Global diversity and biogeography of bacterial communities in wastewater treatment plants

Autotrophic denitrification in coking wastewater treatment systems: Comprehensive comparative study of full-scale systems in China

The biological treatment of coking wastewater faces challenges due to high toxicity, high nitrogen loading, and excessive carbon demand. This study comprehensively investigated the pollutant removal performance, microbial community diversity, and metabolic functions of 14 full-scale coking wastewater treatment systems (CWWs) in China, aiming to explore pollutant removal mechanisms to reduce environmental impacts. The dominant functional microorganisms exhibit significant variations across different CWWs. The core autotrophic sulfur-oxidizing denitrifiers Thiobacillus and Arcobacter drive the sulfur-driven autotrophic denitrification process, leading to higher nitrogen removal in mixotrophic systems. Deterministic factors influence microbial community structures, which can enable targeted community structure regulation. Based on sulfide-based pollutants such as thiocyanates, the contribution of sulfur-driven autotrophic denitrification processes to CWWs was revealed. By optimizing the allocation of electron donors, the construction of mixotrophic nitrogen removal systems can improve nitrogen removal efficiency while reducing carbon inputs and greenhouse gas emissions.

Diversity, influential factor, and communication network construction of quorum sensing bacteria in global wastewater treatment plants

Quorum sensing (QS) is widespread in the microbial world and mediates microbial relationships in communities. However, the existing knowledge is far from a full description of the complex communication-based microbial interactions in engineered ecosystems, i.e., wastewater treatment plants (WWTPs). Herein, we conducted a systematic analysis of the diversity and influential factors of the QS-related microflora through the collection of global 1186 activated sludge microbiome samples. We found that the richness of bacteria associated with the universal bacterial secondary messenger presented the highest in QS system, whereas the bacteria related to the degradation of N-Acyl-homoserine lactones occupied the main position in the quorum quenching system. The community turnover of QS microflora was found more likely to be dominated by the deterministic process, such as the dissolved oxygen and resource availability (the ratio of organic matter to microorganisms). Meanwhile, these QS microflora in turn have a profound impact on the functions of WWTPs, especially multilingual intelligencers involving various language systems, such as Nitrospira. By connecting the signal molecule synthesis and acceptance bacteria, we constructed a QS communication network, which can be a robust tool for initial investigation of signaling molecule-mediated microbial interactions. The above results were further integrated into an online access website, named Quorum Sensing Communication Network in Activated Sludge (QSCNAS) (http://www.qscnas.cn/), which allowed users to browse and capture possible QS-based interactions of target bacterium. This work contributes to the understanding of bacterial communication in WWTPs and provides a platform to help in developing potential regulation strategies.

Recruiting high-efficiency denitrifying consortia using Pseudomonas aeruginosa

Synthesizing the microbial community with a high denitrifying capacity is the key for achieving efficient removal of nitrogen species in wastewater treatment plants. Here, we integrated the evolutionary top-down enrichment and bottom-up bioaugmentation to construct a high-efficiency Pseudomonas-recruited denitrifying consortium (PRDC). A PRDC with a high specific denitrification rate of 109.49 ± 10.58 mg N/(g MLVSS·h) was enriched after 181 days of microbiota construction with pre-inoculation of Pseudomonas strain onto carriers. The 16S rRNA gene sequencing analysis suggested that the pre-inoculated Pseudomonas was quickly washed out and replaced by dominant denitrifying genera, such as Halomonas and Thauera, under different hydraulic retention times (HRTs). The pre-inoculated Pseudomonas can facilitate PRDC by providing public goods, but compromising its nutrient requirements. The dominant community assembly processes switched from homogeneous selection to ecological drift and dispersal limitation under shortened HRT. Furthermore, a shortened HRT facilitated the colonization of new immigrants and intensified their competition with the pre-existing dominant denitrifiers. The PRDC carriers achieved a 1.65-fold enhancement in sludge denitrification and reduced the corresponding chemical oxygen demand consumption at a carrier filling ratio of 30%. Overall, our study developed a novel technique using Pseudomonas aeruginosa as a trigger to enrich high-efficiency denitrifying consortia for wastewater treatment.

Insights into the start-up of acidic nitritation using conventional activated sludge: Process dynamics, nitrifiers succession, and pilot-scale demonstration

Acidic nitritation driven by acid-tolerant ammonia-oxidizing bacteria (AOB) has gained wide attention due to its potential in sustainable wastewater and sludge treatment. However, limited knowledge of initiating acidic nitration using conventional activated sludge hindered the wider studies and application of this technology at lab- and field-scale. This study evaluates three strategies for initiating acidic nitritation: a constant low hydraulic retention time (HRT); an extended initial HRT followed by manual HRT reduction; and pH-controlled HRT. All strategies successfully started acidic nitritation using seed sludge from a local wastewater treatment plant (WWTP) containing undetectable acid-tolerant AOB. Among the three strategies, pH-controlled HRT was the most efficient, with a smoother (minimal fluctuations) and faster (around 30 days) start-up process than the other two strategies. This was attributed to an initial redundancy in ammonia oxidation capacity (i.e. making the proton generation rate caused by ammonium oxidation exceed the alkalinity supply rate by influent), allowing AOB to overcome the activity valley during the transition from neutral to acid pH Level. Using pH as a real-time proxy of AOB activity also leveraged the unique low buffer capacity at acidic pH. Based on these findings, a pilot-scale acidic nitritation reactor treating diluted sidestream wastewater was initiated for the first time using the pH-controlled strategy. The pilot reactor immediately achieved nitrite accumulation and reached the target hydraulic loading rate quicker than the lab reactor, indicating higher influent nitrogen concentration may facilitate NOB suppression and a higher growth rate of acid-tolerant AOB. Based on those results, the versatile start-up strategies using both mainstream or sidestream wastewater were further discussed. Overall, this work greatly expands potential applications of acidic nitritation and paves the way for future field-scale applications.

Comparative enrichment of complete ammonium oxidation bacteria in floccular sludge reactors: Sequencing batch reactor vs. continuous stirred tank reactor

This study attempted to compare the enrichment of complete ammonium oxidation (comammox) bacteria, which are affiliated with Nitrospira and not able to generate nitrous oxide (N2O, a potent greenhouse gas) through biological pathways, in two commonly-utilized configurations of floccular sludge reactors, i.e., sequencing batch reactor (SBR) and continuous stirred tank reactor (CSTR), under the ammonium condition of mainstream wastewater (i.e., 40.0 g-N/m3). The results in terms of nitrification performance and microbial analyses during 216-d operation showed that compared with SBR offering a fluctuating but generally higher in-situ ammonium concentration (i.e., 1.0-6.0 g-N/m3) which was favorable for the growth of ammonium-oxidizing bacteria (AOB, belonging to Nitrosomonas in this study), CSTR managed to lower the in-situ ammonium level to < 2.0 g-N/m3, thus creating a competitive advantage for comammox bacteria with a highly oligotrophic lifestyle. Such an argument was further supported by dedicated batch tests which revealed that Nitrospira-dominant sludge had a lower maximum ammonium oxidation rate and lower apparent ammonium and oxygen affinity constants than Nitrosomonas-dominant sludge (i.e., 33.5 ± 2.1 mg-N/h/g-MLVSS vs. 139.9 ± 26.7 mg-N/h/g-MLVSS, 1.1 ± 0.1 g-N/m3 vs. 17.6 ± 4.6 g-N/m3, and 0.017 ± 0.002 g-O2/m3 vs. 0.037 ± 0.013 g-O2/m3, respectively), proving the nature of comammox bacteria as a K-strategist. Overall, this study not only provided useful insights into the effective enrichment of comammox bacteria in floccular sludge but also further revealed the interactions between comammox bacteria and AOB, thereby contributing to the future development of comammox-inclusive biological nitrogen removal technologies for sustainable wastewater treatment.

Global diversity and distribution of antibiotic resistance genes in human wastewater treatment systems

Antibiotic resistance poses a significant threat to human health, and wastewater treatment plants (WWTPs) are important reservoirs of antibiotic resistance genes (ARGs). Here, we analyze the antibiotic resistomes of 226 activated sludge samples from 142 WWTPs across six continents, using a consistent pipeline for sample collection, DNA sequencing and analysis. We find that ARGs are diverse and similarly abundant, with a core set of 20 ARGs present in all WWTPs. ARG composition differs across continents and is distinct from that of the human gut and the oceans. ARG composition strongly correlates with bacterial taxonomic composition, with Chloroflexi, Acidobacteria and Deltaproteobacteria being the major carriers. ARG abundance positively correlates with the presence of mobile genetic elements, and 57% of the 1112 recovered high-quality genomes possess putatively mobile ARGs. Resistome variations appear to be driven by a complex combination of stochastic processes and deterministic abiotic factors.

