A robust approach to estimate relative phytoplankton cell abundances from metagenomes.
psbO
18S rRNA
Tara Oceans
metabarcoding
metagenomics
metatranscriptomics
photosynthesis
phytoplankton
Journal
Molecular ecology resources
ISSN: 1755-0998
Titre abrégé: Mol Ecol Resour
Pays: England
ID NLM: 101465604
Informations de publication
Date de publication:
Jan 2023
Jan 2023
Historique:
revised:
09
01
2022
received:
19
09
2021
accepted:
25
01
2022
pubmed:
3
2
2022
medline:
7
12
2022
entrez:
2
2
2022
Statut:
ppublish
Résumé
Phytoplankton account for >45% of global primary production, and have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found among prokaryotes (cyanobacteria) and multiple eukaryotic lineages containing chloroplasts. Genetic surveys of phytoplankton communities generally consist of PCR amplification of bacterial (16S), nuclear (18S) and/or chloroplastic (16S) rRNA marker genes from DNA extracted from environmental samples. However, our appreciation of phytoplankton abundance or biomass is limited by PCR-amplification biases, rRNA gene copy number variations across taxa, and the fact that rRNA genes do not provide insights into metabolic traits such as photosynthesis. Here, we targeted the photosynthetic gene psbO from metagenomes to circumvent these limitations: the method is PCR-free, and the gene is universally and exclusively present in photosynthetic prokaryotes and eukaryotes, mainly in one copy per genome. We applied and validated this new strategy with the size-fractionated marine samples collected by Tara Oceans, and showed improved correlations with flow cytometry and microscopy than when based on rRNA genes. Furthermore, we revealed unexpected features of the ecology of these ecosystems, such as the high abundance of picocyanobacterial aggregates and symbionts in the ocean, and the decrease in relative abundance of phototrophs towards the larger size classes of marine dinoflagellates. To facilitate the incorporation of psbO in molecular-based surveys, we compiled a curated database of >18,000 unique sequences. Overall, psbO appears to be a promising new gene marker for molecular-based evaluations of entire phytoplankton communities.
Identifiants
pubmed: 35108459
doi: 10.1111/1755-0998.13592
pmc: PMC10078663
doi:
Substances chimiques
RNA, Ribosomal, 16S
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
16-40Subventions
Organisme : FFEM - French Facility for Global Environment (Fonds Français pour l'Environnement Mondial)
Organisme : Université de Recherche Paris Sciences et Lettres (PSL)
ID : ANR-1253 11-IDEX-0001-02
Organisme : European Research Council (ERC) European Research Council (ERC) under the European Union's Horizon 2020
ID : 835067
Organisme : CNRS Momentum Fellowship 2019-2021
Organisme : French Government "Investissements d'Avenir" Programmes MEMO LIFE
ID : ANR-10-LABX-54
Organisme : OCEANOMICS
ID : ANR-11-BTBR-0008
Organisme : France Genomique
ID : ANR-10-INBS-09
Informations de copyright
© 2022 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.
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