For the appropriate stock management of fish species, it is essential to investigate ecological information, such as species distribution and migration patterns. Recent studies have shown the usefulness of elemental and stable isotopic composition in fish otoliths as a natural tag for reconstructing the migratory ecology of fish. To provide guidance for the use elemental and stable isotopic composition of otoliths in ecological studies of fish, this study focuses on quantitatively describing the process and degree of variations of each chemical composition of otoliths, primarily by describing their geochemical aspects. The types of factors that are responsible for variations in elemental and stable isotopic composition of otoliths are discussed based on biological and latest geochemical findings. Additional detailed discussions are provided regarding things to be considered when interpreting data. Finally, some of our views are discussed as to the selection of optimal otolith elements and analysis methods required for providing new insights into the ecological studies of fish.

The coastal sea area affected by both outer sea and land area has had a variable environmental state. Additionally, influences of human economic activities make it more complicated. Analyzing using a numerical model is an effective way to figure out the relationship between the fluctuation of the environmental state and fish population dynamics quantitatively. On the other hand, there has not been enough ecological knowledge to develop a numerical model. The purpose of this study is to develop a numerical model using statistics. This model is applied to Ammodytes personatus sp in Osaka Bay as an example. Apparently, non-linear responses of fish population to environmental factors are revealed by optimal transformation method and are formulated as a population dynamics model, including environmental effects based on the responses. Additionally, MCMC method is used to estimate optimal parameters for many unknown parameters in the developed model. These results allow the quantitative evaluation of the imact of fisheries and the environmental state on fish population dynamics of Ammodytes personatus sp in Osaka Bay.

The phenomenon of hypoxia distribution off the Banzu tidal flat of Tokyo Bay was classified into two patterns from 2007–2008 observation data. One pattern occurred when cold and heavy seawater entered the bottom layer from outside the bay when a south wind persisted. At this time, hypoxia that was distributed in the bottom layer of the bay center moved to the middle layer in the same sea area and also moved off the Banzu tidal flat. In the offshore area of the Banzu tidal flat, hypoxia was distributed very shallowly, so the risk of this spreading to the Banzu tidal flat increased. The other pattern was that when a north wind continued blowing for more than a few days, hypoxia distributed in the bottom layer of the bay center moved off the Banzu tidal flat. At this time, hypoxia was distributed only in the bottom layer off the Banzu tidal flat, so it was unlikely that hypoxia affected shellfish in the tidal flat. However, fishery resources such as Japanese cockles are located in this area, and it seemed that these fishing ground formations could be influenced by hypoxia.

We examined the effects of nutrient discharge from land areas to nori farms around the Kako River estuary, eastern part of Seto Inland Sea, off Hyogo Prefecture. Horizontal distribution of high DIN concentration water at the surface was frequently observed along the east coast of the Kako River estuary, off the Befunishi area in Higashiharima Port. The water with high DIN concentration originated from the port with industrial and sewage treatment plant effluents, and the river. These results suggest that nutrient discharge from the river and port influenced nori production in the coastal farms in the eastern Kako River estuary.

To investigate spatio-temporal responses of mega-benthos species to hypoxia, we conducted a bottom trawl survey with environmental observation in Mikawa Bay monthly from June to October. The number of deaths for each main mega-benthos species was estimated from standing stock in relation to fishing, recruitment, and growth. Further, natural mortality coefficient (M_t) and death ratio (Dn_ratio) under hypoxia expansion (i.e., June to September) were calculated. Distribution areas and standing stocks of each mega-benthos species decreased as hypoxia developed. Although M_t (month^-1) changed with the calculation period, the mean from June to September was estimated at 0.41–0.85, 0.42–0.46, 0.46–0.76 and 1.16–1.26 in flounder, swimming crab, mantis shrimp, and cockle, respectively. These values were higher than well-known natural mortality coefficients, which were calculated from biological parameters or observations conducted in normoxic regions. Calculated Dn_ratio was more than 50% in all analyzed species. The results of this study indicate that developed hypoxia causes mass mortality of main mega-benthos species. Moreover, expansion of hypoxic areas incidental to coastal development have potentially deteriorated the ecological corridor for the stone flounder and kuruma prawn populations, which use the inner area of the bay as a nursery.

Izonoura—located in the inner area of Matoya Bay in Shima City, Mie Prefecture―prospered in the aquaculture of Monostroma nitidum, whose amount of production was over 300 tons per year in the 1970s. However, the production decreased rapidly after the 1980s, and the fishermen have demanded an investigation into its cause. We conducted observations of several environmental elements, including turbidity and weather, throughout the spring and summer of 2014 and analyzed the generation mechanism of high turbidity. It was found that the turbidity was higher than 7 FTU―17–66% and 26–73% of the time in spring and summer, respectively―which is considered to affect the growth of Monostroma nitidum. The following factors were considered to cause high turbidity: i) Decrease in river flow accompanied by dam construction reduced the mean flow from the inner to the central area, which would induce a clockwise circulation flow, ii) The surface residual outflow current through the canal weakened. Then, SS (Suspended Solid) from the river and that produced and re-suspended in Izonoura, does not readily outflow from Izonoura, iii) SS was re-suspended not only by the wind but also by the usual tidal current, and iv) Excess sedimentation of SS has caused the deterioration of bottom environments, benthic communities, and the self-purification function of the bottom.