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Global climate change occurs not only at the ocean surface but also at the ocean bottom, which is the main habitat of demersal fish. To clarify the current status of bottom temperature warming off the Pacific coast of northeastern Japan, we examined gridded bottom temperature fields from 2003 to 2019. These fields were created by a newly developed gridding method using flexible Gaussian filter weighting with time, distance, and depth. Spatially averaged bottom temperature had a strong, significant warming trend of 0.083 to 0.115°C yr-1 in depth zones of 150-300 m, indicating bottom temperature warming. Corresponding to the warming, increases in landing amounts were found for warm-water species such as searobin in the middle region of our study area (37°50’-39°N). Seasonal catch amounts suggest that ribbon fish and swimming crab recently began to overwinter and reproduce in the area. The distribution shifts of non-target species in fisheries were also analyzed using bottom otter trawl survey data from the area from 2003 to 2019. Northward distribution shifts and increases in density were observed in blackbelly lantern shark and bighand grenadier, indicating that bottom temperature warming led to habitat expansion. Conversely, darkfin sculpin and jelly eelpout shifted northward with decreasing density, suggesting that bottom temperature warming had a negative effect on them. Deepsea bonefish shifted deeper into colder waters with increasing density and mean body weight. Thus, changes and responses of demersal fish to bottom temperature warming in the area were revealed.

We investigated how the nutrient status of Matsushima Bay was affected when a wastewater plant was destroyed by a tsunami in March 2011. The nutrient concentrations in the seawater and the treated water from the wastewater plant increased just after the tsunami, but decreased again to pre-tsunami levels after 2013. The amount of untreated water that passed through the wastewater plant decreased just after the tsunami. It was estimated that approximately 40.7 × 103 m3/day of the treated water from the wastewater plant was discharged to Matsushima Bay; therefore, the quantity of effluent from the wastewater plant was less than one percent of the water inflow from Takagi River and Sendai Bay (which are outside Matsushima Bay) to Matsushima Bay. The nutrient concentrations of seawater in Sendai Bay were lower than those in Matsushima Bay. The results suggest that nutrient concentrations in Matsushima Bay after the tsunami did not increase because any untreated or poorly treated effluent was easily diluted by the river flow and the inflow of seawater. Many people were concerned about eutrophication, therefore, because of the decreased functioning of the wastewater plant in Matsushima Bay. Marked eutrophication in the bay was not observed after August 2011.

Seasonal changes in habitat use in terms of depth and temperature were estimated for Japanese flounder Paralichthys olivaceus from the Pacific coast of northeastern Japan from 2006 to 2008, using data from trawl and gillnet fisheries logbooks, to which we assigned monthly estimates of bottom temperature. Estimated distributions of flounder for depth and temperature were validated by actual depth and temperature readings from data storage tags (DSTs) attached to flounder, and from collection records by trawl survey. Year-round, flounder > 300 mm in total length were present mainly in areas

The Pacific saury (Cololabis saira) is a fish of commercial importance subject to unpredictable epidemics of infection by Pennella sp., a parasitic copepod. We analyzed the distribution of fish presenting with newly attached Pennella to determine the region and season in which Pennella first infect the fish. Pacific sauries migrate northward in the spring to spend the summer in the subarctic region, successively crossing the Subarctic Boundary (SAB) and the Subarctic Front (SAF). The fish then return to subtropical waters in the fall and overwinter there. Pacific sauries infected with Pennella were observed on both the north and south sides of the SAF from May to December. Newly attached Pennella, however, were observed mainly to the south of the SAF during the northward migration of the fish in May and June, and only to the south of the SAB during the southward migration in November and December. These results indicate that the intermediate host or hosts of Pennella inhabit the region south of the SAF, with infection of Pacific saury occurring during late fall and spring. Such information may assist in identifying the intermediate host(s).

The Oyashio–Kuroshio Transitional Region (OKTR) is a nursery ground for pelagic fishes; thus, community succession of mesozooplankton is pivotal to understand prey availability, and it subsequently affects recruitment success. We investigated the surface distribution, biomass, and species composition of thaliaceans (salps and doliolids) that potentially have a significant impact on the food web and biogeochemical cycle by forming intensive blooms. A total of 11 thaliacean species were recorded from 62 locations along two transects at 36° N and 38.5° N extending from 142° E to 180° in May to June 1993. Salps and doliolids were found at 93% and 84% of the stations, respectively, and their biomass values varied widely in space (0.00011–79.56 and 0.00001–5.11 mg C m−3 for salps and doliolids, respectively). Thalia democratica was the most dominant salp and particularly abundant at stations east of 165°E on the 36°N-line; the abundance varied from 103 to 1379 ind m−3. Dolioletta gegenbauri and Doliolum denticulatum were dominant doliolids, although their biomass values were far lower than that of salps. Multivariate statistical analysis with PRIMER revealed that the distribution of thaliaceans in the OKTR was not uniform in space and was affected by oceanographic conditions; doliolids tended to occur in much warmer (14.10–15.63 °C) and saline water mass (34.54–34.72) than salps (13.16–14.95 °C and 34.40–34.53). In terms of population clearance rates, the most dense salp blooms have the potential to sweep > 200% of their resident water per day, indicating that salp blooms cause deleterious feeding conditions for pelagic fishes through non-selective filter feeding.

