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1. Data From: Active sinking particles: Flow and transport dynamics due to sessile suspension feeders on sinking aggregates

   https://doi.org/10.5061/dryad.j6q573nf8  

   Pepper, Rachel; Krishnamurthy, Deepak; Prakash, Manu (January 2021, Dryad)

   Sinking or sedimentation of biological aggregates plays a critical role in carbon sequestration in the ocean and in vertical material fluxes in waste-water treatment plants. In both these contexts, the sinking aggregates are “active,” since they are biological hot-spots and are densely colonized by microorganisms including bacteria and sessile protists, some of which generate feeding currents. However, the effect of these feeding currents on the sinking rates, trajectories, and mass transfer to these "active sinking particles," has not previously been studied. Here we use a novel scale-free vertical-tracking microscope (a.k.a. Gravity Machine, Krishnamurthy et al. "Scale-free vertical tracking microscopy." Nature Methods (2020)) to follow model sinking aggregates (agar spheres) with attached protists (Vorticella convallaria), sinking over long distances while simultaneously measuring local flows. We find that activity due to attached \vortc causes significant changes to the flow around aggregates in a dynamic manner and reshapes mass transport boundary layers. Furthermore, we find that activity-mediated local flows along with sinking modify the encounter and plume cross-sections of the aggregate and induce sustained aggregate rotations. Overall our work shows the important role of biological activity in shaping the near-field flows around aggregates with potentially important effects on aggregate fate and material fluxes. 

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2. Nitrogen and Isotope Flows Through the Costa Rica Dome Upwelling Ecosystem: The Crucial Mesozooplankton Role in Export Flux

   https://doi.org/10.1029/2018GB005968  

   Stukel, Michael_R; Décima, Moira; Landry, Michael_R; Selph, Karen_E (December 2018, Global Biogeochemical Cycles)

   Abstract The Costa Rica Dome (CRD) is an open‐ocean upwelling ecosystem, with high biomasses of picophytoplankton (especiallySynechococcus), mesozooplankton, and higher trophic levels. To elucidate the food web pathways supporting the trophic structure and carbon export in this unique ecosystem, we used Markov Chain Monte Carlo techniques to assimilate data from four independent realizations of δ¹⁵N and planktonic rate measurements from the CRD into steady state, multicompartment ecosystem box models (linear inverse models). Model results present well‐constrained snapshots of ecosystem nitrogen and stable isotope fluxes. New production is supported by upwelled nitrate, not nitrogen fixation. Protistivory (rather than herbivory) was the most important feeding mode for mesozooplankton, which rely heavily on microzooplankton prey. Mesozooplankton play a central role in vertical nitrogen export, primarily through active transport of nitrogen consumed in the surface layer and excreted at depth, which comprised an average 36–46% of total export. Detritus or aggregate feeding is also an important mode of resource acquisition by mesozooplankton and regeneration of nutrients within the euphotic zone. As a consequence, the ratio of passively sinking particle export to phytoplankton production is very low in the CRD. Comparisons to similar models constrained with data from the nearby equatorial Pacific demonstrate that the dominant role of vertical migrators to the biological pump is a unique feature of the CRD. However, both regions show efficient nitrogen transfer from mesozooplankton to higher trophic levels (as expected for regions with large fish, cetacean, and seabird populations) despite the dominance of protists as major grazers of phytoplankton. 

