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Metagenetics is a rapid and taxonomically comprehensive method for revealing community structures within environmental samples, based on large amounts of sequence data produced by high-throughput sequencers. Because community structures of planktonic copepods are important in the ocean owing to their high diversity and abundance, a metagenetic analysis of the 28S D2 region using Roche 454 was previously developed. However, the Illumina MiSeq platform with a high sequence output is being used more frequently in metagenetics, and non-calanoid copepods have not previously been fully evaluated. Here, we evaluated an Illumina MiSeq-based metagenetic analysis using a mock community and field-collected samples that were examined in a previous study using Roche 454, and the community structure, including non-calanoid copepods, was compared among morphological and metagenetic analyses. We removed a singleton read and applied an appropriate abundance threshold to remove erroneous Molecular Operational Taxonomic Units (MOTUs) with low-abundance sequences in the MiSeq-based analysis. Results showed that the copepod community was successfully characterized using Illumina MiSeq. Higher-quality sequences were obtained using MiSeq than by Roche 454, which reduced the overestimation of diversity, especially at a strict 99% similarity threshold for MOTU clustering. Taxonomic compositions in terms of both biomass and presence/absence of species, including non-calanoids, were more appropriately represented in the MiSeq- than in Roche 454-based analysis. Our data showed that metagenetic analysis using Illumina MiSeq is more useful for revealing copepod communities than Roche 454, owing to the lower cost and higher quality.

Nitrogen-fixing microorganisms (diazotrophs) significantly influence marine productivity by reducing nitrogen gas into bioavailable nitrogen. Recently, non-cyanobacterial diazotrophs (NCDs) have been identified as important contributors to marine nitrogen fixation. Among them, Gamma A is one of the best-studied marine NCDs because of its ubiquitous occurrence; however, the factors controlling its distribution remain unknown. In particular, the importance of microzooplankton grazing as a top-down control has not yet been examined. In this study, we investigated the diazotroph community structure using nifH amplicon sequencing and quantified the growth and microzooplankton grazing mortality rate of Gamma A using a combination of dilution experiments and quantitative polymerase chain reaction (PCR) in well-lit waters at the northern edge of the Kuroshio Current off the southern coast of Japan. In the study region, Gamma A was ubiquitous and dominant in the diazotroph communities, whereas cyanobacterial diazotrophs had lower relative abundances. The microzooplankton grazing rate of Gamma A was significantly higher than that of the whole phytoplankton community and was generally balanced with its growth rate, suggesting the efficient transfer of fixed nitrogen by Gamma A to higher trophic levels. Although the growth rates of Gamma A did not show clear responses to nutrient amendments, Gamma A abundance had a significant relationship with nutrient concentration and microzooplankton grazing mortality rate. This suggests that microzooplankton grazing, as well as nutrient concentration, plays a vital role in constraining the Gamma A distribution in the Kuroshio region. Our findings highlight the importance of the further in situ quantification of microzooplankton grazing rates to understand the distribution of diazotrophs and the associated nitrogen transfer into the food web.

During August 2017, the Kuroshio began to follow its large meander (LM) path, and this was 12 years after the last LM event. Such LM events lead to the formation of an inshore cyclonic eddy (ICE) within the Kuroshio inshore region between the Kuroshio and the southern coast of Japan. We analyzed data from repeated seasonal surveys along a transect that followed 138°E, and from additional surveys, satellite observations, Argo floats, and a high-resolution reanalysis dataset to describe the temporal variation of the LM and ICE between 2017 and 2021. Cross sections from the repeated surveys highlighted the variations in the water mass structures. The time series of the indicators of the ICE intensity such as the Kuroshio volume transport and the planetary contribution of potential vorticity ( Q ) in the ICE revealed a maintenance trend in their intensity during the observation period. High- Q water was distributed in the ICE during the LM period compared to the non-LM period, and showed a clear seasonality within the shallower layers, suggesting the injection of Q via the advection from the upstream region in summer. Additional surveys captured an eddy that became detached from the ICE during summer 2020. This detached eddy had a Q value greater than the ICE and velocity similar to the Kuroshio, suggesting that the main stream had become temporarily separated. The structures and volume transport of warm water intrusions into the inshore region were also examined, and centrifugal instability was considered to be one of their generation mechanism.

