanoparticles versus species-specific oligonucleotide probes alone, and (iv) amplified DNA fragments versus unamplified genomic DNA. We demonstrate that LTS is a highly sensitive technique for rapid target species detection, with detection limits in the picomolar range, capable of successful identification in multispecies samples containing target and non-target species DNA. These results indicate that the LTS DNA detection platform will be useful for field application of target species. Additionally, we find that LTS detection is effective with species-specific oligonucleotide tags alone or when they are attached to polystyrene nanobeads and with both amplified and unamplified DNA, indicating that the technique may also have versatility for broader applications.
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Affiliation(s)
- A R Mahon
- 1Department of Biology, Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, MI, USA.
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