Rivers In Japan Research Articles

July 2020 heavy rainfall in Japan: effect of real-time river discharge on ocean circulation based on a coupled river-ocean model

In July 2020, a stationary atmospheric front over Japan caused persistent, nearly continuous rain for most of the month that resulted in new historical highest rainfall records in several areas and caused serious river floods, landslides, and debris-flow events. An existing hindcast and forecast ocean circulation model that includes climatological discharge information of major rivers failed to represent the extreme river discharge under heavy rainfall. New experiments were conducted using real-time river discharge information based on Today's Earth CaMa-Flood simulation that includes 368 rivers in Japan. The inclusion of real-time river discharge improved the salinity bias in the near-surface waters. The differences were significant compared to the observations in the heavy rain region (i.e., Ariake Bay and Tosa Bay), and insignificant at offshore stations. The ensemble experiments of real-time river discharge cases suggested the difference between the climatological and the real-time river discharge experiments was not random, but was robust. The freshening water changed the shelf circulation, and its far-reaching effect appeared hundreds of kilometers away from the shore. Passive particle tracking was conducted for examining the cross-shelf exchange. More particles released from Bungo Channel went offshore in near-surface water when the real-time river discharge was used compared to using the climatology discharge. Particles released in Tosa Bay, Seto Inland Sea, and Kii Channel showed the opposite tendency. The real-time river discharge not only changed the modeled coastal salinity distribution, but also the coastal and offshore currents. The role of the real-time river discharge on modeling normal flow periods or drought events, and its influence on a longer time scale model simulation remain to be explored.

Modelling fish co-occurrence patterns in a small spring-fed river using a machine learning approach

Stopping biodiversity loss due to human activities is of great concern for ensuring ecosystem services for sustainable development. While species-habitat relationships are an important aspect of species conservation, considering species interactions remains challenging in habitat suitability modelling due to the complex nature of the species’ ecology and uncertainties present in ecological data. To cope with this challenge, a Random Forests (RF) multi-class classifier is built using a data set comprised of monthly fish habitat surveys conducted over a period of two years for analyzing the 16 co-occurrence patterns among four fish species, including endangered species and translocated domestic alien species, in a small spring-fed river in Japan. This multi-class habitat suitability model allows for assessing the instream habitat conditions under which multiple species co-occur. Variable importance and partial dependence plots are generated to extract ecological information for a deeper understanding of the species co-occurrence patterns. Results show that the model performance is greatly influenced by data prevalence as reported for single-species habitat suitability models. Ecological information extracted from the RF model illustrates instream habitat conditions that are important for each of the co-occurrence patterns. Such information can be used for prioritizing conservation sites and better designing habitat conditions in order for multiple native species to co-occur or for preventing non-native species to expand their distribution ranges.

Application of Running Water-Type Retarding Basin to Old Kinu River Floodplain, Japan

In the upper and middle reaches of rivers in Japan, river channels used to meander in a comparatively narrow floodplain and heavy rain runoff used to naturally expand over the entire floodplain, retarding floods toward the downstream. Recent continuous levee building to prevent river overflow has had two kinds of negative effects, namely an increase in flood damage in areas of a floodplain closed by levees and river terraces at the time of runoff over the river channel capacity, and an increase in the flood peak toward the downstream. This study introduces the concept of a running water-type retarding basin that mitigates flood damage by allowing excess runoff to pass through the floodplain, restoring a natural hydrological process. After a description of the concept of the facility design, a design example is presented for a closed floodplain of the Kinu River Floodplain, where excess runoff caused severe flood damage in 2015, to quantify the performance and effects of the running water-type retarding basin.

Roseomonas fluvialis sp. nov., an aerobic bacteriochlorophyll a-containing freshwater bacterium isolated from river epilithic biofilm.