A continuous flow method for the determination of ammonium concentration in seawater from a nanomolar to a micromolar level is described. To prevent spurious peaks derived from salinity difference, a gas-permeable hydrophobic membrane filter was used to separate the manifold into an outgassing section and an indophenol blue reaction section. The indophenol blue reaction section was adopted for colorimetric analysis and is equipped with a 1-m path length liquid capillary cell and a fiber-optic spectrometer, which is able to record the absorbance at multiple wavelengths. The minimum detection limit at wavelength 630 nm is 5.5 ± 1.8 nM, and the calibration curves are linear to at least 2,000 nM. In addition, the minimum detection limit at wavelength 530 nm was 13 ± 5.3 nM, and linear calibration curves were observed until at least 10,000 nM. The slopes of the calibration curves were similar for standards prepared using filtered seawater and ultrapure water. The ammonium concentration of the ultrapure water was similar to those of ion-exchanged water and unfiltered low-nutrient seawater, but was significantly lower than those of filtered seawater and solutions that contained sodium hydroxide. Therefore, ultrapure water is optimal for both blank and standard preparations because of its stable quality and availability. Given its large concentration range and the use of readily available blanks, this method is suitable for the determination of ammonium concentration and helps our understanding of ammonium dynamics in the ocean.

We examined the degradation of discarded appendicularian houses due to feeding by oncaeid copepods in surface waters of the Kuroshio region. Vertical distributions of oncaeid copepods and discarded houses were investigated by optical sampling using a video plankton recorder (VPR). In situ VPR observations revealed that oncaeid copepods were commonly associated with discarded houses: the proportion of individuals attached to discarded houses reached saturated values of 25-39% at house concentrations above 2000 houses m−3, suggesting that feeding by oncaeids was not limited by encounters at house concentrations typically observed in the upper 50 m. Laboratory observations confirmed that oncaeid copepods attached to the surface of discarded houses and ingested both house membranes and adhering particles. Individual feeding rates of the dominant Oncaea species, O. venusta and O. media, determined by measuring fecal pellet production and assimilation efficiency, varied from 0.13 μg C ind.−1 d−1 to 1.3 μg C ind.−1 d−1 (10-37% body C d−1). Our results indicate that the oncaeid copepod community consumed up to 10% of house biomass each day in the upper 100 m of the water column, and show that through their close trophic coupling with discarded appendicularian houses, the oncaeids contribute significantly to house degradation in surface waters.

The Kuroshio Current, a western boundary current in the North Pacific Ocean, is regarded as a hotspot of nitrogen fixation that drives marine primary productivity and biogeochemical cycles. However, this assumption is based on limited, spatiotemporally biased data. We curated nitrogen fixation data and applied a generalized additive model to revisit the distribution and total amount of nitrogen fixation in the Kuroshio region. We found a substantial spatial variation, with lower nitrogen fixation in southern Japan and higher rates in the more upstream areas. These variations were explained by nitrate concentration, sea surface temperature, and the distance along the Kuroshio from its origin. We calculated the total nitrogen fixation for the Kuroshio region to be approximately half of the previous estimate. This study provides a more precise estimate of the regional nitrogen fixation and highlights its biogeochemical importance in the Kuroshio region and the western North Pacific Ocean.

A continuous survey examined short-term variations in the zooplankton community and physical ocean environment from the northeastern Izu Islands to Boso Peninsula in Japan. High copepod abundance and small upwellings in the surface layer and salinity minimum layer in the subsurface were observed on the north side of coastal fronts in the westernmost transect, moving southward as the Kuroshio Current left the Boso Peninsula. Thus, the salinity minimum layer might be a key factor forming upwelling and the fronts, leading to large abundance of coastal copepods off the northeastern Izu Islands. A community structure analysis of calanoid copepods revealed an intermediate belt assemblage between coastal and offshore (Kuroshio) assemblages. Copepod abundance was remarkably low and Ctenocalanus vanus dominated (nearly 37%) in the intermediate belt zone, indicating that C. vanus has a relatively high tolerance to adverse environments for calanoid copepods. As the Kuroshio Current left the Boso Peninsula, the coastal assemblage expanded in the same direction, and the intermediate belt assemblage off the northeastern Izu Islands disappeared. The largest population of Calanus sinicus was found along the two western transects off the northeastern Izu Islands (>1000 m depth), which was assumed to be transported from Sagami Bay and advanced southwestward while growing from copepodite stages CIII to CV. Larvae of C. sinicus would be an important food for fish larvae in addition to Paracalanus parvus  s.l., the numerically dominant species in the coastal assemblage, and C. vanus under the adverse conditions for coastal copepods.

