Involvement of Rhodocyclus-related organisms in phosphorus removal in full-scale wastewater treatment plants

Refinement of the "Candidatus Accumulibacter" genus based on metagenomic analysis of biological nutrient removal (BNR) pilot-scale plants operated with reduced aeration

Members of the "Candidatus Accumulibacter" genus are widely studied as key polyphosphate-accumulating organisms (PAOs) in biological nutrient removal (BNR) facilities performing enhanced biological phosphorus removal (EBPR). This diverse lineage includes 18 "Ca. Accumulibacter" species, which have been proposed based on the phylogenetic divergence of the polyphosphate kinase 1 (ppk1) gene and genome-scale comparisons of metagenome-assembled genomes (MAGs). Phylogenetic classification based on the 16S rRNA genetic marker has been difficult to attain because most "Ca. Accumulibacter" MAGs are incomplete and often do not include the rRNA operon. Here, we investigate the "Ca. Accumulibacter" diversity in pilot-scale treatment trains performing BNR under low dissolved oxygen (DO) conditions using genome-resolved metagenomics. Using long-read sequencing, we recovered medium- and high-quality MAGs for 5 of the 18 "Ca. Accumulibacter" species, all with rRNA operons assembled, which allowed a reassessment of the 16S rRNA-based phylogeny of this genus and an analysis of phylogeny based on the 23S rRNA gene. In addition, we recovered a cluster of MAGs that based on 16S rRNA, 23S rRNA, ppk1, and genome-scale phylogenetic analyses do not belong to any of the currently recognized "Ca. Accumulibacter" species for which we propose the new species designation "Ca. Accumulibacter jenkinsii" sp. nov. Relative abundance evaluations of the genus across all pilot plant operations revealed that regardless of the operational mode, "Ca. A. necessarius" and "Ca. A. propinquus" accounted for more than 40% of the "Ca. Accumulibacter" community, whereas the newly proposed "Ca. A. jenkinsii" accounted for about 5% of the "Ca. Accumulibacter" community.IMPORTANCEOne of the main drivers of energy use and operational costs in activated sludge processes is the amount of oxygen provided to enable biological phosphorus and nitrogen removal. Wastewater treatment facilities are increasingly considering reduced aeration to decrease energy consumption, and whereas successful BNR has been demonstrated in systems with minimal aeration, an adequate understanding of the microbial communities that facilitate nutrient removal under these conditions is still lacking. In this study, we used genome-resolved metagenomics to evaluate the diversity of the "Candidatus Accumulibacter" genus in pilot-scale plants operating with minimal aeration. We identified the "Ca. Accumulibacter" species enriched under these conditions, including one novel species for which we propose "Ca. Accumulibacter jenkinsii" sp. nov. as its designation. Furthermore, the MAGs obtained for five additional "Ca. Accumulibacter" species further refine the phylogeny of the "Ca. Accumulibacter" genus and provide new insight into its diversity within unconventional biological nutrient removal systems.

The effects of per- and polyfluoroalkyl substances on environmental and human microorganisms and their potential for bioremediation

Utilised in a variety of consumer products, per- and polyfluoroalkyl substances (PFAS) are major environmental contaminants that accumulate in living organisms due to their highly hydrophobic, lipophobic, heat-resistant, and non-biodegradable properties. This review summarizes their effects on microbial populations in soils, aquatic and biogeochemical systems, and the human microbiome. Specific microbes are insensitive to and even thrive with PFAS contamination, such as Escherichia coli and the Proteobacteria in soil and aquatic environments, while some bacterial species, such as Actinobacteria and Chloroflexi, are sensitive and drop in population. Some bacterial species, in turn, have shown success in PFAS bioremediation, such as Acidimicrobium sp. and Pseudomonas parafulva.

Light and oxygen facilitating the directly treatment food wastewater and poly-β-hydroxybutyrate, 5-aminolevulinic acid, pigment productions by Rubrivivax gelatinosus

Rubrivivax gelatinosus has the advantage of using wastewater to realize biomass recovery. However, they still cannot be applied large scale because they cannot directly treat the wastewater containing macromolecular organics. Thus, this article investigated the effects of light-oxygen conditions on R. gelatinosus by directly recycling wastewater containing macromolecular organics to produce biomass, poly-β-hydroxybutyrate (PHB), 5-aminolevulinic acid (5-ALA), and pigment. Results showed that R. gelatinosus directly treated the macromolecule organic (soybean protein and starch) wastewaters and achieved biomass recovery under light-anaerobic and light-micro-oxygen in six conditions. Chemical oxygen demand, protein, and starch removals for two wastewaters all reached above 70%. Renewable bio-resources such as biomass, PHB, 5-ALA, and pigment production were 10 times the initial content. Theoretical analysis indicated that light activated the synthesis of protease and amylase. However, oxygen concentration decided the number of enzymes. When oxygen was at micro-oxygen or anaerobic, the aforementioned expression and synthesis were conducted. In summary, this study expanded the viewpoint ignored by traditional theory. It was realized that R. gelatinosus directly treated wastewater and accumulated nutrients (biomass, PHB, pigment, and 5-ALA) for recycling, which reduced the secondary pollution of excess sludge into the environment.

Biogas production and nutrients removal from slaughterhouse wastewater using integrated anaerobic and aerobic granular intermittent SBRs - Bioreactors stability and microbial dynamics

Slaughterhouse wastewater (SWW) was effectively treated in sequential anaerobic and aerobic granular intermittent sequencing batch reactors (ASBR+ISBR) for 665 days at different HRTs (48 h, 32 h, 24 h, and 12 h). The ASBR was stable at each HRT but performed relatively well at 12 h (OLR - 7.8-9.8 kg COD/m³-d) in terms of pollutants removal and biogas production than previously conducted research. The average biogas production was about 17.3 L/day having 70-76 % of CH₄ which could subsidize around 52 % of electricity demand while saving 103 US dollars/day if installed at full scale. In the case of post aerobic granular ISBR, carbon and nutrients removal (N&P) was achieved by enriching granules (1.7-2.2 mm) at low DO (0.5-0.8 mg/L) via the nitrite pathway. The ISBR was also well stable at 12 h HRT (average OLR of 2.1 kg COD/m³-d) and met the effluent discharge guidelines recommended by the Central Pollution Control Board of India. During steady-state conditions (12 h HRT), the average removal efficiencies for COD, TSS, O&G, TN, and PO₄-P were 98.8 %, 96.4 %, 98.7 %, 93.4 %, and 86.6 % respectively from combined ASBR and ISBR. The microbial analysis confirmed Euryarchaeota, Proteobacteria, Firmicutes, Chloroflexi, Bacteroidetes, Planctomycetes, and Synergistetes as the dominant phyla in ASBR. Methanosaeta (21.56 %) and Methanosarcina (6.48 %) were the prevailing methanogens for CH₄ production. The leading phyla observed in ISBR were Bacteroidetes, Proteobacteria, Firmicutes, Armatimonadetes, Verrucomicrobia, Chloroflexi, and Planctomycetes. Heterotrophic AOB (Thauera, Xanthomonadaceae, Pseudomonas, Sphingomonadaceae, and Rhodococcus) were mainly detected in the system for ammonia oxidation besides common autotrophic AOB. Similarly, a known PAO (Accumulibacter) was not identified but other PAO (Rhodocyclaceae, Dechloromonas, Pseudomonas, Flavobacteriaceae, and Sphingobacteriaceae) were prevalent inside aerobic granular ISBR that contributed to both carbon and nutrients removal. The results obtained would help implement the investigated reactor configurations at the pilot and full scale for SWW treatment.

