Deterministic mechanisms drive bacterial communities assembly in industrial wastewater treatment system

Regulatory of salinity on assembly of activated sludge microbial communities and nitrogen transformation potential in industrial plants of the lower Yangtze River basin

This study aims to thoroughly investigate the impact mode of salinity carried by industrial wastewater on the anaerobic-anoxic-oxic (A2O) sludge in wastewater treatment plants (WWTPs). Through comprehensive investigation of the A2O stage activated sludge (AS) from 19 industrial WWTPs in the downstream area of the Yangtze River, China, A total of 38 samples of anaerobic sludge and oxic sludge were collected and analyzed. We found that salinity stress significantly inhibits the growth of the AS community, particularly evident in the anaerobic sludge community. Furthermore, the high-saline environment induces changes in the structure and functional patterns of the AS community, leading to intensive interactions and resource exchanges among microorganisms. Halophilic microorganisms may play a crucial role in this process, significantly impacting the overall community structure, especially in the oxic sludge community. Additionally, salinity stress not only suppresses the nitrogen transformation potential of the AS but also leads to the accumulation of nitrite, thereby increasing the emission potential of both NO and N2O, exacerbating the greenhouse effect of the A2O process in industrial WWTPs. The findings of this study provide necessary theoretical support for maintaining the long-term stable operation of the A2O sludge system in industrial WWTPs, reducing carbon footprint, and improving nitrogen removal efficiency.

Dynamic patterns of carbohydrate metabolism genes in bacterioplankton during marine algal blooms

Carbohydrates play a pivotal role in nutrient recycling and regulation of algal-bacterial interactions. Despite their ecological significance, the intricate molecular mechanisms governing regulation of phycosphere carbohydrates by bacterial taxa linked with natural algal bloom have yet to be fully elucidated. Here, a comprehensive temporal metagenomic analysis was conducted to explore the carbohydrate-active enzyme (CAZyme) genes in two discrete algal bloom microorganisms (Gymnodinium catenatum and Phaeocystis globosa) across three distinct bloom stages: pre-bloom, peak bloom, and post-bloom. Elevated levels of extracellular carbohydrates, primarily rhamnose, galactose, glucose, and arabinose, were observed during the initial and post-peak stages. The prominent CAZyme families identified-glycoside hydrolases (GH) and carbohydrate-binding modules (CBMs)-were present in both algal bloom occurrences. In the G. catenatum bloom, GH23/24 and CBM13/14 were prevalent during the pre-bloom and peak bloom stages, whereas GH2/3/30 and CBM12/24 exhibited increased prevalence during the post-bloom phase. In contrast, the P. globosa bloom had a dominance of GH13/23 and CBM19 in the initial phase, and this was succeeded by GH3/19/24/30 and CBM54 in the later stages. This gene pool variation-observed distinctly in specific genera-highlighted the dynamic structural shifts in functional resources driven by temporal alterations in available substrates. Additionally, ecological linkage analysis underscored a correlation between carbohydrates (or their related genes) and phycospheric bacteria, hinting at a pattern of bottom-up control. These findings contribute to understanding of the dynamic nature of CAZymes, emphasizing the substantial influence of substrate availability on the metabolic capabilities of algal symbiotic bacteria, especially in terms of carbohydrates.

From disinfection to pathogenicity: Occurrence, resistome risks and assembly mechanism of biocide and metal resistance genes in hospital wastewaters

