Denitrification of nitrate and nitrite by 'Candidatus Accumulibacter phosphatis' clade IC

An integrated system combining Tetrasphaera-dominated enhanced biological phosphorus removal with sulfur autotrophic denitrification to enhance biological nutrients removal

This study developed a two-stage process, including Tetrasphaera-dominated enhanced biological phosphorus-removal (EBPR(T)) sequencing batch reactor (SBR), followed by sulfur autotrophic denitrification (SADN) SBR, to achieve advanced nutrients removal from low VFAs wastewater. The removal efficiencies of nitrogen and phosphorus (PO43--P) reached 99 % with effluent PO43--P and total inorganic nitrogen (TIN) below 0.5 mg/L and 1 mg/L in EBPR(T) and SADN SBR, respectively. Mechanism analysis indicated that as increasing drainage ratio and complex carbon sources, free amino acids, glycogen, and PHA served as the endogenous carbon sources of Tetrasphaera to store energy. SADN contributed to approximately 80 % of nitrogen removal. DNA and cDNA results indicated Tetrasphaera was shifted from clade 2 to clade 1 after increasing the drainage ratio and the complexity of the carbon source, and Tetrasphaera (50.95 %) and Ca. Accumulibacter (9.12 %) were the most important functional microorganisms synergized to remove phosphorus at the transcriptional level in EBPR(T). Thiobacillus (45.97 %) and Sulfuritalea (9.24 %) were the dominant sulfur autotrophic denitrifiers at gene and transcriptional level in SADN. The results suggested that the EBPR(T) - SADN SBRs have great nutrient removal performance in treating low VFAs wastewater without additional carbon sources.

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.

A review of the phosphorus removal of polyphosphate-accumulating organisms in natural and engineered systems

Increasing eutrophication has led to a continuous deterioration of many aquatic ecosystems. Polyphosphate-accumulating organisms (PAOs) can provide insight into the human response to this challenge, as they initiate enhanced biological phosphorus removal (EBPR) through cyclical anaerobic phosphorus release and aerobic phosphorus uptake. Although the limiting environmental factors for PAO growth and phosphorus removal have been widely discussed, there remains a gap in the knowledge surrounding the differences in the type and phosphorus removal efficiencies of natural and engineered PAO systems. Furthermore, due to the limitations of PAOs in conventional wastewater treatment environments, there is an urgent need to find functional PAOs in extreme environments for better wastewater treatment. Therefore, it is necessary to explore the effects of extreme conditions on the phosphorus removal efficiency of PAOs as well as the types, sources, and characteristics of PAOs. In this paper, we summarize the response mechanisms of PAOs, denitrifying polyphosphate-accumulating organisms (D-PAOs), aerobic denitrifying polyphosphate-accumulating organisms (AD-PAOs), and sulfur-related PAOs (S-PAOs). The mechanism of nitrogen and phosphorus removal in PAOs is related to the coupling cycles of carbon, nitrogen, phosphorus, and sulfur. The genera of PAOs differ in natural and engineered systems, but PAOs have more diversity in aquatic environments and soils. Recent studies on the impact of several parameters (e.g., temperature, carbon source, pH, and dissolved oxygen) and extracellular polymer substances on the phosphorus removal efficiency of PAOs in natural and engineered systems are further discussed. Most of the PAOs screened under extreme conditions still had high phosphorus removal efficiencies (>80.0 %). These results provide a reference for searching for PAOs with different adaptations to achieve better wastewater treatment.

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.

Expanding the Diversity of Accumulibacter with a Novel Type and Deciphering the Transcriptional and Morphological Features among Co-Occurring Strains

"Candidatus Accumulibacter" is the major polyphosphate-accumulating organism (PAO) in global wastewater treatment systems, and its phylogenetic and functional diversity have expanded in recent years. In addition to the widely recognized type I and II sublineages, we discovered a novel type enriched in laboratory bioreactors. Core gene and machine learning-based gene feature profiling supported the assertion that type III "Ca. Accumulibacter" is a potential PAO with the unique function of using dimethyl sulfoxide as an electron acceptor. Based on the correlation between ppk1 and genome similarity, the species-level richness of Accumulibacter was estimated to be over 100, suggesting that the currently recognized species are only the tip of the iceberg. Meanwhile, the interstrain transcriptional and morphological features of multiple "Ca. Accumulibacter" strains co-occurring in a bioreactor were investigated. Metatranscriptomics of seven co-occurring strains indicated that the expression level and interphasic dynamics of PAO phenotype-related genes had minimal correlation with their phylogeny. In particular, the expression of denitrifying and polyphosphate (poly-P) metabolism genes exhibited higher interstrain and interphasic divergence than expression of glycogen and polyhydroxyalkanoate metabolic genes. A strategy of cloning rRNA genes from different strains based on similar genomic synteny was successfully applied to differentiate their morphology via fluorescence in situ hybridization. Our study further expands the phylogenetic and functional diversity of "Ca. Accumulibacter" and proposes that deciphering the function and capability of certain "Ca. Accumulibacter" should be tailored to the environment and population in question. IMPORTANCE In the last 2 decades, "Ca. Accumulibacter" has garnered significant attention as the core functional but uncultured taxon for enhanced biological phosphorus removal due to its phylogenetic and functional diversity and intragenus niche differentiation. Since 2002, it has been widely known that this genus has two sublineages (type I and II). However, in this study, a metagenomic approach led to the discovery of a novel type (type III) with proposed novel functional features. By comparing the average nucleotide identity of "Ca. Accumulibacter" genomes and the similarity of ppk1, a phylogenetic biomarker largely deposited in databases, the global species-level richness of "Ca. Accumulibacter" was estimated for the first time to be over 100. Furthermore, we observed the co-occurrence of multiple "Ca. Accumulibacter" strains in a single bioreactor and found the simultaneous transcriptional divergence of these strains intriguing with regard to their niche differentiation within a single community. Our results indicated a decoupling feature between transcriptional pattern and phylogeny for co-occurring strains.

