Application of molecular tools to update aquatic ecotoxicology monitoring
The field of aquatic ecotoxicology studies the structural and functional disturbances induced in the short, medium, and long-term by contamination factors on ecological aquatic systems. Traditionally, organisms selected for the ecotoxicity studies are identified morphologically. Zooplankton communit...
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| Format: | Thesis (University of Nottingham only) |
| Language: | English |
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2024
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| Online Access: | https://eprints.nottingham.ac.uk/79437/ |
| _version_ | 1848801117534683136 |
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| author | Manfredi, Valeria |
| author_facet | Manfredi, Valeria |
| author_sort | Manfredi, Valeria |
| building | Nottingham Research Data Repository |
| collection | Online Access |
| description | The field of aquatic ecotoxicology studies the structural and functional disturbances induced in the short, medium, and long-term by contamination factors on ecological aquatic systems. Traditionally, organisms selected for the ecotoxicity studies are identified morphologically. Zooplankton communities are frequently employed as indicators of ecological shifts in water quality, serving to monitor such changes (Hemraj et al., 2017; Parmar et al., 2016). Because of their quick and prolific reproduction, zooplankton respond promptly to environmental alterations (Parmar et al., 2016), although they are still poorly studied.
This study aimed to apply conventional microscopy and metabarcoding detection to identify and quantify the zooplankton genera that are known indicators within mesocosms. Protocols for the identification of zooplankton genera by metabarcoding were developed. Within a mesocosm system, both methods were used to monitor seasonal changes in communities and also applied to an ecotoxicity trial using the herbicide glyphosate. The final part of the study compared metabarcoding analysis between NGS platforms: Illumina vs Nanopore sequencing.
The comparison between morphological and metabarcoding identification showed a similar number of genera when monitoring zooplankton over a season, even though both methods have detected genera absent in the other. In the pilot-study ecotoxicity trial, the selected doses of glyphosate were expected to reduce zooplankton populations (Hebert et al., 2020). However, the effects seen by both morphological and metabarcoding analysis methods were relatively subtle. The effects of glyphosate were found to be different when applying the two methodologies used to monitor community composition and significant differences were found only in metabarcoding analyses. 10 However, both methodologies established a NOEC lower than 5.5mg a.i./L, based on effects at the community and/or taxa level. When Illumina and Nanopore sequencing data were compared, it was demonstrated that, as expected, Nanopore metabarcoding did not generate metabarcodes with Illumina-like quality.
Overall, it was deduced that by combining both morphology and metabarcoding techniques, more extensive descriptions of zooplankton populations can be obtained. However, metabarcoding detected more genera than morphological analyses and an effect was found as expected for the Roundup™ doses on community composition, indicating that metabarcoding could potentially replace traditional morphological analysis. |
| first_indexed | 2025-11-14T21:02:21Z |
| format | Thesis (University of Nottingham only) |
| id | nottingham-79437 |
| institution | University of Nottingham Malaysia Campus |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-14T21:02:21Z |
| publishDate | 2024 |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | nottingham-794372025-02-18T14:32:02Z https://eprints.nottingham.ac.uk/79437/ Application of molecular tools to update aquatic ecotoxicology monitoring Manfredi, Valeria The field of aquatic ecotoxicology studies the structural and functional disturbances induced in the short, medium, and long-term by contamination factors on ecological aquatic systems. Traditionally, organisms selected for the ecotoxicity studies are identified morphologically. Zooplankton communities are frequently employed as indicators of ecological shifts in water quality, serving to monitor such changes (Hemraj et al., 2017; Parmar et al., 2016). Because of their quick and prolific reproduction, zooplankton respond promptly to environmental alterations (Parmar et al., 2016), although they are still poorly studied. This study aimed to apply conventional microscopy and metabarcoding detection to identify and quantify the zooplankton genera that are known indicators within mesocosms. Protocols for the identification of zooplankton genera by metabarcoding were developed. Within a mesocosm system, both methods were used to monitor seasonal changes in communities and also applied to an ecotoxicity trial using the herbicide glyphosate. The final part of the study compared metabarcoding analysis between NGS platforms: Illumina vs Nanopore sequencing. The comparison between morphological and metabarcoding identification showed a similar number of genera when monitoring zooplankton over a season, even though both methods have detected genera absent in the other. In the pilot-study ecotoxicity trial, the selected doses of glyphosate were expected to reduce zooplankton populations (Hebert et al., 2020). However, the effects seen by both morphological and metabarcoding analysis methods were relatively subtle. The effects of glyphosate were found to be different when applying the two methodologies used to monitor community composition and significant differences were found only in metabarcoding analyses. 10 However, both methodologies established a NOEC lower than 5.5mg a.i./L, based on effects at the community and/or taxa level. When Illumina and Nanopore sequencing data were compared, it was demonstrated that, as expected, Nanopore metabarcoding did not generate metabarcodes with Illumina-like quality. Overall, it was deduced that by combining both morphology and metabarcoding techniques, more extensive descriptions of zooplankton populations can be obtained. However, metabarcoding detected more genera than morphological analyses and an effect was found as expected for the Roundup™ doses on community composition, indicating that metabarcoding could potentially replace traditional morphological analysis. 2024-12-11 Thesis (University of Nottingham only) NonPeerReviewed application/pdf en cc_by https://eprints.nottingham.ac.uk/79437/1/FINAL%20THESIS%20VM%20VIVA%20CORRECTIONS.pdf Manfredi, Valeria (2024) Application of molecular tools to update aquatic ecotoxicology monitoring. PhD thesis, University of Nottingham. Aquatic ecotoxicology; Aquatic systems; Zooplankton; Metabarcoding analysis; Morphology |
| spellingShingle | Aquatic ecotoxicology; Aquatic systems; Zooplankton; Metabarcoding analysis; Morphology Manfredi, Valeria Application of molecular tools to update aquatic ecotoxicology monitoring |
| title | Application of molecular tools to update aquatic ecotoxicology monitoring |
| title_full | Application of molecular tools to update aquatic ecotoxicology monitoring |
| title_fullStr | Application of molecular tools to update aquatic ecotoxicology monitoring |
| title_full_unstemmed | Application of molecular tools to update aquatic ecotoxicology monitoring |
| title_short | Application of molecular tools to update aquatic ecotoxicology monitoring |
| title_sort | application of molecular tools to update aquatic ecotoxicology monitoring |
| topic | Aquatic ecotoxicology; Aquatic systems; Zooplankton; Metabarcoding analysis; Morphology |
| url | https://eprints.nottingham.ac.uk/79437/ |