Can eDNA be an indicator of tree groundwater use? A perspective
L. Pollitt A C , K. Korbel A , J. Dabovic B , A. Chariton A and G. C. Hose AA School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia.
B Department of Planning and Environment, Water, Parramatta, NSW 2124, Australia.
C Corresponding author. Email: loren.pollitt@hdr.mq.edu.au
Marine and Freshwater Research - https://doi.org/10.1071/MF21293
Submitted: 11 August 2021 Accepted: 25 February 2022 Published online: 12 April 2022
Journal Compilation © CSIRO 2022 Open Access CC BY-NC-ND
Abstract
A major challenge of managing groundwater-dependent ecosystems is determining when and where plants are accessing and using groundwater. Addressing this knowledge gap is particularly pertinent where remnant stands of old growth trees reside within areas where groundwater is being used at an unsustainable rate. The aim of this paper is to investigate what it means to find tree DNA in the groundwater and provide a perspective on whether the detection of tree DNA in groundwater could provide an indicator of groundwater use by trees. This idea arose from recent DNA-based surveys that routinely detected tree DNA in groundwater samples, which may be unexpected given the general absence of plants in dark, subsurface environments. We discuss the likely sources and fate of tree DNA in groundwater and the knowledge needed to progress the development of tree DNA as a robust indicator. If successful, such an indicator would help managers better understand the water requirements of groundwater-dependent vegetation, meet legislative obligations for monitoring and assessment, and improve the conservation and management of groundwater-dependent ecosystems.
Keywords: environmental DNA, riparian vegetation, phreatophytes, groundwater-dependent ecosystems, GDE.
References
Alsos, I. G., Lammers, Y., Yoccoz, N. G., Jørgensen, T., Sjögren, P., Gielly, L., and Edwards, M. E. (2018). Plant DNA metabarcoding of lake sediments: how does it represent the contemporary vegetation. PLoS One 13, e0195403.| Plant DNA metabarcoding of lake sediments: how does it represent the contemporary vegetation.Crossref | GoogleScholarGoogle Scholar | 29664954PubMed |
Anglès d’Auriac, M. B., Strand, D. A., Mjelde, M., Demars, B. O., and Thaulow, J. (2019). Detection of an invasive aquatic plant in natural water bodies using environmental DNA. PLoS One 14, e0219700.
| Detection of an invasive aquatic plant in natural water bodies using environmental DNA.Crossref | GoogleScholarGoogle Scholar | 31299064PubMed |
Australian Bureau of Statistics (2019). Water use on Australian farms, Australia, 2017–2018. (ABS: Canberra, ACT, Australia.) Available at https://www.abs.gov.au/statistics/industry/agriculture/water-use-australian-farms/2017-18#data-download
Baird, D. J., and Hajibabaei, M. (2012). Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing. Molecular Ecology 21, 2039–2044.
| Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing.Crossref | GoogleScholarGoogle Scholar | 22590728PubMed |
Barnes, M. A., and Turner, C. R. (2016). The ecology of environmental DNA and implications for conservation genetics. Conservation Genetics 17, 1–17.
| The ecology of environmental DNA and implications for conservation genetics.Crossref | GoogleScholarGoogle Scholar |
Barnes, M. A., Turner, C. R., Jerde, C. L., Renshaw, M. A., Chadderton, W. L., and Lodge, D. M. (2014). Environmental conditions influence eDNA persistence in aquatic systems. Environmental Science & Technology 48, 1819–1827.
| Environmental conditions influence eDNA persistence in aquatic systems.Crossref | GoogleScholarGoogle Scholar |
Beng, K. C., and Corlett, R. T. (2020). Applications of environmental DNA (eDNA) in ecology and conservation: opportunities, challenges and prospects. Biodiversity and Conservation 29, 2089–2121.
| Applications of environmental DNA (eDNA) in ecology and conservation: opportunities, challenges and prospects.Crossref | GoogleScholarGoogle Scholar |
Benson, J. S. (2008). New South Wales Vegetation Classification and assessment: Part 2 plant communities of the NSW South-western Slopes bioregion and update of NSW Western Plains plant communities, version 2 of the NSWVCA database. Cunninghamia 10, 599–673.
Bioregional Assessment Programme (2016). Namoi hydraulic conductivity measurements. Bioregional Assessment Source Dataset. Available at http://data.bioregionalassessments.gov.au/dataset/5f88517d-8154-411d-907f-4e2c2d12a912 [Verified 12 March 2019].
Bohmann, K., Evans, A., Gilbert, M. T. P., Carvalho, G. R., Creer, S., Knapp, M., Douglas, W. Y., and De Bruyn, M. (2014). Environmental DNA for wildlife biology and biodiversity monitoring. Trends in Ecology & Evolution 29, 358–367.
| Environmental DNA for wildlife biology and biodiversity monitoring.Crossref | GoogleScholarGoogle Scholar |
Boulton, A. J., Bichuette, M. E., Korbel, K., Stoch, F., Niemiller, M. L., Hose, G. C., and Linke, S. (in press). Recent concepts and approaches for conserving groundwater biodiversity. In ‘Groundwater Ecology and Evolution’. (Eds F. Malard, C. Griebler, and S. Retaux.) (Elsevier.)
