Vertical distribution and assemblages of microbial communities and their potential effects on sulfur metabolism in a black-odor urban river

Spatial distribution of cable bacteria in nationwide organic-matter-polluted urban rivers in China

An overload of labile organic matter triggers the water blackening and odorization in urban rivers, leading to a unique microbiome driving biogeochemical cycles in these anoxic habitats. Among the key players in these environments, cable bacteria interfere directly with C/N/S/O cycling, and are closely associated with phylogenetically diverse microorganisms in anoxic sediment as an electron conduit to mediate long-distance electron transport from deep-anoxic-layer sulfide to oxic-layer oxygen. Despite their hypothesized importance in black-odorous urban rivers, the spatial distribution patterns and roles of cable bacteria in large-scale polluted urban rivers remain inadequately understood. This study examined the diversity and spatial distribution pattern of cable bacteria in sediment samples from 186 black-odorous urban rivers across China. Results revealed the co-existence of two well-characterized cable bacteria (i.e., Candidatus Electrothrix and Candidatus Electronema), with Candidatus Electrothrix exhibiting a comparatively wider distribution in the polluted urban rivers. Concentrations of DOC, SS, sulfate, nitrate, and heavy metals (e.g., Ni and Cr) were correlated with the cable bacteria diversity, indicating their essential role in biogeochemical cycles. The activation energy of cable bacteria was 0.624 eV, close to the canonical 0.65 eV. Furthermore, cable bacteria were identified as key connectors and module hubs, closely associated with denitrifiers, sulfate-reducing bacteria, methanogens and alkane degraders, highlighting their role as keystone functional lineages in the contaminated urban rivers. Our study provided the first large-scale and comprehensive insight into the cable bacteria diversity, spatial distribution, and their essential function as keystone species in organic-matter-polluted urban rivers.

Comprehensive profiles of sulfur cycling microbial communities along a mangrove sediment depth

The sulfur (S) cycle is an important biogeochemical cycle with profound implications for both cellular- and ecosystem-level processes by diverse microorganisms. Mangrove sediments are a hotspot of biogeochemical cycling, especially for the S cycle with high concentrations of S compounds. Previous studies have mainly focused on some specific inorganic S cycling processes without paying specific attention to the overall S-cycling communities and processes as well as organic S metabolism. In this study, we comprehensively analyzed the distribution, ecological network and assembly mechanisms of S cycling microbial communities and their changes with sediment depths using metagenome sequencing data. The results showed that the abundance of gene families involved in sulfur oxidation, assimilatory sulfate reduction, and dimethylsulfoniopropionate (DMSP) cleavage and demethylation decreased with sediment depths, while those involved in S reduction and dimethyl sulfide (DMS) transformation showed an opposite trend. Specifically, glpE, responsible for converting S2O32- to SO32-, showed the highest abundance in the surface sediment and decreased with sediment depths; in contrast, high abundances of dmsA, responsible for converting dimethyl sulfoxide (DMSO) to DMS, were identified and increased with sediment depths. We identified Pseudomonas and Streptomyces as the main S-cycling microorganisms, while Thermococcus could play an import role in microbial network connections in the S-cycling microbial community. Our statistical analysis showed that both taxonomical and functional compositions were generally shaped by stochastic processes, while the functional composition of organic S metabolism showed a transition from stochastic to deterministic processes. This study provides a novel perspective of diversity distribution of S-cycling functions and taxa as well as their potential assembly mechanisms, which has important implications for maintaining mangrove ecosystem functions.

Effect of incubation temperature on identification of key odorants of sewage sludge using headspace GC analysis

Currently, headspace gas chromatography-mass spectrometry is a widely used method to identify the key odorants of sludge. However, the effect of incubation temperature on the generation and emission of key odorants from sludge was still uncertain. Thus, in this paper, headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS) and headspace gas chromatography-coupled ion mobility spectrometry (HS-GC-IMS) were carried out to analyze the volatiles emitted from the sludge incubated at different temperatures (30 °C, 50 °C, 60 °C, and 80 °C). The results indicated that the total volatile concentration of the sludge increased with temperatures, which affected the identified proportion of sludge key odorants to a certain extent. Differently from the aqueous solutions, the variation of volatile emission from the sludge was inconsistent with temperature changes, suggesting a multifactorial influence of incubation temperature on the identification of sludge odorants. The microbial community structure and adenosine triphosphate (ATP) metabolic activity of the sludge samples were analyzed at the initial state, 30 °C, and 80 °C. Although no significant effect of incubation temperature on the microbial community structure of the sludge, the incubation at 80 °C led to a noticeable decrease in microbial ATP metabolic activity, accompanied by a significant change in the proportion of odor-related microorganisms with low relative abundances. Changes in the composition and activity of these communities jointly contributed to the differences in odor emission from sludge at different temperatures. In summary, the incubation temperature affects the production and emission of volatiles from sludge through physicochemical and biochemical mechanisms, by which the microbial metabolism playing a crucial role. Therefore, when analyzing the key odorants of sludge, these factors should be considered.

Integrating experiments with modeling to understand key bacterial taxa dynamics after episodic mixing of a stratified water column

Hydraulic mixing of stratified reservoirs homogenizes physicochemical gradients and microbial communities. This has potential repercussions for microbial metabolism and water quality, not least in dams and hydraulically controlled waters. A better understanding of how key taxa respond to mixing of such stratified water bodies is needed to understand and predict the impact of hydraulic operations on microbial communities and nutrient dynamics in reservoirs. We studied taxa transitions between cyanobacteria and sulfur-transforming bacteria following mixing of stratified water columns in bioreactors and complemented the experimental approach with a biogeochemical model. Model predictions were consistent with experimental observations, suggesting that stable stratification of DO is restored within 24 h after episodic and complete mixing, at least in the absence of other more continuous disturbances. Subsequently, the concentration of S2- gradually return to pre-mixing states, with higher concentration at the surface and lower in the bottom waters, while the opposite pattern was seen for SO42-. The total abundance of sulfate-reducing bacteria and phototrophic sulfur bacteria increased markedly after 24h of mixing. The model further predicted that the rapid re-oxygenation of the entire water column by aeration will effectively suppress the water stratification and the growth of sulfur-transforming bacteria. Based on these results, we suggest that a reduction of thermocline depth by optimal flow regulation in reservoirs may also depress sulfur transforming bacteria and thereby constrain sulfur transformation processes and pollutant accumulation. The simulation of microbial nutrient transformation processes in vertically stratified waters can provide new insights about effective environmental management measures for reservoirs.

Revealing microbial community assembly patterns and succession process in the blackening process of black-odor water

Human-imported pollutants could induce water black, changing microbial community structure and function. Employed 16S rRNA high-throughput sequencing, field-scale investigations and laboratory-scale experiments were successively conducted to reveal mechanistic insights into microbial community assembly and succession of black-odor waters (BOWs). In the field-scale investigation, livestock breeding wastewater (56.7 ± 3.2%) was the most critical microbial source. Moreover, fermentation (27.1 ± 4.4%) was found to be the dominant function. Combined with laboratory experiments, the critical environmental factors, such as total organic carbon (30-100 mg/L), ammonia nitrogen (2.5-9 mg/L), initial dissolved oxygen (2-8 mg/L) and chlorophyll a (0-90 mg/L), impacted the intensity of blackening. The differentiation of ecological niches within the microbial community played a significant role in driving the blackening speed. In laboratory-scale experiments, the microbial ecological niche determined the blackening timing and dominations of the stochastic processes in the microbial assembly process (88 - 51%). The three stages, including the anaerobic degradation stage, blackening stage and slow recovery stage, were proposed to understand the assembly of the microbial communities. These findings enhance our understanding of microorganisms in BOWs and provide valuable insights for detecting and managing heavily organic polluted waters.

Response of microbial communities to exogenous nitrate nitrogen input in black and odorous sediment

Since nitrate nitrogen (NO3--N) input has proved an effective approach for the treatment of black and odorous river waterbody, it was controversial whether the total nitrogen concentration standard should be raised when the effluent from the sewage treatment plant is discharged into the polluted river. To reveal the effect of exogenous nitrate (NO3--N) on black odorous waterbody, sediments with different features from contaminated rivers were collected, and the changes of physical and chemical characteristics and microbial community structure in sediments before and after the addition of exogenous NO3--N were investigated. The results showed that after the input of NO3--N, reducing substances such as acid volatile sulfide (AVS) in the sediment decreased by 80 % on average, ferrous (Fe2+) decreased by 50 %, yet the changing trend of ammonia nitrogen (NH4+-N) in some sediment samples increased while others decreased. High-throughput sequencing results showed that the abundance of Thiobacillus at most sites increased significantly, becoming the dominant genus in the sediment, and the abundance of functional genes in the metabolome increased, such as soxA, soxX, soxY, soxZ. Network analysis showed that sediment microorganisms evolved from a single sulfur oxidation ecological function to diverse ecological functions, such as nitrogen cycle nirB, nirD, nirK, nosZ, and aerobic decomposition. In summary, inputting an appropriate amount of exogenous NO3--N is beneficial for restoring and maintaining the oxidation states of river sediment ecosystems.

