Comparison of Spatio‐Temporal Dynamics and Composition in Size‐Fractionated and Unfractionated Northwestern Atlantic Microbial Communities

Size fractionation, filtering water sequentially through a large (3 μm) and fine (0.2 μm) pore size filter, is a widely applied approach to target specific microbial size ranges, differentiating between particle-associated, and free-living microorganisms. To characterise its impact on microbial diversity and its comparability to unfractionated samples, we analysed 16 weekly ocean samples across five depths during a phytoplankton spring bloom. We used a universal marker to characterise prokaryotes, eukaryotes and chloroplasts in unfractionated (> 0.2 μm), fractionated (large > 3 μm, small 0.2-3 μm) and de-fractionated samples, the reconstitution of the small and large fractions. The particle-associated fraction was the most different community from all other samples, and de-fractionating before or after sequencing results in a community that is most similar to unfractionated samples in terms of composition and richness with the exception of very rare taxa. Across all depths and weeks, 75%-97% of ASVs were shared, but some discrepancies in relative abundances were unresolved, including for some lineages of free-living Bacteroidota. Community composition differences from size fractionation were more pronounced during the bloom period in comparison to pre-bloom. Differential-abundance analysis detected at most one significantly different ASV between fractionated and de-fractionated samples, highlighting the similarity in community composition and temporal dynamics between the fractionated and de-fractionated sets.