Bacterial community and "Candidatus Accumulibacter" population dynamics in laboratory-scale enhanced biological phosphorus removal reactors

Research advances of the phosphorus-accumulating organisms of Candidatus Accumulibacter, Dechloromonas and Tetrasphaera: Metabolic mechanisms, applications and influencing factors

Phosphorus-accumulating organisms (PAOs), which harbor metabolic mechanisms for phosphorus removal, are widely applied in wastewater treatment. Recently, novel PAOs and phosphorus removal metabolic pathways have been identified and studied. Specifically, Dechloromonas and Tetrasphaera can remove phosphorus via the denitrifying phosphorus removal and fermentation phosphorus removal pathways, respectively. As the main PAOs in biological phosphorus removal systems, the conventional PAO Candidatus Accumulibacter and the novel PAOs Dechloromonas and Tetrasphaera are thoroughly discussed in this paper, with a specific focus on their phosphorus removal metabolic mechanisms, process applications, community abundance and influencing factors. Dechloromonas can achieve simultaneous nitrogen and phosphorus removal in an anoxic environment through the denitrifying phosphorus removal metabolic pathway, which can further reduce carbon source requirements and aeration energy consumption. The metabolic pathways of Tetrasphaera are diverse, with phosphorus removal occurring in conjunction with macromolecular organics degradation through anaerobic fermentation. A collaborative oxic phosphorus removal pathway between Tetrasphaera and Ca. Accumulibacter, or a collaborative anoxic denitrifying phosphorus removal pathway between Tetrasphaera and Dechloromonas are future development directions for biological phosphorus removal technologies, which can further reduce carbon source and energy consumption while achieving enhanced phosphorus removal.

Resource recovery in aerobic granular sludge systems: is it feasible or still a long way to go?

Lately, wastewater treatment plants are much often being designed as wastewater-resource factories inserted in circular cities. Among biological treatment technologies, aerobic granular sludge (AGS), considered an evolution of activated sludge (AS), has received great attention regarding its resource recovery potential. This review presents the state-of-the-art concerning the influence of operational parameters on the recovery of alginate-like exopolysaccharides (ALE), tryptophan, phosphorus, and polyhydroxyalkanoates (PHA) from AGS systems. The carbon to nitrogen ratio was identified as a parameter that plays an important role for the optimal production of ALE, tryptophan, and PHA. The sludge retention time effect is more pronounced for the production of ALE and tryptophan. Additionally, salinity levels in the bioreactors can potentially be manipulated to increase ALE and phosphorus yields simultaneously. Some existing knowledge gaps in the scientific literature concerning the recovery of these resources from AGS were also identified. Regarding industrial applications, tryptophan has the longest way to go. On the other hand, ALE production/recovery could be considered the most mature process if we take into account that existing alternatives for phosphorus and PHA production/recovery are optimized for activated sludge rather than granular sludge. Consequently, to maintain the same effectiveness, these processes likely could not be applied to AGS without undergoing some modification. Therefore, investigating to what extent these adaptations are necessary and designing alternatives is essential.

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.

Genome-centric metagenomics resolves microbial diversity and prevalent truncated denitrification pathways in a denitrifying PAO-enriched bioprocess