Although numerous metagenome, amplicon sequencing-based studies have been conducted to date to characterize marine microbial communities, relatively few have employed full metagenome shotgun sequencing to obtain a broader picture of the functional features of these marine microbial communities. Moreover, most of these studies only performed sporadic sampling, which is insufficient to understand an ecosystem comprehensively. In this study, we regularly conducted seawater sampling along the northeastern Pacific coast of Japan between March 2012 and May 2016. We collected 213 seawater samples and prepared size-based fractions to generate 454 subsets of samples for shotgun metagenome sequencing and analysis. We also determined the sequences of 16S rRNA (n = 111) and 18S rRNA (n = 47) gene amplicons from smaller sample subsets. We thereafter developed the Ocean Monitoring Database for time-series metagenomic data (http://marine-meta.healthscience.sci.waseda.ac.jp/omd/), which provides a three-dimensional bird’s-eye view of the data. This database includes results of digital DNA chip analysis, a novel method for estimating ocean characteristics such as water temperature from metagenomic data. Furthermore, we developed a novel classification method that includes more information about viruses than that acquired using BLAST. We further report the discovery of a large number of previously overlooked (TAG)n repeat sequences in the genomes of marine microbes. We predict that the availability of this time-series database will lead to major discoveries in marine microbiome research.

The taxonomic compositions of marine prokaryotic communities are known to follow seasonal cycles, but functional metagenomic insights into this seasonality is still limited. We analyzed a total of 22 metagenomes collected at 11 time points over a 14-month period from two sites in Sendai Bay, Japan to obtain seasonal snapshots of predicted functional profiles of the non-cyanobacterial prokaryotic community. Along with taxonomic composition, functional gene composition varied seasonally and was related to chlorophyll a concentration, water temperature, and salinity. Spring phytoplankton bloom stimulated increased abundances of putative genes that encode enzymes in amino acid metabolism pathways. Several groups of functional genes, including those related to signal transduction and cellular communication, increased in abundance during the mid- to post-bloom period, which seemed to be associated with a particle-attached lifestyle. Alternatively, genes in carbon metabolism pathways were generally more abundant in the low chlorophyll a period than the bloom period. These results indicate that changes in trophic condition associated with seasonal phytoplankton succession altered the community function of prokaryotes. Our findings on seasonal changes of predicted function provide fundamental information for future research on the mechanisms that shape marine microbial communities.

Yield from fisheries is a tangible benefit of ecosystem services and sustaining or restoring a fish stock level to achieve a maximum sustainable yield (MSY). Snow crab (Chionoecetes opilio) off Tohoku has been managed by a total allowable catch since 1996, although their abundance has not increased even after 2011, when fishing pressure rapidly decreased because of the Great East Japan Earthquake. This implies that their biological characteristics, such as recruits, natural mortality coefficient (M), and terminal molting probabilities (p), might have changed. We developed “just another state-space stock assessment model (JASAM)” to estimate the MSY of the snow crab off Tohoku, Japan, considering interannual variations inMandp. The multi-model inference revealed thatMincreased from 0.2 in 1997 to 0.59 in 2018, although it was not different among the instars, sex, nor terminal molt of crabs. The parameterpalso increased by 1.34–2.46 times depending on the instar growth stages from 1997 to 2018. We estimated the MSYs in three scenarios, which drastically changed ifMandpwere set as they were in the past or at the current values estimated from this study. This result indicated that the MSY of snow crab would also be time-varying based on their time-varying biological characteristics.

This chapter reviews interdecadal variations of the Oyashio from the 1960s to the 2010s and the impacts of the Oyashio on coastal waters with a focus on the Extreme Cold Water Events (ECWEs) that occur during winter–spring near the Japanese coast adjacent to the Oyashio. The southernmost latitude of the First Oyashio Intrusion migrated southward in response to the basin-scale wind stress from the mid-1960s to the mid-1980s, while it changed less interdecadally from the mid-1990 to the mid-2010s. For the latter period, the Oyashio transport/velocity, including the intensity of the Western Subarctic Gyre, decreased interdecadally. Representative ECWEs occurred during winter–spring in 1963, 1974, 1981, 1984, 2006, and 2014. These ECWEs occurred under different conditions during the two periods; the ECWEs in 1963, 1974, 1981, and 1984 were accompanied by extreme southward intrusions of the Oyashio, whereas the ECWEs in 2006 and 2014 were not. The ECWEs in 2006, 2014, 1974, and 1984 occurred concomitantly with an extreme intensification of wind-induced circulation in the Okhotsk Sea that lasted a few months. Hence, the ECWEs could be caused by either or both of extreme southward intrusion of the Oyashio and extreme intensification of wind-induced circulation in the Okhotsk Sea.

Natural seedling collection is widely used in the culture of various bivalve species. For successful natural seedling collection, collectors must be installed when larvae appear in the water column at a stage immediately before attachment. Aquaculture farmers generally identify target larvae by morphological features through microscopic examination in a time- and labor-expensive exercise, which also requires a level of expertise to ensure accurate larval identification. We develop a deep-learning-based object-detection technique that ultimately might reduce the time and effort required to accurately identify and count Pacific oyster larvae, render their identification more consistent, and negate the need for expertise. Images of plankton net samples collected in Matsushima and Sendai bays, Japan, were taken using a new photographic device with a CMOS image sensor. Images of oyster larvae identified by an expert were used to create a library of labeled images to train a deep-learning model, which proved to be 82.4% accurate in precision, 90.8% in recall, and 86.4% in F-measure. A further method for estimating larval shell height from the rectangular shape of oyster larval images is also developed. The standardized mean difference in shell height between measurements and estimates is 3.3%. This deep-learning model has the potential to significantly reduce the time and effort required to identify oyster larvae in plankton samples, and thereby costs of this exercise.

