Population dynamics of filamentous bacteria in Danish wastewater treatment plants with nutrient removal

Integrating enhanced biological phosphorus removal in adsorption-stage to treat real domestic sewage

Wastewater treatment innovation toward resource recovery facilities raises concerns about the adsorption and bio-degradation (A-B) process. This study integrated enhanced biological phosphorus removal (EBPR) into the A-stage for real domestic sewage treatment using the short sludge retention time (S-SRT) approach. The S-SRT approach resulted in outstanding phosphorus (over 90 %) and COD removal (approximately 88 %), increased sludge yield and organic matter content, and a 1.68-fold increase in energy recovery efficiency by sludge anaerobic digestion. The inhibition of nitrification relieved competition for carbon sources between denitrification and phosphorus removal, allowing for the enrichment of phosphorus-accumulating organisms (PAOs) such as Tetrasphaera and Halomonas, leading to enhanced phosphorus removal activities. Biological adsorption also plays a significant role in achieving steady phosphorus removal performance. This study demonstrates the potential of the S-SRT approach as an effective strategy for simultaneous carbon and phosphorus capture in the A-stage, contributing to energy and nutrient recovery from sewage.

Meta-omic profiling reveals ubiquity of genes encoding for the nitrogen-rich biopolymer cyanophycin in activated sludge microbiomes

Recovering nitrogen (N) from municipal wastewater is a promising approach to prevent nutrient pollution, reduce energy use, and transition toward a circular N bioeconomy, but remains a technologically challenging endeavor. Existing N recovery techniques are optimized for high-strength, low-volume wastewater. Therefore, developing methods to concentrate dilute N from mainstream wastewater will bridge the gap between existing technologies and practical implementation. The N-rich biopolymer cyanophycin is a promising candidate for N bioconcentration due to its pH-tunable solubility characteristics and potential for high levels of accumulation. However, the cyanophycin synthesis pathway is poorly explored in engineered microbiomes. In this study, we analyzed over 3,700 publicly available metagenome assembled genomes (MAGs) and found that the cyanophycin synthesis gene cphA was ubiquitous across common activated sludge bacteria. We found that cphA was present in common phosphorus accumulating organisms (PAO) Ca. 'Accumulibacter' and Tetrasphaera, suggesting potential for simultaneous N and P bioconcentration in the same organisms. Using metatranscriptomic data, we confirmed the expression of cphA in lab-scale bioreactors enriched with PAO. Our findings suggest that cyanophycin synthesis is a ubiquitous metabolic activity in activated sludge microbiomes. The possibility of combined N and P bioconcentration could lower barriers to entry for N recovery, since P concentration by PAO is already a widespread biotechnology in municipal wastewater treatment. We anticipate this work to be a starting point for future evaluations of combined N and P bioaccumulation, with the ultimate goal of advancing widespread adoption of N recovery from municipal wastewater.

Dynamic calibration of a new secondary settler model using Cand. Microthrix as a predictor of settling velocity

Climate change is projected to increase the frequency of hydraulic shocks on urban water systems, affecting water resource recovery facilities (WRRFs). In these facilities, the settleability of activated sludge is a critical hydraulic bottleneck. However, to date, the dynamic prediction of hindered settling velocity (v0/rH) has remained unresolved. To address this significant knowledge gap, this study presents an assessment of microbial community predictors of hindered settling velocity. Through a regression analysis of independent laboratory and full-scale experimental data, we identified a close association between the relative abundance of Candidatus Microthrix filamentous bacteria and hindered settling velocity parameter values. While no direct association was observed between filamentous abundance and compression settling parameters, we propose linking the dynamic calibration of the compressive solid stress function to v0/rH. Notably, our results demonstrate, for the first time, the efficacy of dynamic calibration of SST models using the relative abundance of filamentous microbial predictors in a simulation model of the Kloten-Opfikon full-scale WRRF. Furthermore, besides Cand. Microthrix, Thiothrix is found to be a putative predictor for biomolecular SST calibration. These findings shed light on the potential of microbial communities to predict hindered settling velocity in WRRFs and offer valuable insights for improving wastewater treatment processes in the face of climate change challenges.

A review of filamentous sludge bulking controls from conventional methods to emerging quorum quenching strategies

Filamentous bulking, which results from the overgrowth of filamentous microorganisms, is a common issue that frequently disrupts the stable operation of activated sludge processes. Recent literature has paid attention to the relationship between quorum sensing (QS) and filamentous bulking highlighting that the morphological transformations of filamentous microbes are regulated by functional signal molecules in the bulking sludge system. In response to this, a novel quorum quenching (QQ) technology has been developed to control sludge bulking effectively and precisely by disturbing QS-mediated filamentation behaviors. This paper presents a critical review on the limitations of classical bulking hypotheses and traditional control methods, and provides an overview of recent QS/QQ studies that aim to elucidate and control filamentous bulking, including the characterization of molecule structures, the elaboration of QS pathways, and the precise design of QQ molecules to mitigate filamentous bulking. Finally, suggestions for further research and development of QQ strategies for precise bulking control are put forward.

Genome-centric metagenomic insights into the role of Chloroflexi in anammox, activated sludge and methanogenic reactors

BACKGROUND

The phylum Chloroflexi is highly abundant in a wide variety of wastewater treatment bioreactors. It has been suggested that they play relevant roles in these ecosystems, particularly in degrading carbon compounds and on structuring flocs or granules. Nevertheless, their function is not yet well understood as most species have not been isolated in axenic cultures. Here we used a metagenomic approach to investigate Chloroflexi diversity and their metabolic potential in three environmentally different bioreactors: a methanogenic full-scale reactor, a full-scale activated sludge reactor and a lab scale anammox reactor.

RESULTS

Differential coverage binning approach was used to assemble the genomes of 17 new Chloroflexi species, two of which are proposed as new Candidatus genus. In addition, we recovered the first representative genome belonging to the genus 'Ca. Villigracilis'. Even though samples analyzed were collected from bioreactors operating under different environmental conditions, the assembled genomes share several metabolic features: anaerobic metabolism, fermentative pathways and several genes coding for hydrolytic enzymes. Interestingly, genome analysis from the anammox reactor indicated a putative role of Chloroflexi in nitrogen conversion. Genes related to adhesiveness and exopolysaccharides production were also detected. Complementing sequencing analysis, filamentous morphology was detected by Fluorescent in situ hybridization.