Enhanced Bio-P removal: Past, present, and future - A comprehensive review

Excess amounts of phosphorus (P) and nitrogen (N) from anthropogenic activities such as population growth, municipal and industrial wastewater discharges, agriculture fertilization and storm water runoffs, have affected surface water chemistry, resulting in episodes of eutrophication. Enhanced biological phosphorus removal (EBPR) based treatment processes are an economical and environmentally friendly solution to address the present environmental impacts caused by excess P present in municipal discharges. EBPR practices have been researched and operated for more than five decades worldwide, with promising results in decreasing orthophosphate to acceptable levels. The advent of molecular tools targeting bacterial genomic deoxyribonucleic acid (DNA) has also helped us reveal the identity of potential polyphosphate-accumulating organisms (PAO) and denitrifying PAO (DPAO) responsible for the success of EBPR. Integration of process engineering and environmental microbiology has provided much-needed confidence to the wastewater community for the successful implementation of EBPR practices around the globe. Despite these successes, the process of EBPR continues to evolve in terms of its microbiology and application in light of other biological processes such as anaerobic ammonia oxidation and on-site carbon capture. This review provides an overview of the history of EBPR, discusses different operational parameters critical for the successful operation of EBPR systems, reviews current knowledge of EBPR microbiology, the influence of PAO/DPAO on the disintegration of microbial communities, stoichiometry, EBPR clades, current practices, and upcoming potential innovations.

Phosphorus removal performance, intracellular metabolites and clade-level community structure of Tetrasphaera-dominated polyphosphate accumulating organisms at different temperatures

Tetrasphaera are polyphosphate accumulating organisms (PAOs) that play an important role in enhanced biological phosphorus removal (EBPR) from wastewater. The effect of a wide range of temperature changes (1-30 °C) on phosphorus removal, metabolism and clade-level community structure of Tetrasphaera-dominated PAOs was investigated. At 10 °C, the bioactivities of Tetrasphaera-dominated communities were obviously inhibited and the EBPR efficiency was only 73 %. Yet at 20-30 °C, EBPR efficiency reached 99 % and the relative abundance of Tetrasphaera was up to 90 %. The temperature variation changed the community distribution of Tetrasphaera clades, which was possibly a main reason for EBPR performance. Amino acids and PHA with different contents were intracellular metabolite of Tetrasphaera-dominated communities during phosphorus release and uptake at different temperatures. Moreover, Tetrasphaera fermented protein and amino acids and released VFAs. The outcomes suggested the great potential of Tetrasphaera-PAOs in the treatment of wastewater with varying temperatures and limited carbon sources.

Unveiling organic loading shock-resistant mechanism in a pilot-scale moving bed biofilm reactor-assisted dual-anaerobic-anoxic/oxic system for effective municipal wastewater treatment

Microbial biomass and activity are frequently subjected to organic loading shock (OLS) from decentralized municipal wastewater. A hybrid moving bed biofilm reactor-assisted dual-anaerobic-anoxic/oxic system (D-A²MBBR) was established by integrating dual-anaerobic-anoxic/oxic with moving bed biofilm reactor to resist OLS for stable nutrients removal. The D-A²MBBR achieved 91.57% of chemical oxygen demand, 93.33% of ammonia-nitrogen, 80.20% of total nitrogen and 92.68% of total phosphorus removal, respectively, under the fluctuation of organic loading rate from 417.9 to 812.0 g COD m^-3 d^-1. The 16S rRNA gene sequencing revealed that Gemmobacter (7.28%) was identified as dominating anoxic denitrifying genus in oxic chamber, confirming the coexistence of aerobic and anaerobic/anoxic micro-environments. This circumstance boosted simultaneous nitrification-denitrification and phosphorus removal and the microbial community evolution inside the multilayer biocarrier-attached biofilms. In general, the D-A²MBBR was able to provide unique, cooperative and robust bacterial consortia to form a buffer against OLS, and ensuring effluent stability.

