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Although environmental DNA (eDNA) of aquatic species has been widely explored, the quantitative assessments of fish remain a challenge. eDNA approach proposed by Fukaya et al. (2021) gave a reliable abundance (the total fish population in the study area) estimates of coastal fish but was not as useful for assessing spatial distribution because of fewer eDNA samples relative to the study area. Hence, we evaluated the ability of the eDNA approach to estimate the abundance and distribution of fish in a semi-enclosed bay based on a numerical study. The evaluation was conducted as a case study on the ability of the eDNA approach according to the number of eDNA samples. Our study revealed that the eDNA approach can reliably estimate fish abundance regardless of the number of eDNA samples, if outliers of the fish density estimates are eliminated. However, when estimating spatial distribution, significant estimates were obtained only under those conditions wherein the eDNA concentration was identified in more than 70% of the study area. Therefore, it is necessary to explore other methodologies for broadly estimating eDNA concentrations with fewer samples. We have confirmed that the eDNA approach can reflect fish abundance but has limitations in estimating fish distribution. From above results, we expect our results to provide researchers with more insights into estimating the abundance and spatial distribution of fish using eDNA.

Chum salmon (Oncorhynchus keta) are distributed widely in the subarctic North Pacific. The Japanese stock is maintained by artificial release procedures. Chum salmon, including the Japanese stock, provide important ecosystem services for humans that are related to provisioning, culture and support. These ecosystem services are supported by the supply of prey and habitat that the fish use. We regard the supply of prey and habitat as supporting services for salmon. We developed a procedure to estimate supporting services quantitatively, based on the prey biomass consumed by individual salmon, by coupling a bioenergetics model and a lower trophic level ecosystem model. Using this procedure, we estimated the prey biomass consumed by a cohort of Japanese chum salmon released in a single year. The phytoplankton biomass indirectly consumed by a cohort was also estimated and considered to be the primary production supporting the fish. The Japanese chum salmon cohort was estimated to consume ca. 4.2–4.7 × 109 kg wet weight of zooplankton, of which more than half is eaten in the Bering Sea. The Japanese chum salmon cohort is supported by an estimated primary production of 2.0–2.2 × 109 kg C, which amounts to 0.17%–0.19% of primary production in the areas and periods through which the fish migrate. We also attempted to calculate the monetary value of supporting services for the growth of Japanese chum salmon.

Here, we report a 16S rRNA gene amplicon sequence analysis presenting the microbial community in sediments from the Suyeong River and Suyeong Bay, Republic of Korea. The dominant phyla in all sediment samples were Proteobacteria (39.69 to 53.62%) and Bacteroidetes (29.78 to 33.89%).

Several oyster farms are concentrated in Geoje-Hansan Bay, Republic of Korea, and there is concern about marine pollution. Hence, we monitored the sediment at this site for a year using 16S rRNA gene sequencing. The predominant phyla were Proteobacteria (69.9 to 79.1%) and Bacteroidetes (8.2 to 10.6%) in all seasons.

Aquaculture places contamination pressure on the coastal environment. We investigated the microbial community structure changes in sediment in an ascidian Styela clava farm. Data profiling of the 16S rRNA gene amplicon sequence shows that the microbial diversity of sediment in the Styela clava farm is dominated by Proteobacteria phyla (relative abundance, 95.34 to 97.85%).

The Taehwa River Estuary is one of the largest enclosed bays in east Korea. In order to understand the environment of the Taehwa River Estuary, the microbial diversity in the sediment of the estuary was investigated through 16S rRNA gene sequencing. The predominant phyla were Proteobacteria and Bacteroidetes in all locations., The Taehwa River Estuary is one of the largest enclosed bays in east Korea. In order to understand the environment of the Taehwa River Estuary, the microbial diversity in the sediment of the estuary was investigated through 16S rRNA gene sequencing. The predominant phyla in all locations were Proteobacteria and Bacteroidetes.

