Modeling the Biodegradation of Bacterial Community Assembly Linked Antibiotics in River Sediment Using a Deterministic-Stochastic Combined Model

External circuit loading mode regulates anode biofilm electrochemistry and pollutants removal in microbial fuel cells

This study investigated the effects of different external circuit loading mode on pollutants removal and power generation in microbial fuel cells (MFC). The results indicated that MFC exhibited distinct characteristics of higher maximum power density (Pmax) (named MFC-HP) and lower Pmax (named MFC-LP). And the capacitive properties of bioanodes may affect anodic electrochemistry. Reducing external load to align with the internal resistance increased Pmax of MFC-LP by 54.47 %, without no obvious effect on MFC-HP. However, intermittent external resistance loading (IER) mitigated the biotoxic effects of sulfamethoxazole (SMX) (a persistent organic pollutant) on chemical oxygen demand (COD) and NH4+-N removal and maintained high Pmax (424.33 mW/m2) in MFC-HP. Meanwhile, IER mode enriched electrochemically active bacteria (EAB) and environmental adaptive bacteria Advenella, which may reduce antibiotic resistance genes (ARGs) accumulation. This study suggested that the external circuit control can be effective means to regulate electrochemical characteristics and pollutants removal performance of MFC.

Does exposure timing of macrolide antibiotics affect the development of river periphyton? Insights into the structure and function

Discharged sewage is the dominant source of urban river pollution. Macrolide antibiotics have emerged as prominent contaminants, which are frequently detected in sewage and rivers and pose a threat to aquatic microbial community. As a typical primary producer, periphyton is crucial for maintaining the biodiversity and functions of aquatic ecosystem. However, effects of antibiotic exposure time as well as the recovery process of periphyton remain undetermined. In the present study, five exposure scenarios of two typical macrolides, erythromycin (ERY) and roxithromycin (ROX) were investigated at 50 µg/L, dose to evaluate their potential detrimental effects on the structure and function of periphyton and the subsequent recovery process in 14 days. Results revealed that the composition of periphytic community returned to normal over the recovery period, except for a few sensitive species. The antibiotics-caused significant photodamage to photosystem II, leading to continuous inhibition of the photosynthetic capacity of periphyton. Furthermore, no significant difference in carbon metabolism capacity was observed after direct antibiotic exposure, while the amine carbon utilization capacity of periphyton remarkably increased during the recovery process. These results indicated that periphyton community was capable of coping with the periodic exposure of antibiotic pollutants and recovering on its own. However, the ecological functions of periphyton can be permanently disturbed due to macrolide exposure. Overall, this study sheds light on the influence of macrolide exposure on the development, structure and function of the periphytic microbial community in rivers.

Land use/cover drive functional patterns of bacterial communities in sediments of a subtropical river, China

The bacterial community in sediment serves as an important indicator for assessing the environmental health of river ecosystems. However, the response of bacterial community structure and function in river basin sediment to different land use/cover changes has not been widely studied. To characterize changes in the structure, composition, and function of bacterial communities under different types of land use/cover, we studied the bacterial communities and physicochemical properties of the surface sediments of rivers. Surface sediment in cropland and built-up areas was moderately polluted with cadmium and had high nitrogen and phosphorus levels, which disrupted the stability of bacterial communities. Significant differences in the α-diversity of bacterial communities were observed among different types of land use/cover. Bacterial α-diversity and energy sources were greater in woodlands than in cropland and built-up areas. The functional patterns of bacterial communities were shown that phosphorus levels and abundances of pathogenic bacteria and parasites were higher in cropland than in the other land use/cover types; Urban activities have resulted in the loss of the denitrification function and the accumulation of nitrogen in built-up areas, and bacteria in forested and agricultural areas play an important role in nitrogen degradation. Differences in heavy metal and nutrient inputs driven by land use/cover result in variation in the composition, structure, and function of bacterial communities.