Denitrification is the stepwise microbial reduction of nitrate or nitrite (NO₂^-) to nitrogen gas via the obligate intermediates nitric oxide (NO) and nitrous oxide (N₂O). Substantial N₂O accumulation has been reported in denitrifying enhanced biological phosphorus removal (EBPR) bioreactors enriched in denitrifying polyphosphate accumulating organisms (DPAOs), but little is known about underlying mechanisms for N₂O generation, prevalence of complete versus truncated denitrification pathways, or the impact of NO₂^- feed on DPAO-enriched consortia. To address this knowledge gap, we employed genome-resolved metagenomics to investigate nitrogen transformation potential in a NO₂^- fed denitrifying EBPR bioreactor enriched in Candidatus Accumulibacter and prone to N₂O accumulation. Our analysis yielded 41 near-complete metagenome-assembled genomes (MAGs), including two co-occurring Accumulibacter strains affiliated with clades IA and IC (the first published genome from this clade) and 39 non-PAO flanking bacterial genomes. The dominant Accumulibacter clade IA encoded genes for complete denitrification, while the lower abundance Accumulibacter clade IC harbored all denitrification genes except for a canonical respiratory NO reductase. Analysis of the 39 non-PAO MAGs revealed a high prevalence of taxa harboring an incomplete denitrification pathway. Of the 27 MAGs harboring capacity for at least one step in the denitrification pathway, 10 were putative N₂O producers lacking N₂O reductase, 16 were putative N₂O reducers that lacked at least one upstream denitrification gene, and only one harbored a complete denitrification pathway. We also documented increasing abundance over the course of reactor operation of putative N₂O producers. Our results suggest that the unusually high levels of N₂O production observed in this Accumulibacter-enriched consortium are linked in part to the selection for non-PAO flanking microorganisms with truncated denitrification pathways.

The difference of morphological characteristics and population structure in PAO and DPAOgranular sludges

We examined how long-term operation of anaerobic-oxic and anaerobic-anoxic sequencing batch reactors (SBRs) affects the enhanced biological phosphorus removal (EBPR) performance and sludge characteristics. The microbial characteristics of phosphorus accumulating organism (PAO) and denitrifying PAO (DPAO) sludge were also analyzed through a quantitative analysis of microbial community structure. Compared with the initial stage of operation characterized by unstable EBPR, both PAO and DPAO SBR produced a stable EBPR performance after about 100-day operation. From day 200 days (DPAO SBR) and 250 days (PAO SBR) onward, sludge granulation was observed, and the average granule size of DPAO SBR was approximately 5 times larger than that of PAO SBR. The DPAO granular sludge contained mainly rod-type microbes, whereas the PAO granular sludge contained coccus-type microbes. Fluorescence in situ hybridization analysis revealed that a high ratio of Accumulibacter clade I was found only in DPAO SBR, revealing the important role of this organism in the denitrifying EBPR system. A pyrosequencing analysis showed that Accumulibacter phosphatis was present in PAO sludge at a high proportion of 6%, whereas it rarely observed in DPAO sludge. Dechloromonas was observed in both PAO sludge (3.3%) and DPAO sludge (3.2%), confirming that this organism can use both O₂ and NO₃^- as electron acceptors. Further, Thauera spp. was identified to have a new possibility as denitrifier capable of phosphorous uptake under anoxic condition.

Community structures and population dynamics of "Candidatus Accumulibacter" in activated sludges of wastewater treatment plants using ppk1 as phylogenetic marker

Candidatus Accumulibacter has been identified as dominant polyphosphate-accumulating organisms (PAOs) in enhanced biological phosphorus (P) removal (EBPR) from wastewater. This study revealed the relevance of community structure, abundance and seasonal population dynamics of Candidatus Accumulibacter to process operation of wastewater treatment plants (WWTPs) in China using ppk1 gene as phylogenetic marker. All sludge samples had properties of denitrifying P removal using nitrate as an electron acceptor. Accumulibacter abundance in the anaerobic-anoxic-oxic (A²O) process was the highest (26% of total bacteria), and higher in winter than in summer with a better EBPR performance. Type-II was the dominant Accumulibacter in all processes, and type-I accounted for a small proportion of total Accumulibacter. The abundance of Clade-IIC as the most dominant clade reached 2.59×10⁹ cells/g MLSS and accounted for 87.3% of total Accumulibacter. Clade IIC mainly contributed to denitrifying P removal. Clades IIA, IIC and IID were found in all processes, while clade-IIF was only found in oxidation ditch process through phylogenetic analysis. High proportion of clade IID to total Accumulibacter led to poor performance of aerobic P-uptake in inverted A²O process. Therefore, Accumulibacter clades in WWTPs were diverse, and EBPR performance was closely related to the clade-level community structures and abundances of Accumulibacter.

