Rivers In Japan Research Articles

First detection of VEB-1 extended-spectrum β-lactamase-producing Escherichia coli clinical isolate in Japan.

ESBLs are plasmid-mediated enzymes that confer resistance to clinically significant antimicrobial agents, such as broad-spectrum cephalosporins. Recently, the rapid spread of CTX-M-type ESBL-producing E. coli has become a global issue, including in Japan, where ESBL production in human pathogenic E. coli, such as the ExPEC and UPEC lineages, which typically harbor several virulence genes, is a severe public health concern. To date, VEB (Vietnamese extended-spectrum β-lactamase) producers have been found only in hospital wastewater and rivers in Japan. Thus, we describe the first detection of a very rare human-derived blaVEB-1 gene in the E. coli B2-ST95 pandemic clonal lineage that is highly associated with ExPEC and UPEC in a Japanese clinical setting. Furthermore, we characterized the genomic features of plasmids harboring the class 1 integron-borne blaVEB-1. Our findings highlight the significance of closely monitoring ESBL-producing E. coli isolates to prevent the potential dissemination of this resistance determinant in Japan.

Impact of the Japanese traditional river training structure “Seigyu (Crib spur dike)” on river morphology and its geometrical changes

The traditional Japanese river training structure, known as “Seigyu”, designed to divert flow, reduce flow velocity, and promote geomorphological changes, is expected to contribute to the management of river morphology. Seigyu is highly impervious at the bottom giving it a unique function. Twelve Seigyus were installed in the Kizu River in Japan to assess their ability to serve as a sediment management structure, which is necessary when considering sediment replenishment from upstream dams constructed upstream. Images and videos were recorded by a UAV to assess the flow and morphology around Seigyu via image-based analysis. Additionally, the shift in its function caused by the transformation of Seigyu itself, such as tilting and clogging, was investigated. The detected geomorphological changes indicated that Seigyu contributed to the formation of complex morphological patterns and the continuous shift in the sediment budget from erosional to depositional. Even after tilting approximately 25°, Seigyus’ effects were sustained. High-velocity flow, which occurred between two Seigyus in the early stages after implementation, did not appear or at least decreased in velocity after debris was trapped between the Seigyus. These results suggest that the effects of Seigyu persist even after its transformation, and future simulations and implementations should consider these changes.

Comparative performance of electronegative membrane filtration and automated concentrating pipette for detection of antibiotic resistance genes and microbial markers in river water samples

The target viral and bacterial concentrations in river water are essential for environmental monitoring and public health studies. Filtration-based methods are commonly employed, yet challenges arise due to recoverability and filter pore size. This study aimed to compare the performance of electronegative membrane filtration (EMF) and automated Concentrating Pipette (CP) Select (InnovaPrep) methods for quantifying antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and bacterial and viral markers in river water samples. Fifty-four river water samples were collected from upstream and downstream locations in a river in Japan. The CP Select method was modified by adding MgCl2 and using different tips. The recovery efficiencies for total coliforms and Escherichia coli were assessed, and class 1 integron-integrase gene (intI1), 16S rRNA, gene encoding sulfonamide resistance (sul1), cross-assembly phage (crAssphage), pepper mild mottle virus (PMMoV), and Escherichia coli gene (sfmD) were detected. CP Select showed recovery efficiencies of 45 %–63 % for total coliforms and 17 %–35 % for E. coli. The intI1, 16S rRNA, sul1, crAssphage, PMMoV, and sfmD concentrations using the modified CP Select method were 10.1 ± 0.5, 8.7 ± 0.2, 7.7 ± 0.2, 6.7 ± 0.2, 5.4 ± 0.2, and 3.5 ± 0.5 log10 copies/L, respectively. Higher intI1 and sul1 concentrations were observed downstream, with the highest contribution percentage (22 % and 21 %) using CP Select or EMF. The modified CP Select method with 0.05 μm tips yielded more quantifiable results for all target genes and greater PMMoV concentrations (p < 0.05). Positive correlations were found among bacterial, ARG/MGE, and viral markers (Spearman's ρ = 0.71 for 16S rRNA and sfmD, 0.88 for intI1 and sul1, and 0.64 for PMMoV and crAssphage). The modified CP Select method demonstrated effective recovery of bacteria and quantification of ARGs, MGEs, and microbial markers in river water. Further studies are required to validate these methods and confirm their applicability in diverse environmental contexts.

