TY - JOUR

T1 - Inter-comparison of marine microbiome sampling protocols

AU - Pascoal, Francisco

AU - Tomasino, Maria Paola

AU - Piredda, Roberta

AU - Quero, Grazia Marina

AU - Torgo, Luís

AU - Poulain, Julie

AU - Galand, Pierre E.

AU - Fuhrman, Jed A.

AU - Mitchell, Alex

AU - Tinta, Tinkara

AU - Turk Dermastia, Timotej

AU - Fernandez-Guerra, Antonio

AU - Vezzi, Alessandro

AU - Logares, Ramiro

AU - Malfatti, Francesca

AU - Endo, Hisashi

AU - Dąbrowska, Anna Maria

AU - De Pascale, Fabio

AU - Sánchez, Pablo

AU - Henry, Nicolas

AU - Fosso, Bruno

AU - Wilson, Bryan

AU - Toshchakov, Stephan

AU - Ferrant, Gregory Kevin

AU - Grigorov, Ivo

AU - Vieira, Fabio Rocha Jimenez

AU - Costa, Rodrigo

AU - Pesant, Stéphane

AU - Magalhães, Catarina

N1 - © 2023. ISME Publications B.V.

PY - 2023

Y1 - 2023

N2 - 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.

AB - 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.

U2 - 10.1038/s43705-023-00278-w

DO - 10.1038/s43705-023-00278-w

M3 - Journal article

C2 - 37598259

VL - 3

JO - ISME communications

JF - ISME communications

SN - 2730-6151

M1 - 84

ER -