The ecological role of microbiome at community-, taxonomic - and genome-levels in black-odorous waters

Black-odorous waters (BOWs) are heavily polluted waters where microbial information remains elusive mechanistically. Based on gene amplicon and metagenomics sequencing, a comprehensive study was conducted to investigate the microbial communities in urban and rural BOWs. The results revealed that microbial communities' assembly in urban and rural BOWs was predominantly governed by stochastic factors at the community level. At the taxonomic level, there were 62 core species (58.48%) in water and 207 core species (44.56%) in sediment across urban and rural areas. Notably, significant differences were observed in the functional genetic composition of BOWs between urban and rural areas. Specifically, rural areas exhibited an enhanced abundance of genes involved in nitrogen fixation, Fe2+ transport, and sulfate reduction. Conversely, urban areas showed higher abundances of some genes associated with carbon fixation, nitrification and denitrification. A sulfur-centered ecological model of microbial communities was constructed by integrating data from the three levels of analysis, and 14 near-complete draft genomes were generated, representing a substantial portion of the microbial community (35.04% in rural BOWs and 29.97% in urban BOWs). This research provides significant insights into the sustainable management and preservation of aquatic ecosystems affected by BOWs.

Spatial gradients and molecular transformations of DOM, DON and DOS in human-impacted estuarine sediments

Dissolved organic matter (DOM) constitutes the most active fraction in global carbon pools, with estuarine sediments serving as significant repositories, where DOM is susceptible to dynamic transformations. Anthropogenic nitrogen (N) and sulfur (S) inputs further complicate DOM by creating N-bearing DOM (DON) and S-bearing DOM (DOS). This study delves into the spatial gradients and transformation mechanisms of DOM, DON, and DOS in Pearl River Estuary (PRE) sediments, China, using combined techniques of UV-visible spectroscopy, Excitation-emission matrix (EEM) fluorescence spectroscopy, Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), and microbial high-throughput sequencing. Results uncovered a distinct spatial gradient in DOM concentration, aromaticity (SUVA254), hydrophobicity (SUVA260), the content of substituent groups including carboxyl, carbonyl, hydroxyl and ester groups (A253/A203) of chromophoric DOM (CDOM), and the abundances of tyrosine/tryptophan-like protein and humic-like substances in fluorophoric DOM (FDOM). These all decreased from upper to lower PRE, accompanied by a decrease in O3S and O5S components, indicating seaward reduction in the contribution of terrestrial OM, especially anthropogenic inputs. Additionally, sediments exhibited a reduction in molecular diversity (number of formulas) of DOM, DON, and DOS from upper to lower PRE, with molecules tending towards a lower nominal oxidation state of carbon (NOSC) and higher bio-reactivity (MLBL), molecular weight (m/z) and saturation (H/C). While molecular composition of DOM remained similar in PRE sediments, the relative abundance of lignin-like substances decreased, with a concurrent increase in protein-like and lipid-like substances in DON and DOS from upper to lower PRE. Mechanistic analysis identified the joint influence of terrestrial OM, anthropogenic N/S inputs, and microbial processes in shaping the spatial gradients of DOM, DON, and DOS in PRE estuarine sediments. This study contributes valuable insights into the intricate spatial gradients and transformations of DOM, DON, and DOS within human-impacted estuarine sediments.

Seasonal changes driving shifts in microbial community assembly and species coexistence in an urban river

Microbial communities play a vital role in urban river biogeochemical cycles. However, the seasonal variations in microbial community characteristics, particularly phylogenetic group-based community assembly and species coexistence, have not been extensively investigated. Here, we systematically explored the microbiome characteristics and assembly mechanisms of urban rivers in different seasons using 16S rRNA gene sequencing and multivariate statistical methods. The results indicated that the microbial community presented significant temporal heterogeneity in different seasons, and the diversity decreased from spring to winter. The phylogenetic group-based microbial community assembly was governed by dispersal limitation and drift in spring, summer, and autumn but was structured by homogeneous selection in winter. Moreover, the main functions of nitrification, denitrification, and methanol oxidation were susceptible to dispersal limitation and drift processes, whereas sulfate respiration and aromatic compound degradation were controlled by dispersal limitation and homogeneous selection. Network analyses indicated that network complexity decreased and then increased with seasonal changes, while network stability showed the opposite trend, suggesting that higher complexity and diversity reduced community stability. Temperature was determined to be the primary driver of microbial community structure and assembly processes in different seasons based on canonical correspondence analysis and linear regression analysis. In conclusion, seasonal variation drives the dynamics of microbial community assembly and species coexistence patterns in urban rivers. This study provides new insights into the generation and maintenance of microbial community diversity in urban rivers under seasonal change conditions.

A review of the formation conditions and assessment methods of black and odorous water

Black and odorous water is an extreme pollution phenomenon. This article reviews the formation process, formation conditions, and evaluation methods of black and odorous water. The results indicate that N, P, and TOC are the key nutrients inducing black and odorous water while S, Fe, and Mn are key elements forming blackening and odorizing pollutants. In addition, Cyanobacteria, Proteobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, and Actinobacteria participate in the biogeochemistry cycles of key elements and play important roles in the blackening and odorizing process of water. The black and odorous thresholds that need further verification are as follows: 1.0 g/L of organic matrix, 2.0-8.0 mg/L of NH3-N, 0.6-1.2 mg/L of TP, 0.05 mg/L of Fe2+, 0.3 mg/L of Mn2+, 1.2-2.0 mg/L of DO, and -50 to 50 mV of the ORP. In order to propose a universal assessment method, it is suggested that NH3-N, DO, COD, BOD, and TP serve as the assessment indicators, and the levels of pollutions are I (not black odor), II (mild black odor), III (moderate black odor), IV (severe black odor), and inferior IV (extremely black odor).

Linking ecological niches to bacterial community structure and assembly in polluted urban aquatic ecosystems

Introduction

Bacterial communities play crucial roles in the functioning and resilience of aquatic ecosystems, and their responses to water pollution may be assessed from ecological niches. However, our understanding of such response patterns and the underlying ecological mechanisms remains limited.

Methods

In this study, we comprehensively investigated the effects of water pollution on the bacterial structure and assembly within different ecological niches, including water, sediment, submerged plant leaf surfaces, and leaf surfaces, using a 16S high-throughput sequencing approach.

Results

Ecological niches had a greater impact on bacterial community diversity than pollution, with a distinct enrichment of unique dominant phyla in different niches. This disparity in diversity extends to the bacterial responses to water pollution, with a general reduction in α-diversity observed in the niches, excluding leaf surfaces. Additionally, the distinct changes in bacterial composition in response to pollution should be correlated with their predicted functions, given the enrichment of functions related to biogeochemical cycling in plant surface niches. Moreover, our study revealed diverse interaction patterns among bacterial communities in different niches, characterized by relatively simply associations in sediments and intricate or interconnected networks in water and plant surfaces. Furthermore, stochastic processes dominated bacterial community assembly in the water column, whereas selective screening of roots and pollution events increased the impact of deterministic processes.

Discussion

Overall, our study emphasizes the importance of ecological niches in shaping bacterial responses to water pollution. These findings improve our understanding of the complicated microbial response patterns to water pollution and have ecological implications for aquatic ecosystem health.

Assessing the impacts of fine sediment removal on endogenous pollution release and microbial community structure in the shallow lakes

Resuspension is a crucial process for releasing endogenous pollution from shallow lakes into the overlying water. Fine particle sediment, which has a higher contamination risk and longer residence time, is the primary target for controlling endogenous pollution. To this end, a study coupling aqueous biogeochemistry, electrochemistry, and DNA sequencing was conducted to investigate the remediation effect and microbial mechanism of sediment elution in shallow eutrophic water. The results indicated that sediment elution can effectively remove some fine particles in situ. Furthermore, sediment elution can inhibit the release of ammonium nitrogen and total dissolved phosphorous into the overlying water from sediment resuspension in the early stage, resulting in reductions of 41.44 %-50.45 % and 67.81 %-72.41 %, respectively. Additionally, sediment elution greatly decreased the concentration of nitrogen and phosphorus pollutants in pore water. The microbial community structure was also substantially altered, with an increase in the relative abundance of aerobic and facultative aerobic microorganisms. Redundancy analysis, PICRUSt function prediction, and the correlation analysis revealed that loss on ignition was the primary factor responsible for driving changes in microbial community structure and function in sediment. Overall, the findings provide novel insights into treating endogenous pollution in shallow eutrophication water.

