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Comparative Analysis of Environmental DNA Metabarcoding and Spectro-Fluorescence for Phytoplankton Community Assessments

Salis, Romana LU orcid and Hansson, Lars Anders LU orcid (2025) In Environmental DNA 7(2).
Abstract

Quantifications of phytoplankton biomass and species composition are crucial for monitoring biodiversity and population dynamics in aquatic environments, and both direct microscopic counts and fluorescence-based methods have been widely used for monitoring. Recent advancements in DNA metabarcoding offer an alternative way of easily assessing diversity and species composition. However, a comprehensive comparison of the relative merits and limitations of DNA- and fluorescence-based methods is currently lacking. Here we compare phytoplankton community composition measured via fluorescence and DNA metabarcoding in an outdoor, replicated mesocosm experiment. We show that there is a positive correlation between fluorescence-measured biomass... (More)

Quantifications of phytoplankton biomass and species composition are crucial for monitoring biodiversity and population dynamics in aquatic environments, and both direct microscopic counts and fluorescence-based methods have been widely used for monitoring. Recent advancements in DNA metabarcoding offer an alternative way of easily assessing diversity and species composition. However, a comprehensive comparison of the relative merits and limitations of DNA- and fluorescence-based methods is currently lacking. Here we compare phytoplankton community composition measured via fluorescence and DNA metabarcoding in an outdoor, replicated mesocosm experiment. We show that there is a positive correlation between fluorescence-measured biomass and DNA read and amplicon sequence variants (ASV) numbers for cyanobacteria, but either weak or no correlation for the other phytoplankton groups assessed (cryptophytes, chromophytes, and green algae). In addition, DNA metabarcoding was systematically better at detecting cryptophytes, which were rarely detected via fluorescence. Hence, while DNA metabarcoding may not provide reliable biomass estimates for the majority of phytoplankton groups, metabarcoding analysis offers higher taxonomic resolution and the capability to detect rare phytoplankton groups. Overall, our findings provide new insights into the strengths and limitations of each method and highlight the considerable potential and importance of including DNA barcoding in freshwater ecosystem assessment and biomonitoring programmes with a focus on biodiversity assessments.

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author
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type
Contribution to journal
publication status
published
subject
keywords
16S, 18S, ALA, biomonitoring, cyanobacteria, eDNA, freshwater plankton, microbial eukaryotes, protists, spectral fluorescence
in
Environmental DNA
volume
7
issue
2
article number
e70097
publisher
Wiley
external identifiers
  • scopus:105003265140
ISSN
2637-4943
DOI
10.1002/edn3.70097
language
English
LU publication?
yes
id
5458979f-3cb8-40f3-8691-25a90b841b33
date added to LUP
2025-08-15 12:39:35
date last changed
2025-08-15 12:39:35
@article{5458979f-3cb8-40f3-8691-25a90b841b33,
  abstract     = {{<p>Quantifications of phytoplankton biomass and species composition are crucial for monitoring biodiversity and population dynamics in aquatic environments, and both direct microscopic counts and fluorescence-based methods have been widely used for monitoring. Recent advancements in DNA metabarcoding offer an alternative way of easily assessing diversity and species composition. However, a comprehensive comparison of the relative merits and limitations of DNA- and fluorescence-based methods is currently lacking. Here we compare phytoplankton community composition measured via fluorescence and DNA metabarcoding in an outdoor, replicated mesocosm experiment. We show that there is a positive correlation between fluorescence-measured biomass and DNA read and amplicon sequence variants (ASV) numbers for cyanobacteria, but either weak or no correlation for the other phytoplankton groups assessed (cryptophytes, chromophytes, and green algae). In addition, DNA metabarcoding was systematically better at detecting cryptophytes, which were rarely detected via fluorescence. Hence, while DNA metabarcoding may not provide reliable biomass estimates for the majority of phytoplankton groups, metabarcoding analysis offers higher taxonomic resolution and the capability to detect rare phytoplankton groups. Overall, our findings provide new insights into the strengths and limitations of each method and highlight the considerable potential and importance of including DNA barcoding in freshwater ecosystem assessment and biomonitoring programmes with a focus on biodiversity assessments.</p>}},
  author       = {{Salis, Romana and Hansson, Lars Anders}},
  issn         = {{2637-4943}},
  keywords     = {{16S; 18S; ALA; biomonitoring; cyanobacteria; eDNA; freshwater plankton; microbial eukaryotes; protists; spectral fluorescence}},
  language     = {{eng}},
  number       = {{2}},
  publisher    = {{Wiley}},
  series       = {{Environmental DNA}},
  title        = {{Comparative Analysis of Environmental DNA Metabarcoding and Spectro-Fluorescence for Phytoplankton Community Assessments}},
  url          = {{http://dx.doi.org/10.1002/edn3.70097}},
  doi          = {{10.1002/edn3.70097}},
  volume       = {{7}},
  year         = {{2025}},
}