Insights into microbial diversity in wastewater treatment systems: How far have we come?

Metabolic evolution and bottleneck insights into simultaneous autotroph-heterotroph anammox system for real municipal wastewater nitrogen removal

When biological nitrogen removal (BNR) systems shifted from treating simulated wastewater to real wastewater, a microbial succession occurred, often resulting in a decline in efficacy. Notably, despite their high nitrogen removal efficiency for real wastewater, anammox coupled systems operating without or with minimal carbon sources also exhibited a certain degree of performance reduction. The underlying reasons and metabolic shifts within these systems remained elusive. In this study, the simultaneous autotrophic/heterotrophic anammox system demonstrated remarkable metabolic resilience upon exposure to real municipal wastewater, achieving a nitrogen removal efficiency (NRE) of 82.83 ± 2.29 %. This resilience was attributed to the successful microbial succession and the complementary metabolic functions of heterotrophic microorganisms, which fostered a resilient microbial community. The system's ability to harness multiple electron sources, including NADH oxidation, the TCA cycle, and organics metabolism, allowed it to establish a stable and efficient electron transfer chain, ensuring effective nitrogen removal. Despite the denitrification channel's nitrite supply capability, the analysis of the interspecies correlation network revealed that the synergistic metabolism between AOB and AnAOB was not fully restored, resulting in selective functional bacterial and genetic interactions and the system's PN/A performance declined. Additionally, the enhanced electron affinity of PD increased interconversion of NO3--N and NO2--N, limiting the efficient utilization of electrons and thereby constraining nitrogen removal performance. This study elucidated the metabolic mechanism of nitrogen removal limitations in anammox-based systems treating real municipal wastewater, enhancing our understanding of the metabolic functions and electron transfer within the symbiotic bacterial community.

Unveiling the mechanism underlying in-situ enhancement on anammox system by sulfide: Integration of biological and isotope analysis

The in-situ utilization of sulfide to remove the nitrate produced during the anaerobic ammonium oxidation (anammox) process can avoid prolonged sludge acclimatization, facilitating the rapid initiation of coupled nitrogen removal processes. However, the understanding of in-situ enhancement on anammox system by sulfide remains unclear. Herein, sulfide (Na2S) was introduced as an additional electron donor to remove the nitrate derived from the anammox under varying sulfide/nitrogen (S/N, S2--S/NO3--N, molar ratio) ratios (0.004-4.375). The underlying mechanisms were elucidated by molecular biology techniques including flow cytometry, quantitative polymerase chain reaction, and 16S rRNA amplicon sequencing, alongside isotope tracer analysis. Results revealed that anammox reactors, when operated with in-situ sulfide addition, exhibited a significant enhancement in total nitrogen removal efficiency (NRE) ranging from 11.5 %-41.7 % (achieved 96 %), with the optimal S/N ratios of 0.01-0.8. Isotope tracer analysis indicated the successful coupling of the anammox, sulfur autotrophic denitrification (SADN), and dissimilatory nitrate reduction to ammonium (DNRA) processes within the system, with their contributions to nitrogen removal being 46 %-50 %, 24 %-30 %, and 20 %-22 %, respectively. Moreover, a notable increase in the abundance of sulfur-oxidizing bacteria (SOB) (20 %-40 % increase) and DNRA bacteria (10 %-20 % increase) were observed. Effective collaboration was further supported by the sustained viability of microbial communities. It is speculated that the heightened presence of SOB and DNRA bacteria created a low toxicity environment by converting sulfide to biogenic sulfur, thereby promoting the well-being of anammox bacteria. However, the excessive dosage of sulfide (S/N = 1.8) intensified the DNRA process (contribution>35 %) and weakened the anammox process, leading to an increase in effluent NH4+-N concentration and a decline in NRE. This study confirms that the in-situ adding an appropriate amount of sulfide favors achieving complete nitrogen removal in anammox system, which provides a novel avenue to resolve the issue of the residual nitrate in anammox process.

16S rRNA gene amplicon sequencing data from an Australian wastewater treatment plant

Amplicon sequencing data of the 16S rRNA (V1-V3) gene from 56 effluent and sediment samples from an Australian wastewater treatment plant are reported. Proteobacteria (3.50%-90.09%), Actinobacteria (0.02%-45.71%), and Cyanobacteria (0.05%-63.73%) were dominant in the effluent. The sediment samples were dominated by Proteobacteria (13.14%-84.83%), Chloroflexi (0.84%-42.52%), and Firmicutes (1.54%-17.21%).

Microbiome analysis reveals Microcystis blooms endogenously seeded from benthos within wastewater maturation ponds

Toxigenic Microcystis blooms periodically disrupt the stabilization ponds of wastewater treatment plants (WWTPs). Dense proliferations of Microcystis cells within the surface waters (SWs) impede the water treatment process by reducing the treatment efficacy of the latent WWTP microbiome. Further, water quality is reduced when conventional treatment leads to Microcystis cell lysis and the release of intracellular microcystins into the water column. Recurrent seasonal Microcystis blooms cause significant financial burdens for the water industry and predicting their source is vital for bloom management strategies. We investigated the source of recurrent toxigenic Microcystis blooms at Australia's largest lagoon-based municipal WWTP in both sediment core (SC) and SW samples between 2018 and 2020. Bacterial community composition of the SC and SW samples according to 16S rRNA gene amplicon sequencing showed that Microcystis sp. was dominant within SW samples throughout the period and reached peak relative abundances (32%) during the summer. The same Microcystis Amplicon sequence variants were present within the SC and SW samples indicating a potential migratory population that transitions between the sediment water and SWs during bloom formation events. To investigate the potential of the sediment to act as a repository of viable Microcystis cells for recurrent bloom formation, a novel in-vitro bloom model was established featuring sediments and sterilized SW collected from the WWTP. Microcystin-producing Microcystis blooms were established through passive resuspension after 12 weeks of incubation. These results demonstrate the capacity of Microcystis to transition between the sediments and SWs in WWTPs, acting as a perennial inoculum for recurrent blooms.IMPORTANCECyanobacterial blooms are prevalent to wastewater treatment facilities owing to the stable, eutrophic conditions. Cyanobacterial proliferations can disrupt operational procedures through the blocking of filtration apparatus or altering the wastewater treatment plant (WWTP) microbiome, reducing treatment efficiency. Conventional wastewater treatment often results in the lysis of cyanobacterial cells and the release of intracellular toxins which pose a health risk to end users. This research identifies a potential seeding source of recurrent toxigenic cyanobacterial blooms within wastewater treatment facilities. Our results demonstrate the capacity of Microcystis to transition between the sediments and surface waters (SWs) of wastewater treatment ponds enabling water utilities to develop adequate monitoring and management strategies. Further, we developed a novel model to demonstrate benthic recruitment of toxigenic Microcystis under laboratory conditions facilitating future research into the genetic mechanisms behind bloom development.

Response of partial nitritation and denitrification processes to high levels of free ammonia in a pilot mature landfill leachate treatment system: Stability and microbial community dynamics

The high levels of free ammonia (FA) challenge the application of partial nitritation (PN) and denitrification (DN) in the treatment of ammonia-rich wastewater. This study explored the impact of high levels of FA on the PN and DN stability and microbial community dynamics. By reducing reflux and increasing influent load, the concentrations of FA in PN and DN reactors increased from 28.9 mg/L and 140.0 mg/L to 1099.8 mg/L and 868.4 mg/L, respectively. During this process, the performance of PN and DN remained stable. The microbial analysis revealed that the Nitrosomonas exhibited strong tolerance to high levels of FA, and its relative abundance was positively correlated with amoABC (R2 0.984) and hao (R2 0.999) genes. The increase in microbial diversity could enhance the resistance ability of PN against the FA impact. In contrast, high levels of FA had scant influence on the microbial community and performance of DN.

