Microbial community assembly responses to polycyclic aromatic hydrocarbon contamination across water and sediment habitats in the Pearl River Estuary

Divergences of granules and flocs microbial communities and contributions to nitrogen removal under varied carbon to nitrogen ratios

Aerobic granular sludge (AGS) reactors are promising for treating high ammonia wastewaters, yet the roles of granules and flocs in nitrogen removal under varying carbon to nitrogen (COD/N) ratios remain unclear. This study investigated microbial communities and their contributions to N removal as the COD/N ratio shifted from 6 to 4, and to 2. Results showed granules contributed 53-64 % nitrification capacity at higher COD/N ratios (6 and 4), but flocs contributed more (50-63 %) at a ratio of 2. Granules consistently exhibited higher denitrification capacity (>50 %). Heterotrophic bacteria dominated in both granules and flocs across all ratios. As the COD/N ratio reduced, the relative abundance of anaerobic ammonia oxidation microorganisms (Candidatus Anammoximicrobium) and filamentous bacteria increased in granules, while ammonia oxidizing bacteria (Nitrosomonas) and complex organic degraders increased in flocs. These findings highlight the importance of selectively retaining granules or flocs under varying COD/N ratios to optimize nitrogen removal efficiency.

Dissolved organic matter mediates the interactions between bacterial community and heavy metal fractionation in contaminated coal mine soils

Heavy metal (HM) contamination in coal mine soils disrupts local bacterial networks, leading to prolonged soil deterioration. Dissolved organic matter (DOM), a crucial soil component, actively modulates both bacterial metabolism and HM mobilization. Despite its significance, our understanding of the complex interactions among bacterial communities, soil chemical and DOM properties, and HM fractionation remains limited. In this study, DOM and bacterial communities from three contaminated mines with varying HM levels and soil properties were analyzed using optical methods and high-throughput sequencing technique. Our results revealed pH and DOM composition, especially the ratio of recalcitrant to labile substances, as key environmental drivers of HM mobilization. Moreover, the composition of bacterial community, particularly the keystone and abundant species, exhibits pronounced site-specificity and HM-dependency. Distinct characteristic genera that are pertinent to HM tolerance/mobility were identified across three mines. Specifically, in Zibo (ZB) soils, Rhodococcus, Acinetobacter, and Pseudomonas significantly regulated the fractionation of Pb, Cu, Se, and Hg possibly via protein-like exudates releasing. In Zaozhuang (ZZ) soils, relationships were recognized between Reyranella, oxides associated Pb, and soil cation exchange capacity. Paenibacillus and Fictibacillus contributed to Se mobilization/tolerance in Linyi (LY) soils. Based on these field findings, two mechanisms were identified for how DOM mediates interactions between HM fractionation and bacterial communities. First, metal-resistant bacteria can produce labile DOM compounds, modifying HM fractionation and reducing metal bioavailability, as observed in ZB soils. Second, humic substances in DOM promoted the development of cohesive bacterial networks featuring metal-resistant keystone bacteria, thereby enhancing community resistance to metal contamination, as evidenced in LY and ZZ soils. Overall, this study provides field evidence elucidating the multilateral interactions among bacterial communities, soil chemical and DOM properties, and HM fractionation, underscoring the significant role of DOM in connecting soil bacterial activity and HM mobilization.

The effects of perfluoroalkyl substance pollution on microbial community and key metabolic pathways in the Pearl River Estuary

The extensive use of perfluoroalkyl substances (PFASs) has raised significant concerns regarding their adverse environmental implications. However, the understanding of their behaviors and biological effects in natural estuarine ecosystems remain limited. This study employed a multidisciplinary approach integrating chemical analysis, biological sequencing, and statistical modeling to comprehensively investigate the distribution of PFASs, as well as their intrinsic relationship with microbial community in the Pearl River Estuary (PRE), a rapidly urbanized area. Our findings demonstrate that the total PFAS concentrations ranged from 52-127 ng L-1 in water, and 2-70 μg kg-1 dry weight in sediment, with notably distinct compositions across habitats. Aquatic microbial communities exhibited higher sensitivity to environmental variables, including PFAS concentrations, attributed to increased stochasticity and reduced spatial turnover. Conversely, sediments harbored microbial communities with higher phylogenetic diversity, rendering them less susceptible to PFAS-induced stress. Furthermore, PFAS concentrations significantly affected microbial carbon, nitrogen, and phosphorus cycling, predominantly through indirect alterations in characteristic genus composition. Importantly, noteworthy variations in impacts were observed between perfluorinated carboxylic acids (PFCAs) and perfluorinated sulfonic acids (PFSAs), which might contingent upon C-F bond dissociation energies. The findings shed light on PFAS ecological roles and interaction patterns with microbial communities in human-impacted estuarine environments.

Convergence and divergence of microbial communities in river- Qinghai lake sediment continuum on Tibetan Plateau

Microbiota within interconnected river-lake systems define cycles of carbon and nutrients, yet the mechanisms underlying the assembly of microbial communities during their transition from tributaries to lake remains to be deciphered. This study examined the communities of protists, fungi and bacteria in sediments of Qinghai Lake - a saline lake on the Tibetan Plateau, China - and its connected upstream freshwater tributaries, using high-throughput amplicon sequencing targeting the 18S, ITS2 and 16S rDNA regions. Our findings reveal divergent assembly mechanisms across microbial groups: communities of microeukaryotes (protists and fungi) in tributaries were predominantly shaped by stochastic processes (∼85% contribution), shifting to environmental selection dominance in the lake (∼55%). In contrast, bacterial community assembly in tributaries was primarily deterministic (∼60% environmental selection), shifting to stochastic dominance (∼70%) in the lake. Despite the differences, all groups exhibited congruent biogeographic patterns in terms of diversity and network complexity. The tributary-to-lake transition enhanced the complexity of microbial co-occurrence network but resulted in significant species loss, with α-diversity reduced by 56%-62%. β-diversity increased from tributaries to the estuary but decreased within the lake. Microbial α- and β-diversity correlated positively with sediment C: N ratio but negatively with total sediment C content. Notably, only 1% to 13% of microbial taxa in lake sediments originated from tributaries, suggesting alternative pathways that warrant further geological investigation. This study provides new insights into the convergent biogeographical patterns of diversity and network complexity, coupled with divergent assembly mechanisms, among protist, fungal, and bacterial communities along the river-Qinghai Lake sediment continuum.