We used salinity and potential alkalinity data from hydrographic observations to investigate surface mixing ratios in the Kuroshio-Oyashio mixed water region in the western North Pacific. In addition to mixing between the Kuroshio Extension (KE) and Oyashio, we assessed freshwater input/removal. A mixing scenario with three end-members was assumed in the surface layer ≤100 m. The results indicate that water masses near the sea surface in the Kuroshio-Oyashio mixed water region were mainly the result of mixing between the KE and Oyashio. The freshwater contribution was approximately 2.2% at depth 10 m. The volume of freshwater estimated from this percentage was consistent with surface water budgets estimated from reanalysis precipitation and evaporation data. The estimated mixing ratio of the KE (rk) along the quasi-stationary jet in the western North Pacific, which splits from the KE and flows northeastward toward the subarctic region, decreased downstream from 95% to 27% in only 42 days, suggesting that water properties were changed rapidly by mixing. Correlation between rk around the quasi-stationary jet and nutrients concentration was significantly negative in the layer where photosynthesis was negligible, indicating that the mixing between the KE and Oyashio is an important determinant of the horizontal distribution of nutrients in this area.

To investigate the influence of a river discharging outside a bay on circulation in the bay, we carried out current and salinity measurements from mooring systems and hydrographic observations in Matsushima Bay, Japan, and off the Naruse River, which discharges outside the bay. Previously, enhancement of horizontal circulation in the bay induced by increased freshwater input from the Naruse River was reported to have degraded the seedling yield of wild Pacific oysters in the bay, but the freshwater inflow from the river was not directly measured. Our hydrographic observations in Katsugigaura Strait, approximately 3 km southwest of the Naruse River mouth, detected freshwater derived from the river. The mooring data revealed that freshwater discharged by the river flowed into Matsushima Bay via the strait and that the freshwater transport increased when the river was in flood. The inflow through straits other than Katsugigaura was estimated by a box model analysis to be 26–145 m3 s−1 under normal river discharge conditions, and it decreased to 6 m3 s−1 during flood conditions. During flood events, the salt and water budgets in the bay were maintained by the horizontal circulation: inflow occurred mainly via Katsugigaura Strait, and outflow was mainly via other straits.

To understand long-term mean and seasonal variations of the Oyashio transport off the southeastern coast of Hokkaido, time series of estimated transports were generated by combining satellite altimetry and CTD data from the period 1993–2014 along a monitoring transect referred to as the “A-line”. Linear regressions between CTD-derived geostrophic transport and altimetry-derived sea level anomaly differences were calculated by minimizing a cost function newly proposed in this study. The horizontal structure of 21-year mean transport was characterized by a southwestward flow on the continental slope (SW-1) associated with the First Oyashio Intrusion, a northeastward flow (NE-2) likely trapped against the Kuril-Kamchatka trench, a southwestward flow (SW-3) related to the Second Oyashio Intrusion, and a very stable northeastward flow (NE-4) corresponding to a combination of the Oyashio Return Flow and quasi-stationary Jet. Analysis of long-term mean monthly transports revealed four alternating flows that were present throughout all seasons of the year. The boundaries between adjacent pairs of the four flows on the A-line did not change on a seasonal timescale as much as the southernmost latitude of the First Oyashio Intrusion. At a 0-month (1-month) time lag, the sum of the SW-1, NE-2, and SW-3 (SW-1 and NE-2) transports, which corresponds to net Oyashio transport (partial net Oyashio transport related to the southernmost latitude of the First Oyashio Intrusion), was correlated with Sverdrup transport more robustly than was each of the four alternating flows. This result suggests that as the Oyashio crossed the A-line, it responded barotropically to basin-scale wind stress by adjusting transports composed of both southwestward and northeastward flows.

The relationships between the spatiotemporal variation in phytoplankton community structure and environmental variables were investigated in the Kuroshio Extension (KE) region from winter to spring by analysing biomarker pigments. In winter, when the mixed layer was deep, phytoplankton communities were characterised by low biomass and a relatively high dominance of cryptophytes, followed by chlorophytes and pelagophytes. In spring, phytoplankton biomass generally increased with shoaling of the mixed layer. In April, when nitrate was not exhausted, chlorophytes became the most dominant group throughout the KE region, followed by cryptophytes. In May, in the south of the KE, phytoplankton biomass decreased with the depletion of nitrate and cyanobacteria dominated, whereas at the northern edge of the KE, phytoplankton biomass remained high. A predominance of diatoms occurred sporadically at the northern edge of the first ridge with a shallow mixed layer and an elevated nutricline. In contrast, the contribution of diatoms was low at the northern edge of the second ridge, despite high levels of nitrate and silicic acid, suggesting that factors other than macronutrient depletion limited diatom production. In general, the contribution of diatoms to the total phytoplankton biomass in the KE region was small in both winter (2.9%) and spring (16%). This study showed that the phytoplankton communities in the KE region during the spring bloom were generally composed of non-diatom phytoplankton groups, chlorophytes, cryptophytes, and prasinophytes. It is necessary to identify the roles of non-diatoms in grazing food chains to more accurately evaluate the KE as a nursery area for pelagic fish.

To address various fisheries science problems around Japan, the Japan Fisheries Research and Education Agency (FRA) has developed an ocean forecast system by combining an ocean circulation model based on the Regional Ocean Modeling System (ROMS) with three-dimensional variational analysis schemes. This system, which is called FRA-ROMS, is a basic and essential tool for the systematic conduct of fisheries science. The main aim of FRA-ROMS is to realistically simulate mesoscale variations over the Kuroshio-Oyashio region. Here, in situ oceanographic and satellite data were assimilated into FRA-ROMS using a weekly time window. We first examined the reproducibility through comparison with several oceanographic datasets with an Eulerian reference frame. FRA-ROMS was able to reproduce representative features of mesoscale variations such as the position of the Kuroshio path, variability of the Kuroshio Extension, and southward intrusions of the Oyashio. Second, using a Lagrangian reference frame, we estimated position errors between ocean drifters and particles passively transported by simulated currents, because particle tracking is an essential technique used in applications of reanalysis products to fisheries science. Finally, we summarize recent and ongoing fisheries studies that use FRA-ROMS and mention several new developments and enhancements that will be implemented in the near future.

