Environmental sequencing provides reasonable estimates of the relative abundance of specific picoeukaryotes
High-throughput sequencing (HTS) is revolutionizing environmental surveys of microbial diversity in the three domains of life by providing detailed information on which taxa are present in microbial assemblages. However, it is still unclear how the relative abundance of specific taxa gathered by HTS correlates with cell abundances. Here, we quantified the relative cell abundance of 6 picoeukaryotic taxa in 13 planktonic samples from six European coastal sites using epifluorescence microscopy on TSA-FISH preparations. These relative abundance values were then compared with HTS data obtained in three separate molecular surveys: 454 sequencing the V4 region of the 18S rDNA using DNA and RNA extracts (DNA-V4 and cDNA-V4), and Illumina sequencing the V9 region (cDNA-V9). The microscopic and molecular signals were generally correlated, indicating that a relative increase in specific 18S rDNA was the result of a large proportion of cells in the given taxa. Despite these positive correlations, the slopes often deviated from 1, precluding a direct translation of sequences to cells. Our data highlighted clear differences depending on nucleic-acid template or the 18S rDNA region targeted. Thus, the molecular signal obtained using cDNA templates was always closer to relative cell abundances, while the V4 and V9 regions gave better results depending on the taxa. Our data supports the quantitative use of HTS data but warn about considering it as direct proxy of cell abundances.
© extrait de l'introduction du document :
"[...] "Samples were taken during the BioMarKs project ( http://www.biomarks.org ) in six 117 European coastal sites: Blanes [...], Gijon [...], Naples [...], Oslo [...] , Roscoff 119 (France, 48° 46’ N, 3° 57’ W) and Varna [...]"
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|keyboard_arrow_right||Titre :||Environmental sequencing provides reasonable estimates of the relative abundance of specific picoeukaryotes|
|keyboard_arrow_right||Type de documentation :||Articles|
|keyboard_arrow_right||Auteur(s) personne(s) :||Ramon Massana , De Vargas Colomban, Ramiro Logares , Sarah Romac , Irene Forn , R. Giner Caterina|
|keyboard_arrow_right||Date de publication :||20 mai 2016|
|keyboard_arrow_right||Nombre de pages :||39p|
|keyboard_arrow_right||Editeur(s) :||American society for microbiology (ASM)|
|keyboard_arrow_right||Tags thématiques :||biosphère, organisme marin, plancton|
|keyboard_arrow_right||Mots-clés libres :||Protistologie/biodiversité/picoeucaryote/picoeucaryotes/18S rDNA/454 pyrosequencing/FISH/Illumina sequencing/picoeukaryotes/specific abundance|
|keyboard_arrow_right||N° d'édition (ISBN,DOI...) :||10.1128/AEM.00560-16|
|keyboard_arrow_right||Collection :||Applied and environmental microbiology|