Polycyclic Aromatic Hydrocarbons (PAHs) in Freshwater Systems: A Comprehensive Review of Sources, Distribution, and Ecotoxicological Impacts

This comprehensive review offers new perspectives on the distribution, sources, and ecotoxicological impacts of polycyclic aromatic hydrocarbons (PAHs) in freshwater systems. Unlike previous reviews, this work integrates recent findings on PAH dynamics within environmental matrices and emphasizes spatiotemporal variability across geographic regions. It critically examines both anthropogenic and natural sources, as well as the physical, chemical, and biological mechanisms driving PAH transport and fate. Special attention is given to the ecotoxicological effects of PAHs on freshwater organisms, including bioaccumulation, endocrine disruption, and genotoxicity. Notably, this review identifies key knowledge gaps and proposes an interdisciplinary framework to assess ecological risk and guide effective monitoring and management strategies for the protection of freshwater ecosystems.

The effects of polycyclic aromatic hydrocarbons on ecological assembly processes and co-occurrence patterns differ between soil bacterial and fungal communities

Polycyclic aromatic hydrocarbons (PAHs) are hazardous organic pollutants prevalent in soil ecosystems. Bacteria and fungi play important roles in the degradation of PAHs in the soils. However, little is known about the differences between the bacterial and fungal community assemblies in PAH-contaminated soils. In this study, soil bacterial and fungal community distributions were investigated in maize farmlands and roadside barelands around nine coking plants in Shanxi, China. Most of the soil samples were severely polluted with PAHs. A clear microbial biogeographic pattern was observed. Bacterial communities are primarily affected by environmental factors, whereas fungal communities are primarily affected by spatial factors. Null modeling showed that homogeneous selection (deterministic processes) and dispersal limitation (stochastic processes) dominated the bacterial and fungal community assemblages, respectively. PAH concentrations were closely linked to community assembly processes, and influenced microbial co-occurrence by mediating specific network modules. Overall, the effects of PAHs on bacterial community assembly and co-occurrence relationships were greater than those on fungal communities. Some microbial taxa associated with PAH degradation can be considered potential biomarkers that reflect the degree of PAH pollution. These results expand the understanding of the mechanisms underlying the assembly and maintenance of soil microbial communities in response to PAH contamination.

Description of Albidovulum litorale sp. nov., Albidovulum marisflavi sp. nov., Albidovulum salinarum sp. nov., and Albidovulum sediminicola sp. nov., and proposal for reclassification of the genus Defluviimonas as a later heterotypic synonym of Albidovulum

Four Gram-stain-negative, aerobic, rod-shaped bacteria, designated WL0002T, WL0024T, WL0050T, and WL0075T, were isolated from sediment in the coastal areas of Nantong City, China. Metagenomic analysis revealed higher relative abundance of taxa closely related to the four strains in sediment (0.79-2.0 %) than in water (0.34-1.3 %) (Mann-Whitney U test: p < 0.001). Phylogenetic analysis based on 16S rRNA gene and the bac120 gene set both suggested that the four strains are closely related to the genus Defluviimonas. Additionally, Albidovulum inexpectatum DSM 12048T formed a distinct branch within Defluviimonas. The evolutionary distance (ED) and percentage of conserved proteins (POCP) analysis indicated that the four strains and the genus strains of Albidovulum and Defluviimonas should be recognized as a single genus. Genomic relatedness analysis among the four strains and type strains of the genera Albidovulum and Defluviimonas was below species delimitation thresholds, except for strains WL0024T and "D. salinarum" CAU 1641T, which should belong to the same species. Based on phenotypic and genotypic characterization, the four strains should be recognized as novel species in Albidovulum, and it is reasonable to reclassify the genus Defluviimonas as a later heterotypic synonym of Albidovulum, consistent with the classification of the Genome Taxonomy Database (GTDB). Four names are proposed as follows: Albidovulum marisflavi sp. nov. (type strain WL0002T = MCCC 1K06013T = JCM 34653T = GDMCC 1.2437T), Albidovulum salinarum sp. nov. (WL0024T = MCCC 1K06062T = JCM 34656T = GDMCC 1.2438T), Albidovulum litorale sp. nov. (WL0050T = MCCC 1K07524T = JCM 35566T = GDMCC 1.3084T), and Albidovulum sediminicola sp. nov. (WL0075T = MCCC 1K06064T = JCM 34660T = GDMCC 1.2419T).