Development and validation of an in situ high-resolution technique for measuring antibiotics in sediments

Important biogeochemical processes occur in sediments at fine scales. Sampling techniques capable of yielding information with high resolution are therefore needed to investigate chemical distributions and fluxes and to elucidate key processes affecting chemical fates. In this study, a high-resolution diffusive gradients in thin-films (DGT) technique was systematically developed and tested in a controlled sediment system to measure organic contaminants, antibiotics, for the first time. The DGT probe was used to resolve compound distributions at the mm scale. It also reflected the fluxes from the sediment pore-water and remobilization from the solid phase, providing more dynamic information. Through the fine scale detection, a reduction of re-supply was observed over time, which was concentration and location dependent. Compared to the Rhizon sampling method, antibiotic concentrations obtained by DGT probes were less than the pore-water concentrations, as DGT measures the labile fraction of the compounds. The DGT probe was also tested on an intact sediment core sampled from a lake in China and used to measure the distribution of labile antibiotics with depth in the core at the mm scale. ENVIRONMENTAL IMPLICATION: The abuse of antibiotics and widespread of their residues influences the ecosystem, induces the generation of super-bacteria, and finally poses threat to human health. Sediments adsorbs pollutants from the aquatic environment, while may also release them back to the environment. We systematically developed DGT probe approach for measuring antibiotics in sediment in situ in high resolving power, it provides information at fine scale to help us investigate biogeochemical processes take place in sediment and sediment-water interface.

Nitrate input inhibited the biodegradation of erythromycin through affecting bacterial network modules and keystone species in lake sediments

Antibiotic contamination and excessive nitrate loads are generally concurrent in aquatic ecosystems. However, little is known about the effects of nitrate input on the biodegradation of antibiotics. In this study, the effects of nitrate input on microbial degradation of erythromycin, a typical macrolide antibiotic widely detected in lake sediments, were investigated. The results showed that the nitrate input significantly inhibited the erythromycin removal and such an inhibitory effect was strengthened with the increased input dosages. Nitrate input significantly increased sediment nitrite concentration, indicating enhanced denitrification under high nitrate pressure. Bacterial network module and keystone species analysis showed that nitrate input enriched the keystone species involved in denitrification (e.g., Simplicispira and Denitratisoma). In contrast, some potential erythromycin-degrading bacteria (e.g., Desulfatiglandales, Pseudomonadales, Nitrospira) were inhibited by nitrate input. The variations in dominant bacterial groups implied competition between denitrification and erythromycin degradation in response to nitrate input. Based on the partial least squares path modeling analysis, keystone species (total effect: 0.419) and bacterial module (total effect: 0.403) showed strong association with erythromycin removal percentage. This indicated that the inhibitory effect of nitrate input on erythromycin degradation was mainly explained by bacterial network modules and keystone species. These findings will help us to assess the bioremediation potential of antibiotic-contaminated sediments suffering from excessive nitrogen discharge concurrently.

Bacteria drive soil multifunctionality while fungi are effective only at low pathogen abundance

The positive correlation between soil biodiversity and multifunctionality has gained widespread recognition. However, the impact of plant pathogens on soil multifunctionality and its relationship with microbial diversity remains understudied. To address this knowledge gap, we collected soil samples from three Hami melon (Cucumis melo L.) planting sites with varying monoculture durations (1, 3, and 5 years). We sequenced the bacterial and fungal communities in these samples and quantified multifunctionality. The results revealed a significant increase in the relative abundance of fungal pathogens over the years of planting, which influenced the correlations between microbial diversity and multifunctionality at a threshold value of 0.01. Both bacterial and fungal richness positively influenced multifunctionality when fungal pathogen abundance was low (< 0.01), whereas only bacterial richness showed a positive correlation with multifunctionality under high fungal pathogen abundance (> 0.01) conditions. Both bacterial and fungal communities were primarily governed by deterministic processes. However, only bacterial community assembly drove soil multifunctionality, showing positive correlations with multifunctionality dissimilarity under low fungal pathogen abundance condition and negative correlations under high fungal pathogen abundance condition, reflecting distinct pathogen pressures. Structural equaling modeling further confirmed the distinct roles of bacterial and fungal richness and composition in promoting multifunctionality under different fungal pathogen condition. Our findings provide evidence that shifts in fungal pathogen abundance alter the balance and interactions between biodiversity and multifunctionality and highlight the importance of engineering biotic interactions in determining soil functioning in agroecosystems.

