Journal Article
Taking eDNA underground: factors affecting eDNA detection of subterranean fauna in groundwater
van der Heyde, M., White, N.E., Nevill, P., Austin, A.D., Stevens, N., Jones, M. and Guzik, M.T.
Record Number:
6137
Year:
2023
Journal:
Molecular Ecology
Pages:
yy
Volume:
xx
Notes:
This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process which may lead to differences between this version and the Version of Record.
Abstract:
Stygofauna are aquatic fauna that have evolved to live underground. The impacts of
anthropogenic climate change, extraction and pollution on groundwater pose major threats to
groundwater health, prompting the need for efficient and reliable means to detect and monitor
stygofaunal communities. Conventional survey techniques for these species rely on
morphological identification and can be biased, labour intensive, and often indeterminate to
lower taxonomic levels. By contrast, environmental DNA (eDNA)-based methods have the
potential to dramatically improve on existing stygofaunal survey methods in a large range of
habitats and for all life stages, reducing the need for the destructive manual collection of
often critically endangered species or specialized taxonomic expertise. We compared eDNA
and haul-net samples collected in 2020 and 2021 from 19 groundwater bores and a cave on
Barrow Island, located north-west of Western Australia, and assessed how sampling factors influenced the quality of eDNA detection of stygofauna. The two detection methods were
complementary, eDNA metabarcoding was able to detect soft-bodied taxa and fish often
missed by nets, but only detected seven of the nine stygofaunal crustacean orders identified
from haul-net specimens. Our results also indicated that eDNA metabarcoding could detect
54-100% of stygofauna from shallow water samples and 82-90% from sediment samples.
However, there was significant variation in stygofaunal diversity between sample years and
sampling types. The findings of this study demonstrate that haul net sampling has a tendency
to underestimate stygofaunal diversity and that eDNA metabarcoding of groundwater can
substantially improve efficiency of stygofaunal surveys
Times Cited:
3
Relevent Species:
Related Records:
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Halse, S. (2018)Subterranean fauna of the arid zone
Halse, S. (2018)Subterranean fauna of the arid zone
Page, T.J.,Stevens, M.I., Adams, M., Foster, R. Velasco-Castrillón, A. and Humphreys, W.F. (2018)Multiple molecular markers reinforce the systematic framework of unique Australian cave fishes (Milyeringa : Gobioidei)
Page, T.J.,Stevens, M.I., Adams, M., Foster, R. Velasco-Castrillón, A. and Humphreys, W.F. (2018)Multiple molecular markers reinforce the systematic framework of unique Australian cave fishes (Milyeringa : Gobioidei)
Page, T.J.,Stevens, M.I., Adams, M., Foster, R. Velasco-Castrillón, A. and Humphreys, W.F. (2018)Multiple molecular markers reinforce the systematic framework of unique Australian cave fishes (Milyeringa : Gobioidei)
Perina, G., Camacho, A.I., Huey, J., Horwitz, P., and Koenders, A. (2018)Understanding subterranean variability: the first genus of Bathynellidae (Bathynellacea, Crustacea) from Western Australia described through a morphological and multigene approach
Perina, G., Camacho, A.I., Huey, J., Horwitz, P., and Koenders, A. (2018)Understanding subterranean variability: the first genus of Bathynellidae (Bathynellacea, Crustacea) from Western Australia described through a morphological and multigene approach
Perina, G., Camacho, A.I., Huey, J., Horwitz, P., and Koenders, A. (2018)Understanding subterranean variability: the first genus of Bathynellidae (Bathynellacea, Crustacea) from Western Australia described through a morphological and multigene approach