Microeukaryotic predators shape the wastewater microbiome

The physicochemical parameters that shape the prokaryotic community composition in wastewater have been extensively studied. In contrast, it is poorly understood whether and how biotic interactions affect the prokaryotic community composition in wastewater. We used metatranscriptomics data from a bioreactor sampled weekly over 14 months to investigate the wastewater microbiome, including often neglected microeukaryotes. Our analysis revealed that while prokaryotes are unaffected by seasonal changes in water temperature, they are impacted by a seasonal, temperature-induced change in the microeukaryotic community. Our findings suggest that selective predation pressure exerted by microeukaryotes is a significant factor shaping the prokaryotic community in wastewater. This study underscores the importance of investigating the entire wastewater microbiome to develop a comprehensive understanding of wastewater treatment.

Microbial indicators of efficient performance in an anaerobic/anoxic/aerobic integrated fixed-film activated sludge (A2O-IFAS) and a two-stage mesophilic anaerobic digestion process

An analysis of the community structure, diversity and population dynamics of Bacteria and Archaea in the suspended and attached biomass fractions of a pilot-scale anaerobic/anoxic/aerobic integrated fixed-film activated sludge (A²O-IFAS) was executed. Along with this, the effluents of the acidogenic (AcD) and methanogenic (MD) digesters of a two-stage mesophilic anaerobic (MAD) system treating the primary sludge (PS) and waste activated sludge (WAS) generated by the A²O-IFAS were also analyzed. Non-metric multidimensional scaling (MDS) and Biota-environment (BIO-ENV) multivariate analyses were performed to link population dynamics of Bacteria and Archaea to operating parameters and removal efficiencies of organic matter and nutrients, in search of microbial indicators associated with optimal performance. In all samples analyzed, Proteobacteria, Bacteroidetes and Chloroflexi were the most abundant phyla, while the hydrogenotrophic methanogens Methanolinea, Methanocorpusculum and Methanobacterium were the predominant archaeal genera. BIO-ENV analysis disclosed strong correlations between the population shifts observed in the suspended and attached bacterial communities of the A²O-IFAS and the removal rates of organic matter, N and P. It is noteworthy that the incorporation of carriers combined with a short sludge retention time (SRT = 4.0 ± 1.0 days) enhanced N removal performance of the A²O by favoring the enrichment of bacterial genera able to denitrify (Bosea, Dechloromonas, Devosia, Hyphomicrobium, Rhodobacter, Rhodoplanes, Rubrivivax, and Sulfuritalea) in the attached biomass fraction. In addition, operation at short SRT enabled the generation of a highly biodegradable WAS, which enhanced the biogas and methane yields in the two-stage MAD. An increase in the relative abundance of Acetobacteroides (uncultured Blvii28 wastewater-sludge group of Rikenellaceae family) correlated positively with the volatile solids removal rate (%VSR), CH₄ recovery rate and %CH₄ in the biogas (r > 0.8), supporting their relevance for an efficient methanogenesis in two-stage systems.

Model-based fractionation of biomass in a biological nutrient removal system and its effect on the removal efficiencies

Fractionation of active biomass in a five-stage Bardenpho process was accomplished using an MS Excel wastewater treatment plant modeling tool based on Activated Sludge Model No. 3 extended with a bio-P module. The biomass fractions within the treatment system were predicted as autotrophs, ordinary heterotrophs, and phosphorus accumulating organisms (PAOs). Several simulations were performed in a Bardenpho process using various C/N/P ratios in primary effluent. Biomass fractionation was obtained from steady-state simulation results. The results suggest that the mass percentage of autotrophs, heterotrophs, and PAOs in active biomass range from 1.7 to 7.8%, 5.7-69.0%, and 23.2-92.6%, respectively, depending on characteristics of primary effluent. Results of principal component analysis showed that TKN/COD ratio in primary effluent determines the population of autotrophs and ordinary heterotrophs whereas PAO population is mainly a function of TP/COD ratio.

High-throughput sequencing as a tool for monitoring prokaryote communities in a wastewater treatment plant

In this study, the DNA metabarcoding technique was used to explore the prokaryote diversity and community structure in wastewater collected in spring and winter 2020-2021 as well as the efficiency of the treatment in a wastewater treatment plant (WWTP) in Ría de Vigo (NW Spain). The samplings included raw wastewater from the inlet stream (M1), the discharge water after the disinfection treatment (M3) and mussels used as bioindicators of possible contamination of the marine environment. Significant differences were discovered in the microbiome of each type of sample (M1, M3 and mussels), with 92 %, 45 % and 44 % of exclusive OTUs found in mussel, M3 and M1 samples respectively. Seasonal differences were also detected in wastewater samples, with which abiotic parameters (temperature, pH) could be strongly involved. Bacteria present in raw wastewater (M1) were associated with the human gut microbiome, and therefore, potential pathogens that could be circulating in the population in specific periods were detected (e.g., Arcobacter sp. and Clostridium sp.). A considerable decrease in putative pathogenic organisms from the M1 to M3 wastewater fractions and the scarce presence in mussels (<0.5 % total reads) confirmed the effectiveness of pathogen removal in the wastewater treatment plant. Our results showed the potential of the DNA metabarcoding technique for monitoring studies and confirmed its application in wastewater-based epidemiology (WBE) and environmental contamination studies. Although this technique cannot determine if the infective pathogens are present, it can characterize the microbial communities and the putative pathogens that are circulating through the population (microbiome of M1) and also confirm the efficacy of depuration treatment, which can directly affect the aquaculture sector and even human and veterinary health.

Response of sediment microbial communities to different levels of PAC contamination and exposure time

Coagulants such as polyaluminium chloride (PAC) are widely used for removing phosphorus from eutrophic water, but its application for water treatment can potentially harm the environment. In this study, a four-timepoint exposure experiment was performed at week 1, 3, 7 and 10 to investigate how microbial communities in lake sediments respond to different concentrations of PAC (RS (raw lake water with nothing added), Low, Medium and High). The results showed that, while PAC can efficiently decrease the amount of C, N and P in lake water, the presence of residual aluminum and aluminum precipitates can greatly affect the microbial communities in lake sediments. In particular, different concentrations of PAC and exposure time affected the microbial diversity and structure of lake sediments, with changes being especially obvious at high concentration of PAC after 10 weeks of exposure. Moreover, the use of PAC significantly increased the relative abundances of Gammaproteobacteria and Competibacter, while reducing those of Thermodesulfovibrionia, Vicinamibacterales, and BSV26 in time- and concentration-dependent manners. Network analysis further showed strong correlations between differential bacterial species of PAC in high concentration at 10 weeks, which further suggested that PAC treatment changed the complex structure of microbiota in lake sediment. Finally, correlation analysis indicated a close connection between water parameters and differential species induced by PAC treatment. Overall, PAC contamination changed the microbial communities at different taxonomy levels and influenced the functional pathways to potentiate the P removal, and the results offered interesting insights into the use of PAC in water treatment and its impact on biogeochemical cycling. These results indicated that more attention need to be paid to the potential impact of chemical phosphorus removing reagents on the environment, including eutrophic water.

