Planktonic prokaryotes are further defined into two categories, free-living or particle associated. The two are separated by filtration. Particle-associated bacteria are often difficult to study because marine snow aggregates are often ranging in sizes from 0.2 to 200 μm, often rendering sampling efforts difficult. These aggregates are hotspots for microbial activity. Marine bacteria are the most abundant organisms in aggregates followed by cyanobacteria and then nanoflagellates. Aggregates can be enriched about one thousand times more than the surrounding seawater. Seasonal variability can also have an effect on microbial communities of marine snow aggregates with concentrations being the highest during the summer.
As illustrated in the diagram, phytoplankton fix carbon dioxide in the euphotic zone using solar energy and produce particulate organic carbon. The particulate organic carbon formed in the euphotic zone is processed by marine microorganisms (microbes), zooplankton and their consumers into organic aggregates (marine snow), which is then exported to the mesopelagic (200–1000 m depth) and bathypelagic zones by sinking and vertical migration by zooplankton and fish.
Export flux is defined as the sedimentation out of the surface layer (at approximately 100 m depth) and sequestration flux is the sedimentation out of the mesopelagic zone (at approximately 1000 m depth). A portion of the particulate organic carbon is respired back to CO in the oceanic water column at depth, mostly by heterotrophic microbes and zooplankton, thus maintaining a vertical gradient in concentration of dissolved inorganic carbon (DIC). This deep-ocean DIC returns to the atmosphere on millennial timescales through thermohaline circulation. Between 1% and 40% of the primary production is exported out of the euphotic zone, which attenuates exponentially towards the base of the mesopelagic zone and only about 1% of the surface production reaches the sea floor.
The largest component of biomass are marine protists (eukaryotic microorganisms). Marine snow aggregates collected from the bathypelagic zone were found to consist largely of fungi and labyrinthulomycetes. Smaller aggregates do not harbor as many eukaryotic organisms which is similar to what is found in the deep ocean. The bathypelagic aggregates mostly resembled those found in the surface ocean. It implies higher rates of remineralization in the bathypelagic zone.
Numerically, the largest component of marine snow are the prokaryotes that colonize the aggregates. Bacteria are largely responsible for the remineralisation and fragmentation of aggregates. Remineralization occurs typically below 200 m depth.
Microbial communities that form on the aggregates vary from the communities in the water column. The concentration of attached microbes are typically orders of magnitude larger than free-living microbes. Isolated bacterial cultures have up to 20 times more enzymatic activity within 2 hours of aggregate attachment. The dark ocean harbors around 65% of all pelagic Bacteria and Archaea.(Whitman et al., 1998)
It was previously thought that due to fragmentation, bacterial communities would shift as they travel down the water column. As seen in experiments, it now appears that the communities that form during aggregation remain associated with the aggregate and any community changes are due to grazing or fragmentation rather than new bacterial colony formation.