Cockroach Microbiome Disrupts Indoor Environmental Microbial Ecology with Potential Public Health Implications

Cockroaches pose a significant global public health concern. However, besides the well-recognized cockroach-induced allergy, the potential impact of the cockroach microbiome on human health through various means is not yet fully elucidated. This study aimed to clarify the health impacts of cockroaches by investigating the microbial interactions among cockroaches, the indoor environment, and humans. We simultaneously collected cockroach, indoor environment (indoor air and floor dust), and human (exhaled breath condensate and skin) samples from residential areas in five cities representing distinct climate zones in China. The 16S rDNA sequencing results revealed that cockroaches harbor diverse bacterial populations that vary across different cities. The prevalence of potential pathogenic bacteria (PPB) in cockroaches ranged from 1.1% to 58.9%, with dominant resistance genes conferring resistance to tetracycline, macrolide, and beta-lactam. The relationships between the cockroach microbiome and the associated environmental and human microbiomes were explored by using fast expectation-maximization microbial source tracking (FEAST). The potential contribution of cockroach bacteria to the floor dust-borne microbiome and indoor airborne microbiome was estimated to be 5.6% and 1.3%, respectively. Similarly, the potential contribution of cockroach PPB to the floor dust-borne microbiome and indoor airborne microbiome was calculated to be 4.0% and 1.2%, respectively. In residences with cockroach infestations, the contribution of other sources to the indoor environment was slightly increased. Collectively, the role of cockroaches in the transmission of microorganisms, particularly pathogenic bacteria and antibiotic resistance genes, cannot be overlooked.

Model-driven high-throughput zebrafish embryo assay for evaluating whole effluent toxicity variation across 100 full-scale wastewater treatment plants

The zebrafish embryo is a valuable model for evaluating whole effluent toxicity (WET). However, the widely recognized acute toxicity indicator, based on International Organization of Standardization (ISO) methods, requires large numbers of embryos and is often time-consuming due to its complex experimental procedures. In this study, we propose an alternative to the conventional reliance on ISO standards by developing a model-driven high-throughput assay that utilizes actual wastewater, enabling rapid LC10 (the lethal concentration at which 10 % of the test organisms are affected) prediction through machine learning techniques and multidimensional indicators derived from streamlined experimental procedures. We compared three streamlined toxicity assays-developmental toxicity, behavioral toxicity, and vascular toxicity-along with five different models. Among these, the Lasso model based on behavioral toxicity emerged as the most effective, achieving an R2 value of 0.893 while reducing experimental time by 5- to 8-fold. Furthermore, fivefold cross-validation confirmed its robust predictive accuracy. The application of this model-driven high-throughput assay across 100 wastewater treatment plants in China highlights the crucial role of biological treatment, particularly aerobic processes and secondary sedimentation, in reducing toxicity, thereby providing valuable insights into their functions. This high-throughput assay not only surpasses the ISO standard method in efficiency but also substantially decreases embryo usage, facilitating rapid WET assessments of actual wastewater with larger sample sizes.

Disturbance and stability dynamics in microbial communities for environmental biotechnology applications

Microbial communities are corner stones of environmental biotechnology, driving essential processes such as waste degradation, pollutant removal, and nutrient cycling, all fundamental to industrial bioprocesses and sustainability. The structure and functions of these communities are influenced by environmental disturbances, which can arise from changes in operational conditions. Understanding disturbance-stability dynamics, including the roles of rare taxa and gene potential, is crucial for optimizing processes such as wastewater treatment, bioenergy production, and environmental bioremediation. This review highlights recent theoretical, technical, and experimental advances - including ecological theory, multiscale approaches, and the use of machine learning and artificial intelligence - to predict community responses to disturbances. Together, these insights offer a valuable outlook for developing scalable and robust biotechnology applications.

A benchmark analysis of feature selection and machine learning methods for environmental metabarcoding datasets

Next-Generation Sequencing methods like DNA metabarcoding enable the generation of large community composition datasets and have grown instrumental in many branches of ecology in recent years. However, the sparsity, compositionality, and high dimensionality of metabarcoding datasets pose challenges in data analysis. In theory, feature selection methods improve the analyzability of eDNA metabarcoding datasets by identifying a subset of informative taxa that are relevant for a certain task and discarding those that are redundant or irrelevant. However, general guidelines on selecting a feature selection method for application to a given setting are lacking. Here, we report a comparison of feature selection methods in a supervised machine learning setup across 13 environmental metabarcoding datasets with differing characteristics. We evaluate workflows that consist of data preprocessing, feature selection and a machine learning model by their ability to capture the ecological relationship between the microbial community composition and environmental parameters. Our results demonstrate that, while the optimal feature selection approach depends on dataset characteristics, feature selection is more likely to impair model performance than to improve it for tree ensemble models like Random Forests. Furthermore, our results show that calculating relative counts impairs model performance, which suggests that novel methods to combat the compositionality of metabarcoding data are required.

Quantitative microbial risk assessment for on-site employees in a wastewater treatment plant and implicated surrounding residents exposed to S. aureus bioaerosols

Wastewater treatment plants (WWTPs) have increased dramatically in number due to rapid urbanization. However, these facilities release significant amounts of potentially hazardous airborne microorganisms, including Staphylococcus aureus bioaerosol, which poses health risks to employees and nearby residents. Therefore, this study estimated the direct exposure risks of bioaerosols in WWTPs using a quantitative microbial risk assessment (QMRA) framework evaluated through sensitivity analysis methods. The results showed that the sludge yard had the highest mean bioaerosol concentration but the lowest aerosolization ratio. The disease health risk burden values followed a descending order: residential area > office > sludge yard > inverted umbrella aeration tank > microporous aeration tank > control room. Meanwhile, the risk values were shrunken by 14.1-17.3 times when personal protective equipment (PPE) was used. Sensitivity analysis for individual and multifarious contributions showed that the removal fraction achieved by using PPE was consistently the most influential parameter, followed by aerosol ingestion rate or exposure concentration. This suggests that isolation strips, such as green belts, between the WWTP and residential area is alternative effective measures for residents and wearing masks is essential measure for on-site employees. Furthermore, the multifarious contribution analysis showed that stepwise risk mitigation approaches were equally effective as one-step solutions, as indicated by their identical sensitivity coefficient rankings. This indicates that, when resources for mitigating risk are limited, taking a stepwise approach to risk reduction can be equally effective as allocating all resources at once. This study can advance the understanding of the characteristics and health risks of WWTP bioaerosol emissions and supplement the multifarious contributions of the sensitivity analysis implemented in the QMRA model, which contributes to public wellness development. The findings of this study will help in the optimization of control strategies for local wastewater utilities and implicated surrounding residents.

Revealing real impact of microalgae on seasonal dynamics of bacterial community in a pilot-scale microalgal-bacterial consortium system

The microalgal-bacterial consortium (MBC) system is recognized as an advanced approach for nitrogen and phosphorus removal in wastewater treatment. However, the influence of microalgae on bacterial community dynamics and niche differentiation across varying seasonal conditions remains unexplored. In this study, we established a pilot-scale continuous-flow MBC system to disentangle, for the first time, the impact of microalgae on seasonal bacterial community succession by conducting monthly time-series sampling over a full seasonal cycle. Notably, a core microbiome consisting of 528 ASVs displaying significant seasonal rhythms was identified in both activated sludge (AS) and MBC systems. Unlike the random drift-driven assembly observed in the AS system, microalgae can recruit dominant species that respond to environmental fluctuations to form a core microbiome (heterogeneous selection), thereby enhancing community stability. Concurrently, microalgae facilitated niche differentiation within the core microbiome, driving transition from generalist to specialist species, which in turn promoted synergistic interactions that can improve nitrification and denitrification functions. Additionally, microalgae strengthened the correlation between functional species in the core microbiome and seasonal variations in light and temperature, as well as with regulating the efficiency of nitrogen and phosphorus removal by influencing the abundance of these functional species. These findings deepen our understanding of bacterial ecology based on microalgae management and provide a foundation further for the study of community regulation strategy of MBC systems.

Metagenomic insights into the assembly, function, and key taxa of bacterial community in full-scale pesticide wastewater treatment processes

Pesticide wastewater emerges as a typical refractory wastewater, characterized by complex composition and high toxicity, posing significant treatment challenges. Bacterial communities are responsible for biological treatment of refractory wastewater in full-scale pesticide wastewater treatment plants (PWWTPs), providing important implications for optimizing system performance and improving management strategies. However, the knowledge of their composition, diversity, function, assembly patterns, and biological interactions remains limited. Therefore, this study applied high-throughput sequencing, machine learning models, and statistical analysis to investigate key features of bacterial communities in eight PWWTPs. We found that Proteobacteria and Bacteroidota were the most abundant phyla, with Pseudomonas, Hyphomicrobium, Comamonas, and Thauera being dominant genera. Bacterial community distribution and diversity varied significantly among influents, sludges, and effluents, with sludges and effluents exhibiting higher diversity, richness, and evenness compared to influents. Deterministic processes primarily shaped the bacterial communities, accounting for 77.12%, 61.44%, and 64.05% of variation in influents, sludges, and effluents, respectively. Homogeneous selection explained 47.71%, 31.37%, and 31.37% of variation across these communities. Key modules (Module 1 in influents, Modules 3 and 4 in sludges, and Module 1 in effluents) were significantly associated with various metabolic and degradative functions (p < 0.05). Core taxa identified by Random Forest analysis were strongly linked to key metabolic and degradation functions, such as the metabolism of cofactors and vitamins, carbohydrates, and amino acids as well as the degradation of benzoate, aminobenzoate, nitrotoluene, chloroalkane, and chloroalkene. This study deepens our understanding of bacterial community dynamics and key features in pesticide wastewater treatment systems, offering scientific guidance for process optimization, efficiency improvement, and system stability assessment.