Achieving enhanced biological phosphorus removal utilizing waste activated sludge as sole carbon source and simultaneous sludge reduction in sequencing batch reactor

Achieving enhanced biological phosphorus removal dominated by Tetrasphaera utilizing waste activated sludge (WAS) as carbon source could solve the problems of insufficient carbon source and excessive discharge of WAS in biological phosphorus removal. Up to now, the sludge reduction ability of Tetrasphaera remained largely unknown. Furthermore, the difference between traditional sludge fermentation and sludge fermentation dominated by Tetrasphaera was still unclear. In this study, two different sequencing batch reactors (SBRs) were operated. WAS from SBR-parent was utilized as sole carbon source to enrich Tetrasphaera with the relative abundance of 91.9% in SBR-Tetrasphaera. PO₄^3--P removal and sludge reduction could simultaneously be achieved. The effluent concentration of PO₄^3--P was 0, and the sludge reduction efficiency reached about 44.14% without pretreatment of sludge. Cell integrity detected by flow cytometry, the increase of DNA concentration in the sludge supernatant and decrease of particle size of activated sludge indicated that cell death and lysis occurred in sludge reduction dominated by Tetrasphaera. Stable structure of activated sludge was also damaged in this process, which led to the sludge reduction. By analyzing the excitation-emission matrix spectra of extracellular polymeric substances and the changes of carbohydrate and protein concentration, this study proved that slowly biodegradable organics (e.g., soluble microbial byproduct, tyrosine and tryptophan aromatic protein) could be better hydrolyzed and acidized to volatile fatty acids (VFAs) in sludge fermentation dominated by Tetrasphaera than traditional sludge fermentation, which provided carbon source for biological nutrients removal and saved operation cost in wastewater treatment.

Pairing denitrifying phosphorus accumulating organisms with anaerobic ammonium oxidizing bacteria for simultaneous N and P removal

Coupling of denitrifying polyphosphate accumulating organisms (DPAO) with anaerobic ammonium oxidizing (Anammox) bacteria in a single treatment scheme has so far been unsuccessful but could offer substantial energy savings, minimize sludge production, while achieving simultaneous carbon, nitrogen and phosphate removal. However, both organisms compete for nitrite and have vastly different growth rates and therefore the goal of this study was to uncouple their solid retention time (SRT) by growing them in different sludge fractions and to determine their biomass specific kinetic properties. Anammox bacteria were grown in a biofilm for longer SRTs and DPAO in flocs to allow shorter SRTs. Exposure of DPAO to anaerobic conditions was accomplished by recycling the flocs to a separate reactor by which simultaneous P, N, and C removal was accomplished. The diffusion limited biofilm lowered the biomass specific nitrite affinity for Anammox (K_s^AMX = 0.091 mM), which gave DPAO a competitive edge to consume nitrite (K_s^DPAO = 0.022 mM) in the suspended floc fraction. However, DPAO are more sensitive to nitrite (K_i^DPAO = 0.377 mM) than Anammox bacteria and (K_i^AMX > 1.786 mM), and therefore the DPAO would be better suited to grow in the protective biofilm, showing that both biomass growth types (flocs and granules) have advantages (and disadvantages) depending on the setting. This work is an important steppingstone to understanding resource competition amongst Anammox and DPAO and SRT management strategies to allow their pairing in combined reactor configurations.

Accumulibacter diversity at the sub-clade level impacts enhanced biological phosphorus removal performance

Accumulibacter is a well-known group of organisms, typically considered to be polyphosphate accumulating organisms (PAOs), but potentially capable of glycogen accumulating organism (GAO) metabolism under limiting influent phosphate levels. Metabolic features of Accumulibacter are typically linked to its phylogenetic identity at the Type or clade level, though it is unclear the extent to which Accumulibacter diversity can correlate with its capacity to perform P removal. This paper investigates the fine-scale diversity of Accumulibacter and its link with enhanced biological phosphorus removal (EBPR) performance under various operating conditions, to understand the conditions and community structure leading to successful and unsuccessful EBPR operation. For this purpose, the organic carbon feeding rate and total organic carbon concentration were varied during three distinct operational periods, where influent phosphate was never limiting. Accumulibacter was always the dominant microbial group (>80% of all bacteria according to quantitative fluorescence in situ hybridisation - FISH) and low levels of Competibacter and other GAOs were consistently observed (<15% of all bacteria). Steady state was achieved in each of the three periods, with average phosphorus removal levels of 36%, 99% and >99%, respectively. Experimentally determined stoichiometric activity supported the expression of a mixed PAO/GAO metabolism in the first steady state period and the typical PAO metabolism in the other two steady state periods. FISH quantification and amplicon sequencing of the polyphosphate kinase (ppk1) functional gene indicated that Accumulibacter clade IIC was selected in the first steady state period, which shifted to clade IA after decreasing the carbon feeding rate in steady state period 2, and finally shifted back to clade IIC in the third steady state period. Fine-resolution Ppk-based phylogenetic analysis revealed three different clusters within Accumulibacter clade IIC, where clusters IICii and IICiii were linked to poor EBPR performance in period 1, and cluster IICi was linked to good EBPR performance in period 3. This study shows that the deterioration of EBPR processes through GAO activity at non-limiting P concentrations can be linked to organisms that are typically classified as PAOs, not only to known GAOs such as Competibacter. Intra-clade phylogenetic diversity within Accumulibacter showed that some clusters actually behave similarly to GAOs even without influent phosphate limitation. This study highlights the need to closely re-examine traditional interpretations regarding the link between the microbial community composition and identity with the performance and metabolism of EBPR systems.

