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Serving as a vital linkage between surface water and groundwater, the hyporheic zone (HZ) plays a fundamental role in improving water quality and maintaining ecological security. In arid or semi-arid areas, effluent discharge from wastewater treatment facilities could occupy a predominant proportion of the total base flow of receiving rivers. Nonetheless the relationship between microbial activity, abundance and environmental factors in the HZ of effluent-receiving rivers appear to be rarely addressed. In this study, a spatiotemporal field study was performed in two representative effluent-dominated receiving rivers in Xi'an, China. Land use data, physical and chemical water quality parameters of surface and subsurface water were used as predictive variables, while the microbial respiratory electron transport system activity (ETSA), the Chao1 and Shannon index of total microbial community, as well as the Chao1 and Shannon index of denitrifying bacteria community were used as response variables, while ETSA was used as response variables indicating ecological processes and Shannon and Chao1 were utilized as parameters indicating microbial diversity. Two machine learning models were utilized to provide evidence-based information on how environmental factors interact and drive microbial activity and abundance in the HZ at variable depths. The models with Chao1 and Shannon as response variables exhibited excellent predictive performances (R 2 : 0.754-0.81 and 0.783-0.839). Dissolved organic nitrogen (DON) was the most important factor affecting the microbial functions, and an obvious threshold value of ∼2 mg/L was observed. Credible predictions of models with Chao1 and Shannon index of denitrifying bacteria community as response variables were detected (R 2 : 0.484-0.624 and 0.567-0.638), with soluble reactive phosphorus (SRP) being the key influencing factor. Fe (Ⅱ) was favorable in predicting denitrifying bacteria community. The ESTA model highlighted the importance of total nitrogen in the ecological health monitoring in HZ. These findings provide novel insights in predicting microbial activity and abundance in highly-impacted areas such as the HZ of effluent-dominated receiving rivers., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

We lack a clear understanding of how anthropogenic pressures, exemplified by effluent discharge from wastewater treatment plants, destabilize microbial communities in the hyporheic zone (HZ) of receiving rivers. In this study, the spatiotemporal characteristics of hydrological parameters, and the physicochemical properties of surface and subsurface water in a representative effluent-dominated river were monitored. Sequencing of 16S rRNA amplicons and metagenomes revealed the microbial community structure in the HZ of both effluent discharge area and downstream region. The keystone taxa (taxa vital in determining the composition of each microbial cluster) and the keystone functions they controlled were subsequently identified. Effluent discharge amplified the depth of the oxic/suboxic zone and the hyporheic exchange fluxes in the effluent discharge area, which was 50-120% and 40-300% higher than in the downstream region, respectively. Microbial community structure pattern analysis demonstrated an enhancement in the rate of dispersal, an increase in microbial diversity, and an improved community network complexity in the effluent discharge area. By contrast, the number of keystone taxa in the effluent discharge area was 50-70% lower than that of the downstream region, resulting in reduced community network stability and functionality. The keystone taxa controlling metabolic functions in the networks categorized to effluent discharge area were comprised of more genera related to nitrogen and sulfur cycling, e.g., Dechloromonas, Desulfobacter, Flavobacterium, Nitrosomonas, etc., highlighting a research need in monitoring species associated with nutrient element cycling in the HZ of receiving waterbodies. The results showed that the keystone taxa could contribute positively to network stability, which was negatively correlated to hyporheic exchange fluxes and redox gradients. This study provides valuable insights that will improve our understanding of how river ecosystems respond to changes in anthropogenic pressures., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