CONCLUSION

Our results suggest that Chloroflexi participate in organic matter degradation, nitrogen removal and biofilm aggregation, playing different roles according to the environmental conditions.

Insights into rapidly recovering the autotrophic nitrogen removal performance of single-stage partial nitritation-anammox systems: Reconstructing granular sludge and its functional microbes synergy

Partial nitritation-anammox (PNA) deteriorates easily and is difficult to recover. After an airlift inner-circulation partition bioreactor was impacted by low NH₄⁺-N wastewater containing organic matter, Nitrospira and Denitratisoma propagated rapidly, granular sludge disintegrated, and the total nitrogen removal efficiency (TNRE) decreased from 68.27 % to 5.97 %. This study used a unique strategy to recover deteriorated single-stage PNA systems and explored the mechanism of rapid performance recovery. The TNRE of the system recovered up to 61.77 % in 43 days. The high nitrogen loading rate and hydraulic shear force from the airlift caused the sludge in the reactor to granulate again. The microbial community structure recovered, with a decrease in the abundance of Nitrospira (0.05 %) and enrichment of Candidatus Brocadia (8.82 %). A favorable synergy among functional microbes in the reactor was thus re-established, promoting the rapid recovery of the nitrogen removal performance. This study provides a feasible recovery strategy for PNA processes.

Negative impacts of cleaning agent DEPTAL MCL® on activated sludge wastewater treatment system

DEPTAL MCL® is a professional cleaning agent approved by the Portuguese Food Regulatory Authority and is used in agro-food industries, namely in fish canning industries in the north of Portugal. Its extensive use during cleaning procedures results in potential significant negative impacts on the performance of the downstream municipal wastewater treatment plant (WWTP). A lab-scale extended areation activated sludge wastewater treatment system, continuously fed by influent collected at a municipal WWTP, was used to assess the impact of a range of DEPTAL MCL® concentrations during 72 h. Despite distinct activated sludge community composition (due to its dynamic nature) and variations in real influent characteristics, a relevant impact was observed. DEPTAL MCL® effect was underscored through the use of a multivariate analysis using seventeen physicochemical operational factors and nineteen quantitative image analysis (QIA) parameters. DEPTAL MCL® exerted a severe negative impact on phosphorous (P-PO₄) removal, total nitrogen (TN) removal and sludge volume index (SVI). With increasing DEPTAL MCL® concentrations, both P-PO₄ and TN removal were affected and diminished proportionally. Moreover, several QIA parameters indicate defloculation when DEPTAL MCL® was present, in particular for intermediate size aggregates with significant impacts. Optical density of the effluent (Od_e), displayed an increase of effluent turbidity. Percentage of area covered by small aggregates (%Area_sml) was also significantly higher for the intermediate and higher DEPTAL MCL® concentrations tested. Principal component analysis exhibited 3 distinct ordenations: (i) control without addition of DEPTAL MCL®; (ii) addition of 0.03% and 0.06% and of (iii) 0.13 and 0.26% (v DEPTAL MCL®/v aeration tank). Canonical correspondence analysis (CCA) was used to correlate the physicochemical data, QIA and the filamentous bacteria species prevalence to DEPTAL MCL® concentration and incubation time. A time persistent DEPTAL MCL® effect was observed, underscoring the need of a pretreatment of wastewater containing this cleaning agent.

Metabolic Potential of the Superphylum Patescibacteria Reconstructed from Activated Sludge Samples from a Municipal Wastewater Treatment Plant

Patescibacteria are widely distributed in various environments and often detected in activated sludge. However, limited information is currently available on their phylogeny, morphology, and ecophysiological role in activated sludge or interactions with other microorganisms. In the present study, we identified microorganisms that interacted with Patescibacteria in activated sludge via a correlation ana-lysis using the 16S rRNA gene, and predicted the metabolic potential of Patescibacteria using a metagenomic ana-lysis. The metagenome-assembled genomes of Patescibacteria consisted of three Saccharimonadia, three Parcubacteria, and one Gracilibacteria, and showed a strong positive correlation of relative abundance with Chitinophagales. Metabolic predictions from ten recovered patescibacterial and five Chitinophagales metagenome-assembled genomes supported mutualistic interactions between a member of Saccharimonadia and Chitinophagales via N-acetylglucosamine, between a member of Parcubacteria and Chitinophagales via nitrogen compounds related to denitrification, and between Gracilibacteria and Chitinophagales via phospholipids in activated sludge. The present results indicate that various interactions between Patescibacteria and Chitinophagales are important for the survival of Patescibacteria in activated sludge ecosystems.

Seasonal microbial community dynamics complicates the evaluation of filamentous bulking mitigation strategies in full-scale WRRFs

The activated sludge wastewater treatment process has been thoroughly researched in more than 100 years, yet there are still operational challenges that have not been fully resolved. Such a challenge is the control of filamentous bulking caused by the overgrowth of certain filamentous bacteria. In this study, we tested different mitigation strategies to reduce filamentous bulking, caused by two common filamentous genera found in full-scale water resource recovery facilities (WRRF), Candidatus Microthrix and Candidatus Amarolinea. PAX dosing, ozone addition, hydrocyclone implementation, and the addition of nano-coagulants were tested as mitigation strategies in four parallel treatment lines in a full-scale WRRF over three consecutive years. Unexpectedly, the activated sludge settleability was not affected by any of the mitigation strategies. Some of the strategies appeared to have a strong mitigating effect on the two filamentous species. However, detailed analyses of the microbial communities revealed strong recurrent seasonal variations in all four lines, including the control line which masked the real effect. After removing the effect of the seasonal variation by using a time-series decomposition approach, it was clear that the filamentous bacteria were mostly unaffected by the mitigation strategies. Only PAX dosing had some effect on Ca. Microthrix, but only on one species, Ca. Microthrix subdominans, and not on the most common Ca. Microthrix parvicella. Overall, our study shows the importance of long-term monitoring of microbial communities at species level to understand the normal seasonal pattern to effectively plan and execute full-scale experiments. Moreover, the results highlight the importance of using parallel reference treatment lines when evaluating the effect of mitigation strategies in full-scale treatment plants.

