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Through the eDNA looking glass: Responses of fjord benthic foraminiferal communities to contrasting environmental conditions

Brinkmann, Inda LU orcid ; Schweizer, Magali ; Singer, David ; Quinchard, Sophie ; Barras, Christine ; Bernhard, Joan M. and Filipsson, Helena L. LU orcid (2023) In Journal of Eukaryotic Microbiology 70(4).
Abstract

The health of coastal marine environments is severely declining with global changes. Proxies, such as those based on microeukaryote communities, can record biodiversity and ecosystem responses. However, conventional studies rely on microscopic observations of limited taxonomic range and size fraction, missing putatively ecologically informative community components. Here, we tested molecular tools to survey foraminiferal biodiversity in a fjord system (Sweden) on spatial and temporal scales: Alpha and beta diversity responses to natural and anthropogenic environmental trends were assessed and variability of foraminiferal environmental DNA (eDNA) compared to morphology-based data. The identification of eDNA-obtained taxonomic units was... (More)

The health of coastal marine environments is severely declining with global changes. Proxies, such as those based on microeukaryote communities, can record biodiversity and ecosystem responses. However, conventional studies rely on microscopic observations of limited taxonomic range and size fraction, missing putatively ecologically informative community components. Here, we tested molecular tools to survey foraminiferal biodiversity in a fjord system (Sweden) on spatial and temporal scales: Alpha and beta diversity responses to natural and anthropogenic environmental trends were assessed and variability of foraminiferal environmental DNA (eDNA) compared to morphology-based data. The identification of eDNA-obtained taxonomic units was aided by single-cell barcoding. Our study revealed wide diversity, including typical morphospecies recognized in the fjords, and so-far unrecognized taxa. DNA extraction method impacted community composition outputs significantly. DNA extractions of 10 g sediment more reliably represented present diversity than of 0.5-g samples and, thus, are preferred for environmental assessments in this region. Alpha- and beta diversity of 10-g extracts correlated with bottom-water salinity similar to morpho-assemblage diversity changes. Sub-annual environmental variability resolved only partially, indicating damped sensitivity of foraminiferal communities on short timescales using established metabarcoding techniques. Systematically addressing the current limitations of morphology-based and metabarcoding studies may strongly improve future biodiversity and environmental assessments.

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Please use this url to cite or link to this publication:
author
; ; ; ; ; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
barcoding, biodiversity, coastal ecosystems, environmental DNA, foraminifera, hypoxia, metabarcoding
in
Journal of Eukaryotic Microbiology
volume
70
issue
4
publisher
Wiley-Blackwell
external identifiers
  • pmid:36972021
  • scopus:85152359166
ISSN
1066-5234
DOI
10.1111/jeu.12975
project
Tracing past bottom water oxygenation in the sea: a microanalytical approach to improve calcium carbonate based proxies (TOPICaL)
language
English
LU publication?
yes
additional info
Funding Information: We acknowledge funding from the Swedish Research Council VR (grant number 2017‐04190), the Crafoord Foundation, and the Royal Physiographic Society in Lund, Sweden. JMB's participation was supported by the at Woods Hole Oceanographic Institution.
id
b43b2b01-f6c1-43e1-a00d-a4ce2f73e604
date added to LUP
2023-05-03 15:37:49
date last changed
2024-02-19 19:15:44
@article{b43b2b01-f6c1-43e1-a00d-a4ce2f73e604,
  abstract     = {{<p>The health of coastal marine environments is severely declining with global changes. Proxies, such as those based on microeukaryote communities, can record biodiversity and ecosystem responses. However, conventional studies rely on microscopic observations of limited taxonomic range and size fraction, missing putatively ecologically informative community components. Here, we tested molecular tools to survey foraminiferal biodiversity in a fjord system (Sweden) on spatial and temporal scales: Alpha and beta diversity responses to natural and anthropogenic environmental trends were assessed and variability of foraminiferal environmental DNA (eDNA) compared to morphology-based data. The identification of eDNA-obtained taxonomic units was aided by single-cell barcoding. Our study revealed wide diversity, including typical morphospecies recognized in the fjords, and so-far unrecognized taxa. DNA extraction method impacted community composition outputs significantly. DNA extractions of 10 g sediment more reliably represented present diversity than of 0.5-g samples and, thus, are preferred for environmental assessments in this region. Alpha- and beta diversity of 10-g extracts correlated with bottom-water salinity similar to morpho-assemblage diversity changes. Sub-annual environmental variability resolved only partially, indicating damped sensitivity of foraminiferal communities on short timescales using established metabarcoding techniques. Systematically addressing the current limitations of morphology-based and metabarcoding studies may strongly improve future biodiversity and environmental assessments.</p>}},
  author       = {{Brinkmann, Inda and Schweizer, Magali and Singer, David and Quinchard, Sophie and Barras, Christine and Bernhard, Joan M. and Filipsson, Helena L.}},
  issn         = {{1066-5234}},
  keywords     = {{barcoding; biodiversity; coastal ecosystems; environmental DNA; foraminifera; hypoxia; metabarcoding}},
  language     = {{eng}},
  number       = {{4}},
  publisher    = {{Wiley-Blackwell}},
  series       = {{Journal of Eukaryotic Microbiology}},
  title        = {{Through the eDNA looking glass: Responses of fjord benthic foraminiferal communities to contrasting environmental conditions}},
  url          = {{http://dx.doi.org/10.1111/jeu.12975}},
  doi          = {{10.1111/jeu.12975}},
  volume       = {{70}},
  year         = {{2023}},
}