The impacts of effluent discharge on receiving waterbodies have been a research hotspot. Nonetheless, limited information is available on the microbial community assembly patterns in the hyporheic zones (HZ) responding to the changes in the microenvironments, e.g., solute transport and redox gradient variations. Using two representative effluent-dominated rivers as model systems, the spatio-temporal bacterial community dynamics and assembly patterns in oxic and suboxic zones in the shallow riverbed sediments were disentangled via null model- and neutral model-based approaches. Bacterial dynamics in community composition were observed driven by environmental filtering, i.e., impacts of environmental variables, more than geographic distances, i.e., the depths of sediments. The communities in samples collected in summer were largely shaped by stochasticity, in which homogeneous selection occupied a higher proportion in oxic (∼39%) than in suboxic zone (∼23%). Deterministic processes contributed to a more complex community structure for samples from oxic zones, whereas weakened the interspecies interactions in suboxic zones. The richness and abundances of non-neutral community were confirmed governing the deterministic assembly in oxic zones. Key species ascribed to 'connectors' and 'network hubs' dominated the community assembly variations in samples collected in winter, and in oxic zones, respectively. Significant positive relationships between β-nearest taxon index and dissolved organic nitrogen (DON) and nitrate highlighted their vital roles in community assembly via deterministic selective pressures in oxic zones. The significance thresholds of nitrogen species for community transition in winter (ΔDON: 2.81 mg-N/L, ΔNO 3 - : 1.09 mg-N/L) were lower than in summer, probably implying that stricter effluent quality standards should be established in colder seasons. Combined, our work poses first insights on the roles of redox zonation in driving microbial community assembly in HZ, which is of significance in guiding ecological remediation processes in effluent-dominated rivers., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Artificial aeration, a widely used method of restoring the aquatic ecological environment by enhancing the re-oxygenation capacity, typically relies upon empirical models to predict ecological dynamics and determine the operating scheme of the aeration equipment. Restoration through artificial aeration is involved in oxic-anoxic transitions, whether these transitions occurred in the form of a regime shift, making the development of predictive models challenging. Here, we confirmed the existence of alternative states in microbial communities during artificial aeration through aeration incubation experiment for the first time and considered its existence in neural network modeling in order to improve model performance. By aeration incubation experiment, it was confirmed that the alternative states exist in microbial communities during artificial aeration by two independent approaches, potential analysis and "enterotyping" approach. Comparing neural network models with and without considering the existence of alternative states, it was found that considering the existence of alternative states in modeling could improve the performance of neural network model. Our study provides a reference for the prediction of systems containing time series data where the current state will have an impact on later states. The developed model could be used for optimizing the operating scheme of the artificial aeration., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Riparian wetlands can be used as "sentinels" of environmental changes and play pivotal roles in ecological and biogeochemical processes. The bacterial community is an essential and rapidly responding component in riparian areas. However, the co-occurrence patterns and phylogenetic group-based ecological processes during wet-dry periods are still open questions. Here, we compared the co-occurrence patterns and phylogenetic group-based assembly mechanisms of soil bacterial communities in typical riparian wetlands across wet and dry seasons, which are subjected to intensive agricultural activities. The results showed that the potential functions, community composition, network structure, and phylogenetic group-based ecological processes of the bacterial community were distinct between the wet and dry seasons. The stability and complexity of the wet season bacterial network were significantly higher than those of the dry season bacterial network. Moreover, the phylogenetic group-based null model analysis showed that homogeneous selection (HoS), dispersal limitation (DL), and drift (DR) were the most important ecological processes for the bacterial community assemblages, with a higher proportion of DL in the wet season (36.7%) than in the dry season (25.5%) but lower contributions of the HoS (36.1% versus 41.3%) and DR (20.8% versus 25.4%). The communities dominated by Flavobacteriales , Burkholderiales , and Sphingomonadales in the wet season were controlled more by dispersal limitation, whereas they were significantly negatively correlated with precipitation, dissolved organic carbon, and total carbon in the dry season, respectively. These findings expand our understanding of the network vulnerability and assembly mechanisms in fragile anthropologically affected riparian wetland ecosystems. IMPORTANCE Riparian wetlands comprise microbial communities that are easily affected by the surrounding conditions, especially in agricultural landscapes with a wide range of ecosystem services. After comparing the wet and dry season microbiota, we found that the soil bacterial community of the wet season exhibited a higher complexity and stability of soil bacterial network and stronger dispersal limitations than that of the dry season; however, the dry season bacteria showed stronger homogeneous selection than the wet season bacteria. The co-occurrence and phylogenetic group-based bacterial community assembly mechanisms were mainly shaped by the divergence in temperature and precipitation between seasons. Revealing the variations in the potential functions, co-occurrence, and community assembly processes between wet and dry seasons is critical to understanding the maintenance of soil microbial diversity in riparian wetlands with regard to environmental sceneries.

Community coalescence, i.e., the mixing and merging of microbial communities and their surrounding environments, is prevalent in various ecosystems and potentially acts on ecological processes. River bends are distinguished by significant cross-stream velocities and spiral flow. The flow in river bends causes the mixing of microbial communities, thus making the resultant community (after mixing) different from its precursors (before mixing) through ecological processes. However, so far, no studies have explored the effect of community coalescence on ecological processes and network stability under the hydrodynamic processes of river bends. Here, we explored bacterial community assembly and community coalescence in river bends by coupling hydrodynamic profiling, aqueous biogeochemistry, DNA sequencing, and ecological theory. The results showed that the water flow dominated the community coalescence by regulating the movement of suspended sediments. The main ecological process determining the bacterial community compositions in water was the dispersal process, whereas in sediments it was the selection process. Furthermore, the negative cohesion results showed that community coalescence determined the stability of bacterial networks through competition and predation. This study depicted the bacterial community coalescence in river bends and highlighted their associations with network stability, which might provide new insights into bacterial community assembly and coalescence under complex hydrodynamics in the aquatic environment., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022. Published by Elsevier B.V.)