Mechanistic insights into dissolved organic matter-driven protistan and bacterial community dynamics influenced by vegetation restoration

Vegetation restoration projects can not only improve water quality by absorbing and transferring pollutants and nutrients from non-vegetation sources, but also protect biodiversity by providing habitat for biological growth. However, the mechanism of the protistan and bacterial assembly processes in the vegetation restoration project were rarely explored. To address this, based on 18 S rRNA and 16 S rRNA high-throughput sequencing, we investigated the mechanism of protistan and bacterial community assembly processes, environmental conditions, and microbial interactions in the rivers with (out) vegetation restoration. The results indicated that the deterministic process dominated the protistan and bacterial community assembly (94.29% and 92.38%), influenced by biotic and abiotic factors. For biotic factors, microbial network connectivity was higher in the vegetation zone (average degree = 20.34) than in the bare zone (average degree = 11.00). For abiotic factors, the concentration of dissolved organic carbon ([DOC]) was the most important environmental factor affecting the microbial community composition. [DOC] was lower significantly in vegetation zone (18.65 ± 6.34 mg/L) than in the bare zone (28.22 ± 4.82 mg/L). In overlying water, vegetation restoration upregulated the protein-like fluorescence components (C1 and C2) by 1.26 and 1.01-folds and downregulated the terrestrial humic-like fluorescence components (C3 and C4) by 0.54 and 0.55-folds, respectively. The different DOM components guided bacteria and protists to select different interactive relationships. The protein-like DOM components led to bacterial competition, whereas the humus-like DOM components resulted in protistan competition. Finally, the structural equation model was established to explain that DOM components can affect protistan and bacterial diversity by providing substrates, facilitating microbial interactions, and promoting nutrient input. In general, our study provides insights into the responses of vegetation restored ecosystems to the dynamics and interactives in the anthropogenically influenced river and evaluates the ecological restoration performance of vegetation restoration from a molecular biology perspective.

The investigation of the physiochemical factors and bacterial communities indicates a low-toxic infectious risk of the Qiujiang River in Shanghai, China

The overall water quality of urban rivers is closely related to the community structure and the physiochemical factors in them. In this study, the bacterial communities and physiochemical factors of the Qiujiang River, an important urban river in Shanghai, were explored. Water samples were collected from nine sites of the Qiujiang River on November 16, 2020. The water quality and bacterial diversity were studied through physicochemical detection, microbial culture and identification, luminescence bacteria method, and 16S rRNA Illumina MiSeq high-throughput sequencing technology. The water pollution of the Qiujiang River was quite serious with three water quality evaluation indexes, including Cd²⁺, Pb²⁺, and NH₄⁺-N, exceeding the Class V standard set by the Environmental Quality Standards for Surface Water (China, GB3838-2002), while the luminescent bacteria test indicated low toxicity of nine sampling sites. Through 16S rRNA sequencing, a total of 45 phyla, 124 classes, and 963 genera were identified, in which Proteobacteria, Gammaproteobacteria, and Limnohabitans were the most abundant phylum, class, and genus, respectively. The Spearman correlation heatmap and redundancy analysis showed that the bacterial communities in the Qiujiang River were correlated with pH; the concentrations of K⁺, and NH₄⁺-N, and the Limnohabitans were significantly correlated with the concentrations of K⁺, and NH₄⁺-N in the Zhongyuan Road bridge segment. In addition, opportunistic pathogens Enterobacter cloacae complex and Klebsiella pneumoniae in the samples collected in the Zhongyuan Road bridge segment and Huangpu River segment, respectively, were successfully cultured. The Qiujiang River was a heavily polluted urban river. The bacterial community structure and diversity were greatly affected by the physiochemical factors of the Qiujiang River, and it displayed low toxicity while a relatively high infectious risk of intestinal and lung infectious diseases.

Analysis of bacterial community distribution characteristics in the downstream section of a cross confluence in a polluted urban channel

Channel confluences are common in urban rivers and caused complex hydrodynamic conditions in the downstream section, significantly influencing the distribution of pollutants and the microbial community. So far, the principles of bacterial community assembly and their linkages with environmental factors are poorly understood. In the present study, the hydrodynamic and pollution conditions were investigated in a typical channel confluence of an urban river in the Yangtze River delta area, China, and their impacts on the bacterial community structure in the water and sediment were characterized using 16S rRNA gene high-throughput sequencing technology. Based on the results, the flow velocity was the crucial factor influencing the dispersal of nutrients, organic compounds, and bacterial communities in the river water. Moreover, the sediments exhibited higher α-diversity and bacterial richness for nitrogen and sulfur cycling than the water. In addition to flow velocity, the contents of total organic carbon, total phosphorus, and heavy metals determined the sediment bacterial communities at varying depths. The predictive analysis of functional gene category indicated differences between the water and sediment communities in metabolic potentials and pathogen risk and provided guidance for water pollution control and the eco-remediation of urban rivers.

Determinants and Assembly Mechanism of Bacterial Community Structure in Ningxia Section of the Yellow River

The Yellow River is a valuable resource in the Ningxia Hui Autonomous Region and plays a vital role in local human activities and biodiversity. Bacteria are a crucial component of river ecosystems, but the driving factors and assembly mechanisms of bacterial community structure in this region remain unclear. Herein, we documented the bacterial community composition, determinants, co-occurrence pattern, and assembly mechanism for surface water and sediment. In comparison to sediment, the bacterioplankton community showed significant seasonal variation, as well as less diversity and abundance. The network topology parameters indicated that the sediment bacterial network was more stable than water, but the bacterioplankton network had higher connectivity. In this lotic ecosystem, COD_Mn, Chl a, and pH affected the structure of the bacterioplankton community, while TP was the primary factor influencing the structure of the sediment bacterial community. The combined results of the neutral community model and the phylogenetic null model indicate that Bacterial communities in both habitats were mainly affected by stochastic processes, with ecological processes dominated by ecological drift for bacterioplankton and dispersal limitation for sediment bacteria. These results provide essential insights into future research on microbial ecology, environmental monitoring, and classified management in the Ningxia section of the Yellow River.

Differences in Carbon and Nitrogen Migration and Transformation Driven by Cyanobacteria and Macrophyte Activities in Taihu Lake

The metabolic activities of primary producers play an important role in the migration and transformation of carbon (C) and nitrogen (N) in aquatic environments. This study selected two typical areas in Taihu Lake, a cyanobacteria-dominant area (Meiliang Bay) and a macrophyte-dominant area (in the east area of the lake), to study the effects of cyanobacteria and macrophyte activities on C and N migration and transformation in aquatic environments. The results showed that total N and total particulate N concentrations in the water of the cyanobacteria-dominant area were much higher than those in the macrophyte-dominant area, which was mainly due to the assimilated intracellular N in cyanobacteria. Macrophyte activity drove a significantly higher release of dissolved organic C (DOC) in the water than that driven by cyanobacteria activity, and the DOC contents in the water of the macrophyte-dominant area were 2.4~4.6 times the DOC contents in the cyanobacteria-dominant area. In terms of the sediments, organic matter (OM), sediment total N and N species had positive correlations and their contents were higher in the macrophyte-dominant area than in the cyanobacteria-dominant area. Sediment OM contents in the macrophyte-dominant area increased from 4.19% to 9.33% as the sediment deepened (0~10 cm), while the opposite trend was presented in the sediments of the cyanobacteria-dominant area. Sediment OM in the macrophyte-dominant area may contain a relatively high proportion of recalcitrant OC species, while sediment OM in the cyanobacteria-dominant area may contain a relatively high proportion of labile OC species. Compared with the macrophyte-dominant area, there was a relatively high richness and diversity observed in the bacterial community in the sediments in the cyanobacteria-dominant area, which may be related to the high proportion of labile OC in the OM composition in its sediments. The relative abundances of most OC-decomposing bacteria, denitrifying bacteria, Nitrosomonas and Nitrospira were higher in the sediments of the cyanobacteria-dominant area than in the macrophyte-dominant area. These bacteria in the sediments of the cyanobacteria-dominant area potentially accelerated the migration and transformation of C and N, which may supply nutrients to overlying water for the demands of cyanobacteria growth. This study enhances the understanding of the migration and transformation of C and N and the potential effects of bacterial community structures under the different primary producer habitats.

