Published Papers - Yasumoto Jun

Coral Decline Linked to Exchangeable Phosphate in Seawater from Coastal Calcareous Sediments, as Evidenced in Sekisei Lagoon, Japan

Jun Yasumoto, Mariko Iijima, Akira Iguchi, Takashi Nakamura, Ryogo Takada, Mina Yasumoto-Hirose, Yuichi Iwasaki, Tetsuo Yasutaka, Kanami Mori-Yasumoto, Ryuichi Shinjo, Ryota Ide, Alice Yamazaki, Nanami Mizusawa, Yoshikazu Ohno, Atsushi Suzuki, Shugo Watabe, Ko Yasumoto

Marine Biotechnology ( Springer Nature )    2025.03 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

Adverse effects of total phosphate load from the environment on the skeletal formation of coral juveniles

Mariko Iijima, Ko Yasumoto, Jun Yasumoto, Akira Iguchi, Mina Yasumoto-Hirose, Kanami Mori-Yasumoto, Nanami Mizusawa, Mitsuru Jimbo, Kazuhiko Sakai, Atsushi Suzuki, Shugo Watabe

Marine Pollution Bulletin ( Elsevier )    2025.02 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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Effect of Groundwater Flow on Microbial Activity in a Porous Limestone Groundwater

Nakaya, S; Deno, T; Yasumoto, J; Takada, R

ECOHYDROLOGY   18 ( 1 )   2025.01 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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The Role of Polyamines in pH Regulation in the Extracellular Calcifying Medium of Scleractinian Coral Spats

Azusa Kubota, Yoshikazu Ohno, Jun Yasumoto, Mariko Iijima, Michio Suzuki, Akira Iguchi, Kanami Mori-Yasumoto, Mina Yasumoto-Hirose, Tsuyoshi Sakata, Takaaki Suehiro, Kaho Nakamae, Nanami Mizusawa, Mitsuru Jimbo, Shugo Watabe, Ko Yasumoto

Environmental Science & Technology ( American Chemical Society )    2024.12 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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Polyamine impact on physiology of early stages of reef-building corals–Insights from rearing experiments and RNA-Seq analysis

Kodai Gibu*, Nanami Mizusawa, Mariko Iijima, Yoshikazu Ohno, Jun Yasumoto, Ko Yasumoto, Akira Iguchi

Scientific Reports ( Springer Nature )    2024.10 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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Reply to discussion of "An assessment of small Island hydrological research activity conducted in the Oceania Region"<SUP>1</SUP>

Leong, C; Solomone, M; Shinjo, R; Tomojiri, D; Uchiyama, C; Yasumoto, J; Razafindrabe, B

HYDROLOGICAL SCIENCES JOURNAL ( Hydrological Sciences Journal )  69 ( 11 ) 1557 - 1559   2024.08 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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Live imaging of center of calcification formation during septum development in primary polyps of Acropora digitifera

Yoshikazu Ohno, Anan Takahashi, Motosuke Tsutsumi, Azusa Kubota, Akira Iguchi, Mariko Iijima, Nanami Mizusawa, Takashi Nakamura, Atsushi Suzuki, Michio Suzuki, Jun Yasumoto, Shugo Watabe, Kazuhiko Sakai, Tomomi Nemoto, Ko Yasumoto

Frontiers in Marine Science   11   1406446   2024.08 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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Recent studies have revealed that stony corals create their extracellular skeletons via biologically controlled calcification, in which amorphous calcium carbonate (ACC), regarded as precursors of aragonite crystals, have been observed at nanoscale using electron microscopy. However, the exact mechanism by which ACC is generated, and how it contributes to skeletal growth in coral calcifying tissue, remains enigmatic. The septal skeleton of an individual polyp is composed of radially aligned plates extending upward from the aboral calcifying tissue. This structure includes microstructure known as the centers of calcification (CoC). However, despite its importance, direct in vivo observation of septal growth has not been reported. Observations under transmitted illumination using polarized light microscopy on calcifying tissue of young Acropora digitifera revealed small crystals, a few micrometers in size, that accompany subtle movements and that emerge exclusively on the inner wall of the pocket in extracellular calcifying fluid (ECF). Crystal growth initiated from small, scattered crystals on a glass plate resembles this phenomenon observed in coral skeletons. Time-lapse photographs of 12 individuals in early primary polyp settlement revealed this process in three individuals, documenting 13 of these crystal events. This phenomenon occurred solely at the bases of subsequently formed septa. These crystals differ notably from fusiform crystals and from dumbbell-like or rod-like crystals growing individually. Upright two-photon microscopy captured movement of sub-micron-sized fluorescent calcein-accumulating particles, emphasizing their presence on the surface of the growing fronts of septa. Methodological advances that facilitate comprehensive in vivo observation of sub-micron-sized structures, calcein-accumulating particles to the skeleton, are needed to develop a more detailed understanding of coral skeletal growth.