Bravo, A. G., Wildi, W., and Poté, J. (2010). Kinetics of plant material mass loss and DNA release in freshwater column. Ecotoxicology and Environmental Safety 73, 1548–1552.
| Kinetics of plant material mass loss and DNA release in freshwater column.Crossref | GoogleScholarGoogle Scholar | 20570352PubMed |
Brown, J., Bach, L., Aldous, A., Wyers, A., and DeGagné, J. (2010). Groundwater-dependent ecosystems in Oregon: an assessment of their distribution and associated threats. Frontiers in Ecology and the Environment 9, 97–102.
| Groundwater-dependent ecosystems in Oregon: an assessment of their distribution and associated threats.Crossref | GoogleScholarGoogle Scholar |
Carøe, C., and Bohmann, K. (2020). Tagsteady: a metabarcoding library preparation protocol to avoid false assignment of sequences to samples. Molecular Ecology Resources 20, 1620–1631.
| Tagsteady: a metabarcoding library preparation protocol to avoid false assignment of sequences to samples.Crossref | GoogleScholarGoogle Scholar | 32663358PubMed |
Ceccherini, M. T., Ascher, J., Agnelli, A., Borgogni, F., Pantani, O. L., and Pietramellara, G. (2009). Experimental discrimination and molecular characterization of the extracellular soil DNA fraction. Antonie van Leeuwenhoek 96, 653–657.
| Experimental discrimination and molecular characterization of the extracellular soil DNA fraction.Crossref | GoogleScholarGoogle Scholar | 19533410PubMed |
Chariton, A. A., Stephenson, S., Morgan, M. J., Steven, A. D., Colloff, M. J., Court, L. N., and Hardy, C. M. (2015). Metabarcoding of benthic eukaryote communities predicts the ecological condition of estuaries. Environmental Pollution 203, 165–174.
| Metabarcoding of benthic eukaryote communities predicts the ecological condition of estuaries.Crossref | GoogleScholarGoogle Scholar | 25909325PubMed |
Chimento, A., Cacciola, S. O., and Garbelotto, M. (2012). Detection of mRNA by reverse‐transcription PCR as an indicator of viability in Phytophthora ramorum. Forest Pathology 42, 14–21.
| Detection of mRNA by reverse‐transcription PCR as an indicator of viability in Phytophthora ramorum.Crossref | GoogleScholarGoogle Scholar |
Christina, M., Nouvellon, Y., Laclau, J. P., Stape, J. L., Bouillet, J. P., Lambais, G. R., and Le Maire, G. (2017). Importance of deep water uptake in tropical eucalypt forest. Functional Ecology 31, 509–519.
| Importance of deep water uptake in tropical eucalypt forest.Crossref | GoogleScholarGoogle Scholar |
Cleverly, J., Vote, C., Isaac, P., Ewenz, C., Harahap, M., Beringer, J., Campbell, D. I., Daly, E., Eamus, D., He, L., and Hunt, J. (2020). Carbon, water and energy fluxes in agricultural systems of Australia and New Zealand. Agricultural and Forest Meteorology 287, 107934.
| Carbon, water and energy fluxes in agricultural systems of Australia and New Zealand.Crossref | GoogleScholarGoogle Scholar |
Coble, A. A., Flinders, C. A., Homyack, J. A., Penaluna, B. E., Cronn, R. C., and Weitemier, K. (2019). eDNA as a tool for identifying freshwater species in sustainable forestry: a critical review and potential future applications. The Science of the Total Environment 649, 1157–1170.
| eDNA as a tool for identifying freshwater species in sustainable forestry: a critical review and potential future applications.Crossref | GoogleScholarGoogle Scholar | 30308887PubMed |
Coissac, E., Riaz, T., and Puillandre, N. (2012). Bioinformatic challenges for DNA metabarcoding of plants and animals. Molecular Ecology 21, 1834–1847.
| Bioinformatic challenges for DNA metabarcoding of plants and animals.Crossref | GoogleScholarGoogle Scholar | 22486822PubMed |
Collins, R. A., Wangensteen, O. S., O’Gorman, E. J., Mariani, S., Sims, D. W., and Genner, M. J. (2018). Persistence of environmental DNA in marine systems. Communications Biology 1, 185.
| Persistence of environmental DNA in marine systems.Crossref | GoogleScholarGoogle Scholar | 30417122PubMed |
Cook, P. G., and Eamus, D. (2018). The potential for groundwater use by vegetation in the Australian arid zone. Northern Territory Department of Environmental and Natural Resources Water Resources Division. (Northern Territory Government, Darwin, NT, Australia.) https://depws.nt.gov.au/__data/assets/pdf_file/0004/498883/The-Potential-Use-for-Groundwater-Use-by-Vegetation-in-the-Aust.-Arid-Zone.pdf [Verified 15 June 2019].
