Inter-comparison of marine microbiome sampling protocols
17 pages, 10 figures, supplementary data https://doi.org/10.1038/s43705-023-00278-w.-- Data Availability: All raw sequences from the EMOSE dataset, which includes all data used in this article, are available in the European Nucleotide Archive under the accession number ERP090011. The abundance tables are available at MGnify platform under accession number MGYS00001935. Note that both Versions 5 and 4.1 include all sequencing strategies (MetaB16SV4V5, MetaB18SV9 and metagenomes). The metadata for each sample database was recorded in PANGEA [71], but a cleaner version is available at Supplementary Table S2. The R scripts for all data manipulation, statistical tests and figures is available in github (https://github.com/pascoalf/Inter-comparison-of-marine-microbiome-sampling-protocols), no manipulation of data was done outside the scripts provided, except for manual curation of taxonomy, because it needs human experts’ evaluation
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International Society for Microbial Ecology
2023-12
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| Subjects: | Conserve and sustainably use the oceans, seas and marine resources for sustainable development, |
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Conserve and sustainably use the oceans, seas and marine resources for sustainable development Conserve and sustainably use the oceans, seas and marine resources for sustainable development |
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Conserve and sustainably use the oceans, seas and marine resources for sustainable development Conserve and sustainably use the oceans, seas and marine resources for sustainable development Pascoal, Francisco Tomasino, Maria Paola Piredda, Roberta Quero, Grazia Marina Torgo, Luís Poulain, Julie Galand, Pierre E. Fuhrman, Jed A. Mitchell, Alex Tinta, Tinkara Turk Dermastia, Timotej Fernández-Guerra, Antonio Vezzi, Alessandro Logares, Ramiro Malfatti, Francesca Endo, Hisashi Dąbrowska, Anna Maria De Pascale, Fabio Sánchez Fernández, Pablo Henry, Nicolas Fosso, Bruno Wilson, Brian Toshchakov, Stepan V. Ferrant, Gregory Kevin Grigorov, Ivo Rocha Jimenez Vieira, Fabio Costa, Rodrigo Pesant, Stéphane Magalhães, Catarina M. Inter-comparison of marine microbiome sampling protocols |
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17 pages, 10 figures, supplementary data https://doi.org/10.1038/s43705-023-00278-w.-- Data Availability: All raw sequences from the EMOSE dataset, which includes all data used in this article, are available in the European Nucleotide Archive under the accession number ERP090011. The abundance tables are available at MGnify platform under accession number MGYS00001935. Note that both Versions 5 and 4.1 include all sequencing strategies (MetaB16SV4V5, MetaB18SV9 and metagenomes). The metadata for each sample database was recorded in PANGEA [71], but a cleaner version is available at Supplementary Table S2. The R scripts for all data manipulation, statistical tests and figures is available in github (https://github.com/pascoalf/Inter-comparison-of-marine-microbiome-sampling-protocols), no manipulation of data was done outside the scripts provided, except for manual curation of taxonomy, because it needs human experts’ evaluation |
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Agencia Estatal de Investigación (España) Pascoal, Francisco Tomasino, Maria Paola Piredda, Roberta Quero, Grazia Marina Torgo, Luís Poulain, Julie Galand, Pierre E. Fuhrman, Jed A. Mitchell, Alex Tinta, Tinkara Turk Dermastia, Timotej Fernández-Guerra, Antonio Vezzi, Alessandro Logares, Ramiro Malfatti, Francesca Endo, Hisashi Dąbrowska, Anna Maria De Pascale, Fabio Sánchez Fernández, Pablo Henry, Nicolas Fosso, Bruno Wilson, Brian Toshchakov, Stepan V. Ferrant, Gregory Kevin Grigorov, Ivo Rocha Jimenez Vieira, Fabio Costa, Rodrigo Pesant, Stéphane Magalhães, Catarina M. |
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Conserve and sustainably use the oceans, seas and marine resources for sustainable development |
| author |
