Maximising environmental pressure-response relationship signals from diatom-based metabarcoding in rivers

Kelly, Martyn G.; Mann, David G.; Taylor, Joe D. ORCID: https://orcid.org/0000-0003-0095-0869; Juggins, Stephen; Walsh, Kerry; Pitt, Jo-Anne; Read, Daniel ORCID: https://orcid.org/0000-0001-8546-5154. 2024 Maximising environmental pressure-response relationship signals from diatom-based metabarcoding in rivers. Science of The Total Environment, 914, 169445. 15, pp. https://doi.org/10.1016/j.scitotenv.2023.169445

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Official URL: http://dx.doi.org/10.1016/j.scitotenv.2023.169445

Abstract/Summary

•DNA metabarcoding has been performed on a large number of river phytobenthos samples collected from the UK, using rbcL primers optimised for diatoms. Within this dataset the composition of non-diatom sequence reads was studied and the effect of including these in models for evaluating the nutrient gradient was assessed. Whilst many non-diatom taxonomic groups were detected, few contained the full diversity expected in riverine environments. This may be due to the performance of the current primers in characterising the wider phytobenthic community and influenced by the sampling method employed, as both were developed specifically for diatoms. Nevertheless, the study identified considerable diversity in some groups, e.g. Eustigmatophyceae and a wider distribution than previously thought for freshwater Phaeophyceae. These results offer a strong case for the benefits of metabarcoding for expanding knowledge of aquatic biodiversity in the UK and elsewhere. •Many of the ASVs associated with non-diatoms showed significant pressure responses; however, models that included non-diatoms had similar predictive strength to those based on diatoms alone. Whilst limitations of the primers for assessing non-diatoms may play a role in explaining these results, the diatoms provide a strong signal along the nutrient gradient and other algae, therefore, add little unique information. •We recommend that future developments should use ASVs to calculate metrics, with links to reference databases made as a final step to generate lists of taxa to support interpretation. Any further exploration of the potential of non-diatoms would benefit from access to a well-curated reference database, similar to diat.barcode. Such a database does not yet exist, and we caution against the indiscriminate use of NCBI GenBank as a taxonomic resource as many rbcL sequences deposited have not been curated.

Item Type:	Publication - Article
Digital Object Identifier (DOI):	https://doi.org/10.1016/j.scitotenv.2023.169445
UKCEH and CEH Sections/Science Areas:	Soils and Land Use (Science Area 2017-)
ISSN:	0048-9697
Additional Keywords:	diatoms, algae, rivers, metabarcoding, rbcL, monitoring
NORA Subject Terms:	Ecology and Environment Biology and Microbiology Data and Information
Date made live:	09 Jan 2024 15:54 +0 (UTC)
URI:	https://nora.nerc.ac.uk/id/eprint/536621

Item Type:

Publication - Article

Digital Object Identifier (DOI):

https://doi.org/10.1016/j.scitotenv.2023.169445

UKCEH and CEH Sections/Science Areas:

Soils and Land Use (Science Area 2017-)

ISSN:

0048-9697

Additional Keywords:

diatoms, algae, rivers, metabarcoding, rbcL, monitoring

NORA Subject Terms:

Ecology and Environment
Biology and Microbiology
Data and Information