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Metagenomic analysis of the microbial communities and associated network of nitrogen metabolism genes in the Ryukyu limestone aquifer

Maruyama, R; Yasumoto, K; Mizusawa, N; Iijima, M; Yasumoto-Hirose, M; Iguchi, A; Hermawan, OR; Hosono, T; Takada, R; Song, KH; Shinjo, R; Watabe, S; Yasumoto, J

SCIENTIFIC REPORTS ( Scientific Reports )  14 ( 1 ) 4356 - 14   2024.02 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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Abstract While microbial biogeochemical activities such as those involving denitrification and sulfate reduction have been considered to play important roles in material cycling in various aquatic ecosystems, our current understanding of the microbial community in groundwater ecosystems is remarkably insufficient. To assess the groundwater in the Ryukyu limestone aquifer of Okinawa Island, which is located in the southernmost region of Japan, we performed metagenomic analysis on the microbial communities at the three sites and screened for functional genes associated with nitrogen metabolism. 16S rRNA amplicon analysis showed that bacteria accounted for 94–98% of the microbial communities, which included archaea at all three sites. The bacterial communities associated with nitrogen metabolism shifted by month at each site, indicating that this metabolism was accomplished by the bacterial community as a whole. Interestingly, site 3 contained much higher levels of the denitrification genes such as narG and napA than the other two sites. This site was thought to have undergone denitrification that was driven by high quantities of dissolved organic carbon (DOC). In contrast, site 2 was characterized by a high nitrate-nitrogen (NO₃-N) content and a low amount of DOC, and this site yielded a moderate amount of denitrification genes. Site 1 showed markedly low amounts of all nitrogen metabolism genes. Overall, nitrogen metabolism in the Ryukyu limestone aquifer was found to change based on environmental factors.

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Mechanism of denitrification in subsurface-dammed Ryukyu limestone aquifer, southern Okinawa Island, Japan

Oktanius Richard Hermawan, Takahiro Hosono, Jun Yasumoto, Ko Yasumoto, Ke-Han Song, Rio Maruyama, Mariko Iijima, Mina Yasumoto-Hirose, Ryogo Takada, Kento Hijikawa, Ryuichi Shinjo

Science of The Total Environment ( Elsevier BV )  912   169457 - 169457   2023.12 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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Denitrification crucially regulates the attenuation of groundwater nitrate and is unlikely to occur in a fast-flowing aquifer such as the Ryukyu limestone aquifer in southern Okinawa Island, Japan. However, evidences of denitrification have been observed in several wells within this region. This study analyzed environmental isotopes (δ15NNO3 and ẟ18ONO3) to derive the rationale for denitrification at this site. Additionally, the presence of two subsurface dams in the study area may influence the processes involved in nitrate attenuation. Herein, we analyzed 150 groundwater samples collected spatially and seasonally to characterize the variations in the groundwater chemistry and stable isotopes during denitrification. The values of δ15NNO3 and δ18ONO3 displayed a progressive trend up to +59.7 ‰ and + 21 ‰, respectively, whereas the concentrations of NO3−–N decreased to 0.1 mg L−1. In several wells, the enrichment factors of δ15NNO3 ranged from −6.6 to −2.1, indicating rapid denitrification, and the δ15NNO3 to δ18ONO3 ratios varied from 1.3:1 to 2:1, confirming the occurrence of denitrification. Denitrification intensively proceeds under conditions of depleted dissolved oxygen concentrations (<2 mg L−1), sluggish groundwater flow with longer residence times, high concentrations of dissolved organic carbon (>1.2 mg L−1), and low groundwater levels during the dry season with precipitation rates of <100 mm per month (Jun–Sep). SF6 analysis indicated the exclusive occurrence of denitrification in specific wells with groundwater residence times exceeding 30 years. These wells are located in close proximity to the major NE–SW fault system in the Komesu area, where the hydraulic gradient was below 0.005. Detailed geological and lithological investigations based on borehole data revealed that subsurface dams did not cause denitrification while the major NE–SW fault system uplifted the impermeable basement rock of the Shimajiri Group, creating a lithological gap at an equivalent depth that ultimately formed a sluggish groundwater area, promoting denitrification.