Achieving robust nitritation in a modified continuous-flow reactor: From micro-granule cultivation to nitrite-oxidizing bacteria elimination

In this study, a modified continuous-flow nitrifying reactor was successfully operated for rapid cultivation of micro-granules and achieving robust nitritation. Results showed that sludge granulation with mean size of ca. 100 µm was achieved within three weeks by gradually increasing settling velocity-based selection pressure from 0.48 to 0.9 m/hr. Though Nitrospira like nitrite-oxidizing bacteria (NOB) were enriched in the micro-granules with a ratio between ammonia-oxidizing bacteria (AOB) and NOB of 5.7%/6.5% on day 21, fast nitritation was achieved within one-week by gradually increasing of influent ammonium concentration (from 50 to 200 mg/L). Maintaining ammonium in-excess was the key for repressing NOB in the micro-granules. Interestingly, when the influent ammonium concentration switched back to 50 mg/L still with the residual ammonium of 15-25 mg/L, the nitrite accumulation efficiency increased from 90% to 98%. Experimental results suggested that the NOB repression was intensified by both oxygen and nitrite unavailability in the inner layers of micro-granules. Unexpectedly, continuous operation with ammonium in excess resulted in overproduction of extracellular polysaccharides and overgrowth of some bacteria (e.g., Nitrosomonas, Arenimonas, and Flavobacterium), which deteriorated the micro-granule stability and drove the micro-granules aggregation into larger ones with irregular morphology. However, efficient nitritation was stably maintained with extremely high ammonium oxidation potential (> 50 mg/g VSS/hr) and nearly complete washout of NOB was obtained. This suggested that smooth and spherical granule was not a prerequisite for achieving NOB wash-out and maintaining effective nitritation in the granular reactor. Overall, the micro-granules exhibited a great practical potential for high-rate nitritation.

Co-treatment of landfill leachate with urban wastewater by chemical, physical and biological processes: Fenton oxidation preserves autochthonous bacterial community in the activated sludge process

The impact of Fenton oxidation (FO) and Air stripping (AS) pre-treatments on the bacterial community of a biological activated sludge (B-AS) process for the co-treatment of mature landfill leachate (MLL) and urban wastewater (UWW) was assessed. In this work high-throughput sequencing was used to identify changes in the composition of the bacterial communities when exposed to different landfill leachate's pre-treatments. The combination of FO and AS to increase biodegradability (BOD₅/COD) and reduce ammonia concentration (NH₃) respectively, allowed to successfully operate the B-AS and effectively treat MLL. In particular, BOD₅/COD resulted to be the key factor for bacterial community shifting. The microbiological community of the B-AS, mainly composed by the phylum Bacteroidota (Saprospiraceae, PHOS-HE51, Chitinophagaceae) after FO pre-treatment, shifted to Pseudomonadota (Caulobacteraceae and Hyphomicrobiaceae) when FO was not used. At the same time a drastic reduction in BOD₅ removal was observed (90%-58%). On the other hand, high NH₃ concentration affected the abundance of the family Saprospiraceae, known to play a key role in the degradation of complex organic compounds in B-AS. The results obtained suggest that a suitable combination of pre-treatments can reduce the negative effect of MLL on the B-AS process, reducing the pressure on autochthonous bacteria and therefore the acclimatization time of the biological process.

Selection, Identification and Functional Performance of Ammonia-Degrading Microbial Communities from an Activated Sludge for Landfill Leachate Treatment

The increasing amounts of municipal solid waste and their management in landfills caused an increase in the production of leachate, a liquid formed by the percolation of rainwater through the waste. Leachate creates serious problems to municipal wastewater treatment plants; indeed, its high levels of ammonia are toxic for bacterial cells and drastically reduce the biological removal of nitrogen by activated sludge. In the present work, we studied, using a metagenomic approach based on next-generation sequencing (NGS), the microbial composition of sludge in the municipal wastewater treatment plant of Porto Sant'Elpidio (Italy). Through activated sludge enrichment experiments based on the Repetitive Re-Inoculum Assay, we were able to select and identify a minimal bacterial community capable of degrading high concentrations of ammonium (NH₄⁺-N ≅ 350 mg/L) present in a leachate-based medium. The analysis of NGS data suggests that seven families of bacteria (Alcaligenaceae, Nitrosomonadaceae, Caulobacteraceae, Xanthomonadaceae, Rhodanobacteraceae, Comamonadaceae and Chitinophagaceae) are mainly responsible for ammonia oxidation. Furthermore, we isolated from the enriched sludge three genera (Klebsiella sp., Castellaniella sp. and Acinetobacter sp.) capable of heterotrophic nitrification coupled with aerobic denitrification. These bacteria released a trace amount of both nitrite and nitrate possibly transforming ammonia into gaseous nitrogen. Our findings represent the starting point to produce an optimized microorganisms's mixture for the biological removal of ammonia contained in leachate.

Novel database and cut-off value for bacterial amoA gene revealed a spatial variability pattern of the ammonia-oxidizing bacteria community from river to sea

Ammonia-oxidizing bacteria (AOB) catalyze the first step of nitrification, oxidizing ammonia to nitrite, and are characterized by amoA gene encoding ammonia monooxygenase. To analyze the AOB community effectively, an integral taxonomy database containing 14,058 amoA sequences and the optimal cut-off value at 95 % for OTU clustering were determined. This method was evaluated to be efficient by the analysis of environmental samples from the river, estuary, and sea. Using this method, a significant spatial variance of the AOB community was found. The diversity of AOB was highest in the estuary and lowest in the ocean. Nitrosomonas were the predominant AOB in the sediments of the freshwater river and estuary. Nearly all the AOB-amoA sequences belonged to uncultured bacterium in the sediments of deep sea. In general, an integral AOB taxonomic database and a suitable cut-off value were constructed for the comprehensive exploration of the diversity of AOB from river to sea.

Simultaneous nitrification and denitrification in membrane bioreactor: Effect of dissolved oxygen

Membrane bioreactor with the floc activated sludge (mixed liquor suspended solids (MLSS) = 7500 mg/L) was constructed in this work for simultaneously nitrification and denitrification (SND). The effect of dissolved oxygen (DO) on SND process and the nitrogen pathways were investigated. The average TN removal efficiencies were 63.05%, 91.17%, 87.04% and 70.02% for DO 0.5, 1, 2 and 3 mg/L systems, respectively. The effluent ammonia concentration was continuously lower than 5.0 mg/L when the DO was higher than 1 mg/L. Nitrogen in DO 1 and DO 2 mg/L systems was mainly removed via the SND process. The rise of DO concentration increased the abundance of nitrite oxidizing bacteria (NOB) and Nitrospira was the predominant NOB in all the four MBRs. Dechloromonas and Azoarcus were the dominant denitrifying bacteria (DNB) in DO 1 systems responsible for nitrite denitrification. The dominant aerobic DNB Pseudomonas also contributed SND via nitrate denitrification and was little affected by DO changes. Nitrate reductase was the main enzyme for the reduction of NO₃^--N to NO₂^--N, and narG was the main responsible gene. Nitrite oxidoreductase was the main enzyme for the oxidation of NO₂^--N to NO₃^--N, and nxrA was the main responsible gene in all the four MBR systems.

Polyaniline-Derived Nitrogen-Containing Carbon Nanostructures with Different Morphologies as Anode Modifier in Microbial Fuel Cells

Anode modification with carbon nanomaterials is an important strategy for the improvement of microbial fuel cell (MFC) performance. The presence of nitrogen in the carbon network, introduced as active nitrogen functional groups, is considered beneficial for anode modification. In this aim, nitrogen-containing carbon nanostructures (NCNs) with different morphologies were obtained via carbonization of polyaniline and were further investigated as anode modifiers in MFCs. The present study investigates the influence of NCN morphology on the changes in the anodic microbial community and MFC performance. Results show that the nanofibrillar morphology of NCNs is beneficial for the improvement of MFC performance, with a maximum power density of 40.4 mW/m2, 1.25 times higher than the anode modified with carbonized polyaniline with granular morphology and 2.15 times higher than MFC using the carbon cloth-anode. The nanofibrillar morphology, due to the well-defined individual nanofibers separated by microgaps and micropores and a better organization of the carbon network, leads to a larger specific surface area and higher conductivity, which can allow more efficient substrate transport and better bacterial colonization with greater relative abundances of Geobacter and Thermoanaerobacter, justifying the improvement of MFC performance.