The effect of malathion on the activity, performance, and microbial ecology of activated sludge

This study evaluated the effect of a VX (O-ethyl S-[2-(diisopropylamino)ethyl] methylphosphonothioate) surrogate (malathion) on the activity, performance, and ecology of activated sludge bioreactors. In the presence of malathion, the maximum observed respiration rates varied between 43 and 53 μg/O2 min, generally similar to the 49 μg O2/min rates observed in controls. Malathion did not alter the respiration ratio of O2 consumed-to-CO2 produced nor did it impact the shape of the oxygen consumption curves during respirometry. Shorter term (12 h) batch tests showed that both chemical oxygen demand (COD) and ammonia removal were not negatively impacted by the presence of 0.1-3 mg/L malathion. Longer term continuous addition (i.e. 40 days) of 0.1 mg/L of malathion also had no effect on COD and ammonia removal. In contrast to shorter term exposures, longer term continuous addition of 3 mg/L of malathion negatively impacted both COD and nitrogen removal and was associated with shifts in the abundance of species that are common to activated sludge. These results illustrate the impact that chemicals like malathion may have on COD removal, and nitrification, as well as the robustness of activated sludge microbial communities.

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.

Denitrifying phosphorus removal from municipal wastewater and dynamics of "Candidatus Accumulibacter" and denitrifying bacteria based on genes of ppk1, narG, nirS and nirK

Relevance of clade-level population dynamics of "Candidatus Accumulibacter" to performance of denitrifying phosphorus (P) removal from municipal wastewater was investigated. Stable denitrifying P removal in anoxic zone of continuous-flow reactor was achieved, accounting for 90% of total P removal. Clades IIC and IIF affiliated with Accumulibacter lineage were the dominant clades during denitrifying P removal, reaching 90% of ppk1 clone library. NarG gene library indicated Gamma and Beta-proteobacteria played an important role in nitrate reduction. Diversity and abundance of nirS library was much more than nirK, and thus became the main functional gene to execute nitrite reduction. Based on abundance of nirS, nirK and ppk1, the ratio of Accumulibacter capable of denitrifying P removal to total Accumulibacter was 22%. No matter whether Accumulibacter had narG gene or not, high abundance of narG at a level of 10(9)cells/(g dried-sludge) promoted nitrate reduced to nitrite, ensuring performance of denitrifying P removal.

Influence of nitrite accumulation on "Candidatus Accumulibacter" population structure and enhanced biological phosphorus removal from municipal wastewater

A modified University of Cape Town (MUCT) process was used to treat real municipal wastewater with low carbon to nitrogen ratio (C/N). To our knowledge, this is the first study where the influence of nitrite accumulation on "Candidatus Accumulibacter" clade-level population structure was investigated during nitritation establishment and destruction. Real time quantitative PCR assays were conducted using the polyphosphate kinase 1 gene (ppk1) as a genetic marker. Abundances of total "Candidatus Accumulibacter", the relative distributions and population structure of the five "Candidatus Accumulibacter" clades were characterized. Under complete nitrification, clade I using nitrate as electron acceptor was below 5% of total "Candidatus Accumulibacter". When the reactor was transformed into nitritation, clade I gradually disappeared. Clade IID using nitrite as electron acceptor for denitrifying phosphorus (P) removal was always the dominant "Candidatus Accumulibacter" throughout the operational period. This clade was above 90% on average in total "Candidatus Accumulibacter", even up to nearly 100%, which was associated with good performance of denitrifying P removal via nitrite pathway. The nitrite concentrations affected the abundance of clade IID. The P removal was mainly completed by anoxic P uptake of about 88%. The P removal efficiency clearly had a positive correlation with the nitrite accumulation ratio. Under nitritation, the P removal efficiency was 30% higher than that under complete nitrification, suggesting that nitrite was appropriate as electron acceptor for denitrifying P removal when treating carbon-limited wastewater.

