To prevent extinction of species in currently threatened stream ecosystems, it is important not only to increase the number of high-quality habitats, but also to ensure the connectivity of these habitats. Gene flow (exchange of genes between populations) is the "functional connectivity" of habitats and can be assessed using population/landscape genetics approaches. In this paper, I have (i) checked the function of gene flow on species and regional populations, (ii) reviewed methods for estimating gene flow that have been developed in the field of landscape genetics, and (iii) discussed the applicability of these approaches for riverine organisms. Gene flow has been shown to enhance population resilience in a changing environment and to have a positive effect on the viability of species and regional populations. Regarding the approaches to estimating gene flow, many methods have been proposed, most of which are based on the idea that interpopulation genetic differentiation decreases with an increasing number of migrants, while there were also multiple methods inferring recent and/or bidirectional gene flow using individual information. Each proposed method for estimating genetic differentiation and gene flow has assumptions; it should be important to use the appropriate method according to the characteristics of the data and the purpose of research. Stream ecosystems are unique systems with up-down-stream asymmetry and hierarchical and dendritic structures, sometimes making it difficult to apply the same methods developed in landscape genetics for riverine organisms. This led to the establishment of an exceptional field called "riverscape genetics", where some analysis methods specialized for riverine organisms are being developed. As an example of riverscape genetics, I introduced the case of fluvial sculpin in the upper reaches of the Sorachi River, confirming that the estimation of gene flow can provide useful knowledge for conservation.

Hypolimnion hypoxia in reservoirs is a significant water quality issue. Thermocline formation, caused by natural solar heating and operating aeration systems, contributes to this phenomenon. However, the relationship between the position and strength of the thermocline and the progression of oxygen reduction in hypolimnion has not been fully elucidated, especially in the early stages of thermal stratification. As the position of the thermocline may be artificially controlled, strategic adjustment of the thermocline position may mitigate oxygen reduction in the hypolimnion and provide benefits such as shortening the operation time of water quality improvement devices. In this study, we investigated the relationship between the depth and strength of the thermocline and the DO decline rate of hypolimnion during the early stages of thermal stratification in Miharu Dam. Water temperature and DO data were collected using an automated water quality monitoring system. The position and strength of the thermocline were estimated from the vertical water temperature profile, while the DO decline rate below the thermocline was determined from continuous DO measurement. The results showed a significant positive correlation between the thermocline strength and the DO decline rate (correlation coefficient: about 0.8). A power function well describes this relationship, indicating that the stronger the thermocline, the faster the rate of DO decline. This finding is consistent with previous studies that showed that the vertical diffusion coefficient is inversely proportional to the square of the thermocline strength. The vertical diffusion coefficient can be used as a linear variable to simulate oxygen depletion in hypolimnion. Based on data from a single reservoir, this study provides valuable insights into the relationship between thermocline characteristics and DO decline during the early stages of thermal stratification. Future research will focus on extending this analysis to multiple reservoirs to generalize these findings.

Environmental DNA (eDNA) analysis, now an indispensable tool for monitoring macro-organisms, was first reported to be performed on microorganisms in 1987 and subsequently used to analyze ancient DNA. In 2008, Ficetola et al. successfully detected bullfrog DNA in water, revolutionized the monitoring of macro-organisms. Japanese researchers independently started eDNA studies and have achieved many important results. Of note are the work on eDNA quantification by Takahara et al. and the development of the fish eDNA metabarcoding primer "MiFish" by Miya et al. Environmental DNA analysis is particularly effective for large-scale monitoring because it is easy to perform in the field and does not require expertise. In Japan, multiple large scale surveys have been conducted, and a large amount of data has been accumulated. Early eDNA sudies mainly targeted eDNA in water, but in recent years, efforts have been made to extract DNA from various media, including underwater sediments and surfaces of plants. Applications to the monitoring of infectious diseases and the spatiotemporal understanding of the reproductive behavior of organisms are also in progress. These applications are expected to be useful in the prevention and control of infectious diseases and in the conservation of rare organisms. However, there are several challenges in eDNA analysis. The biggest challenge is the richness and accuracy of the reference DNA sequence database, and the uncertainty of the spatiotemporal range exhibited by eDNA is also a major issue. Environmental DNA analysis is still a young technology that requires further development. We must also remember that eDNA analysis is not a substitute for physical sampling and that the fundamentals of biological monitoring should not be neglected. Conveying the richness of ecosystems to the next generation is also crucial for nature conservation.