Controlled surface water systems, including those with dams lead to dynamic stage changes that alter the fluctuation directions of flow exchange in the hyporheic zones (HZ). However, the nitrogen transformation, dissolved organic matter (DOM) composition, and microbial community responding to variable scenarios of water source and hyporheic exchange are poorly studied. The present work investigated nitrogen transformation in HZ sediments, focusing on how microbial community structure and biological functions related to nitrogen transformation and sediment-attached DOM compositions. Upwelling of synthesized groundwater, downwelling of synthesized river water and exchangeable elution of both feed water created distinct microbial zonation and N-transformation processes. Mixing of river water and groundwater enhanced microbial diversity, microbial co-occurrence network complexity and N-transformation functions. In terms of the sediment-attached DOM properties after hyporheic exchanges, humic fractions occupied the predominant chromophoric DOM. Correlation analysis implied that there were more DOM properties, e.g., tryptophan-like proteins, humic-like fractions, and the source of humic fractions, involved in affecting the microbial community under downwelling flow. Co-occurrence network analysis verified that fluorescent components, protein-like and lignin-like fractions in sediment-detached DOM were clustered with microbial communities in one module in downwelling column, implying closer interactions among microbial communities and DOM fractions. The strains of Nitrospinae, Dinghuibacter, and Lentimicrobium etc. were key species collaborating to metabolize both nitrogen and DOM in HZ sediments. The work provides insights into how the nitrogen transformation, DOM compositional changes, as well as the linkages between community structure and DOM factions, response to the changes in water chemistry, leading to valuable insights into hyporheic zone functions., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Expanding the stress tolerance and adaptation potential of primary producers is of importance for the restoration and management of aquatic ecosystems. Microorganisms have been reported to mediate improved resistance toward different abiotic stresses of primary producers in terrestrial and marine ecosystems. However, it is not clear about the role of microbial communities in the turbidity resistance of primary producers, when aquatic ecosystems are under turbidity pressure. In this study, key microbes and the action path which enhance turbidity tolerance of primary producers were recognized by mesocosm and various multivariate statistical methods. Remarkable decrease of the biomass of primary producers was found with the increase of turbidity. Significant differences in microbial community under different turbidity pressure were recognized and key microbes which may expand the turbidity tolerance of primary producers were further identified. Rhodobacter and Rhodoferax were selected as key microbes by the investigation of keystone species in the microbial ecological network and significant discriminant taxa under different turbidity stress. The action path for microbial communities to help primary producers cope with turbidity pressure was found through structural equation model, and in which the increase of key microbes may expand the turbidity tolerance of primary producers through enhancing the microbial loop. The results may provide a new insight for aquatic ecosystems to resist turbidity stress, and provide a theoretical basis for the management and restoration of aquatic ecosystems., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Understanding how the structures and functions of bacterial and microeukaryotic communities vary within cross-sections will improve managements aimed at restoring river ecological functions. However, no comprehensive investigation has examined how microbial community characteristics vary within cross-sections, which makes the accurate calculation and prediction of microbial metabolic processing of substances in rivers difficult. Here, the distributions, co-occurrence networks, and assemblies of bacterial and microeukaryotic communities and their feedback to nitrogen transformation in cross-sections of the Yangtze River were studied by coupling ecological theory, biogeochemistry, and DNA meta-barcoding methods. The study found that depth in cross-sections was the primary driving factor regulating the composition of sediment bacterial and microeukaryotic communities. Co-occurrence network analysis indicated that the effect of bacteria on the co-occurrence network decreased and the network become more simplified and instability with depth in river cross-sections. Quantified using the β-nearest taxon index, the H2 layer sediment (depth 10-20 m) displayed the largest variation in selection processes for microbial assemblies, while homogeneous selection and homogenizing dispersal contributed most to the bacterial and microeukaryotic assemblies in the H3 layer (depth >20 m). Cross-sectional depth and denitrification genes had a significant quadratic correlation, with the highest microbial nitrogen-removal potential occurring in the H2 layer sediment. Structural equation models showed that the sediment nitrogen distributions were regulated by distinct environmental pathways at different depths, and that the H2 layer sediment was primary driven by bacterial community. In this layer, river cross-sectional depth influenced nitrogen transformation by regulating the distribution of sediment particle sizes, which then influenced the assembly of the multitrophic microbial communities. This study will improve river management by clarifying the importance of cross-sectional depth to the ecological function of rivers., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Maintaining hydrophyte growth has been a major focus of aquatic ecological research. The hydrophyte microbiome plays a key role in the growth and health of hydrophytes, but the ecological processes regulating the assembly and function of hydrophyte microbial communities remain unclear. This knowledge gap limits the efficacy of managing microbiomes to enhance the capacity of hydrophytes to restore the aquatic environment. Here, we sampled three typical hydrophytes (Ceratophyllum demersum, Nymphoides peltatum, and Potamogeton crispus) to study the ecological process governing hydrophyte-associated bacterial communities. The results demonstrated that hydrophyte-associated bacterial communities were affected more by the hydrophyte host species (HEEI = 2.40) than by the environment (HEEI = 1.00). The hydrophyte host species not only affected bacterial community assembly, but reduced the diversity and network complexity of the bacterial community relative to that of the environment. Furthermore, the core taxa of two hydrophytes were identified. Chryseobacterium was the core taxon of N. peltatum, and Burkholderia-Caballeronia-Paraburkholderia, Pseudolabrys, and Pajaroellobacter were the core taxa of P. crispus. The core taxa of P. crispus were closely related to potential denitrification-related functions of bacteria and revealed that P. crispus played a role in denitrification during aquatic ecological restoration. Overall, the results of this study highlight the need to develop approaches employing hydrophyte-associated bacteria to promote the development of hydrophytes, which will be essential for increasing the utility of hydrophyte microbiomes in the future and enhancing aquatic ecological restoration., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Identifying sediment phosphorus sources in river-lake coupled system is a question in developing preferential control strategies for phosphorus. As sediments adsorbed phosphorus and microbes would be transported with changing hydrodynamic, the phosphorus source-specific microbial community fingerprints shed light on determining the major sediment phosphorus sources. However, the identification of microbial community fingerprints is a challenge because both microbial succession and hydrological characteristics of river-lake systems would affect the stability of fingerprints. Therefore, this study provided a framework for optimizing phosphorus source-specific microbial community fingerprints, and attempted to identify the major sources of sediment phosphorus in river-lake coupled ecosystem. Meiliang Lake is one of the highly eutrophic area in Taihu Lake, where the sediments, bacterial communities, and phosphorus had a close relationship. Through analyzing the connectivity of microbes along water continuum, a microbial fingerprints candidate database was constructed. The phosphorus-related bacterial communities were screened and optimized by comparing the difference of predicted results between upstream and downstream, forming the stable microbial community fingerprints which consisted of Bacteroidia, Bacilli, Clostridia, and other species at the class level. SourceTracker results that based on the optimized phosphorus source-specific microbial community fingerprints indicated that the major sediment phosphorus sources to Meiliang Lake were Liangxi River, Wujingang River, and Donghuandi River, with the relative standard deviations ranging from 2.59% to 27.56%. The accuracy of phosphorus source apportionments was further confirmed based on the composite pollution index and hydrodynamic condition. This study put forward suggestions on how to improve the stability of microbial community fingerprints, and would help to improve the understanding of applying microbial source tracking method to identify the sources of abiotic pollution like sediment phosphorus., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Diverging area is widespread in river networks, and understanding its biogeochemical process characteristics is of great significance to river ecological restoration and environmental quality improvement. Microbial communities affected by hydrodynamics play an important role in biogeochemical processes, but their relationship in diverging area is little known. Here, the composition of microbial community and its feedback to hydrodynamics and nitrogen conversion in the diverging area of river networks were first studied by coupling ecological theory, biogeochemical theory, microbial DNA sequencing and mathematical model of water environment. The results showed that there were five hydrodynamic zones with significant velocity differences in the diverging area, namely low velocity zone, maximum velocity zone, stagnant zone, separation zone, and deflection zone. According to the flow velocity grouping, there were significant differences in the microbial diversity and abundance among low velocity group, maximum velocity group and stagnant group had significant differences (p < 0.05, stress = 0.1207). In the low velocity group, Firmicutes was the dominant phylum which had a highest abundance and may promot the conversion of organic nitrogen into ammonia nitrogen. In the maximum velocity group, Bdellovibrionota was the dominant phylum which had a highest abundance and may promot the conversion of nitrate and nitric oxide to nitrogen. In the stagnant zone, Methylomirabilota was the dominant phylum which had a highest abundance and may promot the conversion of nitrogen into nitrate and ammonium. In addition, dissolved oxygen was the most sensitive environmental factor for shaping microorganisms and nitrogen conversion in the diverging area of the river networks by canonical correlation analysis. The denitrifying bacteria Rhodocyclaceae, was shown to negatively correlated with the flow velocity. This research improves the scientific basis for the study of the ecosystem in river networks, which will guide the construction of river ecological projects., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Microplastics are frequently detected in natural aquatic systems proximate to populated areas, such as urban rivers and lakes, and can be rapidly colonized by microbial communities. Microplastics and silver nanoparticles (AgNPs) share similar pathways into natural waters and tend to form heteroaggregations. However, very little is known about the long-term impacts on the structure and function of microplastic biofilms when chronically exposed to silver nanoparticles. Thus, the present study assessed the accumulation property of AgNPs on polymethyl methacrylate (PMMA) microplastics via adsorption tests and studied the chronic effects of AgNPs on the structure and function of microplastic biofilms via 30-day microcosmic experiments in eutrophic water. The adsorption tests showed that the biofilms-colonized PMMA microplastics presented the highest adsorption of 0.98 mg/g in the 1 mg/L AgNPs microcosms. After the 30-day exposure, lactic dehydrogenase release and reactive oxygen species generation of PMMA biofilms increased by 33.23% and 23.98% compared to the MPs-control group with no-AgNPs, indicating that the number of dead cells colonizing microplastics significantly increased. Network analysis suggested that the stabilization of the bacterial community declined with the long-term exposure to AgNPs through the reduction of the modularity and average path length of the network. Compared to the MPs-control group, long-term exposure to AgNPs caused cumulatively inhibitory effects on the nitrogen removal and the N 2 O emissions in eutrophic water. The isotopomer analysis revealed that the contribution rate of NO 2 - reduction to N 2 O emissions was gradually increasing with the AgNPs exposure. Real-time PCR analysis showed that denitrification genes were less sensitive to AgNPs than the nitrification genes, with gene nosZ performed the most negligible response. Overall, our results revealed that long-term exposure to AgNPs could alter biogeochemical cycling involved by microplastic biofilms and cumulatively reduce the self-recovery of the eutrophic ecosystem., (Copyright © 2021 Elsevier Inc. All rights reserved.)

