National Institute for Agro-Environmental Sciences

The concept of the ecological niche, defined as the basic habitat requirements for a species, is central to understanding species geographic distributions and predicting their responses to environmental change. However, identifying the essential niche for large regional communities remains a challenge because niche axes can be "hidden" by the complexity of the underlying ecological processes. Here, applying advanced species distribution modelling to nationwide environmental DNA survey data, we identified hidden niche axes of the Japanese coastal fish community and investigated the response diversity to these axes. Our survey detected 1,220 coastal fish species. The hidden niche axes collectively explained most of the variation in fish biodiversity and revealed five biogeographic boundaries for the regional community. These niches of the Japanese fish community may primarily relate to several processes due to ocean currents, such as environmental filters, transport from source areas and dispersal barriers. We also found that the response diversity to niche axes was positively correlated with species richness, although local communities with particularly high response diversity were geographically biased. A better understanding of the niche axes of the regional ecological community should help to mitigate the loss of biodiversity and ecosystem services caused by ongoing environmental change.

Climate change mitigation and biodiversity loss are closely linked challenges, yet agricultural strategies often address them separately. Focusing on rice farming, this article shows that widely promoted water-saving practices can reduce greenhouse gas emissions but may also harm freshwater biodiversity that depends on flooded fields. We highlight alternative management approaches and the need for spatially and seasonally targeted strategies that balance climate goals, biodiversity conservation, and food production.

Agricultural soils are a major source of nitrous oxide (N₂O), a potent greenhouse gas. Legume pastures, such as white clover (Trifolium repens), and non-legume pastures, like tall fescue (Festuca arundinacea), can emit N₂O as a result of soil nitrogen (N) transformations. However, N fertilizer application typically amplifies these emissions by increasing nitrogen availability for nitrification and denitrification. Biochar a carbon-rich amendment derived from crop residues, may mitigate N₂O through modifying soil physicochemical and microbial processes. However, its interaction with different N fertilizers in not well understood in perennial pastures. We conducted a 12-month field experiment in white clover and tall fescue pastures using ammonium sulphate (AS) and urea (U), applied alone or with rice husk biochar (5 and 10 t ha⁻¹). AS had significantly lower soil pH more than U in tall fescue. Furthermore, AS maintained higher ammonium (NH4+-N) than U in tall fescue and lower nitrate (NO₃⁻-N) than U in white clover, corresponding to its lower annual average daily N₂O fluxes (57 vs. 107 µg N m⁻² h⁻¹), and 40.8% cumulative emissions than U in white clover. ASB5 treatment had the lowest cumulative and yield-scaled N₂O emissions in white clover accompanied also by the higher NH4+-N concentration than sole AS. The significant negative correlation between NH4+-N and NO₃⁻-N in tall fescue could suggest that, biochar co-applied with N fertilizer reduced nitrification and N₂O emissions. However further analyses for N2O associated functional genes is required to elucidate the processes. These findings highlight the importance of pasture species and the potential of AS co-applied with optimum biochar rate of 5 t ha⁻¹ to reduce N₂O emissions in white clover.

Carbon dioxide removal (CDR) via enhanced rock weathering (ERW) strongly depends on rock particle size. While ERW models typically link finer particle size to greater CDR, their tendency to aggregate with soil components such as organic matter (OM) may impede weathering. The inconsistent effects of ERW on soil OM storage in recent studies reinforce the need to clarify underlying mechanisms. We thus tested if finer basaltic rock promotes organo-mineral association while lowering CDR through incubation experiments (rock alone and rock-plant residue-sand mixture) under water regimes with or without weekly leaching. After six months, we analyzed total carbon, extractable metal(loid)s, organo-mineral aggregate formation (by density fractionation), and inorganic carbon contents (by XANES and leachates). Coarse basaltic rock (106–150 μm) showed faster abiotic and biologically induced weathering. Contrarily, fine basaltic rock (20–38 μm) led to greater organo-mineral aggregation and OM accrual, which was attributable to higher particle numbers, geometric surface area, and binding agents (inherent and increased reactive metal(loid)s). The amount of organic carbon stabilized in meso-density aggregates by basaltic rock was one order of magnitude higher than the estimated CDR, regardless of the water regimes. These results exhibit the first direct evidence that rock particle size could induce the trade-off between CO2 removal and OM stabilization, which implies that the current ERW models may severely overestimate CDR potential due to basaltic rock interaction with OM and its weathering products. Further research into rock interactions with soil components is essential for improving model prediction and optimizing ERW applications.

