Polyphosphate kinase from activated sludge performing enhanced biological phosphorus removal

Demystifying polyphosphate-accumulating organisms relevant to wastewater treatment: A review of their phylogeny, metabolism, and detection

Currently, the most cost-effective and efficient method for phosphorus (P) removal from wastewater is enhanced biological P removal (EPBR) via polyphosphate-accumulating organisms (PAOs). This study integrates a literature review with genomic analysis to uncover the phylogenetic and metabolic diversity of the relevant PAOs for wastewater treatment. The findings highlight significant differences in the metabolic capabilities of PAOs relevant to wastewater treatment. Notably, Candidatus Dechloromonas and Candidatus Accumulibacter can synthesize polyhydroxyalkanoates, possess specific enzymes for ATP production from polyphosphate, and have electrochemical transporters for acetate and C4-dicarboxylates. In contrast, Tetrasphaera, Candidatus Phosphoribacter, Knoellia, and Phycicoccus possess PolyP-glucokinase and electrochemical transporters for sugars/amino acids. Additionally, this review explores various detection methods for polyphosphate and PAOs in activated sludge wastewater treatment plants. Notably, FISH-Raman spectroscopy emerges as one of the most advanced detection techniques. Overall, this review provides critical insights into PAO research, underscoring the need for enhanced strategies in biological phosphorus removal.

The role and mechanism of Bacillus megaterium strain A14 in inhibiting the cadmium uptake by peanut plants in acidic red soil

AIMS

This study explores the potential of cadmium (Cd)-resistant bacteria, specifically Bacillus megaterium A14, to decrease Cd accumulation in peanuts, a crop susceptible to metal uptake from contaminated soils, by understanding the bacterium's impact on plant Cd absorption mechanisms.

METHODS AND RESULTS

Through pot experiments, we observed that A14 inoculation significantly increased peanut biomass under Cd stress conditions, primarily by immobilizing the metal and reducing its bioavailability. The bacterium effectively changed the distribution of Cd, with a notable 46.53% reduction in the exchangeable fraction, which in turn limited the expression of genes related to Cd transport in peanuts. Additionally, A14 enhanced the plant's antioxidant response, improving its tolerance to stress. Microbial analysis through 16S sequencing demonstrated that A14 inoculation altered the peanut rhizosphere, particularly by increasing populations of Firmicutes and Proteobacteria, which play crucial roles in soil remediation from heavy metals.

CONCLUSION

The A14 strain effectively counters Cd toxicity in peanuts, promoting growth through soil Cd sequestration, root barrier biofilm formation, antioxidant system enhancement, suppression of Cd transport genes, and facilitation of Cd-remediating microorganisms.

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

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

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

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

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.

Streptomyces pactum and Bacillus consortium influenced the bioavailability of toxic metals, soil health, and growth attributes of Symphytum officinale in smelter/mining polluted soil

Soil microbes influence the uptake of toxic metals (TMs) by changing soil characteristics, bioavailability and translocation of TMs, and soil health indicators in polluted environment. The potential effect of Streptomyces pactum (Act12) and Bacillus consortium (B. subtilis and B. licheniformis; 1:1) on soil enzymes and bacterial abundance, bioavailability and translocation of Zn and Cd by Symphytum officinale, and physiological indicators in soil acquired from Fengxian (FX) mining site. Act12 and Bacillus consortium were applied at 0 (CK), 0.50 (T1), 1.50 (T2), and 2.50 (T3) g kg^-1 in a split plot design and three times harvested (H). Results showed that soil pH significantly dropped, whereas, electrical conductivity increased at higher Act12 and Bacillus doses. The extractable Zn lowered and Cd increased at each harvest compared to their controls. Soil β-glucosidase, alkaline phosphatase, urease and sucrase improved, whereas, dehydrogenase reduced in harvest 2 and 3 (H2 and H3) as compared to harvest 1 (H1) after Act12 and Bacillus treatments. The main soil phyla individually contributed ∼5-55.6%. Soil bacterial communities' distribution was also altered by Act12 and Bacillus amendments. Proteobacteria, Acidobacteria, and Bacteroidetes increased, whereas, the Actinobacteria, Chloroflexi, and Gemmatimonadetes decreased during the one-year trial. The Zn and Cd concentration significantly decreased in shoots at each harvest, whereas, the roots concentration was far higher than the shoots, implicating the rhizoremediation by S. officinale. Accumulation factor (AF) and bioconcentration ratio (BCR) of Zn and Cd in shoots were lower and remained higher in case of roots than the standard level (≥1). BCR values of roots indicated that S. officinale can be used for rhizoremediation of TMs in smelter/mines-polluted soils. Thus, field trials in smelter/mines contaminated soils and the potential role of saponin and tannin exudation in metal translocation by plant will broaden our understanding about the mechanism of rhizoremediation of TMs by S. officinale.

