The life history of the myodocopid ostracod Vargula hilgendorfii was investigated by size-frequency distribution analysis in Akita Port, Japan, from April to December, 2003. Vargula hilgendorfii individuals were collected using baited traps, and the carapace length was measured by computer analysis of a digital photograph of each individual taken under a stereomicroscope. The population was divided into seven groups based on carapace length. These groups corresponded to the five juvenile stages, the adult male stage, and the adult female stage. Each peak in the number of V. hilgendorfii individuals is related to the growth of the population. Our field data clearly suggest that the Akita Port population of V. hilgendorfii produces two generations per year. Adults that survived the winter became sexually active in May and released free-living juveniles in July. After reproducting, they died without having entered a second reproductive cycle. The first-generation juveniles reached the adult stage after five molts and released second-generation juveniles in September. By winter, these second-generation juveniles reached maturity without releasing any new juveniles; they become sexually active in the following spring.

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To examine upstream dispersal and the resultant upstream-downstream variation in demography of the amphidromous shrimp Caridina leucosticta Stimpson, 1860, we collected shrimp from six sites along the lower to middle reaches of the Murasaki River in Kitakyushu city monthly over one year. Spatio-temporal variation in carapace length distribution revealed that recruitment occurred from August to November. Newly recruited individuals finished their upstream migration by winter. The population density decreased gradually after winter, but the rate of decrease was uniform among sites. This suggests that there is neither intensive migration up- or downstream nor variation in survivorship among sites after overwintering. The shrimp grew rapidly from April to August, but growth rates weremuch higher in females than males. Females that migrated to upstream sites kept growing for longer periods than those remaining in downstream ones, resulting in larger body sizes and therefore higher fecundity for the former. Moreover, a higher proportion of ovigerous females was found in upstream sites during the peak of the reproductive season (June to October), which suggests a higher fertility upstream. Such intrapopulation variation in growth and fertility seems likely to have been caused by environmental differences among sites. The proximate factors for this were not clear, but the fact that growth and reproduction performances farther upstream were higher suggests that the upward migration of this shrimp is adaptive.

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In April, 1997, construction of a dike in the inner part of Ariake Sound to close off the innermost area of Isahaya Bay was completed. In June of both 1991 and 2002, benthic surveys were conducted using a Smith-McIntyre grab sampler at 88 stations over the entire sublittoral area of Ariake Sound. The structure of the gammaridean amphipod assemblage was compared between 1997 and 2002 with regard to any change in grain-size composition of the substrates and dissolved oxygen concentration of the bottom waters. No noticeable changes were observed in the distribution of the median particle diameter and silt-clay content, nor in the spatial arrangement of the sediment types of the substrates. Hypoxic water masses were observed in the bottom waters in 1997 in and around Isahaya Bay and in the southern part of Ariake Sound. Other studies also recorded hypoxic water masses in the former area in 1999 and 2001. For the amphipod assemblage, a total of 12, 434 individuals of 94 species belonging to 24 families was collected in 1997; the most dominant species was Photis longicaudata (family Isaeidae). In 2002, those values had changed to 37, 649 individuals, 89 species, and 27 families, with the most dominant species being Corophium sp. A (family Corophiidae). In both years, the amphipod assemblage was dominated by six families, including Isaeidae, Ampeliscidae, Corophiidae, Priscomilitaridae, Melitidae, and Aoridae, although the dominance order changed partially. The amphipod assemblage in both years inclusive was divided into eight groups using group-averaged clustering and non-metric multidimensional scaling. The group with the highest number of stations occupied the largest bottom area, composed of poorly-sorted medium to coarse sand along the longitudinal axis of Ariake Sound; the number of stations in this group increased from 41 in 1997 to 57 in 2002. Increase in individual density and expansion of distribution range of seven species of the superfamily Corophioidea (Corophiidae, Isaeidae, Priscomilitaridae), which occurred around the two hypoxic areas, contributed most to the range extension. For the above-mentioned six most dominant families, density of individuals and proportional composition of number of individuals in each of the two hypoxic areas and other, non-hypoxic areas were compared between the two years. In particular, both values remarkably increased for several members of the Corophiidae, including Corophium sp. A and C. crassicorne, in 2002; the exception was the value for density of individuals in the southern hypoxic area. The Shannon-Wiener species diversity index values were lower in 2002 for both the two hypoxic areas and the combined non-hypoxic areas, and for the three main groups of the amphipod assemblage.