The effect of salinity on ammonium-assimilating biosystems in hypersaline wastewater treatment

The ammonium-assimilating biosystem is a promising solution to improve the susceptible biological nitrogen removal (BNR) and to achieve nitrogen recovery in saline wastewater treatment. However, the treatment performance and functional stability of ammonium-assimilating biosystems have not been fully illuminated in hypersaline wastewater. In this study, although the dramatic decrease of removal efficiency of NH₄⁺-N and PO₄^3--P was observed in ammonium-assimilating biosystems under the salinity from 3% to 7%, the direction of nitrogen conversions through assimilation was insusceptible to high salinity. The extremely low concentrations of nitrite and nitrate accumulation and abundances of nitrification functional genes confirmed that the process of nitrification was negligible in all biosystems. Ammonium-assimilating biosystems maintained robustness and functional stability in hypersaline wastewater. The increase of salinity stimulated the production of EPS and changed the microbial community by enriching Proteobacteria and halophilic genera. We anticipate that the ammonium-assimilating biosystem could be a promising strategy for hypersaline wastewater treatment and future practical applications.

Biological phosphorus removal and its microbial community in a modified full-scale activated sludge system under dry and wet weather dynamics

Enhanced biological phosphorus removal (EBPR) performance and microbial community dynamics during dry and wet-weather conditions of a full-scale treatment plant was evaluated by converting a section of activated sludge basins using low-cost operational modifications into an anoxic/anaerobic zone to promote EBPR. Two trains of the activated sludge system at the Des Moines, Iowa Metropolitan Wastewater Reclamation Facility were used for the study with one train modified for EBPR, and the other remained as nitrification-only for comparison. In addition to measuring the modification effectiveness for phosphorus removal, performance was compared during dry and wet weather conditions over the course of two summer seasons to improve understanding of wet and dry weather dynamics for EBPR. DNA sequencing and qPCR tests were conducted to develop an understanding of microbial population changes between control and modified basins and wet and dry weather conditions. Basin hydraulic retention times varied from 2.6 to 12.7 hours with an average of 8.9 hours. EBPR activity was successfully established in the modified basins with average phosphorus content of the return activated sludge 0.032 ± 0.002 compared to 0.016 ± 0.001 mg TP/mg TSS (95% confidence) in the control basins. Phosphorus removal was significantly decreased by prolonged wet weather conditions, particularly in year two of the study, however the modified basin maximum removal of 96% and average of 43.7 ± 5.3% remained significantly higher than the maximum of 46% and average 12.6 ± 2.4% removal in the control basins. DNA sequencing showed a significant increase in relative abundance of phyla Chloroflexi, Nitrospirae, and Verrucomicrobia in the modified basins, but no correlation to EBPR performance. qPCR indicated significant increase in relative quantity of Accumulibacter, but not for Actinetobacter-like phosphorus accumulating organisms (PAOs), which includes the PAO Tetrasphaera. Significant abundance of some Accumulibacter clades found within the modified basins was contrary to previous literature which focused on small-scale and batch studies. A higher than expected dominance of clade I and increased relative quantities of clades IIB and IIC during extended wet weather was observed which may have contributed to rapid recovery of phosphorus removal when dry weather resumed. The abundance of PAOs did not significantly correlate with changes in phosphorous removal performance, contrary to reports from previous small-scale and batch studies.

Ammonium-assimilating microbiome: A halophilic biosystem rationally optimized by carbon to nitrogen ratios with stable nitrogen conversion and microbial structure

The contradiction between theoretical metabolism of ammonium assimilation and experiential understanding of conventional biosystems makes the rational optimization of the ammonium-assimilating microbiome through carbon to nitrogen (C/N) ratios perplexing. The effect of different C/N ratios on ammonium-assimilating biosystems was investigated in saline wastewater treatment. C/N ratios significantly hindered the nutrient removal efficiency, but ammonium-assimilating biosystems maintained functional stability in nitrogen conversions and microbial communities. With sufficient biomass, higher than 86% ammonium and 73% phosphorus were removed when C/N ratios were higher than 25. Ammonium assimilation dominated the nitrogen metabolism in all biosystems even under relatively low C/N ratios, evidenced by the extremely low abundances of nitrification functional genes. Different C/N ratios did not significantly change the bacterial community structure of ammonium-assimilating biosystems. It is anticipated that the ammonium-assimilating biosystem with advantages of clear metabolic pathway and easy optimization can be applied to nutrient removal and recovery in saline environments.

Microeukaryotic gut parasites in wastewater treatment plants: diversity, activity, and removal

BACKGROUND

During wastewater treatment, the wastewater microbiome facilitates the degradation of organic matter, reduction of nutrients, and removal of gut parasites. While the latter function is essential to minimize public health risks, the range of parasites involved and how they are removed is still poorly understood.

RESULTS

Using shotgun metagenomic (DNA) and metatranscriptomic (RNA) sequencing data from ten wastewater treatment plants in Switzerland, we were able to assess the entire wastewater microbiome, including the often neglected microeukaryotes (protists). In the latter group, we found a surprising richness and relative abundance of active parasites, particularly in the inflow. Using network analysis, we tracked these taxa across the various treatment compartments and linked their removal to trophic interactions.

CONCLUSIONS

Our results indicate that the combination of DNA and RNA data is essential for assessing the full spectrum of taxa present in wastewater. In particular, we shed light on an important but poorly understood function of wastewater treatment - parasite removal. Video Abstract.

Towards better process management in wastewater treatment plants: Process analytics based on SHAP values for tree-based machine learning methods

Understanding the mechanisms of pollutant removal in Wastewater Treatment Plants (WWTPs) is crucial for controlling effluent quality efficiently. However, the numerous treatment units, operational factors, and the underlying interactions between these units and factors usually obfuscate the comprehensive and precise understanding of the processes. We have previously proposed a machine learning (ML) framework to uncover complex cause-and-effect relationships in WWTPs. However, only one interpretable ML model, Random forest (RF), was studied and the interpretation method was not granular enough to reveal very detailed relationships between operational factors and effluent parameters. Thus, in this paper, we present an upgraded framework involving three interpretable tree-based models (RF, XGboost and LightGBM), three metrics (R², Root mean squared error (RMSE), and Mean absolute error (MAE)) and a more advanced interpretation system SHapley Additive exPlanations (SHAP). Details of the framework are provided along with a demonstration of its practical applicability based on a case study of the Umeå WWTP in Sweden. Results show that, for both labels TSS_e (Total suspended solids in effluent) and PO4_e (Phosphate in effluent), the XGBoost models are optimal whereas the RF models are the least optimal, due to overfitting and polarized fitting. This study has yielded multiple new and significant findings with respect to the control of TSS_e and PO4_e in the Umeå WWTP and other similarly configured WWTPs. Additionally, this study has produced two important generic findings relating to ML applications for WWTPs (or even other process industries) in terms of cause-and-effect investigations. First, the model comparison should be carried out from multiple perspectives to ensure that underlying details are fully revealed and examined. Second, using a precise, robust, and granular (feature attribution available for individual instances) explanation method can bring extra insight into both model comparison and model interpretation. SHAP is recommended as we found it to be of great value in this study.

