Development of a Shizugawa Bay Digital Twin using an integrated watershed-ocean-ecosystem model (part 3)

School of Environment and Society, Institute of Science Tokyo

Asso.Prof.Takashi Nakamura

I would like to express my sincere gratitude for your consideration in awarding me the EMECS Grants-in-Aid for young researchers. I am deeply appreciative of the invaluable support provided by the International EMECS Center, which has enabled me to continue my research on the coastal ecosystem in Shizugawa Bay, Minamisanriku, Miyagi.
It has been observed that semi-closed bays, such as Shizugawa Bay, are characterized by a complex flow and water quality environment, influenced by various factors, including the inflow of freshwater from land, nutrients, organic matter, sediment, and biochemical reactions within the bay, as well as the intrusion of open-ocean water. To sustainably utilize marine resources and aquaculture, it is essential to understand these processes and the bay environment with a high degree of accuracy. Furthermore, it is possible that global warming and ocean acidification associated with recent increases in atmospheric CO2 concentrations may enhance stratification, especially in summer, and induce serious hypoxia and acidification in the bottom layer. We need to recognize that ongoing acidification has the potential to have significant consequences for marine ecosystems, particularly for calcifying organisms, such as oysters. This study aims to develop a digital twin of Shizugawa Bay to seek the optimal sustainable use of marine resources and aquaculture in the present and the future under climate change. The proposed approach involves the utilization of an integrated watershed-ocean-ecosystem model, intending to comprehensively reproduce the bay environment and ecosystem, including the dynamics of marine resources.
One of the interesting phenomena of oyster farming in Shizugawa Bay is that oyster yield increased when the number of oyster rafts was reduced with the great decision of local fishermen after the earthquake disaster. This means that it is very important to understand the negative impact of overcrowded aquaculture and to know the best density for aquaculture. The effects of overcrowding in aquaculture must be biological, such as competition for the availability of oyster food (phytoplankton), and physical, such as the weakening of water circulation by the drag of oyster rafts. Additionally, we need to think about how wakame seaweed and phytoplankton, which are a food source for oysters, compete for nutrients. Considering both physical and biological aspects, we try to seek the optimum aquaculture density and the best solution for sustainable aquaculture in Shizugawa Bay.

Elucidating the Carbon Budget in Coastal Areas: A Case Study of Toyama Bay

Faculty of Science, University of Toyama

Special Assit.Prof.Hidetaka Kobayashi

The ocean functions as one of the Earth’s largest carbon reservoirs, absorbing roughly 30% of anthropogenic CO2 emissions. Understanding the mechanisms behind this variability is essential for predicting future atmospheric concentrations. Coastal regions play a particularly important role as dynamic CO2 sinks. Within this context, my research centers on Toyama Bay, where I aim to uncover the processes that shape carbon-centered material cycles through a combination of long-term field observations and numerical modeling.
Over the past research period, I have focused on building a comprehensive observational dataset. This includes continuous monitoring of major rivers in Toyama Prefecture as well as bay waters, measuring discharge, water quality, dissolved inorganic carbon, nutrient concentrations, and chlorophyll. These records highlight both seasonal and interannual variability in nutrient delivery from land, which previous studies suggest may account for up to 20% of phytoplankton blooms. By extending these observations across multiple years, I seek to narrow the uncertainty surrounding this contribution.
These observational efforts provide the foundation for my modeling work. By constraining terrestrial inputs such as riverine discharge and submarine groundwater, I aim to improve the reproducibility of primary production and CO2 fluxes in the bay. Although the modeling system is still in progress, gradually incorporating field data is beginning to reveal the unique structure of material cycles in Toyama Bay. Looking ahead, I intend to combine observations and modeling in a complementary way to quantify the causal relationships between terrestrial fluxes of nutrients and carbon and the oceanic responses they trigger. Such results will not only advance our understanding of carbon cycling in coastal zones but also contribute to more accurate projections of global climate change. Beyond the global perspective, the findings will also provide a scientific basis for sustaining fisheries resources and protecting coastal environments, ensuring that the research contributes to both regional communities and the broader Earth system.