Initial-alkaline motivated fermentation of fine-sieving fractions and its effect on properties of cellulosic components

Exploration of value-added products from wastewater treatment plants (WWTPs) was promising for its sustainable development. This study simultaneously addressed the possibility of volatile fatty acids (VFAs) production boost and cellulosic components recovery from fine-sieving fractions (FSF) under initial alkaline conditions. The step utilization of FSF was relatively untapped in similar literatures. The effect of different initial pH values with 8.5, 9.5 and 10.5 (defined as F-8.5, F-9.5 and F-10.5) on fermentation performance were investigated. Then, the fermentation residues were collected to evaluate the changes in chemical structure and thermodynamic properties by fourier transform infrared spectroscopy (FTIR) and thermo-gravimetric (TG) analysis. Furthermore, analysis of the changes in microbial community structure and the interaction between functional genus and performance parameters were undertaken by high throughput sequencing and canonical correspondence analysis (CCA). Results showed that F-10.5 obtained the highest VFAs yields of 234 mg/g VSS, due to efficient polysaccharides release and inhibited methane production. However, high alkaline intensity caused proteins denaturation. Acidogenesis kinetics suggested that the fermentation rate was chemical-dominated. Although crystalline structure was more disordered with increasing alkalinity, the weight loss was lower than 2.5%, making it possible to recover cellulose from fermented residues. Interaction between functional genus and performance parameters revealed the microbial mechanism during the alkaline fermentation. Consequently, the initial-alkaline motivated fermentation was proved to be a promising technology in value-added products recovery to be cost economic, energy positive and environmental friendly.

Nitrite and nitrate inhibition thresholds for a glutamate-fed bio-P sludge

Enhanced biological phosphorus removal (EBPR) is an efficient and sustainable technology to remove phosphorus from wastewater. A widely known cause of EBPR deterioration in wastewater treatment plants (WWTPs) is the presence of nitrate/nitrite or oxygen in the anaerobic reactor. Moreover, most existing studies on the effect of either permanent aerobic conditions or inhibition of EBPR by nitrate or free nitrous acid (FNA) have been conducted with a "Candidatus Accumulibacter" or Tetrasphaera-enriched sludge, which are the two major reported groups of polyphosphate accumulating organisms (PAO) with key roles in full-scale EBPR WWTPs. This work reports the denitrification capabilities of a bio-P microbial community developed using glutamate as the sole source of carbon and nitrogen. This bio-P sludge exhibited a high denitrifying PAO (DPAO) activity, in fact, 56% of the phosphorus was uptaken under anoxic conditions. Furthermore, this mixed culture was able to use nitrite and nitrate as electron acceptor for P-uptake, being 1.8 μg HNO₂-N·L^-1 the maximum FNA concentration at which P-uptake can occur. Net P-removal was observed under permanent aerobic conditions. However, this microbial culture was more sensitive to FNA and permanent aerobic conditions compared to "Ca. Accumulibacter"-enriched sludge.

The storage compounds associated with Tetrasphaera PAO metabolism and the relationship between diversity and P removal

In enhanced biological phosphorus removal (EBPR), Tetrasphaera can potentially be an abundant and important polyphosphate accumulating organism (PAO), however ongoing questions remain concerning its storage compounds, phosphorus (P) removal capabilities and metabolic behaviour. This study investigated each of these points in an enriched Tetrasphaera culture (95% biovolume). The enriched Tetrasphaera culture fermented amino acids, while also converting and storing diverse amino acids as aspartic and glutamic acid within cells. Subsequent intracellular consumption of these two amino acids during the aerobic phase supports their importance in the metabolism of Tetrasphaera. Polyhydroxyalkanoate (PHA) cycling was also observed in this study, in contrast to some previous studies on Tetrasphaera. While exhibiting anaerobic phosphorus release and aerobic uptake, the highly enriched Tetrasphaera culture was unable to completely remove phosphorus in sequencing batch reactors (SBR) cycles, with an average removal efficiency of 72.3 ± 7.8%. This is unlike a previous study containing both Tetrasphaera (70%) and Accumulibacter (22%), which regularly performed complete phosphorus removal under otherwise similar operational conditions, at efficiencies of > 99%. Notably, the phylodiversity of organisms belonging to Tetrasphaera was substantially different in the present work, consisting mainly of organisms within Clade 2, likely impacting PHA cycling. These results suggest that the contribution of Tetrasphaera towards P removal is highly dependent on the composition of its Clades within this microbial group and an observed higher abundance of Tetrasphaera in WWTPs does not necessarily imply overall higher P removal. This study improves our understanding of the role of Tetrasphaera within EBPR systems and key factors impacting its metabolism.

