Oligotyping and metagenomics reveal distinct Candidatus Accumulibacter communities in side-stream versus conventional full-scale enhanced biological phosphorus removal (EBPR) systems

Comammox and unknown ammonia oxidizers contribute to nitrite accumulation in an integrated A-B stage process that incorporates side-stream EBPR (S2EBPR)

A novel integrated pilot-scale A-stage high rate activated sludge, B-stage short-cut biological nitrogen removal and side-stream enhanced biological phosphorus removal (A/B-shortcut N-S2EBPR) process for treating municipal wastewater was demonstrated with the aim to achieve simultaneous and carbon- and energy-efficient N and P removal. In this studied period, an average of 7.62 ± 2.17 mg-N/L nitrite accumulation was achieved through atypical partial nitrification without canonical known NOB out-selection. Network analysis confirms the central hub of microbial community as Nitrospira, which was one to two orders of magnitude higher than canonical aerobic oxidizing bacteria (AOB) in a B-stage nitrification tank. The contribution of comammox Nitrospira as AOB was evidenced by the increased amoB/nxr ratio and higher ammonia oxidation activity. Furthermore, oligotyping analysis of Nitrospira revealed two dominant sub-clusters (microdiveristy) within the Nitrospira. The relative abundance of oligotype II, which is phylogenetically close to Nitrospira_midas_s_31566, exhibited a positive correlation with nitrite accumulation in the same operational period, suggesting its role as comammox Nitrospira. Additionally, the phylogenetic investigation suggested that heterotrophic organisms from the family Comamonadacea and the order Rhodocyclaceae embedding ammonia monooxygenase and hydroxylamine oxidase may function as heterotrophic nitrifiers. This is the first study that elucidated the impact of integrating the S2EBPR on nitrifying populations with implications on short-cut N removal. The unique conditions in the side-stream reactor, such as low ORP, favorable VFA concentrations and composition, seemed to exert different selective forces on nitrifying populations from those in conventional biological nutrient removal processes. The results provide new insights for integrating EBPR with short-cut N removal process for mainstream wastewater treatment.

Revisiting the role of Acinetobacter spp. in side-stream enhanced biological phosphorus removal (S2EBPR) systems

We piloted the incorporation of side-stream enhanced biological phosphorus removal (S2EBPR) with A/B stage short-cut nitrogen removal processes to enable simultaneous carbon-energy-efficient nutrients removal. This unique configuration and system conditions exerted selective force on microbial populations distinct from those in conventional EBPR. Interestingly, effective P removal was achieved with the predominance of Acinetobacter (21.5 ± 0.1 %) with nearly negligible level of known conical PAOs (Ca. Accumulibacter and Tetrasphaera were 0.04 ± 0.10 % and 0.47 ± 0.32 %, respectively). Using a combination of techniques, such as fluorescence in situ hybridization (FISH) coupled with single cell Raman spectroscopy (SCRS), the metabolic tracing of Acinetobacter-like cells exerted PAO-like phenotypic profiling. In addition, comparative metagenomics analysis of the closely related Acinetobacter spp. revealed the EBPR relevant metabolic pathways. Further oligotyping analysis of 16s rRNA V4 region revealed sub-clusters (microdiversity) of the Acinetobacter and revealed that the sub-group (oligo type 1, identical (100 % alignment identity) hits from Acinetobacter_midas_s_49494, and Acinetobacter_midas_s_55652) correlated with EBPR activities parameters, provided strong evidence that the identified Acinetobacter most likely contributed to the overall P removal in our A/B-shortcut N-S2EBPR system. To the best of our knowledge, this is the first study to confirm the in situ EBPR activity of Acinetobacter using combined genomics and SCRS Raman techniques. Further research is needed to identify the specific taxon, and phenotype of the Acinetobacter that are responsible for the P-removal.