Insights into the synergy between functional microbes and dissolved oxygen partition in the single-stage partial nitritation-anammox granules system

The rapid start-up and stable operation of the single-stage partial nitritation-anammox (PNA) process remains a challenge in practical applications. An integrated investigation of nitrogen removal performance, sludge characteristics, activity and abundance, and microbial dynamics was implemented for 360 days via an airlift internal circulation reactor. During long-term operation, the reactor realized a stable dissolved oxygen (DO) partition and cultivated granular sludge. The nitrogen removal rate increased from 0.15 kg-N/m³/d to 1.24 kg-N/m³/d, and a high nitrogen removal efficiency of 82.6% was obtained. A stable DO partition further accelerated the bioreaction rates and enhanced the activity of functional microbes. The activities of ammonia oxidation and anammox reached 1.21 g-N/g-VSS/d and 1.43 g-N/g-VSS/d, respectively. Sludge granulation efficiently enriched the abundances of Candidatus Brocadia (7.4%) and Nitrosomonas (5.2%). These results demonstrated that efficient DO partition and stable culture of granular sludge could enhance the synergy of functional microbes for autotrophic nitrogen removal.

Dynamic anaerobic membrane bioreactor coupled with sulfate reduction (SrDMBR) for saline wastewater treatment

This study investigated organic removal performance, characteristics of the membrane dynamics, membrane fouling and the effects of biological sulfate reduction during high-salinity (1.0%) and high-sulfate (150 mgSO₄^2--S/L) wastewater treatment using a laboratory-scale upflow anaerobic sludge bed reactor integrated with cross-flow dynamic membrane modules. Throughout the operational period, dynamic membrane was formed rapidly (within 5-10 min) following each backwashing cycle (21-16 days), and the permeate turbidity of <5-7 NTU was achieved with relatively high specific organic conversion (70-100 gTOC/kgVSS·d) and specific sulfate reduction (50-70 gSO₄^2--S/kgVSS·d) rates. The sulfide from sulfate reduction can be reused for downstream autotrophic denitrification. 16S rRNA gene amplicon sequencing revealed that the microbial communities enriched in the sludge were different than those accumulated on the dynamic layer. Overall, this study demonstrates that the anaerobic dynamic membrane bioreactor coupled with sulfate reduction (SrDMBR) shows promising applicability in saline wastewater treatment.

Low Global Diversity of Candidatus Microthrix, a Troublesome Filamentous Organism in Full-Scale WWTPs

Candidatus Microthrix is one of the most common bulking filamentous microorganisms found in activated sludge wastewater treatment plants (WWTPs) across the globe. One species, Ca. M. parvicella, is frequently observed, but global genus diversity, as well as important aspects of its ecology and physiology, are still unknown. Here, we use the MiDAS ecosystem-specific 16S rRNA gene database in combination with amplicon sequencing of Danish and global WWTPs to investigate Ca. Microthrix spp. diversity, distribution, and factors affecting their global presence. Only two species were abundant across the world confirming low diversity of the genus: the dominant Ca. M. parvicella and an unknown species typically present along with Ca. M. parvicella, although usually in lower abundances. Both species were mostly found in Europe at low-to-moderate temperatures and their growth was favored in municipal WWTPs with advanced process designs. As no isolate is available for the novel species, we propose the name "Candidatus Microthrix subdominans." Ten high-quality metagenome-assembled genomes recovered from Danish WWTPs, including 6 representing the novel Ca. M. subdominans, demonstrated high genetic similarity between the two species with a likely preference for lipids, a putative capability to reduce nitrate and nitrite, and the potential to store lipids and poly-P. Ca. M. subdominans had a potentially more versatile metabolism including additional sugar transporters, higher oxygen tolerance, and the potential to use carbon monoxide as energy source. Newly designed fluorescence in situ hybridization probes revealed similar filamentous morphology for both species. Raman microspectroscopy was used to quantify the in situ levels of intracellular poly-P. Despite the observed similarities in their physiology (both by genomes and in situ), the two species showed different seasonal dynamics in Danish WWTPs through a 13-years survey, possibly indicating occupation of slightly different niches. The genomic information provides the basis for future research into in situ gene expression and regulation, while the new FISH probes provide a useful tool for further characterization in situ. This study is an important step toward understanding the ecology of Ca. Microthrix in WWTPs, which may eventually lead to optimization of control strategies for its growth in this ecosystem.

Foam shares antibiotic resistomes and bacterial pathogens with activated sludge in wastewater treatment plants

Foaming is a common operational problem that occurs in activated sludge (AS) from many wastewater treatment plants (WWTPs), but the characteristic of antibiotic resistance genes (ARGs) and human pathogenic bacteria (HPB) in foams is generally lacking. Here, we used a metagenomic approach to characterize the profile of ARGs and HPB in foams and AS from full-scale WWTPs receiving pesticide wastewater. No significant difference in the microbial communities was noted between the AS and foam samples. The diversity and abundance of ARGs in the foams were similar to those in the pertinent AS samples. Procrustes analysis suggested that the bacterial community is the major driver of ARGs. Metagenomic assembly also indicated that most ARGs (e.g., multidrug, rifamycin, peptides, macrolide-lincosamide-streptogramin, tetracycline, fluoroquinolone, and beta-lactam resistance genes) were carried by chromosomes rather than mobile genetic elements. Moreover, the relative abundances of HPB, Pseudomonas putida and Mycobacterium smegmatis, were enriched in the foam samples. Nine HPB were identified as carriers of 21 ARG subtypes, of which Pseudomonas aeruginosa could carry 12 ARG subtypes. Overall, this study indicates the prevalence of ARGs, HPB, and ARG-carrying HPB in foams, which highlights the potential risk of foams in spreading ARGs and HPB into the surrounding environments.

Use of biochar/persulfate for accelerating the stabilization process and improving nitrogen stability of animal waste digestate

In China, the growing amount of digestate from anaerobic digestion produced by animal husbandry is an emerging challenge. A common treatment used to eliminate this digestate is long-term stabilization ponds. However, this process can lead to a shortage of digestate storage space and loss of nitrogen nutrients within the digestate. To alleviate those shortcomings, this study developed an efficient stabilization pond using biochar and persulfate (BC/PS treatment). Using this treatment, the germination index (GI) of the digestate increased from 56% to 85% and the stabilization efficiency increased nearly 2.7 times. In addition, the dehydrogenase activity (DHA) in the BC/PS treatment remained between 0.47 and 0.91 μg/(g·h) across the 40 days, which indicated that BC/PS had a positive effect on microbial inactivation. In the traditional stabilization process (CK treatment), dissolved organic nitrogen (DON) decreased from 47.77 mg/L to 0.81 mg/L and ammonium nitrogen almost disappeared. The BC/PS treatment led to the promotion of nitrogen nutrient composition. Particulate total nitrogen (21.49% of total nitrogen) decomposed into dissolved total nitrogen and the DON increased from 47.77 to 58.89 mg/L. The BC/PS treatment showed a faster stabilization time, good microbial inactivation, lower toxicity, and stable nitrogen nutrient composition of the digestate compared to traditional methods.