The co-occurrence networks and interactions of bacterial communities in sediments are highly variable with environmental factors, which are vital to the nutrient biogeochemical cycle, pollutants biodegradation, and microbial community stability in lake ecosystems. Although pollution gradients reflect environmental variation comprehensively, few studies have characterized the changes in co-occurrence networks and interactions of bacterial communities along sediment pollution gradients. In order to investigate the impact of pollution gradients on compositions, co-occurrence networks, and interactions of sedimentary microbial communities, we studied the bacterial communities in the sediments of a typical shallow eutrophic lake, Taihu Lake, along pollution gradients using 16S rRNA gene high-throughput sequencing technology. All the sediment sampling sites were classified into mild, moderate, and severe pollution groups according to the sediments' physicochemical properties. Our results showed that the taxon richness was lowest in the severe pollution group, and the diversity of species decreased with the level of pollution. The complexity of the co-occurrence network decreased as the level of pollution increased, and the severe pollution group was characterized by a small-world network. The relative abundance of Proteobacteria, Bacteroidetes, and Chlorobi increased significantly as the level of pollution increased (P < 0.05). Strong inter-phyla co-occurrence or co-exclusion patterns demonstrated that the strength of interactions was enhanced in the severe pollution group, indicating stronger cooperative or competitive relationships. Chloroflexales and Chlorobiales were unique keystone taxa in the severe pollution group. The results of this study indicate that severe pollution reduces microbial diversity and network complexity, which may lead to community instability. The competition for nutrients of some copiotrophic bacteria may be enhanced as the level of pollution increased. The unique keystone taxa may contribute to photosynthesis and pollutant degradation in the severe pollution group. These findings expand our understanding of variation in bacterial co-occurrence networks and interactions along sediment pollution gradients., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

