Copepods were collected using a Norpac net (0.315 mm mesh aperture, 0.45 m mouth diameter) in the summers from 1992 to 2010 at Stn A (700 m depth) in Tosa Bay, western Japan. Among the summer samples collected in July and August, there were 19 net samples during periods of upwelling and 27 net samples during periods of non-upwelling, judged by criteria of water temperature. Total abundance of adult copepods in the upwelling samples was not significantly different from the abundance in the non-upwelling samples, while the number of species and species diversity in the upwelling samples was lower than in the non-upwelling samples. Adults of four species (Calanus sinicus, Clausocalanus parapergens, Paracalanus parvus s.l. and Corycaeus affinis) in the upwelling samples were significantly more abundant than those in the non-upwelling samples. The changes of the copepod community structure during periods of upwelling may be produced because of increases of species preferring low water temperatures and decreases of species preferring warm water temperatures.

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Samples containing algal cells were collected from the bottom layers of sea-ice in Saroma-Ko Lagoon, Hokkaido, Japan in early spring 2010–2012. The physical and biogeochemical parameters of brine and sea ice, the structure of the ice algal community, and their photosynthetic characteristics were determined. Light responses of the relative electron transport rate (rETR) of the communities were estimated by quantum yield (ΔF/F_m′) of photosystem II at various light intensities with a pulse amplitude modulation (PAM) fluorometer. Although the compositions of the communities were different between the three years, their maximum quantum yields (F_v/F_m) were well correlated to in situ light attenuation. In contrast, their light acclimation index (E_k), the ratios of maximum rETR to the efficiency of the relative electron transport (α), varied year by year. This suggests that the ice algal communities have effective light-harvesting capabilities and their photoacclimation strategy might be related to the structure of the community.

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We examined the species compositions and community structures of halophytic plants, gastropods, and brachyurans in salt marshes (52 sites) in the Ariake and Yatsushiro seas of the western Japan, and assessed the abiotic and biotic environmental factors driving the community structures. Moreover, differences in community structures were compared among the three main study areas: the Ariake sea area, Yatsushiro sea area, and Uto-Amakusa area (shoreline sites located between the Ariake and Yatsushiro seas). A total of 11 halophytic plant species, 19 gastropod species (groups), and 19 brachyuran species were recorded. The average number of halophytic plant species was the highest in the Uto-Amakusa area, but the numbers of gastropod species (groups) and brachyuran species were similar among the three areas. For each halophytic plant species, gastropod species (groups) and brachyuran species, the community composition in the Uto-Amakusa area differed greatly from that in the Ariake and Yatsushiro sea areas; however, those of the Ariake and Yatsushiro sea areas were similar. The dissimilarities in halophytic plant species among the areas were driven mainly by the presence of tall, dense Phragmites australis. Moreover, the most important environmental factor that affected community structure was interstitial water salinity in halophytic plants and brachyurans, and distance from the open shoreline in gastropods.

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The proliferation of drifting macroalgae and the accompanying occurrence of the impoverishment of zoobenthic species has become a major problem worldwide. We examined the temperature dependency of the effects of macroalgae on the survival of Manila clams in Nakaumi Lagoon in western Japan. We conducted (i) semi-monthly field surveys to clarify seasonal changes in macroalgal abundance and clam density and (ii) 7-day macroalgal enclosing and excluding experiments in two temperature settings (mean water temperatures: 19 and 29°C) to test temperature-induced differences in algal effects on bottom-water redox conditions and clam survival. Clam density decreased during summer (July–September), when increased coverage and thickness of drifting macroalgae was observed. In contrast, clam density increased from autumn to spring as macroalgal abundance decreased. Further, reducing conditions (Eh<0) were only detected in bottom waters in the presence of macroalgae during summer (water temperature >29°C), suggesting that drifting macroalgae induced hypoxia under summer temperatures and consequently led to clam mortality. The 7-day algal enclosure experiment resulted in reducing bottom water conditions when mean water temperature was 29°C. Further, clam survival decreased in the algal enclosure at 29°C, whereas no such changes were detected at 19°C. These results indicate that the effects of drifting macroalgae on the geochemical environment and clam survival are temperature dependent; therefore, global warming may enhance the likelihood of macroalgae-induced hypoxia with its associated adverse consequences in marine life.

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Currently, no tool is available that precisely identifies and quantifies all 48 species of Pseudo-nitzschia simultaneously. In the present study, we used massively parallel sequencing-based technology with genus-specific Pseudo-nitzschia primers to investigate the distribution and population dynamics of the genus in Tokyo Bay, Japan. Furthermore, we attempted to quantify the abundance of each species using both relative abundance data detected in the massively parallel sequencing-based survey, and cell count data, obtained by light microscopy. Several species of Pseudo-nitzschia were detected continuously from July 10 to September 9, 2016 in the sampling location. Cell densities ranged from 2–300 cells mL^－1 (sample no.=10). Fourteen operational taxonomic units (OTUs) attributable to Pseudo-nitzschia were detected, and 99.9% of sequences detected by massively parallel sequencing belonged to the genus. Each of the most abundant OTUs comprised a single species, and were identified, in decreasing order of abundance, as P. multistriata (Takano) Takano, P. pungens (Grunow ex Cleve) Hasle, P. fraudulenta (Cleve) Hasle, P. multiseries (Hasle) Hasle, and P. galaxiae Lundholm & Moestrup. Species identification was possible in 9 of the 14 OTUs detected, of which several were detected in Tokyo Bay for the first time. The cell abundance ranges of the five most abundant species were estimated as 1,976–246,395, 0.03–52,999, 5–42,820, 4–24,617, and 0.03–1,007 cells L^－1, respectively. The detection limit was 0.03 cells L^－1.

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Ammonia-oxidizing marine archaea (mAOA) have been divided into two groups based on ammonia monooxygenase subunit A gene (amoA) phylogeny and they link to preferred habitat (depth in the water column); one is the Shallow Marine Clade (SMC) and the other is the Deep Marine Clade (DMC). Several determinative factors have been proposed to account for their depth-dependent distributions, including light intensity, ammonia concentration, water temperature, and dissolved oxygen concentration. Here, we report the change in abundance of SMC and DMC mAOA in response to nitrogen source and water temperature in a long-term incubation experiment using natural seawaters obtained from mesopelagic and bathypelagic layers. The abundance of each type of mAOA was determined by Q-PCR assay targeting amoA. We found that the abundance of SMC after 266 days of incubation increased at all three incubation temperatures (4, 10, 20°C), whereas the abundance of DMC was stable at low temperatures (4°C and sometimes 10°C) or decreased to below the detection limit at high temperatures (20°C and sometimes 10°C). The SMC abundance was higher in seawater cultures supplied with ammonium than in those supplied with nitrite, although DMC abundance was not responsive to ammonium concentration. These results imply that water temperature and ammonia concentration are significant factors in determining the vertical distribution of the SMC and DMC ecotypes of mAOA in the water column.

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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.

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