Shift in activated sludge microbiomes associated with nitrite accumulation and high nitrous oxide emissions

Nitrous oxide (N2O) emissions can constitute over half of the carbon footprint of a wastewater treatment plant (WWTP), and emission peaks frequently correlate with nitrite (NO2-) concentrations. However, connections between the microbiome and high N2O and NO2- levels are not well-documented. Here, we characterize the microbiomes in several parallel lines of a WWTP during massive N2O emissions (20 % of influent nitrogen load) with prolonged NO2- accumulation in most lines, aiming to identify key differences between communities in lines with high and low NO2- concentrations. The abundance of nitrite-oxidizing bacteria (NOB) was extremely low in the lines with NO2- accumulation, which also had slightly lower abundances of ammonia-oxidizing bacteria (AOB). Some incomplete denitrifiers were more abundant in the lines with NO2- accumulation. Lines without NO2- had a higher relative abundance of filamentous bacteria and better floc formation. These findings confirmed our hypothesis that loss of NOB caused NO2- accumulation, inducing increased N2O emissions. AOB are suspected to be the main source of N2O during the studied period, with a likely contribution from heterotrophic denitrifiers. A few species were identified as interesting candidates for further study regarding their potential role in increased N2O emission from WWTPs. Long-term microbiome monitoring is necessary to understand the changes in the microbiome that might initiate NO2- accumulation and high N2O emissions.

Impacts of chlorine disinfection of municipal sewage effluent on receiving rivers: Changes in organic matter and microbial communities

Effluents from wastewater treatment plants (WWTPs) can impact various aspects of receiving aquatic ecosystems, yet the specific effects of chlorine disinfection of effluents on these ecosystems remain poorly understood. In this study, a simulated flow-through channel system was employed to evaluate the changes in water quality and microbial community in receiving rivers resulting from the discharge of WWTP effluent, with or without chlorination. Results showed that dissolved organic matter (DOM) in secondary effluent from WWTPs exhibited higher fluorescence intensity and elevated levels of biopolymers, humic acids, and low molecular weight compounds compared to river water. Microbial analysis revealed that the input of secondary effluent promoted the proliferation of diverse microbial communities in periphyton of the receiving water, while the chlorinated effluents selectively inhibited chlorine-sensitive taxa in periphyton and favored chlorine-tolerant ones. Chlorine disinfection effectively reduced most pathogens in effluents; however, certain genera, such as Neisseriaceae and Escherichia-Shigella, persisted. Moreover, exposure to chlorinated effluent significantly elevated the relative abundance of Pseudomonas in periphyton compared to other conditions, raising concerns about the persistence of chlorine-tolerant pathogens in aquatic environments. These findings highlight the critical need to further evaluate the impact of the disinfection process in WWTPs on the long-term health and stability of riverine ecosystems.

Miscellaneous salt management based on saline-microbial interaction mechanisms: Technology salt reduction strategies

Fluctuations in salinity have a significant impact on the ability of microorganisms to degrade target pollutants during water treatment. However, the interactions between salinity and microorganisms in industrial wastewater treatment have been explored in only a limited number of studies. Therefore, taking the actual coking wastewater treatment project as an example, the internal relationship between salinity, microbial community and pollutant removal was explored, and the technology salt reduction strategy was put forward. It was found that pollutants in wastewater treatment showed co-removal phenomenon and changes in salinity firstly elicited the response of denitrifying and phosphorus-removing carbon-utilizing microbial populations of Ottowia/Diaphorobacter, Alicycliphilus/Pseudomonas and Nitrosomonas/Nitrospira. The increase of salinity will lead to the destabilization of the microbial system, and the migration rate indicates that the aerobic unit (R2 = 0.8214) is more adaptable to the salt stress brought by the foreign environment than the anaerobic/anoxic unit (R2 = 0.2129). Meanwhile, the Beta Nearest Taxon Index indicates that the OHO (oxic - hydrolytic & heterotrophic denitrification - oxic) process, characterized by the stochastic assembly of microbial communities during salinity increases, exhibits a greater capacity to withstand the potential impacts of water quality fluctuations and uncertainties. The effects of salinity increase on nitrogen removal path were as follows: nitrification (p = -1.9204) > DNR (p = -1.668) > denitrification (p = -0.1226) > anaerobic ammoxidation (p = -0.0448), based on which the concept of technology salt reduction was proposed. Technology salt reduction was realized in A-OHO process, which provided a scientific basis for the salt reduction function of microorganisms in water treatment technology.

Earth's most needed uncultivated aquatic prokaryotes

Aquatic ecosystems house a significant fraction of Earth's biosphere, yet most prokaryotes inhabiting these environments remain uncultivated. While recently developed genome-resolved metagenomics and single-cell genomics techniques have underscored the immense genetic breadth and metabolic potential residing in uncultivated Bacteria and Archaea, cultivation of these microorganisms is required to study their physiology via genetic systems, confirm predicted biochemical pathways, exploit biotechnological potential, and accurately appraise nutrient turnover. Over the past two decades, the limitations of culture-independent investigations highlighted the importance of cultivation in bridging this vast knowledge gap. Here, we collected more than 80 highly sought-after uncultivated lineages of aquatic Bacteria and Archaea with global ecological impact. In addition to fulfilling critical roles in global carbon, nitrogen, and sulfur cycling, many of these organisms are thought to partake in key symbiotic relationships. This review highlights the vital contributions of uncultured microbes in aquatic ecosystems, from lakes and groundwater to the surfaces and depths of the oceans and will guide current and future initiatives tasked with cultivating our planet's most elusive, yet highly consequential aquatic microflora.

Filamentous bacteria in activated sludge: Geographic distribution and impact of treatment processes

In this study, a global activated sludge communities database was used to investigate the global distribution of filamentous bacteria. The dominant filamentous bacteria worldwide were Zoogloea ramigera and Eikelboom type 1863. The incidence of sludge bulking in samples from Europe (22.4%), South America (18.8%), and North America (15.6%) was significantly higher than in other continents. The distribution of remaining filamentous bacteria shows significant regional variability. In addition, climate significantly affects the distribution of filamentous bacterial populations. The filamentous bacterial abundance in samples from polar climates (7.36%) and cold climates (4.13%) was significantly higher than in other climates. Candidatus Microthrix parvicella and Tetrasphaera spp. were the dominant filamentous bacteria in cold region. Wastewater treatment processes are also key factors affecting filamentous bacterial populations. The incidence of sludge bulking (21.6%) and the average abundance of filamentous bacteria (5.08%) in samples from CM processes were the highest, mainly induced by Thiothrix spp. In addition, filamentous sludge bulking is easily induced by Thiothrix spp. in SBR processes, and sludge bulking is easily induced by Zoogloea ramigera in PFR processes. This study provides new insights into preventing and controlling filamentous sludge bulking globally.

Combined semi-continuous feeding and stripping: Improving volatile fatty acid production and sulfate reduction in a two-phase anaerobic sulfate reduction system

This study developed a two-phase anaerobic sulfate reduction system with semi-continuous feeding, integrated with vapor stripping, to assess its treatment performance at varying chemical oxygen demand (COD)/SO42- ratios. At a COD/SO42- ratio of 2, the system achieved high removal efficiencies of 91.85 % for COD and 92.70 % for sulfate, respectively. Vapor stripping effectively maintained low free H2S concentrations, remaining below 50 mg/L in the first-phase reactor (Ra) and below 30 mg/L in the second-phase reactor (Rm). Additionally, the scouring effect of vapor stripping altered the functional group composition on the sludge surface, promoting the formation of sulfate-reducing granular sludge. Microbial analysis revealed a synchronized enrichment of Desulfovibrio and Enterococcus in Ra, as well as Methanosaeta and Enterococcus in Rm under a semi-continuous feeding regime combined with vapor stripping. Conductivity measurements and correlation analyses suggested that electroactive Methanosaeta and Enterococcus engaged in syntrophic metabolism via extracellular electron transfer, which was particularly beneficial for organic removal under low COD/SO42- ratio conditions. At a COD/SO42- ratio of 2, dissimilatory sulfate reduction (DSR) prevailed in Ra, whereas assimilatory sulfate reduction (ASR) dominated in Rm. This balance optimized sulfate removal efficiency while mitigating sulfide toxicity toward methanogens. Overall, this study presents a promising approach for the efficient treatment of high-sulfate organic wastewater with low COD/SO42- ratio.