Distribution and diversity of filamentous bacteria in wastewater treatment plants exhibiting foaming of Taihu Lake Basin, China

Foaming caused by filamentous bacteria in activated sludge (AS) is a common phenomenon in municipal wastewater treatment plants (WWTPs) in Taihu Lake Basin of South China. In this study, total bacterial and filamentous bacterial communities were comprehensively characterized in AS and foams from eight municipal WWTPs by high-throughput sequencing technology. Results showed that alpha diversities of total bacterial communities in foams were obviously lower than those in AS samples. The bacterial community structures were significantly different between WWTPs rather than sample types (AS vs. foam). For most WWTPs, the Actinobacteria phylum was highly enriched in foams and the most abundant genera in foams were common mycolata. Sixteen filamentous bacteria were identified against the improved bulking and foaming bacteria (BFB) database. Abundance and composition of BFB in different WWTPs and different sample types were significantly different. 'Nostocoida limicola' I Trichococcus and Microthrix were generally dominant in AS samples. The dominant BFB in foams were associated with Microthrix, Skermania, Gordonia, and Mycobacterium. A new Defluviicoccus spp. in cluster III was identified in severe and continuous foams. Moreover, dominant BFB in stable and continuous foams with light level in one typical WWTP were diverse, even, and dynamic. Bacterial co-occurrence network analysis implied that the bacterial community of AS was more sensitive to disturbance than that of foam.

Membrane fouling caused by biological foams in a submerged membrane bioreactor: Mechanism insights

Though sludge foaming often occurs and thus causes serious membrane fouling in membrane bioreactors (MBRs), the fouling mechanisms related with the foaming phenomenon have not been well addressed, hindering better understanding and solving foaming problem. In this work, it was interestingly found that, the foulants during the foaming period possessed extremely high specific filtration resistance (SFR) (over 10¹⁶ m kg^-1) and strong adhesion ability to membrane surface. Chemical characterization showed that the proteins (178.57 mg/L) and polysaccharides (209.21 mg/L) in the foaming sample were about 6.4 times and 5.4 times of those in the supernatant sample, suggesting existence of a mechanism permitting continuous production of these foulants in the MBR during the foaming period. It was revealed that the fouling caused by foams was associated with gel layer filtration process, and the extremely high SFR can be interpreted by chemical potential change in the gel filtration process depicted in Flory-Huggins theory. Meanwhile, analyses by the extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory showed that the strong adhesion ability stemmed from the high interaction energy between the foaming foulants and membrane surface. In addition, 16S rDNA gene sequencing identified that the abundance of the foaming related bacteria species in the sludge suspension during the foaming period was more than 10 times of that during the non-foaming period. This study offered new mechanism insights into foaming fouling in MBRs.

Formation and characteristics of filamentous granular sludge

Aerobic granular sludge process as a promising biotechnology has been one of the research hotspots in the area of wastewater treatment during the last two decades. In our study, after around 60 days' operation, filamentous granular sludge (FGS) was formed under low aeration (SAV = 0.085 cm/s) and multi-feeding conditions. The characteristics of FGS and the performance of the FGS system for organic matter and nutrients removal were investigated. The results showed that chemical oxygen demand (COD) and total organic carbon (TOC) removal efficiencies were relatively stable, while COD removal efficiency increased from 82% to 94% in the presence of sulfamethoxazole (SMZ) at low concentration (1 mg/L). At the same time, the TP removal efficiency could be improved and maintained at around 75%, while TN removal efficiency was flocculated at around 50%. The analysis of microbial diversity showed that Thiothrix and Trichococcus as typical filamentous species were detected and dominant in the FGS system. The abundance of Thiothrix increased from 15% to 34%, while Trichococcus decreased from 23% to 3% in the presence of SMZ.

Stochasticity in microbiology: managing unpredictability to reach the Sustainable Development Goals

Pure (single) cultures of microorganisms and mixed microbial communities (microbiomes) have been important for centuries in providing renewable energy, clean water and food products to human society and will continue to play a crucial role to pursue the Sustainable Development Goals. To use microorganisms effectively, microbial engineered processes require adequate control. Microbial communities are shaped by manageable deterministic processes, but also by stochastic processes, which can promote unforeseeable variations and adaptations. Here, we highlight the impact of stochasticity in single culture and microbiome engineering. First, we discuss the concepts and mechanisms of stochasticity in relation to microbial ecology of single cultures and microbiomes. Second, we discuss the consequences of stochasticity in relation to process performance and human health, which are reflected in key disadvantages and important opportunities. Third, we propose a suitable decision tool to deal with stochasticity in which monitoring of stochasticity and setting the boundaries of stochasticity by regulators are central aspects. Stochasticity may give rise to some risks, such as the presence of pathogens in microbiomes. We argue here that by taking the necessary precautions and through clever monitoring and interpretation, these risks can be mitigated.

Norfloxacin-induced effect on enhanced biological phosphorus removal from wastewater after long-term exposure

In this study, long-term experiments were performed under synthetic wastewater conditions to evaluated the potential impacts of norfloxacin (NOR) (10, 100 and 500 μg/L) on enhanced biological phosphorus removal (EBPR). Experimental result showed that long-term exposure to 10 μg/L NOR induced negligible effects on phosphorus removal. The presence of 100 μg/L NOR slightly decreased phosphorus removal efficiency to 94.41 ± 1.59 %. However, when NOR level further increased to 500 μg/L, phosphorus removal efficiency was significantly decreased from 97.96 ± 0.8 5% (control) to 82.33 ± 3.07 %. The mechanism study revealed that the presence of 500 μg/L NOR inhibited anaerobic phosphorus release and acetate uptake as well as aerobic phosphorus uptake during long-term exposure. It was also found that 500 μg/L NOR exposure suppressed the activity of key enzymes related to phosphorus removal but promoted the transformations of intracellular polyhydroxyalkanoate and glycogen. Microbial analysis revealed that that the presence of 500 μg/L NOR reduced the abundances of polyphosphate accumulating organisms but increased glycogen accumulating organisms, as compared the control.