Genetic variability of Myxobolus nagaraensis (Bivalvulida: Myxobolidae) infecting freshwater gobies Rhinogobius Gill 1859 (Gobiiformes: Oxudercidae) from rivers in Japan

Myxobolus nagaraensis is a myxozoan parasite first reported in freshwater gobies (Rhinogobius spp.) from the Nagara River, Gifu Prefecture, Japan. Myxospores of M. nagaraensis form plasmodia in the visceral cavities of gobies, commonly presenting as distended abdomens. Although Rhinogobius is a common fish genus in Japan, details of M. nagaraensis, including genetic information, remain unknown. We compared the nucleotide sequences of the ribosomal RNA gene (rDNA) of M. nagaraensis from three different host species (R. fluviatilis, R. nagoyae, and R. similis) caught in three different rivers in Japan (Sakai, Sagami, and Kaname). The ITS region (ITS-1, 5.8S rDNA, and ITS-2) and large subunit (LSU) rDNA exhibited 49 and 55 variable sites, respectively. The highest nucleotide diversity was observed in the ITS region (0.00962), whereas that of the LSU rDNA was 0.00187. Differences in host species, rather than rivers, were a significant factor for genetic variation in both the ITS region (62.58%; P < 0.001) and LSU rDNA (55.22%; P < 0.01). Significant genetic variation was observed in M. nagaraensis from R. similis compared to R. fluviatilis (P < 0.001) or R. nagoyae (P < 0.001) from the same river. Such details are valuable for understanding parasite dispersal and its ecological impact on Rhinogobius hosts.

Mesoclimate scale effects of river intermittency on aquatic insects in Seto Inland Sea watersheds, Western Japan

AbstractThe responses of assemblages and ecosystems to river intermittency are often considered on large spatial scales, such as those associated with the Köppen climate classification. However, river intermittency may naturally occur even in humid regions, and the effects may differ from those where intermittency occurs throughout the area. This study aimed to examine the differences in taxonomic and trait composition of aquatic insects between intermittent rivers in the Seto Inland Sea watersheds and neighboring humid-temperate rivers in Japan using national census data. While the climate in the most part of the Japanese Archipelago is categorized as humid-temperate, and rivers are usually perennial, local climate in the Seto Inland Sea watersheds has low summer precipitation compared with that in neighboring regions, thereby resulting in river intermittency. Consistent with the previous studies in the regions where rivers are intermittent on a large spatial scale, we observed that aquatic insects with multivoltinism and/or aerial respiration notably tolerated river intermittency. In contrast, the aquatic insect fauna in Japanese intermittent rivers represented subsets of those in the humid-temperate rivers, although previous studies such in Mediterranean regions have reported high endemism and species diversity in intermittent rivers. These results highlight the importance of exploring the role of river intermittency on small to medium spatial scales, as well as on large scales, to project effects of ongoing and future climate changes on species diversity.

Testing the applicability of environmental DNA metabarcoding to landscape genetics.

Landscape genetics is a field dealing with local genetic differences and contributes to strategic conservation planning. Recently, environmental DNA (eDNA) metabarcoding has proven useful not only for detecting species but also for assessing genetic diversity and genetic structure on a large scale such as in phylogeography. However, it remains unclear whether eDNA analysis also has sufficient power to perform the landscape genetics, which focuses on a local scale. To reveal the applicability of eDNA to landscape genetics, we conducted an eDNA metabarcoding analysis of the mitochondrial DNA D-loop region of the fluvial sculpin Cottus nozawae in the upper Sorachi River in Japan and compared the results with inferences based on traditional tissue-based approaches by the same D-loop region and genome-wide SNP data. As a result, the spatial distribution of haplotypes was generally consistent between the eDNA- and tissue-based approaches. In addition, the genetic differentiation statistics calculated using eDNA and tissue samples were highly correlated when comparing both in the D-loop region. The removal of low-frequency reads or the conversion to semi-quantitative rankings of eDNA data did not alter the correlation of genetic diversity and differentiation statistics with tissue-based approaches much. Finally, we confirmed that analyses using eDNA data can reveal patterns such as isolation-by-distance shown in previous studies on this species, indicating the applicability of eDNA to basic landscape genetics. Even though some limitations remain, eDNA may have great potential for conducting basic landscape genetics.