Hospital wastewaters (HWWs) represent critical reservoir for the accumulation and propagation of resistance genes. However, studies on biocide and metal resistance genes (BMRGs) and their associated resistome risks and driving mechanisms in HWWs are still in their infancy. Here, metagenomic assembly was firstly used to investigate host pathogenicity and transferability profiles of BMGRs in a typical HWWs system. As a result, genes conferring resistance to Ethidium Bromide, Benzylkonium Chloride, and Cetylpyridinium Chloride dominated biocide resistance genes (BRGs), whereas Cu resistance gene was the largest contributor of metal resistance genes (MRGs). Most BMRGs experienced significant reduction from anoxic-aerobic treatment to sedimentation stages but exhibited enrichment after chlorine disinfection. Network analysis indicated intense interactions between BMRGs and virulence factors (VFs). Polar_flagella, belonging to the adherence was identified to play important role in the network. Contig-based analysis further revealed noteworthy shifts in host associations along the treatment processes, with Pseudomonadota emerging as the primary carrier, hosting 91.1% and 85.3% of the BRGs and MRGs. A total of 199 opportunistic pathogens were identified to carry 285 BMRG subtypes, which mainly included Pseudomonas alcaligenes, Pseudomonas lundensis, and Escherichia coli. Notably, ruvB conferring resistance to Cr, Cetylpyridinium Chloride, and Dodine were characterized with the highest frequency carried by pathogens. Diverse co-occurrence patterns between BMRGs and mobile genetic elements (MGEs) were found from the raw influent to final effluent. Overall, 10.5% BRGs and 8.84% MRGs were mobile and among the 4 MGEs, transposase exhibited the greatest potential for the BMRGs dissemination. Furthermore, deterministic processes played a dominant role in bacterial communities and BMRGs assembly in HWWs. Bacterial communities contributed more than MGEs in shaping the resistome. Taken together, this work demonstrated widespread BMRGs pollution throughout the HWWs treatment system, emphasizing the potential for informing resistome risk and ecological mechanism in medical practice.

Microbial community assembly in engineered bioreactors

Microbial community assembly (MCA) processes that shape microbial communities in environments are being used to analyze engineered bioreactors such as activated sludge systems and anaerobic digesters. The goal of studying MCA is to be able to understand and predict the effect of design and operation procedures on bioreactor microbial composition and function. Ultimately, this can lead to bioreactors that are more efficient, resilient, or resistant to perturbations. This review summarizes the ecological theories underpinning MCA, evaluates MCA analysis methods, analyzes how these MCA-based methods are applied to engineered bioreactors, and extracts lessons from case studies. Furthermore, we suggest future directions in MCA research in engineered bioreactor systems. The review aims to provide insights and guidance to the growing number of environmental engineers who wish to design and understand bioreactors through the lens of MCA.

Deciphering the core bacterial community structure and function and their response to environmental factors in activated sludge from pharmaceutical wastewater treatment plants

Pharmaceutical wastewater is recognized for its heightened concentrations of organic pollutants, and biological treatment stands out as an effective technology to remove these organic pollution. Therefore, a comprehensive exploration of core bacterial community compositions, functions, and their responses to environmental factors in pharmaceutical wastewater treatment plants (PWWTPs) is important for understanding the removal mechanism of these organic pollutants. This study comprehensively investigated 36 activated sludge (AS) samples from 15 PWWTPs in China. The results revealed that Proteobacteria (45.41%) was the dominant phylum in AS samples, followed by Bacteroidetes (19.54%) and Chloroflexi (4.13%). While the dominant genera were similar in both aerobic and anaerobic treatment processes, their relative abundances exhibited significant variations. Genera like HA73, Kosmotoga, and Desulfovibrio were more abundant during anaerobic treatment, while Rhodoplanes, Bdellovibrio, and Hyphomicrobium dominated during aerobic treatment. 13 and 10 core operational taxonomic units (OTUs) were identified in aerobic and anaerobic sludge, respectively. Further analysis revealed that core OTUs belonging to genera Kosmotoga, Desulfovibrio, Thauera, Hyphomicrobium, and Chelativorans, were associated with key functions, including sulfur metabolism, methane metabolism, amino acid metabolism, carbohydrate metabolism, toluene degradation, and nitrogen metabolism. Furthermore, this study highlighted the crucial roles of environmental factors, such as COD, NH4+-N, SO42-, and TP, in shaping both the structure and core functions of bacterial communities within AS of PWWTPs. Notably, these factors indirectly affect functional attributes by modulating the bacterial community composition and structure in pharmaceutical wastewater. These findings provide valuable insights for optimizing the efficiency of biochemical treatment processes in PWWTPs.

