The link between the microbial ecology, gene expression, and biokinetics of denitrifying polyphosphate-accumulating systems under different electron acceptor combinations

Strategic carbon source supplementation enhances nitrite degradation by Pantoea sp. A5 in variable temperature conditions

The expanding global demand for sustainable aquaculture underscores the need for efficient water quality management, particularly in controlling harmful nitrogenous compounds like nitrites. This study explores the effectiveness of Pantoea sp. A5, a nitrite-degrading bacterium isolated from food waste, reduces nitrite levels in aquaculture systems, focusing on the role of carbon sources like glucose and glycerol. The experiments showed that these carbon sources, especially glycerol, significantly enhanced the bacterium's ability to degrade nitrites across a range of temperatures without promoting growth, suggesting a cost-effective alternative to glucose. Unlike acetic acid, which did not enhance nitrite degradation, glycerol and glucose regulated metabolic pathways, evidenced by reduced malate dehydrogenase (MDH) activity and increased glutamate dehydrogenase (GDH) levels, facilitating efficient ammonia assimilation. These findings highlight the potential of using targeted carbon sources to manage nitrite levels in aquaculture, improving sustainability and contributing to global food supply efforts.

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

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

Deciphering the roles of attached and suspended sludges in simultaneous nitrogen and phosphorus removal in an IFAS system based on metagenomic analysis

Integrated fixed-film activated sludge (IFAS) system, an improvement of the activated sludge process, combines the advantages of both attached sludge (AS) and suspended sludge (SS). This study aimed to fully decipher the roles of AS and SS in simultaneous N and P removal in an IFAS system through metagenomic analysis. It was found that AS contributed about 84.04%, 97%, and 95.12% to exogenous NO3--N reduction, endogenous NO3--N reduction, and endogenous NO2--N reduction, respectively. Compared with AS, SS exhibited a greater contribution to anaerobic P release (69.06%) and aerobic P uptake (73.48%). Nitrate and nitrite reductase enzymes showed higher activities in AS, while the activities of exopolyphosphatase and alkaline phosphatase D were more active in SS. P content further indicated that in AS, only a small amount of P was stored in EPS, with most presented intracellularly. In SS, the amount of P stored in EPS was found to be higher. Metagenomic analysis revealed genes related to the synthesis and degradation of endogenous carbon were higher in AS, whereas the TCA cycle exhibited higher activity in SS. P removal-related genes (such as ppk2, ppx, and adk) was significantly higher in SS than in AS. The alteration of genes associated with nitrogen metabolism suggested that the microbes in AS had a higher capacity for nitrification and denitrification. In summary, the discrepancy in the roles of AS and SS in N and P removal in IFAS can be attributed to variations in enzyme activity, P storage in EPS, microbial community composition, and functional gene abundance.

Effect of enrichment conditions of secondary feeding on the synthesis of polyhydroxyalkanoates (PHAs) by activated sludge

Polyhydroxyalkanoates (PHAs) are biodegradable plastics with great performance and development prospects. However, their traditional anaerobic/aerobic enrichment process requires a high concentration of dissolved oxygen (DO), resulting in high energy consumption. In this study, an anaerobic/oxygen-limited with secondary feeding enrichment mode was used to enhance the synthesis of PHAs while reducing energy consumption. The enrichment process of PHAs-synthesizing bacteria lasted up to 100 days, and the experiment was conducted to investigate the change of the PHAs synthesizing ability of the system in this mode by detecting the PHAs content and community distribution of the activated sludge under different stages. Under these conditions, the system enriched two major genera of PHAs-synthesizing bacteria, Thauera (30.21%) and Thiothrix (21.30%). The content of PHAs in the sludge increased from 4.51% to 30.87% and was able to achieve a concomitant increase in poly(3-hydroxyvalerate) (PHV) monomer content. After nitrogen limitation (C/N = 150) treatment, the content of PHAs reached 63.05%. The results showed that the enrichment mode of anaerobic/oxygen-limited with secondary feeding could enrich more PHAs-synthesizing bacteria and significantly increase the synthesis amount of PHAs, which revealed the great potential of this mode in solid waste value-added and reduce the production cost of PHAs and could provide a theoretical basis for the production of PHAs from activated sludge.