Occurrence and ecological risk assessment of 16 plasticizers in the rivers and estuaries in Japan

Owing to growing concerns about the adverse effects of phthalate plasticizers, non-phthalate plasticizers are being increasingly used as their replacement. However, information on the residual environmental concentrations and ecological risks posed by these plasticizers is limited. In this study, we analyzed the environmental contamination of 11 phthalates and 5 non-phthalate plasticizers in Class A and B rivers in Japan. In the considered river water samples, phthalates and non-phthalates were detected in the following order of detection frequency: phthalates (DEHP > DMP > DMEP > BBP > DNPP > DNP > DEEP > DBEP = DNOP) and non-phthalates (ATBC > DEHS > DEHA > TOTM = DIBA). Phthalate plasticizers were the most abundant and included DEHP (157–859 ng/L), DMP (<MQL–3680 ng/L), DMEP (<MQL–4600 ng/L), and BBP (<MQL–1080 ng/L); non-phthalates included ATBC (<MQL–1550 ng/L) and DEHS (<MQL–220 ng/L). The risk quotient for DEHP and ATBC was found to be more than one, suggesting an emerging concern regarding their contamination and adverse effects on aquatic organisms. This study is the first to shed light on the persistence of non-phthalate plasticizers in freshwater environments in Japan; the findings could help develop strategies to mitigate the environmental effects of plasticizers.

Complete genome sequence of Tornadovirus japonicus, a relative of Pacmanvirus, isolated from the Tamagawa River in Japan.

Here, we report the isolation and genome sequencing of a new Pacmanvirus-related isolate, Tornadovirus japonicus, from the Tamagawa River in Japan. This icosahedral virus has a genome of approximately 380 kb and 465 open reading frames, including two tRNA genes. The name "tornado" is based on its morphological features revealed by transmission electron microscopy analysis.

Anthropogenic gadolinium in the Tone River (Japan): an update showing a 7.7-fold increase from 1996 to 2020

BackgroundAnthropogenic gadolinium (Gd), originating from Gd-based contrast agents (GBCAs) used in magnetic resonance imaging (MRI), is widely identified in the aquatic environment with concerns about toxicity and accumulation. We aimed to present new data on anthropogenic Gd in the Tone River, which has the largest drainage area in Japan, and then to compare the current data with those obtained in 1996.MethodsThe water samples were collected on August 9−10, 2020, at 15 different locations of the Tone River in Japan. The concentrations of the rare earth elements (REEs) were measured by inductively coupled plasma-mass spectrometry and normalized to Post-Archean Australian Shale to construct shale-normalized REE patterns. The degree of Gd-anomaly was defined as the percentage of anthropogenic Gd to the geogenic background and used to compare the water samples from different locations. Pearson’s correlation coefficients were calculated.ResultsAll the samples displayed positive Gd anomalies. The Gd-anomaly ranged from 121 to 6,545% and displayed a repeating decrease-and-increase trend. The Gd-anomaly showed strong positive correlations to the number of hospitals (r = 0.88; p < 0.001) and their MRI units (r = 0.89; p < 0.001).ConclusionsOur study revealed notable anomalies of Gd concentrations in river water in Japan, with strong positive correlations to the number of major hospitals and their MRI units. Compared with the previous report in 2000, the Gd-anomaly in Tone River increased from 851% (sampled in 1996) to 6,545%, i.e., 7.7 times, reflecting the increased use of GBCAs in hospitals.Relevance statementNotable Gd concentration anomalies in river water in Japan were observed. This result underlines the importance of more extensive research on anthropogenic gadolinium, and investigations of risks to human health as well as the development of effective removal technologies may be necessary.Key points• All water samples from Tone River displayed positive Gd anomalies.• The Gd anomalies increased to 7.7 times higher over the past 24 years.• Correlations between Gd values and the number of hospitals and MRI units were observed.Graphical

Temporal variables improve a spatiotemporal species distribution model for the non-native freshwater fish Candidia temminckii

Ecosystem conservation requires a deeper understanding of species-habitat relationships and population dynamics at a fine spatiotemporal resolution. We propose a new distribution modeling method based on a 5-year monthly survey that considers the temporal continuity of species distributions and physical habitat datasets by inputting continuous time-related variables. We employed random forests to relate the presence/absence of the non-native freshwater fish Candidia temminckii to physical habitat data at 15 sampling sites along a 1.4km spring-fed river in Japan. The proposed method outperforms all conventional methods using datasets split into a specific time period to incorporate temporality into the model. The order of variable importance and shape of the partial dependence plots of the proposed method reflect species ecology and show a gradual shift over time compared to the conventional methods. These results demonstrate the applicability of the proposed method to species distribution modeling using fine-scale spatiotemporal data.