Effects of Different Types of Human Disturbance on Total and Nitrogen-Transforming Bacteria in Haihe River

Haihe River is the largest water system in North China and is injected into the Bohai Sea in Tianjin City. In this study, different types of human disturbance (urban sewage, industrial pollution, ship disturbance) were selected from the upper reaches of Haihe river Tianjin section down to the estuary that connected with Bohai Sea for evaluation. By metagenomic sequencing, the effects of different types of disturbances on bacteria communities in Haihe sediments were studied, with a special focus on the function of nitrogen-cycling bacteria that were further analyzed through KEGG comparison. By analyzing the physical and chemical characteristics of sediments, results showed that human disturbance caused a large amount of nitrogen input into Haihe River, and different types of human disturbance led to distinct spatial heterogeneity in different sections of Haihe River. The bacteria community was dominated by Proteobacteria, followed by Chloroflexi, Bacteroidetes, Actinobacteria and Acidobacteria. The relative abundance of each phylum varied at different sites as a response to different types of human disturbances. In nitrogen cycling, microorganisms including nitrogen fixation and removal were detected at each site, which indicated the active potential for nitrogen transformation in Haihe River. In addition, a large number of metabolic pathways relating to human diseases were also revealed in urban and pollution sites by function potential, which provided an important basis for the indicative role of urban river ecosystem for public health security. In summary, by evaluating both the ecological role and function potential of bacteria in Haihe River under different types of human disturbance, the knowledge of microorganisms for healthy and disturbed river ecosystems has been broadened, which is also informative for further river management and bioremediation.

Management of biogenic taste and odour: From source water, through treatment processes and distribution systems, to consumers

Biogenic taste and odour (T&O) have become a global concern for water utilities, due to the increasing frequency of algal blooms and other microbial events arising from the combined effects of climate change and eutrophication. Microbially-produced T&O compounds impact source waters, drinking water treatment plants, and drinking water distribution systems. It is important to manage across the entire biogenic T&O pathway to identify key risk factors and devise strategies that will safeguard the quality of drinking water in a changing world, since the presence of T&O impacts consumer confidence in drinking water safety. This study provides a critical review of current knowledge on T&O-causing microbes and compounds for proactive management, including the identification of abiotic risk factors in source waters, a discussion on the effectiveness of existing T&O barriers in drinking water treatment plants, an analysis of risk factors for biofilm growth in water distribution systems, and an assessment of the impacts of T&O on consumers. The fate of biogenic T&O in drinking water systems is tracked from microbial production pathways, through the release of intracellular T&O by cell lysis, to the treatment of microbial cells and dissolved T&O. Based on current knowledge, five impactful research and management directions across the T&O pathway are recommended.

Partial nitrification in free nitrous acid-treated sediment planting Myriophyllum aquaticum constructed wetland strengthens the treatment of black-odor water

Black-odor water pollution in rural areas, especially swine wastewater, can lead to the deterioration of water quality and thus seriously affect the daily life of people in the area. However, there is a lack of effective treatment measures with simultaneous attention to carbon, nitrogen and sulfur pollution in rural black-odor water bodies. This study evaluated the feasibility of an in-situ pilot-scale constructed wetland (CW) for the synchronous removal of COD, ammonium, and sulfur compounds in the swine wastewater. In this study, the operation strategy of CW sediment pretreated with free nitrous acid (FNA) and Myriophyllum aquaticum plantation was established. Throughout the 114-day operation, the total removal efficiencies of COD and ammonium nitrogen in experimental groups were 81.2 ± 4.2 % and 72.8 ± 1.8 %, respectively, which were significantly higher than CW without any treatment. Removal efficiencies of Sulfur compounds, i.e. sulfide, sulfate, thiosulfate, and sulfite, were 92.3 ± 1.9 % (61.2 % higher than the no-treatment group), 42.1 ± 3.8 %, 97.9 ± 1.7 %, and 42.7 ± 4.5 % respectively. High-throughput sequencing and qPCR revealed that experimental group significantly increased denitrification genes (nirK, nosZ) and sulfur oxidation genes (soxB, fccAB) and enriched the corresponding microbial taxa (Bacillus, Conexibacter and Clostridium sensu stricto). Moreover, metabolic pathways related to nitrogen and sulfur and the degradation of organic matter were up-regulated. These results indicated that partial nitrification in CW planted with M. aquaticum promoted sulfur oxidation denitrification and heterotrophic denitrification. Overall, the in-situ pilot-scale study revealed that the cultivation of M. aquaticum in FNA-treated CW can be a sustainable approach to treat black-odor water bodies.

The degradation of dissolved organic matter in black and odorous water by humic substance-mediated Fe(II)/Fe(III) cycle under redox fluctuation

In nature, the hydroxyl radical (•OH) is produced during the anaerobic-aerobic transition when groundwater level fluctuates. In addition, the •OH is also detected in iron-bearing clay minerals and iron oxides during the redox process. Goethite is one of the most stable iron oxides involved in biogeochemical cycles. In this study, the coexisting humic acid (HA) enhanced the generation of Fe(II) during the iron reduction process and accelerated the generation of •OH in the redox process of goethite. The organic contaminants in black and odorous water were decomposed by constructing an iron-reducing bacteria-HA-Fe(II)/Fe(III) reaction system under anaerobic-aerobic alternation. The results demonstrated that in the anaerobic stage, HA could promote the reduction and dissolution of goethite through the complexation effect and electron shuttle mechanism, as well as significantly strengthening the iron reduction process in water. Under aerobic conditions, Fe(II) in the reaction system would activate O₂ to generate •O₂^-. The •OH, formed by Fe (II) and •O₂^- via Fenton reaction and Haber-Weiss mechanism, oxidized dissolved organic matter (DOM) in water. The characterization of DOM by three-dimensional fluorescence spectroscopy (3DEEM) indicated that after four redox fluctuations, the organic contaminants in water samples were effectively degraded. Generally, this study provides new approaches and insights into the biogeochemical cycling of Fe and C elements and water pollution remediation at the anoxic-anoxic interface.

Distinct Composition and Assembly Processes of Bacterial Communities in a River from the Arid Area: Ecotypes or Habitat Types?

The composition, function, and assembly mechanism of the bacterial community are the focus of microbial ecology. Unsupervised machine learning may be a better way to understand the characteristics of bacterial metacommunities compared to the empirical habitat types. In this study, the composition, potential function, and assembly mechanism of the bacterial community in the arid river were analysed. The Dirichlet multinomial mixture method recognised four ecotypes across the three habitats (biofilm, water, and sediment). The bacterial communities in water are more sensitive to human activities. Bacterial diversity and richness in water decreased as the intensity of human activities increased from the region of water II to water I. Significant differences in the composition and potential function profile of bacterial communities between water ecotypes were also observed, such as higher relative abundance in the taxonomic composition of Firmicutes and potential function of plastic degradation in water I than those in water II. Habitat filtering may play a more critical role in the assembly of bacterial communities in the river biofilm, while stochastic processes dominate the assembly process of bacterial communities in water and sediment. In water I, salinity and mean annual precipitation were the main drivers shaping the biogeography of taxonomic structure, while mean annual temperature, total organic carbon, and ammonium nitrogen were the main environmental factors influencing the taxonomic structure in water II. These results would provide conceptual frameworks about choosing habitat types or ecotypes for the research of microbial communities among different niches in the aquatic environment.