Side-Stream Enhanced Biological Phosphorus Removal (S2EBPR) enables effective phosphorus removal in a pilot-scale A-B stage shortcut nitrogen removal system for mainstream municipal wastewater treatment

While the adsorption/bio-oxidation (A/B) process has been widely studied for carbon capture and shortcut nitrogen (N) removal, its integration with enhanced biological phosphorus (P) removal (EBPR) has been considered challenging and thus unexplored. Here, full-scale pilot testing with an integrated system combining A-stage high-rate activated sludge with B-stage partial (de)nitrification/anammox and side-stream EBPR (HRAS-P(D)N/A-S2EBPR) was conducted treating real municipal wastewater. The results demonstrated that, despite the relatively low influent carbon load, the B-stage P(D)N-S2EBPR system could achieve effective P removal performance, with the carbon supplement and redirection of the A-stage sludge fermentate to the S2EBPR. The novel process configuration design enabled a system shift in carbon flux and distribution for efficient EBPR, and provided unique selective factors for ecological niche partitioning among different key functionally relevant microorganisms including polyphosphate accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs). The combined nitrite from B-stage to S2EBPR and aerobic-anoxic conditions in our HRAS-P(D)N/A-S2EBPR system promoted DPAOs for simultaneous internal carbon-driven denitrification via nitrite and P removal. 16S rRNA gene-based oligotyping analysis revealed high phylogenetic microdiversity within the Accumulibacter population and discovered coexistence of certain oligotypes of Accumulibacter and Competibacter correlated with efficient P removal. Single-cell Raman micro-spectroscopy-based phenotypic profiling showed high phenotypic microdiversity in the active PAO community and the involvement of unidentified PAOs and internal carbon-accumulating organisms that potentially played an important role in system performance. This is the first pilot study to demonstrate that the P(D)N-S2EBPR system could achieve shortcut N removal and influent carbon-independent EBPR simultaneously, and the results provided insights into the effects of incorporating S2EBPR into A/B process on metabolic activities, microbial ecology, and resulted system performance.

Two new clades recovered at high temperatures provide novel phylogenetic and genomic insights into Candidatus Accumulibacter

Candidatus Accumulibacter, a key genus of polyphosphate-accumulating organisms, plays key roles in lab- and full-scale enhanced biological phosphorus removal (EBPR) systems. A total of 10 high-quality Ca. Accumulibacter genomes were recovered from EBPR systems operated at high temperatures, providing significantly updated phylogenetic and genomic insights into the Ca. Accumulibacter lineage. Among these genomes, clade IIF members SCELSE-3, SCELSE-4, and SCELSE-6 represent the to-date known genomes encoding a complete denitrification pathway, suggesting that Ca. Accumulibacter alone could achieve complete denitrification. Clade IIC members SSA1, SCUT-1, SCELCE-2, and SCELSE-8 lack the entire set of denitrifying genes, representing to-date known non-denitrifying Ca. Accumulibacter. A pan-genomic analysis with other Ca. Accumulibacter members suggested that all Ca. Accumulibacter likely has the potential to use dicarboxylic amino acids. Ca. Accumulibacter aalborgensis AALB and Ca. Accumulibacter affinis BAT3C720 seemed to be the only two members capable of using glucose for EBPR. A heat shock protein Hsp20 encoding gene was found exclusively in genomes recovered at high temperatures, which was absent in clades IA, IC, IG, IIA, IIB, IID, IIG, and II-I members. High transcription of this gene in clade IIC members SCUT-2 and SCUT-3 suggested its role in surviving high temperatures for Ca. Accumulibacter. Ambiguous clade identity was observed for newly recovered genomes (SCELSE-9 and SCELSE-10). Five machine learning models were developed using orthogroups as input features. Prediction results suggested that they belong to a new clade (IIK). The phylogeny of Ca. Accumulibacter was re-evaluated based on the laterally derived polyphosphokinase 2 gene, showing improved resolution in differentiating different clades.