Genetic compatibility and ecological connectivity drive the dissemination of antibiotic resistance genes

The dissemination of mobile antibiotic resistance genes (ARGs) via horizontal gene transfer is a significant threat to public health globally. The flow of ARGs into and between pathogens, however, remains poorly understood, limiting our ability to develop strategies for managing the antibiotic resistance crisis. Therefore, we aim to identify genetic and ecological factors that are fundamental for successful horizontal ARG transfer. We used a phylogenetic method to identify instances of horizontal ARG transfer in ~1 million bacterial genomes. This data was then integrated with >20,000 metagenomes representing animal, human, soil, water, and wastewater microbiomes to develop random forest models that can reliably predict horizontal ARG transfer between bacteria. Our results suggest that genetic incompatibility, measured as nucleotide composition dissimilarity, negatively influences the likelihood of transfer of ARGs between evolutionarily divergent bacteria. Conversely, environmental co-occurrence increases the likelihood, especially in humans and wastewater, in which several environment-specific dissemination patterns are observed. This study provides data-driven ways to predict the spread of ARGs and provides insights into the mechanisms governing this evolutionary process.

A novel fluidized-bed reactor with multi-stage oxygen distribution: Application to toxic and recalcitrant wastewater

The development of efficient and low-energy consumption processes and reactors for the treatment of highly concentrated, recalcitrant, and toxic organic wastewater has been a significant challenge. This study presents a novel fluidized-bed reactor, equipped with multi-stage oxygen distribution zones, designed to enhance detoxification, carbon removal, and nitrogen removal. Experimental investigations using coking wastewater demonstrated that the multi-stage oxygen fluidized-bed reactor achieved COD and TN removal rates of 86.9 ± 1.2% and 93.1 ± 2.7% at a hydraulic retention time (HRT) of 70 h, significantly outperforming the traditional aerobic fluidized-bed reactor (84.4 ± 1.6% and 41.8 ± 2.2%). The multi-stage oxygen distribution in the reactor facilitated the enrichment of various functional microorganisms in activated sludge, leading to the formation of a highly diverse microbial community. This community simultaneously performed organic degradation, nitrification, and denitrification, enhancing the COD degradation and TN removal efficiency in coking wastewater. The fluidized-bed reactor with multi-stage oxygen distribution exhibited performance in treating coking wastewater, offering valuable insights for the design of reactors intended for bio-processing toxic, recalcitrant, and high-concentration industrial wastewater.

Geochemical speciation and activation risks of Cd, Ni, and Zn in soils with naturally high background in karst regions of southwestern China

Agricultural soils in karst regions present a remarkable paradox where high geochemical background levels of heavy metals correspond with unexpectedly low crop uptake, challenging traditional risk assessment frameworks and limiting agricultural development. To decode this paradox, we investigated the geochemical speciation of cadmium (Cd), nickel (Ni), and zinc (Zn) in soil-rice systems in southwestern China, which collectively constitute the world's largest continuous karst region and represent diverse soil weathering stages. We employed three chemical extraction methods that revealed reactive pools ranking as Cd (58.74 %) > Zn (7.31 %) > Ni (4.65 %) and risk patterns varying with soil type (Andosols > Cambisols/Gleysols > Lithosols), while multi-surface speciation model (MSM) elucidated the underlying mechanisms. We identified a stage activation-contamination model (SACM) that demonstrates how pH-dependent weathering controlled heavy metal distribution among dissolved, surface-active, semi-stable carbonate, and nonactive species, thereby explaining the observed risk patterns. Specifically, in alkaline soils (pH > 7.50), Cd and Zn were primarily humic acid (HA)- and carbonate-bound, while Ni was goethite-bound. As weathering intensified, the reactive pool shifted to more active HA- and hydrous ferric oxide (HFO)-bound species. In acidic soils (pH < 6.50), dissolved and HA-bound species dominated. Both random forest, offering robust predictions using readily available data, and MSM stepwise regression models, providing high accuracy with mechanistic insights, effectively predicted rice risks. This study from speciation and activation model to prediction model clarifies why standardized risk assessments fail in karst regions and offers practical tools for accurate risk evaluation and management in these agricultural environments.

Quantifying patterns of microbial community assembly processes in bioreactors using different approaches leads to variable results

Engineered bioreactors play a vital role in many processes to convert wastes to resources, such as biological wastewater treatment, bioremediation, and conversion of solid waste to methane in landfills. These biological systems rely on communities of microbes to convert waste to valuable resources. A central aspect of the design and operation of bioreactors involves an understanding of microbial community composition and dynamics, including the assembly processes through which they form. However, there remains a significant gap in our fundamental understanding of microbial community dynamics and microbial community assembly (MCA) processes, especially in engineered bioreactor settings. Here, we propose and employ a tool set that can be used by the research community, assess multiple bioreactor systems across a range of process types and ranges, and connect MCA patterns to relevant microbial groups in each bioreactor system. We applied multiple MCA assessment methods using available tools, layering on a trait-based approach, to seven experiments involving different engineered bioreactor systems. The calculated relative contributions of MCA processes varied by the method used, with null modeling approaches estimating a higher influence of stochastic MCA than neutral modeling. While most patterns of MCA were not discernible by general rules, anaerobic generalists assembled more deterministically than anaerobic specialists. Finally, statistical modeling of confidence levels suggests a minimum of 30-40 samples should be used for neutral modeling while a minimum 50-60 samples should be used for null modeling. Overall, we suggest caution when applying and interpreting the results of any one MCA assessment method.

Stochastic and deterministic mechanisms jointly drive the assembly of microbial communities in cold-rolling wastewater across China

Microorganisms play a pivotal role in industrial wastewater treatment, serving as a critical barrier to water purification and safeguarding human and environmental health. Despite their importance, the biogeographic distribution and assembly mechanisms of microbial communities in cold-rolling wastewater treatment systems remain poorly understood. This study analyzed 101 microbial samples from nine regions using high-throughput sequencing, revealing rich microbial diversity and distinct regional aggregation patterns. Random forest analysis identified key biomarkers, often low-abundance species, while a unique core microbial community was strongly correlated with pollutant removal efficiencies, including chemical oxygen demand (COD), total organic carbon (TOC), and total nitrogen (TN). Neutral community model analysis demonstrated that microbial community assembly is driven by both stochastic and deterministic processes. Co-occurrence network analysis further highlighted o__1-20 and g__Ellin6067 as pivotal taxa influencing community structure. Among environmental factors, nitrite nitrogen (NO₂-N) and COD were identified as critical drivers of community assembly. This study provides the first comprehensive characterization of microbial biogeographic patterns in cold-rolling wastewater treatment plants across China. The findings deepen our understanding of microbial diversity, distribution, and community dynamics in industrial wastewater systems, offering valuable insights for optimizing treatment processes.

Dechloromonas aquae sp. nov., A Novel Species Isolated from Aquaculture Water of Grass Carp

A novel bacterial strain, designated Dechloromonas aquae ZY10T, was isolated from the aquaculture water of grass carp. The colonies exhibited diameters ranging from approximately 1 to 3 mm and were characterized by a creamy-white coloration, circular shape, smooth texture, translucency, and a convex profile. The cells were facultatively anaerobic and motile, utilizing a single polar flagellum for movement. They were rod-shaped, reproduced through binary fission, and were identified as Gram-negative, oxidase-negative, and catalase-positive. Optimal growth was observed between 37 and 40 °C, within a pH range of 7.0-9.0, and at a NaCl concentration of 0% (w/v). The respiratory quinone was ubiquinone-8 (97.6%) and ubiquinone-7 (2.4%), and the major polar lipids were phosphatidylethanolamine (PE), aminophospholipid (APL), diphosphatidylglycerol (DPG), and phosphatidylglycerol (PG). Phylogenetic analysis based on 16S rRNA gene sequences suggested that ZY10T formed a lineage within the genus Dechloromonas and showed the highest 16S rRNA gene sequence similarity to "D. hankyongensis" XY25T (96.5%), followed by D. denitrificans ED1T (96.4%), D. hortensis MA-1T (96.1%) and D. agitata CKBT (96.0%) and Azonexus. caeni Slo-05T (95.5%). The predominant fatty acids of ZY10T were summed feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c) and C16:0. The whole genome of ZY10T was 3,568,927 bp in size, including 3,275 protein-coding genes, 72 tRNA genes, and 15 rRNA genes, and the genomic DNA G + C content was 62.0 mol%. The orthologous average nucleotide identity, average amino acid identity, and digital DNA-DNA hybridization values between ZY10T and other species within the family Azonexaceae were 78.0-81.5%, 71.8-73.9%, and 20.3-23.0%, respectively. Therefore, based on phenotypic, chemotaxonomic, and phylogenetic analyses, the isolated ZY10T (= MCCC 1K08699T = KCTC 72749 T) is proposed as type strain of the novel species Dechloromonas aquae sp. nov.

