The presence of zooplankton swimmers and carcasses in sediment trap samples has long been a concern in particle flux studies. We successfully developed a protocol using the vital stain Neutral Red to distinguish between copepod swimmers and carcasses in conventional cylindrical sediment traps. Swimmers were stained red whereas carcasses were pale or unstained. The color distinction allowed easy quantification of the two. We subsequently used the protocol in Otsuchi Bay, Japan, on 4 consecutive days in May and again in July 2013. Carcasses were present in the sediment traps on all occasions, and calanoid and cyclopoid copepods accounted for 60.0− 93.6% of all carcasses. Swimmers were 1−2 orders of magnitude more abundant than carcasses, with cyclopoid copepods accounting for up to 75.6% of all swimmers. Copepod carcass flux was negatively related to current velocity at the trap depth. Overall, inclusion of copepod carcasses added no more than 10% to the total particulate organic flux, whereas inclusion of swimmers increased the particulate carbon flux by as much as 87.4%. The low C:N ratio of the other trap materials suggests that sinking particles were a high-quality food source for the benthos in Otsuchi Bay.

Temporal changes in mesozooplankton abundance affect planktonic food web interactions and biogeochemistry. We enumerated mesozooplankton from monthly day and night tows in the epipelagic zone at the Bermuda Atlantic Time-series Study (BATS) site in the Sargasso Sea (1999–2010). Abundances of each taxon were determined using a ZooScan imaging system and microscopy. Generalized linear models were used to determine environmental parameters that best explained abundance patterns. Taxa with pronounced diel vertical migration included euphausiids, amphipods, Limacina spp. pteropods, and other shelled pteropods. Taxa with a pronounced spring abundance peak included euphausiids, appendicularians, and Limacina spp., while harpacticoid copepods peaked in late summer, and calanoid copepods in late winter/early spring and summer. Many taxa increased in 2003, coincident with a diatom bloom and the largest primary production peak in the time series. Long-term, increasing trends occurred in calanoid and oncaeid copepods, and ostracods, with barnacle nauplii significantly increasing. Sub-decadal-scale climate oscillations and long-term warming may be driving decreases in shelled pteropods and appendicularians. Chaetognath abundance increased in response to increased density of a major prey taxon, calanoid copepods. Calanoid copepods and ostracods increased with increasing water column stratification index and the Atlantic Multidecadal Oscillation index, indicating warmer sea surface temperatures favour these taxa.

Understanding global warming effects on marine zooplankton is key to proper management of marine resources and fisheries. This is particularly urgent for Japan where the coastal water temperature has been increasing faster than the global average over the past decade. Conventional sampling and monitoring programmes, by ignoring the in situ vital status of the zooplankton, produce incomplete information about the state of the ecosystem. We showed that marine copepod carcasses were ubiquitous along a latitudinal gradient of 34–39°N of the Japanese coasts. On average, 4.4–18.1% of the individuals of the main copepod genera (Acartia, Paracalanus, Oithona, and Pseudocalanus) were carcasses, equivalent to 19–250 µg C m−3. Higher fractions of dead copepods tended to occur at higher water temperatures, implicating temperature-dependent non-predation mortality. Carcass occurrence may represent a loss of copepod production for the traditional predation-based food chain. On average, 49.5% of the carcass carbon would be remineralized in the water column via bacteria respiration, with the remainder potentially exported to the seafloor. Continuous warming in the Japanese coasts is expected to accelerate non-predation copepod mortality, with unknown consequences for the local marine food web.

Eastern boundary systems support major fisheries of species whose early stages depend on upwelling production. However, upwelling can be highly variable at the regional scale, leading to complex patterns of feeding, growth, and survival for taxa that are broadly distributed in space and time. The northern California Current (NCC) is characterized by latitudinal variability in the seasonality and intensity of coastal upwelling. We examined the diet and larval growth of a dominant myctophid (Stenobrachius leucopsarus) in the context of their prey and predators in distinct NCC upwelling regimes. Larvae exhibited significant differences in diet and growth, with greater seasonal than latitudinal variability. In winter, during reduced upwelling, growth was substantially slower, guts less full, and diets dominated by copepod nauplii. During summer upwelling, faster-growing larvae had guts that were more full from feeding on calanoid copepods and relying less heavily on lower trophic level prey. Yet, our findings revealed a dome-shaped relationship with the fastest growth occurring at moderate upwelling intensity. High zooplanktivorous predation pressure led to above average growth, which may indicate the selective loss of slower-growing larvae. Our results suggest that species whose spatio-temporal distributions encompass multiple regional upwelling regimes experience unique feeding and predation environments throughout their range with implications for larval survivorship.