Removal of per- and poly-fluoroalkyl substances (PFASs) by wetlands: Prospects on plants, microbes and the interplay

Per- and polyfluoroalkyl substances (PFASs) represent a large family of synthetic organofluorine aliphatic compounds. They have been extensively produced since 1940s due to enormous applications as a surface-active agent, and water and oil repellent characteristics. PFASs are made to be non-biodegradable, therefore, many of them have been found in the environment albeit strict regulations have been in place since 2002. PFASs are extremely toxic compounds that can impart harm in both fauna and flora. Recent investigations have shown that wetlands might be useful for their removal from the environment as a passive and nature-based solution. To this end, understanding the role of plants, microbes, and their combined plant-microbe interplay is crucial because it could help design a sophisticated passive treatment wetland system. This review focuses on how these components (plants, microbe, substrate) can influence PFASs removal in wetlands under natural and controlled conditions. The information on underlying removal mechanisms is mostly retrieved from laboratory-based studies; however, pilot- and field-scale data are also presented to provide insights on their real-time performance. Briefly, a traditional wetland system works on the principles of phytouptake, bioaccumulation, and sorption, which are mainly due to the fact that PFASs are synthetic compounds that have very low reactivity in the environment. Nevertheless, recent investigations have also shown that Feammox process in wetlands can mineralize the PFASs; thus, opens new opportunities for PFASs degradation in terms of effective plant-microbe interplay in the wetlands. The choice of plants and bacterial species is however crucial, and the system efficiency relies on species-specific, sediment-specific and pollutant-specific principles. More research is encouraged to identify genetic elements and molecular mechanisms that can help us harness effective plant-microbe interplay in wetlands for the successful removal of PFASs from the environment.

Production of nonulosonic acids in the extracellular polymeric substances of "Candidatus Accumulibacter phosphatis"

Nonulosonic acids (NulOs) are a family of acidic carbohydrates with a nine-carbon backbone, which include different related structures, such as sialic acids. They have mainly been studied for their relevance in animal cells and pathogenic bacteria. Recently, sialic acids have been discovered as an important compound in the extracellular matrix of virtually all microbial life and in "Candidatus Accumulibacter phosphatis", a well-studied polyphosphate-accumulating organism, in particular. Here, bioaggregates highly enriched with these bacteria (approx. 95% based on proteomic data) were used to study the production of NulOs in an enrichment of this microorganism. Fluorescence lectin-binding analysis, enzymatic quantification, and mass spectrometry were used to analyze the different NulOs present, showing a wide distribution and variety of these carbohydrates, such as sialic acids and bacterial NulOs, in the bioaggregates. Phylogenetic analysis confirmed the potential of "Ca. Accumulibacter" to produce different types of NulOs. Proteomic analysis showed the ability of "Ca. Accumulibacter" to reutilize and reincorporate these carbohydrates. This investigation points out the importance of diverse NulOs in non-pathogenic bacteria, which are normally overlooked. Sialic acids and other NulOs should be further investigated for their role in the ecology of "Ca. Accumulibacter" in particular, and biofilms in general. KEY POINTS: •"Ca. Accumulibacter" has the potential to produce a range of nonulosonic acids. •Mass spectrometry and lectin binding can reveal the presence and location of nonulosonic acids. •The role of nonulosonic acid in non-pathogenic bacteria needs to be studied in detail.

Phenotypic dynamics in polyphosphate and glycogen accumulating organisms in response to varying influent C/P ratios in EBPR systems

This study employed molecular tools and single cell Raman micro-spectroscopy techniques to reveal the single cell- and population-level phenotypic dynamics and changes in functionally relevant organisms, namely polyphosphate accumulating organisms (PAOs) and glycogen accumulating organisms (GAOs), in response to influent loading readily biodegradable carbon to phosphorus ratio (C/P) changes in enhanced biological phosphorus removal (EBPR) systems. The results, for the first time, provided direct and cellular evidence confirming the adaptive anaerobic metabolic pathway shifts in PAOs in response to influent loading variations. Increase in influent readily biodegradable carbon to phosphorus (C/P) ratio from 20 to 50 led to nearly 50% decline in polyphosphate content and drastic rise of intracellular polyβhydroxybutyrate (PHB) to polyphosphate (polyP) ratio by nearly 6 times in PAOs, indicating corresponding diminishing reliance on polyP hydrolysis for energy as P becomes limiting. Influent carbon availability surge also impacted the intracellular carbon polymers in GAOs, with significant increase in the mean PHB content level but no observed changes in the intracellular glycogen level. Furthermore, the Raman-based quantification of differentiated intracellular polymer content associated with PAOs and GAOs, revealed new insights into the quantitative shift in intracellular carbon storage distribution between the two populations and their variations between the two carbon polymers (PHB, Glycogen). In summary, this investigation revealed high-resolution cellular level information regarding the metabolic flexibility in PAOs, phenotypic stoichiometry changes and carbon flux and distribution among PAOs and GAOs, in response to influent loading conditions. The new information will contribute to improvement in mechanistic EBPR modeling and design.

Survey of full-scale sidestream enhanced biological phosphorus removal (S2EBPR) systems and comparison with conventional EBPRs in North America: Process stability, kinetics, and microbial populations

Sidestream EBPR (S2EBPR) is an emerging alternative process to address common challenges in EBPR related to weak wastewater influent and may improve EBPR process stability. A systematic evaluation and comparison of the process performance and microbial community structure was conducted between conventional and S2EBPR facilities in North America. The statistical analysis suggested higher performance stability in S2EBPR than conventional EBPR, although possible bias associated with other plant-specific factors might have affected the comparison. Variations in stoichiometric values related to EBPR activity and discrepancies between the observed values and current model predictions suggested a varying degree of metabolic versatility of PAOs in S2EBPR systems that warrant further investigation. Microbial community analysis using various techniques suggested comparable known candidate PAO relative abundances in S2EBPR and conventional EBPR systems, whereas the relative abundance of known candidate GAOs seemed to be consistently lower in S2EBPR facilities than conventional EBPR facilities. 16S rRNA gene sequencing analysis revealed differences in the community phylogenetic fingerprints between S2EBPR and conventional facilities and indicated statistically higher microbial diversity index values in S2EBPR facilities than those in conventional EBPRs. PRACTITIONER POINTS: Sidestream EBPR (S2EBPR) can be implemented with varying and flexible configurations, and they offer advantages over conventional configurations for addressing the common challenges in EBPR related to weak wastewater influent and may improve EBPR process stability. Survey of S2EBPR plants in North America suggested statistically more stable phosphorus removal performance in S2EBPR plants than conventional EBPRs, although possible bias might affect the comparison due to other plant-specific factors. The EBPR kinetics and stoichiometry of the S2EBPR facilities seemed to vary and are associated with metabolic versatility of PAOs in S2EBPR systems that warrant further investigation. The abundance of known candidate PAOs in S2EBPR plants was similar to those in conventional EBPRs, and the abundance of known candidate GAOs was generally lower in S2EBPR than conventional EBPR facilities. Further finer-resolution analysis of PAOs and GAOs, as well as identification of other unknown PAOs and GAOs, is needed. Microbial diversity is higher in S2EBPR facilities compared with conventional ones, implying that S2EBPR microbial communities could show better resilience to perturbations due to potential functional redundancy.