Biogeographic patterns of viral communities, ARG profiles and virus-ARG associations in adjacent paddy and upland soils across black soil region

Biogeographic distribution of prokaryotic and eukaryotic communities has been extensively studied. Yet, our knowledge of viral biogeographic patterns, the corresponding driving factors and the virus-resistome associations is still limited. Here, using metagenomic analysis, we explored the viral communities and profiles of antibiotic resistance genes (ARGs) in 30 fields of paddy (rice soils, RS) and upland soils (corn soils, CS) at a regional scale across black soil region of Northeast China. Our finding revealed that viral communities displayed significant distance-decay relationships, and environmental variables largely dominated viral community patterns in agricultural soils. Compared to RS, viral community in CS harbored significantly higher viral α-diversity and distinct β-diversity, and exhibited a higher turnover along with environmental gradients and spatial distance. However, no clear latitudinal diversity gradient (LDG) pattern was observed in viral diversity over large-scale sampling for RS and CS, and heterogeneous distribution of soil viruses was well maintained over large-scale sampling. Soil pH was the important influential factor driving viral community, and the high soil nutrient levels negatively affected viral diversity. Uroviricota, Nucleocytoviricota and Artverviricota were the main viral phyla in agricultural soils, and virus-host linkages spanned 17 prokaryotic phyla, including Actinobacteriota and Proteobacteria. Besides, 2578 ARG subtypes were retrieved and conferred resistance to 27 types of antibiotics, in which multidrug was the predominant ARG type in Mollisols. Procrustes analysis showed the significant contribution of viral community to ARG profiles, which was more obvious in CS compared to RS. We identified 9.61 % and 11.4 % of soil viruses carried at least one ARG can infect multi-host in RS and CS. Furthermore, 43 and 77 complete viral metagenome-assembled genome (vMAG) were reconstructed in RS and CS, respectively. Notably, the lysogenic phages in RS contained 29.7 % of ARGs, a higher proportion than the 12.5 % found in CS. Overall, our study underscored the prevalent distribution of viral communities and ARG profiles at a large spatial scale, and the distinct ecological strategies of virus-ARG associations in adjacent paddy and upland soils.

Are adding carbon sources and activated sludge helpful to the full-scale packing-reinforced multistage biological contact oxidation process?

The performance of wastewater treatment plants (WWTPs) is closely related to the structure and function of microbial communities which are frequently regulated by inoculating carbon source or new microbes. However, the status of microbial communities may be determined by the homeostasis of the bioreactors or properties of the influent especially in full-scale wastewater treatment plants. In this study, a full-scale packing-reinforced multistage biological contact oxidation process (PMBCOP) was used for investigating the durative impacts of carbon source addition and new sludge inoculation on the structure, stability and metabolic pathways of microbial communities. The results showed that inoculation of carbon sources or new sludge significantly increased the diversity (Chao1 and Shannon index) and reciprocal cooperations among microorganisms which further improved the stability of microbial communities and the COD (by 15%) and NH3-N (by 3%) removal efficiencies. Proteobacteria and Bacteroidota were two dominant phyla in the system and were responsible for the main metabolic pathway, i.e. amino acid metabolism. Nevertheless, the modifications of key genera, stability, up-regulated metabolites and enriched metabolic pathways as well as the improved removal efficiencies were not able to persist. The resistant ability of microbial community declined after stopping adding carbon source and new sludge which resulted in the instability and low removal efficiencies of the PMBCOP and aroused the requirements on exploring deep homeostatic mechanism of microbial communities and new promoting strategies. This study provided new insights on the durative effects on the succession and metabolism of microbial communities combing with the performances of the full-scale wastewater treatment plant which is helpful for the management of full-scale WWTPs.

Metatranscriptomes of activated sludge microbiomes from saline wastewater treatment plant

The activated sludge microbiome (ASM) drives the biological wastewater treatment process in wastewater treatment plants. It has been established in the literature that the ASM is characterized by a high degree of taxonomic and metabolic diversity. However, meta-omics datasets have been derived from domestic wastewater treatment plants with little attention to saline wastewater treatment plants (SWWTP). Existing knowledge of how activated sludge microorganisms impact water quality, interrelate within habitat networks, and respond to environmental perturbations remains limited. Here we present datasets of the metatranscriptomes of SWWTP in The Netherlands, coupled with process data. The dataset represents a two-year and four-month time series of data collected from 2014 to 2017, with samples taken at approximately monthly intervals from the facultative zone in the activated sludge process of an SWWTP. In total, 32 activated sludge samples were analyzed. This dataset can be used to enhance understanding of the unique microbiome composition in SWWTPs, its dynamic responses to environmental variables, and the metabolic functions within the ASM.

A powerful but frequently overlooked role of thermodynamics in environmental microbiology: inspirations from anammox

Thermodynamics has long been applied in predicting undiscovered microorganisms or analyzing energy flows in microbial metabolism, as well as evaluating microbial impacts on global element distributions. However, further development and refinement in this interdisciplinary field are still needed. This work endeavors to develop a whole-cycle framework integrating thermodynamics with microbiological studies, focusing on representative nitrogen-transforming microorganisms. Three crucial concepts (reaction favorability, energy balance, and reaction directionality) are discussed in relation to nitrogen-transforming reactions. Specifically, reaction favorability, which sheds lights on understanding the diversity of nitrogen-transforming microorganisms, has also provided guidance for novel bioprocess development. Energy balance, enabling the quantitative comparison of microbial energy efficiency, unravels the competitiveness of nitrogen-transforming microorganisms under substrate-limiting conditions. Reaction directionality, revealing the niche-differentiating patterns of nitrogen-transforming microorganisms, provides a foundation for predicting biogeochemical reactions under various environmental conditions. This review highlights the need for a more comprehensive integration of thermodynamics in environmental microbiology, aiming to comprehensively understand microbial impacts on the global environment from micro to macro scales.

Application of the nitrogen-to-argon ratio to understand nitrogen transformation pathways in landfills under in-situ stabilization

The ratio of nitrogen (N2) to argon (Ar) in landfill gas was compared to the atmospheric gas ratio to quantify the balance between N2 generating (anaerobic ammonium oxidation, denitrification) and N2 consuming (nitrogen fixation) processes on three landfills undergoing in-situ stabilization. In the aerated landfills, as much as 22% of the extracted N2 could be explained by net denitrification, with coexisting aerobic and anaerobic domains fostering nitrification-dependent denitrification. Nitrogen fixation was also occasionally observed. Removal of nitrogen via the gas phase exceeded nitrogen removed via the leachate by up to a factor of 33. Contrastingly, the anaerobic landfill under leachate recirculation showed a net reduction of N2 in relation to Ar, indicating nitrogen fixation as the dominant mechanism, equivalent up to 28% of the nitrogen in the extracted landfill gas. The balance between denitrification and nitrogen fixation in the aerated sites varied seasonally, likely caused by increased evapotranspiration in the summer, allowing greater air intrusion through the cover soil, resulting in higher NO3- and NO2- availability for denitrification and anammox. No such variability was observed for the landfill under liquid recirculation. The nitrogen transforming microbial community comprised of species responsible for nitrification, ammonification, denitrification, and anammox, indicating all processes may coexist. The findings show aeration supports nitrogen removal through the gas phase, but also suggest that nitrogen fixation adds nitrogen to the waste body in anaerobic domains. This could delay reaching environmental compliance criteria for leachate nitrogen, both for in-situ treatment by aeration and by leachate recirculation.

Eukaryotic plankton community and assembly processes in a large-scale water diversion project in China

The Middle Route of the South to North Water Diversion Project (MRP) and its water source, the Danjiangkou Reservoir (DJK), play a pivotal role in mitigating the chronic water scarcity challenges faced by northern China. Eukaryotic plankton are widespread in aquatic ecosystems, which are crucial for the water quality stability of DJK and MRP, yet comparative studies on their contemporaneous dynamics and assembly processes are scarce. In this study, amplicon sequencing was used to investigate the eukaryotic plankton communities. The results revealed that the similarity in community composition of DJK is significantly higher than that of MRP, exhibiting distance-decay patterns. Environmental heterogeneity exhibits significant differences between DJK and MRP, and it significantly influences community composition and alpha diversity. Additionally, the assembly processes of eukaryotic plankton in both DJK and MRP are predominantly influenced by stochastic processes. However, in comparison to DJK, deterministic processes have a more pronounced impact on MRP, accounting for 39.29% and 1.82%, respectively. The variations in total nitrogen (TN), chlorophy IIa (Chl.a), and conductivity (Spc) have led to a transition in the assembly of eukaryotic phytoplankton communities in MRP from a stochastic process to a deterministic process. This study extends insights into the dynamics and assembly processes of eukaryotic plankton communities in the large, engineered drinking water diversion project and its water source, which is also useful for the management and regulation of the DJK and MRP.