Dale, P. J., Clarke, B., and Fontes, E. M. (2002). Potential for the environmental impact of transgenic crops. Nature Biotechnology 20, 567–574.
| Potential for the environmental impact of transgenic crops.Crossref | GoogleScholarGoogle Scholar | 12042859PubMed |
Darling, J. A., and Mahon, A. R. (2011). From molecules to management: adopting DNA-based methods for monitoring biological invasions in aquatic environments. Environmental Research 111, 978–988.
| From molecules to management: adopting DNA-based methods for monitoring biological invasions in aquatic environments.Crossref | GoogleScholarGoogle Scholar | 21353670PubMed |
de Vet, W. W. J. M., Dinkla, I. J. T., Muyzer, G., Rietveld, L. C., and Van Loosdrecht, M. C. M. (2009). Molecular characterization of microbial populations in groundwater sources and sand filters for drinking water production. Water Research 43, 182–194.
| Molecular characterization of microbial populations in groundwater sources and sand filters for drinking water production.Crossref | GoogleScholarGoogle Scholar |
Deagle, B. E., Eveson, J. P., and Jarman, S. N. (2006). Quantification of damage in DNA recovered from highly degraded samples: a case study on DNA in faeces. Frontiers in Zoology 3, 11.
| Quantification of damage in DNA recovered from highly degraded samples: a case study on DNA in faeces.Crossref | GoogleScholarGoogle Scholar | 16911807PubMed |
Deiner, K., and Altermatt, F. (2014). Transport distance of invertebrate environmental DNA in a natural river. PLoS One 9, e88786.
| Transport distance of invertebrate environmental DNA in a natural river.Crossref | GoogleScholarGoogle Scholar | 24523940PubMed |
Deiner, K., Bik, H. M., Mächler, E., Seymour, M., Lacoursière‐Roussel, A., Altermatt, F., Creer, S., Bista, I., Lodge, D. M., De Vere, N., and Pfrender, M. E. (2017). Environmental DNA metabarcoding: transforming how we survey animal and plant communities. Molecular Ecology 26, 5872–5895.
| Environmental DNA metabarcoding: transforming how we survey animal and plant communities.Crossref | GoogleScholarGoogle Scholar | 28921802PubMed |
Dejean, T., Valentini, A., Duparc, A., Pellier-Cuit, S., Pompanon, F., Taberlet, P., and Miaud, C. (2011). Persistence of environmental DNA in freshwater ecosystems. PLoS One 6, e23398.
| Persistence of environmental DNA in freshwater ecosystems.Crossref | GoogleScholarGoogle Scholar | 21858099PubMed |
Díaz-Ferguson, E. E., and Moyer, G. R. (2014). History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments. Revista de Biología Tropical 62, 1273–1284.
| History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments.Crossref | GoogleScholarGoogle Scholar | 25720166PubMed |
Doi, H., Watanabe, T., Nishizawa, N., Saito, T., Nagata, H., Kameda, Y., Maki, N., Ikeda, K., and Fukuzawa, T. (2021). On-site environmental DNA detection of species using ultrarapid mobile PCR. Molecular Ecology Resources 21, 2364–2368.
| On-site environmental DNA detection of species using ultrarapid mobile PCR.Crossref | GoogleScholarGoogle Scholar | 34139102PubMed |
Eamus, D. (2009). ‘Identifying groundwater dependent ecosystems: a guide for land and water managers.’ (Land and Water Australia: Sydney, NSW, Australia.)
Eamus, D., Froend, R., Loomes, R., Hose, G., and Murray, B. (2006). A functional methodology for determining the groundwater regime needed to maintain the health of groundwater-dependent vegetation. Australian Journal of Botany 54, 97–114.
| A functional methodology for determining the groundwater regime needed to maintain the health of groundwater-dependent vegetation.Crossref | GoogleScholarGoogle Scholar |
Eamus, D., Zolfaghar, S., Villalobos-Vega, R., Cleverly, J., and Huete, A. (2015). Groundwater-dependent ecosystems: recent insights from satellite and field-based studies. Hydrology and Earth System Sciences 19, 4229–4256.
| Groundwater-dependent ecosystems: recent insights from satellite and field-based studies.Crossref | GoogleScholarGoogle Scholar |
Erostate, M., Huneau, F., Garel, E., Ghiotti, S., Vystavna, Y., Garrido, M., and Pasqualini, V. (2020). Groundwater dependent ecosystems in coastal Mediterranean regions: characterization, challenges and management for their protection. Water Research 172, 115461.
| Groundwater dependent ecosystems in coastal Mediterranean regions: characterization, challenges and management for their protection.Crossref | GoogleScholarGoogle Scholar | 31951946PubMed |
Evans, N. T., Shirey, P. D., Wieringa, J. G., Mahon, A. R., and Lamberti, G. A. (2017). Comparative cost and effort of fish distribution detection via environmental DNA analysis and electrofishing. Fisheries 42, 90–99.
| Comparative cost and effort of fish distribution detection via environmental DNA analysis and electrofishing.Crossref | GoogleScholarGoogle Scholar |
Ficetola, G. F., Pansu, J., Bonin, A., Coissac, E., Giguet‐Covex, C., De Barba, M., Gielly, L., Lopes, C. M., Boyer, F., Pompanon, F., and Rayé, G. (2015). Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data. Molecular Ecology Resources 15, 543–556.
| Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data.Crossref | GoogleScholarGoogle Scholar | 25327646PubMed |
Froend, R., and Sommer, B. (2010). Phreatophytic vegetation response to climatic and abstraction-induced groundwater drawdown: examples of long-term spatial and temporal variability in community response. Ecological Engineering 36, 1191–1200.
| Phreatophytic vegetation response to climatic and abstraction-induced groundwater drawdown: examples of long-term spatial and temporal variability in community response.Crossref | GoogleScholarGoogle Scholar |
Furlan, E. M., Davis, J., and Duncan, R. P. (2020). Identifying error and accurately interpreting environmental DNA metabarcoding results: a case study to detect vertebrates at arid zone waterholes. Molecular Ecology Resources 20, 1259–1276.
| Identifying error and accurately interpreting environmental DNA metabarcoding results: a case study to detect vertebrates at arid zone waterholes.Crossref | GoogleScholarGoogle Scholar | 32310337PubMed |
Gillmore, M. L., Golding, L. A., Chariton, A. A., Stauber, J. L., Stephenson, S., Gissi, F., Greenfield, P., Juillot, F., and Jolley, D. F. (2021). Metabarcoding reveals changes in benthic eukaryote and prokaryote community composition along a tropical marine sediment nickel gradient. Environmental Toxicology and Chemistry 40, 1892–1905.
| Metabarcoding reveals changes in benthic eukaryote and prokaryote community composition along a tropical marine sediment nickel gradient.Crossref | GoogleScholarGoogle Scholar |
Goldberg, C. S., Strickler, K. M., and Pilliod, D. S. (2015). Moving environmental DNA methods from concept to practice for monitoring aquatic macroorganisms. Biological Conservation 183, 1–3.
| Moving environmental DNA methods from concept to practice for monitoring aquatic macroorganisms.Crossref | GoogleScholarGoogle Scholar |
Goldberg, C. S., Turner, C. R., Deiner, K., Klymus, K. E., Thomsen, P. F., Murphy, M. A., Spear, S. F., McKee, A., Oyler‐McCance, S. J., Cornman, R. S., and Laramie, M. B. (2016). Critical considerations for the application of environmental DNA methods to detect aquatic species. Methods in Ecology and Evolution 7, 1299–1307.
| Critical considerations for the application of environmental DNA methods to detect aquatic species.Crossref | GoogleScholarGoogle Scholar |
Griebler, C., and Lueders, T. (2009). Microbial biodiversity in groundwater ecosystems. Freshwater Biology 54, 649–677.
| Microbial biodiversity in groundwater ecosystems.Crossref | GoogleScholarGoogle Scholar |
Groom, P. K., Froend, R. H., Mattiske, E. M., and Koch, B. L. (2000). Myrtaceous shrub species respond to long-term decreasing groundwater levels on the Gnangara Groundwater Mound, northern Swan Coastal Plain. Journal of the Royal Society of Western Australia 83, 75–82.
Gulden, R. H., Lerat, S., Hart, M. M., Powell, J. R., Trevors, J. T., Pauls, K. P., Klironomos, J. N., and Swanton, C. J. (2005). Quantitation of transgenic plant DNA in leachate water: real-time polymerase chain reaction analysis. Journal of Agricultural and Food Chemistry 53, 5858–5865.
| Quantitation of transgenic plant DNA in leachate water: real-time polymerase chain reaction analysis.Crossref | GoogleScholarGoogle Scholar | 16028966PubMed |
Hadziavdic, K., Lekang, K., Lanzen, A., Jonassen, I., Thompson, E. M., and Troedsson, C. (2014). Characterization of the 18S rRNA gene for designing universal eukaryote specific primers. PLoS One 9, e87624.
| Characterization of the 18S rRNA gene for designing universal eukaryote specific primers.Crossref | GoogleScholarGoogle Scholar | 24516555PubMed |
Harper, L. R., Buxton, A. S., Rees, H. C., Bruce, K., Brys, R., Halfmaerten, D., Read, D. S., Watson, H. V., Sayer, C. D., Jones, E. P., and Priestley, V. (2019). Prospects and challenges of environmental DNA (eDNA) monitoring in freshwater ponds. Hydrobiologia 826, 25–41.
| Prospects and challenges of environmental DNA (eDNA) monitoring in freshwater ponds.Crossref | GoogleScholarGoogle Scholar |
Harrington, N., and Cook, P. (2014). ‘Groundwater in Australia.’ (National Centre for Groundwater Research and Training: Adelaide, SA, Australia.)
Hollingsworth, P. M., Graham, S. W., and Little, D. P. (2011). Choosing and using a plant DNA barcode. PLoS One 6, e19254.
| Choosing and using a plant DNA barcode.Crossref | GoogleScholarGoogle Scholar | 21637336PubMed |
Hoogland, T., Heuvelink, G. B., and Knotters, M. (2010). Mapping water-table depths over time to assess desiccation of groundwater-dependent ecosystems in the Netherlands. Wetlands 30, 137–147.
| Mapping water-table depths over time to assess desiccation of groundwater-dependent ecosystems in the Netherlands.Crossref | GoogleScholarGoogle Scholar |
Humphreys, W. F. (2006). Aquifers: the ultimate groundwater-dependent ecosystems. Australian Journal of Botany 54, 115–132.