The importance of suspended particulate matter (SPM) in nitrogen removal from aquatic environments has been acknowledged in recent years by recognizing the role of attached microbes. However, the succession of attached microbes on suspended particles and their role in nitrogen removal under specific surface microenvironment are still unknown. In this study, the causation among characteristics of SPM, composition and diversity of particle-attached microbial communities, and abundances of nitrogen-related genes in urban rivers was firstly quantitatively established by combing spectroscopy, 16 S rRNA amplicon sequencing, absolute gene quantification and supervised integrated machine learning. SPM in urban rivers, coated with organic layers, was mainly composed of silt and clay (87.59-96.87%) with D50 (medium particle size) of 8.636-30.130 μm. In terms of material composition of SPM, primary mineral was quartz and the four most abundant elements were O, Si, C, Al. The principal functional groups on SPM were hydroxyl and amide. Furthermore, samples with low, medium and high levels of ammoxidation potential were classified into three groups, among which significant differences of microbial communities were found. Samples were also separated into three groups with low, medium and high levels of denitrification potential and significant differences occurred among groups. The particle size, content of functional groups and concentration of SPM were identified as the most significant factors related with microbial communities, playing an important role in succession of particle-attached microbes. In addition, the path model revealed the significantly positive effect of organic matter and particle size on the microbial communities and potential nitrogen removal. The content of hydroxyl and temperature were identified as the most effective predicting factors for ammoxidation potential and denitrification potential respectively by Random Forests Regression models, which had good predictive performances for potential of ammoxidation (R 2  = 0.71) and denitrification (R 2  = 0.61). These results provide a basis for quickly assessing the ability of nitrogen removal in urban rivers., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Prioritizing the relationship between heterogeneity of sediment habitats and river bends is critical when planning and reconstructing urban rivers. However, the exact relationship between ecological heterogeneity and river bends remains ambiguous. Therefore, this research proposed a new approach to quantify and predict bend-induced ecological heterogeneity, incorporating the bacteria-based index of biotic integrity (Ba-IBI), path model, and random forest regression model. The developed Ba-IBI quantified heterogeneity in sediment microbial communities, ranging from low (1.40) to high (3.97). A path model was developed and validated in order to further investigate the relative contributions of environmental factors to the Ba-IBI. The established path model, which was considered acceptable with a CMIN/df = 1.949 < 4, suggested that primary environmental factors affecting the sediment bacterial communities were flow velocity and ammonium concentration in sediment. To further characterize the relationship between environmental factors and the Ba-IBI, a function was constructed using the random forest regression model that predicts the responses of sediment bacterial communities to environmental factors with R 2  = 0.6126. The proposed approach and prediction tools will provide knowledge to improve natural channel design and post-project evaluations in river restoration projects., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Cascade dams have exerted significant effects on river ecosystems. To quantitatively assess dam-induced effects on river ecological status, a novel multi-species interaction-based index of biotic integrity (Mt-IBI) was developed. Benthic microbiota was selected as a bio-indicator for its sensitivity to the environmental disturbance. An environmental DNA metabarcoding tool was used to identify microbiota (bacteria, protozoan, and metazoan). The Mt-IBI was applied to assess the ecological status of the Hanjiang River, a representative dam-affected river in China. Fifteen sampling sites along the Hanjiang River were sampled in June 2018. Seven core metrics were screened from a total of 364 candidate metrics to calculate the value of the Mt-IBI. The Mt-IBI of the Hanjiang River ranged from 1.90 to 6.39, with a mean value of 4.02. The mean values of Mt-IBI at the reservoir and riverine side of dams were 2.11 and 3.81, respectively. The downstream reach without dam constructions had the highest mean Mt-IBI (5.79). Thus, the continuity of the river was strongly related to the Mt-IBI. Structural equation models (SEMs) were further established to identify the dominant environmental variables in the dam-affected river. The SEMs indicated that flow velocity (coefficient 0.749) was the most important determinant of ecological status in the Hanjiang River. Water organic matter also played a vital role in determining the ecological status of the Hanjiang River, and exerted the strongest direct effect (P < 0.001, r = 0.712). The reliability of SEMs was verified by building a support vector regression model (R 2  = 0.8141). This study can provide new tools for ecological assessment and diagnosis, and provide a new perspective for the management of cascade dams., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

The nitrogen (N) cycle is one of the most important nutrient cycles in river systems, and it plays an important role in maintaining biogeochemical balance and global climate stability. One of the main ways that humans have altered riverine ecosystems is through the construction of hydropower dams, which have major effects on biogeochemical cycles. Most previous studies examining the effects of damming on N cycling have focused on the whole budget or flux along rivers, and the role of river as N sources or sinks at the global or catchment scale. However, so far there is still lack of comprehensive and systematic summarize on N cycling and the controlling mechanisms in reservoirs affected by dam impoundment. In this review, we firstly summarize N cycling processes along the longitudinal riverine-transition-lacustrine gradient and the vertically stratified epilimnion-thermocline-hypolimnion gradient. Specifically, we highlight the direct and indirect roles of multi-trophic microbiota and their interactions in N cycling and discuss the main factors controlling these biotic processes. In addition, future research directions and challenges in incorporating multi-trophic levels in bioassessment, environmental flow design, as well as reservoir regulation and restoration are summarized. This review will aid future studies of N fluxes along dammed rivers and provide an essential reference for reservoir management to meet ecological needs., (Copyright © 2021. Published by Elsevier Ltd.)