Interactions between suspended sediments and submerged macrophytes-epiphytic biofilms under water flow in shallow lakes

Suspended sediments (SS) pollution is one of the factors affecting the transfer from turbid water state to clear water state in shallow lakes. However, the interactions between suspended sediments and submerged plants are far from clear. In this study, we investigated the settlement laws of SS in overlying water and its impact on the epiphytic biofilm of Myriophyllum verticillatum and Vallisneria natans under water flow. At least 90% of turbidity can be removed from overlying water, and the decreasing trend of water turbidity fitted the logarithmic decay model in all treatments. The size distribution of SS fit the log-normal distribution model in the first 240 min after SS addition. It should be noted that the main peak particle sizes were lower in treatments with submerged macrophytes (8.71-13.18 μm) than without plants (15.14-19.95 μm). Water flow and SS addition significantly increased the thickness of biofilms attached to M. verticillatum (p < 0.05), but they together significantly reduced the biofilm thickness on V. natans (p < 0.05). SS increased the bacterial α-diversity but decreased eukaryotic one in epiphytic biofilms. However, water flow had a more significant impact on microbial communities (especially eukaryotes) than SS and plant species. The relative abundances of dominant phylum Proteobacteria, class Alphaproteobacteria and Betaproteobacteria, and class Verrucomicrobiae increased in epiphytic biofilms after SS addition. Co-occurrence networks reveal that photosynthetic microbes in epiphytic biofilms played an important role in microbial communities under water flow and SS, and many hub microbes were increased by SS addition but reduced by water flow. These data highlight that SS decline can be predicted by the logarithmic decay model and, SS and water flow can affect the epiphytic-biofilm on submerged macrophytes.

Per-, poly-fluoroalkyl substances (PFASs) and planktonic microbiomes: Identification of biotic and abiotic regulations in community coalescence and food webs

The importance of per-, poly-fluoroalkyl substances (PFASs) effects on riverine microbiomes is receiving increased recognition in the environmental sciences. However, few studies have explored how PFASs affect microbiomes across trophic levels, specifically through predator-prey interactions. This study examined the community profiles of planktonic archaea, bacteria, fungi, algae, protozoa, and metazoa in a semi-industrial and agricultural river alongside their interactions with 15 detected PFASs. As abiotic factors, PFASs affected community coalescence more than biogenic substances (p < 0.05). For biotic regulations, sub-communities in rare biospheres (including always rare taxa-ART and critically rare taxa-CRT) contributed to spatial community coalescence more than sub-communities in abundant biospheres (always abundant taxa-AAT and critically abundant taxa-CAT) (p < 0.05). Metazoa-bacteria (Modularity = 1.971) and protozoa-fungi (1.723) were determined to be the most stable predator-prey networks. Based on pathway models, short-chain PFBA (C4) was shown to weaken the trophic transfer efficiencies from heterotrophic bacteria (HB) to heterotrophic flagellates (HF) (p < 0.05). Long-chain PFTeDA (C14) promoted HB to amoeba (p < 0.05), which we postulate is the pathway for PFTeDA to enter the microbial food chain. Our preliminary results elucidated the influence of PFASs on planktonic microbial food webs and highlighted the need to consider protecting and remediating riverine ecosystems containing PFASs.

Biodeposition of oysters in an urbanized bay area alleviates the black-malodorous compounds in sediments by altering microbial sulfur and iron metabolism

The occurrence of the 'black-malodorous phenomenon' in a waterbody is a clear sign of a highly eutrophic bay, the formation of which is associated with microbial sulfur and iron metabolism in the sediments. Oyster farming restoration has been widely studied as an important method for treating eutrophication and related ecological problems. However, few studies focus on the ecosystem-level consequences of oyster farming concerning microbial sulfur and iron cycles in the sediment. Here, we compared the physicochemical features and microbial functions of oyster farms with those of reference areas using the Geochip5.0 technique. Our results showed a significant reduction of acid volatile sulfide (AVS) content associated with oyster farming, thus alleviating the black-malodorous status of Shenzhen Bay in China. Oyster farming created loose and porous sedimentary structures and stimulated the oxidation of black-odorous compounds. Moreover, we observed that the introduction of oysters changed microbial biodiversity significantly based on gyrB gene structure, with typical sulfur- and iron-cycling microbes being enriched. We also demonstrated that microbial abilities involved in sulfur and iron metabolism were greatly increased in oyster farming areas compared with reference areas. Under such circumstances, some cascading processes (AVS uptake and rates of organic matter turnover) were improved, which eventually contributed to black odor reduction. From the microecological perspective, we conclude that the biodeposition of oysters was the key factor for water retention and improvement of microbial metabolism. This study suggests that biodeposition shapes the microbial functional communities in adjacent territories and presumably alleviates the black-malodorous compounds in sediments.

Insight into variations of DOM fractions in different latitudinal rural black-odor waterbodies of eastern China using fluorescence spectroscopy coupled with structure equation model

The structural compositions of dissolved organic matter (DOM) could profoundly affect formation and evolution of black-odor waterbodies (BOWs). In this study, 81 samples of BOWs were collected from three different latitudinal rural regions in eastern China, including low, middle and high latitude regions. Based on fluorescence index (FI) and biological index (BIX) deduced from excitation-emission matrices (EEMs) of rural BOWs, biological source of DOM was dominant in low latitude, while DOM derived from both biological and terrestrial in mid-latitude and high-latitude. Furthermore, humification degree of DOM in the former was lower than those in the latter based on humification index (HIX) deduced from EEMs. Seven fluorescence components of DOM were extracted by EEMs combined with parallel factor analysis: components 1 and 2 (C1 and C2) known as tryptophan-like substances, C3 and C4 associated with tyrosine-like, C5 related with biological byproducts, C6 relative to fulvic-like, and C7 referred as humic-like. The roughly decreasing order of percentages in DOM fractions from the rural BOWs was tyrosine-like > tryptophan-like > fulvic-like > microbial byproduct > humic-like in three regions. According to hierarchical cluster analysis and redundancy analysis, the autochthonous fresh DOM was dominant in low latitudinal rural BOWs, which was relative to actions of phytoplankton and microorganisms. However, humification degree of DOM increased with a rise in latitude, which could attribute to variations of climate and agriculture industrial structure. Based on structure equation model, the C5 and FI were the potential factors of the rural BOWs, which suggested that microbial activity and pollution sources should affect formation and evolution of rural BOWs. These findings are conductive to reveal composition and fluorescence properties of DOM and in recognizing the potential factors of forming mechanism in rural BOWs, which could provide basic theoretical support for policymakers to regulate and treat it.

A unique microbiome in a highly polluted and alkalic lake in a seasonally frozen area

Highly polluted waters profoundly promoted microbial activities and vice versa. Although microbial community structures and bioprocesses in polluted environments have been fully investigated, they are rarely uncovered in abandoned and highly polluted aquatic environment, especially in a seasonally frozen area. East Lake had been polluted by surrounding paper mills and dairy plants from the 1960s to the early 2000s. Under low biodegradability (BOD₅/COD ratio<0.2) and alkalic (pH > 9) conditions, a unique microbiome was discovered in East lake. Proteobacteria was the largest taxonomic group in the microbial community, covering almost half of the top-100 genera. Among them, seven genera are sulfate-reducing bacteria, including Desulfuromusa, Desulfuromonas, Desulfobulbus, Desulfocapsa, Desulfurivibrio, Desulfatiglans, and Desulfomicrobium. Functional analysis revealed abundant predicted functional genes for the respiration of sulfur compounds and sulfate respiration. Great vertical variations were found to both microbial community structures and predicted functions. This work provides unique evidence for future microbiome studies of nutrient-rich, alkalic, and seasonally frozen water habitats.

Evolution of urban black and odorous water: The characteristics of microbial community and driving-factors

Urban black blooms that are primarily caused by organic carbon are deleterious environmental problems. However, detailed studies on the microbial characteristics that form urban black blooms are lacking. In this study, we observed the composition, diversity, and function of bacterial community in the overlying water and sediments during the occurrence and remediation of urban black blooms using high-throughput 16S rRNA gene amplicon sequencing analysis. First, we found that pivotal consortia in the overlying water increased significantly during the formation of black blooms, including the genera Acidovorax, Brevundimonas, Pusillimonas, and Burkholderiales involved in the degradation of refractory organics, as well as the genera Desulfovibrio, Dechloromonas, and Rhizobium related to the production of black and odorous substances. An RDA analysis revealed that chemical oxygen demand, dissolved oxygen, and oxidation reduction potential were related to the changes in microbial community composition. Furthermore, aeration was found to accelerate the removal of ammonia nitrogen and enhance the function of microbial community by stimulating the growth of order Planktomycetes during the remediation of black blooms, but aeration substantially damaged the microbial diversity and richness. Therefore, the health of the aquatic ecosystem should be comprehensively considered when aeration is applied to restore polluted waterbodies. Notably, we observed a large number of pathogenic bacteria in urban black blooms, which emphasizes the importance of treating domestic sewage so that it is harmless. Together, these findings provide new insights and a basis to prevent and manage urban black blooms.