Nitrogen species control the interaction between NO3--N reduction and aniline degradation and microbial community structure in the oxic-anoxic transition zone

Contrary to the fact that NO₃^--N can serve as electron acceptor to promote organics degradation, it was also found NO₃^--N reduction does not necessarily promote organics degradation. We speculate nitrogen (N) species may control the interaction between NO₃^--N reduction and organics degradation via shifting related microbial community structure. To prove the hypothesis, oxic-anoxic transition zone (OATZ) microcosms simulated by lake water and sediment were conducted with the addition of N species (NO₃^--N, NO₂^--N, and NH₄⁺-N) and aniline as typical organics. High-throughput sequencing was used to analyze the microbial community structure and functional enzyme in the microcosms. Results show that, NO₂^--N inhibited NO₃^--N reduction while enhanced aniline degradation. For NH₄⁺-N, it promoted NO₃^--N reduction when NH₄⁺-N/NO₃^--N concentration ratio ≤ 2 and inhibited aniline degradation when NH₄⁺-N/aniline concentration ratio ≥ 0.5. The presence of NO₂^--N or NH₄⁺-N weakened the interaction between NO₃^--N reduction and aniline degradation, which might be caused by significant changes in the diversity and abundance of microbial communities controlled by N species. The microbial mechanism indicates that NO₂^--N weakened the interaction by affecting both denitrification enzyme activity and electron transfer capability, while NH₄⁺-N weakened the interaction mainly by affecting electron transfer capability. These results imply that N species, as well as other electron acceptors and donors, in the contaminated OATZ should be fully considered, when performing in situ remediation technology of NO₃^--N reduction.

Effects of substrate stress and light intensity on enhanced biological phosphorus removal in a photo-activated sludge system

Photo-activated sludge (PAS) systems are an emerging wastewater treatment technology where microalgae provide oxygen to bacteria without the need for external aeration. There is limited knowledge on the optimal conditions for enhanced biological phosphorus removal (EBPR) in systems containing a mixture of polyphosphate accumulating organisms (PAOs) and microalgae. This research aimed to study the effects of substrate composition and light intensity on the performance of a laboratory-scale EBPR-PAS system. Initially, a model-based design was developed to study the effect of organic carbon (COD), inorganic carbon (HCO₃) and ammonium-nitrogen (NH₄-N) in nitrification deprived conditions on phosphorus (P) removal. Based on the mathematical model, two different synthetic wastewater compositions (COD:HCO₃:NH₄-N: 10:20:1 and 10:10:4) were examined at a light intensity of 350 µmol m^-2 sec^-1. Add to this, the performance of the system was also investigated at light intensities: 87.5, 175, and 262.5 µmol m^-2 sec^-1 for short terms. Results showed that wastewater having a high level of HCO₃ and low level of NH₄-N (ratio of 10:20:1) favored only microalgal growth, and had poor P removal due to a shortage of NH₄-N for PAOs growth. However, lowering the HCO₃ level and increasing the NH₄-N level (ratio of 10:10:4) balanced PAOs and microalgae symbiosis, and had a positive influence on P removal. Under this mode of operation, the system was able to operate without external aeration and achieved a net P removal of 10.33 ±1.45 mg L^-1 at an influent COD of 100 mg L^-1. No significant variation was observed in the reactor performance for different light intensities, indicating the EBPR-PAS system can be operated at low light intensities with a positive influence on P removal.

Revealing the Metabolic Flexibility of "Candidatus Accumulibacter phosphatis" through Redox Cofactor Analysis and Metabolic Network Modeling

Environmental fluctuations in the availability of nutrients lead to intricate metabolic strategies. "Candidatus Accumulibacter phosphatis," a polyphosphate-accumulating organism (PAO) responsible for enhanced biological phosphorus removal (EBPR) from wastewater treatment systems, is prevalent in aerobic/anaerobic environments. While the overall metabolic traits of these bacteria are well described, the nonavailability of isolates has led to controversial conclusions on the metabolic pathways used. In this study, we experimentally determined the redox cofactor preferences of different oxidoreductases in the central carbon metabolism of a highly enriched "Ca Accumulibacter phosphatis" culture. Remarkably, we observed that the acetoacetyl coenzyme A reductase engaged in polyhydroxyalkanoate (PHA) synthesis is NADH preferring instead of showing the generally assumed NADPH dependency. This allows rethinking of the ecological role of PHA accumulation as a fermentation product under anaerobic conditions and not just a stress response. Based on previously published metaomics data and the results of enzymatic assays, a reduced central carbon metabolic network was constructed and used for simulating different metabolic operating modes. In particular, scenarios with different acetate-to-glycogen consumption ratios were simulated, which demonstrated optima using different combinations of glycolysis, glyoxylate shunt, or branches of the tricarboxylic acid (TCA) cycle. Thus, optimal metabolic flux strategies will depend on the environment (acetate uptake) and on intracellular storage compound availability (polyphosphate/glycogen). This NADH-related metabolic flexibility is enabled by the NADH-driven PHA synthesis. It allows for maintaining metabolic activity under various environmental substrate conditions, with high carbon conservation and lower energetic costs than for NADPH-dependent PHA synthesis. Such (flexible) metabolic redox coupling can explain the competitiveness of PAOs under oxygen-fluctuating environments.IMPORTANCE Here, we demonstrate how microbial storage metabolism can adjust to a wide range of environmental conditions. Such flexibility generates a selective advantage under fluctuating environmental conditions. It can also explain the different observations reported in PAO literature, including the capacity of "Ca Accumulibacter phosphatis" to act like glycogen-accumulating organisms (GAOs). These observations stem from slightly different experimental conditions, and controversy arises only when one assumes that metabolism can operate only in a single mode. Furthermore, we also show how the study of metabolic strategies is possible when combining omics data with functional cofactor assays and modeling. Genomic information can only provide the potential of a microorganism. The environmental context and other complementary approaches are still needed to study and predict the functional expression of such metabolic potential.