Primary production of microphytobenthos on tidal flats influenced 　　　　　　　　by tides and submarine groundwater discharge (Part II)

Prefectural University of Kumamoto
Graduate School of Environmental & Symbiotic Sciences　Division of Environmental & Symbiotic Sciences

Doctoral Degree ProgramsTatsuya Ozaki

I would like to offer my sincere gratitude regarding my selection for EMECS Grants-in-Aid for young researchers. I belong to the doctoral course of the Graduate School of Environmental Symbiosis, Prefectural University of Kumamoto, and I am working on quantifying the primary producers of tidal flats in the Midori River tidal flat of the Ariake Bay, which has the largest tidal flat area in Japan.
Tidal flats support high fishery productivity, mainly through the harvest of bivalves. The growth of these bivalves is sustained by the horizontal transport of primary producers within the tidal flats. In this system, bivalve habitats function as “sinks” that consume primary producers, whereas muddy flats without bivalves and submarine groundwater discharge (SGD) areas act as “sources” that supply them. Recent studies have suggested that nutrient-rich SGD, particularly in nearshore areas adjacent to subterranean estuaries, promotes primary production and significantly contributes to its spatial distribution. Thus, conserving the tidal flat ecosystem requires not only the protection of bivalve habitats but also the preservation of these sources. However, because such sources are often located nearshore, they are increasingly threatened by coastal development worldwide. Furthermore, the quantification of primary production in tidal flats and its relationship with SGD have not been sufficiently evaluated scientifically, and evaluating the production balance between sources and sinks is an urgent research priority.
The Ariake Bay, which serve as my study site, contains approximately 40 % of Japan’s tidal flats. Although it was once a major bivalve fishing ground, its catches have drastically declined in recent decades. The tidal flats of the Ariake Bay are broadly categorized into sandy and muddy flats: the sandy flats serve as bivalve habitats, while the muddy flats function as sources of primary producers. In my research last year, I successfully quantified long-term primary production in sandy flats (i.e., the sink) of the Ariake Bay. Comparison with the secondary production of Ruditapes philippinarum at the same site revealed that primary production was substantially lower than the clam’s secondary production, demonstrating that an external supply of primary producers is indispensable for sustaining bivalve populations. Field investigations have also confirmed the presence of nutrient-rich SGD in the southern Ariake Bay, leading me to hypothesize that “SGD areas, together with muddy flats, function as important sources of primary producers.” In the present study, I aim to quantify primary production within these sources and conduct a broad-scale assessment of primary production across the Ariake Bay. Through this research, I seek to contribute to a deeper understanding of the mechanisms sustaining tidal flat ecosystems and provide knowledge essential for their conservation.

Effects of Dissolved Silica on the Growth and Eicosapentaenoic Acid (EPA) Production of Benthic Diatoms in Tidal Flats

Department of Urban and Environmental Engineering
Faculty of Engineering　Kyushu University

Asso.Prof.Megumu Fujibayashi

I am honored to have been selected for the EMECS Grants-in-Aid for young researchers, and I am deeply grateful for this opportunity to pursue my research.
My interest lies in the dynamics and ecological roles of fatty acids in aquatic ecosystems, with a particular focus on highly unsaturated fatty acids such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). These fatty acids are essential nutrients for many aquatic animals; however, animals cannot synthesize them de novo or cannot meet their requirements through endogenous synthesis. EPA is mainly synthesized by diatoms and supplied to aquatic food webs through trophic transfer. Adequate dietary EPA has been shown to enhance the fitness of aquatic animals and potentially increase community diversity. In this study, I aim to clarify how dissolved silica (DSi)—an essential nutrient for diatoms—affects their growth and EPA production.
Diatoms, the primary producers of EPA, require silica to build their siliceous frustules. In Japanese rivers, the concentration of silica is generally higher relative to nitrogen and phosphorus, so DSi has rarely been considered a limiting factor for diatom growth. Here, the comparison “silica is relatively more abundant than nitrogen and phosphorus” is based on the Redfield ratio, which estimates that diatoms require N:P:Si ≈ 16:1:15 (molar). According to Liebig’s law of the minimum, the nutrient in shortest supply—typically nitrogen or phosphorus—would limit growth. However, recent culture experiments have yielded results inconsistent with this Redfield requirement, and concepts such as multiple-nutrient limitation have been proposed. This suggests that it is necessary to investigate the nutrient requirements of benthic diatoms in tidal flats, which underpin coastal food webs and supply EPA.
The purpose of this project is to elucidate, through field surveys of nutrient concentrations (nitrogen, phosphorus, and silica) and laboratory culture experiments, the nutrient requirements of benthic diatoms in tidal flats, focusing mainly on sites in Kyushu, Japan. I have already received valuable advice from my advisors and am proceeding with field and laboratory work with the utmost commitment.