Impact of solid residence time (SRT) on functionally relevant microbial populations and performance in full-scale enhanced biological phosphorus removal (EBPR) systems

Investigations of the impact of solid residence time (SRT) on microbial ecology and performance of enhanced biological phosphorus removal (EBPR) process in full-scale systems have been scarce due to the challenges in isolating and examining the SRT from other complex plant-specific factors. This study performed a comprehensive evaluation of the influence of SRT on polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs) dynamics and on P removal performance at Clark County Water Reclamation District Facility in Las Vegas, USA. Five parallel treatment trains with separated clarifiers were operated with five different SRTs ranging from 6 to 40 days. Microbial community analysis using multiple molecular and Raman techniques suggested that the relative abundances and diversity of PAOs and GAOs in EBPR systems are highly affected by the SRT. The resultant EBPR system stability and performance can be potentially controlled and optimized by manipulating the system SRT, and shorter SRT (<10 days) seems to be preferred. PRACTITIONER POINTS: Phosphorus removal performance and kinetics are highly affected by the operational solid residence time (SRT), with lower and more stable effluent P level achieved at SRT < 10 days. Excessive long SRTs above that needed for nitrification may harm EBPR performance; additionally, excessive long SRT may favor GAOs to dominate over PAOs and thus further reducing efficient use of rbCOD for EBPR. Microbial population abundance and diversity, especially those functionally relevant PAOs and GAOs, can impact the P removal performances, and they are highly dependent on the operational solid residence time. EBPR performance can be potentially controlled and optimized by manipulating the system SRT, and shorter SRT (≤10 days) seems to be preferred at the influent rbCOD/P ratio and environmental conditions as in the plant studied.

Distribution of perfluoroalkyl substances (PFASs) in aquatic plant-based systems: From soil adsorption and plant uptake to effects on microbial community

This study systematically explored the distribution of perfluoroalkyl substances (PFASs) through soil adsorption and plant bioaccumulation in aquatic plant-based systems, derived from a surface flow constructed wetland (CW) planted with Typha angustifolia. The water-soil-plant systems were fortified with eight perfluoroalkyl subsntances (PFASs) at different concentrations. The potential for individual PFAS adsorption onto soil substrate and bioaccumulation in the plants increased with the increasing PFAS initial concentrations. Longer-chain PFASs exhibited higher affinity to soil substrate compared to shorter-chain PFASs. The highest concentration in the soil was observed for PFOS (51.3 ng g^-1), followed by PFHxS (9.39 ng g^-1), and PFOA (5.53 ng g^-1) at low PFAS level. The perfluoroalkyl chain length dependent trend was also seen in the roots with the highest individual PFAS concentration for PFOS (68.9 ng g^-1), followed by PFOA (18.5 ng g^-1) and PFHxS (13.4 ng g^-1). By contrast, shorter-chain PFASs were preferentially translocated from roots to shoots in Typha angustifolia. A significant (p < 0.05) positive correlation between bioaccumulation factor (BAF_plant/water) (whole plant) and perfluoroalkyl chain length was observed. PFASs content in the plant compartments increased with increasing PFAS concentrations in the soil. Mass balance analysis indicates that approximately 40.7-99.6% of PFAS mass added to the system was adsorbed onto the soil and bioaccumulated in the plant tissues of T. angustifolia. Soil adsorption played a vital role in PFAS mass distribution. The results of Illumina high-throughput sequencing show that the bacterial diversity decreased upon PFAS exposure. The most predominant phyla retrieved were Proteobacteria (24.7-39.3%), followed by Actinobacteria (4.2-41.1%), Verrucomicrobia (7.9-25.1%), Bacteroidetes (10.2-20.4%), Cyanobacteria (0.4-16.5%), and Firmicutes (1.1-6.4%). The PFAS enrichment caused the changes (p > 0.05) in the structure and composition of bacterial community. This study helps to gain insight into a better understanding of the potential for PFASs distribution in an aquatic plant-based system and the impact on dynamic of microbial community exposed to PFASs.

Density-Based Separation of Microbial Functional Groups in Activated Sludge

Mechanistic understanding of how activated sludge (AS) solids density influences wastewater treatment processing is limited. Because microbial groups often generate and store intracellular inclusions during certain metabolic processes, it is hypothesized that some microorganisms, like polyphosphate-accumulating organisms (PAOs), would have higher biomass densities. The present study developed a density-based separation approach and applied it to suspended growth AS in two full-scale domestic water resource recovery facilities (WRRFs). Incorporating quantitative real-time PCR (qPCR) and fluorescence in situ hybridization (FISH) analyses, the research demonstrated the effectiveness of density-based separation in enriching key microbial functional groups, including ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB) and PAOs, by up to 90-fold in target biomass fractions. It was observed that WRRF process functionalities have significant influence on density-based enrichment, such that maximum enrichments were achieved in the sludge fraction denser than 1.036 g/cm³ for the enhanced biological phosphorus removal (EBPR) facility and in the sludge fraction lighter than 1.030 g/cm³ for the non-EBPR facility. Our results provide important information on the relationship between biomass density and enrichment of microbial functional groups in AS, contributing to future designs of enhanced biological treatment processes for improved AS settleability and performance.

Side-stream enhanced biological phosphorus removal (S2EBPR) process improves system performance - A full-scale comparative study

To address the common challenges in enhanced biological phosphorus removal (EBPR) related to stability and unfavorable influent carbon to phosphorus ratio, a side-stream EBPR (S2EBPR) process that involves a side-stream anaerobic biological sludge hydrolysis and fermentation reactor was proposed as an emerging alternative. In this study, a full-scale pilot testing was performed with side-by-side operation of a conventional anaerobic-anoxic-aerobic (A2O) process versus a S2EBPR process. A comparison of the performance, activity and microbial community between the two configurations was performed. The results demonstrated that, with the same influent wastewater characteristics, S2EBPR configuration showed improved P removal performance and stability than the conventional A2O configuration, especially when the mixers in the side-stream anaerobic reactor were operated intermittently. Mass balance analysis illustrated that both denitrification and EBPR were enhanced in S2EBPR configuration, where return activated sludge was diverted into the anaerobic zone to promote fermentation and enrichment of polyphosphate accumulating organisms (PAOs), and the influent was bypassed to the anoxic zone for enhancing denitrification. A relatively higher PAO activity and total PAO abundance were observed in S2EBPR than in A2O configuration, accompanied by a higher degree of dependence on glycolysis pathway than tricarboxylic acid cycle. No significant difference in the relative abundances of putative PAOs, including Ca. Accumulibacter and Tetrasphaera, were observed between the two configurations. However, higher microbial community diversity indices were observed in S2EBPR configuration than in conventional one. In addition, consistently lower relative abundance of known glycogen accumulating organisms (GAOs) was observed in S2EBPR system. Extended anaerobic retention time and conditions that generate continuous and more complex volatile fatty acids in the side-stream anaerobic reactor of S2EBPR process likely give more competitive advantage for PAOs over GAOs. PAOs exhibited sustained EBPR activity and delayed decay under extended anaerobic condition, likely due to their versatile metabolic pathways depending on the availability and utilization of multiple intracellular polymers. This study provided new insights into the effects of implementing side-stream EBPR configuration on microbial populations, EBPR activity profiles and resulted system performance.

