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Inter-comparison of marine microbiome sampling protocols [Elektronski vir]Pascoal, Francisco ...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.Source: ISME communications [Elektronski vir]. - ISSN 2730-6151 (Vol. 3, art. no. 84, 2023, str. [1]-16)Type of material - e-articlePublish date - 2023Language - englishCOBISS.SI-ID - 161933059
Author
Pascoal, Francisco |
Tomasino, Maria Paola |
Piredda, Roberta |
Quero, Grazia Marina |
Torgo, Luís |
Poulain, Julie |
Tinta, Tinkara |
Turk Dermastia, Timotej
Topics
morski mikrobiom |
standardizirano vzorčenje |
primerjalna analiza |
sekvenciranje amplikonov |
mikrobna diverziteta |
vzorčenje morske vode |
marine microbiome |
standardized sampling |
inter-comparison |
amplicon sequencing |
microbial diversity |
seawater sampling
Author | Pascoal, Francisco ... |
Title | Inter-comparison of marine microbiome sampling protocols [Elektronski vir] |
Publication date | 2023-08-19 |
COBISS.SI-ID | 161933059 |
Publication version in repository | Publisher's version |
Publication licence | Creative Commons Attribution 4.0 International |
Embargo | Immediate publication for public |
Project(s) from which the publication was funded
Title | Acronym | Project ID | Funder |
---|---|---|---|
Connecting Atlantic and Arctic Oceans to Decipher Climate Change Impact on Plankton Microbiome Functions. | PTDC/CTA-AMB/4946/2020 | PTDC/CTA-AMB/4946/2020 |
Fundação para a Ciência e a Tecnologia, I.P. |
Nitrogen Microbiome in the Changing Arctic | 2022.02983.PTDC |
Fundação para a Ciência e a Tecnologia, I.P. |
|
Interdisciplinary Centre of Marine and Environmental Research | UIDP/04423/2020 | UIDP/04423/2020 |
Fundação para a Ciência e a Tecnologia, I.P. |
Institute for Bioengineering and Biosciences | UIDB/04565/2020 | UIDB/04565/2020 |
Fundação para a Ciência e a Tecnologia, I.P. |
Raziskave obalnega morja | P1-0237-2020 |
Javna agencija za znanstvenoraziskovalno in inovacijsko dejavnost Republike Slovenije |
Files that belong to the publication
Link |
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https://doi.org/10.1038/s43705-023-00278-w |
https://d.cobiss.net/repository/si/files/161933059/140093/43705_2023_article_278_161933059.pdf |
https://dirros.openscience.si/IzpisGradiva.php?id=19265 |
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Database name | Field | Year |
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Pascoal, Francisco | |
Tomasino, Maria Paola | |
Piredda, Roberta | |
Quero, Grazia Marina | |
Torgo, Luís | |
Poulain, Julie | |
Tinta, Tinkara | 29618 |
Turk Dermastia, Timotej | 39120 |
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