Candidatus Amarolinea and Candidatus Microthrix Are Mainly Responsible for Filamentous Bulking in Danish Municipal Wastewater Treatment Plants

Filamentous bulking is a common serious operational problem leading to deteriorated sludge settling that has long been observed in activated sludge biological wastewater treatment systems. A number of bacterial genera found therein possess filamentous morphology, where some have been shown to be implicated in bulking episodes (e.g., Ca. Microthrix), the impact of many others is still not clear. In this study we performed a survey of 17 Danish municipal wastewater treatment plants (WWTPs) with nutrient removal using 16S rRNA amplicon sequencing over a period of 13 years, where all known filamentous bacteria from 30 genera were analyzed. The filamentous community constituted on average 13 ± 6%, and up to 43% of total read abundance with the same genera common to all plants. Ca. Microthrix and several genera belonging to phylum Chloroflexi were among the most abundant filamentous bacteria. The effect of filamentous bacteria on sludge settling properties was analyzed using measurements of the diluted sludge volume index (DSVI). Strong positive correlations with DSVI were observed only for Ca. Microthrix and Ca. Amarolinea, the latter being a novel, recently characterized genus belonging to the phylum Chloroflexi. The bulking potential of other filamentous bacteria was not significant despite their presence in many plants. Low phylogenetic diversity was observed for both Ca. Microthrix and Ca. Amarolinea, making physiological characterization of individual species and potential development of control strategies more feasible. In this study we show that, despite the high diversity of filamentous phylotypes in Danish WWTPs, only few of them were responsible for severe bulking episodes.

Impact of dissolved oxygen and loading rate on NH3 oxidation and N2 production mechanisms in activated sludge treatment of sewage

Microaerobic activated sludge (MAS) is a one-stage process operated at 0.5-1.0 mg l^-1 dissolved oxygen (DO) aiming at simultaneous nitrification and denitrification. We used molecular techniques and a comprehensive nitrogen (N)-transformation activity test to investigate the dominant NH₃ -oxidizing and N₂ -producing mechanism as well as the dominant ammonia-oxidizing bacteria (AOB) species in sludge samples individually collected from an MAS system and a conventional anoxic/oxic (A/O) system; both systems were operated at a normal loading rate (i.e. 1.0 kg chemical oxygen demand (COD) m^-3  day^-1 and 0.1 kg NH₄ ⁺ -N m^-3  day^-1 ) in our previous studies. The DO levels in both systems (aerobic: conventional A/O system; microaerobic: MAS system) did not affect the dominant NH₃ -oxidizing mechanism or the dominant AOB species. This study further demonstrated the feasibility of a higher loading rate (i.e. 2.30 kg COD m^-3  day^-1 and 0.34 kg NH₄ ⁺ -N m^-3  day^-1 ) with the MAS process during sewage treatment, which achieved a 40% reduction in aeration energy consumption than that obtained in the conventional A/O system. The increase in loading rates in the MAS system did not affect the dominant NH₃ -oxidizing mechanism but did impact the dominant AOB species. Besides, N₂ was predominantly produced by microaerobic denitrification in the MAS system at the two loading rates.

Performance and microbial community analysis of two sludge type reactors in achieving mainstream deammonification with hydrazine addition

The deammonification process is a promising and energy efficient nitrogen removal technology. Since deammonification process has succeeded in high-strength ammonia nitrogen wastewater treatment (sidestream deammonification) but its application in treating low-strength ammonium nitrogen wastewater (mainstream deammonification) remains a great challenge. In this study, mainstream deammonification process in two reactors maintained stability with hydrazine (N₂H₄) addition. The two reactors consisted of a deammonification granular reactor and a mixed ammonia oxidizing bacteria (AOB) flocculent with anaerobic ammonia oxidizing bacteria (AnAOB) granular reactor. Deammonification granular reactor had a more efficient total nitrogen removal efficiency (TNRE, 80.5 ± 5.8%) and nitrogen removal rate (NRR, 0.33 ± 0.04 g/(L·day)). The advantage of retain biomass in granular sludge reactor lead to a more balanced ex-situ activity between AOB (0.37 mg N/(g VSS·h)) and AnAOB (0.43 mg N/(g VSS·h)). Candidatus Brocadia and Nitraspira were detected the dominant genus responsible for the observed AnAOB and nitrite oxidizing bacteria (NOB), respectively. The more obvious effect of N₂H₄ on enhancing AnAOB and suppressing NOB both in ex-situ activity and genus abundances in mixed sludge reactor were also founded may due to loose spatial distribution among species.

Exploring the operating factors controlling Kouleothrix (type 1851), the dominant filamentous bacterial population, in a full-scale A2O plant

This study reveals that the abundance of the filament Kouleothrix (Eikelboom type 1851) correlated positively with poor settleability of activated sludge biomass in a Japanese full-scale nutrient removal wastewater treatment plant sampled over a one-year period. 16S rRNA amplicon sequence data confirmed that Kouleothrix was the dominant filament in the plant, with a relative abundance of 3.06% positively correlated with sludge volume index (SVI) (R = 0.691). Moreover, Kouleothrix (type 1851) appeared to form interfloc bridges, typical of bulking sludge, regardless of season. Together with earlier studies that indicated the responsibility of Kouleothrix (type 1851) on bulking events, these data suggest that their high relative abundances alone may be responsible for sludge bulking. 16S rRNA qPCR data for this filament showed changes in its relative abundance correlated with changes in several operational parameters, including mixed liquor temperature, sludge retention time, and suspended solids concentration, and it may be that manipulating these may help control Kouleothrix bulking.