Effect of Varying Nitrate Concentrations on Denitrifying Phosphorus Uptake by DPAOs With a Molecular Insight Into Pho Regulon Gene Expression

Bacterial Pho regulon is a key regulator component in biological phosphorus-uptake. Poly-phosphate accumulating bacteria used in enhanced biological phosphorus removal (EBPR) system encounter negative regulation of the Pho regulon, resulting in reduced phosphorus-uptake from phosphorus-replete waste effluents. This study demonstrates possible trends of overcoming the PhoU negative regulation, resulting in excessive PO4 3--P uptake at varying concentrations of NO3 --N through denitrifying phosphorus removal process. We investigated the Pho regulon gene expression pattern and kinetic studies of P-removal by denitrifying phosphate accumulating organisms (DPAOs) which are able to remove both PO4 3--P and NO3 --N in single anoxic stage with the utilization of external carbon sources, without the use of stored polyhydroxyalkanoate (PHA) and without any anaerobic-aerobic or anaerobic-anoxic switches. Our study establishes that a minimum addition of 100 ppm NO3 --N leads to the withdrawal of the negative regulation of Pho regulon and results in ∼100% P-removal with concomitant escalated poly-phosphate accumulation by our established DPAO isolates and their artificially made consortium, isolated from sludge sample of PO4 3- -rich parboiled rice mill effluent, in a settling tank within 12 h of treatment. The same results were obtained when a phosphate rich effluent (stillage from distillery) mixed with a nitrate rich effluent (from explosive industry) was treated together in a single phase anoxic batch reactor, eliminating the need for alternating anaerobic/aerobic or anaerobic/anoxic switches for removing both the pollutants simultaneously. The highest poly-phosphate accumulation was observed to be more than 17% of cell dry weight. Our studies unequivocally establish that nitrate induction of Pho regulon is parallely associated with the repression of PhoU gene transcription, which is the negative regulator of Pho regulon. Based on earlier observations where similar nitrate mediated transcriptional repression was cited, we hypothesize the possible involvement of NarL/NarP transcriptional regulator proteins in PhoU repression. At present, we propose this denitrifying phosphorus removal endeavor as an innovative methodology to overcome the negative regulation of Pho regulon for accelerated unhindered phosphorus remediation from phosphate rich wastewater in India and the developing world where the stringency of EBPR and other reactors prevent their use due to financial reasons.

"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.

Widespread detection of Candidatus Accumulibacter phosphatis, a polyphosphate-accumulating organism, in sediments of the Columbia River estuary

Enhanced biological phosphorus removal (EBPR) exploits the metabolism of polyphosphate-accumulating organisms (PAOs) to remove excess phosphorus (P) from wastewater treatment. Candidatus Accumulibacter phosphatis (Accumulibacter) is the most abundant and well-studied PAO in EBPR systems. In a previous study, we detected polyphosphates throughout peripheral bay sediments, and hypothesized that an estuary is an ideal setting to evaluate PAOs in a natural system, given that estuaries are characterized by dynamic dissolved oxygen fluctuations that potentially favour PAO metabolism. We detected nucleotide sequences attributable to Accumulibacter (16S rRNA, ppk1) in sediments within three peripheral bays of the Columbia River estuary at abundances rivalling those observed in conventional wastewater treatment plants (0.01%-2.6%). Most of the sequences attributable to Accumulibacter were Type I rather than Type II, despite the fact that the estuary does not have particularly high nutrient concentrations. The highest diversity of Accumulibacter was observed in oligohaline peripheral bays, while the greatest abundances were observed at the mouth of the estuary in mesohaline sediments in the spring and summer. In addition, an approximately 70% increase in polyphosphate concentrations observed at one of the sites between dawn and dusk suggests that PAOs may play an important role in P cycling in estuary sediments.

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.

The Composition and Implications of Polyphosphate-Metal in Enhanced Biological Phosphorus Removal Systems

The individual cellular level and quantitative Polyphosphate (PolyP)-metal compositions in EBPR (enhanced biological phosphorus removal) systems have hardly been investigated and its potential link to EBPR performance therefore remain largely unknown. In this study, we applied scanning electron microscopy combined with energy dispersive X-ray spectroscopy (SEM/EDX) method that enabled detection and semiquantification of metal elemental compositions in intact intracellular PolyP granules in individual PAO (polyphosphate accumulating organism) cells. We, for the first time, revealed diverse and dynamic distributions of different metals ions in the PolyP-metal granules in different EBPR systems operated with the same influent metal composition but varying SRT of 5-30 days. We further demonstrated that the PolyP-metal composition diversity correlated with 16S rRNA gene based PAO phylogenetic diversity, suggesting the possible phylogeny-dependent PolyP-metal composition variation. The impact of PolyP metal composition in EBPR system, especially the Mg content in PolyP granules, was evidenced by the significant and strong positive correlation between PolyP-Mg content and the long-term stability of the four EBPR systems with varying SRTs. The PolyP-Mg content can therefore possibly serve as an indicator for EBPR performance monitoring. The results demonstrated that phenotyping techniques, such as PolyP-metal-based profiling, in compliment, or combined with genotyping techniques such as phylogenetic and functional gene sequencing, can provide more insights into the mechanisms and performance prediction of this important microbial ecosystem.

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.

Toward Better Understanding of EBPR Systems via Linking Raman-Based Phenotypic Profiling with Phylogenetic Diversity

This study reports a proof-of concept study to demonstrate the novel approach of phenotyping microbial communities in enhanced biological phosphorus removal (EBPR) systems using single cell Raman microspectroscopy and link it with phylogentic structures. We use hierarchical clustering analysis (HCA) of single-cell Raman spectral fingerprints and intracellular polymer signatures to separate and classify the functionally relevant populations in EBPR systems, namely polyphosphate accumulating organisms (PAOs) and glycogen accumulating organisms (GAOs), as well as other microbial populations. We then investigated the link between Raman-based community phenotyping and 16S rRNA gene-based phylogenetic characterization of four lab-scale EBPR systems with varying solid retention time (SRT) to gain insights into possible genotype-function relationships. Combined and simultaneous phylogenetic and phenotypic evaluation of EBPR ecosystems revealed SRT-dependent phylogenetic and phenotypic characteristics of the PAOs and GAOs, and their association with EBPR performance. The phenotypic diversity and plasticity of PAO populations, which otherwise could not be obtained with phylogenetic analysis alone, showed complex but potentially crucial association with EBPR process stability.

Genome-Enabled Insights into the Ecophysiology of the Comammox Bacterium "Candidatus Nitrospira nitrosa"

Nitrospira-like bacteria are among the most diverse and widespread nitrifiers in natural ecosystems and the dominant nitrite oxidizers in wastewater treatment plants (WWTPs). The recent discovery of comammox-like Nitrospira strains, capable of complete oxidation of ammonia to nitrate, raises new questions about specific traits responsible for the functional versatility and adaptation of this genus to a variety of environments. The availability of new Nitrospira genome sequences from both nitrite-oxidizing and comammox bacteria offers a way to analyze traits in different Nitrospira functional groups. Our comparative genomics analysis provided new insights into the adaptation of Nitrospira strains to specific lifestyles and environmental niches.

The recently discovered comammox bacteria have the potential to completely oxidize ammonia to nitrate. These microorganisms are part of the Nitrospira genus and are present in a variety of environments, including biological nutrient removal (BNR) systems. However, the physiological traits within and between comammox and nitrite-oxidizing bacterium (NOB)-like Nitrospira species have not been analyzed in these ecosystems. In this study, we identified Nitrospira strains dominating the nitrifying community of a sequencing batch reactor (SBR) performing BNR under microaerobic conditions. We recovered metagenome-derived draft genomes from two Nitrospira strains: (i) Nitrospira sp. strain UW-LDO-01, a comammox-like organism classified as “Candidatus Nitrospira nitrosa,” and (ii) Nitrospira sp. strain UW-LDO-02, a nitrite-oxidizing strain belonging to the Nitrospira defluvii species. A comparative genomic analysis of these strains with other Nitrospira-like genomes identified genomic differences in “Ca. Nitrospira nitrosa” mainly attributed to each strain’s niche adaptation. Traits associated with energy metabolism also differentiate comammox from NOB-like genomes. We also identified several transcriptionally regulated adaptive traits, including stress tolerance, biofilm formation, and microaerobic metabolism, which might explain survival of Nitrospira under multiple environmental conditions. Overall, our analysis expanded our understanding of the genetic functional features of “Ca. Nitrospira nitrosa” and identified genomic traits that further illuminate the phylogenetic diversity and metabolic plasticity of the Nitrospira genus.