A strictly aerobic bacteriochlorophyll a-containing alphaproteobacterium, designated strain S08T, was isolated from a biofilm sampled at Tama River in Japan. The non-motile and rod-shaped cells formed pink-beige pigmented colonies on agar plates containing organic compounds and showed in vivo absorption maxima at 798 and 866 nm in the near-infrared region, typical for the presence of bacteriochlorophyll a. The new bacterial isolate is Gram-negative, oxidase-negative and catalase-positive. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S08T was closely related to species in the genus Roseomonas. The closest phylogenetic relative of strain S08T was Roseomonas lacus TH-G33T (98.2 % sequence similarity). The major cellular fatty acids were C16 : 0, C18 : 1 2-OH and summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c). The predominant respiratory quinone was ubiquinone-9. The major polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an aminolipid. The G+C content of the genomic DNA was 70.6 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain S08T and the related Roseomonas type strains were all far lower than the cut-off value for the delineation of species. The results of polyphasic comparisons showed that strain S08T was clearly distinguishable from other members of the genus Roseomonas. Therefore, we propose a new species in the genus Roseomonas, namely, Roseomonas fluvialis sp. nov. The type strain is S08T (=DSM 111902T=NBRC 112025T).

Complete Genome Sequences of Three Limnohabitans sp. (Lhab-A3) Strains, INBF002, TEGF004, and MORI2, Isolated from Two Lakes and a River in Japan.

Freshwater bacterioplankton of the genus Limnohabitans represent a dominant group that has worldwide distribution. Here, we report the complete genome sequences of three Limnohabitans sp. (Lhab-A3 tribe) strains, i.e., INBF002, TEGF004, and MORI2, which were isolated from surface water samples from two shallow eutrophic lakes and a river in Japan.

Complete Genome Sequences of Three Polynucleobacter sp. Subcluster PnecC Strains, KF022, KF023, and KF032, Isolated from a Shallow Eutrophic Lake and a River in Japan.

The genus Polynucleobacter subcluster PnecC consists of bacteria representing the ubiquitous taxon of freshwater bacterioplankton. Here, we report the complete genome sequences of three Polynucleobacter sp. (PnecC) strains, namely, KF022, KF023, and KF032, which were isolated from surface water of a temperate shallow eutrophic lake and its inflow river in Japan.

Experimental uncertainty assessment of meso- and microplastic concentrations in rivers based on net sampling

Meso- and microplastics have been collected via net sampling in marine and freshwater environments, but the effect of net clogging on evaluations of their concentrations (mPC) remains uncertain. We experimentally investigated the mPC uncertainties resulting from net clogging in the Ohori and Tone-unga Rivers, typical urban rivers in Japan, throughout 16 samplings with five filtration durations in one day. The weighted mean concentration in the Ohori River was significantly lower than that in the Tone-unga River, allowing us to examine the effect of clogging in rivers with different contamination levels. The variances in both rivers consistently tended to increase with increasing filtration duration, which can be expressed by applying the integral form of the Weibull reliability function (WRF).Furthermore, application of the WRF successfully revealed the optimal filtration durations in the Ohori and Tone-unga Rivers, which depended on the plastic abundance and sample volume. Since it could be difficult to obtain the plastic contamination level in advance, our suggestion is to predict the time sustained above 85 % filtration efficiency by applying a WRF-based model. In actuality, the sustained time in the Ohori (Tone-unga) River varied between 2.6 and 6.2 min (3.2 and 7.1 min) throughout the experiment, which permitted low mPC uncertainties of 12 % and 9.5 %, respectively. If notable uncertainty exists due to a low contamination level, a net with a high open area ratio should be used to increase the filtration duration. Hence, our results emphasize the importance of considering the open area ratio of nets used for sampling in studies. Our study provides insights into the occurrence of uncertainty due to net clogging to establish a standardized methodology for meso- and microplastic monitoring in aquatic environments via net sampling and consequently contributes to improving the sampling accuracy.

Bacterial cold-water disease in ayu (Plecoglossus altivelis altivelis) inhabiting rivers in Japan.

