Beyond the limits of the unassigned protist microbiome: inferring large-scale spatio-temporal patterns of Syndiniales marine parasites

Type Article
Date 2023-02-28
Language English
Author(s) Rizos IrisORCID1, 2, Debeljak Pavla1, Finet ThomasORCID1, Klein Dylan1, Ayata Sakina-Dorothée3, Not Fabrice2, Bittner Lucie1, 4
Affiliation(s) 1 : Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
2 : Sorbonne Université, CNRS, AD2M-UMR7144 Station Biologique de Roscoff, 29680, Roscoff, France
3 : Sorbonne Université, Laboratoire d’Océanographie et du Climat: Expérimentation et Analyses Numériques (LOCEAN, SU/CNRS/IRD/MNHN), 75252, Paris Cedex 05, France
4 : Institut Universitaire de France, Paris, France
Source ISME Communications (2730-6151) (Springer Science and Business Media LLC), 2023-02-28 , Vol. 3 , N. 1 , P. 16 (11p.)
DOI 10.1038/s43705-022-00203-7
Abstract

Marine protists are major components of the oceanic microbiome that remain largely unrepresented in culture collections and genomic reference databases. The exploration of this uncharted protist diversity in oceanic communities relies essentially on studying genetic markers from the environment as taxonomic barcodes. Here we report that across 6 large scale spatio-temporal planktonic surveys, half of the genetic barcodes remain taxonomically unassigned at the genus level, preventing a fine ecological understanding for numerous protist lineages. Among them, parasitic Syndiniales (Dinoflagellata) appear as the least described protist group. We have developed a computational workflow, integrating diverse 18S rDNA gene metabarcoding datasets, in order to infer large-scale ecological patterns at 100% similarity of the genetic marker, overcoming the limitation of taxonomic assignment. From a spatial perspective, we identified 2171 unassigned clusters, i.e., Syndiniales sequences with 100% similarity, exclusively shared between the Tropical/Subtropical Ocean and the Mediterranean Sea among all Syndiniales orders and 25 ubiquitous clusters shared within all the studied marine regions. From a temporal perspective, over 3 time-series, we highlighted 39 unassigned clusters that follow rhythmic patterns of recurrence and are the best indicators of parasite community’s variation. These clusters withhold potential as ecosystem change indicators, mirroring their associated host community responses. Our results underline the importance of Syndiniales in structuring planktonic communities through space and time, raising questions regarding host-parasite association specificity and the trophic mode of persistent Syndiniales, while providing an innovative framework for prioritizing unassigned protist taxa for further description.

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How to cite 

Rizos Iris, Debeljak Pavla, Finet Thomas, Klein Dylan, Ayata Sakina-Dorothée, Not Fabrice, Bittner Lucie (2023). Beyond the limits of the unassigned protist microbiome: inferring large-scale spatio-temporal patterns of Syndiniales marine parasites. ISME Communications, 3(1), 16 (11p.). Publisher's official version : https://doi.org/10.1038/s43705-022-00203-7 , Open Access version : https://archimer.ifremer.fr/doc/00823/93480/