Origin and composition of Transparent Exopolymer Particles (TEPs) produced in eelgrass meadows

Akkeshi Marine Station
Field Science Center for Northern Biosphere
Hokkaido University

Asso.Prof.Tomonori Isada

Firstly, I express my sincere gratitude to the International EMECS Center for its generous Grants-in-Aid for young researchers. My research focuses on the dynamics of marine phytoplankton and seagrass in Akkeshi-ko estuary and Akkeshi Bay, located in the eastern region of Hokkaido, Japan. My objective is to obtain a better understanding of the carbon cycle within the coastal marine ecosystem.
Macroalgae beds and seagrass meadows play an important role in carbon burial and sequestration, serving as blue carbon that mitigate climate change. Notably, Japan is recognized as a significant blue carbon area due to its extensive coastline, ranking sixth globally. Consequently, elucidating the carbon cycle of macroalgae beds and seagrass meadows in estuarine and shallow coastal areas is of paramount importance.
This project focuses on the dynamics of Transparent Exopolymer Particles (TEPs) within eelgrass meadows in Akkeshi-ko estuary and Akkeshi Bay. TEPs are composed of acid polysaccharides and are characterized by their sticky particles with > 0.4 µm diameter. This particle aggregation phenomenon closely relates to marine snow. Our previous surveys have shown that the TEP concentrations in the eelgrass meadows of Akkeshi-ko estuary and Akkeshi Bay were highest in summer. We have also found that TEPs contribute to the particle flux in the eelgrass meadow. Next, we aim to investigate the origin and composition of TEPs produced in eelgrass meadows for better understanding the carbon cycle in eelgrass meadows.

Restoration of stock of asari clams and tidal flats ecosystem through nutrient management -A study of ecosystem response and function in　　 tidal flat mesocosm experiments

Aichi Fisheries Research Institute

Chief researcherRyota Sone

The stock of asari clams Ruditapes philippinarum, a key marine species, has significantly declined, impacting coastal fisheries and recreational activities such as clam digging. Moreover, asari clams play an important role in coastal carbon cycling, raising concerns that their decline may lead to the degradation of tidal flats and seagrass beds-ecosystems recognized as part of the blue carbon framework. One major factor contributing to the decline in asari crams stocks is thought to be a shortage of food due to reduced nutrient levels. In response, wastewater treatment facilities in Ise and Mikawa Bays have begun operating with increased nitrogen or phosphorus levels to improve the feeding environment for asari clams. These efforts are expected not only to enhance biological productivity but also to restore ecosystem functions and promote healthy material cycling. Increased primary production may also contribute to decarbonization by enhancing CO₂ absorption at the air–sea interface and increasing carbon sequestration in sediments through the growth of benthic organisms. However, the extent to which differences in nutrient supply and food availability affect biological productivity and ecosystem functions in tidal flats-and how these changes influence material cycling-remains poorly understood. Field surveys in natural coastal areas are often complicated by disturbances such as weather variability and fishing activity, making it difficult to evaluate these processes. Aichi Fisheries Research Institute possesses large-scale tidal flat mesocosms, which have been used to study biological colonization, ecosystem development, and material cycling. This study aims to use these mesocosms to eliminate natural disturbances and conduct controlled experiments manipulating nutrient levels and primary production. We will assess the responses and functions of tidal flat ecosystems, focusing on asari clams. Experimental plots will be established with varying nutrient or food supply conditions, and changes in species composition and biomass of benthic organisms will be monitored. Simultaneously, we will track changes of carbon and nitrogen in water and sediment and evaluate shifts in material cycling driven by ecosystem functions. Direct measurements of CO₂ flux at the air–sea interface will also be conducted to examine carbon budgets, including atmospheric exchange. Through this research, we hope to evaluate how nutrient management can support both productive coastal ecosystems and broader environmental goals such as decarbonization. Ultimately, we aim to contribute to the advancement of integrated fisheries and environmental policies.