The accumulation of estrogens in aquatic environments has drawn increasing public concern due to their adverse effects on aquatic ecosystems and human health. Bacteria play important roles in eliminating estrogens from the environment, but knowledge of the identity and functions of the microorganisms involved in metabolizing these steroid hormones in the natural microbial communities is lacking. Here, we added 13 C-17β-estradiol ( 13 C-E2) to sediments collected from Zhushan (ZS) Bay, Meiliang (ML) Bay, Gonghu (GH) Bay, and the central area (CA) of the Taihu Lake. The indigenous assimilators of E2 in the sediments were recognized using 13 C-DNA stable isotope probing (DNA-SIP), and their effects on 13 C-E2 mineralization were studied under aerobic condition. During the 30-day incubation period, ZS Bay had the highest cumulative percentage of 13 C-E2 mineralization to 13 CO 2 (65.5%), while CA presented the lowest (51.4%). Based on DNA-SIP, we saw that Novosphingobium, Ralstonia, Pseudomonas, Sphingomonas, Nitrosomonas, and Alcaligenes were involved in E2-derived 13 C assimilation for the entire incubation period. Acinetobacter, Flavobacterium, and Mycobacterium only assimilated 13 C for the first half of the incubation. H16 was identified as an E2 assimilator for the first time in this study. In addition, the temporal changes in assimilator abundances during the incubation period indicated that these genera played dominant roles at different stages in the process of E2 biodegradation. The bacteria engaged in the assimilation of E2 in situ were identified, and the rate of increase in the relative abundance of assimilators was significantly (P < 0.05) and positively correlated with the E2 mineralization in sediments. This information enhances our knowledge of in situ E2 biodegradation and provides a potential resource that could be used to eliminate estrogens in sediments., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Black carbon is considered as a promising material for thin-layer capping for sediment remediation. However, the effects of black carbon-based thin-layer capping on microbial communities have not been thoroughly studied. Here, the preparation conditions of capping material were optimized, and the interaction and assembly mechanisms of the microbial community in sediment under black carbon capping were studied. The results showed that concentration of NH 4 + -N in the overlying water was stably lower than 0.5 mg/L after capping. The abundance of key genes related to nitrogen transformation in the sediment was increased. Denitrification was the dominant nitrogen removal pathway under coarse granule capping, while aromatic compound degradation was dominant under fine granule capping and dissimilatory N reduction to ammonium was regarded as the dominant nitrogen removal pathway. Community assembly was mainly driven by deterministic processes (≥ 80%). Interactions between rare and common operational taxonomic units were most frequent. The functional zoning of nitrogen transformation in the vertical aerobic, hypoxic, and anaerobic zones of the sediment was strengthened because of black carbon capping. Overall, these results expand our current understanding of the ecological significance of black carbon capping for remediating contaminated sediment., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021. Published by Elsevier B.V.)

Catastrophic shifts in river ecosystems can abruptly degrade their structures and functions, often reducing the efficacy of traditional remediation targeting physicochemical properties. Alternative stable states theory can not only explain this phenomenon but also provide a new insight into river restoration; however, little is known about the existence and implications of alternative stable states in a river. Considering the important role of benthic microbiota in sustaining river ecosystem structures and functions, ecological theory and high-throughput sequencing were combined to firstly investigate multi-stability in microbial communities and its relationship with environmental factors in river sediments. The Nanjing reach of the Yangtze River was selected as the study area because of its huge spatial heterogeneity and varying degrees of pollution. Bimodal distributions combined with temporal variations of microbiota status provided direct evidence of bistability by showing the instability at the intermediate. In addition, environmental stress, particularly concentrations of NH 4 + -N, was identified as an important driver of alternative microbiota states from the perspectives of the behavior of bistable ecosystems. Comparison of α-diversity indices and network properties between two alternative microbiota states revealed that the diversity and co-occurrence pattern of microbial communities will be high if they are settled in favorable environments (i.e., comprehensive sediment quality identification index > 3.7). Key taxa, including Clostridiales, Nitrospirales and Myxococcales, were discerned by combining LEfSe and network analysis, and their strong interspecies interactions were believed to be an important factor in triggering alternative microbiota states. This study suggests alternative stable states theory should be considered in river remediation to better understand the response of river ecosystems to environmental stress and the effect of hysteresis, benefiting the implementation of effective monitoring and restoration strategies in a river of urban area.3 - -N, was identified as an important driver of alternative microbiota states from the perspectives of the behavior of bistable ecosystems. Comparison of α-diversity indices and network properties between two alternative microbiota states revealed that the diversity and co-occurrence pattern of microbial communities will be high if they are settled in favorable environments (i.e., comprehensive sediment quality identification index > 3.7). Key taxa, including Clostridiales, Nitrospirales and Myxococcales, were discerned by combining LEfSe and network analysis, and their strong interspecies interactions were believed to be an important factor in triggering alternative microbiota states. This study suggests alternative stable states theory should be considered in river remediation to better understand the response of river ecosystems to environmental stress and the effect of hysteresis, benefiting the implementation of effective monitoring and restoration strategies in a river of urban area., (Copyright © 2021. Published by Elsevier Ltd.)

Microplastics provide a unique habitat for microorganisms, forming the plastisphere. Yet the ecology of the plastisphere, including the microbial composition, functions, assembly processes, and interaction networks, needs to be understood. Here, we collected microplastics and their surrounding water samples in freshwater and seawater ecosystems. The bacterial and fungal communities of the plastisphere and the aquatic environment were studied based on 16S and internal transcribed spacer (ITS) high-throughput sequencing. We found that the plastisphere had a distinct microbial community and recruited a noteworthy proportion of unique species compared to the aquatic environment community, potentially altering ecosystem microbial community and causing microbial invasion. Using a random-forest machine-learning model, we identified a group of biomarkers that could best distinguish the plastisphere from the aquatic environment. Significant differences exist in microbial functions between the plastisphere and the aquatic environment, including functions of pathogenicity, compound degradation, as well as functions related to the cycling of carbon, nitrogen, and sulfur. And these functional differences were expressed differently in freshwater and seawater ecosystems. The oxidation-reduction potential, salinity, the concentrations of nitrogen-related ions (NO 3 - , NO 2 - , and NH 4 + ), and the concentration of dissolved organic carbon in the surrounding environment drive the variation of the plastisphere. But environmental physicochemical properties explain less of the microbial community variation in the plastisphere than that in the aquatic environment. Niche-based processes govern the assembly of the plastisphere community, while neutral-based processes dominate the community assembly of the aquatic environment. Furthermore, compared to the aquatic environment, the plastisphere has a network of less complexity, more modules, higher modularity, and more competitive links in freshwater ecosystems, but the pattern is reversed in seawater ecosystems. Altogether, the microbial ecology of the new anthropogenic ecosystem-plastisphere-is unique and exerts different effects in freshwater and seawater ecosystems., (Copyright © 2021. Published by Elsevier Ltd.)