Roles of nitrate recycling ratio in the A2/O - MBBR denitrifying phosphorus removal system for high-efficient wastewater treatment: Performance comparison, nutrient mechanism and potential evaluation

The long-term effect of nitrate recycling ratios (R = 100%-500%) on the denitrifying phosphorus removal (DPR) characteristics was studied in a novel two-sludge system, which coupled Anaerobic Anoxic Oxic (A²/O) with Moving Bed Biofilm Reactor (MBBR) for simultaneous nitrogen (N) and phosphorus (P) removals. During the 220 days' operation, effluent COD (30.87-45.15 mg/L) can meet the discharge standard completely, but N and P removals were significantly affected by the R-value, including COD_intra removal efficiency (COD_intra-Re: 56.09-85.98%), TN removal (TN-Re: 52.06-80.50%), anaerobic PO₄^3- release (PO₄^3--An: 10.66-29.02 mg/L) and oxic PO₄^3- absorption (PO₄^3--O: 2.22-6.26 mg/L). Meanwhile, N and P displayed close correlation with the ΔPO₄^3-/ΔNO₃^- ratio of 4.20-4.41 at R = 300%-400%, resulting in the high-efficient anoxic poly-β-hydroxyalkanoates (PHA) utilization (ΔPHA_A: 64.88 mgCOD/gVSS). Based on the stoichiometry methodology, at R of 300%-400%, the percentages of phosphorus accumulation organisms (PAOs) and glycogen accumulating organisms (GAOs) contributed to ΔPHA_An (ΔGly_An) were 71.7%, 28.3% (61.3%, 38.7%) in the anaerobic stage, respectively, while N denitrification rate (NDR_A: 3.91-3.93 mg N/(gVSS·h)) and P uptake rate (PUR_A: 3.76-3.90 mg P/(gVSS·h)) reached the peak, suggesting superior DPR performance with higher contribution of denitrifying PAOs (DPAOs) (70%) than denitrifying GAOs (DGAOs) (30%) in the anoxic stage. Microbial community analysis showed that Accumulibacter (27.66-30.01%) was more enriched than Competibacter (13.41-14.34%) and was responsible for the improved C, N, P removals and DPR characteristics. For optimizing operation, the combined effect of nitrate recycling ratio with other process parameters especially economic evaluation should be considered.

Transcriptional responses of Candidatus Accumulibacter clades to environmental dynamics in enhanced biological phosphorus removal

The dynamic response mechanism of Candidatus Accumulibacter clades to environmental factors in enhanced biological phosphorus removal (EBPR) was unclear. This study investigated the relationship between the transcriptional responses of Candidatus Accumulibacter clades and environmental dynamics. Results suggested that Candidatus Accumulibacter clade IIA only responded in initial 20 and 30 min of P-release and P-uptake stage, respectively, and was also the first clade to stop responding among the six Candidatus Accumulibacter clades. Clade IIC and IID responded at rising stage of P-release and P-uptake rate. Clade IA and IIB responded at decreasing stage of P-release and P-uptake rate. The transcriptional response duration of clade IIF was the longest, which constantly responded throughout anaerobic, anoxic and oxic phase. The transcriptional responses of Candidatus Accumulibacter clades to environmental dynamics revealed the microorganisms actually working in P-release and P-uptake, and gave a new insight into the transcriptional responses related to the EBPR performance.

A novel metabolic-ASM model for full-scale biological nutrient removal systems

This study demonstrates that META-ASM, a new integrated metabolic activated sludge model, provides an overall platform to describe the activity of the key organisms and processes relevant to biological nutrient removal (BNR) systems with a robust single-set of default parameters. This model overcomes various shortcomings of existing enhanced biological phosphorous removal (EBPR) models studied over the last twenty years. The model has been tested against 34 data sets from enriched lab polyphosphate accumulating organism (PAO)-glycogen accumulating organism (GAO) cultures and experiments with full-scale sludge from five water resource recovery facilities (WRRFs) with two different process configurations: three stage Phoredox (A2/O) and adapted Biodenitro™ combined with a return sludge sidestream hydrolysis tank (RSS). Special attention is given to the operational conditions affecting the competition between PAOs and GAOs, capability of PAOs and GAOs to denitrify, metabolic shifts as a function of storage polymer concentrations, as well as the role of these polymers in endogenous processes and fermentation. The overall good correlations obtained between the predicted versus measured EBPR profiles from different data sets support that this new model, which is based on in-depth understanding of EBPR, reduces calibration efforts. On the other hand, the performance comparison between META-ASM and literature models demonstrates that existing literature models require extensive parameter changes and have limited predictive power, especially in the prediction of long-term EBPR performance. The development of such a model able to describe in detail the microbial and chemical transformations of BNR systems with minimal adjustment to parameters suggests that the META-ASM model is a powerful tool to predict and mitigate EBPR upsets, optimise EBPR performance and to evaluate new process designs.