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An assessment of small Island hydrological research activity conducted in the Oceania Region

Chris Leong, Maletina Solomone, Ryuichi Shinjo, Daiki Tomojiri, Christmas Uchiyama, Jun Yasumoto &Bam Razafindrabe

Hydrological Sciences Journal ( Taylor & Francis )    2023.09 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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Effective use of farmland soil samples for N and O isotopic source fingerprinting of groundwater nitrate contamination in the subsurface dammed limestone aquifer, Southern Okinawa Island, Japan

28. Oktanius Richard Hermawan, Takahiro Hosono, Jun Yasumoto, Ko Yasumoto, Ke-Han Song, Rio Maruyama, Mariko Iijima, Mina Yasumoto-Hirose, Ryogo Takada, Kento Hijikawa, Ryuichi Shinjo

Journal of Hydrology     2023.04 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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Effect of groundwater residence time on geogenic fluoride release into groundwater in the Mt. Meru slope area, Tanzania, the Great Rift Valley, East Africa

Shinji Nakaya, Ryogo Takada, Jun Yasumoto, Harue Masuda, Junichi Yoshitani, Ryuichi Shinjo, Innocent Lugodisha, Hans Komakech

Journal of Contaminant Hydrology ( Elsevier )    2023.02 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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Visualization of Phosphate in Subcalicoblastic Extracellular Calcifying Medium and on a Skeleton of Coral by Using a Novel Probe, Fluorescein-4-Isothiocyanate-Labelled Alendronic Acid

Mariko Iijima, Jun Yasumoto, Kanami Mori-Yasumoto, Mina Yasumoto-Hirose, Akira Iguchi, Atsushi Suzuki, Nanami Mizusawa, Mitsuru Jimbo, Shugo Watabe & Ko Yasumoto

Marine Biotechnology ( Springer Nature )    2022.04 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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Phosphate bound to calcareous sediments hampers skeletal development of juvenile coral

Mariko Iijima, Jun Yasumoto, Akira Iguchi, Kiyomi Koiso, Sayaka Ushigome, Natsuki Nakajima, Yuko Kunieda, Takashi Nakamura, Kazuhiko Sakai, Mina Yasumoto-Hirose, Kanami Mori-Yasumoto, Nanami Mizusawa, Haruna Amano, Atsushi Suzuki, Mitsuru Jimbo, Shugo Watabe and Ko Yasumoto

Royal Society Open Science ( Royal Society )    2021.03 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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Evaluation of recharge areas of Arusha Aquifer, Northern Tanzania: Application of water isotope tracers

Innocent Lugodisha, Hans C. Komakech, Shinji Nakaya, Ryogo Takada, Junichi Yoshitani, Jun Yasumoto

Hydrology Research   51 ( 6 ) 1490 - 1505   2020.12 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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In Arusha urban, northern Tanzania, groundwater contributes about 80% of the water supply. However, elevated fluoride levels and evidence of anthropogenic pollution have been reported in the groundwater around Mount Meru which is a water source for Arusha urban. This study aims at understanding the recharge areas and flow pathways of groundwater in what has been a poorly monitored area. The study uses the isotopic ratio of oxygen and hydrogen to estimate the groundwater recharge area and flow pathway. The results show the recharge elevation of groundwater is between 1,800 and 3,500 m above mean sea level on the slopes of Mount Meru. The average fluoride contents in the study area are 5.3 ± 0.4 mg/L greater than the limits of 1.5 mg/L set by the World Health Organization (WHO) and Tanzania. The nitrate concentration of 83.9 mg/L at the lower elevation areas (<1,400 m above mean sea level) exceeds the 50 mg/L WHO limit. The relationship of F- with δ18O and NO3- suggests the leaching of fluoride in high altitudes and dilution in lower altitudes.

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Phosphate Enrichment Hampers Development of Juvenile Acropora digitifera Coral by Inhibiting Skeleton Formation.