Carrying capacity for tree biomass of a subtropical mangrove along a river in Japan inferred from forest structural features

AbstractA subtropical mangrove along the Miyara River in Ishigaki Island, Japan was studied for evaluating the carrying capacity for biomass of the mangrove stands. The stem diameters D, tree height H, and fine roots mass were measured, while aboveground biomass (AGB) and belowground coarse root biomass (BGBcoarse) were estimated. The AGB, BGBcoarse, and fine root mass were estimated as 130, 31, and 13 Mg ha−1 in the Rhizophora stylosa; 271, 94, and 11 Mg ha−1 in the downstream Bruguiera gymnorrhiza; and, 228, 81, and 6.4 Mg ha−1 in the upstream B. gymnorrhiza stand, respectively. The AGB and BGBcoarse in the R. stylosa stand were significantly lower than B. gymnorrhiza stands, and fine root mass was significantly higher than upstream B. gymnorrhiza stand. Significantly lower mean individual phytomass wt specific to tree density ρ of R. stylosa stand than B. gymnorrhiza stand in the ρ − wt relationship denoted the lower carrying capacity for AGB of R. stylosa than that of B. gymnorrhiza. The results showed that high soil pore water salinity and low pH at the downstream did not limit biomass and potential canopy height Hmax of mangrove along a river gradient but AGB and BGBcoarse differed between different species at the same edaphic environment. Analysis of aboveground and belowground biomass variations between stands of two mangrove species along environmental gradients from upstream to downstream could be useful in assessing the consequences of sea level rise in relation to climate change on the evolution of blue carbon dynamics.

Inter-event and intra-event dynamics of microplastic emissions in an urban river during rainfall episodes

Urban rivers represent the major conduits for land-sourced microplastics in the global oceans, yet the real-time dynamics of their emissions in rivers during rainfall (and runoff) events are poorly understood. Herein, we report the results of high-frequency sampling of microplastic particles (MPs) and fibers (MPFs) in the surface water of an urban river in Japan over the course of three rainfall events (i.e., light, moderate, and heavy rainfalls). The event mean concentrations (EMCs) of MPs amounted to 35,000 items/m3, 929,000 items/m3, and 331,000 items/m3; and the corresponding total loads were 0.5 kg, 19.8 kg, and 35.0 kg for light, moderate and heavy rainfalls, respectively. The inter-event total loads of MPs correlate well with the total rainfall, while the concentrations were linked with the number of antecedent dry days. The dynamic trends show that <2000 μm MPs displayed first flush effects during light to moderate rainfall events (>50% mass discharged with the initial 20–40% of flow). Small-sized MPs (10–40 μm) mobilized rapidly at lower rainfall intensities, whereas MPs over 2000 μm discharged immediately after the peak rainfall intensity. Moreover, <70 μm MPs depicted a surge following heavy rainfall events due to turbulent flow conditions reverting the deposited MPs into suspension. Overall, the three events increased the loads by 4–110 folds, and EMCs by 10–350 folds compared to the concentrations during dry weather while portraying a significant impact on 300–1000 μm MPs. The dynamics of MPs were correlated with those of suspended solids in river water, and the characteristics were comparable to the same of road dust sampled in Japan. Although the dynamic trends between MPs and MPFs in river water were comparable, MPFs were relatively less impacted by rain, likely due to the intervention of separate sewer systems in the study area.

Comparison Between the Plastic Waste Influx of Rural Rivers: Mlese River in Indonesia and Hamada River in Japan

Marine plastic pollution has become a global concern as plastic wastes continue to accumulate in the world’s oceans. Usually, such accumulation occurs due to garbage leakage from land, which eventually flow into the river pathways through surface runoff or wind. This study aims to draw a parallel between the garbage influx of two rural rivers in Indonesia and Japan. Data collections were carried out at one of the river points in Indonesia’s Mlese River and Japan’s Hamada River when the weather was not rainy. The river characteristics and influx of plastic litter into the river streams were analysed at a specific time of a day. In Mlese River, trashboom method and, in Hamada River, manual netting method were used to trap the plastics. The waste outflow was 370 g/hr from Mlese River and 0.25 g/hr from Hamada River. Despite the average discharge of the two rivers being quite similar (0.34 m3/s), the plastic outflow in Mlese River was about 1400 times compared to the plastic outflow of Hamada River, proving the waste leakage problem in Indonesia to be greater. Data must be collected in rainy days as well to better understand the complete situation of waste influx in these rivers.