Microbial communities exhibit distinct diversities and assembly mechanisms in rainwater and tap-water storage systems

Roof-harvested rainwater stored for potable and nonpotable usages represent a clean and sustainable water supply resource. However, the microbial dynamics and mechanisms of community assembly in long-termed operated rainwater storage systems remain elusive. In this study, characteristics of microbial communities in different habitats were systematically compared within rainwater and tap-water simulated storage systems (SWSSs) constructed with different tank materials (PVC, stainless steel and cement). Distinct microbial communities were observed between rainwater and tap-water SWSSs for both water and biofilm samples (ANOSIM, p < 0.05), with lower diversity indexes noted in rainwater samples. Notably, a divergent potential pathogen profile was observed between rainwater and tap-water SWSSs, with higher relative abundances of potential pathogens noted in rainwater SWSSs. Moreover, tank materials had a notable impact on microbial communities in rainwater SWSSs (ANOSIM, p < 0.05), rather than tap-water SWSSs, illustrating the distinct interplay between water chemistry and engineering factors in shaping the SWSS microbiomes. Deterministic processes contributed predominantly to the microbial community assembly in cement rainwater SWSSs and all tap-water SWSSs, which might be ascribed to the high pH levels in cement rainwater SWSSs and low-nutrient levels in all tap-water SWSSs, respectively. However, microbial communities in the PVC and stainless-steel rainwater SWSSs were mainly driven by stochastic processes. Overall, the results provided insights to the distinct microbial assembly mechanisms and potential health risks in stored roof-harvested rainwater, highlighting the importance of developing tailored microbial management strategies for the storage and utilization of rainwater.

Unveiling the power of COD/N on constructed wetlands in a short-term experiment: Exploring microbiota co-occurrence patterns and assembly dynamics

Constructed wetlands (CWs) are a cost-effective and environmentally friendly wastewater treatment technology. The influent chemical oxygen demand (COD)/nitrogen (N) ratio (CNR) plays a crucial role in microbial activity and purification performance. However, the effects of CNR changes on microbial diversity, interactions, and assembly processes in CWs are not well understood. In this study, we conducted comprehensive mechanistic experiments to investigate the response of CWs to changes in influent CNR, focusing on the effluent, rhizosphere, and substrate microbiota. Our goal is to provide new insights into CW management by integrating microbial ecology and environmental engineering perspectives. We constructed two groups of horizontal subsurface flow constructed wetlands (HFCWs) and set up three influent CNRs to analyse the microbial responses and nutrient removal. The results indicated that increasing influent CNR led to a decrease in microbial α-diversity and niche width. Genera involved in nitrogen removal and denitrification, such as Rhodobacter, Desulfovibrio, and Zoogloea, were enriched under medium/high CNR conditions, resulting in higher nitrate (NO3--N) removal (up to 99 %) than that under lower CNR conditions (<60 %). Environmental factors, including water temperature (WT), pH, and phosphorus (P), along with CNR-induced COD and NO3--N play important roles in microbial succession in HFCWs. The genus Nitrospira, which is involved in nitrification, exhibited a significant negative correlation (p < 0.05) with WT, COD, and P. Co-occurrence network analysis revealed that increasing influent CNR reduced the complexity of the network structure and increased microbial competition. Analysis using null models demonstrated that the microbial community assembly in HFCWs was primarily driven by stochastic processes under increasing influent CNR conditions. Furthermore, HFCWs with more stochastic microbial communities exhibited better denitrification performance (NO3--N removal). Overall, this study enhances our understanding of nutrient removal, microbial co-occurrence, and assembly mechanisms in CWs under varying influent CNRs.