A novel SNPR process for advanced nitrogen and phosphorus removal from mainstream wastewater based on anammox, endogenous partial-denitrification and denitrifying dephosphatation

For achieving energy-efficient wastewater treatment, a novel simultaneous nitrogen and phosphorus removal (SNPR) process, which integrated anammox, endogenous partial-denitrification and denitrifying dephosphatation in a sequencing batch reactor with granular sludge was developed to treat mainstream wastewater. After 200 days of operation, a simultaneous high-level nitrogen and phosphorus removal of 93.9% and 94.2%, respectively was achieved with an average influent C/N ratio of 2.9. Anammox pathway contributed 82.9% of the overall nitrogen removal because of the stable nitrite production from nitrate via endogenous partial-denitrification. In addition, phosphorus was mainly removed via denitrifying dephosphatation utilizing nitrate as the electron acceptor, resulting in a significant saving of carbon sources and oxygen demands. Further, adsorption/precipitation of phosphorus occurred in this novel SNPR process, which displaced the energy source to the metabolism of glycogen accumulating organisms (GAOs) for nitrite production and alleviated competition between phosphorus accumulating organisms (PAOs) and anammox for electron acceptor. Using 16S rRNA gene amplicon sequencing analysis, the study found that anammox bacteria (8.4%), GAOs (1.5%) and PAOs (1.1%) co-existed in this system, potentially resulting in simultaneous endogenous partial-denitrification, anammox and denitrifying dephosphatation. The above results demonstrated that the novel SNPR process is a promising technique for energy-efficient wastewater treatment.

Abundance of total and metabolically active Candidatus Microthrix and fungal populations in three full-scale wastewater treatment plants

The abundances of total and metabolically active populations of Candidatus Microthrix and Fungi were evaluated by quantitative PCR (qPCR) and retrotranscribed qPCR of ribosomal molecular markers in three different full-scale wastewater treatment plants (WWTPs), in absence of bulking/foaming episodes. Significant differences of the abundance of rDNAs and rRNAs of Candidatus Microthrix and Fungi were observed among the three WWTPs. The average relative abundances of 16S rDNA copies of Candidatus Microthrix to those of Bacteria ranged 3.4-8.9%. Biota-environment analysis (BIO-ENV) demonstrated that the number of copies of both 16S rDNA and rRNA of Candidatus Microthrix increased at longer hydraulic and solids' retention times and with higher nitrate concentrations in the activated sludge. The abundance of Candidatus Microthrix correlated strongly and positively with the removal efficiencies of organic matter and total nitrogen in the tested WWTPs, highlighting the role of these particular microbial group in the performance of these engineered systems.

The Phylogeny, Biodiversity, and Ecology of the Chloroflexi in Activated Sludge

It is now clear that several of the filamentous bacteria in activated sludge wastewater treatment plants globally, are members of the phylum Chloroflexi. They appear to be more commonly found in treatment plants designed to remove nitrogen (N) and phosphorus (P), most of which operate at long sludge ages and expose the biomass to anaerobic conditions. The Chloroflexi seem to play an important beneficial role in providing the filamentous scaffolding around which flocs are formed, to feed on the debris from lysed bacterial cells, to ferment carbohydrates and to degrade other complex polymeric organic compounds to low molecular weight substrates to support their growth and that of other bacterial populations. A few commonly extend beyond the floc surface, while others can align in bundles, which may facilitate interfloc bridging and hence generate a bulking sludge. Although several recent papers have examined the phylogeny and in situ physiology of Chloroflexi in activated sludge plants in Denmark, this review takes a wider look at what we now know about these filaments, especially their global distribution in activated sludge plants, and what their functional roles there might be. It also attempts to outline why such information might provide us with clues as to how their population levels may be manipulated, and the main research questions that need addressing to achieve these outcomes.

Comparative investigation on carbon-based moving bed biofilm reactor (MBBR) for synchronous removal of phenols and ammonia in treating coal pyrolysis wastewater at pilot-scale

By regulating the extraction solvent and alkali in pretreatment, two carbon-based MBBRs were compared in pilot-scale to synchronously remove phenols and ammonia of coal pyrolysis wastewater (CPW) under fluctuant phenols-ammonia loadings. It revealed that lignite activated coke (LAC)-based MBBR performed more stable with phenols increasing (250-550 mg/L), and reached higher tolerance limit to ammonia (>320 mg/L) than activated carbon (AC)-based MBBR under fluctuant ammonia loadings. During the phenols-ammonia synchronous removal process, the LAC provided the firm basis for shock resistance due to superior resilient adsorption capacity, enhanced sludge property and microbial cooperation. Furthermore, microbial analysis revealed that the strengthened collaboration between archaea and facultative bacteria played the primary role in phenols-ammonia synchronous degradation. Specifically, the heterotrophic bacteria consumed phenols-ammonia by partial nitrification process and ammonia assimilation, following by denitrifying process to further eliminate phenols. The multifunctional Comamonas was the critical genus participating in all procedures.

Denitrification activity of polyphosphate accumulating organisms (PAOs) in full-scale wastewater treatment plants

A comprehensive assessment of full-scale enhanced biological phosphorus removal (EBPR) plants (five plants, 19 independent tests) was undertaken to determine their effectiveness in terms of aerobic and anoxic P removal. By comparing parallel P uptake tests under only aerobic or under anoxic-aerobic conditions, results revealed that introducing an anoxic stage led to an overall P removal of on average 90% of the P removed under only aerobic conditions. This was achieved with negligible higher PHA and glycogen requirements, 30% lower overall oxygen consumption and with the simultaneous removal of nitrate, reducing up to an estimate of 70% of carbon requirements for simultaneous N and P removal. Varying fractions of denitrifying polyphosphate accumulating organisms (DPAOs), from an average of 25% to 84%, were found in different plants. No correlation was found between the DPAO fractions and EBPR configuration, season, or the concentration of any of the microbial groups measured via quantitative fluorescence in situ hybridisation. These included Type I and Type II Ca. Accumulibacter and glycogen accumulating organisms, suggesting that chemical batch tests are the best methodology for quantifying the potential of anoxic P removal in full-scale wastewater treatment plants.

