Ariake Bay is located off the west coast of Kyushu, western Japan, and is a typical enclosed coastal sea of approximately 1,700 km² in area. The tidal amplitude reaches approximately 6 m in the inner parts of the bay at the spring tide, and consequently approximately 20,000 ha of tidal flats appear along the coast of the bay at ebb tide. The tidal flats and the shallow waters offshore from the tidal flats are extremely productive areas, and utilized for various fisheries. However, the ecosystem of Ariake Bay is now in critical condition. The abundance of benthic animals has decreased markedly on the sandy tidal flats in the bay. This phenomenon is represented by the drastic decrease in the harvest of the most popular short neck clam, Ruditapes philippinarum, on the sandy tidal flats of Kumatoto Prefecture facing Ariake Bay. The annual harvest on the sandy tidal flats exceeded 50,000 tons until 1980, but decreased to only around 400 tons between 1995 to 1997. On the sandy tidal flats where the dense clam population collapsed, very few macro-benthic animals occurred. Since the 1960s, a large amount of sand and gravel has been collected from the rivers that flow into Ariake Bay. It is apparent that the marked decrease in newly deposited sand on the sandy tidal flats is one of the main causes of the collapse of the dense population of the short neck clam and marked decrease of other macro-benthic animals on the sandy tidal flats, and thus it appears that the only effective measure to recover the benthic communities on the sandy tidal flats is creating sand covers with natural sands collected from the sea floor offshore of the bay.
In the subtidal areas of the bay, the scale of the autumn bloom of phytoplankton has increased markedly and red tides have covered almost the entire inner bay area since 1998, although the nutrient input from the land to the bay through the major rivers has fluctuated stably over the past three decades. The nori culture was seriously damaged by the occurrence of a large-scale autumn red tide on two occasions (2000 and 2002). In early summer, hypoxic bottom water has occurred in the wide areas of the inner parts of the bay since at least 2001, causing a serious environmental disturbance to the benthic ecosystem. Both of these phenomena commonly occurred when the water was stratified mainly due to the decrease of salinity in the surface layers. These facts indicate that the stratification of the water was enforced in the inner parts of the bay from the end of the 1990s. In Isahaya Bay, an inner bay of the west side of Ariake Bay, a big reclamation project of the tidal flats to create land and a fresh water pond of approximately 3,500 ha in total area has been conducted since 1986, and the gates of the dike were closed to lower the water levels inside the dike for reclamation in April 1997. A decrease in the tidal current was recently observed in some parts of the west coast of the bay. It is very likely that the changes of the hydrographical conditions caused by the modification of the topography of Isahaya Bay are responsible for the development of the water stratification in the inner parts of Ariake Bay, following the occurrence of the large-scale autumn red tides without any increase in the nutrient input from the land and the hypoxic bottom water in the summer.

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For understanding larval recruitment processes of Scyllarus and Panulirus lobsters, exact species identification of field-caught phyllosoma larvae, particularly those of the early stages, is essential. Using ichthyoplankton samples from waters along the west coast of Kyushu to the Japan Sea coast of Honshu and the Kuroshio and Kuroshio-Counter Current regions, we described morphological features of the I to VIII (final) stage phyllosoma larvae of S. bicuspidatus and the IV to VIII stage larvae of S. cultrifer. The larvae of equivalent stages of two Scyllarus species are distinguishable from each other by using the combinations of body lengths and morphological features of antennules, pereiopods and pleopods. In addition, a) equivalent larval stages in S. cultifer are always larger than in S. bicuspidatus; b) cephalic shield of S. bicuspidatus is rounder than in S. cultrifer; c) relative to antennule length, the eyestalk is longer in S. cultrifer than in S. bicuspidatus.

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Seasonal occurrence, diel vertical migration (DVM), biomass (dry weight, carbon and nitrogen contents), growth and behavior of the two phytal-dwelling harpacticoid copepods, Ambunguipes rufocincta and Eudactylops spectabilis, were investigated using field samplings and laboratory experiments. The field samplings were conducted at a subtidal station (St. M; ca. 6.5 m depth) in Tanabe Bay, Japan from March 1999 to January 2000. The results from the field revealed that the two species performed DVM between the water column and macroalgal beds of Colpomenia sinuosa (brown algae), and the seasonal occurrence of the two species at St. M were almost identical to that of C. sinuosa, which bloomed only between December and May. The carbon/nitrogen ratios of A. rufocincta (5.00±0.60) and E. spectabilis (3.95±0.66) differed, probably due to the differences in their foods. Laboratory incubation showed that E. spectabilis needed both C. sinuosa and sediments as food for growth, whereas A. rufocincta that was fed only with the macroalgae was able to grow to maturity. Our results suggested that their DVM behaviors of both species were related to the dispersal of copepodids and adults, because 1) the nauplii grew on C. sinuosa, 2) their main food items were C. sinuosa and sediments, and 3) mating might not be the main purpose of the DVM since females with egg sacs emerged into the water column. Moreover, in later field investigations during summer, refuge populations of A. rufocincta were collected from the seagrass Halophila ovalis in an area shallower than St. M, indicating that A. rufocincta might sustain its population by moving to different habitats though the DVM behavior and changing food items from C. sinuosa to H. ovalis during summer. Therefore, at least for A. rufocincta, the DVM behavior might be indispensable in their life strategy for sustaining their population year round.