Performance and population structure of two carbon sources granular enhanced biological phosphorus removal systems at low temperature

This study explored the effect of two carbon sources on performance and population structure of granular enhanced biological phosphorus removal systems at long-term low temperature by using two sequencing batch reactors, with acetate (SBR-1) and propionate (SBR-2) as carbon sources respectively. Results showed that highly efficient EBPR were successfully achieved, and the average PO₄^3--P and COD removal efficiency of SBR-1 and SBR-2 were 94.2%, 87.1% and 98.2%, 87.0%, respectively. Moreover, the acetate system preferred to utilize intracellular Mg/K-polyP to produce ATP for VFA uptake rather than glycogen. High-throughput sequencing analysis revealed that the abundance of Rhodocyclaceae were 31.7% (SBR-1) and 71.7% (SBR-2), and genus Dechloromonas was enriched to 60.5% with propionate, evidently higher than acetate (1.2%). Furthermore, in addition to oxygen, Dechloromonas could use nitrate as electron acceptors for phosphate uptake. The study further provides support to simultaneous nitrogen and phosphorus removal at low temperature.

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

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

"Candidatus Accumulibacter delftensis": A clade IC novel polyphosphate-accumulating organism without denitrifying activity on nitrate

Populations of "Candidatus Accumulibacter", a known polyphosphate-accumulating organism, within clade IC have been proposed to perform anoxic P-uptake activity in enhanced biological phosphorus removal (EBPR) systems using nitrate as electron acceptor. However, no consensus has been reached on the ability of "Ca. Accumulibacter" members of clade IC to reduce nitrate to nitrite. Discrepancies might relate to the diverse operational conditions which could trigger the expression of the Nap and/or Nar enzyme and/or to the accuracy in clade classification. This study aimed to assess whether and how certain operational conditions could lead to the enrichment and enhance the denitrification capacity of "Ca. Accumulibacter" within clade IC. To study the potential induction of the denitrifying enzyme, an EBPR culture was enriched under anaerobic-anoxic-oxic (A2O) conditions that, based on fluorescence in situ hybridization and ppk gene sequencing, was composed of around 97% (on a biovolume basis) of affiliates of "Ca. Accumulibacter" clade IC. The influence of the medium composition, sludge retention time (SRT), polyphosphate content of the biomass (poly-P), nitrate dosing approach, and minimal aerobic SRT on potential nitrate reduction were studied. Despite the different studied conditions applied, only a negligible anoxic P-uptake rate was observed, equivalent to maximum 13% of the aerobic P-uptake rate. An increase in the anoxic SRT at the expenses of the aerobic SRT resulted in deterioration of P-removal with limited aerobic P-uptake and insufficient acetate uptake in the anaerobic phase. A near-complete genome (completeness = 100%, contamination = 0.187%) was extracted from the metagenome of the EBPR biomass for the here-proposed "Ca. Accumulibacter delftensis" clade IC. According to full-genome-based phylogenetic analysis, this lineage was distant from the canonical "Ca. Accumulibacter phosphatis", with closest neighbor "Ca. Accumulibacter sp. UW-LDO-IC" within clade IC. This was cross-validated with taxonomic classification of the ppk1 gene sequences. The genome-centric metagenomic analysis highlighted the presence of genes for assimilatory nitrate reductase (nas) and periplasmic nitrate reductase (nap) but no gene for respiratory nitrate reductases (nar). This suggests that "Ca. Accumulibacter delftensis" clade IC was not capable to generate the required energy (ATP) from nitrate under strict anaerobic-anoxic conditions to support an anoxic EBPR metabolism. Definitely, this study stresses the incongruence in denitrification abilities of "Ca. Accumulibacter" clades and reflects the true intra-clade diversity, which requires a thorough investigation within this lineage.

Mining traits for the enrichment and isolation of not-yet-cultured populations

BACKGROUND

The lack of pure cultures limits our understanding into 99% of bacteria. Proper interpretation of the genetic and the transcriptional datasets can reveal clues for the enrichment and even isolation of the not-yet-cultured populations. Unraveling such information requires a proper mining method.

RESULTS

Here, we present a method to infer the hidden traits for the enrichment of not-yet-cultured populations. We demonstrate this method using Candidatus Accumulibacter. Our method constructs a whole picture of the carbon, electron, and energy flows in the not-yet-cultured populations from the genomic datasets. Then, it decodes the coordination across three flows from the transcriptional datasets. Based on it, our method diagnoses the status of the not-yet-cultured populations and provides strategy to optimize the enrichment systems.

CONCLUSION

Our method could shed light to the exploration into the bacterial dark matter in the environments.

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.