Interdependence between the aerobic degradation of BPA and readily biodegradable substrates by activated sludge in semi-continuous reactors

The objective of the present work was to analyze the interrelationship between the aerobic degradation of BPA and readily biodegradable substrates by activated sludge (AS) in semi-continuous reactors (SCRs). AS were obtained from three SCRs fed with glucose, acetate or peptone. AS from these reactors were used as inocula for three SCRs that were fed with each biogenic substrate, and for three SCRs that were fed with the biogenic substrate and BPA. In all cases, dissolved organic carbon (DOC), BPA, total suspended solids (TSS) and respirometric measurements were performed. Although BPA could be removed in the presence of all the tested substrates, AS grown on acetate exhibited the longest acclimation to BPA. Reactors fed with peptone attained the lowest TSS concentration; however, these AS had the highest specific BPA degradation rate. Specific DOC removal rates and respirometric measurements demonstrated that the presence of BPA had a negligible effect on the removal of the tested substrates. A mathematical model was developed to represent the evolution of TSS and DOC in the SCRs as a function of the operation cycle. Results suggest that the main effect of BPA on AS was to increase the generation of microbial soluble products. This work helps to understand the relationship between the biodegradation of BPA and readily biodegradable substrates.

The threshold of influent ammonium concentration for nitrate over-accumulation in a one-stage deammonification system with granular sludge without aeration

Low-strength ammonium is still a challenge for the mainstream deammonification because of nitrate over-accumulation. In this study, the threshold of influent ammonium concentration of one-stage deammonification system with granular sludge was investigated, by stepwise decreasing influent ammonium from high concentrations (280mg/L to 140mg/L) to the low concentration (70mg/L) in 108d at 32°C without aeration. Results showed that, under 70mg/L NH₄⁺-N, ΔNO₃^--N/ΔNH₄⁺-N ratio increased to 0.2, deviated from the theoretical value of 0.11, with ammonium and TN removal efficiencies of 91% and 71%, respectively. However, under both high ammonium concentrations (280mg/L and 140mg/L), nitrate production stabilized at only 13%. Chloroflexi, Planctomycetes and Proteobacteria contributed >70% of the communities under all three ammonium concentrations. As influent ammonium decreasing, the relative abundances of bacteria for anammox, aerobic oxidizing and denitrifying decreased, while NOB (nitrite oxidizing bacteria) abundance increased greatly. So 70mg/L was the threshold of influent ammonium concentration for stable deammonification without organic influent. It was the decrease of functional bacteria and overgrowth of NOB that worsen the deammonification performance under low-strength ammonium.

Genomic insights into Candidatus Amarolinea aalborgensis gen. nov., sp. nov., associated with settleability problems in wastewater treatment plants

Settleability of particles in activated sludge systems can be impaired by an overgrowth of filamentous bacteria, a problem known as bulking. These filaments are often members of the phylum Chloroflexi, sometimes reaching abundances in excess of 30% of the biovolume. The uncultured Chloroflexi phylotype, Candidatus Amarolinea, has been observed in high abundances in Danish full-scale activated sludge systems by 16S rRNA gene amplicon surveys, where it has been associated with bulking. In this study, fluorescence in situ hybridization was applied to confirm their high abundance, filamentous morphology, and contribution to the interfloc bridging that characterizes filamentous bulking. Furthermore, genome-centric metagenomics using both Illumina and Oxford Nanopore sequencing was used to obtain a near complete population genome (5.7Mbp) of the Ca. Amarolinea phylotype, which belongs to the proposed novel family Amarolineaceae within the order Caldilineales of Chloroflexi. Annotation of the genome indicated that the phylotype is capable of aerobic respiration, fermentation, and dissimilatory nitrate reduction to ammonia. The genome sequence also gives a better insight into the phylogenetic and evolutionary relationships of the organism. The name Candidatus Amarolinea aalborgensis is proposed for the species.

Energy saving control strategies for Haliscomenobacter hydrossis filamentous sludge bulking in the A/O process treating real low carbon/nitrogen domestic wastewater

The control strategies of energy saving for filamentous sludge bulking were investigated in the A/O process under low dissolved oxygen (DO) with low carbon/nitrogen (C/N) ratio, and the dominant filamentous bacteria were identified by using fluorescent in situ hybridization. Initially, the sludge volume index reached nearly 500 mL/g and serious bulking occurred when the DO value was 0.5 mg/L, with Haliscomenobacter hydrossis as the major filamentous bacteria in the bulking sludge. Later on, the compartment number increased in the aerobic zone, increasing by this way DO, to control serious bulking. Increasing DO to 1 mg/L based on the increase of compartment number in the aerobic zone was the favorable controlling method, which solved the sludge loss, improved the effluent quality to the national discharge standard and allowed for energy costs saving. As a result, the effective control method for H. hydrossis filamentous sludge bulking provided the economical, convenient and longstanding method for most municipal wastewater treatment plants treating real low C/N domestic wastewater.

Microbial community structures and functions of wastewater treatment systems in plateau and cold regions

Wastewater treatment plants (WWTPs) in plateau regions have unique microbial community structures. In this study, Illumina high-throughput sequencing technology was applied to investigate microbial communities of plateau WWTPs. The research showed that microbial diversities and richness were negatively associated with the altitude and positively to the water temperature to a certain extent. The dominant phyla of plateau and control WWTPs were similar, which mainly included Proteobacteria, Bacteroidetes, Chloroflexi and Firmicutes. In plateau WWTPs, the LEfSe analysis found 4 biomarkers which can catabolize aromatic compounds, indicating the microorganisms that can degrade refractory organics might survive better in plateau WWTPs. The analysis of functional genera and enzymes showed that there was no significant difference in abundances of organic degrading bacteria, but the nitrogen removal bacteria were less abundant and phosphorus removal bacteria were more abundant in plateau WWTPs.

Insight into the microbial community and its succession of a coupling anaerobic-aerobic biofilm on semi-suspended bio-carriers

This work aims at establishing a coupling anaerobic-aerobic biofilm within a single bioreactor and revealing its microbial community and succession. By using a semi-suspended bio-carrier fabricated with 3D printing technique, an obvious DO gradient was gradually created within the biofilm, which demonstrated that a coupling anaerobic-aerobic biofilm was successfully established on the surface of bio-carriers. The results of metagenomic analysis revealed that the microbial community on the bio-carriers experienced a continuous succession in its structure and dominant species along with the operational time. The formed coupling biofilm created suitable micro multi-habitats for the co-existence of these microorganisms, including nitrifying and denitrifying bacteria, which were beneficial to the removing of organic pollutants and converting nutrients. Along with the succession, the microbial community was gradually dominated by several functional microorganisms. Overall, the results presented an approach to improve the microbial biodiversity by constructing a new structure and floating status of bio-carriers.