Biodegradation of CAHs and BTEX in groundwater at a multi-polluted pesticide site undergoing natural attenuation: Insights from identifying key bioindicators using machine learning methods based on microbiome data

Groundwater pollution, particularly in retired pesticide sites, is a significant environmental concern due to the presence of chlorinated aliphatic hydrocarbons (CAHs) and benzene, toluene, ethylbenzene, and xylene (BTEX). These contaminants pose serious risks to ecosystems and human health. Natural attenuation (NA) has emerged as a sustainable solution, with microorganisms playing a crucial role in pollutant biodegradation. However, the interpretation of the diverse microbial communities in relation to complex pollutants is still challenging, and there is limited research in multi-polluted groundwater. Advanced machine learning (ML) algorithms help identify key microbial indicators for different pollution types (CAHs, BTEX plumes, and mixed plumes). The accuracy and Area Under the Curve (AUC) achieved by Support Vector Machines (SVM) were impressive, with values of 0.87 and 0.99, respectively. With the assistance of model explanation methods, we identified key bioindicators for different pollution types which were then analyzed using co-occurrence network analysis to better understand their potential roles in pollution degradation. The identified key genera indicate that oxidation and co-metabolism predominantly drive dechlorination processes within the CAHs group. In the BTEX group, the primary mechanism for BTEX degradation was observed to be anaerobic degradation under sulfate-reducing conditions. However, in the CAHs&BTEX groups, the indicative genera suggested that BTEX degradation occurred under iron-reducing conditions and reductive dechlorination existed. Overall, this study establishes a framework for harnessing the power of ML alongside co-occurrence network analysis based on microbiome data to enhance understanding and provide a robust assessment of the natural attenuation degradation process at multi-polluted sites.

Comammox Nitrospira act as key bacteria in weakly acidic soil via potential cobalamin sharing

The discovery of comammox Nitrospira in low pH environments has reshaped the ammonia oxidation process in acidic settings, providing a plausible explanation for the higher nitrification rates observed in weakly acidic soils. However, the response of comammox Nitrospira to varying pH levels and its ecological role in these environments remains unclear. Here, a survey across soils with varying pH values (ranging from 4.4 to 9.7) was conducted to assess how comammox Nitrospira perform under different pH conditions. Results showed that comammox Nitrospira dominate ammonia oxidation in weakly acidic soils, functioning as a K-strategy species characterized by slow growth and stress tolerance. As a key species in this environment, comammox Nitrospira may promote bacterial cooperation under low pH conditions. Genomic evidence suggested that cobalamin sharing is a potential mechanism, as comammox Nitrospira uniquely encode a metabolic pathway that compensates for cobalamin imbalance in weakly acidic soils, where 86.8% of metagenome-assembled genomes (MAGs) encode cobalamin-dependent genes. Additionally, we used DNA stable-isotope probing (DNA-SIP) to demonstrate its response to pH fluctuations to reflect how it responds to the decrease in pH. Results confirmed that comammox Nitrospira became dominant ammonia oxidizers in the soil after the decrease in pH. We suggested that comammox Nitrospira will become increasingly important in global soils, under the trend of soil acidification. Overall, our work provides insights that how comammox Nitrospira perform in weakly acidic soil and its response to pH changes.

Phage biocontrol in water treatment and reuse systems: a nascent field with significant innovation opportunities

While the use of phages in the food and biomedical sectors occurs commercially, their application in the water sector is less common and is typically demonstrated at a lower technological readiness level. This is so despite the potential that phages have to enhance the control of problematic bacteria (including pathogens) and protect infrastructure within the water sector. Fulfilling the great potential of this nascent field requires more research and development. Here, we highlight innovation opportunities and discern critical knowledge gaps and research needs to facilitate the use of phages as precise biocontrol agents in the water sector. First, while the advent of sequencing technologies made it easier to identify bacterial communities and understand their functional roles, identifying and cultivating the appropriate phages that can be effective against the bacterial target requires more research. The large volumes of water to be spiked with phages also require optimizing the phage biocontrol strategy, minimizing the associated costs and enhancing scaling up. In addition, bacterial hosts may gain phage resistance after long-term exposure, which is common in most water-engineered systems, and strategies to minimize or delay resistance must be considered. In this opinion, we provide an overview of pertinent literature and bioinformatic tools that help identify appropriate bacterial hosts and phages for water systems applications. We then discuss strategies that can aid in prolonging the efficacy and enhancing the feasibility of phage biocontrol approaches.

Differences in Biogeographic Patterns and Mechanisms of Assembly in Estuarine Bacterial and Protist Communities

As transitional ecosystems between land and sea, estuaries are characterized by a unique environment that supports complex and diverse microbial communities. A comprehensive analysis of microbial diversity and ecological processes at different trophic levels is crucial for understanding the ecological functions of estuarine ecosystems. In this study, we systematically analyzed the diversity patterns, community assembly, and environmental adaptability of bacterial and protist communities using high-throughput sequencing techniques. The results revealed a higher alpha diversity for the bacteria than for protists, and the beta diversity pattern was dominated by species turnover in both communities. In addition, the two community assemblages were shown to be dominated by deterministic and stochastic processes, respectively. Furthermore, our results emphasized the influence of the local species pool on microbial communities and the fact that, at larger scales, geographic factors played a more significant role than environmental factors in driving microbial community variation. The study also revealed differences in environmental adaptability among different microbial types. Bacteria exhibited strong adaptability to salinity, while protists demonstrated greater resilience to variations in dissolved oxygen, nitrate, and ammonium concentrations. These results suggested differences in environmental adaptation strategies among microorganisms at different trophic levels, with bacteria demonstrating a more pronounced environmental filtering effect.

Preparation of a novel organic-inorganic composite sludge bioflocculant (SBF) from dewatered sludge as raw material: Characteristics, flocculation mechanism and application for domestic sewage

In this work, a green sludge bioflocculant (SBF) was prepared via chemical hydrolysis of dewatered sludge and applied to flocculation of domestic wastewater. The process parameters for the preparation of the SBF were 1.80 % hydrochloric acid concentration, 60 min extraction time, and 4000 r/min centrifugation speed. SBF is polymeric flocculant composed of organic and inorganic compounds. Flocculation efficiency reached 97.31 ± 0.26 % under optimal flocculation conditions. Charge neutralization promotes the surface adsorption, bridging and net trapping and sweeping of Fe (OH)3, Al (OH)3 and active functional groups O-H/N-H and C = O in SBF, which together achieve efficient flocculation reactions. SBF had high efficiency and stable flocculation performance for phosphorus in urban domestic wastewater, and the concentration of TP in effluent was lower than 0.30 mg/L. Therefore, SBF prepared from dewatered sludge has efficient flocculation properties and is suitable for removing pollutant phosphorus, which has good application prospects in the field of wastewater treatment.

Selective enrichment of high-affinity clade II N2O-reducers in a mixed culture

Microorganisms encoding for the N2O reductase (NosZ) are the only known biological sink of the potent greenhouse gas N2O and are central to global N2O mitigation efforts. Clade II NosZ populations are of particular biotechnological interest as they usually feature high N2O affinities and often lack other denitrification genes. We focus on the yet-unresolved ecological constraints selecting for different N2O-reducers strains and controlling the assembly of N2O-respiring communities. Two planktonic N2O-respiring mixed cultures were enriched at low dilution rates under limiting and excess dissolved N2O availability to assess the impact of substrate affinity and N2O cytotoxicity, respectively. Genome-resolved metaproteomics was used to infer the metabolism of the enriched populations. Under N2O limitation, clade II N2O-reducers fully outcompeted clade I affiliates, a scenario previously only theorized based on pure-cultures. All enriched N2O-reducers encoded and expressed the sole clade II NosZ, while also possessing other denitrification genes. Two Azonexus and Thauera genera affiliates dominated the culture, and we hypothesize their coexistence to be explained by the genome-inferred metabolic exchange of cobalamin intermediates. Under excess N2O, clade I and II populations coexisted; yet, proteomic evidence suggests that clade II affiliates respired most of the N2O, de facto outcompeting clade I affiliates. The single dominant N2O-reducer (genus Azonexus) notably expressed most cobalamin biosynthesis marker genes, likely to contrast the continuous cobalamin inactivation by dissolved cytotoxic N2O concentrations (400 μM). Ultimately, our results strongly suggest the solids dilution rate to play a pivotal role in controlling the selection among NosZ clades, albeit the conditions selecting for genomes possessing the sole nosZ remain elusive. We furthermore highlight the potential significance of N2O-cobalamin interactions in shaping the composition of N2O-respiring microbiomes.