Insights on biological phosphorus removal with partial nitrification in single sludge system via sidestream free ammonia and free nitrous acid dosing

The sidestream sludge treatment by free ammonium (FA)/free nitrous acid (FNA) dosing was frequently demonstrated to maintain the nitrite pathway for the partial nitrification (PN) process. Nevertheless, the inhibitory effect of FA and FNA would severely influence polyphosphate accumulating organisms (PAOs), destroying the microbe-based phosphorus (P) removal. Therefore, a strategic evaluation was proposed to successfully achieve biological P removal with a partial nitrification process in a single sludge system by sidestream FA and FNA dosing. Through the long-term operation of 500 days, excellent phosphorus, ammonium and total nitrogen removal performance were achieved at 97.5 ± 2.6 %, 99.1 ± 1.0 % and 75.5 ± 0.4 %, respectively. Stable partial nitrification with a nitrite accumulation ratio (NAR) of 94.1 ± 3.4 was attained. The batch tests also reported the robust aerobic phosphorus uptake based on FA and FNA adapted sludge after exposure of FA and FNA, respectively, suggesting the FA and FNA treatment strategy could potentially offer the opportunity for the selection of PAOs, which synchronously have the tolerance to FA and FNA. Microbial community analysis suggested that Accumulibacter, Tetrasphaera, and Comamonadaceae collectively contributed to the phosphorus removal in this system. Summarily, the proposed work presents a novel and feasible strategy to integrate enhanced biological phosphorus removal (EBPR) and short-cut nitrogen cycling and bring the combined mainstream phosphorus removal and partial nitrification process closer to practical application.

Modeling versatile and dynamic anaerobic metabolism for PAOs/GAOs competition using agent-based model and verification via single cell Raman Micro-spectroscopy

Side-stream enhanced biological phosphorus removal process (S2EBPR) has been demonstrated to improve performance stability and offers a suite of advantages compared to conventional EBPR design. Design and optimization of S2EBPR require modification of the current EBPR models that were not able to fully reflect the metabolic functions of and competition between the polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs) under extended anaerobic conditions as in the S2EBPR conditions. In this study, we proposed and validated an improved model (iEBPR) for simulating PAO and GAO competition that incorporated heterogeneity and versatility in PAO sequential polymer usage, staged maintenance-decay, and glycolysis-TCA pathway shifts. The iEBPR model was first calibrated against bulk batch testing experiment data and proved to perform better than the previous EBPR model for predicting the soluble orthoP, ammonia, biomass glycogen, and PHA temporal profiles in a starvation batch testing under prolonged anaerobic conditions. We further validated the model with another independent set of anaerobic testing data that included high-resolution single-cell and specific population level intracellular polymer measurements acquired with single-cell Raman micro-spectroscopy technique. The model accurately predicted the temporal changes in the intracellular polymers at cellular and population levels within PAOs and GAOs, and further confirmed the proposed mechanism of sequential polymer utilization, and polymer availability-dependent and staged maintenance-decay in PAOs. These results indicate that under extended anaerobic phases as in S2EBPR, the PAOs may gain competitive advantages over GAOs due to the possession of multiple intracellular polymers and the adaptive switching of the anaerobic metabolic pathways that consequently lead to the later and slower decay in PAOs than GAOs. The iEBPR model can be applied to facilitate and optimize the design and operations of S2EBPR for more reliable nutrient removal and recovery from wastewater.