IMPORTANCENitrospira-like bacteria are among the most diverse and widespread nitrifiers in natural ecosystems and the dominant nitrite oxidizers in wastewater treatment plants (WWTPs). The recent discovery of comammox-like Nitrospira strains, capable of complete oxidation of ammonia to nitrate, raises new questions about specific traits responsible for the functional versatility and adaptation of this genus to a variety of environments. The availability of new Nitrospira genome sequences from both nitrite-oxidizing and comammox bacteria offers a way to analyze traits in different Nitrospira functional groups. Our comparative genomics analysis provided new insights into the adaptation of Nitrospira strains to specific lifestyles and environmental niches.

Author Video: An author video summary of this article is available.

A Critical Assessment of the Microorganisms Proposed to be Important to Enhanced Biological Phosphorus Removal in Full-Scale Wastewater Treatment Systems

Understanding the microbiology of phosphorus (P) removal is considered essential to knowledge-based optimization of enhanced biological P removal (EBPR) systems. Biological P removal is achieved in these systems by promoting the growth of organisms collectively known as the polyphosphate accumulating organisms (PAOs). Also considered important to EBPR are the glycogen accumulating organisms (GAOs), which are theorized to compete with the PAOs for resources at the expense of P removal efficiency. Numerous studies have sought to identify the PAOs and their GAOs competitors, with several candidates proposed for each over the last few decades. The current study collectively assessed the abundance and diversity of all proposed PAOs and GAOs in 18 Danish full-scale wastewater treatment plants with well-working biological nutrient removal over a period of 9 years using 16S rRNA gene amplicon sequencing. The microbial community structure in all plants was relatively stable over time. Evidence for the role of the proposed PAOs and GAOs in EBPR varies and is critically assessed, in light of their calculated amplicon abundances, to indicate which of these are important in full-scale systems. Bacteria from the genus Tetrasphaera were the most abundant of the PAOs. The “Candidatus Accumulibacter” PAOs were in much lower abundance and appear to be biased by the amplicon-based method applied. The genera Dechloromonas, Microlunatus, and Tessaracoccus were identified as abundant putative PAO that require further research attention. Interestingly, the actinobacterial Micropruina and sbr-gs28 phylotypes were among the most abundant of the putative GAOs. Members of the genera Defluviicoccus, Propionivibrio, the family Competibacteraceae, and the spb280 group were also relatively abundant in some plants. Despite observed high abundances of GAOs (periodically exceeding 20% of the amplicon reads), P removal performance was maintained, indicating that these organisms were not outcompeting the PAOs in these EBPR systems. Phylogenetic diversity within each of the PAOs and GAOs genera was observed, which is consistent with reported metabolic diversity for these. Whether or not key traits can be assigned to sub-genus level clades requires further investigation.

A comparative study of microbial dynamics and phosphorus removal for a two side-stream wastewater treatment processes

A side-stream process with anoxic/aerobic tanks was designed as a denitrifying enhanced biological phosphorus removal process for wastewater treatment as compared to a modified side-stream process using contact/stabilization tanks.

Prevalence of 'Candidatus Accumulibacter phosphatis' type II under phosphate limiting conditions

P-limitation in enhanced biological phosphorus removal (EBPR) systems fed with acetate, has generally been considered as a condition leading to enrichment of organisms of the genotype’ Candidatus Competibacter phosphatis’ expressing the glycogen-accumulating organisms (GAO) phenotype. Recent studies have demonstrated in short-term experiments that organisms of the genotype ‘Candidatus Accumulibacter phosphatis’ clade I and II, known to express the polyphosphate-accumulating organisms (PAO) phenotype can switch to the GAO phenotype when poly-P is absent, but are performing the HAc-uptake at lower kinetic rates, where clade I showed the lowest rates. The objective of this study was to verify whether organisms of the genotype ‘Candidatus Accumulibacter phosphatis’ can also be enriched under P-limiting conditions while expressing a GAO phenotype and more specifically to see which specific clade prevails. A sequencing batch reactor was inoculated with activated sludge to enrich an EBPR culture for a cultivation period of 128 days (16 times the solids retention time) under P-limiting conditions. A mixed culture was obtained comprising of 49 % ‘Candidatus Accumulibacter phosphatis’ clade II and 46 % ‘Candidatus Competibacter phosphatis’. The culture performed a full GAO metabolism for anaerobic HAc-uptake, but was still able to switch to a PAO metabolism, taking up excessive amounts of phosphate during the aerobic phase when it became available in the influent. These findings show that P-limitation, often used as strategy for enrichment of ‘Candidatus Competibacter phosphatis’, does not always lead to enrichment of only ‘Candidatus Competibacter phosphatis’. Furthermore, it demonstrates that ‘Candidatus Accumulibacter phosphatis’ are able to proliferate in activated sludge systems for periods of up to 128 days or longer when the influent phosphate concentrations are just enough for assimilation purposes and no poly-P is formed. The ‘Candidatus Accumulibacter phosphatis’ retain the ability to switch to the PAO phenotype, taking up phosphate from the influent as soon as it becomes available.

Culture-Dependent and -Independent Identification of Polyphosphate-Accumulating Dechloromonas spp. Predominating in a Full-Scale Oxidation Ditch Wastewater Treatment Plant

The oxidation ditch process is one of the most economical approaches currently used to simultaneously remove organic carbon, nitrogen, and also phosphorus (P) from wastewater. However, limited information is available on biological P removal in this process. In the present study, microorganisms contributing to P removal in a full-scale oxidation ditch reactor were investigated using culture-dependent and -independent approaches. A microbial community analysis based on 16S rRNA gene sequencing revealed that a phylotype closely related to Dechloromonas spp. in the family Rhodocyclaceae dominated in the oxidation ditch reactor. This dominant Dechloromonas sp. was successfully isolated and subjected to fluorescent staining for polyphosphate, followed by microscopic observations and a spectrofluorometric analysis, which clearly demonstrated that the Dechloromonas isolate exhibited a strong ability to accumulate polyphosphate within its cells. These results indicate the potential key role of Dechloromonas spp. in efficient P removal in the oxidation ditch wastewater treatment process.

Candidatus Accumulibacter phosphatis clades enriched under cyclic anaerobic and microaerobic conditions simultaneously use different electron acceptors

Lab- and pilot-scale simultaneous nitrification, denitrification and phosphorus removal-sequencing batch reactors were operated under cyclic anaerobic and micro-aerobic conditions. The use of oxygen, nitrite, and nitrate as electron acceptors by Candidatus Accumulibacter phosphatis during the micro-aerobic stage was investigated. A complete clade-level characterization of Accumulibacter in both reactors was performed using newly designed qPCR primers targeting the polyphosphate kinase gene (ppk1). In the lab-scale reactor, limited-oxygen conditions led to an alternated dominance of Clade IID and IC over the other clades. Results from batch tests when Clade IC was dominant (i.e., >92% of Accumulibacter) showed that this clade was capable of using oxygen, nitrite and nitrate as electron acceptors for P uptake. A more heterogeneous distribution of clades was found in the pilot-scale system (Clades IIA, IIB, IIC, IID, IA, and IC), and in this reactor, oxygen, nitrite and nitrate were also used as electron acceptors coupled to phosphorus uptake. However, nitrite was not an efficient electron acceptor in either reactor, and nitrate allowed only partial P removal. The results from the Clade IC dominated reactor indicated that either organisms in this clade can simultaneously use multiple electron acceptors under micro-aerobic conditions, or that the use of multiple electron acceptors by Clade IC is due to significant microdiversity within the Accumulibacter clades defined using the ppk1 gene.

