Journal Article
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.
Record Number:
6324
Year:
2023
Journal:
Environmental DNA
Pages:
1-14
Volume:
xx
Notes:
This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited
Abstract:
Groundwater is an essential source of freshwater that supports surface ecosystems
as well as organisms adapted to living underground. The impacts of anthropogenic
climate change, extraction, and pollution pose major threats to groundwater ecosystem
health, prompting a need for efficient and reliable means to detect and monitor
subterranean faunal communities. Conventional survey of subterranean fauna relies
on the collection of organisms for morphological identification, which can be biased,
labor intensive, and often indeterminate at lower taxonomic levels. Environmental
DNA (eDNA)-based methods can dramatically improve on stygofaunal surveys, but
currently rely on time consuming active water filtration that limits the number of samples
that can be processed. Passive eDNA sampling, which involves submersion of
absorbent material (e.g. filter membrane, sponge etc.) into the sampled environment
for a fixed period, has shown promise as a viable alternative to active filtration in
aquatic ecosystems and may be applicable to groundwater systems. Here, we compared
groundwater eDNA collected from active pump filtered water samples, membranes
submerged in water for 10 min and 24 h, and haul-net samples morphologically
identified from bores at two geographically distinct locations in Western Australia.
Our results show that while the relative abundance of eDNA in groundwater (measured
through qPCR) is 100–800 times lower in passive samples, the species richness
detected is comparable between passive and active eDNA collection. Additionally,
standard metabarcoding assays (18S and COI) of passive eDNA samples detected
most subterranean orders identified morphologically (12/17), and this proportion may
be improved with increased sampling and application of DNA extraction methods that
increase DNA yield. Our findings demonstrate that passive eDNA sample collection is
a non-invasive survey method with the potential to improve the efficiency and replication
level of stygofaunal surveys but will benefit from further development.
Times Cited:
3
Relevent Species:
Related Records:
Whitley, G. P. (1945)
New sharks and fishes from Western Australia. Part 2
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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
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
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
Page, T.J., Hughes, J.M., Real, K.M., Stevens, M.I., King, R.A. and Humphreys, W.F. (2018)Allegory of a cave crustacean: systematic and biogeographic reality of Halosbaena (Peracarida: Thermosbaenacea) sought with molecular data at multiple scales
Page, T.J., Hughes, J.M., Real, K.M., Stevens, M.I., King, R.A. and Humphreys, W.F. (2018)Allegory of a cave crustacean: systematic and biogeographic reality of Halosbaena (Peracarida: Thermosbaenacea) sought with molecular data at multiple scales
Page, T.J., Hughes, J.M., Real, K.M., Stevens, M.I., King, R.A. and Humphreys, W.F. (2018)Allegory of a cave crustacean: systematic and biogeographic reality of Halosbaena (Peracarida: Thermosbaenacea) sought with molecular data at multiple scales
Kuang, T., Tornabene, L., Lia, J., Jiang, J., Chakrabarty, P., Sparks, J.S., Naylor, G.J.P. and Lia, C. (2018)Phylogenomic analysis on the exceptionally diverse fish clade Gobioidei (Actinopterygii: Gobiiformes) and data-filtering based on molecular clocklikeness
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
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
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
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
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
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
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
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)
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., 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
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., 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., 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
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., 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