Response of a sludge-minimizing lab-scale BNR reactor when the operation is changed to real primary effluent from synthetic wastewater

The activated sludge process is the most widely used treatment method for municipal wastewater. However, the excessive amount of biomass generated during the process is a major drawback. Earlier studies using the activated sludge process running in a biomass fasting and feasting mode demonstrated both nutrient removal and a minimization of biomass production. However, these studies were conducted using synthetic wastewater. In this study, we report findings from a lab-scale sludge-minimizing biological nutrient removing (BNR) reactor when its operation was changed from synthetic to real wastewater (primary effluent). Two lab-scale sequencing batch reactors, one in sludge minimization mode (hereafter called modified-SBR), and the other in conventional activated sludge mode (referred as control-SBR), were operated for more than 300 days. Both reactors were started and operated with synthetic feed. Gradually the feed to both reactors was changed to 100% primary effluent collected from a local full-scale wastewater treatment plant. Irrespective of the feed composition, more than 98% NH3-N removal was recorded in both SBRs. However, while 89% of the total dissolved phosphorus was removed from the 100% synthetic feed, only 80% of the total dissolved phosphorus was removed from the 100% primary effluent in both SBRs. The overall observed sludge reduction in the modified-SBR as compared to the control-SBR also decreased from 65% to 39% when the feed was changed from 100% synthetic to 100% primary effluent. The specific oxygen uptake rate for the modified-SBR was 80% higher than that for the control-SBR when the SBRs were fed with primary effluent wastewater. The modified-SBR showed a greater diversity of ammonia-oxidizing bacteria (AOBs) with synthetic wastewater as well as during the transition period than the control-SBR. Yet when the reactors were running on 100% real wastewater, only Nitrosomonas europaea/eutropha were identified in both SBRs. The nitrite-oxidizing bacterial community and the polyphosphate accumulating organisms (PAOs) responded in a similar way in both SBRs.

Multilevel correlations in the biological phosphorus removal process: From bacterial enrichment to conductivity-based metabolic batch tests and polyphosphatase assays

Enhanced biological phosphorus removal (EBPR) from wastewater relies on the preferential selection of active polyphosphate-accumulating organisms (PAO) in the underlying bacterial community continuum. Efficient management of the bacterial resource requires understanding of population dynamics as well as availability of bioanalytical methods for rapid and regular assessment of relative abundances of active PAOs and their glycogen-accumulating competitors (GAO). A systems approach was adopted here toward the investigation of multilevel correlations from the EBPR bioprocess to the bacterial community, metabolic, and enzymatic levels. Two anaerobic-aerobic sequencing-batch reactors were operated to enrich activated sludge in PAOs and GAOs affiliating with "Candidati Accumulibacter and Competibacter phosphates", respectively. Bacterial selection was optimized by dynamic control of the organic loading rate and the anaerobic contact time. The distinct core bacteriomes mainly comprised populations related to the classes Betaproteobacteria, Cytophagia, and Chloroflexi in the PAO enrichment and of Gammaproteobacteria, Alphaproteobacteria, Acidobacteria, and Sphingobacteria in the GAO enrichment. An anaerobic metabolic batch test based on electrical conductivity evolution and a polyphosphatase enzymatic assay were developed for rapid and low-cost assessment of the active PAO fraction and dephosphatation potential of activated sludge. Linear correlations were obtained between the PAO fraction, biomass specific rate of conductivity increase under anaerobic conditions, and polyphosphate-hydrolyzing activity of PAO/GAO mixtures. The correlations between PAO/GAO ratios, metabolic activities, and conductivity profiles were confirmed by simulations with a mathematical model developed in the aqueous geochemistry software PHREEQC.