Metagenome analysis could be a useful tool to monitor biological diversities in marine environments. However, environmental conditions fluctuate widely in coastal areas. We examined bacterial community compositions in coastal seawater from Sendai Bay for 2 years to clarify their temporal variation in relation to physical and biological environmental factors. Sequencing of 16S rRNA gene amplicons revealed obvious annual variation and the significant associations of temperature, salinity, and chlorophyll a concentration with the community composition change. The most dominant operational taxonomic unit (OTU) was assigned to the oceanic bacterium, SAR11. An OTU assigned to Rhodobacteraceae was also dominant during phytoplankton blooms. OTUs assigned to cyanobacteria or Alteromonadaceae were increased in the warm water period after phytoplankton blooming, from June to September. Of the top 20 OTUs, 12 OTUs had a significant correlation with water temperature, indicating seasonal fluctuation. Three OTUs significantly correlated with salinity, indicating that freshwater discharge influenced the bacterial community in the bay. Five OTUs that represented 38% of the total did not show any correlation with environmental factors. The dominant SAR11 OTU was included in this category, implying that hydrographical conditions are very important factors determining microbial community composition in coastal seawater.

Matsushima Bay is one of the famous cultivation area of oysters. However, it is reported that the seedling collection decline in 2013. It is necessary to clarify this cause in order to take a countermeasure. There is some possibility that strong tidal currents through narrow straits cause oyster larvae in the bay to flow out. It is pointed out that increase of river discharge leads to a large flow of them. This research aims to clarify the influence on the movement of larvae in Matsushima Bay, especially focused on currents and river discharge. In this paper, the numerical model for tidal currents around Matsushima Bay is developed as the first step of the study to clarify their influence on them. The model is based on finite volume method with unstructured grid system and generalized terrain-following coordinate system (FVCOM). The model reproduces the influence on tidal currents by heat flux, precipitation, evaporation, surface wind stress and river discharge. The results are compared with some observation data to verify the validity of the model. The characteristics of currents around Matsushima Bay are also investigated from the result reproduced by the model, focused on the influence of fresh water from rivers.

Oyster and scallop aquaculture has flourished in Ofunato Bay, on the Sanriku Coast of Japan. Between 1967 and 2011, this bay was a highly enclosed area by a bay-mouth breakwater, and while the breakwater provided calm conditions suitable for aquaculture, there was concern about water quality deterioration. The Tohoku Earthquake off the Pacific coast and the subsequent major tsunami on 11 March 2011 caused extensive damage to the Sanriku Coast, resulting in the collapse of the breakwater of Ofunato Bay. We analyzed the monthly hydrographic observational data that were collected between 1996 and 2015, supplemented with hydrographic observations and direct current measurements that were carried out after the earthquake. The historical hydrographic observational data showed the lowest dissolved oxygen (DO) concentrations were observed near the bottom in the bay. The average and standard deviation of the lowest DO concentrations of each monthly observation during the period before and after the earthquake were 5.81 ± 3.72 and 7.22 ± 1.49 mg L−1, respectively, and are significantly different. The oceanic water inflow and water exchange rate estimated by a box model based on the salt budget under the steady-state estuarine circulation were also significantly different before and after the earthquake. An increase in the inflow of oceanic water and the more rapid water exchange in the bay after the earthquake induced marked improvements in the bottom DO concentration. These changes are considered to be attributable to the improved circulation of oceanic water in the bay that resulted from the collapse of the bay-mouth breakwater.

We investigated the relationship between adult (age-4) return rates for chum salmon (Oncorhynchus keta) originating from the Iwate Prefecture, Japan, and coastal environmental conditions during their early ocean life in coastal residency. We analyzed distributions of water properties via intensive hydrographic observations using a conductivity–temperature–depth profiler. Both the return rates and water properties vary strongly over interannual time scales. We found that the time when the return rate decreased drastically corresponded well to the time when the frequency of warm waters in the coastal residency increased.

Sendai Bay in northern Japan suffered serious damage from massive tsunamis generated by the 2011 off the Pacific coast of Tohoku earthquake. The physical disturbance caused by a tsunami may affect the coastal ecosystem, including the planktonic diatom community. We investigated seasonal changes in the diatom community structure at a coastal and an offshore station in Sendai Bay, from June 2011 (3 months after the tsunami) to April 2014. Diatom abundance increased at both stations during the spring. Sporadic increases were also recorded at the coastal station during the summer because of silicate input from river discharge. Seasonal succession of the diatom communities was similar at both the coastal and offshore stations. The onset of the spring bloom consisted mainly of Chaetoceros spp. when water temperatures were low. Subsequently, species such as Skeletonema costatum s.l. became dominant as salinity and nutrient concentrations decreased. Cell density decreased from summer into early winter. Leptocylindrus danicus became dominant in the summer, but was replaced by Thalassiosira cf. mala from autumn into winter. Redundancy analysis (RDA) showed that most of the variation in the diatom community could be explained by temperature, salinity, NO3 −, NO2 −, PO4 3−, and SiO2. In addition, the occurrence of diatom species before the tsunami showed a similar pattern to that after the tsunami, suggesting that the tsunami did not have a serious impact on the diatom community in Sendai Bay.