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The spatial distribution and ecological status of the golden mussel, Limnoperna fortunei, in Lake Kasumigaura, Ibaraki Prefecture, Japan, were investigated from June to September, 2006. The mussel was found along half of the Kasumigaura lakefront, from the western to the southern coast. The mussels were attached to hard substrata, such as concrete walls and stones. Most of the mussels were collected from the underside of stones on the lake bottom. The highest density sites of the mussel are in Ami-cho, on the western shore of the lake, where one researcher was able to collect a maximum of 154 individuals in 10 minutes. No mussels were found in the northern and eastern parts of the lake. We could identify two cohorts of the mussel by size-frequency distribution in August and September, 2006. The largest individual among collected specimens was 31.4mm in shelllength. Based on this maximal size and a previous report, the first infestation of the mussel in Lake Kasumigaura must have occurred not later than 2004.

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To date, the panopeid crab Rhithropanopeus harrisii has been found widely in brackish waters in North America and Europe. We report here the first record of R. harrisii as an introduced crab in Japan, on the basis of 86 specimens (47 males and 39 females) collected in July, 2006, from the Nakagawa Canal, which connects with Nagoya Port in the innermost part of Ise Bay on the Pacific coast of central Japan. Fragmentary evidence suggests that this crab may have settled in the area at least by 2000. A brief morphological description of the crab and a comparison between it and the native pilumnid crab Pilumnopeus makianus is made in order to facilitate easy recognition, because the two species are superficially similar and sympatrically occur in local waters.

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The nearshore coastal sea is an important marine ecosystem that includes seagrass beds and tidal flats. These ecosystems provide many kinds of ecological functioning such as high primary production and nutrient cycling and are now facing serious deterioration due to human-induced factors such as eutrophication and land reclamation; therefore, coastal management is needed to promote conservation of these natural ecosystems. To take on increasing demand for conservation, a variety of coastal restoration programs have been undertaken, but in Japan most of these enterprises have not been as successful as expected because they sometimes disregard the ecological processes of coastal organisms and ecosystems. This paper reviews the importance of research on biodiversity and ecosystem functioning for coastal management, and emphasizes effective links among research, management, and decision-making when promoting the conservation and restoration of coastal ecosystems. In any nature restoration program for a particular ecosystem, it is important to take into account biological factors such as traits of the component species, species interactions, community structure, and connectivity of adjacent ecosystems, but such biological factors have until now been inadequately considered in planning an effective restoration programs. To compensate for uncertainties in ecosystem variability and dynamics, broad-scale and long-term monitoring of biodiversity and ecosystem functions in coastal ecosystems are indispensable and also should be useful for adaptive management of coastal ecosystems.

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Long-term variations in water temperature, salinity, transparency, and nutrient and dissolved oxygen concentrations in the whole area of the Seto Inland Sea of Japan were examined using data from a fisheries monitoring program conducted from 1973 to 2002. After 1989/1990, water temperature at 10m depth generally remained at a higher level than in the 1980s. This trend was recognized noticeably in winter, suggesting that the water temperature fluctuations in the Seto Inland Sea were differed seasonally. Transparency generally remained at a high level after the late 1980s. On the other hand, phosphate concentration at the surface dramatically decreased in the late 1970s, probably in reflection of the Areawide Total Pollutant Load Control System, and generally continued to be flat thereafter. Patterns of variation in concentration of dissolved inorganic nitrogen at the surface and dissolved oxygen at the bottom were similar to that of phosphate concentration throughout the viewpoint of the whole area of the Seto Inland Sea.

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The Seto Inland Sea is a semi-enclosed shallow embayment located in the western part of Japan. A great deal of aquaculture is performed in the sea area, and outbreaks of HABs (Harmful Algal Blooms) often cause severe damage to the local fisheries industry. Recently, recurrent winter diatom blooms have come to cause a large-scale reduction in the production of nori culture in Harima Nada (eastern part of the Seto Inland Sea), by depleting dissolved inorganic nitrogen from the coastal waters. The causative species is thought to be Eucampia zodiacus, which is thought to have a holoplanktonic life cycle. E. zodiacus dominates under conditions of relatively low concentration of inorganic nutrients, compared to Skeletonema, Chaetoceros and Thalassiosira species that have a meroplanktonic life cycle. Inorganic nutrient levels in the Seto Inland Sea have fallen since the 1980s, and the causative species of HABs seems to have been changed. We have monitored the number of diatom resting stage cells (Skeletonema, Chaetoceros and Thalassiosira species) in the bottom sediments of the Seto Inland Sea for many years. The results indicate that the dominant species in bottom sediments has changed from Skeletonema (which dominates under relatively high nutrient levels) to Chaetoceros (which dominates under relatively low nutrient levels).