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.

The impact of microbial ecology and chemical profile on the enhanced biological phosphorus removal (EBPR) process: a case study of Northern Wastewater Treatment Works, Johannesburg

The impact of polyphosphate-accumulating organism (PAO) and glycogen-accumulating organism (GAO) populations as well as of the chemical profile on the performance of Unit-3 (open elutriation tanks) and Unit-5 (covered elutriation tank) of the City of Johannesburg Northern Wastewater Treatment Works was determined. Physicochemical parameters of wastewater samples were measured using standard methods. Bacterial diversity was determined using 16S rRNA gene amplicon pyrosequencing of the variable region V1-3. Results showed soluble COD concentrations from settled sewage for Unit-3 at 192.8 mg COD/L and for Unit-5 at 214.6 mg COD/L, which increased to 301.8 mg COD/L and 411.6 mg COD/L in the overflow from elutriation tanks and decreased to 170.9 mg COD/L and 256.3 mg COD/L at the division boxes, respectively. Both long-chain volatile fatty acids (heptanoic acid, isobutyric acid, 3-methylbutanoic acid, pentanoic acid, 4-methylpentanoic acid, methylheptanoic acid) and short-chain volatile fatty acids (acetic acid, propionic acid, isobutyric acid) were present within concentration ranges of 17.19 mg/L to 54.98 mg/L and 13.64 mg/L to 87.6 mg/L for Unit 3 and 38.61 mg/L to58.85 mg/L and 21.63 mg/L to 92.39 mg/L for Unit 5, respectively. In the secondary settling tanks, the phosphate-removal efficiency in Unit-5 appeared to be slightly higher (0.08 mg P/L) compared to that of Unit-3 (0.11 mg P/L). The average DO concentrations (2.1 mg/L and 2.2 mg/L) as well as the pH values (pH 7 to pH 7.5) were found to be slightly higher in Unit-5 in the aerobic zones. The high presence of PAOs in the bioreactors (Unit-5: Dechloromonas (14.96%), Acinetobacter (6.3%), Zoogloea (4.72%) in the anaerobic zone and Dechloromonas (22.37 %) in the aerobic zone; Unit-3: Dechloromonas (37.25%) in the anaerobic zone and Dechloromonas (23.97%) in the aerobic zone) confirmed the phosphate-removal efficiencies of both units. Negligible GAOs were found in the aerobic zones (Defluviicoccus spp.: 0.33% for Unit-5 and 0.68% for Unit-3) and in the anaerobic zones (Defluviicoccus: 9.8% for Unit-3). The high microbial diversity and a negligible percentage of GAOs in Unit-5 could contribute to its high phosphate-removal efficiency, although results did not indicate statistically significant differences between the unit with a covered elutriation tank (Unit-5) and that with open elutriation tanks (Unit-3).

Occurrence of PAOI in a low temperature EBPR system

The occurrence of Accumulibacter Type I (a known phosphorus-accumulating organism, PAO) has received increased attention due to the potential operating benefits associated with their denitrifying activity in enhanced biological phosphorus removal (EBPR) wastewater treatment plants. In this study, after a shift from an enriched glycogen-accumulating organism (GAO) culture (competitors of PAO) to a PAO-enriched system, Accumulibacter Type I (PAO I) became dominant in an anaerobic-aerobic EBPR system fed with acetate and operated at 10°C with a net aerobic solids retention time (SRT) of 6 d. Since Accumulibacter Type II (PAO II) were not detected, the low temperature in combination with the net aerobic SRT applied appeared to have suppressed their growth as well. The stoichiometry of PAO I was in agreement with previous metabolic models, suggesting that it was the main PAO organisms present in previous studies operated under similar conditions. Moreover, under poly-P limiting conditions, PAO I were unable to switch to a GAO-like metabolism at low temperatures. These results contribute to increase the understanding of the physiology, microbial metabolism and microbial ecology of PAO I.