| Aquifers: the ultimate groundwater-dependent ecosystems.Crossref | GoogleScholarGoogle Scholar |
Jane, S. F., Wilcox, T. M., McKelvey, K. S., Young, M. K., Schwartz, M. K., Lowe, W. H., Letcher, B. H., and Whiteley, A. R. (2015). Distance, flow and PCR inhibition: e DNA dynamics in two headwater streams. Molecular Ecology Resources 15, 216–227.
| Distance, flow and PCR inhibition: e DNA dynamics in two headwater streams.Crossref | GoogleScholarGoogle Scholar | 24890199PubMed |
Jo, T., and Minamoto, T. (2021). Complex interactions between environmental DNA (eDNA) state and water chemistries on eDNA persistence suggested by meta‐analyses. Molecular Ecology Resources 21, 1490–1503.
| Complex interactions between environmental DNA (eDNA) state and water chemistries on eDNA persistence suggested by meta‐analyses.Crossref | GoogleScholarGoogle Scholar | 33580561PubMed |
Korbel, K., Chariton, A., Stephenson, S., Greenfield, P., and Hose, G. C. (2017). Wells provide a distorted view of life in the aquifer: implications for sampling, monitoring and assessment of groundwater ecosystems. Scientific Reports 7, 40702.
| Wells provide a distorted view of life in the aquifer: implications for sampling, monitoring and assessment of groundwater ecosystems.Crossref | GoogleScholarGoogle Scholar | 28102290PubMed |
Kunadiya, M. B., Burgess, T. I. A., Dunstan, W., White, D., and Hardy, G. E. S. (2021). Persistence and degradation of Phytophthora cinnamomi DNA and RNA in different soil types. Environmental DNA 3, 92–104.
| Persistence and degradation of Phytophthora cinnamomi DNA and RNA in different soil types.Crossref | GoogleScholarGoogle Scholar |
Larned, S. T. (2012). Phreatic groundwater ecosystems: research frontiers for freshwater ecology. Freshwater Biology 57, 885–906.
| Phreatic groundwater ecosystems: research frontiers for freshwater ecology.Crossref | GoogleScholarGoogle Scholar |
Laroche, O., Wood, S. A., Tremblay, L. A., Lear, G., Ellis, J. I., and Pochon, X. (2017). Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities. PeerJ 5, e3347.
| Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities.Crossref | GoogleScholarGoogle Scholar | 28533985PubMed |
Leblanc, M., Tweed, S., Van Dijk, A., and Timbal, B. (2012). A review of historic and future hydrological changes in the Murray–Darling Basin. Global and Planetary Change 80–81, 226–246.
| A review of historic and future hydrological changes in the Murray–Darling Basin.Crossref | GoogleScholarGoogle Scholar |
Lopes, C. M., Baêta, D., Valentini, A., Lyra, M. L., Sabbag, A. F., Gasparini, J. L., Dejean, T., Haddad, C. F. B., and Zamudio, K. R. (2020). Lost and found: frogs in a biodiversity hotspot rediscovered with environmental DNA. Molecular Ecology 30, 3289–3298.
| 32786119PubMed |
Matsui, K., Honjo, M., and Kawabata, Z. (2001). Estimation of the fate of dissolved DNA in thermally stratified lake water from the stability of exogenous plasmid DNA. Aquatic Microbial Ecology 26, 95–102.
| Estimation of the fate of dissolved DNA in thermally stratified lake water from the stability of exogenous plasmid DNA.Crossref | GoogleScholarGoogle Scholar |
Meier, P., and Wackernagel, W. (2003). Monitoring the spread of recombinant DNA from field plots with transgenic sugar beet plants by PCR and natural transformation of Pseudomonas stutzeri. Transgenic Research 12, 293–304.
| Monitoring the spread of recombinant DNA from field plots with transgenic sugar beet plants by PCR and natural transformation of Pseudomonas stutzeri.Crossref | GoogleScholarGoogle Scholar | 12779118PubMed |
Moorhouse-Gann, R. J., Dunn, J. C., De Vere, N., Goder, M., Cole, N., Hipperson, H., and Symondson, W. O. (2018). New universal ITS2 primers for high-resolution herbivory analyses using DNA metabarcoding in both tropical and temperate zones. Scientific Reports 8, 8542.
| New universal ITS2 primers for high-resolution herbivory analyses using DNA metabarcoding in both tropical and temperate zones.Crossref | GoogleScholarGoogle Scholar | 29867115PubMed |
Murray–Darling Basin Authority (2017). Native vegetation 2017 Basin Plan evaluation. (MDBA: Canberra, ACT, Australia.) Available at https://www.mdba.gov.au/sites/default/files/pubs/BPE-tech-reports-vegetation-2.pdf
Nelson, T. (2020). Factors influencing groundwater microbial communities across an intensive agricultural landscape. M.Res. Thesis, Macquarie University, Sydney, NSW, Australia.
Ngugi, M. R., Neldner, V. J., Dowling, R. M., and Li, J. (2021). Recruitment and demographic structure of floodplain tree species in the Queensland Murray–Darling basin, Australia. Ecological Management & Restoration 23, 64–73.
