The gut content was analyzed in order to clarify the potential food sources of the oyster (Crassostrea gigas) and the clam (Ruditapes philippinarum) in the Akkeshi-ko estuary. Benthic diatoms in the diets of oysters were most abundant and accounted for 70% in 2003 and 67% in 2004, followed by pelagic diatoms and dinoflagellates. In gut of clams, benthic diatoms represented 78% in 2003 and 87% in 2004, also followed by pelagic diatoms and dinoflagellates. There are no differences in dietary preference between oyster and clam. There are no significant correlations between phytoplankton compositions in gut of oyster/clam and water column. The Index of electivity was high particularly in dinoflagellates and several species of benthic diatoms such as Amphora sp., Cocconeis scutellum, Nitzschia sp., Paralia sulcata, Rhoicophenia curvata and Thallasiosira sp., Gramatophora marina, and so on.

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We determined the nucleotide sequences of the non-coding region between the genes for tRNA^Thr and tRNA^Pro in 433 specimens of the deep-sea demersal fish Bothrocara hollandi obtained from the Japan Sea and the Okhotsk Sea. This region consisted of 1–3 copies of sequences, which originated from the duplication of the 5′-region of the tRNA^Pro gene. All the individuals from the Okhotsk Sea have two copies and those from the Japan Sea were shown to have 1–3 copies. Of the individuals obtained from the Japan Sea, those with more than one copy and those with a single copy corresponded to Group A and Group B, respectively, which have been defined in a previous study. On the other hand, a closely related species, Bothrocara tanakae, has a single copy, and no non-coding region was detected for the congeneric species Bothrocara molle. Duplication of the unit might have occurred three times during the evolution of B. hollandi. During the last glacial maximum (LGM) when most of the Japan Sea was anoxic, ancestors of Group A would have inhabited the shallower areas of the Japan Sea which did not become anoxic while those of Group B might have survived in other refuges in the Japan Sea. Low genetic diversity of Group B suggests that a severe bottleneck might have occurred in the population size of an ancestral population of Group B during the LGM.

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2-(4-pyridyl)-5-[(4-(2-dimethylaminoethylaminocarbamoyl)methoxy)-phenyl] oxazole (PDMPO) is a fluorescent compound that accumulates in acidic cell compartments. PDMPO is accumulated with silica under acidic conditions, and the newly developed silica skeletons show green fluorescent light. This study is the first to use PDMPO in polycystine radiolarians, which are unicellular planktonic protists. We tested Acanthodesmia sp., Rhizosphaera trigonacantha, and Spirocyrtis scalaris for emission of green fluorescence. Entire skeletons of Acanthodesmia sp. and Sr. scalaris emitted green fluorescent light, whereas only the outermost shell and radial spines of Rz. trigonacantha showed fluorescence. Two additional species, Spongaster tetras tetras and Rhopalastrum elegans did not show fluorescence. Green fluorescence of the entire skeleton is more like the “skeletal thickening growth” defined by silica deposition throughout the surface of the existing skeleton. The brightness of the fluorescence varied with each cell. This difference in fluorescence may reflect the rate of growth in these cells. Green fluorescence in PDMPO-treated polycystines suggests the presence of similar metabolic systems with controlled pH. The results of this study shed light not only on the feasibility of using PDMPO in diatoms and siliceous sponges, but also in polycystines. Further application of PDMPO could refine polycystine skeletogenic hypotheses and offer new insight on the physiological functions of silica assimilation.

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The initial stage of bloom formation of cyanobacteria was investigated in Hirosawa-no-ike Pond, Kyoto, Japan, from February to May 2006. This pond is prone to periodic heavey blooms of cyanobacteria from spring to autumn, despite the complete draining of water for more than two months every winter. The dominant types of cyanobacteria in the bloom were Aphanizomenon flos-aquae from February to March, followed by Microcystis spp. in April. The planktonic populations of Microcystis spp. increased continuously during April when the water temperature was in the range of 12.0–17.3°C, which was almost below the growth threshold for most Microcystis species. An incubation experiment revealed that the recruitment of Microcystis colonies from the pond sediment increased with temperature, especially at and above 15°C. Recruitment of Anabaena trichomes was also observed, but there was no clear relationship between water temperature and trichome densities of Anabaena spp. The M. aeruginosa colonies in the sediment in winter were likely to be dormant, as implied by the invariable frequencies of the division of cells throughout a day. These results suggest that once water temperature exceeded the growth threshold of Microcystis species, the recruitment of the colonies is enhanced and a bloom is formed by both conspicuous recruitment and active growth.

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Cell volume of Isochrysis galbana (Prymneshiophyceae) was determined with a microscope before and after fixation during storage at 4 and 25°C. The shrinkage effect at 4°C was not detectable but at 25°C. It was described by the exponential equation; Y=0.797+0.224 exp (−0.074 X) for 2% formaldehyde and Y=0.849+0.150 exp (−0.87 X) for 1.6% Lugol's solution where X is hours and Y is the ratio of fixed volume to live volume. Lugol's solution provides 6.5% less shrinkage than formaldehyde (p<0.05). We recommend Lugol's solution as a preservative at 25°C with a shrinkage correction or refrigeration for storage at 4°C, otherwise a species–specific correction should be made for estimating live volume from fixed material.

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Teleaulax amphioxeia (Conrad) Hill is a marine free-living cryptophyte. Here, we report the basic characteristics of the cryptophyte-infecting virus “TampV (Teleaulax amphioxeia virus)”, the host of which is T. amphioxeia, as the first such virus to be successfully cultured. TampV strain 301 (TampV301) is a polyhedral large virus (ca. 203 nm in diameter), propagating in its host's cytoplasm. Because of the virion size, thin-section view and propagation characteristics, TampV301 was assumed to harbor a large double-stranded (ds) DNA genome; i.e., TampV is most likely one of the “nucleo-cytoplasmic large DNA viruses (NCLDVs)” belonging to the family Phycodnaviridae. Its infectivity was ‘strain-specific’ rather than ‘species-specific’ as is the case in other algal viruses. The burst size and latent period were roughly estimated to be 430–530 infectious units cell⁻¹ and <24 h, respectively. Considering the uniqueness of cryptophytes' evolutionary position and the host's unique role within the complicated food chain involving kleptoplastid acquisition (composed of T. amphioxeia, the ciliate Myrionecta rubra and a dinoflagellate Dinophysis species), TampV is of much interest from the viewpoints of both eukaryotic host-virus coevolution and marine microbial ecology.

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A molecular based method for the quantitative detection of larvae of the golden mussel Limnoperna fortunei was developed. Partial nucleotide sequences of the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene in several bivalve species including L. fortunei were analyzed. These nucleotide sequences and the CO1 gene for bivalve species found in habitats similar to L. fortunei (obtained from the EMBL/Genbank/DDBJ databases) were aligned. Based on these results, L. fortunei-specific primers were designed for amplification. DNA extracted from several bivalve species including L. fortunei were subjected to PCR using L. fortunei-specific primers, and amplification of the DNA fragment was confirmed only in PCR assays which utilized template DNA from L. fortunei. No DNA fragments were amplified during the PCR of freshwater planktonic sample lacking golden mussel larvae which were collected from Lake Ohshio (Gunma, Japan). Real-time PCR was performed using fluorescent dye (SYBR Green) detection. Threshold cycles correlated well with the template DNA and number of larvae equivalents, and the R-square values of the standard curves were 0.99 and 0.98, respectively. These results suggest that this real-time PCR-based method can be utilized not only for the identification of L. fortunei in a particular habitat, but also for the quantification of larvae of this species in natural environments.

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