Performance of the melting seawater‐ice elution method on the metabarcoding characterization of benthic protist communities

Autor: Guillaume Reboul, David Moreira, Purificación López-García, Adrià Auladell, Albert Reñé
Přispěvatelé: Ecologie Systématique et Evolution (ESE), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Centre National de la Recherche Scientifique (CNRS)
Jazyk: angličtina
Rok vydání: 2020
Předmět:
Zdroj: Environmental Microbiology Reports
Environmental Microbiology Reports, Wiley, 2020, 12 (3), pp.314-323. ⟨10.1111/1758-2229.12834⟩
Digital.CSIC. Repositorio Institucional del CSIC
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ISSN: 1758-2229
DOI: 10.1111/1758-2229.12834⟩
Popis: 10 pages, 4 figures, 2 tables, supporting Information https://doi.org/10.1111/1758-2229.12834.-- This is the peer reviewed version of the following article: Performance of the melting seawater‐ice elution method on the metabarcoding characterization of benthic protist communities, A, Reñé, A. Auladell, G. Reboul, D. Moreira, P. López‐García, Environmental Microbiology Reports12(3): 314-323 (2020) which has been published in final form at https://doi.org/10.1111/1758-2229.12834. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions
Massive amplicon sequencing approaches to characterize the diversity of microbial eukaryotes in sediments are scarce and controls about the effects introduced by different methods to recover DNA are lacking. In this study, we compare the performance of the melting seawater‐ice elution method on the characterization of benthic protist communities by 18S rRNA gene metabarcoding with results obtained by direct cell lysis and DNA purification from sediments. Even though the most abundant operational taxonomic units were recovered by both methods, eluted samples yielded higher richness than samples undergoing direct lysis. Both treatments allowed recovering the same taxonomic groups, although we observed significant differences in terms of relative abundance for some of them. Dinoflagellata and Ciliophora strongly dominated the community in eluted samples (> 80% reads). In directly lysed samples, they only represented 37%, while groups like Fungi and Ochrophytes were highly represented (> 20% reads respectively). Our results show that the elution process yields a higher protist richness estimation, most likely as a result of the higher sample volume used to recover organisms as compared to commonly used volumes for direct benthic DNA purification. Motile groups, like dinoflagellates and ciliates, are logically more enriched during the elution process
G.R., D.M. and P. L.‐G. were funded by European Research Council Grant ProtistWorld (no. 322669) under the European Union's Seventh Framework Program. A.R. was granted by MINECO Grant COPAS ‘Understanding top‐down control in coastal bloom‐forming protists’ (CTM2017‐86121‐R), and a MECD grant ‘Estancia de Movilidad en el extranjero José Castillejo’ (CAS17/00237)
With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI)
Databáze: OpenAIRE
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