Effect of Lactate on the Microbial Community and Process Performance of an EBPR System

Candidatus Accumulibacter phosphatis is in general presented as the dominant organism responsible for the biological removal of phosphorus in activated sludge wastewater treatment plants. Lab-scale enhanced biological phosphorus removal (EBPR) studies, usually use acetate as carbon source. However, the complexity of the carbon sources present in wastewater could allow other potential poly-phosphate accumulating organism (PAOs), such as putative fermentative PAOs (e.g., Tetrasphaera), to proliferate in coexistence or competition with Ca. Accumulibacter. This research assessed the effects of lactate on microbial selection and process performance of an EBPR lab-scale study. The addition of lactate resulted in the coexistence of Ca. Accumulibacter and Tetrasphaera in a single EBPR reactor. An increase in anaerobic glycogen consumption from 1.17 to 2.96 C-mol/L and anaerobic PHV formation from 0.44 to 0.87 PHV/PHA C-mol/C-mol corresponded to the increase in the influent lactate concentration. The dominant metabolism shifted from a polyphosphate-accumulating metabolism (PAM) to a glycogen accumulating metabolism (GAM) without EBPR activity. However, despite the GAM, traditional glycogen accumulating organisms (GAOs; Candidatus Competibacter phosphatis and Defluvicoccus) were not detected. Instead, the 16s RNA amplicon analysis showed that the genera Tetrasphaera was the dominant organism, while a quantification based on FISH-biovolume indicated that Ca. Accumulibacter remained the dominant organism, indicating certain discrepancies between these microbial analytical methods. Despite the discrepancies between these microbial analytical methods, neither Ca. Accumulibacter nor Tetrasphaera performed biological phosphorus removal by utilizing lactate as carbon source.

Integrated Omic Analyses Provide Evidence that a "Candidatus Accumulibacter phosphatis" Strain Performs Denitrification under Microaerobic Conditions

The ability of "Candidatus Accumulibacter phosphatis" to grow and remove phosphorus from wastewater under cycling anaerobic and aerobic conditions has also been investigated as a metabolism that could lead to simultaneous removal of nitrogen and phosphorus by a single organism. However, although phosphorus removal under cyclic anaerobic and anoxic conditions has been demonstrated, clarifying the role of "Ca. Accumulibacter phosphatis" in this process has been challenging, since (i) experimental research describes contradictory findings, (ii) none of the published "Ca. Accumulibacter phosphatis" genomes show the existence of a complete respiratory pathway for denitrification, and (iii) some genomes lacking a complete respiratory pathway have genes for assimilatory nitrate reduction. In this study, we used an integrated omics analysis to elucidate the physiology of a "Ca. Accumulibacter phosphatis" strain enriched in a reactor operated under cyclic anaerobic and microaerobic conditions. The reactor's performance suggested the ability of the enriched "Ca. Accumulibacter phosphatis" strain (clade IC) to simultaneously use oxygen and nitrate as electron acceptors under microaerobic conditions. A draft genome of this organism was assembled from metagenomic reads ("Ca. Accumulibacter phosphatis" UW-LDO-IC) and used as a reference to examine transcript abundance throughout one reactor cycle. The genome of UW-LDO-IC revealed the presence of a full pathway for respiratory denitrification. The observed transcript abundance patterns showed evidence of coregulation of the denitrifying genes along with a cbb ₃ cytochrome, which has been characterized as having high affinity for oxygen. Furthermore, we identified an FNR-like binding motif upstream of the coregulated genes, suggesting transcription-level regulation of both denitrifying and respiratory pathways in UW-LDO-IC. Taking the results together, the omics analysis provides strong evidence that "Ca. Accumulibacter phosphatis" UW-LDO-IC uses oxygen and nitrate simultaneously as electron acceptors under microaerobic conditions. IMPORTANCE "Candidatus Accumulibacter phosphatis" is widely found in full-scale wastewater treatment plants, where it has been identified as the key organism for biological removal of phosphorus. Since aeration can account for 50% of the energy use during wastewater treatment, microaerobic conditions for wastewater treatment have emerged as a cost-effective alternative to conventional biological nutrient removal processes. Our report provides strong genomics-based evidence not only that "Ca. Accumulibacter phosphatis" is the main organism contributing to phosphorus removal under microaerobic conditions but also that this organism simultaneously respires nitrate and oxygen in this environment, consequently removing nitrogen and phosphorus from the wastewater. Such activity could be harnessed in innovative designs for cost-effective and energy-efficient optimization of wastewater treatment systems.

Color and nitrogen removal from synthetic dye wastewater in an integrated mesophilic hydrolysis/acidification and multiple anoxic/aerobic process

Dye wastewater is one kind of refractory pollutant and it is commonly treated by the integrated anaerobic and aerobic process. A new integrated hydrolysis/acidification and multiple anoxic/aerobic (AO) process was proposed for the removal of color and nitrogen from azo dye wastewater. System performance, the degradation pathway of azo dye and nitrogen metabolic pathway were investigated with quadrupole-time-of-flight and metagenomic analyses. The proposed process removed color and nitrogen efficiently, with the removal percentages of 89.4% and 54.0%, respectively. A colorful intermediate C₁₆H₁₁N₃O₇S₂ during the degradation of azo dye was detected. Controlling a low dissolved oxygen concentration in the multiple AO process could enhance nitrogen removal. The detected bacteria possessing azoreductase for the azo dye degradation included Desulfovibrio aminophilus, Thermoanaerobacter, Lactococcus raffinolactis, Ruminiclostridium and Rhodopirellula. The nitrifying genes of amo and hao were mainly detected in Nitrosomonas, while the denitrifying genes were detected in Thauera, Candidatus Accumulibacter and Rhodothermus marinus.