Iijima M, Yasumoto K, Yasumoto J, Yasumoto-Hirose M, Kuniya N, Takeuchi R, Nozaki M, Nanba N, Nakamura T, Jimbo M, Watabe S

Marine biotechnology (New York, N.Y.) ( Marine Biotechnology )  21 ( 2 ) 291 - 300   2019.04 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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Coral reef degradation due to various local stresses, such as nutrient enrichment and terrestrial run-off into coastal waters, is an increasing global concern. Inorganic phosphates have been considered to possibly inhibit skeleton formation in corals. Despite many studies available on the effects of nutrients on corals, a clear consensus on how nutrients exert deteriorative effects on corals has not been established satisfactorily. In this study, we examined the effects of phosphates and nitrates on in vitro aragonite CaCO3 formation by using biogenic polyamines and in vivo aragonite formation in the skeleton of juvenile Acropora digitifera corals. We showed that the phosphates at similar concentrations clearly inhibited both in vitro and in vivo CaCO3 formation. In contrast, nitrates inhibited neither in vitro aragonite CaCO3 formation nor in vivo aragonite formation in juvenile coral skeleton. Furthermore, our findings showed that inhibition of coral skeleton formation was due to absorption of phosphate on the skeleton, which inorganically inhibited normal development of juvenile coral skeleton.

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Atmospheric CO₂ captured by biogenic polyamines is transferred as a possible substrate to Rubisco for the carboxylation reaction.

Yasumoto K, Sakata T, Yasumoto J, Yasumoto-Hirose M, Sato SI, Mori-Yasumoto K, Jimbo M, Kusumi T, Watabe S

Scientific reports ( Scientific Reports )  8 ( 1 ) 17724   2018.12 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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Biogenic polyamines are involved in a wide range of plant cellular processes, including cell division, morphogenesis and stress responses. However, the exact roles of biogenic polyamines are not well understood. We recently reported that biogenic polyamines that have multiple amino groups can react with CO2 and accelerate calcium carbonate formation in seawater. The ability of biogenic polyamines to capture atmospheric CO2 prompted us to examine their roles in photosynthesis. Here, we demonstrated that atmospheric CO2 captured by biogenic polyamines is a candidate substrate for the carboxylation reaction of ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco), which is an enzyme involved in the first major step of carbon fixation during photosynthesis, and that biogenic polyamines can accelerate the carboxylation reaction of this enzyme because of their specific affinity for CO2. Moreover, the results of our nuclear magnetic resonance (NMR) analysis showed that putrescine, which is the most common biogenic polyamine, reacts with atmospheric CO2 and promotes the formation of carbamate derivatives and bicarbonate in aqueous environments. A sufficient amount of CO2 is well known to be produced by carbonic an hydrase from bicarbonate in vivo. The present study indicates that CO2 would be also produced by the equilibrium reaction from carbonate produced by biogenic polyamines and would be used as a substrate of Rubisco, too. Our results may suggest a new photosynthetic research strategy that involves CO2-concentrating mechanisms and also possibly constitutes a potential tool for reducing atmospheric CO2 levels and, consequently, global warming.

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Hydrochemical behaviour of an underground dammed limestone aquifer in the subtropics

Nakaya Shinji, Yasumoto Jun, Ha Phan Min, Aoki Hideto, Kohara Fumiya, Masuda Harue, Masuoka Kentaroh

HYDROLOGICAL PROCESSES   32 ( 23 ) 3529 - 3546   2018.11 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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<jats:title>Abstract</jats:title><jats:p>In an island area with limited surface water resources, the conservation of fresh groundwater resources is important for the maintenance of the water supply and irrigation system to be used in agricultural activity. In a limestone aquifer used for irrigation on a subtropical island, the progress of the dissolution behaviour of the aquifer and the effects of CO<jats:sub>2</jats:sub> storage and chemical weathering of the aquifer must be understood to ensure sustainable groundwater use. In this study, hydrochemical behaviour of the Ryukyu limestone aquifer was investigated using the residence time of slowly flowing groundwater, which is contained by a 2.3‐km‐long underground man‐made dam constructed in 2005 located at the southern edge of Okinawa Island, Japan. Groundwater dating and horizontal flow velocity measurements indicate that the groundwater horizontal flow is slow in the underground dam area, whereas the saturation index (SI) for calcite indicates that the majority of the limestone exists in a supersaturated condition. The range of SI for gypsum was indicative of subsaturation, and the SI increased with the groundwater residence time, suggesting that the dissolution of CaSO<jats:sub>4</jats:sub> tends to proceed slowly through the common ion effect. The dissolution of CaCO<jats:sub>3</jats:sub>, however, tends to be in suspension within about a residence time of 20 years. The apparent dissolution rate of Ca in the Ryukyu limestone aquifer in this area was estimated to be approximately 2.70–4.06 nmol cm<jats:sup>−2</jats:sup> year<jats:sup>−1</jats:sup>, a value much lower than that of the early stages of the limestone dissolution. The estimated groundwater CO<jats:sub>2</jats:sub> (gas) concentrations are two order high (about 0.3–7%) relative to atmospheric CO<jats:sub>2</jats:sub> (about 0.04%), and the groundwater pH shows a tendency to decrease from 7.4 to 6.9 over the last approximately 20 years, indicating that the hydration reaction of CO<jats:sub>2</jats:sub> occurs in the Ryukyu limestone aquifer. These findings imply that high CO<jats:sub>2</jats:sub> produced in the subtropical zone is consumed slower than CO<jats:sub>2</jats:sub> production during limestone dissolution, with the exclusion of the early stage of the chemical weathering process, and causes groundwater acidification in the underground dammed limestone aquifer.</jats:p>

