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Pascoal F, Tomasino MP, Piredda R, Quero GM, Torgo L, Poulain J, Galand PE, Fuhrman JA, Mitchell A, Tinta T, Turk Dermastia T, Fernandez-Guerra A, Vezzi A, Logares R, Malfatti F, Endo H, Dąbrowska AM, De Pascale F, Sánchez P, Henry N, Fosso B, Wilson B, Toshchakov S, Ferrant GK, Grigorov I, Vieira FRJ, Costa R, Pesant S, Magalhães C. Inter-comparison of marine microbiome sampling protocols. ISME Commun 2023; 3:84. [PMID: 37598259 PMCID: PMC10439934 DOI: 10.1038/s43705-023-00278-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/19/2023] [Accepted: 06/23/2023] [Indexed: 08/21/2023]
Abstract
Research on marine microbial communities is growing, but studies are hard to compare because of variation in seawater sampling protocols. To help researchers in the inter-comparison of studies that use different seawater sampling methodologies, as well as to help them design future sampling campaigns, we developed the EuroMarine Open Science Exploration initiative (EMOSE). Within the EMOSE framework, we sampled thousands of liters of seawater from a single station in the NW Mediterranean Sea (Service d'Observation du Laboratoire Arago [SOLA], Banyuls-sur-Mer), during one single day. The resulting dataset includes multiple seawater processing approaches, encompassing different material-type kinds of filters (cartridge membrane and flat membrane), three different size fractionations (>0.22 µm, 0.22-3 µm, 3-20 µm and >20 µm), and a number of different seawater volumes ranging from 1 L up to 1000 L. We show that the volume of seawater that is filtered does not have a significant effect on prokaryotic and protist diversity, independently of the sequencing strategy. However, there was a clear difference in alpha and beta diversity between size fractions and between these and "whole water" (with no pre-fractionation). Overall, we recommend care when merging data from datasets that use filters of different pore size, but we consider that the type of filter and volume should not act as confounding variables for the tested sequencing strategies. To the best of our knowledge, this is the first time a publicly available dataset effectively allows for the clarification of the impact of marine microbiome methodological options across a wide range of protocols, including large-scale variations in sampled volume.
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Affiliation(s)
- Francisco Pascoal
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, rua do Campo Alegre s/n, 4169- 007, Porto, Portugal
| | - Maria Paola Tomasino
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
| | - Roberta Piredda
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Grazia Marina Quero
- Institute for Biological Resources and Marine Biotechnologies, National Research Council (IRBIM-CNR), Largo Fiera della Pesca 2, 60125, Ancona, Italy
| | - Luís Torgo
- Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Écogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls-sur-Mer, France
| | - Jed A Fuhrman
- Marine & Environmental Biology, Department of Biological Sciences, University of Southern California (USC), Los Angeles, CA, USA
| | - Alex Mitchell
- EMBL's European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Tinkara Tinta
- National Institute of Biology, Marine Biology Station Piran, Piran, Slovenia
| | | | - Antonio Fernandez-Guerra
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Alessandro Vezzi
- Department of Biology, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC. Passeig Marítim de la Barceloneta, 37-49, ES08003, Barcelona, Spain
| | | | - Hisashi Endo
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Japan
| | - Anna Maria Dąbrowska
- Department of Marine Ecology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Fabio De Pascale
- Department of Biology, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy
| | - Pablo Sánchez
- Institute of Marine Sciences (ICM), CSIC. Passeig Marítim de la Barceloneta, 37-49, ES08003, Barcelona, Spain
| | - Nicolas Henry
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M ECOMAP, UMR 7144, Roscoff, France
- CNRS, FR2424, ABiMS, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Bruno Fosso
- Department of Biosciences, Biotechnologies and Environment, University of Bari, 70126, Bari, Italy
| | - Bryan Wilson
- Department of Biology, John Krebs Field Station, University of Oxford, Wytham, OX2 8QJ, UK
| | | | | | - Ivo Grigorov
- Technical University of Denmark, National Institute of Aquatic Resources, Kgs. Lyngby, Denmark
| | | | - Rodrigo Costa
- Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
- Institute for Bioengineering and Biosciences (iBB) and i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Stéphane Pesant
- EMBL's European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, rua do Campo Alegre s/n, 4169- 007, Porto, Portugal.
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