DNA metabarcoding reveals the significant influence of anthropogenic effects on microeukaryotic communities in urban waterbodies

Biological monitoring and assessment are the first and most fundamental steps towards diagnosing ecological or environmental quality. Increasing anthropogenic impact on urban ecosystems has prompted the development of less expensive and more efficient bioassessment approaches. Generally, a morphospecies based approach is effective for plants and large organisms but challenging for the microbial biosphere. To overcome this challenge, we used high-throughput DNA sequencing for predicting anthropogenic effects on microeukaryotic communities in urban waterbodies along a pollution gradient in Wuhan City, central China in summer 2019. Our results indicated that microeukaryotic community structure was distinct between non-urban polluted reservoir and urban polluted waterbodies. The heterogeneity of environmental condition significantly affected the microeukaryotic diversity, community structure, and species interactions. Integrated co-occurring network analysis revealed that the pollution gradient has a significant adverse impact on network complexity and network dissimilarity. These results revealed that the significant variation in anthropogenically-driven environmental condition shaped microeukaryotic communities in urban freshwater ecosystems. Furthermore, we observed that the relative abundance of indicative OTUs were significantly and negatively correlated with pollution level and these indicative OTUs could be used to predict the water quality status with up to 77% success. Thus, our multiple approaches combining 18S rDNA amplicon sequencing, co-occurring network and indicator species analyses suggest that this study gives a novel approach based on microeukaryotic communities to assess and predict the water quality status of urban aquatic environments.

Distinct profile of bacterial community and antibiotic resistance genes on microplastics in Ganjiang River at the watershed level

Microplastics are of great public concern due to their wide distribution and the potential risk to humans and animals. In this study, the microplastic pollution associated with bacterial communities, human pathogenic bacteria, and antibiotic resistance genes (ARGs) were investigated compared to water, sediment, and natural wood particles. Microplastics were widely distributed in surface water of the Ganjiang River at a watershed level with an average value of 407 particles m^-3. The fragment was the main microplastic shape found in the basin. Microplastics had significantly higher observed species and Chao1 index of bacterial communities than those in water, but comparable to wood particles. However, there was no difference in the microplastics pollution and alpha diversity indices of bacterial between different reaches along the Ganjiang River. Flavobacterium, Rhodoferax, Pseudomonas, and Janthinobacterium on the microplastics were all found to be enriched compared with water and sediment. Principal component analysis of the composition and function profile of bacterial communities showed that microplastics provide a new microbial niche in the Ganjiang River, which was distinct from water, sediment, and natural wood. Pseudomonas genus dominated the composition of human pathogenic bacteria on the microplastics, which was significantly different from water and sediment. No difference was observed in the relative abundance of total ARGs among the four media. However, microplastic and wood particles showed similar composition patterns of ARGs compared with water and sediment.

Persistent contamination of polycyclic aromatic hydrocarbons (PAHs) and phthalates linked to the shift of microbial function in urban river sediments

Urban rivers were heavily polluted, which resulted in blackening and odorization (i.e., black-odor rivers). Nevertheless, very limited information is available on sediment contamination levels of black-odor rivers and their linkage to the patterns of microbial functional genes. This study investigated distribution of polycyclic aromatic hydrocarbons (PAHs) and phthalates (PAEs) and their linkages to bacterial community and related functional genes in river sediments. The results demonstrate that higher average levels of ∑16PAHs (1405 μg/kg, dry weight) and ∑6PAEs (7120 μg/kg) were observed in sediments from heavy black-odor rivers than the moderate ones (∑16PAHs: 462 μg/kg; ∑6PAEs: 2470 μg/kg). The taxon composition and diversities of bacterial community in sediments varied with significantly lower diversity indices in heavy black-odor rivers than moderate ones. Sediments from heavy black-odor rivers enriched certain PAH and PAE degrading bacteria and genes. Unfortunately, PAH and PAE contamination demonstrated negative influences on nitrogen and phosphorus metabolism related bacteria and function genes but significant positive influences on certain sulfur metabolism related bacterial taxa and sulfur reduction gene, which might cause nitrogen and phosphorus accumulation and black-odor phenomenon in heavy black-odor rivers. This study highlights PAH and PAE contamination in urban rivers may shift bacterial community and detrimentally affect their ecological functions.

Microbial sulfur metabolism and environmental implications

Sulfur as a macroelement plays an important role in biochemistry in both natural environments and engineering biosystems, which can be further linked to other important element cycles, e.g. carbon, nitrogen and iron. Consequently, the sulfur cycling primarily mediated by sulfur compounds oxidizing microorganisms and sulfur compounds reducing microorganisms has enormous environmental implications, particularly in wastewater treatment and pollution bioremediation. In this review, to connect the knowledge in microbial sulfur metabolism to environmental applications, we first comprehensively review recent advances in understanding microbial sulfur metabolisms at molecular-, cellular- and ecosystem-levels, together with their energetics. We then discuss the environmental implications to fight against soil and water pollution, with four foci: (1) acid mine drainage, (2) water blackening and odorization in urban rivers, (3) SANI® and DS-EBPR processes for sewage treatment, and (4) bioremediation of persistent organic pollutants. In addition, major challenges and further developments toward elucidation of microbial sulfur metabolisms and their environmental applications are identified and discussed.

Water flow and temperature drove epiphytic microbial community shift: Insight into nutrient removal in constructed wetlands from microbial assemblage and co-occurrence patterns

The impacts of water flow and low temperature on nutrient removal and underlying ecological mechanism of epiphytic microbial community in constructed wetlands remain to be fully illustrated. In this study, low temperature inhibited the decrease of TN, NH₄⁺-N, TP, and COD concentrations in water, but water flow decreased NH₄⁺-N and COD concentrations strikingly. The relative conductivity, soluble sugar, and protein of M. spicatum increased, while the total chlorophyll contents decreased significantly under the stress of water flow and low temperature. Temperature affected the alpha-diversity and composition of the microbial community, while water flow caused differences in community distribution. Deterministic processes dominated in microbial community assembly with increasing environmental stress. Co-occurrence network analysis demonstrated that Chlorophyta, Verrucomicrobia, Proteobacteria, Bacteroidetes, and Firmicutes phyla were the dominant hubs in September, however, low temperatures caused a shift to Metazoan dominated network, demonstrating diminished nutrient removal capacity.

Degradation of Nitrogen, Phosphorus, and Organic Matter in Urban River Sediments by Adding Microorganisms

Reducing and remediating endogenous sediment pollution in urban rivers using appropriate microbiological remediation technology is regarded as a safe, effective, and environmentally sustainable mechanism. In this study, the pollutant removal efficiency of three microorganism types at different dosages was studied in the laboratory. To optimize the microbial restoration scheme, a comprehensive analysis of their effectiveness in removing total nitrogen (TN), total phosphorus (TP), total organic matter (OM), and polycyclic aromatic hydrocarbons (PAHs) was conducted, and associated structural changes in the sediment bacteria were analyzed. The results showed that using nitrifying bacteria and Bacillus as microbial agents resulted in superior removal efficiencies of TN and TP in sediments, whereas yeast was not as effective. The removal rates of TN reached 27.65% and 20.88% when 5 mg nitrifying bacteria and 10 mg Bacillus respectively, were used. A comparative analysis showed that nitrifying bacteria exhibited a better TN removal effect; however, Bacillus exhibited a better TP removal effect. The results of high-throughput sequencing revealed no significant changes to the microbial community structures when optimal microorganisms or beneficial microorganisms that thrive using OM as a source of C and energy were added. This study provides insights into the processes and mechanisms involved in the microorganism degradation of black and odorous sediment, and the results can be used as a basis for developing endogenous pollution control policies and methods for urban rivers.

Combined impact of organic matter, phosphorus, nitrate, and ammonia nitrogen on the process of blackwater

Blackwater events are frequently reported over the world and become a serious environmental problem. However, the mechanisms of blackwater occurrence are not fully understood yet. This study simulated the process of blackwater with the combined pollution in an orthogonal experiment, which had 4 factors (TOC, TP, NH4+-N, and NO3--N) and 4 levels (None, Low, Middle, and High). Results showed that the process of water condition changes was divided into two parts, which were "exogenous" and "algae-derived" blackwater, and the influence of four different pollutants on the occurrence of the blackwater was ranked as follows: TOC > TP > NO3--N > NH4+-N. With the increase of organic matter addition, the anaerobic condition in water was prolonged and the concentration of Fe2+ had a significant increase. In addition, under the None phosphorus condition, the descent rates of DO and COD in the water were reduced, and the algae bloom was obviously deferred. Moreover, the addition of organic matter or phosphorus changed the microbial community structure and led to different water processes. Particularly, only on the condition of the high content of TOC and phosphorus, the diversity of sulfate-reducing bacteria (e.g., Pseudomonas, Paludibacter, and Bacteroides) increased significantly, which accounted for 51.4%, causing the significant production of S2- in the water. Water's lack of phosphorus showed a low rate of decomposition of organic matter, which might be the result of a considerable increase in the abundance of aerobic Trichococcus and Malikia. This study shows that organic matter and phosphorus have synergistic effect on blackwater occurrence. In the treatment of blackwater, the exogenous pollutant control should reduce the discharge of organic pollutants, and endogenous control should focus on phosphorus abatement and reduce nitrogen control.