Exploring the microbial influence on seasonal nitrous oxide concentration in a full-scale wastewater treatment plant using metagenome assembled genomes

Nitrous oxide is a highly potent greenhouse gas and one of the main contributors to the greenhouse gas footprint of wastewater treatment plants (WWTP). Although nitrous oxide can be produced by abiotic reactions in these systems, biological N₂O production resulting from the imbalance of nitrous oxide production and reduction by microbial populations is the dominant cause. The microbial populations responsible for the imbalance have not been clearly identified, yet they are likely responsible for strong seasonal nitrous oxide patterns. Here, we examined the seasonal nitrous oxide concentration pattern in Avedøre WWTP alongside abiotic parameters, the microbial community composition based on 16S rRNA gene sequencing and already available metagenome-assembled genomes (MAGs). We found that the WWTP parameters could not explain the observed pattern. While no distinct community changes between periods of high and low dissolved nitrous oxide concentrations were determined, we found 26 and 28 species with positive and negative correlations to the seasonal N₂O concentrations, respectively. MAGs were identified for 124 species (approximately 31% mean relative abundance of the community), and analysis of their genomic nitrogen transformation potential could explain this correlation for four of the negatively correlated species. Other abundant species were also analysed for their nitrogen transformation potential. Interestingly, only one full-denitrifier (Candidatus Dechloromonas phosphorivorans) was identified. 59 species had a nosZ gene predicted, with the majority identified as a clade II nosZ gene, mainly from the phylum Bacteroidota. A correlation of MAG-derived functional guilds with the N₂O concentration pattern showed that there was a small but significant negative correlation with nitrite oxidizing bacteria and species with a nosZ gene (N₂O reducers (DEN)). More research is required, specifically long-term activity measurements in relation to the N₂O concentration to increase the resolution of these findings.

Nitrous oxide formation during simultaneous phosphorus and nitrogen removal in aerobic granular sludge treating different carbon substrates

The impact of different substrates on N₂O dynamics and gene expression of marker enzymes (nirS, nirK and nosZ) involved in denitrifying enhanced biological phosphorus removal (d-EBPR) was investigated. Aerobic granular sludge fed with VFAs led to an anoxic P-uptake (27.7 ± 1.2 mg PO₄^3--P.gVSS^-1) and N₂O emissions up to 80.7 ± 3.4% N₂O-N. A decisive role of Accumulibacter in N₂O formation was observed. Dosage of amino acids (12.0 ± 1.2 mg PO₄^3--P.gVSS^-1) and glucose (1.5 ± 0.9 mg PO₄^3--P.gVSS^-1) as sole substrate did not support d-EBPR activity. Presence of NO₂^- resulted in higher N₂O formation in comparison to nitrate and a nosZ/(nirS + nirK) ratio lower than 0.3. A linear correlation (R² > 0.95) between the nosZ/(nirS + nirK) ratio and the N₂O reductase rate was found only when dosing the same type of substrate. This suggests an interplay between the microbial community composition and different polyhydroxyalkanoates derivatives, when dosing different substrates.

Ameliorating effect of nitrate on nitrite inhibition for denitrifying P-accumulating organisms

Lowered air supply and organic carbon need are the key factors to reduce wastewater treatment costs and thereby, avoid eutrophication. Denitrifying PO43-- removal (DPR) process using nitrate instead of oxygen for PO43- uptake was started up in the sequencing batch reactor (SBR) at a nitrate dosing rate of 20-25 mg N L-1 d-1. Operation with a real municipal wastewater supplied with CH3COONa, K2HPO4 and KNO3 succeeded in the cultivation of biomass containing denitrifying polyphosphate accumulating organisms (DPAOs). The durations of SBR process anaerobic/anoxic/oxic cycles were 1.5 h, 3.5 h and 1 h, respectively. SBR operation resulted in a maximum PO43--P uptake of 17 mg PO43--P g-1 MLSS. The highest TN and PO43- removal efficiencies were observed during the first half of reactor operation at 77 (±10) % and 71 (±5) %, respectively. An average COD removal rate of 172 (±98) mg g-1 MLSS and a high average removal efficiency of 89 (±4) % were achieved. Nitrite effect with/without nitrate as DPR electron acceptor was investigated in batch-scale to show possibilities to use high nitrite and nitrate contents simultaneously as electron acceptors for the anoxic phosphate uptake. Nitrate attenuation against nitrite toxicity can be economically justified in full-scale treatment applications in which wastewater has a high nitrogen content. Nitrate attenuated nitrite toxicity (caused by nitrite content at 5-100 mg NO2--N L-1) when using supplemental additions of nitrate (at concentrations of 45-200 mg NO3--N L-1) in batch tests. Illumina sequencing emphasized that during biomass adaption microbial community changed by lowered aerobic cycle length and by lowered nitrate dosing towards representation of key DPAO/PAO- organisms, such as Candidatus Accumulibacter, Xanthomonadaceae, Comomonadaceae, Saprospiraceae and Rhodocyclaceae. This study showed that DPAO biomass adaption to nitrate maintained an efficient COD, nitrogen and phosphorus removal and the biomass can be applied for treatment of wastewater containing high nitrite and nitrate content.