Understanding the ecological relationship of microbial community under external stimulation is crucial for environmental restoration. Black carbon (e.g., biochar) have been widely deemed as a strategy to enhance pollutants removal because of its structure and redox-active property. However, the underlying ecological mechanism of microbial community under black carbon addition is poorly understood. The major purposes of this study were to determine the microbial assemblage and functional patterns via null model test, network analysis, and function prediction. The results showed that the nitrate removal efficiency of modified black carbon system achieved 46.44%. Both deterministic and stochastic processes were significant for mediating the microbial assemblage and the deterministic process dominated (>95%) the assemblage of community. Keystone taxa in the black carbon systems, involving Sulfuricella, Allorhizobium, and Nitrospira, stimulated the shift of community composition regarding the nitrogen removal. The existence of black carbon and the biotic interactions increased biological nitrate utilization and promoted nitrogen removal. Overall, this study presents the mechanism of bacterial community assembly and provides insight into biological nitrogen removal from microbial ecological perspective., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Understanding the characteristics of biogeochemical processes in urban channel confluences is essential for the evaluation and improvement of water environmental capacity. However, influences of biogeochemical processes in confluence were always overlooked or simply parametrized since the transformation processes controlled by microbial community assembly were hard to quantify. To address this knowledge gap, the present study proposed a novel mathematical modeling system, based on microbial community assembly theory and fluid kinetics, to decouple nitrogen dynamics into flow-induced transport and microorganism-induced transformation processes, and quantified their contributions to nitrogen concentrations. Results revealed that variable selection processes (including hydrodynamic conditions) contributed to significant difference in microbial communities among different hydraulic regions. Variation in microbial communities further shifted transformation processes. Rhodobacterales and Sphingomonadales , which were reported to be vital participants in denitrification process, were enriched in flow separation region, and promoted it as a hotspot for nitrogen removal. In the flow separation region, microorganism-induced transformation processes accounted for 56% of total nitrogen removal, which was significantly higher than that in other regions (12% on average; p < 0.01). Results and findings could provide useful information for the improvement of water environmental capacity.

Hyporheic zones (HZ) are hotspots for biogeochemical reactions where groundwater and surface water mix. River dam buildings and other hydrologic controls alter the sediment grain size distribution and modify the downstream hyporheic exchange, with cascading effects on geochemical and microbial processes in river corridors. In this lab-scale column experiment, the N transformations in HZ filled with sediments in different grain sizes were investigated with a focus on understanding the interplay among variational hydraulic connectivity, microbial community structure, functional potential under frequent groundwater-surface water exchange. Porosity was identified as the main driver determining bacterial community assembly in HZ sediments. Significant microbial zonation was observed along the columns and the degree of co-occurrence of bacterial communities in the Fine column was lower than that in the Coarse and Mix columns. The Coarse column allowed for almost 2.47 times the exchange flux relative to the Fine column, and generates the fastest DO consumption rate (-6.52 μg O 2 /L·s). The enrichment of nitrifiers, i.e., Cytophagaceae and Bacillaceae and nitrification functional genes, i.e., amoA&#95;AOA and amoA&#95;AOB revealed the higher nitrification potential in column filled with coarse sediments. In comparison, the highest NH 4 + production rates (2.4 × 10 -3  μg N/L·s) took place in Fine column. The higher abundancies of denitrifiers such as Comamonadaceae and Lysobacter and enrichment of functional genes of nirK and nirS interestingly suggested the elevated denitrification potential in Fine column in a more anaerobic environment. The results implied that variations in microbial functional potential and associated nitrogen transformation may occur in size-fractioned HZ to dynamic hyporheic exchange, which added new knowledge to the underlying biogeochemical and ecological processes in regulated river corridors., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Phosphorus, one of the primary limiting factors for eutrophication, plays a crucial role in the ecology health of aquatic ecosystems. However, understanding phosphorus bioavailability and source contributions in contaminated lake sediments which could help develop effective eutrophication management plans is limited largely due to the lack of appropriate methods in large catchments with a complex arrangement of sources. Based on the significant relationships between sediment, phosphorus and microbial community, source-specific microbial community fingerprints formed by machine-learning classification SourceTracker might shed light on determining dominant phosphorus sources in the river-lake systems in the era of high-throughput sequencing. This study was conducted in Dongting Lake that suffered accelerated eutrophication due to considerable phosphorus input from the inflow-rivers. The results of phosphorus fractionation according to the Standards, Measurements and Testing harmonized procedure indicated that sediments in the central lake had a higher concentration of non-apatite inorganic phosphorus (Mann-Whitney U test), which deserves greater attention on the risk of phosphorus release. The significant relationships between phosphorus fractionations, sediment and bacterial community were established with the spearman correlation and network analysis. SourceTracker analysis indicated that the major inflow-rivers of phosphorus sources to Dongting Lake were the Songzi, Miluo, and Xinqiang Rivers. The effects of sediment diffusion distance on phosphorus source apportionment were further confirmed. Taken together, our results contribute to an improved understanding of phosphorus fractionations and source contributions in the river-lake systems and its potential impact to eutrophication management plans., Competing Interests: Declaration of competing interest The authors declare that they have no conflict of interest., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Understanding environmental factors driving ecological processes of archaeal communities in heavily contaminated rivers is crucial for improvements in river ecological monitoring and indication. However, succession mechanisms underlying vertical and horizontal archaeal community assemblages in contaminated rivers remains largely unstudied. Here, to investigate ecological processes controlling archaeal community succession in a contaminated urban river, multivariate statistics approaches were applied to fields samples collected from locations representing vertical and horizontal assemblages of archaeal community. Our results revealed that archaeal community in the river showed distinct vertical and horizontal distribution patterns and the differences between water and sediment samples were most significant. Beta-diversity patterns in the vertical and horizontal assemblages are both almost completely caused by species replacement between sampling points (horizontal β SIM  = 0.60 ± 0.09, β NES  = 0.09 ± 0.05; vertical β SIM  = 0.40 ± 0.07, β NES  = 0.10 ± 0.06). Considering phylogenetic turnover deviation, homogenizing dispersal was the most crucial process dominating archaeal community assemblages in water samples while main ecological process in sediment samples was variable selection. Euryarchaeota and Thaumarchaeota were found to prefer high-nutrients and low-nutrients environments, respectively. Analysis of environmental drivers of archaeal phyla distribution and community assemblages indicated that nutrients played a decisive role in driving the sediment archaeal community. Dissolved oxygen (DO) explained the most variation in phylogenetic turnover deviation within all water archaeal community while oxidation reduction potential (ORP) contributed most for horizontal sediment archaeal community assemblages. These findings help to indicate the pollution situation of the river and provide information to predict how archaeal communities would respond to different environmental variations., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