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Hiroshima Bay (Hiroshima Prefecture) and Ishinomaki Bay (Miyagi Prefecture) are representative farming areas for the Pacific oyster Crassostrea gigas in Japan. To sustain the high productivity of oyster aquaculture, it is essential to clarify the characteristic environmental conditions in both areas. In the present study, the differences between Hiroshima Bay and Oginohama Bay (an inlet of Ishinomaki Bay) in environmental conditions, primary productivity and carbon transfer efficiency from primary production to oyster production are summarized. Among the environmental parameters, annual mean temperature, nutrient concentration, and abundance of prey organisms for oysters were higher and salinity was lower, in Hiroshima Bay than in Oginohama Bay. The maximum species number of tintinnid ciliates was the same in both bays, but while clear increases in species number were observed in Oginohama Bay in spring and autumn, the tintinnid species number in Hiroshima Bay was relatively stable in all seasons. The annual mean of primary production in Hiroshima Bay was 3.8 times higher than that in Oginohama Bay, while estimated carbon transfer efficiency from primary production to oyster production in and around Oginohama Bay was 2.6 times higher than that in Hiroshima Bay. All this suggests that food conditions for cultured oysters are more closely related to oyster production rates in the Oginohama area than in Hiroshima Bay. Consequently, oyster production per unit area in Hiroshima Bay was only 1.5 times higher than that in the Oginohama oyster-farming area, in spite of the much higher primary production in Hiroshima Bay.

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Species composition of fish early life stages was compared among different habitats in shallow waters of the Seto Inland Sea. Data from monthly surveys in three habitats (offshore area, inshore area, and fishing port) in the Sea of Hiuchi, central part of the Seto Inland Sea, during the late 1990s was analyzed. In total, 51, 322 fishes belonging to more than 97 taxa in 49 families were collected with a larva-net at eight offshore sampling stations. 9, 521 fishes belonging to more than 38 species in 24 families were collected with a small-triangle net at 10 inshore stations, and 13, 561 fishes belonging to more than 44 species in 26 families were collected by light-trap sampling in the fishing port. The ichthyofauna of the three habitats was diverse and abundant from late spring to early summer. Differences in the composition of the dominant species among the three habitats indicate that each habitat serves as a nursery for different fish species. Intra-habitat comparison of fish species in summer between inshore stations without vegetation (i.e., sandy beaches) and those with vegetation (i.e., seagrass or macroalgal beds) showed a significant effect of vegetation on dominant fish species composition. The differences in composition of young fish species among the habitats indicate that integrated conservation of the different fish habitats in shallow waters is indispensable for sustainable use of fishery resources in the Seto Inland Sea.

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On extensive intertidal sandflats in Ariake Sound, the yield of the Manila clam, Ruditapes philippinarum, considerably increased in the 1970s but has remarkably decreased since the early 1980s. A survey conducted in 2004 of the individual density and distribution of the large-sized members of the macrobenthic community on a sandflat located at the mouth of the Shirakawa River in the central part of the Sound demonstrated four dominant species: two thalassinidean shrimps (Upogebia major and Nihonotrypaea japonica), which inhabit deep-reaching burrows, and two bivalves (Mactra veneriformis and R. philippinarum). In the late 1970s the Manila clam population prevailed in high densities over the entire area, while its distribution was limited to the lowest zone in 2004. By contrast, the other three species have increased their densities and distribution ranges and may have outcompeted the Manila clam through competition for habitat space. In particular, the strong bioturbating activities of the two shrimps probably havenegatively affected the abundance of the Manila clam. The carbon and nitrogen stable isotope compositions of the four species and their potential food sources were analysed in 2003, specifying phytoplankton (mainly diatoms) as the exclusive food source and suggesting that the four species belong to the same feeding guild. The wet biomass of the populations of N. japonica, U. major, M. veneriformis, and R. philippinarum (the whole body for shrimps and the soft tissues for bivalves) over the sandflat was estimated at 315 t, 110 t, 400 t, and 237 t, respectively. In conclusion, it is hypothesized that the amount of phytoplankton determines the carrying capacity for the benthic community on the sandflat, both quantities having attained their maxima in the 1970s, and (2) the subsequent increased competition for space has caused a further decline in the biomass of the Manila clam population.