Bacterial cold-water disease in ayu (Plecoglossus altivelis altivelis) inhabiting rivers in Japan.

Quantitative environmental DNA metabarcoding shows high potential as a novel approach to quantitatively assess fish community

The simultaneous conservation of species richness and evenness is important to effectively reduce biodiversity loss and keep ecosystem health. Environmental DNA (eDNA) metabarcoding has been used as a powerful tool for identifying community composition, but it does not necessarily provide quantitative information due to several methodological limitations. Thus, the quantification of eDNA through metabarcoding is an important frontier of eDNA-based biomonitoring. Particularly, the qMiSeq approach has recently been developed as a quantitative metabarcoding method and has attracted much attention due to its usefulness. The aim here was to evaluate the performance of the qMiSeq approach as a quantitative monitoring tool for fish communities by comparing the quantified eDNA concentrations with the results of fish capture surveys. The eDNA water sampling and the capture surveys using the electrical shocker were conducted at a total of 21 sites in four rivers in Japan. As a result, we found significant positive relationships between the eDNA concentrations of each species quantified by qMiSeq and both the abundance and biomass of each captured taxon at each site. Furthermore, for seven out of eleven taxa, a significant positive relationship was observed between quantified DNA concentrations by sample and the abundance and/or biomass. In total, our results demonstrated that eDNA metabarcoding with the qMiSeq approach is a suitable and useful tool for quantitative monitoring of fish communities. Due to the simplicity of the eDNA analysis, the eDNA metabarcoding with qMiSeq approach would promote further growth of quantitative monitoring of biodiversity.

COPMAN: A novel high-throughput and highly sensitive method to detect viral nucleic acids including SARS-CoV-2 RNA in wastewater

During the coronavirus disease 2019 (COVID-19) pandemic, wastewater-based epidemiology (WBE) attracted attention as an objective and comprehensive indicator of community infection that does not require individual inspection. Although several severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection methods from wastewater have been developed, there are obstacles to their social implementation. In this study, we developed the COPMAN (Coagulation and Proteolysis method using Magnetic beads for detection of Nucleic acids in wastewater), an automatable method that can concentrate and detect multiple types of viruses from a limited volume (∼10 mL) of wastewater. The COPMAN consists of a high basicity polyaluminum chloride (PAC) coagulation process, magnetic bead-based RNA purification, and RT-preamplification, followed by qPCR. A series of enzymes exhibiting a high tolerance to PCR inhibitors derived from wastewater was identified and employed in the molecular detection steps in the COPMAN. We compared the detectability of viral RNA from 10-mL samples of virus-spiked (heat-inactivated SARS-CoV-2 and intact RSV) or unspiked wastewater by the COPMAN and other methods (PEG-qPCR, UF-qPCR, and EPISENS-S). The COPMAN was the most efficient for detecting spiked viruses from wastewater, detecting the highest level of pepper mild mottle virus (PMMoV), a typical intrinsic virus in human stool, from wastewater samples. The COPMAN also successfully detected indigenous SARS-CoV-2 RNA from 12 samples of wastewater at concentrations of 2.2 × 104 to 5.4 × 105 copies/L, during initial stages of an infection wave in the right and the left bank of the Sagami River in Japan (0.65 to 11.45 daily reported cases per 100,000 people). These results indicate that the COPMAN is suitable for detection of multiple pathogens from small volume of wastewater in automated stations.

Genome Sequence of the Edible Green Alga Ulva prolifera, Originating from the Yoshinogawa River in Japan.

ABSTRACTWe report the genome sequence of Ulva prolifera, which originated from the Yoshinogawa River in Japan, using Oxford Nanopore Technologies MinION and Illumina sequencing reads. The genome assembly size is 103.8 Mbp, consisting of 142 scaffolds with an N50 value of 4.11 Mbp.