"Candidatus Propionivibrio aalborgensis": A Novel Glycogen Accumulating Organism Abundant in Full-Scale Enhanced Biological Phosphorus Removal Plants

Enhanced biological phosphorus removal (EBPR) is widely used to remove phosphorus from wastewater. The process relies on polyphosphate accumulating organisms (PAOs) that are able to take up phosphorus in excess of what is needed for growth, whereby phosphorus can be removed from the wastewater by wasting the biomass. However, glycogen accumulating organisms (GAOs) may reduce the EBPR efficiency as they compete for substrates with PAOs, but do not store excessive amounts of polyphosphate. PAOs and GAOs are thought to be phylogenetically unrelated, with the model PAO being the betaproteobacterial “Candidatus Accumulibacter phosphatis” (Accumulibacter) and the model GAO being the gammaproteobacterial “Candidatus Competibacter phosphatis”. Here, we report the discovery of a GAO from the genus Propionivibrio, which is closely related to Accumulibacter. Propionivibrio sp. are targeted by the canonical fluorescence in situ hybridization probes used to target Accumulibacter (PAOmix), but do not store excessive amounts of polyphosphate in situ. A laboratory scale reactor, operated to enrich for PAOs, surprisingly contained co-dominant populations of Propionivibrio and Accumulibacter. Metagenomic sequencing of multiple time-points enabled recovery of near complete population genomes from both genera. Annotation of the Propionivibrio genome confirmed their potential for the GAO phenotype and a basic metabolic model is proposed for their metabolism in the EBPR environment. Using newly designed fluorescence in situ hybridization (FISH) probes, analyses of full-scale EBPR plants revealed that Propionivibrio is a common member of the community, constituting up to 3% of the biovolume. To avoid overestimation of Accumulibacter abundance in situ, we recommend the use of the FISH probe PAO651 instead of the commonly applied PAOmix probe set.

Ancestral genome reconstruction identifies the evolutionary basis for trait acquisition in polyphosphate accumulating bacteria

The evolution of complex traits is hypothesized to occur incrementally. Identifying the transitions that lead to extant complex traits may provide a better understanding of the genetic nature of the observed phenotype. A keystone functional group in wastewater treatment processes are polyphosphate accumulating organisms (PAOs), however the evolution of the PAO phenotype has yet to be explicitly investigated and the specific metabolic traits that discriminate non-PAO from PAO are currently unknown. Here we perform the first comprehensive investigation on the evolution of the PAO phenotype using the model uncultured organism Candidatus Accumulibacter phosphatis (Accumulibacter) through ancestral genome reconstruction, identification of horizontal gene transfer, and a kinetic/stoichiometric characterization of Accumulibacter Clade IIA. The analysis of Accumulibacter's last common ancestor identified 135 laterally derived genes, including genes involved in glycogen, polyhydroxyalkanoate, pyruvate and NADH/NADPH metabolisms, as well as inorganic ion transport and regulatory mechanisms. In contrast, pathways such as the TCA cycle and polyphosphate metabolism displayed minimal horizontal gene transfer. We show that the transition from non-PAO to PAO coincided with horizontal gene transfer within Accumulibacter's core metabolism; likely alleviating key kinetic and stoichiometric bottlenecks, such as anaerobically linking glycogen degradation to polyhydroxyalkanoate synthesis. These results demonstrate the utility of investigating the derived genome of a lineage to identify key transitions leading to an extant complex phenotype.

Ultrasonic waste activated sludge disintegration for recovering multiple nutrients for biofuel production

Waste activated sludge is a valuable resource containing multiple nutrients, but is currently treated and disposed of as an important source of pollution. In this work, waste activated sludge after ultrasound pretreatment was reused as multiple nutrients for biofuel production. The nutrients trapped in sludge floc were transferred into liquid medium by ultrasonic disintegration during first 30 min, while further increase of pretreatment time only resulted in slight increase of nutrients release. Hydrogen production by Ethanoligenens harbinense B49 from glucose significantly increased with the concentration of ultrasonic sludge, and reached maximum yield of 1.97 mol H2/mol glucose at sludge concentration of 7.75 g volatile suspended solids/l. Without addition of any other chemicals, waste molasses rich in carbohydrate was efficiently turned into hydrogen with yield of 189.34 ml H2/g total sugar by E. harbinense B49 using ultrasonic sludge as nutrients. The results also showed that hydrogen production using pretreated sludge as multiple nutrients was higher than those using standard nutrients. Acetic acid produced by E. harbinense B49 together with the residual nutrients in the liquid medium were further converted into hydrogen (271.36 ml H2/g total sugar) by Rhodopseudomonas faecalis RLD-53 through photo fermentation, while ethanol was the sole end product with yield of 220.26 mg/g total sugar. Thus, pretreated sludge was an efficient nutrients source for biofuel production, which could replace the standard nutrients. This research provided a novel strategy to achieve environmental friendly sludge disposal and simultaneous efficient biofuel recovery from organic waste.

Diversity of phosphorus reserves in microorganisms

Phosphorus compounds are indispensable components of the Earth's biomass metabolized by all living organisms. Under excess of phosphorus compounds in the environment, microorganisms accumulate reserve phosphorus compounds that are used under phosphorus limitation. These compounds vary in their structure and also perform structural and regulatory functions in microbial cells. The most common phosphorus reserve in microorganism is inorganic polyphosphates, but in some archae and bacteria insoluble magnesium phosphate plays this role. Some yeasts produce phosphomannan as a phosphorus reserve. This review covers also other topics, i.e. accumulation of phosphorus reserves under nutrient limitation, phosphorus reserves in activated sludge, mycorrhiza, and the role of mineral phosphorus compounds in mammals.

Functional and genomic diversity of methylotrophic Rhodocyclaceae: description of Methyloversatilis discipulorum sp. nov

Three strains of methylotrophic Rhodocyclaceae (FAM1(T), RZ18-153 and RZ94) isolated from Lake Washington sediment samples were characterized. Based on phylogenetic analysis of 16S rRNA gene sequences the strains should be assigned to the genus Methyloversatilis. Similarly to other members of the family, the strains show broad metabolic capabilities and are able to utilize a number of organic acids, alcohols and aromatic compounds in addition to methanol and methylamine. The main fatty acids were 16:1ω7c (49-59%) and 16:0 (32-29%). Genomes of all isolates were sequenced, assembled and annotated in collaboration with the DOE Joint Genome Institute (JGI). Genome comparison revealed that the strains FAM1T, RZ18-153 and RZ94 are closely related to each other and almost equally distant from two previously described species of the genus Methyloversatilis, Methyloversatilis universalis and Methyloversatilis thermotolerans. Like other methylotrophic species of the genus Methyloversatilis, all three strains possess one-subunit PQQ-dependent ethanol/methanol dehydrogenase (Mdh-2), the N-methylglutamate pathway and the serine cycle (isocitrate lyase/malate synthase, Icl/ms(+) variant). Like M. universalis, strains FAM1(T), RZ18-153 and RZ94 have a quinohemoprotein amine dehydrogenase, a tungsten-containing formaldehyde ferredoxin oxidoreductase, phenol hydroxylase, and the complete Calvin cycle. Similarly to M. thermotolerans, the three strains possess two-subunit methanol dehydrogenase (MxaFI), monoamine oxidase (MAO) and nitrogenase. Based on the phenotypic and genomic data, the strains FAM1(T), RZ18-153 and RZ94 represent a novel species of the genus Methyloversatilis, for which the name Methyloversatilis discipulorum sp. nov. is proposed. The type strain is FAM1(T) ( = JCM 30542(T) = VKM = B-2888(T)).