Moore, G.I. (2018)New morphological data and live photographs of the rare subterranean blind cave eel Ophisternon candidum (Synbranchidae) from north‑western Australia
Moore, G.I., Humphreys, W.F. and Foster, R. (2018)New populations of the rare subterranean Blind Cave Eel Ophisternon candidum (Synbranchidae) reveal recent historical connections throughout northwestern Australia
Moore, G.I. (2018)New morphological data and live photographs of the rare subterranean blind cave eel Ophisternon candidum (Synbranchidae) from north‑western Australia
Moore, G.I., Humphreys, W.F. and Foster, R. (2018)New populations of the rare subterranean Blind Cave Eel Ophisternon candidum (Synbranchidae) reveal recent historical connections throughout northwestern Australia
Moore, G.I. (2018)New morphological data and live photographs of the rare subterranean blind cave eel Ophisternon candidum (Synbranchidae) from north‑western Australia
Perina, G., Camacho, A.I., Huey, J., Horwitz, P. and Koenders, A. (2019)New Bathynellidae (Crustacea) taxa and their relationships in the Fortescue catchment aquifers of the Pilbara region, Western Australia, Systematics and Biodiversity
Perina, G., Camacho, A.I., Huey, J., Horwitz, P. and Koenders, A. (2019)New Bathynellidae (Crustacea) taxa and their relationships in the Fortescue catchment aquifers of the Pilbara region, Western Australia, Systematics and Biodiversity
Perina, G., Camacho, A.I., Huey, J., Horwitz, P. and Koenders, A. (2019)New Bathynellidae (Crustacea) taxa and their relationships in the Fortescue catchment aquifers of the Pilbara region, Western Australia, Systematics and Biodiversity
Perina, G., Camacho, A., Huey, J., Horwitz, P. and Koenders, A. (2019)The role of allopatric speciation and ancient origins of Bathynellidae (Crustacea) in the Pilbara (Western Australia): two new genera from the De Grey River catchment
Perina, G., Camacho, A., Huey, J., Horwitz, P. and Koenders, A. (2019)The role of allopatric speciation and ancient origins of Bathynellidae (Crustacea) in the Pilbara (Western Australia): two new genera from the De Grey River catchment
Perina, G., Camacho, A., Huey, J., Horwitz, P. and Koenders, A. (2019)The role of allopatric speciation and ancient origins of Bathynellidae (Crustacea) in the Pilbara (Western Australia): two new genera from the De Grey River catchment
Matthews, E.F., Abrams, K.M., Cooper, S.J.B., Huey, J.A., Hillyer, M.J., Humphreys, W.F., Austin, A.D. and Guzik, M.T. (2019)Scratching the surface of subterranean biodiversity: molecular analysis reveals a diverse and previously unknown fauna of Parabathynellidae (Crustacea: Bathynellacea) from the Pilbara, Western Australia
Matthews, E.F., Abrams, K.M., Cooper, S.J.B., Huey, J.A., Hillyer, M.J., Humphreys, W.F., Austin, A.D. and Guzik, M.T. (2019)Scratching the surface of subterranean biodiversity: molecular analysis reveals a diverse and previously unknown fauna of Parabathynellidae (Crustacea: Bathynellacea) from the Pilbara, Western Australia
Matthews, E.F., Abrams, K.M., Cooper, S.J.B., Huey, J.A., Hillyer, M.J., Humphreys, W.F., Austin, A.D. and Guzik, M.T. (2019)Scratching the surface of subterranean biodiversity: molecular analysis reveals a diverse and previously unknown fauna of Parabathynellidae (Crustacea: Bathynellacea) from the Pilbara, Western Australia
Perina, G. (2019)Ancient origins of a diverse stygofaunal group: The Australian Bathynellidae (Crustacea)
Perina, G. (2019)Ancient origins of a diverse stygofaunal group: The Australian Bathynellidae (Crustacea)
