The true picture of environmental DNA, a case study in harvested fishponds
The application of environmental DNA (eDNA) metabarcoding has revolutionised large scale biodiversity monitoring of aquatic ecosystems. Validation studies have been performed mainly in laboratories and mesocosm experiments, however large-scale field experiments are necessary to verify the robustness...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-09-01
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| Series: | Ecological Indicators |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1470160X22007130 |
| _version_ | 1817999083408719872 |
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| author | Petr Blabolil Nathan P. Griffiths Bernd Hänfling Tomáš Jůza Vladislav Draštík Jelena Knežević-Jarić Romulo dos Santos Tomáš Mrkvička Jiří Peterka |
| author_facet | Petr Blabolil Nathan P. Griffiths Bernd Hänfling Tomáš Jůza Vladislav Draštík Jelena Knežević-Jarić Romulo dos Santos Tomáš Mrkvička Jiří Peterka |
| author_sort | Petr Blabolil |
| collection | DOAJ |
| description | The application of environmental DNA (eDNA) metabarcoding has revolutionised large scale biodiversity monitoring of aquatic ecosystems. Validation studies have been performed mainly in laboratories and mesocosm experiments, however large-scale field experiments are necessary to verify the robustness of eDNA based monitoring for more specific applications and different environmental conditions. Here, eDNA samples were collected from three fishponds with high fish density and broad species diversity during summer and autumn. This sampling design included a large number of spatial replicates evenly spaced across the pond surface and samples from the inflow, while pooled samples were used to test the effect of filtration volumes on detectability. Most common species were detected using eDNA, but rare species were often missed out under these high stocking densities. Average read counts and site occupancy positively correlated strongly with species abundance and biomass, with the exception of samples affected by PCR inhibition. Higher diversity detections were observed in autumn compared to summer samplings and in running compared to standing water. Fish communities detected in pooled samples reflect the overall community structure, and the species detectability increases with higher filtration volumes. This work highlights how eDNA based surveys can be optimised based on sampling conditions to achieve the highest overall detection, which has important implications for applying this method to aid management and policy initiatives. |
| first_indexed | 2024-04-14T03:03:15Z |
| format | Article |
| id | doaj.art-fb2fc411053244a78aaa922046f9d915 |
| institution | Directory Open Access Journal |
| issn | 1470-160X |
| language | English |
| last_indexed | 2024-04-14T03:03:15Z |
| publishDate | 2022-09-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Ecological Indicators |
| spelling | doaj.art-fb2fc411053244a78aaa922046f9d9152022-12-22T02:15:51ZengElsevierEcological Indicators1470-160X2022-09-01142109241The true picture of environmental DNA, a case study in harvested fishpondsPetr Blabolil0Nathan P. Griffiths1Bernd Hänfling2Tomáš Jůza3Vladislav Draštík4Jelena Knežević-Jarić5Romulo dos Santos6Tomáš Mrkvička7Jiří Peterka8Biology Centre CAS, Institute of Hydrobiology, Na Sádkách 7, České Budějovice 370 05, Czech Republic; University of South Bohemia in České Budějovice, Faculty of Science, Branišovská 1760, 370 05 České Budějovice, Czech Republic; Corresponding author at: Biology Centre CAS, Institute of Hydrobiology, Na Sádkách 7, České Budějovice 370 05, Czech Republic.University of Hull, School of Biological and Marine Sciences, EvoHull, Hull HU6 7RX, UKUniversity of Hull, School of Biological and Marine Sciences, EvoHull, Hull HU6 7RX, UK; University of the Highlands and Islands, 12b Ness Walk, Inverness IV3 5SQ, UKBiology Centre CAS, Institute of Hydrobiology, Na Sádkách 7, České Budějovice 370 05, Czech RepublicBiology Centre CAS, Institute of Hydrobiology, Na Sádkách 7, České Budějovice 370 05, Czech RepublicBiology Centre CAS, Institute of Hydrobiology, Na Sádkách 7, České Budějovice 370 05, Czech RepublicBiology Centre CAS, Institute of Hydrobiology, Na Sádkách 7, České Budějovice 370 05, Czech Republic; University of South Bohemia in České Budějovice, Faculty of Science, Branišovská 1760, 370 05 České Budějovice, Czech RepublicUniversity of South Bohemia in České Budějovice, Faculty of Economics Studentská 13, 370 05 České Budějovice, Czech RepublicBiology Centre CAS, Institute of Hydrobiology, Na Sádkách 7, České Budějovice 370 05, Czech RepublicThe application of environmental DNA (eDNA) metabarcoding has revolutionised large scale biodiversity monitoring of aquatic ecosystems. Validation studies have been performed mainly in laboratories and mesocosm experiments, however large-scale field experiments are necessary to verify the robustness of eDNA based monitoring for more specific applications and different environmental conditions. Here, eDNA samples were collected from three fishponds with high fish density and broad species diversity during summer and autumn. This sampling design included a large number of spatial replicates evenly spaced across the pond surface and samples from the inflow, while pooled samples were used to test the effect of filtration volumes on detectability. Most common species were detected using eDNA, but rare species were often missed out under these high stocking densities. Average read counts and site occupancy positively correlated strongly with species abundance and biomass, with the exception of samples affected by PCR inhibition. Higher diversity detections were observed in autumn compared to summer samplings and in running compared to standing water. Fish communities detected in pooled samples reflect the overall community structure, and the species detectability increases with higher filtration volumes. This work highlights how eDNA based surveys can be optimised based on sampling conditions to achieve the highest overall detection, which has important implications for applying this method to aid management and policy initiatives.http://www.sciencedirect.com/science/article/pii/S1470160X22007130BiodiversityeDNAEnvironmental parametersFish communityFreshwater |
| spellingShingle | Petr Blabolil Nathan P. Griffiths Bernd Hänfling Tomáš Jůza Vladislav Draštík Jelena Knežević-Jarić Romulo dos Santos Tomáš Mrkvička Jiří Peterka The true picture of environmental DNA, a case study in harvested fishponds Ecological Indicators Biodiversity eDNA Environmental parameters Fish community Freshwater |
| title | The true picture of environmental DNA, a case study in harvested fishponds |
| title_full | The true picture of environmental DNA, a case study in harvested fishponds |
| title_fullStr | The true picture of environmental DNA, a case study in harvested fishponds |
| title_full_unstemmed | The true picture of environmental DNA, a case study in harvested fishponds |
| title_short | The true picture of environmental DNA, a case study in harvested fishponds |
| title_sort | true picture of environmental dna a case study in harvested fishponds |
| topic | Biodiversity eDNA Environmental parameters Fish community Freshwater |
| url | http://www.sciencedirect.com/science/article/pii/S1470160X22007130 |
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