Pascoal, Francisco Tomasino, Maria Paola Piredda, Roberta Quero, Grazia Marina Torgo, Luís Poulain, Julie Galand, Pierre E. Fuhrman, Jed A. Mitchell, Alex Tinta, Tinkara Turk Dermastia, Timotej Fernández-Guerra, Antonio Vezzi, Alessandro Logares, Ramiro Malfatti, Francesca Endo, Hisashi Dąbrowska, Anna Maria De Pascale, Fabio Sánchez Fernández, Pablo Henry, Nicolas Fosso, Bruno Wilson, Brian Toshchakov, Stepan V. Ferrant, Gregory Kevin Grigorov, Ivo Rocha Jimenez Vieira, Fabio Costa, Rodrigo Pesant, Stéphane Magalhães, Catarina M. |
| author_sort |
Pascoal, Francisco |
| title |
Inter-comparison of marine microbiome sampling protocols |
| title_short |
Inter-comparison of marine microbiome sampling protocols |
| title_full |
Inter-comparison of marine microbiome sampling protocols |
| title_fullStr |
Inter-comparison of marine microbiome sampling protocols |
| title_full_unstemmed |
Inter-comparison of marine microbiome sampling protocols |
| title_sort |
inter-comparison of marine microbiome sampling protocols |
| publisher |
International Society for Microbial Ecology |
| publishDate |
2023-12 |
| url |
http://hdl.handle.net/10261/354925 |
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dig-icm-es-10261-3549252024-04-25T09:30:14Z Inter-comparison of marine microbiome sampling protocols Pascoal, Francisco Tomasino, Maria Paola Piredda, Roberta Quero, Grazia Marina Torgo, Luís Poulain, Julie Galand, Pierre E. Fuhrman, Jed A. Mitchell, Alex Tinta, Tinkara Turk Dermastia, Timotej Fernández-Guerra, Antonio Vezzi, Alessandro Logares, Ramiro Malfatti, Francesca Endo, Hisashi Dąbrowska, Anna Maria De Pascale, Fabio Sánchez Fernández, Pablo Henry, Nicolas Fosso, Bruno Wilson, Brian Toshchakov, Stepan V. Ferrant, Gregory Kevin Grigorov, Ivo Rocha Jimenez Vieira, Fabio Costa, Rodrigo Pesant, Stéphane Magalhães, Catarina M. Agencia Estatal de Investigación (España) European Marine Research Network Fundação para a Ciência e a Tecnologia (Portugal) Slovenian Research Agency European Commission Conserve and sustainably use the oceans, seas and marine resources for sustainable development 17 pages, 10 figures, supplementary data https://doi.org/10.1038/s43705-023-00278-w.-- Data Availability: All raw sequences from the EMOSE dataset, which includes all data used in this article, are available in the European Nucleotide Archive under the accession number ERP090011. The abundance tables are available at MGnify platform under accession number MGYS00001935. Note that both Versions 5 and 4.1 include all sequencing strategies (MetaB16SV4V5, MetaB18SV9 and metagenomes). The metadata for each sample database was recorded in PANGEA [71], but a cleaner version is available at Supplementary Table S2. The R scripts for all data manipulation, statistical tests and figures is available in github (https://github.com/pascoalf/Inter-comparison-of-marine-microbiome-sampling-protocols), no manipulation of data was done outside the scripts provided, except for manual curation of taxonomy, because it needs human experts’ evaluation 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 This study was supported by the Euromarine European Marine Research Network by funding the initiative EMOSE 2017 “Inter-Comparison of Marine Plankton Metagenome Analysis Methods”. The Portuguese Science and Technology Foundation (FCT) funded this study through the grants PTDC/CTA-AMB/4946/2020, 2022.02983.PTDC, 2020.03139 CEECIND to CM and a PhD grant to FP (2020.04453). The work of LT was undertaken, in part, thanks to funding from the Canada Research Chairs program and a Discovery Grant from NSERC. This study was also partially funded by the Strategic Funding UIDP/04423/2020, UIDB/04565/2020 and LA/P/0140/2020 through national funds provided by FCT and carried out under the projects ATLANTIDA (ref. NORTE-01–0145-FEDER-000040) and Ocean3R (NORTE-01-0145-FEDER-000064), supported by the Norte Portugal Regional Operational Program (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement and through the European Regional Development Fund (ERDF). This work was also partially supported by financing attributed to TT from the Slovenian Research Agency (Research Core Funding P1-0237) With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S) Peer reviewed 2024-04-25T09:30:13Z 2024-04-25T09:30:13Z 2023-12 artículo ISME Communications 3(1): 84 (2023) CEX2019-000928-S http://hdl.handle.net/10261/354925 10.1038/s43705-023-00278-w 2730-6151 en Publisher's version https://doi.org/10.1038/s43705-023-00278-w Sí open International Society for Microbial Ecology |