Dynamics of antibiotic resistance genes and bacterial community structure within substrate biofilms

Biofilms that develop on the surface of substrates are critical for treating wastewater. The accumulation of antibiotic resistance genes (ARGs) within these biofilms is particularly noteworthy. Despite their importance, studies that focus on biofilms attached to substrate surfaces remain scarce. This investigation explored the prevalence and succession of ARGs and microbial dynamics in biofilms on different substrates (ceramic, biomass filter, and steel slag) versus water biofilms over a year. Results showed distinct differences in ARG profiles between water and substrate biofilms. Multidrug ARGs constituted 39.14-46.73% of all ARGs in the substrate biofilms, with macrolide ARGs making up 11.98-14.52%. Seasonal variations influenced the diversity of the ARGs, notably increasing during the spring. The neutral community model suggested that the ARG assembly was dominantly driven by stochastic process. Proteobacteria, Actinobacteria and Campylobacter emerged as the predominant phyla within these biofilms. The microbial community distribution was predominantly influenced by ammonium nitrogen (NH4+-N) (R2 = 0.4113), temperature and total nitrogen (TN). Notably, temperature exerted a critical impact on the microbial community distribution (P = 0.001), identifying it as the principal factor for spatial arrangement. Furthermore, the structural variations of ARGs were primarily driven by total organic carbon (TOC) (R2 = 0.3988), temperature, oxidation-reduction potential (ORP) and NH4+-N. Our findings provided new insights into the optimization of substrate selection and ecological management to manage ARG enrichment, offering a promising strategy for aquatic ecological restoration and pollution control.

Differential insights into the distribution characteristics of bacterial communities and their response to typical pollutants in the sediment and soil of large drinking water reservoir

In this study, a large drinking water reservoir (Fengshuba Reservoir) was chosen as a representative case, and the bacterial communities in the sediments and soils of Water-level fluctuating zone (WLFZ) as well as their responses to heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) were systematically investigated. The results indicated that the abundance and diversity of the bacterial community obviously changed with seasonal hydrological variations in sediments, and the absolute abundance and composition of bacteria community differed significantly between the sediment phase and soil phase. Bacteria with the ability to degrade pollutants rapidly proliferate and gain ascendancy in the soil phase, with Burkholderia-Caballeronia-Paraburkholderia (B-C-P) and Bradyrhizobium forming the core of the largest community. Furthermore, Co-occurrence network analysis indicated that a more stable bacterial community composition in the sediment phase. The community assembly pattern of bacteria in sediments exhibit a higher degree of stochasticity than that observed in soils of the WLFZ. Furthermore, the Spearman correlations found that the interaction between physicochemical factors, HMs, and PAHs with bacteria community was stronger in the soils of WLFZ. In total, the structural equation models indicated that PAHs were the main driver in altering the deterministic process of bacterial community in the sediment, while HMs and physicochemical factors had a greater effect on the bacteria community in the WLFZ. This study systematically revealed the differential characteristics of bacterial community and their response to typical pollutants between the sediments and soils of large drinking water reservoir.

Machine learning models reveal how polycyclic aromatic hydrocarbons influence environmental bacterial communities

Polycyclic aromatic hydrocarbons (PAHs) are harmful and widespread pollutants in the environment, posing an ecological threat. However, exploring the influence of PAHs on environmental bacterial communities in different habitats (soil, water, and sediment) remains a major challenge. We collected and reanalyzed 1924 16S rRNA sequencing samples to determine the effects of PAHs on bacterial communities in different habitats and used machine learning to predict potential degrading bacteria. It was found that PAHs had substantial effects on the bacterial community, and that the bacterial community structure changed differently in different habitats. PAH contamination decreased the relative abundance of Proteobacteria in the soil (16.3 %) and sediment (10.1 %), whereas the abundance of Proteobacteria in water increased by 20.2 %. Among the tested models, the random forest model best identified the effects of PAHs on bacterial groups, with an accuracy of 99.51 % for soil, 97.72 % for sediment, and 100 % for water at the genus level. Using the random forest model, we identified 70 biomarkers that respond to PAHs, including potentially degrading microorganisms such as A4b, Bacillus, Flavobacterium and Polynucleobacter. Furthermore, PAH contamination did not significantly alter the functions of bacterial communities in the environment. This study provides a candidate strain set for future screening of PAH-degrading bacteria and contributes to the study of the adaptability of engineered PAH-degrading bacteria to the environment.

Nano-Fe3O4/FeCO3 modified red soil-based biofilter for simultaneous removal of nitrate, phosphate and heavy metals: Optimization, microbial community and possible mechanism

The pollution of nitrogen, phosphorus and heavy metals in surface water is becoming more and more serious, affecting the safety of water quality. In this study, three biofilters were constructed using iron-modified red soil-based filler carriers (RSC, nano-Fe3O4@RSC, and FeCO3@RSC) combined with strain Zoogloea sp. ZP7 to simultaneously remove nitrate (NO3--N), phosphate (PO43--P), copper (Cu2+), and zinc (Zn2+). The long-term operation results showed that the three groups of biofilters could remove 85.0 %, 90.0 %, and 89.8 % of NO3--N, respectively. Furthermore, the addition of iron compounds enhanced the removal of PO43--P and the resistance to the stress of Cu2+ and Zn2+ in the biofilter. The analysis illustrated that iron modification improved the redox activity and zeta potential of RSC surface. The secondary structure analysis of the protein showed that the microbial secreted proteins were more compact on the surface of the iron-modified RSC, which facilitated the formation of biofilm on the carrier surface. In addition, the iron-modified RSC-based biofilter also showed excellent NO3--N and PO43--P removal efficiency in the treatment of actual surface water. The microbial community analysis results showed that Zoogloea became the dominant species in the biofilter. On the other hand, the presence of iron-reducing bacteria and the expression iron cycle-related genes may contribute to denitrification under low nutrient conditions.