Ecological and functional differences of abundant and rare sub-communities in wastewater treatment plants across China

The microbial community in activated sludge is composed of a small number of abundant sub-community with high abundance and a large number of rare sub-community with limited abundance. Our knowledge regarding the ecological properties of both abundant and rare sub-communities in activated sludge is limited. This article presented an analysis of functional prediction, assembly mechanisms, and biogeographic distribution characteristics of abundant and rare sub-communities in 211 activated sludge samples from 60 wastewater treatment plants across China. Moreover, this study investigated the dominant factors influencing the community structure of these two microbial groups. The results showed that the functions associated with carbon and nitrogen cycling were primarily detected in abundant sub-community, while rare sub-community were primarily involved in sulfur cycling. Both microbial groups were mainly influenced by dispersal limitation, which, to some extent, resulted in a distance-decay relationship in their biogeographic distribution. Moreover, a higher spatial turnover rate of rare sub-communities (0.0887) suggested that spatial differences in microbial community structure among different WWTPs may mainly result from rare sub-community. Moreover, SEM showed that geographic locations affected rare sub-communities greatly, which agreed with their higher dispersal limitation and turnover rate. In contrast, influent characteristics showed stronger correlations with abundant sub-communities, suggesting that abundant sub-community may contribute more to the removal of pollutants. This study enhanced our understanding of abundant and rare microorganisms in activated sludge especially the role of rare species and provided scientific evidence for precise regulation and control of wastewater treatment plants.

Insight into the role of niche concept in deciphering the ecological drivers of MPs-associated bacterial communities in mangrove forest

Myriad inherent and variable environmental features are controlling the assembly and succession of bacterial communities colonizing on mangrove microplastics (MPs). However, the mechanisms governing mangrove MPs-associated bacterial responses to environmental changes still remain unknown. Here, we assessed the dissimilarities of MPs-associated bacterial composition, diversity and functionality as well as quantified the niche variations of each taxon on plastispheres along river-mangrove-ocean and mangrove landward-to-seaward gradients in the Beibu Gulf, China, respectively. The bacterial richness and diversity as well as the niche breadth on mangrove sedimentary MPs dramatically decreased from landward to seaward regions. Characterizing the niche variations linked the difference of ecological drivers of MPs-associated bacterial populations and functions between river-mangrove-ocean (microplastic properties) and mangrove landward-to-seaward plastispheres (sediment physicochemical properties) to the trade-offs between selective stress exerted by inherent plastic substrates and microbial competitive stress imposed by environmental conditions. Notably, Rhodococcus erythropolis was predicted to be the generalist species and closely associated to biogeochemical cycles of mangrove plastispheres. Our work provides a reliable pathway for tackling the hidden mechanisms of environmental factors driving MPs-associated microbe from perspectives of niches and highlights the spatial dynamic variations of mangrove MPs-associated bacteria.

Effects of treatments and distribution on microbiome and antibiotic resistome from source to tap water in three Chinese geographical regions based on metagenome assembly

Antibiotic resistance genes (ARGs) represent emerging environmental pollutants that present health risks. Drinking water supply systems (DWSSs), including sources to tap water, play crucial roles in the dissemination and propagation of ARGs. However, there was a paucity of knowledge on the relative abundance, diversity, mobility, and pathogenic hosts of ARGs in DWSSs from source to tap. Therefore, the effects of treatments and distributions on the microbial community and ARGs from three geographical regions (downstream areas of the Yellow, Yangtze, and Pearl Rivers) were elucidated in the present study. Treatment processes lowered the complexity of the microbial community network, whereas transportation increased it. The assembly mechanisms of the microbial community and antibiotic resistome were primarily driven by stochastic processes. Distribution greatly increased the contribution of stochastic processes. Multidrug ARGs (for example, multidrug transporter and adeJ) and bacitracin ARG (bacA) were the primary mobile ARGs in drinking water, as identified by the metagenomic assembly. Achromobacter xylosoxidans, Acinetobacter calcoaceticus, and Acinetobacter junii harbored diverse multidrug ARGs and mobile genetic elements (MGEs) (recombinases, integrases, and transposases) as potential pathogens and were abundant in the disinfected water. Environmental factors, including pH, chlorine, latitude, longitude, and temperature, influenced the ARG abundance by directly regulating the MGEs and microbial community diversity. This study provides critical information on the fate, mobility, host pathogenicity, and driving factors of ARGs in drinking water, which is conducive to ARG risk assessment and management to provide high-quality drinking water to consumers.