Application oriented bioaugmentation processes: Mechanism, performance improvement and scale-up

Bioaugmentation is an optimization method with great potential to improve the treatment effect by introducing specific strains into the biological treatment system. In this study, a comprehensive review of the mechanism of bioaugmentation from the aspect of microbial community structure, the optimization methods facilitating application as well as feasible approaches of scale-up application has been provided. The different contribution of indigenous and exogenous strains was critically analyzed, the relationship between microbial community variation and system performance was clarified. Operation regulation and immobilization technologies are effective methods to deal with the possible failure of bioaugmentation. The gradual expansion from lab-scale, pilot scale to full-scale, the transformation and upgrading of wastewater treatment plants through the combination of direct dosing and biofilm, and the application of side-stream reactors are feasible ways to realize the full-scale application. The future challenges and prospects in this field were also proposed.

Changes in BNR Microbial Community in Response to Different Selection Pressure

This study investigated structural changes in microbial community of biological nutrient removal (BNR) in response to changes in substrate composition (ammonium and phosphate), redox condition, and morphological characteristics (flocs to granules), with a focus on nitrification and phosphate removal. Analyzing treatment performance and 16S rRNA phylogenetic gene sequencing data suggested that heterotrophic nitrification (HN) and autotrophic nitrification (AN) potentially happened in aerobic organic-rich (HN_AS) and aerobic organic-deficient (AN_AS) activated sludge batch reactors, respectively. However, phosphate release and uptake were not observed under alternating anaerobic/aerobic regime. Phosphate release could not be induced even when anaerobic phase was extended, although Accumulibacter existed in the inoculum (5.1% of total bacteria). Some potential HN (e.g., Thauera, Acinetobacter, Flavobacterium), AN (e.g., Nitrosomonas (3.2%) and Nitrospira), and unconventional phosphate-accumulating organisms (PAOs) were identified. Putative HN bacteria (i.e., Thauera (29–36%) and Flavobacterium (18–25%)) were enriched in aerobic granular sludge (AGS) regardless of the granular reactor operation mode. Enrichment of HN organisms in the AGS was suspected to be mainly due to granulation, possibly due to the floc-forming ability of HN species. Thus, HN is likely to play a role in nitrogen removal in AGS reactors. This study is supposed to serve as a starting point for the investigation of the microbial communities of AS- and AGS-based BNR processes. It is recommended that the identified roles for the isolated bacteria are further investigated in future works.

RNA Viromics of Southern California Wastewater and Detection of SARS-CoV-2 Single-Nucleotide Variants

Municipal wastewater provides an integrated sample of a diversity of human-associated microbes across a sewershed, including viruses. Wastewater-based epidemiology (WBE) is a promising strategy to detect pathogens and may serve as an early warning system for disease outbreaks. Notably, WBE has garnered substantial interest during the coronavirus disease 2019 (COVID-19) pandemic to track disease burden through analyses of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. Throughout the COVID-19 outbreak, tracking SARS-CoV-2 in wastewater has been an important tool for understanding the spread of the virus. Unlike traditional sequencing of SARS-CoV-2 isolated from clinical samples, which adds testing burden to the health care system, in this study, metatranscriptomics was used to sequence virus directly from wastewater. Here, we present a study in which we explored RNA viral diversity through sequencing 94 wastewater influent samples across seven wastewater treatment plants (WTPs), collected from August 2020 to January 2021, representing approximately 16 million people in Southern California. Enriched viral libraries identified a wide diversity of RNA viruses that differed between WTPs and over time, with detected viruses including coronaviruses, influenza A, and noroviruses. Furthermore, single-nucleotide variants (SNVs) of SARS-CoV-2 were identified in wastewater, and we measured proportions of overall virus and SNVs across several months. We detected several SNVs that are markers for clinically important SARS-CoV-2 variants along with SNVs of unknown function, prevalence, or epidemiological consequence. Our study shows the potential of WBE to detect viruses in wastewater and to track the diversity and spread of viral variants in urban and suburban locations, which may aid public health efforts to monitor disease outbreaks. IMPORTANCE Wastewater-based epidemiology (WBE) can detect pathogens across sewersheds, which represents the collective waste of human populations. As there is a wide diversity of RNA viruses in wastewater, monitoring the presence of these viruses is useful for public health, industry, and ecological studies. Specific to public health, WBE has proven valuable during the coronavirus disease 2019 (COVID-19) pandemic to track the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) without adding burden to health care systems. In this study, we used metatranscriptomics and reverse transcription-droplet digital PCR (RT-ddPCR) to assay RNA viruses across Southern California wastewater from August 2020 to January 2021, representing approximately 16 million people from Los Angeles, Orange, and San Diego counties. We found that SARS-CoV-2 quantification in wastewater correlates well with county-wide COVID-19 case data, and that we can detect SARS-CoV-2 single-nucleotide variants through sequencing. Likewise, wastewater treatment plants (WTPs) harbored different viromes, and we detected other human pathogens, such as noroviruses and adenoviruses, furthering our understanding of wastewater viral ecology.

Biotechnological potential of microorganisms from textile effluent: isolation, enzymatic activity and dye discoloration

Environmental pollution may be considered one of the main problems affecting the world population. As the effluents from textile industries are the largest representatives of sources of pollution of water bodies due to the disposal of colored compounds in the environment. Microorganisms capable of thriving in textile wastewater may exhibit metabolic machinery to synthesize a wide variety of enzymes and/or secondary metabolites of industrial interest. The present work investigated the biotechnological potential of filamentous fungi from wastewater of a textile industry for the production of laccase, cellulase, amylase and lipase enzymes and their potential for discoloration capacity of Remazol Brilliant Blue R synthetic dye. The isolate Aspergillus sydowii (ITF 30) presented the best cellulase (46.74 U mL-1), amylase, lipase and laccase (0.0273 U L-1) production, as well as RBBR dye discoloration ability in solid medium, followed by isolate Aspergillus sydowii (ITF 27) able to synthesize cellulase, amylase and laccase and had the capacity to discolor 74.7% of RBBR in liquid medium. The results of the present work encourage future studies of characterization, optimization and purification of the enzymes encountered, aiming to be used in bioremediation processes of textile industrial effluents.

The wastewater protist Rhogostoma minus (Thecofilosea, Rhizaria) is abundant, widespread, and hosts Legionellales

Wastewater is treated by concerted actions of the microbial communities within bioreactors. Although protists (unicellular eukaryotes) are good bioindicators and important players influencing denitrification, nitrification, and flocculation, they are the least known organisms in WWTPs. The few recent environmental surveys of the protistan diversity in WWTPs show that the most abundant protistan sequences in WWTPs belong to Thecofilosea (Rhizaria). We re-investigated previously published environmental sequencing data and gathered strains from seven WWTPs to determine which species dominate WWTPs worldwide. We found that all highly abundant thecofilosean sequences represent a single species - Rhogostoma minus. Considering that Thecofilosea are frequent hosts for Legionellales, i.e. bacteria linked to waterborne diseases, we confirm that Rhogostoma minus functions as a host for Legionellales in WWTPs. Whether the highly abundant Rhogostoma minus also serves as a host for known human pathogenic Legionellales requires further attention.

Insights into the microbial diversity and structure in a full-scale municipal wastewater treatment plant with particular regard to Archaea

Due to limited description of the role and diversity of archaea in WWTPs, the aim of the study was to analyze microbial community structures and diversities with particular regard to Archaea in the samples taken from different stages of the full-scale municipal wastewater treatment plant and effluent receiving water (upstream and downstream discharge point). Our study was focused on showing how the treatment processes influenced the Eubacteria and Archaea composition. Alpha and Beta diversity were used to evaluate the microbial diversity changes in the collected samples. Proteobacteria was the largest fraction ranging from 28% to 67% with 56% relative abundance across all samples. Archaea were present in all stages of WWTP ranged from 1 to 8%. Among the Archaea, two groups of methanogens, acetoclastic (Methanosarcina, Methanosaeta) and hydrogenotrophic methanogens (Methanospirillium, Methanoculleus, Methanobrevibacter) were dominant in the technological stages. The obtained results indicate that the treated wastewater did not significantly affect eubacterial and archaeal composition in receiving water. However, differences in richness, diversity and microbial composition of Eubacteria and Archaea between the wastewater samples taken from the primary and secondary treatment were observed.