Bacterial specialists playing crucial roles in maintaining system stability and governing microbial diversity in bioremediation of oil-polluted sediments under typical deep-sea condition

Ecologically, interactions and contributions of microbiota generalists and specialists remain largely unexplored in remediation of deep-sea oil pollution. Herein, ecological and evolutionary characteristics of the two taxa were comprehensively investigated in restoration of oil-polluted sediment at deep-sea microcosm. Niche-specialized taxa exhibited rapid speciation rate, more complex network structure and highly interspecific mutualism. In contrast, generalists possessed higher richness but with poor local performance, as evidenced by higher extinction rate, lower stability, and more interspecific antagonism. Generalists were the primary oil degraders, while specialists acted as auxiliaries promoting degradation via production of biofilm and biosurfactant. Evolutionarily, the continuous transition from specialists to generalists insured the exclusion of generalist at a relatively constant level for ecological trade-offs. Collectively, the findings emphasize the importance of specialists in facilitating oil degradation by elucidating their vital roles in maintaining system stability and regulating microbial diversity during process, and offer valuable guidance for designing remediation plans.

Seasonal dynamics of bacterial communities in a highly polluted coastal lagoon: Dominance of sulfur bacteria in response to elevated H2S levels

This study aims to evaluate the effects of different environmental gradients and seasonality on the bacterial communities of an impacted coastal lagoon. While the community compositions were homogenous in surface waters with the dominance of Candidatus Pelagibacter, diversity showed high vertical variation due to salinity and dissolved oxygen gradients. Anoxic conditions occurred at deeper parts of the lagoon, particularly at 14 m and 18 m, where nutrient enrichment and high H2S concentration were detected resulting in a shift of bacterial community to anoxic species. Sulfurimonas, Sulfurovum, and Desulfobacula were dominant genera at 14 m and 18 m where the H2S concentration was high. The community composition of the sediment did not change over seasons, dominated by Syntrophus species. The insights gained from this study may contribute to understanding how dissolved oxygen, H2S concentrations and salinity drive bacterial community structure in euxinic ecosystems especially the dominance of anoxic bacteria.

Occurrence of polycyclic aromatic hydrocarbons in the Yellow River delta: Sources, ecological risks, and microbial response

This research investigated the distribution, sources, and ecological risks of polycyclic aromatic hydrocarbons (PAHs) in the Yellow River Delta (YRD), China, emphasizing the response of soil microorganisms. The study involved quantitative analyses of 16 PAHs specified by the U.S. Environmental Protection Agency (USEPA) in both water and soil, utilizing metagenomic technique to determine the response of microbial communities and metabolism within the soil. Results noted that PAHs in the water mainly originate from pyrogenic source and in the soil originate from mixture source, with higher concentrations found in wetland areas compared to river regions. The ecological risk assessment revealed low-to-moderate risk. Microbial analysis demonstrated increased diversity and abundance of bacteria associated with PAHs in areas with higher PAHs pollution. Metagenomic insights revealed significant effects of organic carbon on PAHs degradation genes (ko00624 and ko00626), as well as significant differences in specific metabolic pathways including phenanthrene degradation, with key enzymes showing significant differences between the two environments. The study underscores the importance of understanding PAHs distribution and microbial responses to effectively manage and mitigate pollution in estuarine environments.

Enhancing the biodegradation of hydrophobic volatile organic compounds: A study on microbial consortia adaptation and the role of surfactants

The emission of hydrophobic Volatile Organic Compounds (VOCs) is a serious environmental issue. Typically, biofilters (BFs) are employed for their treatment, with the potential enhancement of mass transfer through the addition of surfactants. However, disparate results in previous studies have been observed, attributed to uncontrolled conditions during the introduction of surfactants to BFs. Additionally, there has been limited exploration of microbial consortium adaptation to surfactants. To address these gaps, this study followed two approaches. First, the long-term (247 days) removal of cyclohexane was studied in a stirred tank bioreactor (STBR) inoculated with Rhodococcus erythropolys E1 and using Tween 80 at three times the critical micelle concentration (CMC). Second, the short-term (9 days) impact of two (bio)surfactants [Tween 80 (1 × CMC) and Quillaja Saponin (QS, 1 × CMC)] on the removal of cyclohexane, hexane and toluene was investigated in batch tests using three types of inocula: a pure culture of Rhodococcus erythropolys E1 (X0), a microbial consortium adapted to cyclohexane (X1), and a microbial consortium adapted to cyclohexane with Tween 80 (X2). For long-term operation, the addition of Tween 80 at 3 × CMC improved cyclohexane removal efficiency (RE) to 87 ± 1% (elimination capacity, EC = 145 ± 25 mg m-3 h-1, gas residence time, GRT = 20 min, inlet concentration, Cin = 14.9 ± 2.5 ppmv), compared to a RE of 32 ± 9% (EC = 44 ± 8 mg m-3 h-1, GRT = 20 min, Cin = 15.1 ± 0.7 ppmv) under similar conditions without surfactants. For short-term operation, the addition of QS at 1 × CMC significantly increased biomass growth, resulting in lower maximum specific consumption rates for X1 and X2 compared to scenarios without surfactants or 1 × CMC Tween 80. The most abundant genera in X1 and X2 were Paludisphaera (26-23%), 67-14 genus (17-23%), and Rhodococcus (9-18%), respectively.

Similarities and differences in bacterial communities between the Pearl River (Guangzhou section) and its estuary

BACKGROUND

The Pearl River and its estuary are highly exposed to anthropogenic disturbance. Because bacterial communities play an indispensable role in aquatic ecosystems, there has been an increased research focus on the statuses of these communities under human-induced perturbations.