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.

Hybrid organic-inorganic anion-exchange pore-filled membranes for the recovery of nitric acid from highly acidic aqueous waste streams

Recycling of acid from aqueous waste streams is highly important not only from the environmental point of view but also for developing the sustainable technology. One of the effective ways to recover acid from aqueous waste streams is the anion-exchange membrane based diffusion-dialysis. The work presents the synthesis and characterization of anion-exchange pore-filled membranes for the objective of recovery of high concentration of acid by diffusion dialysis. The membranes were prepared by anchoring the guest organic-inorganic anionic gel in the pores of the host poly(propylene) membrane by in situ UV-initiator induced polymerization of the appropriate monomers along with cross-linker. The removal of nitric acid in the presence of different representative monovalent, divalent and trivalent nitrates and the leakage of these ions through anion exchange membrane have been studied by DD technique for optimizing the chemical composition of the membrane. The nitric acid permeation rate of the membrane with the optimized composition has been found to be considerably faster than the commercial Selemion membrane without sacrificing salt leakage. The performance of the optimized pore-filled anion exchange membranes has been found to be independent of the acid concentration, nature of the anion and substrate and has been observed to be solely dependent on the guest inorganic-organic hybrid anionic gel component. The membranes have been found to be stable and reusable for the acid recovery. Removal of nitric acid as high as 90% from the simulated high level nuclear waste with the optimized grafted pore-filled membrane has been achieved with negligible salt transport.

Cooperation between Candidatus Competibacter and Candidatus Accumulibacter clade I, in denitrification and phosphate removal processes

Although simultaneous P-removal and nitrate reduction has been observed in laboratory studies as well as full-scale plants, there are contradictory reports on the ability of PAO I to efficiently use nitrate as electron acceptor. Such discrepancy could be due to other microbial groups performing partial denitrification from nitrate to nitrite. The denitrification capacities of two different cultures, a highly enriched PAO I and a PAO I-GAO cultures were assessed through batch activity tests conducted before and after acclimatization to nitrate. Negligible anoxic phosphate uptake coupled with a reduction of nitrate was observed in the highly enriched PAO I culture. On the opposite, the PAO I-GAO culture showed a higher anoxic phosphate uptake activity. Both cultures exhibited good anoxic phosphate uptake activity with nitrite (8.7 ± 0.3 and 9.6 ± 1.8 mgPO₄-P/gVSS.h in the PAO I and PAO I-GAO cultures, respectively). These findings suggest that other microbial populations, such as GAOs, were responsible to reduce nitrate to nitrite in this EBPR system, and that PAO I used the nitrite generated for anoxic phosphate uptake. Moreover, the simultaneous denitrification and phosphate removal process using nitrite as electron acceptor may be a more sustainable process as can: i) reduce the carbon consumption, ii) reduce oxygen demand of WWTP, and iii) due to a lower growth yield contribute to a lower sludge production.

Long-term effects of sulphide on the enhanced biological removal of phosphorus: The symbiotic role of Thiothrix caldifontis

Thiothrix caldifontis was the dominant microorganism (with an estimated bio-volume of 65 ± 3%) in a lab-scale enhanced biological phosphorus removal (EBPR) system containing 100 mg of sulphide per litre in the influent. After a gradual exposure to the presence of sulphide, the EBPR system initially dominated by Candidatus Accumulibacter phosphatis Clade I (98 ± 3% bio-volume) (a known polyphosphate accumulating organism, PAO) became enriched with T. caldifontis. Throughout the different operating conditions studied, practically 100% phosphate removal was always achieved. The gradual increase of the sulphide content in the medium (added to the anaerobic stage of the alternating anaerobic-aerobic sequencing batch reactor) and the adjustment of the aerobic hydraulic retention time played a major role in the enrichment of T. caldifontis. T. caldifontis exhibited a mixotrophic metabolism by storing carbon anaerobically as poly-β-hydroxy-alkanoates (PHA) and generating the required energy through the hydrolysis of polyphosphate. PHA was used in the aerobic period as carbon and energy source for growth, polyphosphate, and glycogen formation. Apparently, extra energy was obtained by the initial accumulation of sulphide as an intracellular sulphur, followed by its gradual oxidation to sulphate. The culture enriched with T. caldifontis was able to store approximately 100 mg P/g VSS. This research suggests that T. caldifontis could behave like PAO with a mixotrophic metabolism for phosphorus removal using an intracellular sulphur pool as energy source. These findings can be of major interest for the biological removal of phosphorus from wastewaters with low organic carbon concentrations containing reduced S-compounds like those (pre-)treated in anaerobic systems or from anaerobic sewers.