High-throughput single-cell sequencing of activated sludge microbiome

Wastewater treatment plants (WWTPs) represent one of biotechnology's largest and most critical applications, playing a pivotal role in environmental protection and public health. In WWTPs, activated sludge (AS) plays a major role in removing contaminants and pathogens from wastewater. While metagenomics has advanced our understanding of microbial communities, it still faces challenges in revealing the genomic heterogeneity of cells, uncovering the microbial dark matter, and establishing precise links between genetic elements and their host cells as a bulk method. These issues could be largely resolved by single-cell sequencing, which can offer unprecedented resolution to show the unique genetic information. Here we show the high-throughput single-cell sequencing to the AS microbiome. The single-amplified genomes (SAGs) of 15,110 individual cells were clustered into 2,454 SAG bins. We find that 27.5% of the genomes in the AS microbial community represent potential novel species, highlighting the presence of microbial dark matter. Furthermore, we identified 1,137 antibiotic resistance genes (ARGs), 10,450 plasmid fragments, and 1,343 phage contigs, with shared plasmid and phage groups broadly distributed among hosts, indicating a high frequency of horizontal gene transfer (HGT) within the AS microbiome. Complementary analysis using 1,529 metagenome-assembled genomes from the AS samples allowed for the taxonomic classification of 98 SAG bins, which were previously unclassified. Our study establishes the feasibility of single-cell sequencing in characterizing the AS microbiome, providing novel insights into its ecological dynamics, and deepening our understanding of HGT processes, particularly those involving ARGs. Additionally, this valuable tool could monitor the distribution, spread, and pathogenic hosts of ARGs both within AS environments and between AS and other environments, which will ultimately contribute to developing a health risk evaluation system for diverse environments within a One Health framework.

Diversity and biogeography of the bacterial microbiome in glacier-fed streams

The rapid melting of mountain glaciers and the vanishing of their streams is emblematic of climate change1,2. Glacier-fed streams (GFSs) are cold, oligotrophic and unstable ecosystems in which life is dominated by microbial biofilms2,3. However, current knowledge on the GFS microbiome is scarce4,5, precluding an understanding of its response to glacier shrinkage. Here, by leveraging metabarcoding and metagenomics, we provide a comprehensive survey of bacteria in the benthic microbiome across 152 GFSs draining the Earth's major mountain ranges. We find that the GFS bacterial microbiome is taxonomically and functionally distinct from other cryospheric microbiomes. GFS bacteria are diverse, with more than half being specific to a given mountain range, some unique to single GFSs and a few cosmopolitan and abundant. We show how geographic isolation and environmental selection shape their biogeography, which is characterized by distinct compositional patterns between mountain ranges and hemispheres. Phylogenetic analyses furthermore uncovered microdiverse clades resulting from environmental selection, probably promoting functional resilience and contributing to GFS bacterial biodiversity and biogeography. Climate-induced glacier shrinkage puts this unique microbiome at risk. Our study provides a global reference for future climate-change microbiology studies on the vanishing GFS ecosystem.

Assessment of Bacterial Community Structure, Associated Functional Role, and Water Health in Full-Scale Municipal Wastewater Treatment Plants

The present study collected wastewater samples from fourteen (14) full-scale wastewater treatment plants (WWTPs) at different treatment stages, namely, primary, secondary, and tertiary, to understand the impact of WWTP processes on the bacterial community structure, their role, and their correlation with environmental variables (water quality parameters). The findings showed that the bacterial communities in the primary, secondary, and tertiary treatment stages are more or less similar. They are made up of 42 phyla, 84 classes, 154 orders, 212 families, and 268 genera. Proteobacteria, Bacteroidetes, Cloacimonetes, Firmicutes, Euryarchaeota, Verrucomicrobia, Cyanobacteria, Desulfomicrobium, Thauera, Zavarzinia, and Nitrospirae, among others, dominated the bacterial community structure in all treatment stages. The biochemical oxygen demand was 7-12 times, chemical oxygen demand (COD) was 6 times, and total suspended solids (TSS) was 3.5 times higher in the wastewater than what the Central Pollution Control Board (CPCB) in New Delhi, India, allows as standard discharge. The correlation analysis using the Pearson r matrix and canonical correspondence analysis (CCA) also confirmed the fact that these water quality parameters (especially BOD and COD) play a pivotal role in deciphering the community structure in WWTPs.

Formation and Fate of Reactive Nitrogen during Biological Nitrogen Removal from Water: Important Yet Often Ignored Chemical Aspects of the Nitrogen Cycle

Hydroxylamine, nitrous acid, and nitric oxide are obligate intermediates or side metabolites in different nitrogen-converting microorganisms. These compounds are unstable and susceptible to the formation of highly reactive nitrogen species, including nitrogen dioxide, dinitrogen trioxide, nitroxyl, and peroxynitrite. Due to the high reactivity and cytotoxicity, the buildup of reactive nitrogen can affect the interplay of microorganisms/microbial processes, stimulate the reactions with organic compounds like organic micropollutants (OMP) and act as the precursors of nitrous oxide (N2O). However, there is little understanding of the occurrence and significance of reactive nitrogen during biological nitrogen conversions in engineered water systems. In this review, we evaluate the formation and fate of reactive nitrogen produced by microorganisms involved in biological nitrogen removal (BNR) processes, i.e., nitritation/nitrification, denitratation/denitrification, anammox, and the combined processes. While the formation of reactive nitrogen intermediates is entirely controlled by microbial activities, the consumption can be either biological or purely chemical. Changes in environmental conditions, such as redox transition, pH, and substrate availability, can imbalance the production and consumption of these reactive intermediates, thus leading to the transient accumulation of species. Based on previous experimental evidence, environmental relevance of reactive nitrogen in BNR systems, particularly related to abiotic N2O production and OMP transformation, is demonstrated.

Broad Microbial Community Functions in a Conventional Activated Sludge System Exhibit Temporal Stability

Wastewater microbial communities within conventional activated sludge (CAS) systems can perform hundreds of biotransformations whose relative importance, frequency, and temporal stability remain largely unexplored. To improve our understanding of biotransformations in CAS systems, we collected 24 h composite samples from the influent and effluent of a CAS system over 14 days, analyzed samples using high-resolution mass spectrometry (HRMS), and conducted a nontarget analysis of our HRMS acquisitions. We found that over 50% of the chemical features in the influent were completely removed, and the daily number of detected features exhibited low variability with a coefficient of variation of 0.07. Additionally, we found 352 Core chemical features present in every sample at both locations. We used chemical features to search for evidence of 19 potential biotransformations and detected 9 of these biotransformations at a frequency of over 80 times per day, where evidence for dehydrogenations, hydroxylations, and acetylations was most frequently detected. The daily number of detections for the 9 biotransformations exhibited coefficients of variation ranging from 0.13-0.20, revealing the broad temporal stability for these wastewater microbial community functions. This stability contrasts with the previously observed temporal variability for micropollutant biotransformations, suggesting that micropollutant biotransformations are linked to specialized microbial community functions.

Meta-analysis of ecological and phylogenetic biomass maturity metrics

Although a wide variety of biomass sources have been subjected to 16S rRNA gene sequencing, ecological and phylogenetic signatures of maturity have not been identified quantitatively. In this meta-analysis we reanalyzed data from the only published study with publicly available 16S and temperature data (Zhou et al., 2018), and then applied the Zhou results to 705 samples from 13 additional studies. Using the Zhou data, we found that Faith's alpha diversity index correlated inversely with compost temperature and positively with maturity. We also noted a dramatic shift in the ratios of Bacilliota to Acidobacteriota, Planctomycetota, and Pseudomonadota, as samples cooled below 44 °C (p < 0.001). A negative correlation between Bacillota and Pseudomonadota was also observed in all 705 samples that included compost, sugarcane mill mud, anerobic digestates, and vermicompost. Even in the absence of temperature data for the majority of samples, our meta-analysis shows that microbiomes of diverse residuals converged on similar communities that resemble those of soil, regardless of the starting material or residual management process. We propose that approximately < 0.4 log(Bacillota:Pseudomonadota) and > 43 Faith's phylogenetic diversity indices are indicative of maturity of diverse biomass materials destined for land application.