The effects of environmental concentration silver nanoparticles (ecAgNPs) on microbial communities and the nitrogen cycling in river sediments remain largely uncharacterized. As a fundamental component of sediments, Fe(III) can interact with AgNPs and participate in nitrogen transformation processes. N 2 O is an important intermediate in nitrogen transformation processes and can be a potent greenhouse gas with significant environmental effects. However, the impacts of the co-existence of AgNPs and Fe(III) on microbial communities and N 2 O emission in river sediments are still unclear. In the present study, mesocosm experiments were conducted to assess the changes of microbial communities and N 2 O emission in response to the co-existence of AgNPs and environmental concentration Fe(III). Our results revealed that the microbial community diversity and N 2 O emission in river sediments responded differently to ecAgNPs (0.05 mg/kg) and high-polluting concentration AgNPs (hcAgNPs, 5 mg/kg), which was further regulated by the environmental concentration Fe(III) (1 mg/g and 10 mg/g). After ecAgNPs treatments, a marked increase was observed in microbial diversity compared to hcAgNPs treatments, regardless of the Fe(III) concentration in the sediment. The β-NTI index indicated that AgNPs had stronger impacts on phylogenetic distance of bacterial communities in sediments containing 1 mg/g Fe(III) than that containing 10 mg/g Fe(III). In sediments containing 1 mg/g Fe(III), ecAgNPs did not affect N 2 O emission, but hcAgNPs significantly inhibited the emission of N 2 O. However, in sediments containing 10 mg/g Fe(III), N 2 O emission was significantly stimulated upon exposure to ecAgNPs, but the inhibition effect of hcAgNPs was barely observed. Functional prediction and real-time PCR analyses indicated that AgNPs and Fe(III) predominantly affected N 2 O emissions by affecting the abundance of the nirK gene. Our results provide new insights into the ecological impacts of the co-existence of environmental concentration AgNPs and Fe(III) in altering microbial communities and nitrogen transformation functions in river sediments., (Copyright © 2018. Published by Elsevier B.V.)

Controlling wastewater pollution from centralized industrial zones is important for reducing overall water pollution. Microbial community structure and diversity can adversely affect wastewater treatment plant (WWTP) performance and stability. Therefore, we studied microbial structure, diversity, and metabolic functions in WWTPs that treat industrial or municipal wastewater. Sludge microbial community diversity and richness were the lowest for the industrial WWTPs, indicating that industrial influents inhibited bacterial growth. The sludge of industrial WWTP had low Nitrospira populations, indicating that influent composition affected nitrification and denitrification. The sludge of industrial WWTPs had high metabolic functions associated with xenobiotic and amino acid metabolism. Furthermore, bacterial richness was positively correlated with conventional pollutants (e.g., carbon, nitrogen, and phosphorus), but negatively correlated with total dissolved solids. This study was expected to provide a more comprehensive understanding of activated sludge microbial communities in full-scale industrial and municipal WWTPs.

Black-odor phenomenon in highly urbanized river is increasingly recognized as a global ecological risk. Biotransformation associated with sulfur cycle is a major contributor to the blank-odor phenomenon. The vertical geochemical gradient in black-odor rivers is likely to alter microbial community assemblages and functions in the sulfur cycle. However, the interactions between geochemical gradients and microbial communities, as well as the changes in the process of sulfur biotransformation under different environmental conditions remain largely unknown. The vertical community assembly patterns and the impacts of microbial communities and genes on the biotransformation in the sulfur cycle were revealed in our study for the first time in a typical urban black-odor river, Jinchuan River, in China. Vertical beta-diversity patterns of microbial communities mainly resulted from species replacement that was largely driven by spatial turnover (β SIM  = 0.43) but also influenced by nestedness (β NES  = 0.08). MiSeq sequencing and GeoChip 5.0 microarray chip approaches were applied and identify 41 bacterial genera, 8 archaeal genera, and 26 genes involved in the sulfur cycle in Jinchuan River. The vertical beta-diversity patterns of microbial profile mainly resulted from species replacement. Those sulfur-related bacterial and archaeal genera, accounting for 23.15% and 42.65% of the total bacteria and archaea respectively in analysed samples, were mainly responsible for sulfur reduction. According to redundancy analysis, oxidation-reduction potential (r = -0.8662, P < 0.05), S 2- concentration (r = -0.6288, P < 0.05), and total nitrogen concentration (r = -0.6782, P < 0.05) were identified as factors that significantly affect sulfur-related microbial communities. The highest reaction potential was detected in the dissimilated sulfate reduction action and experienced an increase with depth increasing in the river system. The results indicated that the sulfur biotransformation in a deeper layer in river sediment could make more contribution to the black-odor phenomenon in urban rivers., (Copyright © 2019. Published by Elsevier Ltd.)