Impact of artificial mixing and oxygenation on bacteria in a water transfer reservoir: Community succession and the role in water quality improvement

Artificial mixing and oxygenation induced by water-lifting aerations (WLAs) have the potential to improve water quality in reservoirs. However, there is a limited understanding of the bacterial community composition, assembly, and mechanisms behind water quality improvement under the influence of WLAs, especially in a water transfer reservoir. Here, the dynamics and relationship between water quality, bacterial diversity, and composition during the pre-operation, in-operation, and post-operation stages of WLAs were analyzed using high-throughput sequencing technology to explore the effects of artificially regulated bacteria on water quality improvement. WLAs operation led to the elimination of water stratification, significant bottom oxygenation, and reduction in nutrient concentrations. In addition, the operation of WLAs significantly changed the bacterial community composition, with an increase in richness, negligible difference in diversity, and a significant increase in the abundance of species with pollutant degradation functions, resulting in a shift from stochastic to deterministic processes of the bacterial community assembly. As a result, enhancement of the dominant bacteria responsible for organic matter degradation and denitrification and suppression of the emergence of algae-related bacteria were observed during the WLAs operation, and the ecosystem stability improved. Multiple analyses indicated a direct correlation between artificial mixing and oxygenation; changes in the bacterial community; and the reduction of nitrogen, phosphorus, and permanganate index in the water column. This study provides novel insights into in situ water quality enhancement and a valuable reference for understanding bacterial change patterns under artificially intervened conditions in water transfer reservoirs.

Optimized start-up strategies for elemental sulfur packing bioreactor achieving effective autotrophic denitrification

The start-up efficiency of the elemental sulfur packing bioreactor (S0PB) is constrained by the slow growth kinetics of autotrophic microorganisms, which is essentially optimized. This study aims to optimize start-up procedures and offer scientific guidance for the practical applications of S0PB. Through comparing the start-up efficiencies under various conditions related to inoculation, backwashing, and EBCT, it was found that these conditions did not significantly influence start-up time, but they did impact denitrification performance in detail. Using activated sludge as the inoculum was not recommended as the 2.5 ± 0.2 mg-N/L higher nitrite accumulation and 26.0 ± 5.1 % lower TN removal rate, compared to self-enrichment. Starting with a long-to-short EBCT (1 → 0.33 h) achieved higher nitrate removal of 11.5 ± 0.6 mg-N/L and eliminated nitrite accumulation compared to constantly short EBCT (0.33 h) conditions. Daily and postponed backwashing were suggested for long-to-short EBCT and constantly short EBCT start-up, respectively. Enrichment of Sulfurimonas was beneficial for the effective nitrite reduction process.

Community assembly patterns and processes of bacteria in a field-scale aquaculture wastewater treatment system

Microbial communities are responsible for the biological treatment of wastewater, however, our comprehension of their diversity, assembly patterns, and functions remains limited. In this study, we analyzed bacterial communities in both water and sediment samples. These samples were gathered from a novel field-scale aquaculture wastewater treatment system (FAWTS), which employs a multi-stage purification process to eliminate nutrients from pond culture wastewater. Significant variations were observed in bacterial diversity and composition across various ponds within the system and at different stages of the culture. Notably, the bacterial community in the FAWTS displayed a distinct species abundance distribution. The influence of dispersal-driven processes on shaping FAWTS communities was found to be relatively weak. The utilization of neutral and null models unveiled that the assembly of microbial communities was primarily governed by stochastic processes. Moreover, environmental factors variables such as total nitrogen (TN), dissolved oxygen (DO), and temperature were found to be associated with both the composition and assembly of bacterial communities, influencing the relative significance of stochastic processes. Furthermore, we discovered a close relationship between that bacterial community composition and system functionality. These findings hold significant implications for microbial ecologists and environmental engineers, as they can collaboratively refine operational strategies while preserving biodiversity. This, in turn, promotes the stability and efficiency of the FAWTS. In summary, our study contributes to an enhanced mechanistic understanding of microbial community diversity, assembly patterns, and functionality within the FAWTS, offering valuable insights into both microbial ecology and wastewater treatment processes.