The biotransformation of arsenic by spent mushroom compost - An effective bioremediation agent

Spent mushroom compost (SMC) is a lignocellulose-rich waste material commonly used in the passive treatment of heavy metal-contaminated environments. In this study, we investigated the bioremediation potential of SMC against an inorganic form of arsenic, examining the individual abiotic and biotic transformations carried out by SMC. We demonstrated, that key SMC physiological groups of bacteria (denitrifying, cellulolytic, sulfate-reducing, and heterotrophic) are resistant to arsenites and arsenates, while the microbial community in SMC is also able to oxidize As(III) and reduce As(V) in respiratory metabolisms, although the SMC did not contain any As. We showed, that cooperation between arsenate and sulfate-reducing bacteria led to the precipitation of As_xS_y. We also found evidence of the significant role organic acids may play in arsenic complexation, and we demonstrated the occurrence of As-binding proteins in the SMC. Furthermore, we confirmed, that biofilm produced by the microbial community in SMC was able to trap As(V) ions. We postulated, that the above-mentioned transformations are responsible for the sorption efficiency of As(V) (up to 25%) and As(III) (up to 16%), as well as the excellent buffering properties of SMC observed in the sorption experiments.

Microbial Interactions as Drivers of a Nitrification Process in a Chemostat

This article deals with the inclusion of microbial ecology measurements such as abundances of operational taxonomic units in bioprocess modelling. The first part presents the mathematical analysis of a model that may be framed within the class of Lotka–Volterra models fitted to experimental data in a chemostat setting where a nitrification process was operated for over 500 days. The limitations and the insights of such an approach are discussed. In the second part, the use of an optimal tracking technique (developed within the framework of control theory) for the integration of data from genetic sequencing in chemostat models is presented. The optimal tracking revisits the data used in the aforementioned chemostat setting. The resulting model is an explanatory model, not a predictive one, it is able to reconstruct the different forms of nitrogen in the reactor by using the abundances of the operational taxonomic units, providing some insights into the growth rate of microbes in a complex community.

Metagenomic Sequencing and Quantitative Real-Time PCR for Fecal Pollution Assessment in an Urban Watershed

Microbial contamination of recreation waters is a major concern globally, with pollutants originating from many sources, including human and other animal wastes often introduced during storm events. Fecal contamination is traditionally monitored by employing culture methods targeting fecal indicator bacteria (FIB), namely E. coli and enterococci, which provides only limited information of a few microbial taxa and no information on their sources. Host-associated qPCR and metagenomic DNA sequencing are complementary methods for FIB monitoring that can provide enhanced understanding of microbial communities and sources of fecal pollution. Whole metagenome sequencing (WMS), quantitative real-time PCR (qPCR), and culture-based FIB tests were performed in an urban watershed before and after a rainfall event to determine the feasibility and application of employing a multi-assay approach for examining microbial content of ambient source waters. Cultivated E. coli and enterococci enumeration confirmed presence of fecal contamination in all samples exceeding local single sample recreational water quality thresholds (E. coli, 410 MPN/100 mL; enterococci, 107 MPN/100 mL) following a rainfall. Test results obtained with qPCR showed concentrations of E. coli, enterococci, and human-associated genetic markers increased after rainfall by 1.52-, 1.26-, and 1.11-fold log₁₀ copies per 100 mL, respectively. Taxonomic analysis of the surface water microbiome and detection of antibiotic resistance genes, general FIB, and human-associated microorganisms were also employed. Results showed that fecal contamination from multiple sources (human, avian, dog, and ruminant), as well as FIB, enteric microorganisms, and antibiotic resistance genes increased demonstrably after a storm event. In summary, the addition of qPCR and WMS to traditional surrogate techniques may provide enhanced characterization and improved understanding of microbial pollution sources in ambient waters.

Unravelling metabolism and microbial community of a phytobed co-planted with Typha angustifolia and Ipomoea aquatica for biodegradation of doxylamine from wastewater

Pharmaceutical contaminants in environment induce unexpected effects on ecological systems and human; thus, development of efficient technologies for their removal is immensely necessary. In this study, biodegradation and metabolic fate of a frequently found pharmaceutical contaminant, doxylamine by Typha angustifolia and Ipomoea aquatica was investigated. Microbial community of the plant rhizosphere has been identified to understand the important roles of the functional microbes. The plants reduced 48-80.5 % of doxylamine through hydrolysis/dehydroxylation and carbonylation/decarbonylation. A constructed phytobed co-planted with T. angustifolia and I. aquatica removed 77.3 %, 100 %, 83.67 %, and 61.13 % of chemical oxygen demand, total nitrogen, total phosphorus, and doxylamine respectively from real wastewater. High-throughput sequencing of soil and rhizosphere indicated that the phyla Proteobacteria, Bacteroidetes, Firmicutes, Planctomycetes, Actinobacteria, and Cyanobacteria dominated the microbial communities of the phytobed. Current study has demonstrated the applicability of the developed phytobeds for the treatment of doxylamine from municipal wastewater and provide a comprehensive understanding of its metabolism through plant and its rhizospheric microbial communities.

Performance and microbial community dynamics in anaerobic continuously stirred tank reactor and sequencing batch reactor (CSTR-SBR) coupled with magnesium-ammonium-phosphate (MAP)-precipitation for treating swine wastewater

The impacts of magnesium-ammonium-phosphate (MAP) precipitation on the performance and microbial dynamics in an anaerobic continuously stirred tank reactor (CSTR) coupled with sequencing batch reactor (SBR) for swine wastewater treatment were investigated. In CSTR-SBR systems, an overall higher removal efficiency for COD, NH₄⁺ and PO₄^3-as 98.6%, 98.7% and 97.9% was achieved with MAP precipitation, compared to CSTR-SBR without MAP pretreatment (i.e., 97.5, 74.3% and 19.9% for COD, NH₄⁺ and PO₄^3-, respectively). With MAP precipitation, the high C/N ratio of 6.6 after anaerobic CSTR was observed. The increase in the richness and diversity of microbial communities in CSTR with MAP was conducive to nitrogen and phosphorus removal, as well as biogas production. The core community was affiliated with bacterial phyla Firmicutes, Bacteroidetes, Proteobacteria, Cloacimonetes, and Spirochaetae. The study provide a new insight into the potential application of MAP precipitation as pretreatment for dealing with nutrient recovery from high-strength swine wastewater.

Recent developments and key barriers to microbial CO2 electrobiorefinery

The electrochemical conversion of CO₂ can include renewable surplus electricity storage and CO₂ utilisation. This review focuses on the microbial CO₂ electrobiorefinery based on microbial electrosynthesis (MES) which merges electrochemical and microbial conversion to produce biofuels and higher-value chemicals. In this review, recent developments are discussed about bioelectrochemical conversion of CO₂ into biofuels and chemicals in MES via microbial CO₂-fixation and electricity utilisation reactions. In addition, this review examines technical approaches to overcome the current limitations of MES including the following: engineering of the biocathode, application of electron mediators, and reactor optimisation, among others. An in-depth discussion of strategies for the CO₂ electrobiorefinery is presented, including the integration of the biocathode with inorganic catalysts, screening of novel electroactive microorganisms, and metabolic engineering to improve target productivity from CO₂.