Abstract Mangrove forests form vital interfaces between aquatic and terrestrial ecosystems, supporting a wide variety of organisms, both vertebrates and invertebrates. Although insects have long been underrepresented in mangrove research, particularly compared with studies on plant biology and ecosystem functioning, recent findings suggest that their diversity and ecological importance are greater than previously recognized. Nevertheless, their roles in trophic interactions, especially as prey, remain poorly understood. Here, we document six instances of insect predation from a mangrove habitat on Iriomote Island, the Yaeyama Islands, Japan. These include predation by fish, crabs, spiders, dragonflies, wasps and flies on various insect taxa, some of which are associated with mangrove environments. Although fragmentary, these records indicate that insects contribute to mangrove food webs not only as herbivores and detritivores but also as an important prey resource for a broad range of predators. Our observations underscore the need for further research into insect‐mediated trophic relationships in mangrove ecosystems.

ABSTRACT Dorotsuke, a traditional winter off-season farming practice in the Omiya Upland along the Arakawa River, involved transporting alluvial soil on horseback to the upland, maturing it, and then applying it to Andosol fields. Practiced for an estimated 400–600 years until the early twentieth century, this technique formed a thick anthropogenic horizon. Based on our previous research, we consider this soil to be the first documented example of a plaggen epipedon formed on Andosols. Our study investigated the spatial variation of these Dorotsuke anthropogenic soils, identifying their common feature and classification. We surveyed 81 fields with boring sticks in putative distribution areas, identifying a 56 ± 12-cm thick anthropogenic horizon in 54 fields, with topsoil oxalate-extractable silicon content from 0.5 to 11.7 g kg−1. Thick anthropogenic horizons were concentrated in the north-central area, while thinner horizons and/or larger mixtures of Andosols were concentrated in the south. Four pedons were analyzed to further characterize the anthropogenic soils and to test how the World Reference Base for Soil Resources (WRB) system classifies them. The two anthropogenic horizons exceeded 50 cm in thickness with different soil textures, while one of the other two showed significant mixing with Andosol. The profiles exhibited a vertical attenuation of andic characteristics, including increased bulk density, decreased short-range-order mineral content, and reduced phosphate retention, from the buried Andosol up to the topsoil. The applied alluvial soil was neutral in pH and rich in exchangeable Ca2+, but large amounts of Ca2+ leached from the topsoil, causing acidification owing to decreased base saturation. Under the WRB (2022) system, the anthropogenic horizons with ≥50% base saturation met the terric horizon criteria, and those thicker than 50 cm were classified as Andic Terric Anthrosols. The others were classified as Umbrisols over Andosols. While these results are currently appropriate, the potential for Ca2+ leaching to reduce base saturation below 50% could lead to thick anthropogenic horizons no longer meeting the requirements for terric horizon and thus Anthrosols. Therefore, given their similarity to European plaggen soils in terms of anthropedogenesis, we propose that the diagnostic criteria for terric horizon be modified to ensure their proper classification.

Abstract Issues related to reactive nitrogen (Nr) continue to increase and have exceeded planetary boundaries. Both production- and consumer-level efforts can mitigate Nr loads and inputs. However, only independent evaluations of these efforts have been performed thus far, and the lack of comprehensive evaluations has hindered further reductions in Nr loads and inputs. Therefore, in this study, we applied the food nitrogen footprint to a subtropical island in Japan and evaluated both direct (on-island) and indirect (overseas-related, imported food/feed production) Nr loads and inputs within the food system. The following scenarios were developed: shifting diets toward grains and legumes in imported food, halving food loss and using the remainder as concentrate feed, and replacing chemical fertilizers with cattle manure produced on the island. Altering the composition of imported food, reducing food loss by half, and utilizing the remaining portion as feed effectively reduced the indirect Nr load, while using cattle manure reduced the direct Nr load. Implementing these measures in combination reduced the direct and indirect Nr loads by 15.4% and 30.9% and the direct and indirect Nr inputs by 19.8% and 18.8%, respectively. Therefore, it is essential to implement consumer and production efforts simultaneously rather than independently to optimize the global nitrogen cycle.