The effect of seasonal variations on floc morphology in the activated sludge process

The effect of seasonal variations on floc formation in the activated sludge process (ASP) was studied in a municipal wastewater treatment plant in Finland nearly 16 months. Floc formation was measured with an online optical monitoring device, and results were correlated with the temperature of the upcoming wastewater and the treatment efficiency of the ASP. Results showed that floc formation has a clear, seasonal pattern, with flocs in summer being larger and rounder and having fewer filaments and small particles. In addition, treatment efficiency increased in summer. The study correlated the results of image analysis with the composition (chemical oxygen demand and suspended solids content) and temperature of the wastewater before and after the ASP. Results showed that the composition of upcoming wastewater has no clear correlation with floc morphological parameters. However, the wastewater temperature clearly correlated with floc formation. Results indicated that cold winter conditions enhanced the growth of filamentous bacteria in wastewater, decreasing treatment efficiency. Furthermore, these results confirmed that floc formation has seasonal variations.

Anaerobic digestion of pig manure supernatant at high ammonia concentrations characterized by high abundances of Methanosaeta and non-euryarchaeotal archaea

We examined the effect of ammonium and temperature on methane production in high rate upflow anaerobic sludge bed reactors treating pig manure supernatant. We operated four reactors at two ammonium concentrations (‘low’ at 1.9, ‘high’ at 3.7 g L⁻¹, termed LA and HA reactors, respectively) and at variable temperatures over 358 days. Archaeal and bacterial communities were characterized by Illumina sequencing of 16S rRNA amplicons. Ammonium was a major selective factor for bacterial and archaeal community structure. After ~200 days of adaptation to high ammonium levels, acetate and propionate removal and methane production improved substantially in HA reactors. Aceticlastic Methanosaeta was abundant and positively correlated to methane yield in the HA reactors, whereas Methanosarcina was more abundant in LA reactors. Furthermore, a group of monophyletic OTUs that was related to Thaumarchaeota in phylogenetic analysis was highly abundant in the archaeal communities, particularly in the HA reactors. The most abundant bacterial OTU in LA reactors, representing Syntrophomonadaceae, was also positively correlated to methane yield in the HA reactors, indicating its importance in methane production under ammonia stress. In conclusion, efficient methane production, involving aceticlastic methanogenesis by Methanosaeta took place in the reactors at free ammonia concentrations as high as 1 g L⁻¹.

Can DNA sequencing show differences between microbial communities in Polish and Danish wastewater treatment plants?

The microbial populations in the activated sludge of two Polish wastewater treatment plants (WWTPs) were identified and quantified using Illumina sequencing of 16S ribosomal RNA amplicons over a 2-year period. Their dynamics over time were compared to Danish WWTPs (data collected in previous studies by Center for Microbial Communities, Aalborg University). The bacterial communities in Polish and Danish WWTPs were similar to each other, but the microbial diversity in Polish WWTPs was lower. The dominant genera in Polish WWTPs were more abundant than in Danish WWTPs; 30 of them constituted more than half the of activated sludge community. Polish WWTPs showed a higher abundance of bacteria involved in nitrogen and chemical oxygen demand removal (Proteobacteria and Bacteroidetes), while polyphosphate-acculumating bacteria were the dominant bacterial group in Danish plants. The microbial community structures in the examined Polish WWTPs were relatively similar to each other and showed strong seasonal variations which are not normally observed in Danish WWTPs.

Temporal dynamics of bacterial communities and predicted nitrogen metabolism genes in a full-scale wastewater treatment plant

Dynamics of bacterial communities and nitrogen metabolism genes in a full-scale WWTP as revealed by Illumina sequencing and PICRUSt.

Short-sludge age EBPR process - Microbial and biochemical process characterisation during reactor start-up and operation

The new paradigm for used water treatment suggests the use of short solid retention times (SRT) to minimize organic substrate mineralization and to maximize resource recovery. However, little is known about the microbes and the underlying biogeochemical mechanisms driving these short-SRT systems. In this paper, we report the start-up and operation of a short-SRT enhanced biological phosphorus removal (EBPR) system operated as a sequencing batch reactor (SBR) fed with preclarified municipal wastewater, which is supplemented with propionate. The microbial community was analysed via 16S rRNA amplicon sequencing. During start-up (SRT = 8 d), the EBPR was removing up to 99% of the influent phosphate and completely oxidized the incoming ammonia. Furthermore, the sludge showed excellent settling properties. However, once the SRT was shifted to 3.5 days nitrification was inhibited and bacteria of the Thiothrix taxon proliferated in the reactor, thereby leading to filamentous bulking (sludge volume index up to SVI = 1100 mL/g). Phosphorus removal deteriorated during this period, likely due to the out-competition of polyphosphate accumulating organisms (PAO) by sulphate reducing bacteria (SRB). Subsequently, SRB activity was suppressed by reducing the anaerobic SRT from 1.2 day to 0.68 day, with a consequent rapid SVI decrease to ∼200 ml/g. The short-SRT EBPR effectively removed phosphate and nitrification was mitigated at SRT = 3 days and oxygen levels ranging from 2 to 3 mg/L.

Effects of organic matter in livestock manure digester liquid on microbial community structure and in situ activity of anammox granules

Anaerobic ammonium oxidation (anammox) is a promising process for NH4(+)-rich wastewaters such as anaerobic digester liquids. In the present study, we investigated various properties of an up-flow column reactor containing anammox granules and fed with a real digester liquid at four different concentrations (Phases 1 to 4). The efficiencies of NH4(+) and NO2(-) removal decreased by up to 32% and 42%, respectively, in the digester-liquid-fed reactor (reactor-DL). When the performance of reactor-DL deteriorated, the community structure, spatial distribution, and in situ anammox activity in the two reactors were further investigated using 16S rRNA gene-based phylogenetic analysis, fluorescence in situ hybridization (FISH), and microelectrode measurements. The phylogenetic analysis and FISH results showed that non-anammox bacteria were predominant in the granule outer layers in reactor-DL, whereas anammox bacteria still dominated the granule interiors. Microelectrode measurements showed clear evidence of NH4(+) oxidation activity in the interiors of granules from reactor-DL. Batch experiments using anammox granules at different acetate concentrations indicated that concentrations up to 50 mM had no effects on the anammox activity, whereas inorganic carbon uptake decreased in the presence of acetate. The present study clearly shows that the anammox activity and anammox bacterial density in the granules were maintained after feeding the digester liquid to the reactor for 140 days.