Microbial communities associated with sinking particles across an environmental gradient from coastal upwelling to the oligotrophic ocean

Abstract Complex interactions between microbial communities in the epipelagic and mesopelagic ocean drive variability in sinking carbon flux as part of the biological carbon pump. To investigate the relative contribution of dominant prokaryotic, protistan, and phytoplankton taxa to sinking particles, we used 16S/18S rRNA gene sequencing of particles collected in sediment traps and water column communities. Comparisons were done across a coastal upwelling-to-oligotrophic environmental gradient in the southern California Current Ecosystem to assess effects of natural environmental variability on taxon-specific contributions to sinking particle export. Particle-associated microbial assemblages differ from ambient mixed-layer communities. Gammaproteobacteria, dinoflagellates, and rhizarians were dominant microbes associated with sinking particles at all sampling locations, with diatoms increasing significantly at the inshore mesotrophic site. Parasitic groups, syndiniales and apicomplexans, were also major particle-associated taxa. Relative sequence abundance on exported particles from the mesotrophic inshore site more closely resembled the water-column dominants (especially diatoms) found above, while oligotrophic communities exhibited greater dissimilarity between the microbial communities on sinking particles and in the mixed layer. Protists generally showed greater similarity between mixed-layer and sinking particle communities than prokaryotes. Synechococcus was over-represented on sinking particles (relative to eukaryotic phytoplankton and other cyanobacteria) only in oligotrophic areas. Diatoms were the only phytoplankton group consistently over-represented on sinking particles across the region. Our results highlight important variability in microbial contributions to export that seem to align with differences in dominant grazing pathways. At the upwelling influenced site where export was primarily due to the fecal pellets of large copepods, diatoms were dominant contributors to export and protistan communities on sinking particles resembled those in the water column above. When doliolids were abundant, dinoflagellates contributed substantially to export, while the dominant picoeukaryote (Ostreococcus) was only a minor contributor. In oligotrophic areas, where grazing pathways were dominated by protists and sinking particles were primarily amorphous aged aggregates, there was little similarity between mixed layer and sinking particle communities.