Ammonia-oxidizing microbial communities in reactors with efficient nitrification at low-dissolved oxygen

Ammonia-oxidizing microbial communities involved in ammonia oxidation under low dissolved oxygen (DO) conditions (<0.3 mg/L) were investigated using chemostat reactors. One lab-scale reactor (NS_LowDO) was seeded with sludge from a full-scale wastewater treatment plant (WWTP) not adapted to low-DO nitrification, while a second reactor (JP_LowDO) was seeded with sludge from a full-scale WWTP already achieving low-DO nitrifiaction. The experimental evidence from quantitative PCR, rDNA tag pyrosequencing, and fluorescence in situ hybridization (FISH) suggested that ammonia-oxidizing bacteria (AOB) in the Nitrosomonas genus were responsible for low-DO nitrification in the NS_LowDO reactor, whereas in the JP_LowDO reactor nitrification was not associated with any known ammonia-oxidizing prokaryote. Neither reactor had a significant population of ammonia-oxidizing archaea (AOA) or anaerobic ammonium oxidation (anammox) organisms. Organisms isolated from JP_LowDO were capable of autotrophic and heterotrophic ammonia utilization, albeit without stoichiometric accumulation of nitrite or nitrate. Based on the experimental evidence we propose that Pseudomonas, Xanthomonadaceae, Rhodococcus, and Sphingomonas are involved in nitrification under low-DO conditions.

Impact of inocula and operating conditions on the microbial community structure of two anammox reactors

The microbial community structure of the biomass selected in two distinctly inoculated anaerobic oxidation of ammonium (anammox) reactors was investigated and compared with the help of data obtained from 454-pyrosequencing analyses. The anammox reactors were operated for 550 days and seeded with different sludges: sediment from a constructed wetland (reactor I) and biomass from an aerated lagoon part of the oil-refinery wastewater treatment plant (reactor II). The anammox diversity in the inocula was evaluated by 16S rRNA gene-cloning analysis. The diversity of anammox bacteria was greater in the sludge from the oil-refinery (three of the five known genera of anammox were detected) than in the wetland sludge, in which only Candidatus Brocadia was observed. Pyrosequencing analysis demonstrated that the community enriched in both reactors had differing compositions despite the nearly similar operational conditions applied. The dominant phyla detected in both reactors were Proteobacteria, Chloroflexi, Planctomycetes, and Acidobacteria. The phylum Bacteroidetes, which is frequently observed in anammox reactors, was not detected. However, Acidobacteria and GN04 phyla were observed for the first time, suggesting their importance for this process. Our results suggest that, under similar operational conditions, anammox populations (Ca. Brocadia sinica and Ca. Brocadia sp. 40) were selected in both reactors despite the differences between the two initial inocula. Taken together, these results indicated that the type of inoculum and the culture conditions are key determinants of the general microbial composition of the biomass produced in the reactors. Operational conditions alone might play an important role in anammox selection.

Operation performance and microbial community dynamics of phosphorus removal sludge with different electron acceptors

Operation performances of phosphorus removal sludge with different electron acceptors in three parallel SBRs were firstly compared in the present study, and the effect of post-aeration on denitrifying phosphorus removal was also studied. Moreover, community dynamics of different phosphorus removal sludge was systematically investigated with high-throughput sequencing for the first time. TP removal rates for nitrate-, nitrite-, and oxygen-based phosphorus removal sludge were 84.8, 78.5, and 87.4 %, with an average effluent TP concentration of 0.758, 0.931, and 0.632 mg/l. The average specific phosphorus release and uptake rates were 20.3, 10.8, and 21.5, and 9.43, 8.68, and 10.8 mgP/(gVSS h), respectively. Moreover, electron utilization efficiency of denitrifying phosphorus removal sludge with nitrate as electron acceptor was higher than nitrite, with P/e− were 2.21 and 1.51 mol-P/mol-e−, respectively. With the assistance of post-aeration for nitrate-based denitrifying phosphorus removal sludge, settling ability could be improved, with SVI decreased from 120 to 80 and 72 ml/g when post-aeration time was 0, 10, and 30 min, respectively. Moreover, further phosphorus removal could be achieved during post-aeration with increased aeration time. However, the anoxic phosphorus uptake was deteriorated, which was likely a result of shifted microbial community structure. Post-aeration of approximately 10 min was proposed for denitrifying phosphorus removal. Nitrate- and nitrite-based denitrifying phosphorus removal sludge exhibited similar community structure. More phosphorus accumulating organisms were enriched under anaerobic–aerobic conditions, while anaerobic–anoxic conditions were favorable for suppressing glycogen-accumulating organisms. Significant differences in pathogenic bacterial community profiles revealed in the current study indicated the potential public health hazards of non-aeration activated sludge system.

A comparative study of the bacterial community in denitrifying and traditional enhanced biological phosphorus removal processes

Denitrifying phosphorus removal is an attractive wastewater treatment process due to its reduced carbon source demand and sludge minimization potential. Two lab-scale sequencing batch reactors (SBRs) were operated in alternating anaerobic-anoxic (A-A) or anaerobic-oxic (A-O) conditions to achieve denitrifying enhanced biological phosphate removal (EBPR) and traditional EBPR. No significant differences were observed in phosphorus removal efficiencies between A-A SBR and A-O SBR, with phosphorus removal rates being 87.9% and 89.0% respectively. The community structures in denitrifying and traditional EBPR processes were evaluated by high-throughput sequencing of the PCR-amplified partial 16S rRNA genes from each sludge. The results obtained showed that the bacterial community was more diverse in A-O sludge than in A-A sludge. Taxonomy and β-diversity analyses indicated that a significant shift occurred in the dominant microbial community in A-A sludge compared with the seed sludge during the whole acclimation phase, while a slight fluctuation was observed in the abundance of the major taxonomies in A-O sludge. One Dechloromonas-related OTU outside the 4 known Candidatus “Accumulibacter” clades was detected as the main OTU in A-A sludge at the stationary operation, while Candidatus “Accumulibacter” dominated in A-O sludge.

Carbon mass balance and microbial ecology in a laboratory scale reactor achieving simultaneous sludge reduction and nutrient removal

Solids reduction in activated sludge processes (ASP) at source using process manipulation has been researched widely over the last two-decades. However, the absence of nutrient removal component, lack of understanding on the organic carbon, and limited information on key microbial community in solids minimizing ASP preclude the widespread acceptance of sludge minimizing processes. In this manuscript, we report simultaneous solids reduction through anaerobiosis along with nitrogen and phosphorus removals. The manuscript also reports carbon mass balance using stable isotope of carbon, microbial ecology of nitrifiers and polyphosphate accumulating organisms (PAOs). Two laboratory scale reactors were operated in anaerobic-aerobic-anoxic (A(2)O) mode. One reactor was run in the standard mode (hereafter called the control-SBR) simulating conventional A(2)O type of activated sludge process and the second reactor was run in the sludge minimizing mode (called the modified-SBR). Unlike other research efforts where the sludge minimizing reactor was maintained at nearly infinite solids retention time (SRT). To sustain the efficient nutrient removal, the modified-SBR in this research was operated at a very small solids yield rather than at infinite SRT. Both reactors showed consistent NH3-N, phosphorus and COD removals over a period of 263 days. Both reactors also showed active denitrification during the anoxic phase even if there was no organic carbon source available during this phase, suggesting the presence of denitrifying PAOs (DNPAOs). The observed solids yield in the modified-SBR was 60% less than the observed solids yield in the control-SBR. Specific oxygen uptake rate (SOUR) for the modified-SBR was almost 44% more than the control-SBR under identical feeding conditions, but was nearly the same for both reactors under fasting conditions. The modified-SBR showed greater diversity of ammonia oxidizing bacteria and PAOs compared to the control-SBR. The diversity of PAOs in the modified-SBR was even more interesting in which case novel clades of Candidatus Accumulibacter phosphatis (CAP), an uncultured but widely found PAOs, were found.