Sulfate dependent ammonium oxidation: A microbial process linked nitrogen with sulfur cycle and potential application

Sulfate dependent ammonium oxidation (Sulfammox) is a potential microbial process coupling ammonium oxidation with sulfate reduction under anaerobic conditions, which provides a novel link between nitrogen and sulfur cycle. Recently, Sulfammox was detected in wastewater treatments and was confirmed to occur in natural environments, especially in marine sediments. However, knowledge gaps in the mechanism of Sulfammox, functional bacteria, and their metabolic pathway, make it challenging to estimate its environmental significance and potential applications. This review provides an overview of recent advances in Sulfammox, including possible mechanisms, functional bacteria, and main influential factors, and discusses future challenges and opportunities. Future perspectives are outlined and discussed, such as exploration of microbial community structure and metabolic pathways, possible interactions with other microbes, environmental significance, and potential applications for nitrogen and sulfate removal, to inspire more researches on the Sulfammox process.

Evaluation of the Abundance of Fungi in Wastewater Treatment Plants Using Quantitative PCR (qPCR)

Assessment of the abundance of fungi in environmental samples by quantitative PCR (qPCR) of community DNA is often a difficult task due to biases introduced during PCR amplification, resulting from the differences associated with length polymorphism and the varying number of copies of the rRNA operon among fungal species, the lack of specificity of the primers targeting the different regions of the rRNA operon, or their insufficient coverage of the fungal lineages. To overcome those limitations, it is crucial to test and select the specific primers sets which provide the more accurate approximation to the quantification of the targeted fungal populations in a given set of samples. Fungi are a significant fraction of the microbiota in wastewater treatment plants (WWTPs), but the activated sludge microbial communities comprise many other eukaryotic microorganisms whose molecular markers are often coamplified by primers initially designed as fungal-specific. Here, the use of the FungiQuant primer set is recommended for the quantification of fungal molecular markers (18S rRNA genes) by qPCR in activated sludge samples and the full protocol is described.

Microbiome taxonomic and functional profiles of two domestic sewage treatment systems

Anaerobic systems for domestic sewage treatment, like septic tanks and anaerobic filters, are used in developing countries due to favorable economic and functional features. The anaerobic filter is used for the treatment of the septic tank effluent, to improve the COD removal efficiency of the system. The microbial composition and diversity of the microbiome from two wastewater treatment systems (factory and rural school) were compared through 16S rRNA gene sequencing using MiSeq 2 × 250 bp Illumina sequencing platform. Additionally, 16S rRNA data were used to predict the functional profile of the microbial communities using PICRUSt2. Results indicated that hydrogenotrophic methanogens, like Methanobacterium, were found in higher abundance in both systems compared to acetotrophic methanogens belonging to Methanosaeta genus. Also, important syntrophic microorganisms (Smithella, Syntrophus, Syntrophobacter) were found in the factory and rural school wastewater treatment systems. Microbial communities were also compared between stages (septic tank and anaerobic filter) of each wastewater treatment stage, revealing that, in the case of the rural school, both microbial communities were quite similar most likely due to hydraulic short-circuit issues. Meanwhile, in the factory, microbial communities from the septic tank and anaerobic filter were different. The school system showed lower COD removal rates (2-30%), which were probably related to a higher abundance of Firmicutes members in addition to the hydraulic short-circuit and low abundance of Chloroflexi members. On the other hand, the fiberglass factory presented higher COD removal rates (60-83%), harboring phyla reported as the core microbiome of anaerobic digesters (Bacteroidetes, Chloroflexi, and Proteobacteria phyla). The knowledge of the structure and composition of wastewater treatment systems may provide support for the improvement of the pollutant removal in anaerobic process.

Bioeconomy moving forward step by step - A global journey

Continuous, inspiring and interconnected step-by-step changes in thought and understanding, knowhow, actions and behaviour have often been instrumental in transitions from one particular age to the next in human history. This also applies to the present century and its sustainability challenges at the planetary, regional and local levels. Therefore, it is of great importance and relevance to move forward on the journey which has been started globally to address the not insignificant number of challenges. It is however essential to go beyond descriptive work by continuing with novel, inspiring and interconnected steps to find solutions to overcome these challenges. As this huge task also requires multidimensional communication, understanding and actions across different regions, cultures, disciplines and knowledge areas, the development of a common conceptual framework such as the concept of bioeconomy has been accepted globally as very valuable. The momentum which has been created in more than 50 countries around the world by the growing number of activities, initiatives and strategies in bioeconomy is very encouraging. This offers great opportunities to mobilize even more stakeholders in science and industry, as well as society, to join the bioeconomy journey. Strategic high-level concepts such as preserving the value of the natural capital of planet earth, connecting economy and ecology, sustaining the boundary conditions and habitability of our biosphere are highly important. It is also essential on the bioeconomy journey to connect with highly specific and actionable missions, programs and plans towards sustainable economic growth under the boundary conditions of our planet.

Seasonality and Community Separation of Fungi in a Municipal Wastewater Treatment Plant

Fungi are known to play important roles in pollutant transformation in activated sludge-based wastewater treatment plants (WWTPs). However, the seasonality and distributions of fungal populations in different-sized flocs have still remained largely unknown. In this study, seasonal population dynamics and community separation of fungi in a municipal WWTP across a 1-year period were investigated. We classified all taxa into six categories based on abundances to assess their roles and contributions to the whole community. The results showed that the rare taxa (<0.01%) contributed greatly to species richness (95.27%). Conversely, although low in species diversity, abundant taxa (≥1%) accounted for the majority (89.45%) of the total relative abundance, which suggested that a few core abundant fungi existed in the activated sludge ecosystem. The abundant, conditionally rare, and rare taxa contributed 30.14%, 31.11%, and 38.75%, respectively, to temporal shifts in community structure, and their abundances responded differently to environmental variables, suggesting that these three subcommunities exhibited a large difference in environmental sensitivity. Importantly, the results revealed seasonal dynamics of the whole fungal community and the subcommunities of all the microbial taxon categories, resulting in significant differences in community structures between warm and cold seasons. Furthermore, fungal diversity and the compositions of the whole community and subcommunities differed significantly among flocs of different sizes, which underlined the size-based fungal community separation in activated sludge of WWTPs. The findings of this work improved our understanding of fungal population dynamics and community separation in WWTPs.IMPORTANCE Fungi are important contributors to the various functions of activated sludge in wastewater treatment plants (WWTPs). Unlike previous studies, this work demonstrated the seasonality of the fungal community over a longer time span while it also systematically assessed the contributions of abundant, conditionally rare, and rare taxa to the whole community. Importantly, in the present study, we considered sludge flocs of a certain size range rather than the whole sludge flocs as a community. Our results revealed significant differences in fungal community structure among different-sized flocs, which supported the idea that size-based fungal community segregation is occurring in activated sludge ecosystems. The findings provide new insights into the dynamic changes or distribution of fungi in the bioaggregates of sludge flocs in WWTPs.

Environmental fate of Bacteroidetes, with particular emphasis on Bacteroides fragilis group bacteria and their specific antibiotic resistance genes, in activated sludge wastewater treatment plants

The aim of this study was to determine the effect of the activated sludge process on the abundance of anaerobic bacteria of the phylum Bacteroidetes, with special emphasis on Bacteroides fragilis group (BFG) bacteria, in twelve full-scale wastewater treatment plants. The composition of bacterial phyla and classes in wastewater samples were analyzed by next-generation sequencing. The presence of specific to BFG bacteria genes and the abundance of ARGs and genes encoding class 1 integrase in wastewater samples were determined by qPCR. Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes were dominant bacterial phyla in wastewater samples. Next-generation sequencing revealed similar proportions of Bacteroidia (<1.0-8.2 % of all bacteria) in wastewater influents and effluents, which suggest that these microorganisms are not completely eliminated in the activated sludge process. The average copy numbers of specific to BFG bacteria gene, were 10⁶, and 10⁴ copies in 1 mL of wastewater influents and effluents, respectively. The results revealed a correlation between the abundance of BFG bacteria and BFG-specific genes encoding resistance to antibiotics. The observed changes in the prevalence of BFG-specific genes and ARGs in untreated and treated wastewater indicate that the activated sludge process decreases the number of gene copies in the effluent evacuated to the environment.

