Fishes are the dominant vertebrates in the ocean, yet we know little of their contribution to carbon export flux at regional to global scales. We synthesize the existing information on fish‐based carbon flux in coastal and pelagic waters, identify gaps and challenges in measuring this flux and approaches to address them, and recommend research priorities. Based on our synthesis of passive (fecal pellet sinking) and active (migratory) flux of fishes, we estimated that fishes contribute an average (± standard deviation) of about 16.1% (± 13%) to total carbon flux out of the euphotic zone. Using the mean value of model‐generated global carbon flux estimates, this equates to an annual flux of 1.5 ± 1.2 Pg C yr⁻¹. High variability in estimations of the fish‐based contribution to total carbon flux among previous field studies and reported here highlight significant methodological variations and observational gaps in our present knowledge. Community‐adopted methodological standards, improved and more frequent measurements of biomass and passive and active fluxes of fishes, and stronger linkages between observations and models will decrease uncertainty, increase our confidence in the estimation of fish‐based carbon flux, and enable identification of controlling factors to account for spatial and temporal variability. Better constraints on this key component of the biological pump will provide a baseline for understanding how ongoing climate change and harvest will affect the role fishes play in carbon flux.

The biological pump transports organic carbon produced by photosynthesis to the meso- and bathypelagic zones, the latter removing carbon from exchanging with the atmosphere over centennial time scales. Organisms living in both zones are supported by a passive flux of particles, and carbon transported to the deep-sea through vertical zooplankton migrations. Here we report globally-coherent positive relationships between zooplankton biomass in the epi-, meso-, and bathypelagic layers and average net primary production (NPP). We do so based on a global assessment of available deep-sea zooplankton biomass data and large-scale estimates of average NPP. The relationships obtained imply that increased NPP leads to enhanced transference of organic carbon to the deep ocean. Estimated remineralization from respiration rates by deep-sea zooplankton requires a minimum supply of 0.44 Pg C y⁻¹ transported into the bathypelagic ocean, comparable to the passive carbon sequestration. We suggest that the global coupling between NPP and bathypelagic zooplankton biomass must be also supported by an active transport mechanism associated to vertical zooplankton migration.

Quantification of the actual amount of carbon export to the mesopelagic layer by both zooplankton and micronekton is at present a gap in the knowledge of the biological pump. These organisms perform diel vertical migrations exporting carbon through respiration, excretion, mortality, and egestion during their residence at depth. The role of zooplankton in active flux is nowadays partially assessed. However, micronekton active flux is scarcely known and only a few studies addressed this downward transport. Even less is known about the capacity of both communities to export carbon in the ocean. Here, we show the results of zooplankton and micronekton active flux across a productivity gradient in the tropical and subtropical Atlantic Ocean. Biomass vertical distribution from the surface up to 800 m depth by day and night was studied during April 2015 in a transect from 9°S to 25°N, covering from the quite oligotrophic zone off Brazil to the meso- and eutrophic areas of the equator, Guinea Dome, and the oceanic upwelling off Northwest Africa. Zooplankton and micronekton migrant biomass was estimated from day and night catches at different layers of the water column using MOCNESS-1 (1 m² mouth area) and Mesopelagos (35 m²) nets, respectively. Respiratory flux was assessed by measuring the enzymatic activity of the electron transfer system (ETS) of organisms at depth. Results showed a close relationship between migrant biomass and respiratory flux in zooplankton and micronekton as expected. Using a rather conservative 50% of efficiency for the net used to capture micronekton, respiratory flux resulted in similar values for both communities. Gravitational (passive) flux measured using sediment traps increased from the oligotrophic toward the meso- and eutrophic zones. Total active flux (including respiration and estimated mortality, excretion, and gut flux) by zooplankton and micronekton accounted for about 25% of total flux (passive plus active) in oligotrophic zones. Total active flux also increased toward meso- and eutrophic zones, reaching about 80% of total flux and being at least twofold higher than passive flux. These results alert about an important underestimation of the ocean biological pump using only passive flux measurements.

The plankton outburst during the so‐called late winter bloom in subtropical waters was studied in relation to lunar illumination in the Canary Island waters. Nutrient enrichment by mixing and dust deposition promoted a bloom of phyto‐ and zooplankton. Mesozooplankton biomass increased as the winter mixing progressed but peaked in every full moon and decreased thereafter because of the effect of predation by interzonal diel vertical migrants (DVMs). The pattern was similar to the one described in lakes due to predation by fishes and confirms that this phenomenon is important in the sea. The estimated consumption and subsequent transport of epipelagic zooplankton biomass by DVMs after every full moon is on the order of the mean gravitational export and is an unaccounted flux of carbon to the mesopelagic zone that may play a pivotal role in the efficiency of the biological pump.

Mesozooplankton ammonium excretion rates in the ocean, based on published data, were studied across all latitudes in order to assess the amount of ammonium excretion by this community. Specific ammonium excretion rates were highest in equatorial waters and decreased rapidly pole-ward. Global community excretion in the upper 200 m of the oceans, integrated over all latitudes, accounted in general for 1.78 ± 0.60 Gt N·year⁻¹. Excretion rates showed a decrease from tropical (0.65 ± 0.14 Gt N·year⁻¹) to polar waters (0.05 ± 0.02 Gt N·year⁻¹). The substrate metabolized by organisms as indicated by the O/N ratio showed a protein-based metabolism of mesozooplankton with the exception of the temperate and subpolar regions, which showed a more lipid-based metabolism. The largest contribution of ammonium to autotrophs was observed in the tropical and subtropical areas, decreasing to polar areas. On a global basis, nutrient regeneration by mesozooplankton in the oceanic realm was estimated to be in the range of 12–23% of the requirements for phytoplankton and bacterial production.

The abundance and composition of zooplankton down to 3000 m depth was studied in the subtropical and tropical latitudes across the Atlantic, Pacific and Indian Oceans (35 °N–40 °S). Samples were collected from December 2010 to June 2011 during the Malaspina Circumnavigation Expedition. Usually, low abundances were observed with the highest values found in the North Pacific Ocean, Benguela, and off Mauritania, and the lowest in the South Pacific Ocean. No significant differences in abundance and zooplankton composition were found among oceans, with depth being consistently the most important factor affecting their distribution. Each depth strata were inhabited by distinct copepod assemblages, which significantly differed among the strata. The contribution of copepods to the zooplankton community increased with the depth although, as expected, their abundance strongly decreased. Among the copepods, 265 species were identified but 85% were rare and contributed less than 1% in abundance. Clausocalanus furcatus and Nannocalanus minor dominated the epipelagic strata. Pleuromamma abdominalis and Lucicutia clausi were of importance in the mesopelagic layer, and Pareucalanus, Triconia, Conaea and Metridia brevicauda in the bathypelagic layer. Our results provide a global-scale assessment of copepod biodiversity and distribution, providing a contemporary benchmark to follow future ocean changes at low latitudes.