METHODS AND RESULTS

This study investigated the composition, diversity, and structure of bacterial communities across 29 sites from the Guangzhou section of the Pearl River (GZ) to the Pearl River Estuary (PRE) using 16S rRNA gene amplicons. The results revealed similar dominant phyla of bacteria in both GZ and PRE, as well as significant differences in bacterial community composition and diversity between the two sections. Proteobacteria and Cyanobacteria were identified as the primary drivers of compositional differences between GZ and PRE. The Cyanobacteria Dolichospermum_NIES41 and Cuspidothrix issatschenkoi were only present in GZ, whereas the marine Gram-negative bacteria of Porticoccus litoralis and Thalassolituus oleivorans were unique to PRE.

CONCLUSIONS

Bacterial community composition and diversity exhibit both similarities and differences between GZ and PRE; Proteobacteria and Cyanobacteria are key factors underlying these variations. Bacterial communities in both GZ and PRE are strongly influenced by human activities, and salinity is an important factor in controlling their differences. This study provides a comprehensive analysis of the bacterial communities in GZ and PRE, establishing a foundation for better management of aquatic ecosystems impacted by anthropogenic activities.

Combined influence of the nanoplastics and polycyclic aromatic hydrocarbons exposure on microbial community in seawater environment

Nanoplastics (NPs) and polycyclic aromatic hydrocarbons (PAHs) are recognized as persistent organic pollutant (POPs) with demonstrated physiological toxicity. When present in aquatic environments, the two pollutants could combine with each other, resulting in cumulative toxicity to organisms. However, the combined impact of NPs and PAHs on microorganisms in seawater is not well understood. In this study, we conducted an exposure experiment to investigate the individual and synergistic effects of NPs and PAHs on the composition, biodiversity, co-occurrence networks of microbial communities in seawater. Exposure of individuals to PAHs led to a reduction in microbial community richness, but an increase in the relative abundance of species linked to PAHs degradation. These PAHs-degradation bacteria acting as keystone species, maintained a microbial network complexity similar to that of the control treatment. Exposure to individual NPs resulted in a reduction in the complexity of microbial networks. Furthermore, when PAHs and NPs were simultaneously present, the toxic effect of NPs hindered the presence of keystone species involved in PAHs degradation, subsequently limiting the degradation of PAHs by marine microorganisms, resulting in a decrease in community diversity and symbiotic network complexity. This situation potentially poses a heightened threat to the ecological stability of marine ecosystems. Our work strengthened the understanding of the combined impact of NPs and PAHs on microorganisms in seawater.

Community coalescence under variable hydrochemical conditions of the Chesapeake Bay shaped bacterial diversity and functional traits

Community coalescence related to bacterial mixing events regulates community characteristics and affects the health of estuary ecosystems. At present, bacterial coalescence and its driving factors are still unclear. The present study used a dataset from the Chesapeake Bay (2017) to address how bacterial community coalescence in response to variable hydrochemistry in estuarine ecosystems. We determined that variable hydrochemistry promoted the deterioration of water quality. Temperature, orthophosphate, dissolved oxygen, chlorophyll a, Secchi disk depth, and dissolved organic phosphorus were the key environmental factors driving community coalescence. Bacteria with high tolerance to environmental change were the primary taxa accumulated in community coalescence, and the significance of deterministic processes to communities was revealed. Community coalescence was significantly correlated with the pathways of metabolism and organismal systems, and promoted the co-occurrence of antibiotic resistance and virulence factor genes. Briefly, community coalescence under variable hydrochemical conditions shaped bacterial diversity and functional traits, to optimise strategies for energy acquisition and lay the foundation for alleviating environmental pressures. However, potential pathogenic bacteria in community coalescence may be harmful to human health and environmental safety. The present study provides a scientific reference for ecological management of estuaries.

Enhanced Soil Fertility and Carbon Sequestration in Urban Green Spaces through the Application of Fe-Modified Biochar Combined with Plant Growth-Promoting Bacteria

The soil of urban green spaces is severely degraded due to human activities during urbanization, and it is crucial to investigate effective measures that can restore the ecological functions of the soil. This study investigated the effects of plant growth promoting bacteria (Bacillus clausii) and Fe-modified biochar on soil fertility increases and mechanisms of carbon sequestration. Additionally, the effects on C-cycling-related enzyme activity and the bacterial community were also explored. Six treatments included no biochar or Bacillus clausii suspension added (CK), only Bacillus clausii suspension (BC), only biochar (B), only Fe-modified biochar (FeB), biochar combined with Bacillus clausii (BBC), and Fe-modified biochar combined with Bacillus clausii (FeBBC). Compared with other treatments, the FeBBC treatment significantly decreased soil pH, alleviated soil alkalization, and increased the alkali-hydro nitrogen content in the soil. Compared to the individual application of FeB and BC, the FeBBC treatment significantly improved aggregates' stability and positively improved soil fertility and ecological function. Additionally, compared to the individual application of FeB and BC, the soil organic carbon (SOC), particulate organic carbon (POC), and soil inorganic carbon (SIC) contents for the FeBBC-treated soil increased by 28.46~113.52%, 66.99~434.72%, and 7.34~10.04%, respectively. In the FeBBC treatment, FeB can improve soil physicochemical properties and provide bacterial attachment sites, increase the abundance and diversity of bacterial communities, and promote the uniform distribution of carbon-related bacteria in the soil. Compared to a single ecological restoration method, FeBBC treatment can improve soil fertility and carbon sequestration, providing important reference values for urban green space soil ecological restoration.