Variance and precision of microplastic sampling in urban rivers

Microplastics (MPs), plastic particles <5 mm in diameter, have become an emerging ubiquitous concern for the environment. Rivers are the primary pathways that transport MPs from the land to the ocean; however, standardized methodologies for in-situ sampling in freshwater environments remain undefined. Notably, uncertainties in MP sampling methods lead to errors in estimating MP discharge through rivers. In the present study, the inter-sample variance of plankton net-obtained MP concentrations for two urban rivers in Japan was investigated. Numerical concentrations, expressed in particles·m−3, revealed that variance s2 was proportional to the mean m of replicated estimates of numerical concentrations. A derived statistical model suggested that river MPs disperse according to purely random processes; that is, Poisson point processes. Accordingly, a method was established to project the “precision,” the ratio of the standard error to m, of numerical concentrations based on the number of net sampling repetitions. It was found that the mean of two replicates maintained sufficient precision of <30% for conditions with high concentrations of ≥3 particles·m−3. Projected precisions under different levels of MP concentrations are also presented to help design future field campaigns.

Nutrient limitation of primary production in rivers along a land use gradient in the Lake Biwa Basin, Shiga Prefecture, Japan

Benthic microalgae (BMA) biomass and community structure in freshwater lotic systems are often limited by inorganic nutrient availability. We examined nutrient limitation of benthic algae biomass and community structure using nutrient diffusing substrates in four rivers along a land use gradient in the Lake Biwa basin, Japan. Ambient in-stream nutrient concentrations were correlated to catchment land use, with the highest nitrogen and phosphorus concentrations being found in rivers draining more forested catchments. Nutrient limitation of primary producer biomass and nutrient-driven changes in community structure were evident in all four rivers, regardless of in-stream nutrient concentrations and surrounding land use. BMA biomass (measured as chlorophyll log-response ratio) exhibited the greatest nutrient limitation in rivers with higher in-stream nutrient concentrations. The relationship to catchment land use was less clear, with the highest nutrient limitation being observed in the catchment with moderate amounts of agricultural and forested land use. Nutrient additions resulted in a shift from dominance by Bacillariophyceae (diatoms) to a mixed Bacillariophyceae-Chlorophyceae (chlorophyte) community in all rivers and this shift was most pronounced in the forested catchments. Changes within the diatom community with nutrient additions were also observed, although the shifts in diatom community within a river in response to nutrient additions were much smaller than the differences in diatom community composition among rivers. Diatom taxa classified as highly motile increased with nutrient additions in all rivers. Our results suggest that primary producer community in rivers may be sensitive to nutrient inputs even in areas with elevated nutrient concentrations and catchments dominated by agricultural land use. There is likely widespread nutrient limitation in rivers of Japan, across both in-stream nutrient and land use gradients and any increases in nutrient loading will likely stimulate benthic algal growth. Our findings highlight the importance of looking at both biomass and species composition to assess ecosystem-level impacts of elevated nutrient levels.

Towards control of dam and reservoir systems with forward–backward stochastic differential equations driven by clustered jumps

AbstractWe deal with a new maximum principle‐based stochastic control model for river management through operating a dam and reservoir system. The model is based on coupled forward–backward stochastic differential equations (FBSDEs) derived from jump‐driven streamflow dynamics and reservoir water balance. A continuous‐time branching process with immigration driven by a tempered stable subordinator efficiently describes clustered inflow streamflow dynamics. This is a completely new attempt in hydrology and control engineering. Applying a stochastic maximum principle to the dynamics based on an objective functional for designing cost‐efficient control of dam and reservoir systems leads to the FBSDEs as a system of optimality equations. The FBSDEs under a linear‐quadratic ansatz lead to a tractable model, while they are solved numerically in the other cases using a least‐squares Monte‐Carlo method. Optimal controls are found in the former, while only sub‐optimal ones are computable in the latter due to a hard state constraint. Model parameters are successfully identified from a real data of a river in Japan having a dam and reservoir system. We also show that the linear‐quadratic case can capture the real operation data of the system with underestimation of the outflow discharge. More complex cases with a realistic time horizon are analyzed numerically to investigate impacts of considering the environmental flows and seasonal operational purposes. Key challenges towards more sophisticated modeling and analysis with jump‐driven FBSDEs are discussed as well.