Antibiotic resistance and pathogen spreading in a wastewater treatment plant designed for wastewater reuse

Climate change significantly contributes to water scarcity in various regions worldwide. While wastewater reuse is a crucial strategy for mitigating water scarcity, it also carries potential risks for human health due to the presence of pathogenic and antibiotic resistant bacteria (ARB). Antibiotic resistance represents a Public Health concern and, according to the global action plan on antimicrobial resistance, wastewater role in selecting and spreading ARB must be monitored. Our aim was to assess the occurrence of ARB, antibiotic resistance genes (ARGs), and potential pathogenic bacteria throughout a wastewater treatment plant (WWTP) designed for water reuse. Furthermore, we aimed to evaluate potential association between ARB and ARGs with antibiotics and heavy metals. The results obtained revealed the presence of ARB, ARGs and pathogenic bacteria at every stage of the WWTP. Notably, the most prevalent ARB and ARG were sulfamethoxazole-resistant bacteria (up to 7.20 log CFU mL-1) and sulII gene (up to 5.91 log gene copies mL-1), respectively. The dominant pathogenic bacteria included Arcobacter, Flavobacterium and Aeromonas. Although the abundance of these elements significantly decreased during treatment (influent vs. effluent, p < 0.05), they were still present in the effluent designated for reuse. Additionally, significant correlations were observed between heavy metal concentrations (copper, nickel and selenium) and antibiotic resistance elements (ampicillin-resistant bacteria, tetracycline-resistant bacteria, ARB total abundance and sulII) (p < 0.05). These results underscore the importance of monitoring the role of WWTP in spreading antibiotic resistance, in line with the One Health approach. Additionally, our findings suggest the need of interventions to reduce human health risks associated with the reuse of wastewater for agricultural purposes.

Deep insights into the assembly mechanisms, co-occurrence patterns, and functional roles of microbial community in wastewater treatment plants

The understanding of activated sludge microbial status and roles is imperative for improving and enhancing the performance of wastewater treatment plants (WWTPs). In this study, we conducted a deep analysis of activated sludge microbial communities across five compartments (inflow, effluent, and aerobic, anoxic, anaerobic tanks) over temporal scales, employing high-throughput sequencing of 16S rRNA amplicons and metagenome data. Clearly discernible seasonal patterns, exhibiting cyclic variations, were observed in microbial diversity, assembly, co-occurrence network, and metabolic functions. Notably, summer samples exhibited higher α-diversity and were distinctly separated from winter samples. Our analysis revealed that microbial community assembly is influenced by both stochastic processes (66%) and deterministic processes (34%), with winter samples demonstrating more random assembly compared to summer. Co-occurrence patterns were predominantly mutualistic, with over 96% positive correlations, and summer networks were more organized than those in winter. These variations were significantly correlated with temperature, total phosphorus and sludge volume index. However, no significant differences were found among microbial community across five compartments in terms of β diversity. A core community of keystone taxa was identified, playing key roles in eight nitrogen and eleven phosphorus cycling pathways. Understanding the assembly mechanisms, co-occurrence patterns, and functional roles of microbial communities is essential for the design and optimization of biotechnological treatment processes in WWTPs.

The impact of wastewater treatment plants on the composition and toxicity of pollutants in urban rivers in Nanjing, China

Widespread wastewater pollution is one of the biggest challenges threatening the ecological health of rivers. It is crucial to identify the toxic changes of effluents after entering urban rivers as well as the toxic substances in the complex chemical mixtures found in these urban rivers. This study used HepG2 cell line for cytotoxicity test to evaluate the ecological impact of effluents on urban rivers. Water samples were collected from the Xingwu River and Yunliang River in Nanjing, China. The bacterial communities in the lower reaches of urban rivers were altered due to the differences in total nitrogen and nitrate nitrogen. The complex chemical mixtures collected in the urban rivers were divided into 10 fractions, >100 chemicals were screened in each fraction. The substances with LC50 < 1000 mg/L were listed as toxic substances, and the number of toxic substances dominated the toxicity of urban rivers. Our study highlights toxicity as a comprehensive indicator for assessing river pollutants and reveals relationship between the number of toxic substance and river toxicity. These findings have direct implications for the monitoring and management of environmental stressors and the protection of aquatic organisms and human health.

Microbiome regulation for sustainable wastewater treatment

Sustainable wastewater treatment is essential for attaining clean water and sanitation, aligning with UN Sustainable Development Goals. Wastewater treatment plants (WWTPs) have utilized environmental microbiomes in biological treatment processes in this effort for over a century. However, the inherent complexity and redundancy of microbial communities, and emerging chemical and biological contaminants, challenge the biotechnology applications. Over the past decades, understanding and utilization of microbial energy metabolism and interaction relationships have revolutionized the biological system. In this review, we discuss how microbiome regulation strategies are being used to generate actionable performance for low-carbon pollutant removal and resource recovery in WWTPs. The engineering application cases also highlight the real feasibility and promising prospects of the microbiome regulation approaches. In conclusion, we recommend identifying environmental risks associated with chemical and biological contaminants transformation as a prerequisite. We propose the integration of gene editing and enzyme design to precisely regulate microbiomes for the synergistic control of both chemical and biological risks. Additionally, the development of integrated technologies and engineering equipment is crucial in addressing the ongoing water crisis. This review advocates for the innovation of conventional wastewater treatment biotechnology to ensure sustainable wastewater treatment.

Strain-level multidrug-resistant pathogenic bacteria in urban wastewater treatment plants: Transmission, source tracking and evolution

Wastewater treatment plants (WWTPs) serve as reservoirs for various pathogens and play a pivotal role in safeguarding environmental safety and public health by mitigating pathogen release. Pathogenic bacteria, known for their potential to cause fatal infections, present a significant and emerging threat to global health and remain poorly understood regarding their origins and transmission in the environment. Using metagenomic approaches, we identified a total of 299 pathogens from three full-scale WWTPs. We comprehensively elucidated the occurrence, dissemination, and source tracking of the pathogens across the WWTPs, addressing deficiencies in traditional detection strategies. While indicator pathogens in current wastewater treatment systems such as Escherichia coli are effectively removed, specific drug-resistant pathogens, including Pseudomonas aeruginosa, Pseudomonas putida, and Aeromonas caviae, persist throughout the treatment process, challenging complete eradication efforts. The anoxic section plays a predominant role in controlling abundance but significantly contributes to downstream pathogen diversity. Additionally, evolution throughout the treatment process enhances pathogen diversity, except for upstream transmission, such as A. caviae str. WP8-S18-ESBL-04 and P. aeruginosa PAO1. Our findings highlight the necessity of expanding current biomonitoring indicators for wastewater treatment to optimize treatment strategies and mitigate the potential health risks posed by emerging pathogens. By addressing these research priorities, we can effectively mitigate risks and safeguard environmental safety and public health.

Dissolved organic nitrogen depresses the expected outcome of wastewater treatment upgrading on effluent eutrophication potential mitigation: Molecular mechanistic insight

Continuously tightening total nitrogen (TN) discharge standards in wastewater treatment plants is a common practice worldwide to mitigate eutrophication. However, given the different bioavailability of effluent dissolved organic nitrogen (DON) and inorganic nitrogen, a great inefficiency of the TN-targeted upgrading might be hidden because of the poor understanding of its impact on effluent eutrophication potential mitigation. Here we show that the tightening TN discharge standards could only considerably promote inorganic nitrogen removal, however, DON concentrations remained constant across different effluent TN levels (p > 0.05, Kruskal-Wallis test). Surprisingly, restricting TN in turn increases the reactivity of DON molecules owing to the accumulation of produced DON by acting on the key biotic and abiotic transformation reactions. The difficulty of removing DON and the increased DON reactivity during wastewater treatment upgrading contribute to the practical elimination effect of effluent eutrophication potential exhibiting lower than expected. This work challenges the rationality of the prevailing pursuit for extreme-low TN discharge, calling for shifting the focus of wastewater treatment upgrading towards the more fundamental eutrophication-targeted perspective.

Activated Sludge Combined with Pervious Concrete Micro-Ecosystem for Runoff Rainwater Collection and Pollutant Purification

This study investigated the purification of pollutants in runoff rainwater by constructing a micro-ecosystem using waste-activated sludge (WAS) and riverbed sludge (RBS) as inoculums in combination with pervious concrete. The research results showed that the best hydraulic retention time (HRT) was 9 h. The COD and ammonia nitrogen (NH4+-N) removal of the waste-activated sludge ecosystem (WASE) was 62.67% and 71.21%, respectively, while the riverbed sludge ecosystem (RBSE) showed COD and NH4+-N removal percentages of 46.05% and 66.55%, respectively. The analysis of the genetic metabolism of microbial genes showed that the system was microbially enhanced with extensive and diverse populations. At the phylum level, the microorganisms responsible for degrading organic matter were mainly Firmicutes and Actinobacteriota. At the genus level, the Trichococcus genus was dominant in the WASE, while the Dietzia, norank_f__Sporomusaceae and norank_f__norank_o__norank_c__BRH-c20a genera were the central bacterial populations in the RBSE. The proliferation of phylum-level bacteria in the WASE was relatively large, and the genus-level bacteria demonstrated a better removal efficiency for pollutants. The overall removal effect of the WASE was better than that of the RBSE. The application analyses showed that a WASE is capable of effectively accepting and treating all rainfall below rainstorm levels and at near-full rainstorm levels under optimal removal efficiency conditions. This study innovatively used wastewater plant waste-activated sludge combined with pervious concrete to construct a micro-ecosystem to remove runoff rainwater pollutants. The system achieved pollutant removal comparable to that of pervious concrete modified with adsorbent materials. An effective method for the collection and pollutant treatment of urban runoff rainwater is provided.