Conservation tillage practices affect soil microbial diversity and composition in experimental fields

Introduction

Conservation tillage is a widely used technique worldwide, but the effects of conservation tillage on bacterial community structure are poorly understood. We explored proportional alterations in the bacterial community under different tillage treatments.

Methodology

Hence, this study utilized high-throughput sequencing technique to investigate the structure and assembly processes of microbial communities in different tillage treatments.

Results and discussion

Tillage treatments included tillage no-straw retention (CntWt), no-tillage with straw retention (CntWntS), tillage with straw retention (CntWtS), no-tillage and no-straw retention (CntWnt). The influence of tillage practices on soil bacterial communities was investigated using Illumina MiSeq sequencing. Different tillage methods and straw retention systems significantly influenced soil parameters such as total potassium and pH were not affected by tillage practices, while straw retention significantly affected soil parameters including nitrogen content, available phosphorus and available potassium. Straw retention decreased bacterial diversity while increased bacterial richness. The effect of straw retention and tillage on bacterial communities was greater than with no tillage. Phylogenetic β-diversity analysis showed that deterministic homogeneous selection processes were dominated, while stochastic processes were more pronounced in tillage without straw retention. Ecological network analysis showed that microbial community correlation was increased in CntWntS and CntWnt. Straw retention treatment significantly increased the relative abundance of bacterial taxa Proteobacteria, Bacteroidetes, and OD1, while Nitrospirae, Actinobacteria, and Verrucomicrobia significantly decreased.

Conclusion

The conservation tillage practices significantly affect soil properties, bacterial composition, and assembly processes; however, further studies are required to investigate the impact of different crops, tillage practices and physiological characteristics on bacterial community structure and functions.

Linking bacterial and fungal assemblages to soil nutrient cycling within different aggregate sizes in agroecosystem

Soil aggregates provide spatially heterogeneous microhabitats that support the coexistence of soil microbes. However, there remains a lack of detailed assessment of the mechanism underlying aggregate-microbiome formation and impact on soil function. Here, the microbial assemblages within four different aggregate sizes and their correlation with microbial activities related to nutrient cycling were studied in rice fields in Southern China. The results show that deterministic and stochastic processes govern bacterial and fungal assemblages in agricultural soil, respectively. The contribution of determinism to bacterial assemblage improved as aggregate size decreased. In contrast, the importance of stochasticity to fungal assemblage was higher in macroaggregates (>0.25 mm in diameter) than in microaggregates (<0.25 mm). The association between microbial assemblages and nutrient cycling was aggregate-specific. Compared with microaggregates, the impacts of bacterial and fungal assemblages on carbon, nitrogen, and phosphorus cycling within macroaggregates were more easily regulated by soil properties (i.e., soil organic carbon and total phosphorus). Additionally, soil nutrient cycling was positively correlated with deterministic bacterial assemblage but negatively correlated with stochastic fungal assemblage in microaggregates, implying that bacterial community may accelerate soil functions when deterministic selection increases. Overall, our study illustrates the ecological mechanisms underlying the association between microbial assemblages and soil functions in aggregates and highlights that the assembly of aggregate microbes should be explicitly considered for revealing the ecological interactions between agricultural soil and microbial communities.

Biodegradable microplastics enhance soil microbial network complexity and ecological stochasticity