A NEW SPECIES OF THE AMPHIPOD &lt;i&gt;MELITA&lt;/i&gt; LEACH, 1814 (CRUSTACEA: AMPHIPODA: MELITIDAE) FOR THE AZOV-BLACK SEA BASIN

Amphipods of the genus (Melitidae, Amphipoda) were found in the Kerch Strait (Black Sea) in September 2019 and March, July, November 2020. The material was collected in the formations formed by the polychaete (Fauvel, 1923). The depth ranged from 0.1 to 0.2 m. The individuals found in this site do not belong to the species (Montagu, 1804) known in the Black Sea, but they correspond to the morphological characters of the genus Melita . The species discovered is as close as possible to the species Melita setiflagella Yamato, 1988, whose natural range is located in the estuaries of rivers in Japan. Invasive range covers coastal waters of the Atlantic coast of Europe, the Pacific and Atlantic coasts of the United States and the Atlantic coast of Argentina. Presumably, this invader was accidentally introduced into the Black Sea with ballast waters or by transfer with fouling of ship surfaces. M. cf . setiflagella formed a stable self-reproducing population in the Kerch Strait. Therefore, it is important to monitor the distribution of this amphipod in order to predict the consequences for endemic species and local ecosystems.

High-Throughput Screening of Antimicrobial Resistance Genes and Their Association With Class 1 Integrons in Urban Rivers in Japan

Antimicrobial resistance (AMR) is a serious public health concern. Many countries have implemented AMR surveillance programs for humans and animals, but a scheme for monitoring AMR in the environment has not yet been established. Class 1 integrons, which can acquire antimicrobial resistance genes (ARGs) to gene cassettes, were proposed as a candidate to evaluate the anthropogenic impacts on AMR. However, the association between class 1 integrons and ARGs in aquatic environments is less studied and requires further elucidation. This study used high-throughput quantitative polymerase chain reaction (HT-qPCR) to characterize the pollution profiles of ARGs and mobile gene elements (MGEs) in 24 urban rivers in Tokyo and its surrounding area. The abundance of class 1 integron-integrase gene (intI1) and the array of class 1 integron gene cassettes were also determined. In total, 9–53 target genes were detected per sample, and their abundances increased following effluent discharge from wastewater treatment plants. The river and wastewater samples were categorized based on their HT-qPCR profiles, indicating that this method was useful for characterizing the pollution status in aquatic environments. The prevalence ofintI1in the rivers was observed. Some ARGs and MGEs were positively correlated withintI1, indicating thatintI1could be used as a proxy for monitoring these ARGs and MGEs in urban rivers. Long-read sequencing of class 1 integron gene cassettes revealed that one to three ARGs were present in the gene cassettes. Regardless of the sample type,blaGES-24,aadA2, andqacHwere dominant in the gene cassettes. The source and spread of class 1 integrons carrying these ARGs in aquatic environments should be further monitored.

Burrow utilization by the Japanese mitten crab &lt;i&gt;Eriocheir japonica&lt;/i&gt; in the clay sediment of a freshwater river of Kyushu, Japan

This is the first record of the burrows of the Japanese mitten crab Eriocheir japonica. Morphologies of the burrows found in the clay sediment used by this crab were recorded by excavating them in a small freshwater river in Japan. Only E. japonica was found inside 2 of the 10 burrows examined (15 crabs and one crab, respectively), and the other 8 were empty. Crabs of various sizes (6.1–47.0 mm in carapace width) were collected from inside the occupied burrows. Burrow morphology ranged from single tunnels to complex burrows with multiple openings and tunnels. Openings (2–10 cm in diameter) were mostly located underwater. The single tunnels were 14–65 cm long. Considering the different digging habits of other burrowing animals found in this area, it can be concluded that E. japonica constructed these burrows. Burrows resembled those of the Chinese mitten crab E. sinensis, but were different in their location (freshwater vs. tidal), sediment type (clay vs. sand and silt), opening placement (mainly underwater vs. intertidal) and occupation rate (low vs. high). The low occupation rate suggests that E. japonica do not always rest in their burrows and rather prefer to hide beneath the riverbed’s large rocks. These results reflect the adaptation of E. japonica to the unstable environment of Japanese rivers.