Effect of Pond-Based Rice Floating Bed on the Microbial Community Structure and Quality of Water in Pond of Mandarin Fish Fed Using Artificial Diet

The culture of mandarin fish using artificial feed has been gaining increasing attention in China. Ensuring good water quality in the ponds is crucial for successful aquaculture. Recently, the trial of pond-based rice floating beds (PRFBs) in aquaculture ponds has shown promising results. This research assessed the impact of PRFBs on the microbial community structure and overall quality of the aquaculture pond, thereby enhancing our understanding of its functions. The results revealed that the PRFB group exhibited lower levels of NH4+-N, NO2--N, NO3--N, TN, TP, and Alk in pond water compared to the control group. The microbial diversity indices in the PRFB group showed a declining trend, while these indices were increasing in the control group. At the phylum level, there was a considerable increase in Proteobacteria abundance in the PRFB group throughout the culture period, suggesting that PRFBs may promote the proliferation of Proteobacteria. In the PRFB group, there was a remarkable decrease in bacterial populations related to carbon, nitrogen, and phosphorus metabolism, including genera Rhodobacter, Rhizorhapis, Dinghuibacter, Candidatus Aquiluna, and Chryseomicrobium as well as the CL500_29_marine_group. Overall, the research findings will provide a basis for the application of aquaculture of mandarin fish fed an artificial diet and rice floating beds.

Variations in bacterial community succession and assembly mechanisms with mine age across various habitats in coal mining subsidence water areas

Microorganisms play a pivotal role as catalysts in the biogeochemical cycles of aquatic ecosystems within coal mining subsidence areas. Despite their importance, the succession of microbial communities with increasing mine age, particularly across different habitats, and variations in phylogenetically-based community assembly mechanisms are not well understood. To address this knowledge gap, we collected 72 samples from lake sediments, water, and surrounding topsoil (0-20 cm) at various mining stages (early: 16 years, middle: 31 years, late: 40 years). We analyzed these samples using 16S rRNA gene sequencing and multivariate statistical methods to explore the dynamics and assembly mechanisms of bacterial communities. Our findings reveal that increases in phosphorus and organic matter in sediments, correlating with mining age, significantly enhance bacterial alpha diversity while reducing species richness (P < 0.001). Homogenizing selection (49.9 %) promotes species asynchrony-complementarity, augmenting the bacterial community's ability to metabolize sulfur, phosphorus, and organic matter, resulting in more complex-stable co-occurrence networks. In soil, elevated nitrogen and organic carbon levels markedly influence bacterial community composition (Adonis R2 = 0.761), yet do not significantly alter richness or diversity (P > 0.05). The lake's high connectivity with surrounding soil leads to substantial species drift and organic matter accumulation, thereby increasing bacterial richness in later stages (P < 0.05) and enhancing the ability to metabolize dissolved organic matter, including humic-like substances, fulvic acids, and protein-like materials. The assembly of soil bacterial communities is largely governed by stochastic processes (79.0 %) with species drift (35.8 %) significantly shaping these communities over a broad spatial scale, also affecting water bacterial communities. However, water bacterial community assembly is primarily driven by stochastic processes (51.2 %), with a substantial influence from habitat quality (47.6 %). This study offers comprehensive insights into the evolution of microbial community diversity within coal mining subsidence water areas, with significant implications for enhancing environmental management and protection strategies for these ecosystems.

The response pattern of the microbial community structure and metabolic profile of jiupei to Bacillus subtilis JP1 addition during baijiu fermentation

BACKGROUND

Baijiu brewing is a complex and multifaceted multimicrobial co-fermentation process, in which various microorganisms interact to form an interdependent micro-ecosystem, subsequently influencing metabolic activities and compound production. Among these microorganisms, Bacillus, an important bacterial genus in the liquor brewing process, remains unclear in its role in shaping the brewing microbial community and its functional metabolism.

RESULTS

A baijiu fermentation system was constructed using B. subtilis JP1 isolated from native jiupei (grain mixture) combined with daqu (a saccharifying agent) and huangshui (a fermentation byproduct). Based on high-throughput amplicon sequencing analysis, it was evident that B. subtilis JP1 significantly influences bacterial microbial diversity and fungal community structure in baijiu fermentation. Of these, Aspergillus and Monascus emerge as the most markedly altered microbial genera in the jiupei community. Based on co-occurrence networks and bidirectional orthogonal partial least squares discriminant analysis models, it was demonstrated that the addition of B. subtilis JP1 intensified microbial interactions in jiupei fermentation, consequently enhancing the production of volatile flavor compounds such as heptanoic acid, butyl hexanoate and 3-methylthiopropanol in jiupei.

CONCLUSION

B. subtilis JP1 significantly alters the microbial community structure of jiupei, enhancing aroma formation during fermentation. These findings will contribute to a broader application in solid-state fermentation. © 2024 Society of Chemical Industry.

Differentiated cognition of the effects of human activities on typical persistent organic pollutants and bacterioplankton community in drinking water source

Accelerated urbanization in developing countries led to a typical gradient of human activities (low, moderate and high human activities), which affected the pollution characteristics and ecological functions of aquatic environment. However, the occurrence characteristics of typical persistent organic pollutants, including organochlorine pesticides (OCPs) and polycyclic aromatic hydrocarbons (PAHs), and bacterioplankton associated with the gradient of human activities in drinking water sources is still lacking. Our study focused on a representative case - the upper reaches of the Dongjiang River (Pearl River Basin, China), a drinking water source characterized by a gradient of human activities. A comprehensive analysis of PAHs, OCPs and bacterioplankton in the water phase was performed using gas chromatography-mass spectrometry (GC-MS) and the Illumina platform. Moderate human activity could increase the pollution of OCPs and PAHs due to local agricultural activities. The gradient of human activities obviously influenced the bacterioplankton community composition and interaction dynamics, and low human activity resulted in low bacterioplankton diversity. Co-occurrence network analysis indicated that moderate human activity could promote a more modular organization of the bacterioplankton community. Structural equation models showed that nutrients could exert a negative influence on the composition of bacterioplankton, and this phenomenon did not change with the gradient of human activities. OCPs played a negative role in shaping bacterioplankton composition under the low and high human activities, but had a positive effect under the moderate human activity. In contrast, PAHs showed a strong positive effect on bacterioplankton composition under low and high human activities and a weak negative effect under moderate human activity. Overall, these results shed light on the occurrence characteristics of OCPs, PAHs and their ecological effects on bacterioplankton in drinking water sources along the gradient of human activities.

