The armored dinoflagellate genus Heterocapsa is composed of relatively small species, including a species responsible for harmful red tides, H. circularisquama. Some Heterocapsa species such as H. rotundata and H. triquetra have been well documented as red tide-forming species, but are not recognized as causing harmful effects. Following sequential shellfish mass mortalities in the coastal waters of western Japan due to H. circularisquama red tides, this species has attracted considerable interest. Many properties of this species, such as its distribution and growth characteristics, have been investigated to better understand the mechanisms involved in harmful red tide formation. Related to the need for unambiguous identification of H. circularisquama, several unidentified (or undescribed) Heterocapsa species, which must be distinguished from the harmful taxon, have been detected sympatrically in regions where H. circularisquama blooms occur. However, the taxonomic affiliation of these Heterocapsa species have not yet been determined because several characteristics of Heterocapsa (e.g. body scale ultrastructure) have not yet been reported from all described species due to the changing taxonomic criteria. After the taxonomic ambiguities in this genus were resolved, cellular and body scale morphology of Heterocapsa were reinvestigated and several new species were described. In the present paper, the taxonomic history and morphological characters of the genus Heterocapsa are summarized.

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In this study, we examined seasonal changes in the vertical population density of each developmental stage (nauplius and copepodite) of Oithona and Oncaea species in the surface water of Toyama Bay from 1997 to 1999. Furthermore, we investigated the detailed vertical distribution (0 m, 25 m and 50 m depth) of the naupliar stages, which are regarded as an important food source for fish larvae. Major changes in the community structure of nauplii, which occurred at different sampling depths and in different seasons, are considered to have been influenced by the occurrence of adults and changes in the hydrographic conditions, including temperature and water currents. In winter to early summer (January to June) nauplii of Oithona similis and Oithona atlantica, copepodites and adults, were abundant, while those of Oithona plumifera, and other species of Oithona and Oncaea showed a higher density between August and December.
During the spring season, when many fish larvae appeared, O. similis nauplii occurred at higher densities of more than 10⁵ indiv. m⁻³ in the upper layer (0 m and 25 m depth) than those of O. atlantica. The weighted mean depth of O. atlantica nauplii was significantly deeper than that of O. similis nauplii. The respective vertical distributions of the nauplii of O. atlantica and O. similis were similar to the distributions of adults. Oithona similis nauplii are suggested to be a potentially important food item for fish larvae in spring because of their high density and similar vertical distribution to many fish larvae.

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Species composition and horizontal distribution of appendicularians were investigated in waters adjacent to the Kuroshio, south of Honshu in winter–early spring. Twenty-one species belonging to 5 genera were found and the species composition was characterized by a strong dominance of Oikopleura longicauda and occasional dense occurrence of Fritillaria pellucida. Oikopleura longicauda was distributed rather uniformly throughout the study area while F. pellucida was usually only sparsely distributed, although it was sometimes found in dense concentrations at the stations close to the Kuroshio axis. Occurrence of O. dioica, a well-studied neritic species, was limited to the stations with a relatively shallow bottom and its relative importance in terms of abundance was small. Generally, the appendicularian biomass was less than one tenth of the copepod biomass in carbon. Nevertheless, the role of appendicularians in terms of secondary production was estimated to be smaller but comparable in magnitude to that of copepods, 1.7–202.3 mgC m⁻² d⁻¹ in the former and 30.0–185.2 mgC m⁻² d⁻¹ in the latter, because of their higher somatic growth rates and house production. Clearance rate of appendicularians was also estimated to be comparable to copepods, 3.1–591.3 L m⁻² h⁻¹ in the former and 49.0–462.1 L m⁻² h⁻¹ in the latter, owing to their much higher weight specific clearance rates.

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There are few descriptions of the impact of hypoxic conditions on short-necked clam Ruditapes philippinarum larvae in the natural environment, while a number of reports describe catastrophic mortality of benthic clams caused by coastal upwelling of hypoxic water in the eutrophicated bays in Japan. We conducted seasonal observations of larval density in the water column along with measurement of DO at coastal and off-shore stations in Tokyo Bay during 2001–2003, and also experimental exposure of the clam larvae to low DO to examine the impact of hypoxic water on larval survival. Under hypoxic conditions (<1.0 mgO₂ L⁻¹) in the bay, a marked decline in larval density was consistently detected in the bottom layer at coastal stations adjacent to adult habitats and at off-shore stations of the central bay. In the low DO exposure experiment, the ratio of swimming larvae decreased with exposure period. Larval survival declined within 12 h, and most of the larvae at early developmental stage (shell length <170 μm) died within 24 h under severe hypoxic conditions (<0.2 mgO₂ L⁻¹) at 25°C. These results indicate that larvae being transported to the hypoxic zone may have reduced swimming ability and may inevitably sink to the lower layer and die shortly thereafter. In Tokyo Bay, anoxic or hypoxic conditions in the lower layer during May–October are continuous, and this time period overlaps with the entire spawning period of the short-necked clam. Hypoxic water exerts critical stress on larval survival, and may result in decline of juvenile recruitment to the benthic populations of short-necked clam in Tokyo Bay.

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Galaxea fascicularis is a common reef-building coral in the Indo-Pacific area including the Ryukyu Archipelago. A previous study on nematocyst morphology and mitochondrial genotype suggested that G. fascicularis consists of two genetically differentiated groups. However, the extent of the reproductive barrier between the two groups remains unknown. In the present study, more than 99% of G. fascicularis colonies were classified into two groups based on allelic difference of a nuclear microsatellite locus. Colonies exhibiting the hybrid genotype were rare (only two out of 224 colonies), suggesting that the reproductive barrier between the groups is nearly impermeable. The two groups were highly correlated to different nematocyst types and mitochondrial haplotypes, supporting the previous hypothesis that G. fascicularis consists of two genetically and morphologically differentiated lineages in the Ryukyu Archipelago. However, the frequencies of six color morphs were rather similar between the two groups, indicating that the evolution of the color variation had occurred before the divergence of G. fascicularis into the two lineages.

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We describe a rapid and simple enumeration method for sulphate-reducing bacteria (SRB) from aquatic environments using a quantitative real-time PCR (qPCR) in combination with a rapid DNA isolation method. Enumeration of SRB in the sediment and water samples was performed by quantifying the copy number of the dsrA gene coding for the α-subunit of the dissimilatory sulphite reductase using real-time PCR with the SYBR Green I assay. Using dsrA-specific primers, we demonstrated that quantification of SRB in known numbers of SRB assemblages can be achieved. We compared DNA isolation methods using commercial DNA extraction kits and a published technique. We found two commercial kits were of advantage for extraction of DNA from water or sediment samples, where a large number of samples could be processed at the same time. We showed this newly developed qPCR technique targeting dsrA is rapid, simple and reproducible for the quantification of SRB numbers in situ and is superior to the use of culture-dependent techniques.

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CO₂ ocean storage is proposed as a possible measure to mitigate climate changes caused by increasing atmospheric concentrations of the gas. The feasibility of the measure has been intensively investigated, yet its biological impact on marine animals is still largely unknown. We investigated the acute CO₂ tolerance of juveniles of three marine invertebrates; the cuttlefish, Sepia lycidas, the squid, Sepioteuthis lessoniana, and the prawn, Marsupenaeus japonicus. Median tolerance limits of CO₂ were 8.4% (24 h) for the cuttlefish, 5.9% (24 h) and 3.8% (48 h) for the squid and 14.3% (72 h) for the prawn. Comparison of these and previously reported data suggests an inverse relationship between O₂ requirement and CO₂ tolerance among marine animals.

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