Biodegradable plastics have emerged as an ecological alternative to conventional petroleum-based plastics. Despite the recent advances in the effects of conventional microplastic on soil ecosystems, the ecological impact of biodegradable microplastics in soil environments remains poorly understood. Here, we performed soil microcosms with conventional (polyethylene and polystyrene) and biodegradable (polybutylene succinate and polylactic acid) microplastics to estimate their effects on the success patterns, co-occurrence networks, and the assembly mechanisms of soil bacterial communities. Biodegradable microplastics significantly altered the soil bacterial community composition with steeper temporal turnovers (rate: 0.317 - 0.514) compared to the conventional microplastic treatments (rate: 0.211 - 0.220). Network under biodegradable microplastics showed greater network complexity, including network size, connectivity, average clustering coefficient, and the number of keystone species, as compared with the conventional microplastic treatments. Additionally, the biodegradable microplastic network had higher robustness, which may be potentially due to the enhanced dissolved organic carbon contents in the soil treated with biodegradable microplastics. The bacterial community assembly was initially governed by deterministic homogeneous selection (93 - 100 %) under the stress of microplastics, but was progressively structured by increasing stochastic homogeneous dispersal (17.8 - 73.3 %) over time. The normalized stochasticity ratio also revealed that the application of microplastics increased the importance of stochastic processes following incubation. These findings greatly enhanced our understanding of the ecological mechanisms and interactions of soil bacterial communities in response to microplastic stress.

A review on antibiotics removal: Leveraging the combination of grey and green techniques

Antibiotics are currently a major source of concern around the world due to the serious risks posed to human health and the environment. The performance of the secondary wastewater treatment processes/technologies (representing grey process) and constructed wetlands (CWs) (typical green process) in removing antibiotics and antibiotic resistance genes (ARG) was reviewed. The result showed that the grey process mainly removes antibiotics, but does not significantly remove ARG, and some processes may even cause ARG enrichment. The overall treatment in CWs is better than WWTPs, especially for ARG. Vertical subsurface flow CWs (VFCWs) are more conductive to antibiotics removal, while horizontal subsurface flow CWs (HFCWs) have a better ARG removal. More importantly, this review admits and suggests that the combination of grey process with green process is an effective strategy to remove antibiotics and ARG. The most advantage of the combination lies in realizing complementary advantages, i.e. the grey process as the primary treatment while CWs as the polishing stage. The efficiency of such the hybrid system is much higher than either single treatment process.

The biogeochemical responses of hyporheic groundwater to the long-run managed aquifer recharge: Linking microbial communities to hydrochemistry and micropollutants

Interactions of surface water and groundwater (SW-GW) in hyporheic zones produce biogeochemical hotspots. However, response patterns of hyporheic groundwater to external influences remain unclear. In this study, three datasets (hydrochemistry, antibiotics, and microbiome) were collected over a hydrological year to explore the influence of a 12-year managed aquifer recharge (MAR) project. We observed that the long-term MAR practice elevated nutrient and antibiotic levels while reduced redox potential in hyporheic groundwater, and these impacts depended on decreasing SW-GW interaction intensity with aquifer depth. In contrast, the long-term MAR practice increased community dissimilarity of 30-m groundwater but had little impact on 50-m or 80-m groundwater. Moreover, hyporheic community assembly was dominated by dispersal limitation, and thereby co-varied hydrochemistry and antibiotics only attributed to small community variability. The long-term MAR practice decreased species-interaction intensity and changed the abundance of metabolic functions in hyporheic groundwater. Furthermore, predicted community functions involving carbon, nitrogen, sulfur, and manganese cycles for 30-m groundwater showed higher abundances than those for 50- and 80-m groundwater. Collectively, we showed that hyporheic groundwater was sensitive to the SW-GW interaction and human activities, with the interactions of hydrochemistry, contaminants, and microbiome linking to hyporheic groundwater quality and ecosystem functioning.

Coupling Genomics and Hydraulic Information to Predict the Nitrogen Dynamics in a Channel Confluence

The simulation of nitrogen dynamics in urban channel confluences is essential for the evaluation and improvement of water quality. The omics-based modeling approaches that have been rapidly developed have been increasingly applied to characterize metabolisms of the microbial community and transformation of the associated materials. However, the transport of microorganisms and chemicals within and among different phases, which could be the rate-limiting step for the nitrogen dynamics, are always neglected or oversimplified in omics-based models. Therefore, this study proposes a novel simulation system coupling genomic and hydraulic information to simulate transport and transformation processes and provide predictions of nitrogen dynamics in a confluence. The proposed model was able to capture multiphase mass transport, microbial population dynamics, and nitrogen transformation and accurately predict gene abundances and nitrogen concentrations in both water and sediment; the mean relative errors were all lower than 40%. The model emphasized the importance of transport processes, which contributed more than 90% to gene abundances and chemical concentrations. Moreover, the simulation of reaction rates exhibited the specific nitrogen transformation processes in the confluence. The sulfide oxidation and the nitrate reduction and anaerobic ammonium oxidation, with the participation of the genes nap and hzo, respectively, were promoted as the main processes of nitrate and nitrite reduction.