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Recent analyses of ecological experiments conducted at small spatial scales have revealed that biodiversity measured at various biotic levels, i.e., species and landscape diversity, plays important roles in maintaining various functions of coastal ecosystems. To test whether the same relationship can be found at broader spatial scales, we measured various indices of biodiversity and functions of seagrass beds located along the eastern shore of Tokyo Bay. Based on our field survey and literature information, we collected data on three variables representing biodiversity of seagrass beds, i.e., mean allele richness of eelgrass obtained using microsatellite analysis, species richness of seagrasses, and Simpson's diversity index for epifaunal assemblages. We also obtained data on three variables representing functions of seagrass beds, i.e., bed areas and their temporal variation, and abundance of epifaunal assemblages. Correlation analysis revealed that allele richness was positively correlated with seagrass bed area, and that seagrass species richness tended to increase with seagrass bed area. In contrast, diversity of epifauna tended to decrease with increasing abundance, although this could be ascribed to a massive occurrence of mysids in one seagrass bed. The findings suggest that biodiversity measured at multiple levels is related to environmental settings and functions of seagrass beds, and that this relationship can be used for the evaluation of seagrass bed condition for conservation and management purposes.

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The Manila clam (Ruditapes philippinarum) population of Yamaguchi Bay, Japan, has almost gone extinct. This paper reviews recent findings from an estuary restoration project there concerning factors affecting clam survivorship and patterns of larval transport within the bay. An artificial stocking experiment examining survivorship of clams released with or without protection by a net revealed that predators such as long-headed eagle rays prey heavily on the clams. Spatial comparisons of survivorship showed that the Nakagata tidal flat is the most suitable habitat for the clam if there is no predation. Current modelling showed that the Shinchigata tidal flat received clam larvae from the Nakagata tidal flat, the Nakagata flat received clam larvae from itself by local recirculation as well as larvae arriving from outside the bay, and the Minamigata tidal flat received clam larvae from itself by local recirculation . Based on these findings, we propose several management strategies for the restoration of the R, philippinarum population in Yamaguchi Bay.

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We propose the following 10 guidelines for running nature restoration projects: (1) Organize a scientific committee; (2) Keep the size of the local council small; (3) Assign appropriate roles to its members; (4) Build a consensus for the master plan's long-term plan and objectives; (5) Resolve land problems and vested interests in an appropriate manner; (6) Write compact implementation and master plans with the text reduced to the essentials; (7) Invite public comment on the drafts for the overall design plan and implementation plan; (8) Clarify when and how the project plan shall be reviewed; (9) Build trust by making the project enjoyable for the participants; and (10) Assure that the scientists speak well and positively of the local council. Adaptive management furthermore depends on the following seven ironclad rules: (i) Specify the hypotheses and assumptions that are used; (ii) Determine beforehand a policy for effecting changes; (iii) Establish evaluation criteria; (iv) Conduct risk management on the basis of careful consideration of uncertainties; (v) Increase the scope of the hypotheses; (vi) Build trust between stakeholders; and (vii) Be aware that today's judgments and decisions may prove to be in error. Finally, we urge attention to the following eight Commandments for nature restoration projects: (I) Thou shalt not proceed with an implementation plan without agreement as to its objective; (II) Thou shalt not lose thy focus; (III) Thou shalt not sketch out a unique path into the future; (IV) Thou shalt not conduct any discussions disregarding the budget; (V) Thou shalt not confuse the scientific committee with the stakeholders' council; (VI) Thou shalt not divide into opposing camps; (VII) Thou shalt not disregard the facts and get carried away with ideology; and (VIII) Thou shalt not neglect to imagine what thou must say the following year.

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As a synthesis of the discussions presented in this special issue, we propose possible solutions to the current problems of conservation and sustainable use of coastal ecosystems. We especially focus on three pressing issues: (1) design of monitoring programs, (2) conflict between conservation of biodiversity and ecosystem functioning, and (3) conflict between different types of restoration project. Monitoring of coastal ecosystems can be planned following either of two strategies: an hypothesis-oriented approach to test the effects of specific conservation and restoration projects, and more general approach designed for wider use by citizens or researchers. Not only the establishment of monitoring networks based on reliable sources that are opened to public, but a well-designed hypothesis-testing method is also necessary to utilize the acquired data fully for predictingfuture changes in coastal ecosystems. Conservation and restoration projects to maximize ecosystem functioning such as fisheries yield are not always consistent with those aimed at minimizing biodiversity loss. Recent studies, however, have revealed evidence for a tight link between biodiversity and ecosystem functioning. We suggest that effective management must consider the spatial structure of coastal areas and make use multiple zoning as a management strategy. Most restoration projects in coastal areas rely largely on artificial materials and structures to accelerate the recovery of only certain targeted species. However, such projects will lead to lowered biodiversity and ecosystem functioning in the long run. Restoration of nature should be carried out to maximize the resilience capacity of natural ecosystems. More scientific research is needed for deeper understanding of the spatial and temporal scales of ecosystem variation, and actions based on such scientific findings are necessary for more effective and comprehensive management of coastal ecosystems.

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