A hundred years of activated sludge: time for a rethink

Biological wastewater treatment plants (BWWTPs) based on the activated sludge (AS) process have dramatically improved worldwide water sanitation despite increased urbanization and industrialization. However, current AS-based operations are considered economically and environmentally unsustainable. In this Perspective, we discuss our current understanding of microbial populations and their metabolic transformations in AS-based BWWTPs in view of developing more sustainable processes in the future. In particular, much has been learned over the course of the past 25 years about specialized microorganisms, which could be more comprehensively leveraged to recover energy and/or nutrients from wastewater streams. To achieve this, we propose a bottom-up design approach, focused around the concept of a "wastewater biorefinery column", which would rely on the engineering of distinct ecological niches into a BWWTP in order to guarantee the targeted enrichment of specific organismal groups which in turn will allow the harvest of high-value resources from wastewater. This concept could be seen as a possible grand challenge to microbial ecologists and engineers alike at the centenary of the discovery of the AS process.

Seasonal bacterial community dynamics in a full-scale enhanced biological phosphorus removal plant

Activated sludge is one of the most abundant and effective wastewater treatment process used to treat wastewater, and has been used in developed countries for nearly a century. In all that time, several hundreds of studies have explored the bacterial communities responsible for treatment, but most studies were based on a handful of samples and did not consider temporal dynamics. In this study, we used the DNA fingerprinting technique called automated ribosomal intergenic spacer region analysis (ARISA) to study bacterial community dynamics over a two-year period in two different treatment trains. We also used quantitative PCR to measure the variation of five phylogenetically-defined clades within the Accumulibacter lineage, which is a model polyphosphate accumulating organism. The total bacterial community exhibited seasonal patterns of change reminiscent of those observed in lakes and oceans. Surprisingly, all five Accumulibacter clades were present throughout the study, and the total Accumulibacter community was relatively stable. However, the abundance of each clade did fluctuate through time. Clade IIA dynamics correlated positively with temperature (ρ = 0.65, p < 0.05) while Clade IA dynamics correlated negatively with temperature (ρ = -0.35, p < 0.05). This relationship with temperature hints at the mechanisms that may be driving the seasonal patterns in overall bacterial community dynamics and provides further evidence for ecological differentiation among clades within the Accumulibacter lineage. This work provides a valuable baseline for activated sludge bacterial community variation.

Identification of trigger factors selecting for polyphosphate- and glycogen-accumulating organisms in aerobic granular sludge sequencing batch reactors

Nutrient removal performances of sequencing batch reactors using granular sludge for intensified biological wastewater treatment rely on optimal underlying microbial selection. Trigger factors of bacterial selection and nutrient removal were investigated in these novel biofilm systems with specific emphasis on polyphosphate- (PAO) and glycogen-accumulating organisms (GAO) mainly affiliated with Accumulibacter and Competibacter, respectively. In a first dynamic reactor operated with stepwise changes in concentration and ratio of acetate and propionate (Ac/Pr) under anaerobic feeding and aerobic starvation conditions and without wasting sludge periodically, propionate favorably selected for Accumulibacter (35% relative abundance) and stable production of granular biomass. A Plackett-Burman multifactorial experimental design was then used to screen in eight runs of 50 days at stable sludge retention time of 15 days for the main effects of COD concentration, Ac/Pr ratio, COD/P ratio, pH, temperature, and redox conditions during starvation. At 95% confidence level, pH was mainly triggering direct Accumulibacter selection and nutrient removal. The overall PAO/GAO competition in granular sludge was statistically equally impacted by pH, temperature, and redox factors. High Accumulibacter abundances (30-47%), PAO/GAO ratios (2.8-8.4), and phosphorus removal (80-100%) were selected by slightly alkaline (pH > 7.3) and lower mesophilic (<20 °C) conditions, and under full aeration during fixed 2-h starvation. Nitrogen removal by nitrification and denitrification (84-97%) was positively correlated to pH and temperature. In addition to alkalinity, non-limited organic conditions, 3-carbon propionate substrate, sludge age control, and phase length adaptation under alternating aerobic-anoxic conditions during starvation can lead to efficient nutrient-removing granular sludge biofilm systems.

Microbial contributions to phosphorus cycling in eutrophic lakes and wastewater

Phosphorus is a key element controlling the productivity of freshwater ecosystems, and microbes drive most of its relevant biogeochemistry. Eutrophic lakes are generally dominated by cyanobacteria that compete fiercely with algae and heterotrophs for the element. In wastewater treatment, engineers select for specialized bacteria capable of sequestering phosphorus from the water, to protect surface waters from further loading. The intracellular storage molecule polyphosphate plays an important role in both systems, allowing key taxa to control phosphorus availability. The importance of dissolved organic phosphorus in eutrophic lakes and mineralization mechanisms is still underappreciated and understudied. The need for functional redundancy through biological diversity in wastewater treatment plants is also clear. In both systems, a holistic ecosystems biology approach is needed to understand the molecular mechanisms controlling phosphorus metabolism and the ecological interactions and factors controlling ecosystem-level process rates.

Low acetate concentrations favor polyphosphate-accumulating organisms over glycogen-accumulating organisms in enhanced biological phosphorus removal from wastewater

Glycogen-accumulating organisms (GAOs) are thought to compete with polyphosphate-accumulating organisms (PAOs) in enhanced biological phosphorus removal (EBPR) wastewater treatment systems. A laboratory sequencing batch reactor (SBR) was operated for one year to test the hypothesis that PAOs have a competitive advantage at low acetate concentrations, with a focus on low pH conditions previously shown to favor GAOs. PAOs dominated the system under conventional SBR operation with rapid acetate addition (producing high in-reactor concentrations) and pH values of 7.4-8.4. GAOs dominated when the pH was decreased (6.4-7.0). Decreasing the acetate addition rate led to very low reactor acetate concentrations, and PAOs recovered, supporting the study hypothesis. When the acetate feed rate was increased, EBPR failed again. Dominant PAOs and GAOs were Candidatus Accumulibacter phosphatis and Defluviicoccus Cluster 2, respectively, according to fluorescent in situ hybridization and 454 pyrosequencing. Surprisingly, GAOs were not the immediate causes of PAO failures, based on functional and population measurements. Pyrosequencing results suggested Dechloromonas and Tetrasphaera spp. may have also been PAOs, and additional potential GAOs were also identified. Full-scale systems typically have lower in-reactor acetate concentrations than laboratory SBRs, and so, previous laboratory studies may have overestimated the practical importance of GAOs as causes of EBPR failure.

Population dynamics of bacteria involved in enhanced biological phosphorus removal in Danish wastewater treatment plants

The enhanced biological phosphorus removal (EBPR) process is increasingly popular as a sustainable method for removal of phosphorus (P) from wastewater. This study consisted of a comprehensive three-year investigation of the identity and population dynamics of polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs) in 28 Danish municipal wastewater treatment plants with nutrient removal. Fluorescence in situ hybridization was applied to quantify ten probe-defined populations of PAO and GAO that in total constituted a large fraction (30% on average) of the entire microbial community targeted by the EUBmix probes. Two PAO genera, Accumulibacter and Tetrasphaera, were very abundant in all EBPR plants (average of 3.7% and 27% of all bacteria, respectively), and their abundance was relatively stable in the Danish full-scale plants without clear temporal variations. GAOs were occasionally present in some plants (Competibacter in 11 plants, Defluviicoccus in 6 plants) and were consistent in only a few plants. This shows that these were not core species in the EBPR communities. The total GAO abundance was always lower than that of Accumulibacter. In plants without EBPR design, the abundance of PAO and GAO was significantly lower. Competibacter correlated in general with high fraction of industrial wastewater. In specific plants Accumulibacter correlated with high C/P ratio of the wastewater and Tetrasphaera with high organic loading. Interestingly, the relative microbial composition of the PAO/GAO species was unique to each plant over time, which gives a characteristic plant-specific "fingerprint".