Characteristics of planktonic and sediment bacterial communities in a heavily polluted urban river

Urban rivers represent a unique ecosystem in which pollution occurs regularly, altering the biogeochemical characteristics of waterbodies and sediments. However, little is presently known about the spatiotemporal patterns of planktonic and sediment bacterial community diversities and compositions in urban rivers. Herein, Illumina MiSeq high-throughput sequencing was performed to reveal the spatiotemporal dynamics of bacterial populations in Liangtan River, a heavily polluted urban river in Chongqing City (China). The results showed the richness and diversity of sediment bacteria were significantly higher than those of planktonic bacteria, whereas a strong overlap (46.7%) in OTUs was identified between water and sediment samples. Bacterial community composition remarkably differed in waters and sediments. Planktonic bacterial communities were dominated by Proteobacteria, Bacteroidetes, Cyanobacteria and Actinobacteria, while sediment bacterial communities mainly included Proteobacteria, Actinobacteria, Chloroflexi and Bacteroidetes. Additionally, several taxonomic groups of potential bacterial pathogens showed an increasing trend in water and sediment samples from residential and industrial areas (RI). Variation partition analysis (VPA) indicated that temperature and nutrient were identified as the main drivers determining the planktonic and sediment bacterial assemblages. These results highlight that bacterial communities in the polluted urban river exhibit spatiotemporal variation due to the combined influence of environmental factors associated with sewage discharge and hydropower dams.

Combined bioaugmentation with electro-biostimulation for improved bioremediation of antimicrobial triclocarban and PAHs complexly contaminated sediments

Haloaromatic antimicrobial triclocarban (TCC) is an emerging refractory contaminant that commonly coexisted with conventional contaminants such as polycyclic aromatic hydrocarbons (PAHs). TCC may negatively affect the metabolic activity of sediment microorganisms and persist in environment; however, remediation methods that relieve the TCC inhibitory effect in sediments remain unknown. Here, a novel electro-biostimulation and bioaugmentation combined remediation system was proposed by the simultaneous introduction of a TCC-degrading Ochrobactrum sp. TCC-2 and electrode into the TCC and PAHs co-contaminated sediments. Results indicated the PAHs and TCC degradation efficiencies of the combined system were 2.9-3.0 and 4.6 times respectively higher than those of the control group (no electro-biostimulation and no bioaugmentation treatments). The introduced strain TCC-2 and the enriched electroactive bacteria and PAHs degraders (e.g. Desulfobulbus, Clostridium, and Paenarthrobacter) synergistically contributed to the accelerated degradation of PAHs and TCC. The preferential elimination of the TCC inhibitory effect through bioaugmentation treatment could restore microbial functions by increasing the functional gene abundances related to various metabolic processes. This study offers new insights into the response of sediment functional communities to TCC stress, electro-biostimulation and bioaugmentation operations and provides a promising system for the enhanced bioremediation of the PAHs and TCC co-contaminated sediments.

Seasonal dynamics modifies fate of oxygen, nitrate, and organic micropollutants during bank filtration - temperature-dependent reactive transport modeling of field data