This study reports that the Japanese aucha perch, Coreoperca kawamebari, a domestic alien species, has been found in the Nogawa River in Tokyo. Seven individuals were recorded near the shore in areas with little to no current and abundant aquatic vegetation. Environmental DNA analysis also clearly detected C. kawamebari, suggesting that environmental DNA may be an effective tool for detecting the invasion of nonnative species. In this study, the information provided by local citizens and citizen-researcher collaborations enabled us to promptly identify the invasion of the species.

This paper addresses future challenges related to the quantitative assessment of intertidal habitats, particularly tidal flats and salt marshes, with the aim of conserving estuarine and coastal biodiversity in Japan. Approximately 40% of tidal flats in Japan have been lost since 1945, and the decline has been mainly observed in the foreshore. Quantification of the tidal flats in riverine areas has not performed in depth and is necessary. Intertidal habitats covered with gravelly sediments formed in riverine areas have unique estuarine ecosystems based on the topographic and basin characteristics of Japanese small islands. However, these habitats may be overlooked in the quantification via the habitat assessment system developed recently. Although salt marshes, including reed beds, have been severely degraded and lost due to anthropogenic impacts, this decline throughout Japan has not been assessed. Therefore, we must first address the lack of fundamental data on salt marshes for their effective conservation and restoration planning. Small patches of salt marshes located in small basins should be quantitatively assessed because no significant positive correlation was observed between the area of salt marshes and species richness; i.e., these patches are expected to contribute to biodiversity conservation. Furthermore, adequate biodiversity assessment is difficult using a single evaluation item, such as “tidal flats” or “reed marshes”, because the biota in intertidal habitats is diversified according to biotic and abiotic factors. Developing field-applicable survey methods with simple, rapid, and inexpensive techniques is needed to quantify intertidal habitats or evaluate the current status of a threatened species in more detail. The study of new survey gears and analytical techniques will support this development.

Green Infrastructure (GI) is an idea that systematically integrates ecosystems into societal infrastructure, which could provide several ecosystem services. Recently, government support for promoting GI has been expanding, leading to increased efforts to advance GI initiatives across various regions. However, the broad and abstract nature of the GI concept poses challenges for its concrete implementation, and there is still a lack of information to guide governments in considering specific GI initiatives. When assessing the feasibility of GI implementation, it is necessary to consider both the existing ecosystems and the legal and societal constraints. This study focuses on land use planning as a factor related to the feasibility of GI implementation, particularly concerning existing ecosystems and societal constraints to propose GI types that are easy for local governments to introduce. Using the Basic Land Use Plans based on the National Land Use Planning Act, we classified 1,917 municipalities across Japan through non-hierarchical cluster analysis of land use categories by area. The results showed that municipalities could be divided into three classes when using four categories (forest, urban development areas, urban green spaces, and agricultural land) and into five classes when using three categories (excluding forests). These classes were broadly characterized as areas with active urban development, areas with substantial urban green spaces and agricultural land, and areas predominantly covered by forests and agricultural land. This classification was basically match with the areas of locational condition proposed by the guideline for Green Infrastructure, MILT. Additionally, mapping the classification results revealed a geographical clustering tendency, suggesting that cooperation among municipalities within the same class could significantly enhance GI promotion. Increasing mechanisms to support such collaboration among municipalities is expected to further contribute to the advancement of GI initiatives.