Effects of Escherichia coli pollution on decomposition of aquatic plants: Variation due to microbial community composition and the release and cycling of nutrients

Determination of the effects of Escherichia coli (E. coli) pollution on agricultural pond ecosystems with vegetation at different life stages is essential for the protection of ecological functions. However, no comprehensive study has yet shown the responses of epiphytic microbial communities to E. coli invasion during plant decay. Thus, this study was conducted to clarify variation in the decay of the following aquatic plants-Myriophyllum aquaticum, Nymphaea tetragona and Phragmites australis after E. coli pollution. Exogenous E. coli especially shifted the epiphytic microbial composition and distribution of P. australis. Stronger effects of E. coli on the archaeal community (edges/nodes = 0.818 < 1, modularity = 0.654; lower clustered structure, 0.389) were found than on the bacterial community (edges/nodes = 1.538 > 1, modularity = 1.291 > 0.654; higher clustered, 0.593). During plant decomposition, E. coli weakened methanogenesis by regulating the network of core genera Methanobacterium and Methanospirillum (spearman, P <  0.05), stimulated the accumulation of organic matters in water (P <  0.05). Similarly, nitrification and denitrification increased and decreased through network regulation in relative biomass of genera Devosia and Desulfovibrio (P <  0.05), respectively. The results provided theoretical supports for eutrophication management in pond ecosystems threatened by E. coli pollution.

Disentangling the seasonal co-occurrence patterns and ecological stochasticity of planktonic and benthic bacterial communities within multiple lakes

Both the planktonic bacterial community (PBC) and benthic bacterial community (BBC) are important for biogeochemical processes in freshwater lakes. Despite their ecological significance, little is known about their seasonal co-occurrence patterns and the ecological processes that drive them. In this study, we aimed to investigate the ecological associations among bacterial taxa and assembly processes of PBC and BBC in different seasons. We used 16S rRNA gene high-throughput sequencing of a total of 150 water and sediment samples collected from multiple lakes distributed in an urban region of China during winter and summer. Our results revealed that PBC showed stronger seasonal variations in co-occurrence patterns than BBC, suggesting that BBC had greater temporal stability than PBC. Winter PBC network was characterized by higher connectivity and complexity, and thereby the formation of a highly stable community structure; whereas lower connectivity arising from the presence of fewer predicted keystone taxa (hubs and connectors in a network) was destabilizing to summer PBC network. In addition, the phylum Firmicutes identified as a putative keystone taxon of PBC in both seasons played a non-negligible role in maintaining network structure which may result from strong functional associations with other bacterioplankton. Temperature and pH were the best explanatory factors predicting the seasonal co-occurrence patterns of PBC and BBC, respectively. Normalized stochasticity ratio based on null-model analysis indicated that deterministic processes overwhelmed stochastic processes in governing the assembly of PBC and BBC in both seasons. However, we observed a greater influence of ecological stochasticity on BBC assembly than PBC assembly in both seasons. Taken together, these findings provide insights into understanding the impacts of habitat heterogeneity and seasonal variability on microbial assemblage patterns in lake ecosystems.

Key internal factors leading to the variability in CO2 fixation efficiency of different sulfur-oxidizing bacteria during autotrophic cultivation

Variability in the apparent CO₂ fixation yield of four aerobic sulfur-oxidizing bacteria (Halothiobacillus neapolitanus DSM 15147, Thiobacillus thioparus DSM 505, Thiomonas intermedia DSM 18155, and Starkeya novella DSM 506) in autotrophic culturing was studied, and mutual effects of key intrinsic factors on CO₂ fixation were explored. DSM 15147 and DSM 505 exhibited much higher CO₂ fixation yields than DSM 18155 and DSM 506. The differences in CO₂ fixation yield were determined not only by cbb gene transcription, but also by cell synthesis rate, which was determined by rRNA gene copy number; the rRNA gene copy number had a more significant effect than cbb gene transcription on the apparent CO₂ fixation yield. Moreover, accumulation of EDOC was observed in all four strains during chemoautotrophic cultivation, and the proportion of EDOC accounting for total fixed organic carbon (TOC; EDOC/TOC ratio) was much higher in DSM 18155 and DSM 506 than in DSM 15147 and DSM 505. The accumulation of EDOC led to a significant decrease in the cbb gene transcription efficiency during cultivation, and a further feedback inhibitory effect on CO₂ fixation.

Integrating Microbial Community Assembly and Fluid Kinetics to Decouple Nitrogen Dynamics in an Urban Channel Confluence

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.

Insight into the nitrogen accumulation in urban center river from functional genes and bacterial community

Along with urbanization, the intensified nitrogen pollution in urban rivers and the form of black-odor rivers has become one of the biggest concerns. Better understanding of the nitrogen transformations and microbial mechanisms occurring within urban rivers could help to manage their water quality. In this study, pollution characteristics, potential nitrogen removal rate, composition and function of bacterial community, and abundance of functional genes associated with nitrogen transformation were comparatively investigated in a typical urban river (FC) and a suburban river (LH). Compared with LH, FC was characterized by higher content of nutrients, lower potential nitrogen removal rate and lower abundance of functional genes associated with nitrogen transformation in both overlying water and sediment, especially in summer. Sediment dissolved organic matter characterized by excitation−emission matrix (EEM) showed that FC was more severely polluted by high nitrogen organic matter. Our results revealed that anammox was the main nitrogen removal pathway in both rivers and potential nitrogen removal rates decreased significantly in summer. Bacterial community analysis showed that the benthic communities were more severely influenced by the pollutant than aquatic ones in both rivers. Furthermore, the FC benthic community was dominated by anaerobic respiring, fermentative, sulfate reduction bacteria. Quantitatively, the denitrification rate showed a significant positive correlation with the abundance of denitrification genes, whilst the anammox rate was significantly negatively correlated with bacterial diversity. Meanwhile, NH₄⁺-N had a significant negative correlation to both denitrification and anammox in sediment. Taken together, the results indicated that the increased nitrogen pollutants in an urban river altered nitrogen removal pathways and bacterial communities, which could in turn exacerbate the nitrogen pollution to this river.

Nitrate application decreased microbial biodiversity but stimulated denitrifiers in epiphytic biofilms on Ceratophyllum demersum

Among nitrogen species, nitrate is more stable than ammonium and nitrite, and it is an important nitrogenous pollutant in surface water. However, little is known about the characterization of epiphytic microbial communities on submersed macrophytes under nitrate loading. In this study, we investigated the co-occurring pattern and response of bacteria and microeukaryotes in epiphytic biofilms under nitrate loading. Nitrate loading significantly affected bacterial and eukaryotic communities, and turnover played greater contribution to the total dissimilarity than nestedness by partitioning beta-diversity analysis. Cyanobacteria, α-proteobacteria, β-proteobacteria, Actinobacteria, Planctomycetes, Bacteroidetes, and γ-proteobacteria were dominant bacterial phyla/classes. Metazoan (phylum Arthropoda, Rotifera, Gastrotricha, Annelida, and Nematoda) and algae (phylum Bacillariophyta, Chlorophyta, and Streptophyta) were dominated in eukaryotic communities. The abundances of denitrifying bacteria (Rhodobacter, Acinetobacter, Bacillus, Flavobacterium, and Pseudomonas) and genes (nirS, cnorB, and nosZ) increased with nitrate loading. The network analysis showed there were complex interactions among photosynthetic microbes, metazoan, and bacteria (including denitrifiers) that they were potentially interrelated via photosynthesis, predation or feeding. This study provides new perspectives into understanding the factors affecting nitrate removal mechanisms in wetlands with submersed macrophytes.