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3. Biological composition and microbial dynamics of sinking particulate organic matter at abyssal depths in the oligotrophic open ocean

   https://doi.org/10.1073/pnas.1903080116  

   Boeuf, Dominique; Edwards, Bethanie R.; Eppley, John M.; Hu, Sarah K.; Poff, Kirsten E.; Romano, Anna E.; Caron, David A.; Karl, David M.; DeLong, Edward F. (January 2019, Proceedings of the National Academy of Sciences)

   Sinking particles are a critical conduit for the export of organic material from surface waters to the deep ocean. Despite their importance in oceanic carbon cycling and export, little is known about the biotic composition, origins, and variability of sinking particles reaching abyssal depths. Here, we analyzed particle-associated nucleic acids captured and preserved in sediment traps at 4,000-m depth in the North Pacific Subtropical Gyre. Over the 9-month time-series, Bacteria dominated both the rRNA-gene and rRNA pools, followed by eukaryotes (protists and animals) and trace amounts of Archaea. Deep-sea piezophile-like Gammaproteobacteria, along with Epsilonproteobacteria, comprised >80% of the bacterial inventory. Protists (mostly Rhizaria, Syndinales, and ciliates) and metazoa (predominantly pelagic mollusks and cnidarians) were the most common sinking particle-associated eukaryotes. Some near-surface water-derived eukaryotes, especially Foraminifera, Radiolaria, and pteropods, varied greatly in their abundance patterns, presumably due to sporadic export events. The dominance of piezophile-like Gammaproteobacteria and Epsilonproteobacteria, along with the prevalence of their nitrogen cycling-associated gene transcripts, suggested a central role for these bacteria in the mineralization and biogeochemical transformation of sinking particulate organic matter in the deep ocean. Our data also reflected several different modes of particle export dynamics, including summer export, more stochastic inputs from the upper water column by protists and pteropods, and contributions from sinking mid- and deep-water organisms. In total, our observations revealed the variable and heterogeneous biological origins and microbial activities of sinking particles that connect their downward transport, transformation, and degradation to deep-sea biogeochemical processes. 

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4. Does the settling column method underestimate phytoplankton sinking speeds?

   https://doi.org/10.1098/rsos.231455  

   Du Clos, Kevin T.; Gemmell, Brad J. (February 2024, Royal Society Open Science)

   Phytoplankton sinking is a major component of vertical ocean carbon and nutrient fluxes, and sinking is an integral component of phytoplankton biology and ecology. Much of our understanding of phytoplankton sinking derives from the settling column method (SETCOL) in which sinking speeds are calculated from the proportion of cells reaching the bottom of a water-filled column after a set time. Video-based methods are a recent alternative to SETCOL in which sinking speeds are measured by tracking the movement of individual cells in a salinity-stratified water column. In this study, we present the results of a meta-analysis showing that SETCOL produces significantly and consistently lower sinking speeds than the video method. Next, we perform a particle image velocimetry analysis, which shows that the observed discrepancy in sinking speeds between the two methods can probably be explained by weak convection currents in the SETCOLs. Finally, we discuss the implications of these results for the interpretation of past and future phytoplankton sinking speed measurements and models that rely on those measurements. 

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5. Microscale dynamics promote segregated denitrification in diatom aggregates sinking slowly in bulk oxygenated seawater

   https://doi.org/10.1038/s43247-023-00935-x  

   Ciccarese, Davide; Tantawi, Omar; Zhang, Irene H.; Plata, Desiree; Babbin, Andrew R. (July 2023, Communications Earth & Environment)

   Abstract Sinking marine particles drive the biological pump that naturally sequesters carbon from the atmosphere. Despite their small size, the compartmentalized nature of particles promotes intense localized metabolic activity by their bacterial colonizers. Yet the mechanisms promoting the onset of denitrification, a metabolism that arises once oxygen is limiting, remain to be established. Here we show experimentally that slow sinking aggregates composed of marine diatoms—important primary producers for global carbon export—support active denitrification even among bulk oxygenated water typically thought to exclude anaerobic metabolisms. Denitrification occurs at anoxic microsites distributed throughout a particle and within microns of a particle’s boundary, and fluorescence-reporting bacteria show nitrite can be released into the water column due to segregated dissimilatory reduction of nitrate and nitrite. Examining intact and broken diatoms as organic sources, we show slowly leaking cells promote more bacterial growth, allow particles to have lower oxygen, and generally support greater denitrification. 

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