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Inter-comparison of marine microbiome sampling protocols.

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  • 1Interdisciplinary 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.

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Summary
This summary is machine-generated.

Standardizing marine microbial sampling is crucial for comparable research. Our study found that seawater volume and filter type do not significantly impact microbial diversity, but size fractionation does.

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Area of Science:

  • Marine Microbiology
  • Environmental Science
  • Molecular Ecology

Background:

  • Comparative analysis of marine microbial studies is challenging due to diverse seawater sampling protocols.
  • Standardization is needed to improve inter-comparison of research and guide future sampling strategies.

Purpose of the Study:

  • To develop the EuroMarine Open Science Exploration initiative (EMOSE) to address methodological variations in marine microbiome research.
  • To clarify the impact of different seawater sampling protocols on microbial diversity.

Main Methods:

  • Collected thousands of liters of seawater from a single station in the NW Mediterranean Sea.
  • Applied various filtration methods including different filter types (cartridge and flat membrane) and size fractionations (>0.22 µm, 0.22-3 µm, 3-20 µm, >20 µm).
  • Analyzed microbial diversity across a range of seawater volumes (1 L to 1000 L) using different sequencing strategies.

Main Results:

  • Seawater volume filtered did not significantly affect prokaryotic and protist diversity.
  • Alpha and beta diversity showed significant differences between size fractions and 'whole water' samples.
  • Filter type and volume were not confounding variables for the tested sequencing strategies.

Conclusions:

  • Researchers should exercise caution when merging datasets with differing filter pore sizes.
  • Filter type and sampled volume are unlikely to confound results from standard sequencing strategies.
  • This study provides a unique dataset for understanding the impact of methodological choices in marine microbiome research.