Bank filtration is considered to improve water quality through microbially mediated degradation of pollutants and is suitable for waterworks to increase their production. In particular, aquifer temperatures and oxygen supply have a great impact on many microbial processes. To investigate the temporal and spatial behavior of selected organic micropollutants during bank filtration in dependence of relevant biogeochemical conditions, we have set up a 2D reactive transport model using MODFLOW and PHT3D under the user interface ORTI3D. The considered 160-m-long transect ranges from the surface water to a groundwater extraction well of the adjacent waterworks. For this purpose, water levels, temperatures, and chemical parameters were regularly measured in the surface water and groundwater observation wells over one and a half years. To simulate the effect of seasonal temperature variations on microbial mediated degradation, we applied an empirical temperature factor, which yields a strong reduction of the degradation rate at groundwater temperatures below 11 °C. Except for acesulfame, the considered organic micropollutants are substantially degraded along their subsurface flow paths with maximum degradation rates in the range of 10^-6 mol L^-1 s^-1. Preferential biodegradation of phenazone, diclofenac, and valsartan was found under oxic conditions, whereas carbamazepine and sulfamethoxazole were degraded under anoxic conditions. This study highlights the influence of seasonal variations in oxygen supply and temperature on the fate of organic micropollutants in surface water infiltrating into an aquifer.

Developing a statistical-weighted index of biotic integrity for large-river ecological evaluations

The efficiency, accuracy and universality of ecological assessment methods comprise an important foundation for comprehensive assessment and restoration of large river ecological health at the watershed scale. New evaluation metrics and methods are urgently needed to be developed to adapt the characteristics of large rivers, including geographical differences in surface runoff, regional ecological complexity, and seasonal changes. In this study, a bacteria-weighted index of biotic integrity was developed to assess the ecological health of large rivers (lrBW-IBI) based on compositional and functional characteristics of sediment bacterial communities from 33 sections of the lower mainstream of Yangtze River. Five key metrics were determined by range, responsiveness, and redundancy tests. Principal component analysis (PCA), entropy method, criteria importance through intercriteria correlation and random forest were applied to calculate weighted coefficients of key metrics. The optimal lrBW-IBI was observed through the sum of PCA weighted-metrics: the relative abundance of Latescibacteria (0.234), Gemmatimonadaceae (0.149), Nitrospira spp. (0.234), Rhizobiales (0.228), and nitrogenase NifH (0.156). According to PCA based lrBW-IBI, 12.12%, 24.24%, 39.39%, and 24.24% of river sections were labeled excellent, good, moderate, and relatively poor, respectively. The ecological status of the lower mainstream of the Yangtze River did not change significantly across seasons but declined gradually from upstream to downstream. This study provides a new assessment tool for the ecological health of large rivers and highlights the importance of microbial ecological index in river ecology.

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.

Impact of long-term industrial contamination on the bacterial communities in urban river sediments

BACKGROUND

The contamination of the aquatic environment of urban rivers with industrial wastewater has affected the abiotic conditions and biological activities of the trophic levels of the ecosystem, particularly sediments. However, most current research about microorganism in urban aquatic environments has focused on indicator bacteria related to feces and organic pollution. Meanwhile, they ignored the interactions among microorganisms. To deeply understand the impact of industrial contamination on microbial community, we study the bacterial community structure and diversity in river sediments under the influence of different types of industrial pollution by Illumina MiSeq high-throughput sequencing technology and conduct a more detailed analysis of microbial community structure through co-occurrence networks.

RESULTS

The overall community composition and abundance of individual bacterial groups differed between samples. In addition, redundancy analysis indicated that the structure of the bacterial community in river sediments was influenced by a variety of environmental factors. TN, TP, TOC and metals (Cu, Zn and Cd) were the most important driving factors that determined the bacterial community in urban river sediments (P < 0.01). According to PICRUSt analysis, the bacterial communities in different locations had similar overall functional profiles. It is worth noting that the 15 functional genes related to xenobiotics biodegradation and metabolism were the most abundant in the same location. The non-random assembly patterns of bacterial composition in different types of industrially polluted sediments were determined by a co-occurrence network. Environmental conditions resulting from different industrial pollutants may play an important role in determining their co-occurrence patterns of these bacterial taxa. Among them, the bacterial taxa involved in carbon and nitrogen cycles in module I were relatively abundant, and the bacterial taxa in module II were involved in the repair of metal pollution.

CONCLUSIONS

Our data indicate that long-term potential interactions between different types of industrial pollution and taxa collectively affect the structure of the bacterial community in urban river sediments.