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琉球石灰岩帯水層における脱窒に係わる微生物相解析

安元純，廣瀬(安元)美奈，久手堅剛，宮城雄次，大城要平，聖川健斗，細野高啓，嶋田純，中野拓治

地下水学会誌 ( 公益社団法人 日本地下水学会 )  57 ( 2 ) 153 - 169   2015.05 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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本研究では，沖縄本島南部地域の琉球石灰岩帯水層において，地下水水質データと硝酸中の窒素及び酸素同位体比（δ#U15#URN#DNO#B#D3#DR#BR#DR，δ#U18#URO#DNO#B#D3#DR#BR#DR）を測定することで脱窒ポイントを推定し，PCR法を組み合わせた変性剤濃度勾配ゲル電気泳動法（以下，PCR-DGGE法）及びリアルタイムPCR等を用いた微生物相解析等を実施して，帯水層中の優占種および分離菌株の分子系統解析と脱窒関連遺伝子の検出と定量を試みると共に，その結果とδ#U15#URN#DNO#B#D3#DR#BR#DR，δ#U18#URO#DNO#B#D3#DR#BR#DRの結果を比較し，地下水中の脱窒の有無やその程度の推定に対する微生物相解析の有効性について検討した。<BR>その結果，細菌種は異なるものの，脱窒ポイント，その他のポイントに係わらず，全観測地点で脱窒能を持つと報告されている属と同じ属の細菌が検出された。リアルタイムPCRを用いて脱窒関連遺伝子（nirS/nirK）の定量を行ったところ，nirK遺伝子に比べnirS遺伝子の方が多く検出され，本地域の脱窒にはnirS遺伝子をもつ微生物が優先的にかかわっていることが明らかとなった。さらに，nirS及びnirK遺伝子のDNA コピー数とδ#U15#URN#DNO#B#D3#DR#BR#DR，δ#U18#URO#DNO#B#D3#DR#BR#DRの値との間には比較的高い相関がみられ，δ#U15#URN#DNO#B#D3#DR#BR#DR，δ#U18#URO#DNO#B#D3#DR#BR#DRを用いた同位体的手法とリアルタイムPCRを用いた脱窒関連遺伝子の定量手法を併用することが，地下水中における脱窒環境やその程度を推定する有効な手法となる可能性が示唆された。

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琉球石灰岩帯水層における広域地下水流動モデルの構築

安元純，阿部真己，中野拓治

土木学会論文集B1(水工学) ( 公益社団法人 土木学会 )  71 ( 4 ) I_217-222 - I_222   2015 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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Groundwater model for understanding and predicting hydraulics and contaminant transport in aquifer make assumptions about the distribution and hydraulic properties of geologic features that may not always apply to karst aquifers. In this study, a finite difference groundwater model (MODFLOW-NWT) was applied to construct an equivalent single layer two-dimensional mathematical model of the Ryukyu limestone aquifer, which is located a southern part of Okinawa main islands. In order to handle problems at regional scale groundwater model in the aquifer, automated parameter estimation method (PEST) was used in this model. Groundwater level measurements collected in 1994 were used to calibrate a steady state model of the study area. This study shows the ability of MODFLOW-NWT and PEST to simulate regional groundwater flow in highly karstified aquifer such as Ryukyu limestone aquifer, which is important for water resource and groundwater management in the area.

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