Perina, G. (2019)Ancient origins of a diverse stygofaunal group: The Australian Bathynellidae (Crustacea)
Moore, G. (2019)Milyeringa justitia. Barrow Island cave gudgeon. The IUCN Red List of Threatened Species 2019: e.T128969918A128970120
Shelley, J.J., Swearer, S.E., Dempster, T., Adams, M., Le Feuvre, M.C., Hammer, M.P. and Unmack, P.J. (2020)Plio-Pleistocene sea-level changes drive speciation of freshwater fishes in north-western Australia
Shelley, J.J., Swearer, S.E., Dempster, T., Adams, M., Le Feuvre, M.C., Hammer, M.P. and Unmack, P.J. (2020)Plio-Pleistocene sea-level changes drive speciation of freshwater fishes in north-western Australia
Lintermans, M., Geyle, H.M., Beatty, S., Brown, C., Ebner, B.C., Freeman, R., Hammer, M.P., Humphreys, W.F., Kennard, M.J., Kern, P., Martin, K., Morgan, D.L., Raadik, T.A., Unmack, P.J., Wager, R., Woinarski, J.C.Z. and Garnett, S.T. (2020)Big trouble for little fish: identifying Australian freshwater fishes in imminent risk of extinction
Shelley, J.J., Swearer, S.E., Dempster, T., Adams, M., Le Feuvre, M.C., Hammer, M.P. and Unmack, P.J. (2020)Plio-Pleistocene sea-level changes drive speciation of freshwater fishes in north-western Australia
Lintermans, M., Geyle, H.M., Beatty, S., Brown, C., Ebner, B.C., Freeman, R., Hammer, M.P., Humphreys, W.F., Kennard, M.J., Kern, P., Martin, K., Morgan, D.L., Raadik, T.A., Unmack, P.J., Wager, R., Woinarski, J.C.Z. and Garnett, S.T. (2020)Big trouble for little fish: identifying Australian freshwater fishes in imminent risk of extinction
Lintermans, M., Geyle, H.M., Beatty, S., Brown, C., Ebner, B.C., Freeman, R., Hammer, M.P., Humphreys, W.F., Kennard, M.J., Kern, P., Martin, K., Morgan, D.L., Raadik, T.A., Unmack, P.J., Wager, R., Woinarski, J.C.Z. and Garnett, S.T. (2020)Big trouble for little fish: identifying Australian freshwater fishes in imminent risk of extinction
White, N.E., Guzik, M.T., Austin, A.D., Moore, G.I. Humphreys, W.F., Alexander, J. and Bunce, M. (2020)Detection of rare Australian endemic blind cave eel (Ophisternon candidum) with environmental DNA: implications for threatened species management in subterranean environments
White, N.E., Guzik, M.T., Austin, A.D., Moore, G.I. Humphreys, W.F., Alexander, J. and Bunce, M. (2020)Detection of rare Australian endemic blind cave eel (Ophisternon candidum) with environmental DNA: implications for threatened species management in subterranean environments
White, N.E., Guzik, M.T., Austin, A.D., Moore, G.I. Humphreys, W.F., Alexander, J. and Bunce, M. (2020)Detection of rare Australian endemic blind cave eel (Ophisternon candidum) with environmental DNA: implications for threatened species management in subterranean environments
Eberhard, S.M. and Howarth, F.G. (2021)Undara lava cave fauna in tropical Queensland with an annotated list of Australian subterranean biodiversity hotspots
Eberhard, S.M. and Howarth, F.G. (2021)Undara lava cave fauna in tropical Queensland with an annotated list of Australian subterranean biodiversity hotspots
Eberhard, S.M. and Howarth, F.G. (2021)Undara lava cave fauna in tropical Queensland with an annotated list of Australian subterranean biodiversity hotspots
Tian, H., Hu, Q., Lu, H. and Li, Z. (2021)The complete mitochondrial genome of one breeding strain of Asian swamp eel (Monopterus albus, Zuiew 1793) using PacBio and Illumina sequencing technologies
and phylogenetic analysis in synbranchiformes
Saccò, M., Guzik, M.T., van der Heyde, M., Nevill, P., Cooper, S.J.B., Austin, A.D., Coates, P.J. and Allentoft, M.E. (2022)eDNA in subterranean ecosystems: Applications, technical aspects, and future prospects