Niche differentiation in microbial communities with stable genomic traits over time in engineered systems

Microbial communities in full-scale engineered systems undergo dynamic compositional changes. However, mechanisms governing assembly of such microbes and succession of their functioning and genomic traits under various environmental conditions are unclear. In this study, we used the activated sludge and anaerobic treatment systems of four full-scale industrial wastewater treatment plants as models to investigate the niches of microbes in communities and the temporal succession patterns of community compositions. High-quality representative metagenome-assembled genomes revealed that taxonomic, functional, and trait-based compositions were strongly shaped by environmental selection, with replacement processes primarily driving variations in taxonomic and functional compositions. Plant-specific indicators were associated with system environmental conditions and exhibited strong determinism and trajectory directionality over time. The partitioning of microbes in a co-abundance network according to groups of plant-specific indicators, together with significant between-group differences in genomic traits, indicated the occurrence of niche differentiation. The indicators of the treatment plant with rich nutrient input and high substrate removal efficiency exhibited a faster predicted growth rate, lower guanine-cytosine content, smaller genome size, and higher codon usage bias than the indicators of the other plants. In individual plants, taxonomic composition displayed a more rapid temporal succession than functional and trait-based compositions. The succession of taxonomic, functional, and trait-based compositions was correlated with the kinetics of treatment processes in the activated sludge systems. This study provides insights into ecological niches of microbes in engineered systems and succession patterns of their functions and traits, which will aid microbial community management to improve treatment performance.

Moderate anthropogenic disturbance stimulates versatile microbial taxa contributing to denitrification and aromatic compound degradation

Wastewater treatment plants (WWTPs) effluent often contains a significant amount of residual organic pollutants and nutrients, causing disturbance to the coastal effluent receiving areas (ERA). Microbial communities in coastal ERA sediments may benefit from the coexistence of organic pollutants and nutrients, promoting the emergence of versatile taxa that are capable of eliminating these substances simultaneously. However, the identification and exploration of versatile taxa in natural environments under anthropogenic disturbances remain largely uncharted territory. In this study, we specifically focused on the versatile taxa coupled by the degradation of aromatic compounds (ACs) and denitrification, using Hangzhou Bay in China as our study area. We explored how WWTPs effluent disturbance would affect the versatile taxa, and particularly examined the role of disturbance intensity in shaping their composition. Intriguingly, we found that versatile taxa were mainly derived from denitrifiers like Pseudomonas, suggesting the fulfilled potential of denitrifiers regarding ACs degradation. We also discovered that moderate disturbance stimulated the diversity of versatile taxa, resulting in strengthened functional redundancy. Through correlation network analysis, we further demonstrated that moderate disturbance enhanced the community-level cooperation. Thus, moderate disturbance serves as a catalyst for versatile taxa to maintain community function, making them more resilient to effluent disturbances. Additionally, we identified COD and NO3--N concentrations as significant environmental factors influencing the versatile taxa. Overall, our findings reveal the role of effluent disturbances in the promotion of versatile taxa, and highlight moderate disturbance can foster more robust versatile taxa that are better equipped to handle effluent disturbances.

Seasonal variations of biofilm C, N and S cycling genes in a pilot-scale chlorinated drinking water distribution system

Biofilms in drinking water distribution systems (DWDS) host diverse microorganisms. However, the functional attributes of DWDS biofilms and their associations with seasonality remain unclear. This study aims to characterize variations in the microbial metabolic traits of DWDS biofilms collected during different seasons, using a pilot-scale DWDS in dark under plug-flow conditions during one-year operation period. Network analysis was used to predict the functional gene hosts. The overall functional attributes determined by shotgun metagenomics exhibited significant differences among seasons. Genes associated with aromatic metabolism, fatty acid biosynthesis and degradation, and capsular extracellular polymeric substance (EPS) were significantly upregulated in summer owing to the higher temperatures and chlorine in the influent of the DWDS. Moreover, the pathways associated with nitrogen, sulfur, glycolysis, and tricarboxylic acid (TCA) cycling, as well as carbon fixation were reconstructed and displayed according to the sampling season. Nitrogen reduction pathways [dissimilatory nitrate reduction to ammonium (DNRA) 73 %, assimilatory nitrate reduction to ammonium (ANRA) 21 %] were identified in DWDS biofilms, but nitrogen oxidation pathways were not. Sulfur cycling were involved in diverse pathways and genes. Glycolysis and TCA cycling offered electron donors and energy sources for nitrogen and sulfur reduction in biofilms. Carbon fixation was observed in DWDS biofilms, with the predominant pathway for fixing carbon dioxide being the reductive citrate cycle (38 %). Constructed functional gene networks composed of carbon, nitrogen, and sulfur cycling-related genes demonstrated synergistic effects (Positive proportion: 63.52-71.09 %). In addition, from spring to autumn, the network complexity decreased and network modularity increased. The assembly mechanism of carbon, nitrogen and sulfur cycling-related genes was driven by stochastic processes for all samples. These results highlight the diverse functional genes in DWDS biofilms, their synergetic interrelationships, and the seasonality effect on functional attributes.