In 2013, there was a significant decline in the wild seedling yield of the Pacific oyster Crassostrea gigas in Matsushima Bay, Japan. We used hydrographic observational data obtained from 2009–2014 to determine whether hydrographic conditions explained the low yield and the absence of pre-attachment stage larvae. In August 2013, low salinity water was distributed at the surface resulting in a density difference between the surface and near the seafloor of the bay exceeding 10 kg m−3. This difference generated a strong outward driving force of 10.0 × 10−3 N m−3. We hypothesize that the oyster larvae were transferred out of the bay before they could reach the pre-attachment stage. The low salinity distribution resulted from increased precipitation associated with stagnation of a stationary rain front. In addition to the outflow driven by freshwater inputs into Matsushima Bay, freshwater derived from the Naruse River, located on the east of the bay, flowed into the bay and formed the horizontal circulation with increased water exchange resulting in the acceleration of the outflow of oyster larvae. The influence of freshwater from the Naruse River has likely increased in the bay as a result of topographical changes caused by the 2011 Tohoku earthquake.

Pre-fishing season (June and July) Pacific saury Cololabis saira occur offshore, east of Japan, before migrating west to nearshore waters where they are exploited by Japanese fishers in the autumn (September–November). To forecast the location of these fishing grounds we develop a migration model using oceanographic (temperature and current velocity) and fisheries (pre-fishing Pacific saury distribution obtained from stock assessment surveys) data, and migration characteristics determined from fishery data analysis. We speculate that Pacific saury migrate seasonally, first north, staying within a certain temperature zone from May to July, then west, remaining within a preferred but gradually increasing temperature zone. We tune our model using hindcast calculation to reproduce actual fishing grounds around Japan. In July 2018 we forecast the locations of early Pacific saury fishing grounds from August to September. Our forecast fishing grounds were subsequently validated by actual positions of the fishing grounds. Our model successfully forecast the locations of early fishing grounds along the Kuril Islands archipelago, and forecast particles that reached an offshore region roughly predicted offshore fishing grounds. This model also identified Pacific saury migration route trajectories in detail, and that these two fishing grounds in 2018 were formed from geographically separated pre-fishing season shoals via different migration routes. We believe that applying our model will improve the efficiency of the Pacific saury fishery and fleet operation through savings in vessel fuel and time spent searching for shoals.

The Western Isoguchi Jet, a quasi-stationary baroclinic jet that separates from the Kuroshio Extension, has been detected for a decade. Here we report the first observations of the vertical structure and temporal variations of the jet via moored current meters (September 2011–September 2012) and intensive hydrographic measurements (September 2010, 2011, and 2012). The jet flows northeastward and supplies subtropical water (northeastward velocity was ∼ 0.16 m s−1 and temperature was ∼ 4.4 ° C at 300 m depth, and they were ∼ 0.05 m s−1 and ∼ 2.9 ° C at 1000 m depth). We newly estimated the volume, heat, and salt transports of the jet to be 13.6–26.5 Sv, 0.0745–0.173 PW (reference potential temperature of 4.0 ° C ), and 5.58–9.91 × 10 6 kg s−1 (reference salinity of 33.5), respectively. Year-to-year changes of the jet axis complicated its horizontal distribution. The jet flowed stably northeastward throughout the year with weak seasonal variability. The vertical structure of the jet is quite different from that of the surrounding flow. These observations are consistent with the mechanism proposed by Mitsudera et al. (2018) and Miyama et al. (2018) to be responsible for the formation and maintenance of the jet.

Sendai Bay is located on the Pacific coast of northern Japan and suffered serious damage following the 2011 off the Pacific coast of Tohoku earthquake and tsunami in March 2011. To assess the impact on the marine ecosystem, information was needed on the phytoplankton communities and their seasonal variation. However, such information was limited. Therefore, an intensive monitoring of the phytoplankton was carried out from March 2012 to April 2014. Seasonal variation of the phytoplankton community was similar at coastal and offshore stations. Total phytoplankton biomass, based on Chl a concentration, peaked in spring and then decreased to a minimum in summer, before gradually increasing during early winter and peaking again in the following spring. This seasonal pattern was consistent with previous studies conducted before the earthquake and tsunami. Also, size structure of the phytoplankton community and its four main groups was estimated from the size-fractioned samples of Chl a. Our results also showed that the spring bloom consisted of large diatoms, with their growth ceasing due to nitrogen depletion. The bloom was followed by a summer period where cyanobacteria and picoeukaryote became dominant, with high cell densities in spite of low nutrient concentrations. In addition, sporadic environmental changes, such as those following typhoons, were observed. These resulted in large increases/decreases in individual phytoplankton groups.

A massive tsunami hit the north Pacific coast of Japan on 11 March 2011. We evaluated the effects of the tsunami on the distribution, growth, and survival of young Pacific cod (Gadus macrocephalus) using data from benthic trawl surveys and otolith microstructure analysis. The distribution of Pacific cod juveniles differed between 2011 and 2008–2010. The 2011 year class was smaller in body size than those in 2008–2010. The majority of 2011 year-class juveniles was captured in deeper areas at a smaller body size, whereas those of previous year classes were primarily distributed in shallower water. The peak hatch of the 2011 year-class juveniles was from early to late February, which was several days later than those of the 2008 and 2010 year classes. The 2011 year class grew at the same rate as those from 2008 and 2010 until the day of the tsunami, but had a lower growth rate during the 30 days after the tsunami, resulting in a decrease in fish size at settlement. Growth of the 2011 year class was also inferior soon after the day of the tsunami in almost all groups divided by the hatching period. Growth of juveniles captured in shallower water following the tsunami in 2011 tended to be slower than that of juveniles captured in deeper water. Our results suggest that the tsunami caused a decrease in growth rates for approximately 30 days and a change in the distribution of juvenile fish relative to prior years. The change in distribution was primarily the result of mortality in shallow water caused by physical damage and (or) subsequent decreased growth. Considering these results and the finding that the recruitment level and the recruits per spawning in the 2011 year class were low, the tsunami may have affected the determination of the recruitment level.