Impact of the substrate composition on enhanced biological phosphorus removal during formation of aerobic granular sludge

Performance of enhanced biological phosphorus removal (EBPR) is often investigated with simple synthetic wastewater containing volatile fatty acids (VFAs). In this study, various (fermentable) substrates, individually and in mixtures, were examined during the application of a granulation strategy. In addition, the microbial community and N₂O formation were monitored. Sludge densification was observed in all systems. Stable EBPR, associated with the presence of Accumulibacter and an anaerobic P-release up to 21.9 mgPO₄^3--P.gVSS^-1, was only obtained when VFAs were present as sole substrate or in mixture. Systems fed with VFAs were strongly related to the formation of N₂O (maximum of 6.25% relative to the total available nitrogen). A moderate anaerobic dissolved organic carbon (DOC) uptake was observed when amino acids (64.27 ± 3.08%) and glucose (75.39 ± 5.79%) as sole carbon source were applied. The substrate/species-specific enrichment of Burkholderiaceae and Saccharimonadaceae respectively, resulted in unstable EBPR in those systems.

Full-scale N removal from centrate using a sidestream process with a mainstream carbon source

An innovative approach to treat centrate for rapid nitrogen load discharge reduction was investigated and applied at the Truckee Meadows Water Reclamation Facility (TMWRF) in Reno, NV. This process allowed TMWRF to circumvent an anticipated exceedance of the individual waste load allocation in 2018. Existing infrastructure and equipment were re-purposed in a full-scale suspended growth biological centrate treatment system, attaining simultaneous nitrification, and denitrification with no additional capital investment. Functioning within a few days of start-up, the average ammonia reduction was 81% (1,106 kg/day) and the average total nitrogen reduction in the sidestream was 53% (757 kg/day) using primary effluent as carbon source. Alkalinity and carbon limitations were both anticipated and observed; however, adaptive operations allowed for balancing of nitrification and denitrification processes, providing pH stability and success in meeting treatment goals. Immediately after the sidestream treatment system was placed into service, nitrogen in the mainstream facility was measured at concentrations significantly lower than typical and was sustained at historically low concentrations throughout the operation. This translated into a significant methanol cost savings of $1,500 per day (USD). The system has become a critical supplemental treatment process during upcoming rehabilitation projects to address aging infrastructure of existing nitrogen treatment facilities. PRACTITIONER POINTS: Full scale demonstration of sidestream N removal using a hybrid process. Integration of the sidestream N process to reduce N effluent load without alkalinity or supplementary carbon augmentation. Operational solution to reduce operating costs without new infrastructure.

Treatment of industrial effluents and assessment of their impact on the structure and function of microbial diversity in a unique Anoxic-Aerobic sequential batch reactor (AnASBR)

