Taking eDNA underground : Factors affecting eDNA detection of subterranean fauna in groundwater
© 2023 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd..
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 for 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, northwest 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 the efficiency of stygofaunal surveys.
| Medienart: |
E-Artikel |
|---|
| Erscheinungsjahr: |
2023 |
|---|---|
| Erschienen: |
2023 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:23 |
|---|---|
| Enthalten in: |
Molecular ecology resources - 23(2023), 6 vom: 31. Aug., Seite 1257-1274 |
| Sprache: |
Englisch |
|---|
| Beteiligte Personen: |
van der Heyde, Mieke [VerfasserIn] |
|---|
| Links: |
|---|
| Themen: |
Crustaceans |
|---|
| Anmerkungen: |
Date Completed 06.07.2023 Date Revised 06.07.2023 published: Print-Electronic Citation Status MEDLINE |
|---|
| doi: |
10.1111/1755-0998.13792 |
|---|
| funding: |
|
|---|---|
| Förderinstitution / Projekttitel: |
|
| PPN (Katalog-ID): |
NLM355045109 |
|---|
| LEADER | 01000naa a22002652 4500 | ||
|---|---|---|---|
| 001 | NLM355045109 | ||
| 003 | DE-627 | ||
| 005 | 20231226063522.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 231226s2023 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.1111/1755-0998.13792 |2 doi | |
| 028 | 5 | 2 | |a pubmed24n1183.xml |
| 035 | |a (DE-627)NLM355045109 | ||
| 035 | |a (NLM)36999608 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
| 041 | |a eng | ||
| 100 | 1 | |a van der Heyde, Mieke |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Taking eDNA underground |b Factors affecting eDNA detection of subterranean fauna in groundwater |
| 264 | 1 | |c 2023 | |
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a ƒaComputermedien |b c |2 rdamedia | ||
| 338 | |a ƒa Online-Ressource |b cr |2 rdacarrier | ||
| 500 | |a Date Completed 06.07.2023 | ||
| 500 | |a Date Revised 06.07.2023 | ||
| 500 | |a published: Print-Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a © 2023 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd. | ||
| 520 | |a 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 for 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, northwest 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 the efficiency of stygofaunal surveys | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Crustaceans | |
| 650 | 4 | |a Stygofauna | |
| 650 | 4 | |a environmental DNA | |
| 650 | 4 | |a invertebrates | |
| 650 | 4 | |a subterranean Fauna | |
| 650 | 7 | |a DNA, Environmental |2 NLM | |
| 700 | 1 | |a White, Nicole E |e verfasserin |4 aut | |
| 700 | 1 | |a Nevill, Paul |e verfasserin |4 aut | |
| 700 | 1 | |a Austin, Andrew D |e verfasserin |4 aut | |
| 700 | 1 | |a Stevens, Nicholas |e verfasserin |4 aut | |
| 700 | 1 | |a Jones, Matt |e verfasserin |4 aut | |
| 700 | 1 | |a Guzik, Michelle T |e verfasserin |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t Molecular ecology resources |d 2008 |g 23(2023), 6 vom: 31. Aug., Seite 1257-1274 |w (DE-627)NLM206871481 |x 1755-0998 |7 nnns |
| 773 | 1 | 8 | |g volume:23 |g year:2023 |g number:6 |g day:31 |g month:08 |g pages:1257-1274 |
| 856 | 4 | 0 | |u http://dx.doi.org/10.1111/1755-0998.13792 |3 Volltext |
| 912 | |a GBV_USEFLAG_A | ||
| 912 | |a GBV_NLM | ||
| 951 | |a AR | ||
| 952 | |d 23 |j 2023 |e 6 |b 31 |c 08 |h 1257-1274 | ||