Environmental DNA (eDNA) consists of DNA fragments shed from organisms into the environment, and can be used to identify species presence and abundance. This study aimed to reveal the dispersion and degradation processes of eDNA in the sea. Caged fish were set off the end of a pier in Maizuru Bay, the Sea of Japan, and their eDNA was traced at sampling stations located at the cage and 10, 30, 100, 300, 600 and 1000 m distances from the cage along two transect lines. Sea surface water was collected at each station at 0, 2, 4, 8, 24 and 48 h after setting the cage, and again after removing the cage. Quantitative PCR analyses using a species-specific primer and probe set revealed that the target DNA was detectable while the cage was present and for up to 1 h after removing the cage, but not at 2 h or later. Among the 57 amplified samples, 45 (79%) were collected within 30 m from the cage. These results suggest that eDNA can provide a snapshot of organisms present in a coastal marine environment.

The dominant external forcing factors influencing estuarine circulation differ among coastal environments. A three-dimensional regional circulation model was developed to estimate external influence indices and relative contributions of external forcing factors such as external oceanic forcing, surface heat flux, wind stress, and river discharge to circulation and hydrographic properties in Tango Bay, Japan. Model results show that in Tango Bay, where the Tsushima Warm Current passes offshore of the bay, under conditions of strong seasonal winds and river discharge, the water temperature and salinity are strongly influenced by surface heat flux and river discharge in the surface layer, respectively, while in the middle and bottom layers both are mainly controlled by open boundary conditions. The estuarine circulation is comparably influenced by all external forcing factors, the strong current, surface heat flux, wind stress, and river discharge. However, the influence degree of each forcing factor varies with temporal variations in external forcing factors as: the influence of open boundary conditions is higher in spring and early summer when the stronger current passes offshore of the bay, that of surface heat flux reflects the absolute value of surface heat flux, that of wind stress is higher in late fall and winter due to strong seasonal winds, and that of river discharge is higher in early spring due to snow-melting and summer and early fall due to flood events. (C) 2017 Elsevier Ltd. All rights reserved.

Molecular analysis of DNA left in the environment, known as environmental DNA (eDNA), has proven to be a powerful and cost-effective approach to infer occurrence of species. Nonetheless, relating measurements of eDNA concentration to population abundance remains difficult because detailed knowledge on the processes that govern spatial and temporal distribution of eDNA should be integrated to reconstruct the underlying distribution and abundance of a target species. In this study, we propose a general framework of abundance estimation for aquatic systems on the basis of spatially replicated measurements of eDNA. The proposed method explicitly accounts for production, transport and degradation of eDNA by utilizing numerical hydrodynamic models that can simulate the distribution of eDNA concentrations within an aquatic area. It turns out that, under certain assumptions, population abundance can be estimated via a Bayesian inference of a generalized linear model. Application to a Japanese jack mackerel (Trachurus japonicus) population in Maizuru Bay revealed that the proposed method gives an estimate of population abundance comparable to that of a quantitative echo sounder method. Furthermore, the method successfully identified a source of exogenous input of eDNA (a fish market), which may render a quantitative application of eDNA difficult to interpret unless its effect is taken into account. These findings indicate the ability of eDNA to reliably reflect population abundance of aquatic macroorganisms; when the "ecology of eDNA" is adequately accounted for, population abundance can be quantified on the basis of measurements of eDNA concentration.

Several studies have shown that suspended microphytobenthos are important food source for clams. We hypothesized that the degree of the resuspension flux of microphytobenthos must play important roles in growth rate and size of clams, and investigated it through observations over 2 years at two stations (lake mouth and inner lake) in a subarctic lagoon (Akkeshi Lake) and numerical modeling. Large clams (length >40 mm) were seldom observed at the inner lake. The growth rates of 40 mm clams incubated in cages at two stations were also much greater at the outer station. Resuspension of microphytobenthos occurred frequently at the lake mouth due to the high current speed. These results indicate that differences in food availability due to the current and resuspension were the primary cause of the growth differences between the two stations. The relationships between environmental factors, food availability, and clam growth were also modeled with long-term simulation. Once more, the different clam growth in the two lake zones was ascribed to the resuspension flux of microphytobenthos. The shell growth limited at approximately 40 mm at the inner lake was due to strong growth limitation. Both filed measurements and modeling demonstrated that microphytobenthos resuspension can be a remarkable food source for clams.