Effect of return activated sludge diversion ratio on phosphorus removal performance in side-stream enhanced biological phosphorus removal (S2EBPR) process

In this study, a lab-scale continuous flow side-stream enhanced biological phosphorus (P) removal (S2EBPR) reactor was operated for 247 days treating synthetic wastewater with influent carbon to phosphorus (C/P) ratio of 25.0 g COD/g P and influent PO43--P of 7.4 ± 0.3 mg P/L. The effect of the return activated sludge (RAS) diversion ratio on S2EBPR reactor was investigated by comparing P removal performance, microbial activity, and community structure. The results showed that the RAS diversion ratio of 8.0%, by yielding a side-stream sludge retention time (SRTSS) of ∼60 h, resulted in the lowest effluent PO43--P concentration of 0.5 ± 0.3 mg P/L. The results of in situ process profiles and ex situ P release and uptake batch tests under different RAS diversion conditions showed that the more anaerobic P release was obtained in the side-stream reactor, the higher the P removal efficiency and EBPR activity were achieved. The stoichiometric ratios observed in EBPR activity tests indicated a polyphosphate accumulating organisms (PAOs) metabolism mainly dependent on the glycolysis pathway. The results of microbial ecology analysis revealed that the optimized SRTSS would give a competitive advantage to PAOs in the S2EBPR process. By obtaining statistically reliable results, this study would provide guidance for wastewater treatment plants to achieve optimal P removal performance in S2EBPR configuration.

Toward Integrating EBPR and the Short-Cut Nitrogen Removal Process in a One-Stage System for Treating High-Strength Wastewater

Enhanced biological phosphorus removal (EBPR) is an economical and sustainable process for phosphorus removal from wastewater. Despite the widespread application of EBPR for low-strength domestic wastewater treatment, limited investigations have been conducted to apply EBPR to the high-strength wastewaters, particularly, the integration of EBPR and the short-cut nitrogen removal process in the one-stage system remains challenging. Herein, we reported a novel proof-of-concept demonstration of integrating EBPR and nitritation (oxidation of ammonium to nitrite) in a one-stage sequencing batch reactor to achieve simultaneous high-strength phosphorus and short-cut nitrogen removal. Excellent EBPR performance of effluent 0.8 ± 1.0 mg P/L and >99% removal efficiency was achieved fed with synthetic high-strength phosphorus wastewater. Long-term sludge acclimation proved that the dominant polyphosphate accumulating organisms (PAOs), Candidatus Accumulibacter, could evolve to a specific subtype that can tolerate the nitrite inhibition as revealed by operational taxonomic unit (OTU)-based oligotyping analysis. The EBPR kinetic and stoichiometric evaluations combined with the amplicon sequencing proved that the Candidatus Competibacter, as the dominant glycogen accumulating organisms (GAOs), could well coexist with PAOs (15.3-24.9% and 14.2-33.1%, respectively) and did not deteriorate the EBPR performance. The nitrification activity assessment, amplicon sequencing, and functional-based gene marker quantification verified that the unexpected nitrite accumulation (10.7-21.0 mg N/L) in the high-strength EBPR system was likely caused by the nitritation process, in which the nitrite-oxidizing bacteria (NOB) were successfully out-selected (<0.1% relative abundance). We hypothesized that the introduction of the anaerobic phase with high VFA concentrations could be the potential selection force for achieving nitritation based on the literature review and our preliminary batch tests. This study sheds light on developing a new feasible technical route for integrating EBPR with short-cut nitrogen removal for efficient high-strength wastewater treatment.

Reclaimed water influences bacterioplankton and bacteriobenthos communities differently in river networks