The biological pump that transports carbon from the surface ocean to the ocean interior is an important determinant of ocean carbon absorption from the atmosphere, and of biological activity beneath the euphotic zone. Various factors influence the magnitude and efficiency of this biological pump, such as primary production, particle size, and the composition of consumers of particulate organic carbon (POC). The complex factors influencing the biological pump induce high regional and temporal variability; however, the mechanisms of this variability are not understood and its causes remain unclear. The size of sinking particles has been hypothesized to affect the attenuation of POC flux via reduction of residence time within the water column. Here, we conducted sediment trap experiments in slope and subtropical gyre areas along the Kuroshio in the subtropical North Pacific. The ratio of POC flux at a depth 100 m below the base of the euphotic zone to that at the base of the euphotic zone ( T 100 ) varied from 0.307 to 0.646 and from 0.090 to 0.958 in the slope and subtropical gyre areas, respectively, and was positively correlated with variations in the volume-weighted mean particle diameter (Spearman rank order correlation coefficient: 0.700, p < 0.05, n = 9). However, the variation in T 100 was not correlated with ambient water temperature ( p > 0.05). The results support the hypothesis that attenuation of POC flux is influenced by the size of sinking particles in oligotrophic oceanic areas.

Species composition, diversity and biomass of jellyfish (Cnidaria and Ctenophora), with their spatio-temporal distributions, were analyzed in the upper 1500 m of the Oyashio front, the Transition zone and the Kuroshio extension, off Tohoku, northeastern Japan, between May 2005 and March 2006. Species composition and abundance differed remarkably between the shallower layer and the deeper layer at the boundary of 300-500 m depth, where water density was within the range of the North Pacific Intermediate Water. In the deeper layer, diversity reached its peak with the appearance of 27 taxa common in all the regions throughout the year, though abundance was low. Pantachogon haeckeli and Crossota rufobrunnea were dominant in the deeper layer. The possibility of diel vertical migration was suggested in two midwater species: Euphysa japonica and Atolla vanhoeffeni. In the Oyashio waters, jellyfish abundance was much higher than in the Transition waters and Kuroshio-derived waters, but with low diversity, dominated by large numbers of Aglantha digitale and Dimophyes arctica. High values of diversity were found in the Kuroshio-derived waters with various tropical and warm-water species, especially calycophoran siphonophores being present. In the Transition waters, diversity was relatively high, with co-occurrence of warm-water species and cold-water species. Jellyfish biomass tended to be high in the midwater zone due to the occurrence of large species, particularly Scyphozoa. Carbon-based jellyfish biomass calibrated with other studies exceeded that of other organism groups.

Seasonal and spatial contrasts of nitrate + nitrite (N + N) concentrations in the slope area (the inshore area to the Kuroshio), Kuroshio and subtropical gyre areas were described by using data sets carried out along the O-line (138°E) between 34°45′N and 30°N over 11 years (2002–2013). The mean concentration of N + N in the surface mixed layer during winter was elevated to 4.8 ± 2.7, 1.5 ± 1.6 and 0.7 ± 0.4 µM in the slope, Kuroshio and subtropical gyre areas, respectively, while it was depleted to < 0.1 µM in all areas during summer. Applying regression analyses to the data, a significant negative correlation between N + N concentration and temperature was found at any depths above 1000 m in both summer and winter in these areas, except for the summer surface depletive layers. The analyses also showed that the diffusive upward flux and the depth difference between the surface mixed layer and the 15-µM nitrate-isoconcentration depth were important factors to induce the seasonal contrast between winter and summer and horizontal contrast among the slope, Kuroshio and gyre areas in the N + N concentration in the surface mixed layer. Since the nitrate-isoconcentration depth is much shallower in the slope area than in the other two areas, the developing wintertime mixed layer reaches to the nitrate-rich water in the slope area, and that leads to a several micromolar increase in the surface N + N concentration there.