Chum salmon (Oncorhynchus keta) are predominantly located in the Bering Sea during summer and fall. However, several studies have recently reported a different tendency as follows. Observed densities of chum salmon were higher in the vicinity of the Bering Strait and the Chukchi Sea than the eastern Bering Sea in September 2007, and Japanese chum salmon migrated to northern areas in the Bering Sea during summer 2009. The sea surface temperature (SST) in the Arctic marginal seas has increased since the mid-1960s, and especially since 2000. We speculated that the SST increase directly promoted salmon northing from the Bering Sea to the Western Arctic. In this study, we estimated the potential habitat for chum salmon in the Western Arctic using a bioenergetics model coupled with a three-dimensional lower trophic ecosystem model (3-D NEMURO). “Potential habitat” was defined as “an area where chum salmon could grow (i.e., the growth rate was positive)”. In the bioenergetics model, the growth rate of an individual chum salmon was calculated as a function of water temperature, salinity, and prey density, which were obtained from the 3-D NEMURO model results. To evaluate the habitat responses under a global warming scenario, we used the modeled monthly change of water temperature between 2005 (averaged from 2001 to 2010) and 2095 (averaged from 2091 to 2100) under the IPCC SRES-A1B scenario. Our calculations, following the global warming scenario, suggested that the potential habitat for chum salmon would expand to the north due to the increase in water temperature and prey density. In contrast, south of 71°N during summer, the potential habitat would shrink regionally because the water temperature exceeded the optimal condition.

In the original publication the text in right column of page 330, the sequences of primers were incorrectly published as.

Akkeshi Lake is a subarctic shallow brackish lagoon located in Hokkaido, Japan. The Manila clam, Ruditapes philippinarum, is cultured in sandy sediments at the shallow, intertidal flat near the mouth of the lake. To quantitatively evaluate the effects of environmental factors such as water temperature and food availability on the growth of the Manila clam and to estimate the responses of Manila clam growth and food availability to global warming in Akkeshi Lake, we developed a numerical model by coupling a three-dimensional ecosystem model with a bioenergetics model for the growth of the Manila clam. We ran the model under two different conditions: the present condition and the global warming condition. For the global warming condition, water temperature was increased by 2 °C at the open boundary for the entire computational period. The growth of the Manila clam was limited by water temperature and food availability. The Manila clam grew up to 1.33 g dry weight ind.−1 at the lake mouth (station A) for 5 years, whereas it grew up to 1.00 g dry weight ind.−1 at the lake center (station B). The difference in the biomass of the Manila clam between two stations was due to the difference in food availability. Under the global warming condition, the water temperature limitation for the Manila clam was relaxed with a water temperature increase. The Manila clam grew up to 1.55 g dry weight ind.−1 at station A and 1.10 g dry weight ind.−1 at station B. While the growth of the Manila clam was improved in the lake under the global warming condition, its food sources, especially phytoplankton, decreased because of ingestion increases of grazers.

A lower trophic ecosystem model, which was originally developed for describing the variability in plankton distribution in the western North Pacific, is applied to the global ocean. A realistic time series of dynamically self-consistent circulation fields obtained by a 4-dimensional variational ocean data assimilation experiment is used for the environmental fields in the ecosystem model. An optimization of the bio-ecological parameter values in 40 provinces by a Green’s function approach enables the ecosystem model to represent the observed variabilities of nutrients and surface chlorophyll concentration with a relatively small number (11) of compartments. In addition, artificial trends of the ecosystem variables due to model errors are generally suppressed by the optimization. The obtained parameter values and ecosystem fields are generally consistent with observations in terms of assimilated and non-assimilated metrics. The integrated lower-trophic ecosystem and physical fields in the global ocean offer important information on the mechanisms (such as El Ninos) responsible for the seasonal–interannual variability in the lower trophic ecosystem. Our results demonstrate that, with adequate parameter sets capable of modifying indirectly the model and significance of each pathway to reflect the characteristics of local species, a simple ecosystem model can be applied in quantitative analyses to enhance our understanding of the influence of climate variations on the ocean ecosystem.