Nielsen, K. M., Johnsen, P. J., Bensasson, D., and Daffonchio, D. (2007). Release and persistence of extracellular DNA in the environment. Environmental Biosafety Research 6, 37–53.
| Release and persistence of extracellular DNA in the environment.Crossref | GoogleScholarGoogle Scholar | 17961479PubMed |
Nørgaard, L., Olesen, C. R., Trøjelsgaard, K., Pertoldi, C., Nielsen, J. L., Taberlet, P., Ruiz-González, A., De Barba, M., and Iacolina, L. (2021). eDNA metabarcoding for biodiversity assessment, generalist predators as sampling assistants. Scientific Reports 11, 1–12.
Pang, L., Abeysekera, G., Hanning, K., Premaratne, A., Robson, B., Abraham, P., Sutton, R., Hanson, C., Hadfield, J., Heiligenthal, L., and Stone, D. (2020). Water tracking in surface water, groundwater and soils using free and alginate-chitosan encapsulated synthetic DNA tracers. Water Research 184, 116192.
| Water tracking in surface water, groundwater and soils using free and alginate-chitosan encapsulated synthetic DNA tracers.Crossref | GoogleScholarGoogle Scholar | 32731038PubMed |
Pawlowski, J., Kelly-Quinn, M., Altermatt, F., Apothéloz-Perret-Gentil, L., Beja, P., Boggero, A., Borja, A., Bouchez, A., Cordier, T., Domaizon, I., and Feio, M. J. (2018). The future of biotic indices in the ecogenomic era: integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems. The Science of the Total Environment 637–638, 1295–1310.
| The future of biotic indices in the ecogenomic era: integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems.Crossref | GoogleScholarGoogle Scholar | 29801222PubMed |
Pérez Hoyos, I. C., Krakauer, N. Y., Khanbilvardi, R., and Armstrong, R. A. (2016). A review of advances in the identification and characterization of groundwater dependent ecosystems using geospatial technologies. Geosciences 6, 17.
| A review of advances in the identification and characterization of groundwater dependent ecosystems using geospatial technologies.Crossref | GoogleScholarGoogle Scholar |
Pollitt, L. (2020). The detection of phreatophytic tree DNA in groundwater, and its environmental correlates. M.Res Thesis, Macquarie University, Sydney, NSW, Australia.
Poté, J., Ceccherini, M. T., Rosselli, W., Wildi, W., Simonet, P., and Vogel, T. M. (2003). Fate and transport of antibiotic resistance genes in saturated soil columns. European Journal of Soil Biology 39, 65–71.
| Fate and transport of antibiotic resistance genes in saturated soil columns.Crossref | GoogleScholarGoogle Scholar |
Poté, J., Rossé, P., Rosselli, W., and Wildi, W. (2005). Kinetics of mass and DNA decomposition in tomato leaves. Chemosphere 61, 677–684.
| Kinetics of mass and DNA decomposition in tomato leaves.Crossref | GoogleScholarGoogle Scholar | 15878608PubMed |
Poté, J., Rosselli, W., Wigger, A., and Wildi, W. (2007). Release and leaching of plant DNA in unsaturated soil column. Ecotoxicology and Environmental Safety 68, 293–298.
| Release and leaching of plant DNA in unsaturated soil column.Crossref | GoogleScholarGoogle Scholar | 17187857PubMed |
Poté, J., Ackermann, R., and Wildi, W. (2009a). Plant leaf mass loss and DNA release in freshwater sediments. Ecotoxicology and Environmental Safety 72, 1378–1383.
| Plant leaf mass loss and DNA release in freshwater sediments.Crossref | GoogleScholarGoogle Scholar | 19419763PubMed |
Poté, J., Mavingui, P., Navarro, E., Rosselli, W., Wildi, W., Simonet, P., and Vogel, T. M. (2009b). Extracellular plant DNA in Geneva groundwater and traditional artesian drinking water fountains. Chemosphere 75, 498–504.
| Extracellular plant DNA in Geneva groundwater and traditional artesian drinking water fountains.Crossref | GoogleScholarGoogle Scholar | 19171370PubMed |
Rees, H. C., Gough, K. C., Middleditch, D. J., Patmore, J. R., and Maddison, B. C. (2015). Applications and limitations of measuring environmental DNA as indicators of the presence of aquatic animals. Journal of Applied Ecology 52, 827–831.
| Applications and limitations of measuring environmental DNA as indicators of the presence of aquatic animals.Crossref | GoogleScholarGoogle Scholar |
Rosi-Marshall, E. J., Tank, J. L., Royer, T. V., Whiles, M. R., Evans-White, M., Chambers, C., Griffiths, N. A., Pokelsek, J., and Stephen, M. L. (2007). Toxins in transgenic crop byproducts may affect headwater stream ecosystems. Proceedings of the National Academy of Sciences of the United States of America 104, 16204–16208.
| Toxins in transgenic crop byproducts may affect headwater stream ecosystems.Crossref | GoogleScholarGoogle Scholar | 17923672PubMed |
Ruppert, K. M., Kline, R. J., and Rahman, M. S. (2019). Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: a systematic review in methods, monitoring, and applications of global eDNA. Global Ecology and Conservation 17, e00547.
| Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: a systematic review in methods, monitoring, and applications of global eDNA.Crossref | GoogleScholarGoogle Scholar |
Saccò, M., Guzik, M. T., van der Heyde, M., Nevill, P., Cooper, S. J., Austin, A. D., Coates, P. J., Allentoft, M. E., and White, N. E. (2022). eDNA in subterranean ecosystems: applications, technical aspects, and future prospects. The Science of the Total Environment 820, 153223.
| eDNA in subterranean ecosystems: applications, technical aspects, and future prospects.Crossref | GoogleScholarGoogle Scholar | 35063529PubMed |
Saito, T., and Doi, H. (2021a). A model and simulation of the influence of temperature and amplicon length on environmental DNA degradation rates: a meta-analysis approach. Frontiers in Ecology and Evolution 9, 623831.
| A model and simulation of the influence of temperature and amplicon length on environmental DNA degradation rates: a meta-analysis approach.Crossref | GoogleScholarGoogle Scholar |
Saito, T., and Doi, H. (2021b). Degradation modeling of water environmental DNA: experiments on multiple DNA sources in pond and seawater. Environmental DNA 3, 850–860.
| Degradation modeling of water environmental DNA: experiments on multiple DNA sources in pond and seawater.Crossref | GoogleScholarGoogle Scholar |
Stoeckle, B. C., Beggel, S., Cerwenka, A. F., Motivans, E., Kuehn, R., and Geist, J. (2017). A systematic approach to evaluate the influence of environmental conditions on eDNA detection success in aquatic ecosystems. PLoS One 12, e0189119.
| A systematic approach to evaluate the influence of environmental conditions on eDNA detection success in aquatic ecosystems.Crossref | GoogleScholarGoogle Scholar | 29220394PubMed |
Stone, E. L., and Kalisz, P. J. (1991). On the maximum extent of tree roots. Forest Ecology and Management 46, 59–102.
| On the maximum extent of tree roots.Crossref | GoogleScholarGoogle Scholar |
Strickler, K. M., Fremier, A. K., and Goldberg, C. S. (2015). Quantifying effects of UV-B, temperature, and pH on eDNA degradation in aquatic microcosms. Biological Conservation 183, 85–92.
| Quantifying effects of UV-B, temperature, and pH on eDNA degradation in aquatic microcosms.Crossref | GoogleScholarGoogle Scholar |
Taberlet, P., Gielly, L., Pautou, G., and Bouvet, J. (1991). Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology 17, 1105–1109.
| Universal primers for amplification of three non-coding regions of chloroplast DNA.Crossref | GoogleScholarGoogle Scholar | 1932684PubMed |
Taberlet, P., Coissac, E., Pompanon, F., Gielly, L., Miquel, C., Valentini, A., Vermat, T., Corthier, G., Brochmann, C., and Willerslev, E. (2007). Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Research 35, e14.
| Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding.Crossref | GoogleScholarGoogle Scholar | 17169982PubMed |
Taberlet, P., Coissac, E., Pompanon, F., Brochmann, C., and Willerslev, E. (2012). Towards next‐generation biodiversity assessment using DNA metabarcoding. Molecular Ecology 21, 2045–2050.
| Towards next‐generation biodiversity assessment using DNA metabarcoding.Crossref | GoogleScholarGoogle Scholar | 22486824PubMed |
Taberlet, P., Bonin, A., Coissac, E., and Zinger, L. (2018). DNA metabarcode choice and design. In ‘Environmental DNA: for Biodiversity Research and Monitoring’. pp. 1–5. (Oxford University Press.)
Thomsen, P. F., and Willerslev, E. (2015). Environmental DNA: an emerging tool in conservation for monitoring past and present biodiversity. Biological Conservation 183, 4–18.
| Environmental DNA: an emerging tool in conservation for monitoring past and present biodiversity.Crossref | GoogleScholarGoogle Scholar |
Thomsen, P. F., Kielgast, J., Iversen, L. L., Møller, P. R., Rasmussen, M., and Willerslev, E. (2012a). Detection of a diverse marine fish fauna using environmental DNA from seawater samples. PLoS One 7, e41732.
| Detection of a diverse marine fish fauna using environmental DNA from seawater samples.Crossref | GoogleScholarGoogle Scholar | 22952584PubMed |
Thomsen, P. F., Kielgast, J. O. S., Iversen, L. L., Wiuf, C., Rasmussen, M., Gilbert, M. T. P., Orlando, L., and Willerslev, E. (2012b). Monitoring endangered freshwater biodiversity using environmental DNA. Molecular Ecology 21, 2565–2573.
| Monitoring endangered freshwater biodiversity using environmental DNA.Crossref | GoogleScholarGoogle Scholar | 22151771PubMed |
Tomlinson, M., and Boulton, A. J. (2010). Ecology and management of subsurface groundwater dependent ecosystems in Australia: a review. Marine and Freshwater Research 61, 936–949.
| Ecology and management of subsurface groundwater dependent ecosystems in Australia: a review.Crossref | GoogleScholarGoogle Scholar |
Trebitz, A. S., Hoffman, J. C., Darling, J. A., Pilgrim, E. M., Kelly, J. R., Brown, E. A., Chadderton, W. L., Egan, S. P., Grey, E. K., Hashsham, S. A., and Klymus, K. E. (2017). Early detection monitoring for aquatic non-indigenous species: optimizing surveillance, incorporating advanced technologies, and identifying research needs. Journal of Environmental Management 202, 299–310.