We investigated distribution patterns of a doliolid (Dolioletta gegenbauri) bloom in relation to the physical environment using a video plankton recorder in the Oyashio–Kuroshio mixed water region. Using 12 km transects, doliolid blooms were encountered at a horizontal scale of about 2–3 km, which corresponds to submesoscale physical events. Doliolids were also consistently encountered in the subsurface layer above the pycnocline in warmer (> 14oC) and higher-salinity (> 34) water masses, and seawater density was the most critical factor affecting distribution depth. Compared to previous studies, the density and biomass of the blooms observed in this study (77 mgC m−3 and 4600 inds m−3) were highest in the open ocean. Bloom formation consisted of two phases; first, the seeding population of a nurse stage increased rapidly to 2000 inds m−3 by asexual reproduction, followed by asexual production of phorozooids. Estimated population clearance rates revealed that these dense patches could potentially sweep the surrounding water within 2–3 d. The incidence of exhausted and shrunken zooids was significantly correlated with patch density, suggesting that mortality was due to overgrazing. Shrunken doliolids appeared to sink below the pycnocline, corresponding to 8–17% of the particulate organic carbon flux at 150 m. Hydromedusae, pelagic polycheates, and sapphirinid copepods preyed on the doliolids. These results indicate that doliolids, which were seeded by populations originating from the Kuroshio, formed dense blooms in response to submesoscale physical events and would alter the sinking particle properties (i.e., biological pump) and the epipelagic food web structure through their grazing and mortality.

We investigated the main controlling factors and predictability of extreme sea surface temperature changes along the Sanriku coast (the east coast of the northern part of Japan's main island). We analyzed distributions of water properties and flow fields via intensive observations using a conductivity–temperature–depth profiler and a coastal water-temperature monitoring system from January 1998 to December 2012. Satellite altimetry and tide gauge data were also analyzed to investigate more widespread horizontal and temporal variation of the sea surface flow field. Anomalous temperature events (2 °C lower and higher than climatological monthly values) were observed in winter 2006 and fall 2010 and 2012 along the Sanriku coast. In winter (fall) 2006 (2010, 2012), we observed both unusually thick and wide cold/fresh (warm/saline) waters, corresponding to the Oyashio (Tsugaru Warm Current) waters. At that time, sea surface velocities of the Oyashio (Tsugaru Warm Current) along the Hokkaido coast (Tsugaru Strait) were also high. We propose new methods for predicting extreme temperature changes a few months in advance, based on current observations.

We investigated the interdecadal trend of Oyashio velocity and transport during 1993–2011 based mainly on linear trend analysis of altimetry and in situ temperature-salinity data from a monitoring line (“A-line”) off the southeastern Hokkaido coast. Significant trends of increasing sea level were detected on the continental slope, north of the Kuril-Kamchatka Trench. Sea level anomaly data revealed a localized clockwise circulation centered near the trench, the suggestion being that the strength of the Oyashio on the slope and the offshore return flow had decreased. The Oyashio mainstream seemed to have shifted from a nearshore to an offshore path. Steric heights estimated from the A-line data exhibited an increasing trend north of the trench, where 50–80% of the increase was determined by halosteric components attributable to a trend of decreasing salinity in the subsurface. The trend of decreasing salinity was related to downward displacement of isohaline/isopycnal surfaces. The largest displacement was above the trench. Horizontal pressure gradients associated with southwestward flows on the slope were weakened. The Oyashio transport decreased by 8.9 Sv (106 m3 s−1) in 19 years. A mesoscale eddy analysis revealed that clockwise eddies appeared more frequently in recent years near the trench around the A-line and could decrease the Oyashio transport. A baroclinic, long Rossby-wave model also predicted that a large-scale baroclinic response to the wind stress could weaken the Oyashio velocity in the upper layer. Dynamical linkage between the localized eddies and large-scale response remains to be clarified in future work.

We investigated the elevated chlorophyll-a (Chl-a) zone found along the coast in winter in Sendai Bay, Japan, using hydrographic observations and a one-dimensional ecosystem model. Chlorophyll-a distribution was vertically homogeneous with a horizontal gradient and could be approximated as a power function of bottom depth; Chl-a concentration drastically increased with decreasing bottom depth, despite temperature and salinity being almost vertically and horizontally homogeneous. The observed results revealed significant correlations among Chl-a and nutrients concentrations proportional to the Redfield ratio. Diatoms accounted for more than 99% of the detected total cells, indicating the occurrence of a diato m bloom. A one-dimensional ecosystem model, which incorporated vertical mixing and the self-shading effect of phytoplankton, revealed that bottom depth was responsible for the occurrence of the bloom during the convective season in coastal area where vertical mixing reached the bottom and that there existed the critical bottom depth where the integrated Chl-a in the water column remained constant. A bloom could occur where the bottom depth is shallower than the critical bottom depth, not when the depth of the mixed layer is shallower than the classical critical depth and the stratification is established. From the observational and model results, it is suggested that the diatom bloom was induced by oceanic water intrusion, which transported nutrients to the bay and the elevated Chl-a zone was formed within a month after the intrusion.