Ups and downs of non‐native and native stream‐dwelling salmonids: Lessons from two contrasting rivers

AbstractFreshwater rivers and lakes are particularly vulnerable to anthropogenic disturbance because of their proximity to human occupation. Anthropogenic impacts in fresh water include those caused by dams, water pollution, channelization, and invasive species. One common action to conserve freshwater biodiversity involves supplementing or reintroducing extirpated species, though the benefits of these efforts are controversial. Installation of fishways to dams and removal of invasive alien species has also resulted in recovery of native species. Herein results of long‐term monitoring of salmonids in two rivers in Japan are presented. The first case involves a river above a dam where native white‐spotted charr Salvelinus leucomaenis and masu salmon Oncorhynchus masou declined rapidly in number following dam construction, where non‐native rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta increased in number, and where stocking of native masu salmon was unsuccessful. The second case involves a river formerly dominated by non‐native rainbow trout, in which native Dolly Varden charr Salvelinus curilus and masu salmon increased in numbers following removal of non‐native species and fishway installation. Results reveal natural recovery of masu salmon in a river within which they were once completely extirpated, without stocking. Because salmonids are migratory fish and return to natal rivers, when locally extinct, human intervention to stock or reintroduce them has often been deemed necessary. However, restoration of wildlife would not require stocking or reintroduction if factors that impede the self‐recovery capability of species are removed.

Airborne LiDAR-assisted deep learning methodology for riparian land cover classification using aerial photographs and its application for flood modelling

Abstract In response to challenges in land cover classification (LCC), many researchers have experimented recently with classification methods based on artificial intelligence techniques. For LCC mapping of the vegetated Asahi River in Japan, the current study uses deep learning (DL)-based DeepLabV3+ module for image segmentation of aerial photographs. We modified the existing model by concatenating data on its resultant output port to access the airborne laser bathymetry (ALB) dataset, including voxel-based laser points and vegetation height (i.e. digital surface model data minus digital terrain model data). Findings revealed that the modified approach improved the accuracy of LCC greatly compared to our earlier unsupervised ALB-based method, with 25 and 35% improvement, respectively, in overall accuracy and the macro F1-score for November 2017 dataset (no–leaf condition). Finally, by estimating flow-resistance parameters in flood modelling using LCC mapping-derived data, we conclude that the upgraded DL methodology produces better fit between numerically analyzed and observed peak water levels.

Influence of salinity on the horizontal distribution of soldier crab Mictyris guinotae in a subtropical river in Japan

ABSTRACT The horizontal distribution of Mictyris guinotae was studied in relation to gradients of salinity and sediment characteristics in sandy flats between 0 and 8.2 km from the mouth of a subtropical river. Lower salinity tolerance was also tested at seven salinity levels (0, 2, 4, 8, 12, 24 and 32) by a survival experiment for 14 days. Environmental clines were found in salinity but not in sediment characteristics. The upper limit of the occurrence of crab was 5.07 km upstream where seawater could reach during the spring flood tide. The densities of age-0 crabs tended to be higher at lower stations (0–0.65 km upstream), suggesting more recruits settle near the river mouth. Carapace length was significantly larger in the upper section (2.50–5.07 km upstream) in which salinity fluctuated or remained low (<10) for longer periods. It is unlikely that low salinity has a negative effect on post-larval growth. In contrast, body size was smaller in the lower section, possibly due to the effect of density. Some individuals died at the end of the experiment at salinity ≤12. The upper limit of appearance was explained by the salinity of riverine water and low salinity tolerance of the crab.