Bacterial community responses to tourism development in the Xixi National Wetland Park, China

A large number of urban wetland parks have been established, but knowledge about the effects of tourism development on the microbial diversity and ecosystem functioning remains limited. This study aimed to clarify the responses of bacterial communities to tourism development targeted the Xixi National Wetland Park, China. By analyzing the diversity, composition, assembly pattern, and environmental drivers of bacterial communities, we found that tourism development considerably affected the water quality, which further decreased the α-diversity but increased the β-diversity in open areas for landscaping and recreation. Specifically, there was higher Simpson dissimilarity across functional wetland areas, indicating that species replacement mainly explained β-diversity patterns of bacterial communities. RDA analysis and ecological processes quantification further suggested that TOC and TC were the major factors in the open areas driving bacterial communities in water and sediment, respectively. Also, typical anti-disturbance taxa (Gammaproteobacteria) and potential pathogens (Bacillus) were enriched in the wetlands under more anthropogenic disturbances. Findings of the present study highlighted the effects of tourism development on bacterial communities resulted in obvious spatial variation in the Xixi National Wetland Park. This study gives us useful information for ecological assessments of urban wetlands, and further can provide references in making appropriate strategies to manage wetland ecosystems.

Homogeneous selection dominates the microbial community assembly in the sediment of the Three Gorges Reservoir

Deep-water reservoir sediment is a unique habitat sheltering indispensable microorganisms and facilitating their biogeochemical functions; however, the assembly processes of the microbial community therein remain elusive. This study focuses on the assembly processes in the Three Gorges Reservoir Area (TGRA). A total of 42 sediment samples were collected from the TGRA, both in the mainstream and the tributaries, and in different seasons. Metagenomic analyses of 16S rRNA using Exact Sequence Variants revealed the spatiotemporal distribution patterns of the microbial communities. Linear regressions between dissimilarity of microbial communities, geographic and environmental distance showed that environmental, rather than geographic factors, impacted the microbial community. However, the environmental differences explained little variations (14.14%) in community structure, implying the homogeneity of environmental conditions across the TGRA. From the quantification of ecological processes, homogeneous selection was shown to be a dominating factor (51.34%) in the assembly of the microbial communities. The co-occurrence network showed that keystone species were more important than prevalent abundant species in interspecies interactions. Overall, the assembly of microbial community in the deep-water reservoir sediment is mediated by both deterministic and stochastic processes, and homogeneous selection plays a leading role.

Determination of vertical and horizontal assemblage drivers of bacterial community in a heavily polluted urban river

Identifying vertical and horizontal assemblage drivers of bacterial community is important for improving the efficacies of ecological evaluation and remediation for a huge contaminated river (e.g. black-odor urban river). However, little is known about the effect of stochastic vs. deterministic processes on the reliability of the identification processes. Here, a comprehensive analysis was performed to reveal vertical and horizontal assemblage drivers of bacterial community in a heavily polluted urban river (total area of 4.23 km² and total length of 9.3 km), considering the relative importance of stochastic and deterministic processes. Heterogeneous bacterial community assemblages were observed in both vertical and horizontal profiles and the differences in the bacterial community between depths were relatively significant at genus level. The higher values for the Simpson dissimilarity index (horizontal β_SIM = 0.59 ± 0.02; vertical β_SIM = 0.48 ± 0.03) compared to the nestedness-resultant dissimilarity index (horizontal β_NES = 0.05 ± 0.02; vertical β_NES = 0.05 ± 0.05) showed that species replacement explained both the vertical and horizontal beta-diversity patterns. Comparison of horizontal and vertical Sørensen dissimilarity indices further indicated that the biodiversity of vertical community deserved more attention due to the shorter geographical distance with similar beta-diversity patterns compared to horizontal assemblages. Various traditional analysis without consideration for phylogenetic turnover revealed that TN, TP, NH₄⁺-N, DO, ORP, Conductivity and COD_Mn were all the related environmental factors that influenced bacterial community. However, after taking stochastic vs. deterministic processes into account, only NH₄⁺-N and ORP were identified as the main driving forces of trends in the vertical and in the horizontal assembly of bacterial community in the polluted urban river, respectively. This study is helpful for improving ecological assessment methodology and remediation strategy for contaminated urban rivers.