Vertical and seasonal dynamics of bacterial pathogenic communities at an aged organic contaminated site: Insights into microbial diversity, composition, interactions, and assembly processes

Under the background of the Coronavirus Disease 2019 (COVID-19) pandemic, research on pathogens deserves greater attention in the natural environment, especially in the widely distributed contaminated sites with complicated and severe organic pollution. In this study, the community composition and assembly of soil pathogens identified by the newly-developed 16S-based pipeline of multiple bacterial pathogen detection (MBPD) have been investigated on spatiotemporal scales in the selected organic polluted site. We demonstrated that the richness and diversity of the pathogenic communities were primarily controlled by soil depth, while the structure and composition of pathogenic communities varied pronouncedly with seasonal changes, which were driven by the alterations in both physiochemical parameters and organic contaminants over time. Network analysis revealed that the overwhelmingly positive interactions, identified multiple keystone species, and a well-organized modular structure maintained the stability and functionality of the pathogenic communities under environmental pressures. Additionally, the null-model analysis showed that deterministic processes dominated the pathogenic community assembly across soil profiles. In three seasons, stochasticity-dominated processes in spring and summer changed into determinism-dominated processes in winter. These findings extend our knowledge of the response of the bacterial pathogenic community to environmental disruptions brought on by organic contaminated sites.

Response of aerobic activated sludge to edible oil exposure: Extracellular polymeric substance (EPS) characteristics and microbial community

Aerobic activated sludge is widely used to degrade edible oil wastewater in wastewater treatment plants. During this process, the observed poor organics removal performance might be caused by poor sludge settling performance, which might be influenced by extracellular polymeric substances (EPS) and the structure of the microbial community. However, this hypothesis was not confirmed. Thus, this study investigated the response of activated sludge to 50% and 100% edible oil exposure in comparison to glucose, focusing on organics removal performance, characteristics of sludge, EPS, and microbial community structure. Results showed that both concentrations of edible oil influenced the systems' performance, although 100% edible oil showed more significant negative effects than 50% edible oil. The mechanisms behind the influence of edible oil on the aerobic activated sludge system and the differences between the different concentrations of edible oil were revealed. The worse system performance in the edible oil exposure system was due to the worse sludge settling performance, which was significantly affected by edible oil (p < 0.05). The sludge settling performance was mainly inhibited by promoting the formation of floating particles and the enrichment of filamentous bacteria in the 50% edible oil exposure system; biosurfactant secretion was also speculated as the reason, in addition to the above factors, in the 100% edible oil exposure system. The macroscopic largest floating particles, highest total relative abundance of foaming bacteria and biosurfactant production genera (34.32%), lowest surface tension (43.7 mN/m), and highest emulsifying activity (E₂₄ = 25%) of EPS in 100% edible oil exposure systems provide strong evidence.