After the adoption of the Aichi Target, data accumulation and evaluation regarding biodiversity have progressed rapidly. The use of ecologically and biologically significant areas (EBSAs) criteria to evaluate important areas enables the identification of effective and prioritized areas for ecosystem management. This includes strategic environmental assessment and discussions aimed at establishing protected marine areas based on scientific data. This paper reviews previous and current ideas as well as the methods used, for the identification of EBSAs. In particular, the following issues are addressed: problems associated with different types of marine ecosystems in the Japanese Archipelago, such as seagrass and seaweed beds, coral reefs, offshore pelagic plankton, and deep-sea benthic ecosystems; and problems associated with the integration of multiple criteria that are not totally exclusive. Several candidate variables accounting for each of the 7 criteria used to identify ecologically important areas are presented. Data availability is the most important criterion that allowed for the comprehensive evaluation of different types of ecosystems in the same localities. In particular, for coastal ecosystems such as seagrass, seaweed beds, and coral reefs, it is possible to carry out broad spatial comparisons using variables representing most of these 7 criteria. Regarding methods for the quantitative evaluation of each criterion and their integration, application of these methods to kelp forest ecosystems in Hokkaido, Northern Japan is presented as a case study.

Size-fractionated primary production was investigated in the Kuroshio Extension (KE) and adjacent regions from winter to spring in order to understand dynamics of spring phytoplankton bloom. Primary production in both the Kuroshio and KE regions was low in winter and ranged from 61 to 185 mg C m−2 day−1, and was composed mostly of small phytoplankton ( 10 µm) became major producers in spring with high production of 443–871 mg C m−2 day−1 in the Kuroshio region, the main primary producers remained small in the KE region, and primary production was not elevated as observed in the Kuroshio, ranging from 82 to 492 mg C m−2 day−1. Low production in the KE region in spring was associated with a lack of primary production by large phytoplankton, and this was primarily due to the low availability of nitrate and silicic acid in early spring. Within the KE region, primary production tended to be high in the northern edge and around the axis of the first ridge of the KE meandering compared with other regions of KE. The shoaling of the surface mixed layer produced by intrusion of the southern warmer water was responsible for the high primary productivity.

The Fukushima Dai-ichi nuclear power plant (FNPP) accident that followed the Great East Japan Earthquake in 2011 resulted in the release of enormous quantities of anthropogenic radionuclides, especially radioactive cesium (134Cs and 137Cs) into the ocean off the east coast of Japan. FNPP-derived radioactive Cs may have consequently accumulated within marine food webs via seawater intake and predator–prey interactions. We provide evidence of the temporal variability in 134Cs and 137Cs concentrations in seawater and zooplankton samples collected in coastal waters off Joban-Sanriku, in Sendai Bay, and in the Oyashio region between June 2011 and December 2013. In Sendai Bay, seawater 134Cs and 137Cs concentrations exceeded 1 Bq/kg in June 2011 and rapidly decreased during the study period. 134Cs and 137Cs concentrations in zooplankton were also high in June 2011, up to 23 Bq/kg-wet and also decreased during the study period, although at a slower rate than seawater 134Cs and 137Cs concentrations. Regarding 137Cs concentrations, the difference in the rate of decrease between seawater and zooplankton resulted in a high apparent concentration ratio (aCR) for zooplankton. The observed relation between 137Cs in seawater and the aCR of zooplankton were good indicators of the progress of 137Cs contamination in zooplankton from the beginning of the FNPP accident to the restoration phase.

The hydrographic structure of a quasi-stationary jet separated from the Kuroshio Extension, a phenomenon that possibly leads to deepening of the winter mixed layer, is revealed via intensive observations using a conductivity–temperature–depth profiler and a ship-mounted acoustic Doppler current profiler (ADCP) carried out in September 2009. Data collected from profiling floats set to drift isopycnal layers and time series of sea surface buoys and satellite altimeters were also analyzed to understand the continuity, water characteristics, and time variation of the jet. Although the flow field was complex due to disturbances such as energetic eddies, the jet transported subtropical water to the downstream (northeastern) observation region in a layer shallower than 400 dbar and its highest velocity was concentrated in the mid- and deep layers (≤0.30 m s−1 at the sea surface and ≥0.05 m s−1 at 800-m depth). The velocity axes of the jet detected from the satellite data corresponded to those detected through analysis of the ADCP data, and the intensity of the jet at the sea surface varies over interannual-to-decadal time scales. Part of the interannual-to-decadal variation in the velocity field of the jet is controlled by the dynamic state of the Kuroshio Extension and is correlated with that of the Kuroshio Extension latitude (linear correlation coefficient r ~ 0.67). The relationship between these variations can be interpreted qualitatively as being responsible for the inertial streamers that separate from the crests of meanders of the Kuroshio Extension to the jet region due to the large steering effect.