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Some benthic organisms make burrows that may stimulate bacterial activity by introducing oxygen-rich overlying water. In order to assess this effect quantitatively, it is necessary to establish a suitable method to observe both behavior of the animal and bacterial activities. Here we developed a soft-agar microcosm in which Capitella sp. I successfully created burrows. Bacterial respiratory activity in the microcosm was visualized by using tetrazolium salt, 2-(p-iodophenyl)-3-(p-nitrophenyl)-5-phenyl tetrazolium chloride (INT), which is converted to red insoluble form (INT-formazan) after reduction. Formazan was then extracted and quantified spectrophotometrically. Within a couple of hours after adding INT into overlying water, the red color due to formazan precipitation became apparent in the water column and on the soft agar surface. With incubation time, the red color zone extended to deeper layers along with burrows, indicating the aerobic bacterial respiration on the burrow lining. The newly developed microcosm system composed of seawater soft-agar and INT staining will provide a unique opportunity for visual observation of both benthic organisms and bacterial metabolic activities under various experimental conditions.

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This paper provides the first evidence that Thysanoteuthis rhombus spawns in the Sea of Japan. Five planktonic egg masses were collected in the southern Sea of Japan during 29 October to 24 November 2004 and transported to onshore laboratories for observation. Part of each egg mass was reared in indoor, aerated tanks supplied with filtered running seawater. The egg masses (ca. 60–120 cm in total length and 13–15 cm in diameter) were cylindrical with rounded ends and consisted of a resilient, transparent gelatinous core with a pair of egg rows forming spiral loops around the core. The embryos had dome-shaped mantles covered with many chromatophores and slowly rotated inside the spherical egg capsules. Hatching was observed in all the egg masses 3–10 days after collection. Morphological characteristics of the egg masses, eggs and embryos, especially the large number of chromatophores present in the early embryonic stages, agreed with the descriptions in previous studies. Near the collections sites, surface water temperature and salinity ranged 18–22 °C and 33.3–33.7, respectively, both of which were lower than the optimum conditions for T. rhombus spawning. The early embryonic stages of the egg masses at collection such as cleavage and slow currents at the sea surface suggest the egg masses were spawned near the collection sites. Increased abundance of T. rhombus in the Sea of Japan and increased sampling efforts were proposed as two possible causes for the egg-mass discoveries.

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The respiration rate of large medusae (11–24 cm bell diameter, 2–17 g dry weight) and their metabolic demand were estimated under laboratory conditions. The respiration rate (R; mL O_{2 ind⁻¹} h⁻¹) was defined as a function of water temperature (T; °C) and body dry weight (W; g ind⁻¹) according to the equation, R=10^{(0.11T−3.1)} W^1.093. The weight specific daily carbon demand of medusae, including respiration and growth, in spring, summer, and autumn was 5.74, 17.6, and 7.27% of body carbon weight, respectively, and these were compared with the weight specific daily ration in specimens from the same area of Tokyo Bay.

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Clearance rate of the planktonic cyclopoid copepod Mesocyclops dissimilis on the planktonic calanoid copepod Eodiaptomus japonicus was measured in laboratory experiments. Ontogenetic changes were investigated using several combinations of different developmental stages of the two species. To minimize the side effects of laboratory experiments, predation was examined for a short duration using field-captured animals at natural prey densities and temperatures. Individual predators showed a large variation in the clearance rate even within replicates of the same experiment. The clearance rates of adult female predators on late naupliar prey were similar (about 0.15 L ind.⁻¹ d⁻¹) within a range of prey density 12–31 ind. L⁻¹. Ontogenetic tendencies in clearance rate, though seldom significant, translated to an increase with development of the predators and a decrease with that of the prey. Present clearance rates and the natural densities of predators and prey suggest that M. dissimilis was sometimes an influential predator of E. japonicus in the field.

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