Wastewater treatment plant effluent discharge decreases bacterial community diversity and network complexity in urbanized coastal sediment

The wastewater treatment plant (WWTP) effluent discharge affects the microorganisms in the receiving water bodies. Despite the ecological significance of microbial communities in pollutant degradation and element cycling, how the community diversity is affected by effluent remains obscure. Here, we compared the sediment bacterial communities exposed to different intensities of WWTP effluent discharge in Hangzhou Bay, China: i) a severely polluted area that receives effluent from an industrial WWTP, ii) a moderately polluted area that receives effluent from a municipal WWTP, and iii) less affected area that inner the bay. We found that the sediment bacterial diversity decreased dramatically with pollution levels of inorganic nutrients, heavy metals, and organic halogens. Microbial community assembly model analysis revealed increased environmental selection and decreased species migration rate in the severely polluted area, resulting in high phylogenetic clustering of the bacterial communities. The ecological networks were less complex in the two WWTP effluent receiving areas than in the inner bay area, as suggested by the smaller network size and lower modularity. Fewer negative network associations were detected in the severely (6.7%) and moderately (8.3%) polluted areas than in the less affected area (16.7%), indicating more collaborative inter-species behaviors are required under stressful environmental conditions. Overall, our results reveal the fundamental impacts of WWTP effluents on the ecological processes shaping coastal microbial communities and point to the potential adverse effects of diversity loss on ecosystem functions.

Variations in antibiotic resistance genes and microbial community in sludges passing through biological nutrient removal and anaerobic digestion processes in municipal wastewater treatment plants

Antimicrobial resistance (AMR) represents a relentless, silent pandemic. Contributing to this are wastewater treatment plants (WWTPs), a potential source of antibiotic resistance genes' (ARGs) transmission to the environment, threatening public health. The presence of ARGs in pathogenic bacteria and their release into the environment by WWTPs threatens the public health. The current study investigated changes in ARGs' abundance in biological nutrient removal (BNR) processes and anaerobic digestion (AD) reactors of two WWTPs. Also, microbial community structure, which is known to shape the distribution and abundance of ARGs, was also analyzed. The relative abundance of eight ARGs (tetX, tetA, tetM, TEM, sul1, sul2, ermB and qnrD) was quantified as ARGs' copies/16 S rRNA gene copies using quantitative polymerase chain reaction (qPCR). Microbial community composition was assessed by 16 S rRNA microbiome sequencing analysis. TetX was prevalent among the eight ARGs, followed by TEM and sul1. However, its abundance was decreased in the AD sludges compared to BNR sludges. Proteobacteria was the major bacterial phylum found in all the sludge samples, while Arcobacter, 12up and Acidovorax were the predominant genera. Acinetobacter and Flavobacterium were significantly more abundant in the BNR sludges, while 12up and Aeromonas were predominant in AD sludges. Principal component analysis (PCA) revealed a clear difference in dominant ARGs and bacteria between the sludges in the processes of BNR and AD of the two WWTPs. Clinically relevant bacterial genera, Klebsiella and Enterococcus, found in both the BNR and AD sludges, were significantly correlated with the tetX gene. Throughout this study, the relationship between microbial communities and specific ARGs was revealed, illustrating that the composition of the microbial community could play a vital role in the abundance of ARGs. These results will better inform future studies aimed at controlling the spread of ARGs and their potential hosts from WWTPs.

Different living environments drive deterministic microbial community assemblages in the gut of Alpine musk deer (Moschus chrysogaster)

Substantial variation in the environment directly causes remodeling of the colonized gut microbiota, controlling community diversity, and functions in the host to tune-up their adaptive states. However, the mechanisms of microbial community assembly in response to environmental changes remain unclear, especially in endangered ruminants. In this study, we analyzed the microbial communities of 37 fecal samples collected from captive and wild Alpine musk deer (Moschus chrysogaster) to characterize the complexity and assembly processes using 16S rRNA gene sequencing. We found significantly different diversities and compositions of gut microbiota among both groups associated with different living environments. Heterogeneous selection was the predominant factor regulating the gut microbiota community under similar climatic conditions, indicating that microbial community assembly was largely driven by deterministic mechanisms. The species co-occurrence network showed complex and tight connections with a higher positive correlation in the wild environment. Moreover, the captive group exhibited significant differences in chemoheterotrophy and fermentation compared with the wild group, but the opposite was observed in animal parasites or symbionts, which might be closely related to diet, energy supply, and healthcare of animals. This study provides a framework basis and new insights into understanding gut microbiota in different environments.