Size Fractionation Informs Microbial Community Composition and Interactions in the Eastern Tropical North Pacific Ocean

Marine microorganisms are drivers of biogeochemical cycles in the world’s oceans, including oxygen minimum zones (OMZs). Using a metabarcoding survey of the 16S rRNA gene, we investigated prokaryotic communities, as well as their potential interactions with fungi, at the coastal, offshore, and peripheral OMZ of the eastern tropical North Pacific. Water samples were collected along a vertical oxygen gradient, and large volumes were filtered through three size fractions, 0.22, 2, and 22 µm. The changes in community composition along the oxygen gradient were driven by Planctomycetota, Bacteroidota, Verrucomicrobiota, and Gammaproteobacteria; most are known degraders of marine polysaccharides and usually associated with the large particle-associated (LPA) community. The relative abundance of Nitrososphaerota, Alphaproteobacteria, Actinomycetota, and Nitrospinota was high in free-living and small particle-associated (SPA) communities. Network analyses identified putative interactions between fungi and prokaryotes in the particle-associated fractions, which have been largely overlooked in the ocean. In the SPAnetwork analysis, fungal amplicon sequence variants (ASVs) had exclusively negative connections with SAR11 nodes. In the LPA network analysis, fungal ASVs displayed both negative and positive connections with Pseudomonadota, SAR324, and Thermoplasmatota. Our findings demonstrate the utility of three-stage size-fractioned filtration in providing novel insights into marine microbial ecology.