Bacterial community composition and function shift with the aggravation of water quality in a heavily polluted river

Blackening and odorization of heavily polluted rivers has become a vital aquatic environmental problem in developing countries and has threatened river ecosystems. Monitoring the contamination and functional degradation conditions is important for bioremediation of river ecosystems. In this study, the diversity, composition, co-occurrence pattern, and function of bacterial communities collected from a heavily polluted urban river sediment were investigated using 16S rRNA amplicon sequencing analysis. The degree of pollution in the river was divided into three levels, and the clustering result based on the relative abundance of bacterial communities was consistent with the pollution levels in the river. The community assembly analysis further demonstrated that bacterial community assembly was mainly driven by environmental selection (95.84%) in Jinchuan River. Composition of bacterial communities were clearly different at different pollution level sites, although no apparent changes in alpha diversity were observed. The complexity of the bacterial co-occurrence network decreased with aggravation of the pollution level, as indicated by topological features, suggesting that the interactions among bacterial communities were weakened. A phylogenetic Investigation of Communities by Reconstruction of Unobserved States analysis predicted that the relative abundance of functional genes was negatively correlated with pollution levels, and those related to energy metabolism as well as xenobiotic biodegradation and metabolism decreased significantly. These results provide an ecological reference for monitoring and bioremediation of aquatic ecosystems.

Simultaneous remediation of sediments contaminated with sulfamethoxazole and cadmium using magnesium-modified biochar derived from Thalia dealbata

In situ remediation and assessment of sediments contaminated with both antibiotics and heavy metals remains a technological challenge. In this study, MgCl₂-modified biochar (BCM) was obtained at 500 °C through slow pyrolysis of Thalia dealbata and used for remediation of sediments contaminated by sulfamethoxazole (SMX) and Cd. The BCM showed greater surface area (110.6 m² g^-1) than pristine biochar (BC, 7.1 m² g^-1). The SMX sorption data were well described by Freundlich model while Langmuir model was better for the Cd²⁺ sorption data. The addition of 5.0% BCM significantly increased the sorption of SMX (by 50.8-58.6%) and Cd (by 24.2-25.6%) on sediments in both single and binary systems as compared with 5.0% BC. SMX sorption in sediments was significantly improved by addition of Cd²⁺, whereas SMX has no influence on Cd sorption on sediments. The addition of BCM distinctly decreased both SMX (by 51.4-87.2%) and Cd concentrations (by 56.2-91.3%) in overlying water, as well as in TCLP extracts (by 55.6-86.1% and 58.2-91.9% for SMX and Cd, respectively), as compared with sediments without biochar. Both germination rate and root length of pakchoi increased with increasing doses of BCM in contaminated sediments, 5.0% BCM showed greater promotion on pakchoi growth than 5.0% BC. Overall, BCM in the sediments does not only decrease the bioavailability of SMX and Cd, but it also diminishes the phytotoxicity, and thereby shows great application potential for in situ remediation of sediments polluted with antibiotics and heavy metals.

Initial evenness determines diversity and cell density dynamics in synthetic microbial ecosystems

The effect of initial evenness on the temporal trajectory of synthetic communities in comprehensive, low-volume microcosm studies remains unknown. We used flow cytometric fingerprinting and 16S rRNA gene amplicon sequencing to assess the impact of time on community structure in one hundred synthetic ecosystems of fixed richness but varying initial evenness. Both methodologies uncovered a similar reduction in diversity within synthetic communities of medium and high initial evenness classes. However, the results of amplicon sequencing showed that there were no significant differences between and within the communities in all evenness groups at the end of the experiment. Nevertheless, initial evenness significantly impacted the cell density of the community after five medium transfers. Highly even communities retained the highest cell densities at the end of the experiment. The relative abundances of individual species could be associated to particular evenness groups, suggesting that their presence was dependent on the initial evenness of the synthetic community. Our results reveal that using synthetic communities for testing ecological hypotheses requires prior assessment of initial evenness, as it impacts temporal dynamics.