Reclaimed water reuse is a promising strategy for addressing water scarcity; however, its potential ecological impact remains largely unknown. In particular, the differential effects of reclaimed water on microbial communities in various habitats remain poorly understood. Here, we aimed to elucidate the distinct effects of reclaimed water on bacterioplankton and bacteriobenthos communities in reclaimed water-receiving river networks from multiple perspectives, including community structure, co-occurrence patterns, assembly mechanisms, and nitrogen cycle function. Significant differences in microbial composition were observed between the plankton and benthic habitats, and the average numbers of amplicon sequence variants (ASVs) that originated from the wastewater treatment plants (WWTP) sites were 310.0 and 613.3, respectively, indicating a stronger association between WWTP and benthic habitats. Random forest and network co-occurrence analyses identified the genus Clostridium_sensu_stricto as a biomarker and key module hub. The assembly of bacteriobenthos communities was driven primarily by deterministic processes (58.74% for River-S and 58.94% for WWTP-S), whereas for bacterioplankton communities, this proportion was reduced to 18.02% (River-W) and 19.09% (WWTP-W). The qPCR revealed a large difference in abundance between the N cycling related genes of bacteriobenthos (average 2.47 × 106 copies/ng) and bacterioplankton (average 3.11 × 103 copies/ng) communities, and different interaction patterns with functional genes. Variance partitioning analysis (VPA) indicated that nitrogen was the most important pollutant, affecting the structure and ecological functions of microbial communities. Moreover, pathway analysis suggested that the reuse of reclaimed water may have enhanced the N-cycling functions of microbial communities and the emission of nitrous oxide.

CRISPR-Cas phage defense systems and prophages in Candidatus Accumulibacter

Candidatus Accumulibacter plays a major role in enhanced biological phosphorus removal (EBPR) from wastewater. Although bacteriophages have been shown to represent fatal threats to Ca. Accumulibacter organisms and thus interfere with the stability of the EBPR process, little is known about the ability of different Ca. Accumulibacter strains to resist phage infections. We conducted a systematic analysis of the occurrence and characteristics of clustered regularly interspaced short palindromic repeats and associated proteins (CRISPR-Cas) systems and prophages in Ca. Accumulibacter lineage members (43 in total, including 10 newly recovered genomes). Results indicate that 28 Ca. Accumulibacter genomes encode CRISPR-Cas systems. They were likely acquired via horizontal gene transfer, conveying a distinct adaptivity to phage predation to different Ca. Accumulibacter members. Major differences in the number of spacers show the unique phage resistance of these members. A comparison of the spacers in closely related Ca. Accumulibacter members from distinct geographical locations indicates that habitat isolation may have resulted in the acquisition of resistance to different phages by different Ca. Accumulibacter. Long-term operation of three laboratory-scale EBPR bioreactors revealed high relative abundances of Ca. Accumulibacter with CRISPSR-Cas systems. Their specific resistance to phages in these reactors was indicated by spacer analysis. Metatranscriptomic analyses showed the activation of the CRISPR-Cas system under both anaerobic and aerobic conditions. Additionally, 133 prophage regions were identified in 43 Ca. Accumulibacter genomes. Twenty-seven of them (in 19 genomes) were potentially active. Major differences in the occurrence of CRISPR-Cas systems and prophages in Ca. Accumulibacter will lead to distinct responses to phage predation. This study represents the first systematic analysis of CRISPR-Cas systems and prophages in the Ca. Accumulibacter lineage, providing new perspectives on the potential impacts of phages on Ca. Accumulibacter and EBPR systems.

Redirecting carbon to recover VFA to facilitate biological short-cut nitrogen removal in wastewater treatment: A critical review

Wastewater treatment plants (WWTPs) are facing a great challenge to transition from energy-intensive to carbon-neutral and energy-efficient systems. Biological nutrient removal (BNR) can be severely impacted by carbon limitation, particularly for wastewater with a low carbon-to-nitrogen (C/N) ratio, which can significantly increase the operational costs. Waste activated sludge (WAS) is a valuable byproduct of WWTPs, as it contains high levels of organic matter that can be utilized to improve BNR management by recovering and reusing the fermentative volatile fatty acids (VFAs). This review provides a comprehensive examination of the recovery and reuse of VFAs in wastewater management, with a particular focus on advancing the preferable biological short-cut nitrogen removal process for carbon-insufficient municipal wastewaters. First, the method of carbon redirection for recovering VFAs was reviewed. Carbon could be captured through the two-stage A/B process or via sludge fermentation with different sludge pretreatment and process control strategies to accelerate sludge hydrolysis and inhibit methanogens to enhance VFA production. Second, VFAs can support the metabolism of autotrophic N-cycling microorganisms involved in wastewater treatment, such as AOB, NOB, anammox, and comammox bacteria. However, VFAs can also cause inhibition at high concentrations, leading to the partition of AOB and NOB; and can promote partial denitrification as an efficient carbon source for heterotrophic denitrifiers. Third, the lab- and pilot-scale engineering practices with different configurations (i.e., A²O, SBR, UASB) were summarized that have shown the feasibility of utilizing the fermentate to achieve superior nitrogen removal performance without the need for external carbon addition. Lastly, the future perspectives on leveraging the relationships between mainstream and sidestream, nitrogen and phosphorus, autotrophs and heterotrophs were given for sustainable and efficient BNR management.