Response of Microbial Communities to Naturally Occurring Radioactive Material-Contaminated Sediments: A Microcosm-Based Study

There is a growing need to understand the potential ecological impacts of contaminants in offshore oil and gas infrastructure, especially if that infrastructure is to be left in situ as a decommissioning option. Naturally occurring radioactive material (NORM) is one type of contaminant found in solid deposits on internal surfaces of infrastructure that poses potential ecological harm if released into the marine environment. Microbes are important components of marine sediment ecosystems because they provide ecosystem services, yet the impacts of NORM contamination to these communities are not well understood. The present study aimed to investigate the response of benthic microbial communities to NORM-contaminated scale, collected from an offshore oil and gas system, via controlled laboratory microcosm studies. Changes to microbial communities in natural sediment and sediments spiked with NORM at radium-226 activity concentrations ranging from 9.5 to 59.8 Bq/kg (in partial equilibria with progeny) over 7 and 28 days were investigated using high-throughput sequencing of environmental DNA extracted from experimental sediments. There were no significant differences in microbial community composition between control and scale-spiked sediments over 7 and 28 days. However, we observed a greater presence of Firmicutes in the scale-mixed treatment and Chloroflexi in the scale-surface treatments after 28 days. This could suggest selection for species with contaminant tolerance or potential resilience to radiation and metal toxicity. Further research is needed to explore microbial tolerance mechanisms and their potential as indicators of effects of radionuclide-contaminated sediments. The present study demonstrated that microcosm studies can provide valuable insights about the potential impacts of contamination from oil and gas infrastructure to sediment microbial communities. Environ Toxicol Chem 2024;43:1648-1661. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Life in the PFAS lane: The impact of perfluoroalkyl substances on photosynthesis, cellular exudates, nutrient cycling, and composition of a marine microbial community

Perfluoroalkyl substances (PFAS) are of great ecological concern, however, exploration of their impact on bacteria-phytoplankton consortia is limited. This study employed a bioassay approach to investigate the effect of unary exposures of increasing concentrations of PFAS (perfluorooctane sulfonate (PFOS) and 6:2 fluorotelomer sulfonate (6:2 FTS)) on microbial communities from the northwestern Gulf of Mexico. Each community was examined for changes in growth and photophysiology, exudate production and shifts in community structure (16S and 18S rRNA genes). 6:2 FTS did not alter the growth or health of phytoplankton communities, as there were no changes relative to the controls (no PFOS added). On the other hand, PFOS elicited significant phototoxicity (p < 0.05), altering PSII antennae size, lowering PSII connectivity, and decreasing photosynthetic efficiency over the incubation (four days). PFOS induced a cellular protective response, indicated by significant increases (p < 0.001) in the release of transparent exopolymer particles (TEP) compared to the control. Eukaryotic communities (18S rRNA gene) changed substantially (p < 0.05) and to a greater extent than prokaryotic communities (16S rRNA gene) in PFOS treatments. Community shifts were concentration-dependent for eukaryotes, with the low treatment (5 mg/L PFOS) dominated by Coscinodiscophyceae (40 %), and the high treatment (30 mg/L PFOS) marked by a Trebouxiophyceae (50 %) dominance. Prokaryotic community shifts were not concentration dependent, as both treatment levels became depleted in Cyanobacteriia and were dominated by members of the Bacteroidia, Gammaproteobacteria, and Alphaproteobacteria classes. Further, PFOS significantly decreased (p < 0.05) the Shannon diversity and Pielou's evenness across treatments for eukaryotes, and in the low treatment (5 mg/L PFOS) for prokaryotes. These findings show that photophysiology was not impacted by 6:2 FTS but PFOS elicited toxicity that impacted photosynthesis, exudate release, and community composition. This research is crucial in understanding how PFOS impacts microbial communities.

Indirect Impact of Eutrophication on Occurrence, Air-Water Exchange, and Vertical Sinking Fluxes of Antibiotics in a Subtropical River

A significant challenge that warrants attention is the influence of eutrophication on the biogeochemical cycle of emerging contaminants (ECs) in aquatic environments. Antibiotics pollution in the eutrophic Pearl River in South China was examined to offer new insights into the effects of eutrophication on the occurrence, air-water exchange fluxes (Fair-water), and vertical sinking fluxes (Fsinking) of antibiotics. Antibiotics transferred to the atmosphere primarily through aerosolization controlled by phytoplankton biomass and significant spatiotemporal variations were observed in the Fair-water of individual antibiotics throughout all sites and seasons. The Fsinking of ∑AB14 (defined as a summary of 14 antibiotics) was 750.46 ± 283.19, 242.71 ± 122.87, and 346.74 ± 249.52 ng of m-2 d-1 in spring, summer, and winter seasons. Eutrophication indirectly led to an elevated pH, which reduced seasonal Fair-water of antibiotics, sediment aromaticity, and phytoplankton hydrophobicity, thereby decreasing antibiotic accumulation in sediments and phytoplankton. Negative correlations were further found between Fsinking and the water column daily loss of antibiotics with phytoplankton biomass. The novelty of this study is to provide new complementary knowledge for the regulation mechanisms of antibiotics by phytoplankton biological pump, offering novel perspectives and approaches to understanding the coupling between eutrophication and migration and fate of antibiotics in a subtropical eutrophic river.

