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Título: | A robust approach to estimate relative phytoplankton cell abundances from metagenomes |
Autor: | Pierella Karlusich, Juan J.; Pelletier, Eric; Zinger, Lucie; Lombard, Fabien; Zingone, Adriana; Colin, Sebastien; Gasol, Josep M. CSIC ORCID ; Dorrell, Richard G.; Henry, Nicolas; Scalco, Eleonora; Acinas, Silvia G. CSIC ORCID ; Wincker, Patrick; Vargas, Colomban de; Bowler, Chris | Palabras clave: | 18S rRNA metabarcoding Metagenomics Metatranscriptomics photosynthesis Phytoplankton psbO Tara Oceans |
Fecha de publicación: | ene-2023 | Editor: | John Wiley & Sons | Citación: | Molecular Ecology Resources 23(1): 16-40 (2023) | Resumen: | Phytoplankton account for >45% of global primary production, and have an enor-mous impact on aquatic food webs and on the entire Earth System. Their members are found among prokaryotes (cyanobacteria) and multiple eukaryotic lineages con-taining 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 appre-ciation 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 photosyn-thetic 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 | Descripción: | This article is contribution number 127 of Tara Oceans..-- 25 pages, 8 figures, 2 tables, supporting Information https://doi.org/10.1111/1755-0998.13592.-- Data availability statement: All datasets analysed for this study are of public access as described in Table 1. The curated psbO database was submitted to the EMBL-EBI repository BioStudies (www.ebi.ac.uk/biostudies) under accession S-BSST659. The 18S miTags data set covering size fractions between 0.8 and 2,000 µm was submitted to the same repository under accession S-BSST762. The Supporting Information tables for flow cytometry and optical microscopy as well as the protein sequences used for building the protein similarity networks are available at S-BSST761 | Versión del editor: | https://doi.org/10.1111/1755-0998.13592 | URI: | http://hdl.handle.net/10261/288974 | DOI: | 10.1111/1755-0998.13592 | ISSN: | 1755-098X | E-ISSN: | 1755-0998 |
Aparece en las colecciones: | (ICM) Artículos |
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Pierella_et_al_2023.pdf | 27,31 MB | Adobe PDF | Visualizar/Abrir | |
Pierella_et_al_2023_suppl.pdf | 17,41 MB | Adobe PDF | Visualizar/Abrir |
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