Bank Accumulation of Macroplastic Samples in a Farmland River in Japan

Bank Accumulation of Macroplastic Samples in a Farmland River in Japan

The Disaster Protection System of Mountainous Rivers in Japan: The Example of the Akatani Watershed’s Reconstruction

On 5–6 July 2017, an unstable atmospheric condition caused an unusual concentration of rainfall above the Northern part of Kyushu Island, triggering a set of hydro-meteorological hazards. Within the affected area, the mountainous subwatershed of the Akatani River was significantly impacted by numerous landslides combined with debris flow and floods. National and local agencies deployed a plan of reconstruction to restore the floodplain and protect inhabitants. Regarding the hydrosystem in the Akatani watershed, this reconstruction project mainly focuses on the restoration of damaged protection systems and the construction of new infrastructures. Thus, this paper aims to explain the restoration plan of the Akatani River in terms of the strategic Japanese River System Sabo and then as a model of a national-scale spatial plan. It draws on (i) a literature review based on the historical evolution of Japanese protection systems and the River Sabo System; (ii) field surveys in 2019, 2022 and 2023, in conjunction with (iii) interviews with local, regional, and national officials; and (iv) a Geographical Information System analysis of previously and newly built protection systems through aerial photograph interpretation and geospatial data. Sabo works implemented in the Akatani watershed illustrate the engineering vision of Japanese river management. They also constitute a comprehensive system and include a downstream–upstream logic which echoes that of the River System Sabo. In addition, the disaster of July 2017 and the government’s response emphasize the continuous adaptation and improvement of the Japanese disaster management system, which mitigates severe disasters.

Habitat aging and degradation in terrestrialized floodplains: a need to rejuvenate processes for sustaining freshwater mussel populations

Progressive floodplain terrestrialization leads to the deterioration of floodplain ecosystems. Although the importance of hydrological connectivity between floodplain habitats and river channels for floodplain‐dependent organisms has been emphasized, less attention has been paid to the temporal relationship between habitat degradation and aquatic organisms. In this study, we examined temporal changes in mussel population structures and the hydrological connectivity of pond‐like floodplain water bodies (FWBs) in the terrestrialized floodplains of a lowland river in Japan. We tested the hypothesis that FWB habitats for mussels degrade over time, while newly formed FWBs contribute to providing recruitment sites for mussels. The habitat age for 53 FWBs was determined as of 2018, using historical aerial photographs. Inundation frequency, mussel abundance, and size structures (shell length) were also investigated in the FWBs in 2007 and 2018. Mussel abundance decreased with FWB aging (6–36 years), which coincided with a decrease in inundation frequency. In most existing FWBs, mussel abundance in all size classes decreased over the decade (2007–2018). In contrast, small individuals occurred in the newly formed FWBs at age 6, and in the existing FWBs where inundation frequency slightly increased over the decade (2007–2018), such FWBs were rare. In conclusion, the “young” and “rejuvenated” FWBs were found to be critically important for the recruitment and persistence of mussel populations. This suggests that the floodplain management strategy of “cyclic floodplain rejuvenation” could be applicable for mussel conservation in terrestrialized floodplains of lowland rivers.

THE CASE OF SEDIMENT OUTFLOW FROM MOUNTAIN TO THE COAST DUE TO SMALL AND MEDIUM-SIZE FLOODS

Smaller rivers in Japan can be characterized as having short distances from the mountainous areas of the source of sediment production to the estuary and steep slopes. Therefore, sediment produced from the mountains and river channels at the time of flooding immediately contributes significantly to the sediment dynamics at the estuary and coast in a short period of time. On the other hand, there have been few observations or studies that have measured the volume of landslides and riverbed fluctuations in the mountains in the entire basin before and after the occurrence of flooding, and quantitatively linked them to the amount of landslide movement and shoreline changes in the entire basin. This paper discusses the Chitose River basin (basin area A: 30km2, river channel distance L: 0.179km, stream gradient I: 1/14) and the Niizaki River basin (A: 16km2, L: 0.213km, I:1/17), which have an estuary on the Yugawara coast in Kanagawa Prefecture. The effect of sediment production from mountains and riverbeds at the time of flooding on coastal sediment dynamics on July 3rd, 2021.

Applicability of F-specific bacteriophage subgroups, PMMoV and crAssphage as indicators of source specific fecal contamination and viral inactivation in rivers in Japan.