Regeneration of a warm anticyclonic ring as a result of interaction with cold water masses was observed within the western subarctic gyre of the North Pacific. Satellite, profiling float, and shipboard observations revealed that a warm-core ring originated from the Kuroshio Extension, propagating northeastwards, entrained cold and fresh water masses from the coastal area of Hokkaido, which are typically recognized within the ring as water that is colder than 2.5 °C. The potential temperature and planetary contribution of potential vorticity of the cold water in the coastal area of Hokkaido were

We investigated predatory behavior of sapphirinid copepods on doliolids around the Kuroshio Extension at stations experiencing blooms of Dolioletta gegenbauri. Onboard observations showed that adult Sapphirina nigromaculata was an active predator of doliolids, with a preference for internal tissues. When entering a doliolid body cavity, sapphirinids left a characteristic bite mark around the fringe of oral and atrial aperture or hole on the tunic of the doliolid. In situ observations with a video plankton recorder (VPR) revealed that association between sapphirinids and doliolids was common in the field. Adult sapphirinids and doliolids exhibiting the characteristic evidence of an attack (bite mark or hole) were found in sediment traps at a depth of 50 m, indicating that the association between these taxa was due to predation. Early copepodites, which were not observed in sedimenttrap samples, appeared in the VPR observations to have a semi-parasitic phase when they attached themselves to nurse chains. The maximal daily ration of sapphirinids estimated by onboard experiments ranged between 29% and 37% of their body carbon weight. Although the mean predation effect by sapphirinids on the doliolid population biomass was only 0.7% d21, sapphirinids potentially had a greater effect on doliolid abundance at the termination of doliolid blooms. Some of the attacked doliolids were discarded by the sapphirinids and contributed to the sinking flux below 150 m, the importance of which as a source of detritus likely increased with depth. Sapphirinids, despite their relatively low abundance in the water column, play a specific role in driving community succession and biogeochemical cycling.

We calculated the mass balance of major congeners of dioxins derived from chloronitrophen (CNP) and pentachlorophenol (PCP) found in Sendai Bay, in order to characterize the present status of marine pollution caused by dioxins and enable the establishment of appropriate countermeasures against dioxin contamination. According to published statistics, about 58 000 t of CNP and about 22 000 t of PCP were shipped to Miyagi Prefecture over a 40-year period, and based on the these amounts of CNP and PCP, we estimated that 30.7 t of 1,3,6,8-tetrachlorinated dibenzo-p-dioxin (1,3,6,8-TeCDD), 1,3,7,9-TeCDD, and octa-chlorodibenzo-p-dioxin (OCDD) were introduced into the terrestrial environment as impurities contained in both pesticides. Mass balance analysis results show that most of these dioxins remained in the terrestrial environment and were not transported by runoff into Sendai Bay. Moreover, degradation mainly reduced the amount of dioxins in the terrestrial environment, instead of runoff or volatilization. Although large amounts of CNP and PCP were shipped to Miyagi Prefecture, only 0.8% of the total quantity of 1,3,6,8-TeCDD, 1,3,7,9-TeCDD, and OCDD contained in pesticides that were applied to paddy fields reached Sendai Bay via the discharge of major rivers. Moreover, most dioxins transported to the bay either flowed offshore or settled at the bottom of the bay. And there was very little bioaccumulation in marine organisms, particularly commercially valuable species.

Intensive hydrographic observations obtained with an underwater glider revealed the vertical structure with high horizontal resolution, as well as the temporal variation, of the Subpolar Front and the Tsushima Warm Current in the Japan Sea. Even when sea surface current velocities were large (>0.50 m s−1), the glider was able to completed the observations along the planned straight line. The glider detected changes in the frontal structures and the water mass distributions on spatial scales smaller than O(10 km) and on timescales smaller than O(1 month). We showed that the assimilation of glider data by an ocean dynamic model increased velocity magnitudes in the simulated flow field.

The importance of parentage analysis has been underscored in the conservation genetics. We present a software package for parentage allocation running in Microsoft® EXCEL™, PARFEX (v1.0). It implements exclusion and likelihood-based methods based on microsatellite and/or SNPs markers.

The Oyashio region in the western North Pacific supports high biological productivity and has been well monitored. We applied the NEMURO (North Pacific Ecosystem Model for Understanding Regional Oceanography) model to simulate the nutrients, phytoplankton, and zooplankton dynamics. Determination of parameters values is very important, yet ad hoc calibration methods are often used. We used the automatic calibration software PEST (model-independent Parameter ESTimation), which has been used previously with NEMURO but in a system without ontogenetic vertical migration of the large zooplankton functional group. Determining the performance of PEST with vertical migration, and obtaining a set of realistic parameter values for the Oyashio, will likely be useful in future applications of NEMURO. Five identical twin simulation experiments were performed with the one-box version of NEMURO. The experiments differed in whether monthly snapshot or averaged state variables were used, in whether state variables were model functional groups or were aggregated (total phytoplankton, small plus large zooplankton), and in whether vertical migration of large zooplankton was included or not. We then applied NEMURO to monthly climatological field data covering 1 year for the Oyashio, and compared model fits and parameter values between PEST-determined estimates and values used in previous applications to the Oyashio region that relied on ad hoc calibration. We substituted the PEST and ad hoc calibrated parameter values into a 3-D version of NEMURO for the western North Pacific, and compared the two sets of spatial maps of chlorophyll-a with satellite-derived data. The identical twin experiments demonstrated that PEST could recover the known model parameter values when vertical migration was included, and that over-fitting can occur as a result of slight differences in the values of the state variables. PEST recovered known parameter values when using monthly snapshots of aggregated state variables, but estimated a different set of parameters with monthly averaged values. Both sets of parameters resulted in good fits of the model to the simulated data. Disaggregating the variables provided to PEST into functional groups did not solve the over-fitting problem, and including vertical migration seemed to amplify the problem. When we used the climatological field data, simulated values with PEST-estimated parameters were closer to these field data than with the previously determined ad hoc set of parameter values. When these same PEST and ad hoc sets of parameter values were substituted into 3-D-NEMURO (without vertical migration), the PEST-estimated parameter values generated spatial maps that were similar to the satellite data for the Kuroshio Extension during January and March and for the subarctic ocean from May to November. With non-linear problems, such as vertical migration, PEST should be used with caution because parameter estimates can be sensitive to how the data are prepared and to the values used for the searching parameters of PEST. We recommend the usage of PEST, or other