Gierl, C., Dohrmann, M., Keith, P., Humphreys, W.J., Esmaeili, H.R., Vukić, J., Radek, S. and ReichenbacherI, B. (2022)An integrative phylogenetic approach for inferring relationships of fossil gobioids (Teleostei: Gobiiformes)
Saccò, M., Blyth, A.J., Douglas, G., Humphreys, W.F., Hose, G.C., Davis, J., Guzik, M.T., Martínez, A., Eberhard, S.M. and Halse, S.A. (2022)Stygofaunal diversity and ecological sustainability of coastal groundwater ecosystems in a changing climate: The Australian paradigm
Gierl, C., Dohrmann, M., Keith, P., Humphreys, W.J., Esmaeili, H.R., Vukić, J., Radek, S. and ReichenbacherI, B. (2022)An integrative phylogenetic approach for inferring relationships of fossil gobioids (Teleostei: Gobiiformes)
Saccò, M., Blyth, A.J., Douglas, G., Humphreys, W.F., Hose, G.C., Davis, J., Guzik, M.T., Martínez, A., Eberhard, S.M. and Halse, S.A. (2022)Stygofaunal diversity and ecological sustainability of coastal groundwater ecosystems in a changing climate: The Australian paradigm
Saccò, M., Blyth, A.J., Douglas, G., Humphreys, W.F., Hose, G.C., Davis, J., Guzik, M.T., Martínez, A., Eberhard, S.M. and Halse, S.A. (2022)Stygofaunal diversity and ecological sustainability of coastal groundwater ecosystems in a changing climate: The Australian paradigm
Saccò, M., Guzik, M.T., van der Heyde, M., Nevill, P., Cooper, S.J.B., Austin, A.D., Coates, P.J. and Allentoft, M.E. (2022)eDNA in subterranean ecosystems: Applications, technical aspects, and future prospects
Saccò, M., Guzik, M.T., van der Heyde, M., Nevill, P., Cooper, S.J.B., Austin, A.D., Coates, P.J. and Allentoft, M.E. (2022)eDNA in subterranean ecosystems: Applications, technical aspects, and future prospects
van der Heyde, M., White, N.E., Nevill, P., Austin, A.D., Stevens, N., Jones, M. and Guzik, M.T. (2023)Taking eDNA underground: factors affecting eDNA detection of subterranean fauna in groundwater
Thacker, C.E., McCraney, W.T., Harrington, R.C., Near, T.J., Shelley, J.J., Adams, M., Hammer, M.P. and Unmack, P.J. (2023)Diversification of the sleepers (Gobiiformes: Gobioidei: Eleotridae) and evolution of the root gobioid families
Thacker, C.E., McCraney, W.T., Harrington, R.C., Near, T.J., Shelley, J.J., Adams, M., Hammer, M.P. and Unmack, P.J. (2023)Diversification of the sleepers (Gobiiformes: Gobioidei: Eleotridae) and evolution of the root gobioid families
Webb, J.A., White, S.Q. and Smith, G.K. (2023)Australian caves and karst systems
Webb, J.A., White, S.Q. and Smith, G.K. (2023)Australian caves and karst systems
Webb, J.A., White, S.Q. and Smith, G.K. (2023)Australian caves and karst systems
White, S.Q., Brooks, D. and Webb, J.A. (2023)Cape Range
White, S.Q., Brooks, D. and Webb, J.A. (2023)Cape Range
White, S.Q., Brooks, D. and Webb, J.A. (2023)Cape Range
van der Heyde, M., Alexander, J., Nevill, P., Austin, A.D., Stevens, N., Jones, M. and Guzik, M.T. (2023)Rapid detection of subterranean fauna from passive sampling of groundwater eDNA
van der Heyde, M., Alexander, J., Nevill, P., Austin, A.D., Stevens, N., Jones, M. and Guzik, M.T. (2023)Rapid detection of subterranean fauna from passive sampling of groundwater eDNA
van der Heyde, M., White, N.E., Nevill, P., Austin, A.D., Stevens, N., Jones, M. and Guzik, M.T. (2023)Taking eDNA underground: factors affecting eDNA detection of subterranean fauna in groundwater
van der Heyde, M., Alexander, J., Nevill, P., Austin, A.D., Stevens, N., Jones, M. and Guzik, M.T. (2023)Rapid detection of subterranean fauna from passive sampling of groundwater eDNA
van der Heyde, M., White, N.E., Nevill, P., Austin, A.D., Stevens, N., Jones, M. and Guzik, M.T. (2023)Taking eDNA underground: factors affecting eDNA detection of subterranean fauna in groundwater