A widely distributed hydrogenase oxidises atmospheric H2 during bacterial growth

Diverse aerobic bacteria persist by consuming atmospheric hydrogen (H₂) using group 1h [NiFe]-hydrogenases. However, other hydrogenase classes are also distributed in aerobes, including the group 2a [NiFe]-hydrogenase. Based on studies focused on Cyanobacteria, the reported physiological role of the group 2a [NiFe]-hydrogenase is to recycle H₂ produced by nitrogenase. However, given this hydrogenase is also present in various heterotrophs and lithoautotrophs lacking nitrogenases, it may play a wider role in bacterial metabolism. Here we investigated the role of this enzyme in three species from different phylogenetic lineages and ecological niches: Acidithiobacillus ferrooxidans (phylum Proteobacteria), Chloroflexus aggregans (phylum Chloroflexota), and Gemmatimonas aurantiaca (phylum Gemmatimonadota). qRT-PCR analysis revealed that the group 2a [NiFe]-hydrogenase of all three species is significantly upregulated during exponential growth compared to stationary phase, in contrast to the profile of the persistence-linked group 1h [NiFe]-hydrogenase. Whole-cell biochemical assays confirmed that all three strains aerobically respire H₂ to sub-atmospheric levels, and oxidation rates were much higher during growth. Moreover, the oxidation of H₂ supported mixotrophic growth of the carbon-fixing strains C. aggregans and A. ferrooxidans. Finally, we used phylogenomic analyses to show that this hydrogenase is widely distributed and is encoded by 13 bacterial phyla. These findings challenge the current persistence-centric model of the physiological role of atmospheric H₂ oxidation and extend this process to two more phyla, Proteobacteria and Gemmatimonadota. In turn, these findings have broader relevance for understanding how bacteria conserve energy in different environments and control the biogeochemical cycling of atmospheric trace gases.

A novel membrane-aerated biofilter for the enhanced treatment of nitroaniline wastewater: Nitroaniline biodegradation performance and its influencing factors

Nitroaniline (NA) wastewater is known to be highly toxic and biodegradation-resistant. Based on the principles of molecular oxygen supply and biofilm formation, a novel membrane-aerated biofilter (MABF) combining membrane aeration with a biofilter was established for the first time to treat NA wastewater containing the same concentrations of p-nitroaniline (PNA) and o-nitroaniline (ONA). The NA wastewater treatment performance of the MABF was investigated, and the NA biodegradation characteristics were evaluated. When the influent NA concentration was 120 mg/L, the PNA and ONA removal rates reached 100% and 86.56%, respectively. The NA removal loading reached 111.62 g/m³·d, and the total nitrogen (TN) removal rate reached 82.97%. The synergistic effects of the diverse microorganisms in the membrane-aerated and nonaerated zones of the MABF enhanced the removal of NA and nitrogen. This MABF is an economically efficient and environmentally friendly technology for treating wastewater containing toxic and hazardous organic compounds.

Technologies for biological removal and recovery of nitrogen from wastewater

Water contamination is a growing environmental issue. Several harmful effects on human health and the environment are attributed to nitrogen contamination of water sources. Consequently, many countries have strict regulations on nitrogen compound concentrations in wastewater effluents. Wastewater treatment is carried out using energy- and cost-intensive biological processes, which convert nitrogen compounds into innocuous dinitrogen gas. On the other hand, nitrogen is also an essential nutrient. Artificial fertilizers are produced by fixing dinitrogen gas from the atmosphere, in an energy-intensive chemical process. Ideally, we should be able to spend less energy and chemicals to remove nitrogen from wastewater and instead recover a fraction of it for use in fertilizers and similar applications. In this review, we present an overview of various technologies of biological nitrogen removal including nitrification, denitrification, anaerobic ammonium oxidation (anammox), as well as bioelectrochemical systems and microalgal growth for nitrogen recovery. We highlighted the nitrogen removal efficiency of these systems at different temperatures and operating conditions. The advantages, practical challenges, and potential for nitrogen recovery of different treatment methods are discussed.

Casimicrobium huifangae gen. nov., sp. nov., a Ubiquitous "Most-Wanted" Core Bacterial Taxon from Municipal Wastewater Treatment Plants

Microorganisms in wastewater treatment plants (WWTPs) play a key role in the removal of pollutants from municipal and industrial wastewaters. A recent study estimated that activated sludge from global municipal WWTPs harbors 1 × 10⁹ to 2 × 10⁹ microbial species, the majority of which have not yet been cultivated, and 28 core taxa were identified as "most-wanted" ones (L. Wu, D. Ning, B. Zhang, Y. Li, et al., Nat Microbiol 4:1183-1195, 2019, https://doi.org/10.1038/s41564-019-0426-5). Cultivation and characterization of the "most-wanted" core bacteria are critical to understand their genetic, physiological, phylogenetic, and ecological traits, as well as to improve the performance of WWTPs. In this study, we isolated a bacterial strain, designated SJ-1, that represents a novel cluster within Betaproteobacteria and corresponds to OTU_16 within the 28 core taxa in the "most-wanted" list. Strain SJ-1 was identified and nominated as Casimicrobium huifangae gen. nov., sp. nov., of a novel family, Casimicrobiaceae. C. huifangae is ubiquitously distributed and is metabolically versatile. In addition to mineralizing various carbon sources (including carbohydrates, aromatic compounds, and short-chain fatty acids), C. huifangae is capable of nitrate reduction and phosphorus accumulation. The population of C. huifangae accounted for more than 1% of the bacterial population of the activated sludge microbiome from the Qinghe WWTP, which showed seasonal dynamic changes. Cooccurrence analysis suggested that C. huifangae was an important module hub in the bacterial network of Qinghe WWTP.IMPORTANCE The activated sludge process is the most widely applied biotechnology and is one of the best ecosystems to address microbial ecological principles. Yet, the cultivation of core bacteria and the exploration of their physiology and ecology are limited. In this study, the core and novel bacterial taxon C. huifangae was cultivated and characterized. This study revealed that C. huifangae functioned as an important module hub in the activated sludge microbiome, and it potentially plays an important role in municipal wastewater treatment plants.

Microbial community at transcription level in the synergy of GAOs and Candidatus Accumulibacter for saving carbon source in wastewater treatment

The microbial community in endogenous denitrification and denitrifying phosphorus removal treatment at transcription level was unknown. This study first confirmed the expression of actually active bacteria in endogenous denitrification and denitrifying phosphorus removal system to treat low C/N municipal wastewater. No external carbon source was added to influent wastewater. The cDNA high throughput sequencing showed that Candidatus Accumulibacter was the most effective polyphosphate accumulating organisms (PAOs) that actually worked rather than Dechloromonas, which was different from the result at gene level. Reverse transcriptional PCR (RT-PCR) and analysis of Variance (ANOVA) suggested that the ratios of dead or dormant bacteria could monitor wastewater treatment process. Identification of active microbial community at transcription level demonstrated that the synergy of endogenous denitrification by glycogen accumulating organisms (GAOs) and denitrifying phosphorus removal by Candidatus Accumulibacter fully utilized the internal carbon source, and effectively solved the problem of carbon source deficiency in municipal wastewater treatment.