A novel Anoxic-Aerobic Process (AnAP) that eliminated the anaerobic process was optimized and operated for the simultaneous remediation of phosphate, nitrate, and chemical oxygen demand (COD) from industrial effluents. Two sequential batch reactors (SBR) with AnAP were established for the treatment of effluent from two industries; phosphate fertilizer (AnASBR_PPL) and dairy industry (AnASBR_DW). The adaptability of the bacterial consortium in the SBRs, dominated by denitrifying phosphate accumulating organisms (DNPAOs), facilitates the stable performance of AnAP for simultaneous nutrient and COD removal. Up to 90% and ~80% of COD removal were achieved in AnASBR_PPL and AnASBR_DW, respectively. Nearly complete denitrification was observed along with phosphate removal accounted for ~90% in both the reactors. Granulation of sludge has been widely reported in aerobic reactors; however, interestingly, in this study, partial granulation of the sludge was observed in both the AnASBRs which facilitated the microorganisms to uptake a minimal amount of phosphate and nitrate even under the aerobic condition. The underlying mechanism of DNPAOs and other associated microbes in the consortium were investigated for microbial diversity by 16S rDNA based targeted amplicon sequencing using the Illumina platform and imputed metagenomic analysis. The dominance of Betaproteobacteria, Alphaproteobacteria, Gammaproteobacteria, and Bacteroidia was observed in AnASBRs. At steady-state operation, the identity of the core community members remained largly stable, but their relative abundances changed considerably in both the reactors as a function of varying industrial effluent. However, population of few strains such as Lactobacteriales, Enterobacteriales changed drastically with respect to the influent, as these strains were predominat in AnASBR_DW but not present in AnASBR_PPL. The dominant strains were the vital contributor to the gene pool encoding for denitrification, dephosphatation, TCA cycle, glycolysis, EPS production, and polyhydroxyalkanoate (PHA) storage, etc. Few less abundant but persistent species were also detected as contributors to these functional groups. It unveiled the TCA cycle remains preferable over conventional glycolysis in both the SBR irrespective of carbon source. The new AnASBR was proved to be an efficient alternative system that is energy efficient with higher ease of operation for the treatment of different industrial effluents without fail.

Re-evaluating the microbiology of the enhanced biological phosphorus removal process

We have critically assessed some of the dogmas in the microbiology of enhanced biological phosphorus removal (EBPR) and argue that the genus Tetrasphaera can be as important as Ca. Accumulibacter for phosphorus removal; and that proliferation of their competitors, the glycogen accumulating organisms, does not appear to be a practical problem for EBPR efficiency even under tropical conditions. An increasing number of EBPR-related genomes are changing our understanding of their physiology, for example, their potential to participate in denitrification. Rather than trying to identify organisms that adhere to strict phenotype metabolic models, we advocate for broader analyses of the whole microbial communities in EBPR plants by iterative studies with isolates, lab enrichments, and full-scale systems.

Single-stage denitrifying phosphorus removal biofilter utilizing intracellular carbon source for advanced nutrient removal and phosphorus recovery

Advanced nutrient removal of municipal wastewater has insufficient carbon source, and resource recovery is neglected. In this study, a single-stage biofilter based on denitrifying phosphorus removal (DPR) was proposed for advanced nutrient removal and phosphorus recovery, which was operated under alternating anoxic/anaerobic mode with no extracellular carbon source in anoxic period. The results showed that the biofilter achieved efficient and stable performance with low carbon consumption (C/N ≈ 3.7). The average removal efficiency of NO₃^--N, TN and PO₄^3--P were 74.81%, 71.08% and 91.15%, respectively. DPR primarily occurred in the middle of the filtration bed and nutrient removal was driven by intracellular polymers, which was the main carbon source. High-throughput sequencing indicated that Dechloromonas was enriched and contributed to DPR while Zoogloea was responsible for endogenous denitrification. Denitrifying polyphosphate accumulating organisms and endogenous denitrifiers synergistically enhanced the nutrient removal capacity. The study further provides research perspectives for improving nutrient removal.

The link between nitrous oxide emissions, microbial community profile and function from three full-scale WWTPs

Few attempts have been made in previous studies to link the microbial community structure and function with nitrous oxide (N₂O) emissions at full-scale wastewater treatment plants (WWTPs). In this work, high-throughput sequencing and reverse transcriptase-qPCR (RT-qPCR) was applied to activated sludge samples from three WWTPs for two seasonal periods (winter and summer) and linked with the N₂O emissions and wastewater characteristics. The total N₂O emissions ranged from 7.2 to 937.0 g N-N₂O/day, which corresponds to an emission factor of 0.001 to 0.280% of the influent NH₄-N being emitted as N₂O. Those emissions were related to the abundance of Nitrotoga, Candidatus Microthrix and Rhodobacter genera, which were favored by higher dissolved oxygen (DO) and nitrate (NO₃^-) concentrations in the activated sludge tanks. Furthermore, a relationship between the nirK gene expression and N₂O emissions was verified. Detected N₂O emission peaks were associated with different process events, related to aeration transition periods, that occurred during the regular operation of the plants, which could be potentially associated to increased emissions of the WWTP. The design of mitigation strategies, such as optimizing the aeration regime, is therefore important to avoid process events that lead to those N₂O emissions peaks. Furthermore, this study also demonstrates the importance of assessing the gene expression of nosZ clade II, since its high abundance in WWTPs could be an important key to reduce the N₂O emissions.