Accuracy of protist diversity assessments: morphology compared to cloning and direct pyrosequencing of 18S rRNA genes and ITS regions using the conspicuous tintinnid ciliates as a case study

Description :

 Deep-sequencing technologies are becoming nearly routine to describe
                microbial community composition in environmental samples. 18S rDNA pyrosequencing
                has revealed a vast diversity of infrequent sequences, leading to the proposition of
                the existence of an extremely diverse microbial "rare biosphere". While rare
                microbes no doubt exist, critical views suggest that many rare sequences may
                actually be artifacts. However, information about how diversity revealed by
                molecular methods relates to that revealed by classical morphology approaches is
                practically non-existent. To address this issue, we used different approaches to
                assess the diversity of tintinnid ciliates, a species-rich group in which species
                can be easily distinguished morphologically. We studied two Mediterranean marine
                samples with different patterns of tintinnid diversity. We estimated tintinnid
                diversity in these samples employing morphological observations as well as both
                classical cloning and sequencing and pyrosequencing of two different markers, the
                18S rDNA and the ITS regions, applying a variety of computational approaches
                currently used to analyze pyrosequence reads. We found that both molecular
                approaches were efficient in detecting the tintinnid species observed by microscopy
                and revealed similar phylogenetic structures of the tintinnid community at the
                species level. However, depending on the method used to analyze the pyrosequencing
                results, we observed discrepancies with the morphology-based assessments up to
                several orders of magnitude. In several cases, the inferred number of operational
                taxonomic units (OTUs) largely exceeded the total number of tintinnid cells in the
                samples. Such inflation of the OTU numbers corresponded to "rare biosphere" taxa,
                composed largely of artefacts. Our results suggest that a careful and rigorous
                analysis of pyrosequencing datasets, including data denoising and sequence
                clustering with well-adjusted parameters, is necessary to accurately describe
                microbial biodiversity using this molecular approach.

Link GBIF portal : https://www.gbif.org/dataset/3df9766b-ba53-4355-a801-930d89df841a

Project :
Title : Accuracy of protist diversity assessments: morphology compared to cloning
                and direct pyrosequencing of 18S rRNA genes and ITS regions using the conspicuous
                tintinnid ciliates as a case study
Abstract : 
Funding : 
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Le jeu de données diffusé est issu d'un traitement automatique appliqué sur les données issues du GBIF. Les règles de l'INPN et plus globalement du SINP (en termes de périmètre et de contrôle sur les données) peuvent impliquer que l'ensemble des données du jeu source ne soit pas restitué dans le SINP.
 The disseminated dataset stems from an automatic treatment applied to data coming from GBIF. INPN rules, and more generally SINP rules (in terms of perimeter and data quality controls) may imply that the whole of the source dataset might not be provided on the SINP platform. 

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Dates publication :

Premiere diffusion : 26/09/2019 

Dernière mise à jour : 30/11/2023