Metagenomics reveals the metabolism of polyphosphate-accumulating organisms in biofilm sequencing batch reactor: A new model

This study assessed the impact of the operating conditions of the biofilm sequencing batch reactor (BSBR) on the community structure and the growth/metabolic pathways of its polyphosphate-accumulating organisms (PAOs). There are significant difference with reference to the enhanced biological phosphorus removal (EBPR) process. The leading PAOs in BSBR generally are capable of high affinity acetate metabolism, gluconeogenesis, and low affinity phosphate transport, and have various carbon source supplementation pathways to ensure the efficient circulation of energy and reducing power. A new model of the metabolic mechanism of PAOs in the BSBR was formulated, which features low glycogen metabolism with simultaneous gluconeogenesis and glycogenolysis and differs significantly from the classic mechanism based on Candidatus_Accumulibacter and Tetrasphaera. The findings will assist the efficient recovery of low concentration phosphate in municipal wastewater.

Metagenomics illuminated the mechanism of enhanced nitrogen removal and vivianite recovery induced by zero-valent iron in partial-denitrification/anammox process

In this study, a novel strategy of zero-valent iron (ZVI) combined with acetic acid was proposed to optimize partial-denitrification/anammox (PD/A) process, and enhanced nitrogen removal mechanism was elucidated through metagenomics. Results showed that the optimal nitrogen and phosphorus removal were as high as 99.50% and 98.37%, respectively, with vivianite being precipitated as the main byproduct. The occurrence of Feammox was a crucial link for enhanced ammonia removal and vivianite recovery. Metagenomic analysis further certified that long-term acclimation of optimization strategy triggered DNRA-based nitrate reducing genes (narY/Z and nrfA) assigned to Candidatus Brocadia, which allow direct uptake of nitrate by the anammox. Additionally, ZVI might act as a new electron donor to decrease organics dependence of PD by reducing the abundance of genes for electron production involved in carbon metabolism. However, FA addition enhanced the relative abundances of genes involved in anammox including nitrogen reduction and oxidation, thereby accelerating nitrogen removal.

Biologically induced phosphate precipitation in heterotrophic nitrification processes of different microbial aggregates: Influences of nitrogen removal metabolisms and extracellular polymeric substances

Phosphorus (P) removal occurred in heterotrophic nitrification process, but its mechanism has not been fully explored. In this study, the P removal performances, pathways, and mechanisms in heterotrophic nitrification processes of different microbial aggregates (activated sludge and biofilm) were investigated. The results showed that the biofilm reactor had more efficient total nitrogen removal (98.65%) and phosphate removal (94.17%). Heterotrophic nitrification and denitrification processes generated alkalinity for biologically induced phosphate precipitation (BIPP), which contributed to 64.12%-78.81% of the overall P removal. The solid phase P content reached 48.03 mg/gSS with hydroxyapatite and calcium phosphate formation. The study clarified that biofilm was beneficial to BIPP because of the nitrogen removal metabolism and extracellular polymeric substance (EPS). Heterotrophic nitrogen removal metabolism was the driving force of BIPP, while EPS with abundant carboxyl and amide groups promoted the precipitation. The study would provide new insights into simultaneous nutrients removal and P recovery from wastewater.