To date, several microbes have been proposed as potential source-specific indicators of fecal pollution. 16S ribosomal RNA gene markers of the Bacteroidales species are the most widely applied due to their predominance in the water environment and source specificity. F-specific bacteriophage (FPH) subgroups, especially FRNA phage genogroups, are also known as potential source-specific viral indicators. Since they can be quantified by both culture-based and molecular assays, they may also be useful as indicators for estimating viral inactivation in the environment. Pepper mild mottle virus (PMMoV) and crAssphage, which are frequently present in human feces, are also potentially useful as human-specific indicators of viral pollution. This study aimed to evaluate the applicability of FPH subgroups, PMMoV, and crAssphage as indicators of source-specific fecal contamination and viral inactivation using 108 surface water samples collected at five sites affected by municipal and pig farm wastewater. The host specificity of the FPH subgroups, PMMoV, and crAssphage was evaluated by principal component analysis (PCA) along with other microbial indicators, such as 16S ribosomal RNA gene markers of the Bacteroidales species. The viabilities (infectivity indices) of FRNA phage genogroups were estimated by comparing their numbers determined by infectivity-based and molecular assays. The PCA explained 58.2% of the total information and classified microbes into three groups: those considered to be associated with pig and human fecal contamination and others. Infective and gene of genogroup IV (GIV)-FRNA phage were assumed to be specific to pig fecal contamination, while the genes of GII-FRNA phage and crAssphage were identified to be specific to human fecal contamination. However, PMMoV, infective GI-FRNA phage, and FDNA phage were suggested to not be specific to human or pig fecal contamination. FRNA phage genogroups, especially the GIV-FRNA phage, were highly inactivated in the warm months in Japan (i.e., July to November). Comparing the infectivity index of several FRNA phage genogroups or other viruses may provide further insight into viral inactivation in the natural environment and by water treatments.

Steps to Regulatory Science

The research achievements in the field of regulatory science from the beginning of my research are described in an overview. First, I was interested in the complexity of development and pursued my studies on the mechanisms of DNA replication and repair, the mutagenicity of air pollutants, and the oncogene. After researching new phenomena based on the discovery of basic research in molecular/biochemistry, my research interests turned to the field of regulatory science which applies scientific evidence to social systems. I was able to successfully contribute to the field of drinking water quality in Japan through the establishment of drinking water quality standards and standard values, primarily for organic and agricultural chemicals, the development of analysis techniques, and the creation of an organization for ensuring safety. Research on the water quality in public water areas, which are also the sources of drinking water, was another subject in which I was involved. I took part in developing the concept and evaluation methodology for the environmental impact assessment of active pharmaceutical ingredients as well as conducting environmental monitoring on urban rivers in Japan. I have also been engaged in studies on the security and safety of human health with an ecosystem conservation background. It has been a great pleasure to collaborate on research projects with so many people toward a common aim.

Inferring microbial community assembly in an urban river basin through geo-multi-omics and phylogenetic bin-based null-model analysis of surface water

Understanding the community assembly process is a central issue in microbial ecology. In this study, we analyzed the community assembly of particle-associated (PA) and free-living (FL) surface water microbiomes in 54 sites from the headstream to the river mouth of an urban river in Japan, the river basin of which has the highest human population density in the country. Analyses were conducted from two perspectives: (1) analysis of deterministic processes considering only environmental factors using a geo-multi-omics dataset and (2) analysis of deterministic and stochastic processes to estimate the contributions of heterogeneous selection (HeS), homogeneous selection (HoS), dispersal limitation (DL), homogenizing dispersal (HD), and drift (DR) as community assembly processes using a phylogenetic bin-based null model. The variation in microbiomes was successfully explained from a deterministic perspective by environmental factors, such as organic matter–related, nitrogen metabolism, and salinity-related parameters, using multivariate statistical analysis, network analysis, and habitat prediction. In addition, we demonstrated the dominance of stochastic processes (DL, HD, and DR) over deterministic processes (HeS and HoS) in community assembly from both deterministic and stochastic perspectives. Our analysis revealed that as the distance between two sites increased, the effect of HoS sharply decreased while the effect of HeS increased, particularly between upstream and estuary sites, indicating that the salinity gradient could potentially enhance the contribution of HeS to community assembly. Our study highlights the importance of both stochastic and deterministic processes in community assembly of PA and FL surface water microbiomes in urban riverine ecosystems.