Comparative genomics of two 'Candidatus Accumulibacter' clades performing biological phosphorus removal

Members of the genus Candidatus Accumulibacter are important in many wastewater treatment systems performing enhanced biological phosphorus removal (EBPR). The Accumulibacter lineage can be subdivided phylogenetically into multiple clades, and previous work showed that these clades are ecologically distinct. The complete genome of Candidatus Accumulibacter phosphatis strain UW-1, a member of Clade IIA, was previously sequenced. Here, we report a draft genome sequence of Candidatus Accumulibacter spp. strain UW-2, a member of Clade IA, assembled following shotgun metagenomic sequencing of laboratory-scale bioreactor sludge. We estimate the genome to be 80-90% complete. Although the two clades share 16S rRNA sequence identity of >98.0%, we observed a remarkable lack of synteny between the two genomes. We identified 2317 genes shared between the two genomes, with an average nucleotide identity (ANI) of 78.3%, and accounting for 49% of genes in the UW-1 genome. Unlike UW-1, the UW-2 genome seemed to lack genes for nitrogen fixation and carbon fixation. Despite these differences, metabolic genes essential for denitrification and EBPR, including carbon storage polymer and polyphosphate metabolism, were conserved in both genomes. The ANI from genes associated with EBPR was statistically higher than that from genes not associated with EBPR, indicating a high selective pressure in EBPR systems. Further, we identified genomic islands of foreign origins including a near-complete lysogenic phage in the Clade IA genome. Interestingly, Clade IA appeared to be more phage susceptible based on it containing only a single Clustered Regularly Interspaced Short Palindromic Repeats locus as compared with the two found in Clade IIA. Overall, the comparative analysis provided a genetic basis to understand physiological differences and ecological niches of Accumulibacter populations, and highlights the importance of diversity in maintaining system functional resilience.

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.

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".

Phage encoded H-NS: a potential achilles heel in the bacterial defence system

The relationship between phage and their microbial hosts is difficult to elucidate in complex natural ecosystems. Engineered systems performing enhanced biological phosphorus removal (EBPR), offer stable, lower complexity communities for studying phage-host interactions. Here, metagenomic data from an EBPR reactor dominated by Candidatus Accumulibacter phosphatis (CAP), led to the recovery of three complete and six partial phage genomes. Heat-stable nucleoid structuring (H-NS) protein, a global transcriptional repressor in bacteria, was identified in one of the complete phage genomes (EPV1), and was most similar to a homolog in CAP. We infer that EPV1 is a CAP-specific phage and has the potential to repress up to 6% of host genes based on the presence of putative H-NS binding sites in the CAP genome. These genes include CRISPR associated proteins and a Type III restriction-modification system, which are key host defense mechanisms against phage infection. Further, EPV1 was the only member of the phage community found in an EBPR microbial metagenome collected seven months prior. We propose that EPV1 laterally acquired H-NS from CAP providing it with a means to reduce bacterial defenses, a selective advantage over other phage in the EBPR system. Phage encoded H-NS could constitute a previously unrecognized weapon in the phage-host arms race.

Microbiology of 'Candidatus Accumulibacter' in activated sludge

‘Candidatus Accumulibacter’ is a biotechnologically important bacterial group that can accumulate large amounts of intracellular polyphosphate, contributing to biological phosphorus removal in wastewater treatment. Since its first molecular identification more than a decade ago, this bacterial group has drawn significant research attention due to its high abundance in many biological phosphorus removal systems. In the past 6 years, our understanding of Accumulibacter microbiology and ecophysiology has advanced rapidly, largely owing to genomic information obtained through shotgun metagenomic sequencing efforts. In this review, we focus on the metabolism, physiology, fine‐scale population structure and ecological distribution of Accumulibacter, aiming to integrate the information learned so far and to present a more complete picture of the microbiology of this important bacterial group.