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eDNA as a tool for non-invasive monitoring of the fauna of a turbid, well-mixed system, the Elbe estuary in Germany
- Source :
- PLoS ONE, Vol 16, Iss 4, p e0250452 (2021), PLoS ONE
- Publication Year :
- 2021
- Publisher :
- Public Library of Science (PLoS), 2021.
-
Abstract
- The Elbe is one of the longest European rivers and features a large, turbid and well-mixed estuary, which runs through the inner city of Hamburg. The Elbe has been closely monitored using classical catch techniques in the past. Here we tested a COI-based eDNA approach for assessing the biodiversity within the Elbe. We sampled three stations in the Elbe, included low and high tide events, as well as two adjoining lakes to compare the recovered faunas. To analyze the data, we employed two different pipelines: the automated mBRAVE pipeline utilizing the BOLD database and one including NCBI BLAST. The number of OTUs with species or higher-level identifications were similar between both approaches with 352 OTUs and 355 OTUs for BLAST and mBRAVE, respectively, however, BLAST searches recovered another 942 unidentified metazoan OTUs. Many taxa were well represented; however, fish species were poorly represented, especially in the Elbe estuary samples. This could be a result of the universal COI primers, which also yielded high read numbers for non-metazoan OTUs, and small-bodies taxa like Rotifera, which might have been sampled together with the eDNA. Our results show a strong tidal influence on the recovered taxa. During low tide, downstream stations resembled sites further upstream, but the former showed a very different OTU composition during high tide and early tide. Such differences might be due to varying impacts of upstream-originating eDNA during tide cycles. Such factors need to be considered when routinely employing eDNA for monitoring programs.
- Subjects :
- Fauna
Biodiversity
Marine and Aquatic Sciences
Artificial Gene Amplification and Extension
Tides
Polymerase Chain Reaction
Germany
Data Management
Multidisciplinary
geography.geographical_feature_category
biology
Physics
Database and informatics methods
Sequence analysis
Fishes
Eukaryota
Freshwater Fish
Geophysics
Oceanography
Physical Sciences
Vertebrates
Freshwater fish
Medicine
Taxonomy (biology)
Estuaries
Research Article
Freshwater Environments
Environmental Monitoring
Computer and Information Sciences
Bioinformatics
Science
Mixed systems
Rivers
Surface Water
Animals
DNA Barcoding, Taxonomic
Molecular Biology Techniques
Molecular Biology
BLAST algorithm
Taxonomy
Invertebrate
geography
Ecology and Environmental Sciences
Organisms
Biology and Life Sciences
Aquatic Environments
Estuary
Bodies of Water
biology.organism_classification
Research and analysis methods
Lakes
Fish
Taxon
Earth Sciences
Hydrology
Zoology
Subjects
Details
- Language :
- English
- ISSN :
- 19326203
- Volume :
- 16
- Issue :
- 4
- Database :
- OpenAIRE
- Journal :
- PLoS ONE
- Accession number :
- edsair.doi.dedup.....6ebf3e367548703384f8e982f432bc12