Interaction patterns and keystone taxa of bacterial and eukaryotic communities during sulfamethoxazole mineralization in lake sediment

Sulfamethoxazole (SMX) is a common antibiotic pollutant in aquatic environments, which is highly persistent under various conditions and significantly contributes to the spread of antibiotic resistance. Biodegradation is the major pathway to eliminate antibiotics in the natural environment. The roles of bacteria and eukaryotes in the biodegradation of antibiotics have received considerable attention; however, their successions and co-occurrence patterns during the biodegradation of antibiotics remain unexplored. In this study, 13C-labled SMX was amended to sediment samples from Zhushan Bay (ZS), West Shore (WS), and Gonghu Bay (GH) in Taihu Lake to explore the interplay of bacterial and eukaryotic communities during a 30-day incubation period. The cumulative SMX mineralization on day 30 ranged from 5.2 % to 19.3 %, which was the highest in WS and the lowest in GH. The bacterial community showed larger within-group interactions than between-group interactions, and the positive interactions decreased during incubation. However, the eukaryotic community displayed larger between-group interactions than within-group interactions, and the positive interactions increased during incubation. The proportion of negative interactions between bacteria and eukaryotes increased during incubation. Fifty genera (including 46 bacterial and 4 eukaryotic genera) were identified as the keystone taxa due to their dominance in the co-occurrence network and tolerance to SMX. The cumulative relative abundance of these keystone taxa significantly increased during incubation and was consistent with the SMX mineralization rate. These taxa closely cooperated and played vital roles in co-occurrence networks and microbial community interactions, signifying their crucial role in SMX mineralization. These findings broadened our understanding of the complex interactions of microorganisms under SMX exposure and their potential functions during SMX mineralization, providing valuable insights for in situ bioremediation.

Residual effects of chlorinated organic pollutants on microbial community and natural redox processes in coastal wetlands

Chlorinated organic pollutants (COPs) are common in flooded environments. To examine the residual status and effects of COPs on flooded environments, a survey of 7 coastal wetlands in Zhejiang, East China was conducted. Total COP concentrations detected from 95.69 to 412.76 ng g-1 dw. Gamma-HCH and o,p'-DDT posed the greatest risk with exceedance rates of 100% according to sediment quality guidelines. Samples with higher COP pollution had higher microbial diversity, more complex microbial networks, more deterministic community assembly processes and lower microbiome stability, indicating an improved soil function for balance cycle of substances, especially for COP degradation. Further analysis using quantitative real-time PCR suggested COP-dechlorination interacted with natural redox processes, especially sulfate reduction and methanogenesis. The positive correlation between CH4 and pentachlorobenzene indicated a potential increase in greenhouse gas emissions caused by COP pollution. Correlation between dsr gene and COPs demonstrated the ability of sulfate-reducing bacteria to degrade COPs. Particularly, facultative OHRB such as sulfate-reducing bacteria hold significant importance in the process of COP-dechlorination. This finding provides a reference for COP pollution remediation. Collectively, our study offers new insight into the residual effect of COPs in coastal wetlands and contributes to an improved understanding of bioremediation strategies for COP pollution.

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.

Functional keystone taxa promote N and P removal of the constructed wetland to mitigate agricultural nonpoint source pollution

Characterized by irregular spatial and temporal variations of pollutant loading and complex occurrence mechanisms, agricultural nonpoint source pollution (ANPSP) has always been a great challenge in field restoration worldwide. Returning farmlands to wetlands (RFWs) as an ecological restoration mode among various constructed wetlands was selected to manage ANPSP in this study. Triarrhena lutarioriparia, Nelumbo nucifera and Zizania latifolia monocultures were designed and the water pollutants was monitored. N. nucifera and Z. latifolia could reach the highest TN (53.28 %) and TP (53.22 %) removal efficiency, respectively. By 16s high-throughput sequencing of rhizosphere bacteria, 45 functional species were the main contributors for efficient N and P removal, and 38 functional keystone taxa (FKT) were found with significant ecological niche roles and metabolic functions. To our knowledge, this is the first study to explore the microbial driving N and P removal mechanism in response to ANPSP treated by field scale RFWs.

Toward an intensive understanding of sewer sediment prokaryotic community assembly and function

Prokaryotic communities play important roles in sewer sediment ecosystems, but the community composition, functional potential, and assembly mechanisms of sewer sediment prokaryotic communities are still poorly understood. Here, we studied the sediment prokaryotic communities in different urban functional areas (multifunctional, commercial, and residential areas) through 16S rRNA gene amplicon sequencing. Our results suggested that the compositions of prokaryotic communities varied significantly among functional areas. Desulfomicrobium, Desulfovibrio, and Desulfobacter involved in the sulfur cycle and some hydrolytic fermentation bacteria were enriched in multifunctional area, while Methanospirillum and Methanoregulaceae, which were related to methane metabolism were significantly discriminant taxa in the commercial area. Physicochemical properties were closely related to overall community changes (p < 0.001), especially the nutrient levels of sediments (i.e., total nitrogen and total phosphorus) and sediment pH. Network analysis revealed that the prokaryotic community network of the residential area sediment was more complex than the other functional areas, suggesting higher stability of the prokaryotic community in the residential area. Stochastic processes dominated the construction of the prokaryotic community. These results expand our understanding of the characteristics of prokaryotic communities in sewer sediment, providing a new perspective for studying sewer sediment prokaryotic community structure.