A model to integrate urban river thermal cooling in river restoration

River water quality and habitats are degraded by thermal pollution from urban areas caused by warm surface runoff, lack of riparian forests, and impervious channels that transfer heat and block cool subsurface flows. This study updates the i-Tree Cool River model to simulate restoration of these processes to reverse the urban river syndrome, while using the HEC-RAS model water surface profiles needed for flood hazard analysis in restoration planning. The new model was tested in a mountain river within the New York City drinking water supply area (Sawmill, SM, Creek), and then used for base case and restoration scenarios on the 17.5 km reach of the Los Angeles (LA) River where a multi-million dollar riverine restoration project is planned. The model simulated the LA River average temperature in the base case decreased from 29.5 °C by 0.3 °C when warm surface inflows were converted to cooler groundwater inflows by terrestrial green infrastructure; by 0.7 °C when subsurface hyporheic exchange was increased by removal of armoring and installation of riffle-pool bedforms; by 3.6 °C when riparian forests shaded the river; and by 6.4 °C when floodplain forests were added to riparian forests to cool surface reservoirs and local air temperatures. Applying all four restoration treatments lowered river temperature by 7.2 °C. The simulated decreases in river temperature lead to increased saturated dissolved oxygen levels, reaching 8.7 mg/L, up from the 7.6 mg/L in the base case scenario, providing improved fish habitat and reducing eutrophication and hypoxic zones. This study evaluating the performance of environmental management scenarios could help managers control the thermal pollution in rivers.

Environmental amenities of urban rivers and residential property values: A global meta-analysis

Environmental amenities and disamenities of urban rivers and their capitalization in property prices have been a major subject of empirical investigation in the hedonic price method (HPM) literature for several decades. Primary studies across the globe have nonetheless adopted varying valuation scenarios and modelling approaches. And systematic variation has been shown in homeowners' marginal willingness-to-pay (WTP) for urban rivers' amenities and disamenities, ranging between -12.2% and 63.58% price premium. To identify which valuation scenarios, socio-economic variables, and modelling characteristics might affect the quantification of urban rivers' impacts on property values, we conducted a very first meta-analysis of existing evidence to extract additional information concerning the heterogeneity in WTP estimates pertaining to urban rivers' environmental amenities and disamenities. A total of 53 observations from 30 primary studies that adopted HPM to provide WTP estimates for three prominent valuation scenarios, i.e., proximity, view and water quality, were synthesized using a random effects model. Our meta-analysis results revealed several important factors in explaining the heterogeneity in empirical WTP estimates pertaining to urban rivers' environmental amenities/disamenities. First, while all three valuation scenarios could capture urban rivers' impacts on residential property values, river view was associated with the greatest premium, followed by river water quality, and river proximity the least. Second, we found that WTP estimates were significantly higher after the year of 2000, indicating the widespread and successful river restoration and rehabilitation projects in the 21st century has driven up homeowners' environmental perception and appreciation of urban rivers' amenities, especially their clear depreciation of negative environmental disamenities, to a high level. Third, our results showed that homeowners' valuation of urban rivers was not sensitive to the macro-geographical locations of their residences, suggesting a universal overall appreciation/depreciation of urban rivers across varying cultures and societies. Instead, household income level and population density should be systematically controlled if value transfer across countries is necessary. The findings of this meta-analysis could help refine urban rivers' attributes to be incorporated into HPM studies so as to adequately quantify people's sophisticated valuation of intertwined amenities and disamenities. On the practical front, our results supported two arguments from a very utilitarian point of view. First, it appears that the visual impacts might be prioritized for river restoration projects, such as through careful revegetation of riparian areas using native species. This could harbor rich diversity of ecological functions and in the meantime maximize environmental amenities that homeowners would like to pay for. And second, cost-effective river restoration in urbanized contexts should be prioritized in densely populated areas over places with relatively low population densities. This approach might maximize the number of people who can enjoy rivers for a given budget.

Trophic Status Is Associated With Community Structure and Metabolic Potential of Planktonic Microbiota in Plateau Lakes

Microbes in various aquatic ecosystems play a key role in global energy fluxes and biogeochemical processes. However, the detailed patterns on the functional structure and the metabolic potential of microbial communities in freshwater lakes with different trophic status remain to be understood. We employed a metagenomics workflow to analyze the correlations between trophic status and planktonic microbiota in freshwater lakes on Yun-Gui Plateau, China. Our results revealed that microbial communities in the eutrophic and mesotrophic-oligotrophic lake ecosystems harbor distinct community structure and metabolic potential. Cyanobacteria were dominant in the eutrophic ecosystems, mainly driving the processes of aerobic respiration, fermentation, nitrogen assimilation, nitrogen mineralization, assimilatory sulfate reduction and sulfur mineralization in this ecosystem group. Actinobacteria, Proteobacteria (Alpha-, Beta-, and Gammaproteobacteria), Verrucomicrobia and Planctomycetes, occurred more often in the mesotrophic-oligotrophic ecosystems than those in the eutrophic ecosystems, and these taxa potentially mediate the above metabolic processes. In these two groups of ecosystems, a difference in the abundance of functional genes involved in carbohydrate metabolism, energy metabolism, glycan biosynthesis and metabolism, and metabolism of cofactors and vitamins significantly contribute to the distinct functional structure of microbiota from surface water. Furthermore, the microbe-mediated metabolic potentials for carbon, nitrogen and sulfur transformation showed differences in the two ecosystem groups. Compared with the mesotrophic-oligotrophic ecosystems, planktonic microbial communities in the eutrophic ecosystems showed higher potential for aerobic carbon fixation, fermentation, methanogenesis, anammox, denitrification, and sulfur mineralization, but they showed lower potential for aerobic respiration, CO oxidation, nitrogen fixation, and assimilatory sulfate reduction. This study offers insights into the relationships of trophic status to planktonic microbial community structure and its metabolic potential, and identifies the main taxa responsible for the biogeochemical cycles of carbon, nitrogen and sulfur in freshwater lake environments.

The effect of temperature on sulfate release from Pearl River sediments in South China

Sulfate (SO₄^2-) has received attention as means of monitoring water quality and pollution. However, the SO₄^2- content of rivers, lakes, and reservoirs varies significantly by season, so environmental factors such as temperature can affect it. An experiment was conducted with a series of aerobic and anaerobic tanks containing Pearl River sediments and distilled water to assess the release of SO₄^2- from sediments under controlled conditions. "Black-odor river" refers to near anoxic conditions in the water column and foul odors emanating from affected rivers in southeastern China. These river systems typical have sediments containing ammonia (NH₃), hydrogen sulfide (H₂S), and organic sulfide compounds in excess, and precipitates of sulfide (S^2-), with ferrous (Fe²⁺) or manganese (Mn²⁺). SO₄^2- concentration was measured at various depths in pore water and in the water column while controlling temperature and dissolved oxygen (DO) concentrations. Interpolation of study results revealed that SO₄^2- content was highest between temperatures of 20 °C and 25 °C. The relationship between SO₄^2- concentration, which varied with temperature and time, was fit using a linearized Michaelis-Menten function (R² = 0.69). The release of SO₄^2- to the water column was accelerated during the experiment (for temperatures higher than 20 °C), and led to higher SO₄^2- content in the water column than in pore water. The maximum concentration of SO₄^2- within the sediment occurred at a temperature of 20 °C. Comparing aerated and non-aerated tanks at 20 °C, we found that O₂ restricted SO₄^2- content in the water column; DO could, in turn, also be controlled by temperature. Fe²⁺ and Mn²⁺ had a negative correlation with SO₄^2-.

Shift of Sediments Bacterial Community in the Black-Odor Urban River during In Situ Remediation by Comprehensive Measures

The phenomenon of black-odor urban rivers with rapid urbanization has attracted extensive attention. In this study, we investigated the water quality and composition of sediment-associated bacteria communities in three remediation stages (before remediation, 30 days after remediation, and 90 days after remediation) based on the in situ remediation using comprehensive measures (physical, chemical, and biological measures). The results show that the overlying water quality was notably improved after in situ remediation, while the diversity and richness of sediment-associated bacterial communities decreased. A growing trend of some dominant genus was observed following the remediation of a black-odor river, such as Halomonas, Pseudomonas, Decarbonamis, Leptolina, Longilina, Caldiseericum, Smithella, Mesotoga, Truepera, and Ralstonia, which play an important role in the removal of nitrogen, organic pollutants and hydrogen sulfide (H2S) during the sediment remediation. Redundancy analysis (RDA) showed that the bacterial community succession may accelerate the transformation of organic pollutants into inorganic salts in the sediment after in situ remediation. In a word, the water quality of the black-odor river was obviously improved after in situ remediation, and the bacterial community in the sediment notably changed, which determines the nutrients environment in the sediment.