水田の畑地化における地力維持および作物の安定的生産のため，堆肥の有無，および休閑の有無を組み合わせた3年間のダイズ・コムギ輪作体系試験を実施した．堆肥処理により，土壌中の熱水抽出性窒素，可給態リン酸，交換性カリウムが増加した．しかし，堆肥の有無によって，ダイズやコムギの乾物生産や収量が大きく異なることは無かった．ダイズ作においては，コムギ作後は休閑後と比較して，2年目，3年目ともに，播種時の土壌中の硝酸態窒素が低く，根粒重は増加する傾向が認められた．しかし，前作の有無によりダイズの乾物生産や収量が異なることはほとんど無かった．コムギ作においては，ダイズ作後と休閑後の間には，初年目，3年目ともに乾物生産や収量に差異はほとんど認められなかった．ただし，コムギ作の3年目においては，ダイズ作後は休閑後と比較して，土壌中の硝酸態窒素が低く，登熟期間の葉色値が低く，子実蛋白が低かった．土壌中の全窒素は，窒素施肥，窒素固定，子実蛋白からの推定によると，堆肥有区で増加し，堆肥無区で減少したが，実際の土壌の分析値によると，堆肥有区で増加したが，堆肥無区で大きく変化しなかった．結論として，堆肥は土壌の化学的特性に変化をもたらしたが，前作や堆肥は作物の収量にほとんど影響しなかった．

Direct seeding of rice is increasingly used to grow the most suitable cultivars under the best cropping schedule in the face of changing climatic and weather conditions. Although crop modeling can be used to optimize these factors, models developed for transplanted rice are not directly applicable, owing to differences in crop development due to weather conditions. Here, we present a method for estimating a parameter set for a crop development model applicable to direct-seeded rice from a set developed for transplanted rice. We hypothesized that model parameters C and D, which are related to the initial development index, can describe the difference in crop development between direct seeding and transplanting. The method estimates the values of C and D for each practice independently using shared parameters A, Th, and G, which are related to the temperature response of development and the days required for panicle initiation and heading in transplanted rice. We used data from field trials conducted in Iwate Prefecture between 2015 and 2019 with ‘Ginga no Shizuku’ to establish and verify the method. The estimated parameter set was accurate within a root mean square error (RMSE) range of 1.08 to 3.85 days at the heading stage and 2.96 to 3.11 days at the panicle initiation stage. When we tested the validity of the method by growing ‘Ten no Tsubu’ in both practices, the estimated parameter accuracy was 2.06 to 3.37 days RMSE at heading. We conclude that our method supplies a suitable parameter set for crop development models of direct-sown rice with an acceptable degree of accuracy. It will contribute to the estimation of optimal combinations of cultivars and cropping schedules for direct-sown rice under climate change, using historical field trial data and estimated parameter sets for transplanted rice.

<strong class="journal-contentHeaderColor">Abstract.</strong> Accurate assessment of leaf functional traits is crucial for a diverse range of applications from crop phenotyping to parameterizing global climate models. Leaf reflectance spectroscopy offers a promising avenue to advance ecological and of robust hyperspectral models for predicting leaf photosynthetic capacity and associated traits from reflectance data has been hindered by limited data availability across species and environments. Here we introduce the Global Spectra-Trait Initiative (GSTI), a collaborative repository of paired leaf hyperspectral and gas exchange measurements from diverse ecosystems. The GSTI repository currently encompasses over 7500 observations from 397 species and 41 sites gathered from 36 published and unpublished studies, thereby offering a key resource for developing and validating hyperspectral models of leaf photosynthetic agricultural research by complementing traditional, time-consuming gas exchange measurements. However, the development capacity. The GSTI database is developed on GitHub (<a href="https://github.com/plantphys/gsti" target="_blank" rel="noopener">https://github.com/plantphys/gsti</a>) and published to ESS-dive <a href="https://data.ess-dive.lbl.gov/datasets/doi:10.15485/2530733" target="_blank" rel="noopener">https://data.ess-dive.lbl.gov/datasets/doi:10.15485/2530733</a>, Lamour et al., 2025). It includes gas exchange data, derived photosynthetic parameters, and key leaf traits often associated with traditional gas exchange measurements such as leaf mass per area and leaf elemental composition. By providing a standardized repository for data sharing and analysis, we present a critical step towards creating hyperspectral models for predicting photosynthetic traits and associated leaf traits for terrestrial plants.