| Early detection monitoring for aquatic non-indigenous species: optimizing surveillance, incorporating advanced technologies, and identifying research needs.Crossref | GoogleScholarGoogle Scholar | 28738203PubMed |
Turner, C. R., Barnes, M. A., Xu, C. C., Jones, S. E., Jerde, C. L., and Lodge, D. M. (2014). Particle size distribution and optimal capture of aqueous microbial eDNA. Methods in Ecology and Evolution 5, 676–684.
| Particle size distribution and optimal capture of aqueous microbial eDNA.Crossref | GoogleScholarGoogle Scholar |
van Engelenburg, J., Hueting, R., Rijpkema, S., Teuling, A. J., Uijlenhoet, R., and Ludwig, F. (2018). Impact of changes in groundwater extractions and climate change on groundwater-dependent ecosystems in a complex hydrogeological setting. Water Resources Management 32, 259–272.
| Impact of changes in groundwater extractions and climate change on groundwater-dependent ecosystems in a complex hydrogeological setting.Crossref | GoogleScholarGoogle Scholar |
von Ammon, U., Wood, S. A., Laroche, O., Zaiko, A., Lavery, S. D., Inglis, G. J., and Pochon, X. (2019). Linking environmental DNA and RNA for improved detection of the marine invasive fanworm Sabella spallanzanii. Frontiers in Marine Science 6, 621.
| Linking environmental DNA and RNA for improved detection of the marine invasive fanworm Sabella spallanzanii.Crossref | GoogleScholarGoogle Scholar |
Wacker, S., Fossøy, F., Larsen, B. M., Brandsegg, H., Sivertsgård, R., and Karlsson, S. (2019). Downstream transport and seasonal variation in freshwater pearl mussel (Margaritifera margaritifera) eDNA concentration. Environmental DNA 1, 64–73.
| Downstream transport and seasonal variation in freshwater pearl mussel (Margaritifera margaritifera) eDNA concentration.Crossref | GoogleScholarGoogle Scholar |
Wada, Y., Van Beek, L. P., Van Kempen, C. M., Reckman, J. W., Vasak, S., and Bierkens, M. F. (2010). Global depletion of groundwater resources. Geophysical Research Letters 37, L20402.
| Global depletion of groundwater resources.Crossref | GoogleScholarGoogle Scholar |
Walker, J., Bullen, F., and Williams, B. G. (1993). Ecohydrological changes in the Murray–Darling Basin. I. The number of trees cleared over two centuries. Journal of Applied Ecology 30, 265–273.
| Ecohydrological changes in the Murray–Darling Basin. I. The number of trees cleared over two centuries.Crossref | GoogleScholarGoogle Scholar |
Wood, S. A., Biessy, L., Latchford, J. L., Zaiko, A., von Ammon, U., Audrezet, F., Cristescu, M. E., and Pochon, X. (2020). Release and degradation of environmental DNA and RNA in a marine system. The Science of the Total Environment 704, 135314.
| Release and degradation of environmental DNA and RNA in a marine system.Crossref | GoogleScholarGoogle Scholar | 31780169PubMed |
Zencich, S. J., Froend, R. H., Turner, J. V., and Gailitis, V. (2002). Influence of groundwater depth on the seasonal sources of water accessed by Banksia tree species on a shallow, sandy coastal aquifer. Oecologia 131, 8–19.
| Influence of groundwater depth on the seasonal sources of water accessed by Banksia tree species on a shallow, sandy coastal aquifer.Crossref | GoogleScholarGoogle Scholar | 28547514PubMed |
Zhu, B. (2006). Degradation of plasmid and plant DNA in water microcosms monitored by natural transformation and real-time polymerase chain reaction (PCR). Water Research 40, 3231–3238.
| Degradation of plasmid and plant DNA in water microcosms monitored by natural transformation and real-time polymerase chain reaction (PCR).Crossref | GoogleScholarGoogle Scholar | 16945402PubMed |
Zinger, L., Chave, J., Coissac, E., Iribar, A., Louisanna, E., Manzi, S., Schilling, V., Schimann, H., Sommeria-Klein, G., and Taberlet, P. (2016). Extracellular DNA extraction is a fast, cheap and reliable alternative for multi-taxa surveys based on soil DNA. Soil Biology & Biochemistry 96, 16–19.
| Extracellular DNA extraction is a fast, cheap and reliable alternative for multi-taxa surveys based on soil DNA.Crossref | GoogleScholarGoogle Scholar |
Zinger, L., Bonin, A., Alsos, I. G., Bálint, M., Bik, H., Boyer, F., Chariton, A. A., Creer, S., Coissac, E., Deagle, B. E., and De Barba, M. (2019). DNA metabarcoding: need for robust experimental designs to draw sound ecological conclusions. Molecular Ecology 28, 1857–1862.
| DNA metabarcoding: need for robust experimental designs to draw sound ecological conclusions.Crossref | GoogleScholarGoogle Scholar | 31033079PubMed |