Metabolic Differentiation of Co-occurring Accumulibacter Clades Revealed through Genome-Resolved Metatranscriptomics

Natural microbial communities consist of closely related taxa that may exhibit phenotypic differences and inhabit distinct niches. However, connecting genetic diversity to ecological properties remains a challenge in microbial ecology due to the lack of pure cultures across the microbial tree of life. "Candidatus Accumulibacter phosphatis" (Accumulibacter) is a polyphosphate-accumulating organism that contributes to the enhanced biological phosphorus removal (EBPR) biotechnological process for removing excess phosphorus from wastewater and preventing eutrophication from downstream receiving waters. Distinct Accumulibacter clades often coexist in full-scale wastewater treatment plants and laboratory-scale enrichment bioreactors and have been hypothesized to inhabit distinct ecological niches. However, since individual strains of the Accumulibacter lineage have not been isolated in pure culture to date, these predictions have been made solely on genome-based comparisons and enrichments with varying strain compositions. Here, we used genome-resolved metagenomics and metatranscriptomics to explore the activity of coexisting Accumulibacter strains in an engineered bioreactor environment. We obtained four high-quality genomes of Accumulibacter strains that were present in the bioreactor ecosystem, one of which is a completely contiguous draft genome scaffolded with long Nanopore reads. We identified core and accessory genes to investigate how gene expression patterns differed among the dominating strains. Using this approach, we were able to identify putative pathways and functions that may confer distinct functions to Accumulibacter strains and provide key functional insights into this biotechnologically significant microbial lineage. IMPORTANCE "Candidatus Accumulibacter phosphatis" is a model polyphosphate-accumulating organism that has been studied using genome-resolved metagenomics, metatranscriptomics, and metaproteomics to understand the EBPR process. Within the Accumulibacter lineage, several similar but diverging clades are defined by the shared sequence identity of the polyphosphate kinase (ppk1) locus. These clades are predicted to have key functional differences in acetate uptake rates, phage defense mechanisms, and nitrogen-cycling capabilities. However, such hypotheses have largely been made based on gene content comparisons of sequenced Accumulibacter genomes, some of which were obtained from different systems. Here, we performed time series genome-resolved metatranscriptomics to explore gene expression patterns of coexisting Accumulibacter clades in the same bioreactor ecosystem. Our work provides an approach for elucidating ecologically relevant functions based on gene expression patterns between closely related microbial populations.

In-situ remediation of nitrogen and phosphorus of beverage industry by potential strains Bacillus sp. (BK1) and Aspergillus sp. (BK2)

The bioremediation of beverage (treated and untreated) effluent was investigated in the current study by using the potential strains of Bacillus sp. (BK1) and Aspergillus sp. (BK2). Effluent was collected from the beverage industry (initial concentration of nitrogen were 3200 ± 0.5 mg/L and 4400 ± 0.6 mg/L whereas phosphorus were 4400 ± 2 mg/L and 2600 ± 1 mg/L in treated and untreated effluent correspondingly). Further, the BK1 and BK2 exhibited high removal competence after 1 week of incubation; BK1 removed phosphorus 99.95 ± 0.7% and BK2 95.69 ± 1% in treated effluent while nitrogen removed about 99.90 ± 0.4% by BK1 and 81.25 ± 0.8% by BK2 (initial concentration of phosphorus 4400 ± 2 mg/L and nitrogen 3200 ± 0.5 mg/L). Next, in the untreated effluent BK1 removed 99.81 ± 1% and BK2 99.85 ± 0.8% of phosphorus while removed nitrogen 99.93 ± 0.5% by BK1 and 99.95 ± 1.2% by BK2 correspondingly, (initial concentration of phosphorus 2600 ± 1 mg/L and nitrogen 4400 ± 0.6 mg/L). The physiochemical composition of sample such as pH, total carbohydrates, total proteins, total solids of treated and untreated effluent were also analysed before and after treatment of both the samples. BK1 and BK2 increased the pH by 8.94 ± 0.3 and 9.5 ± 0.4 correspondingly in treated effluent whereas 6.34 ± 0.5 and 7.5 ± 0.2 correspondingly in untreated effluent (initial pH of treated and untreated effluent 7.07 ± 0.8 and 4.85 ± 0.3 correspondingly). Total Carbohydrates removed about 17,440 ± 4.6 mg/L and 10,680 ± 3.2 mg/L by BK1 and BK2 correspondingly in treated effluent whereas 18,050 ± 3.5 mg/L and 18,340 ± 2.3 mg/L correspondingly in untreated effluent (initial concentration of treated and untreated effluent 25,780 ± 1.6 mg/L and 35,000 ± 1.5 mg/L correspondingly) while BK1 and BK2 removed total proteins by 30.336 ± 4.6 mg/L and 40.417 ± 2.3 mg/L correspondingly in treated effluent whereas 18.929 ± 1.2 mg/L and 17.526 ± 0.8 mg/L correspondingly in untreated effluent (initial concentration of treated and untreated effluent 49.225 ± 1.5 mg/L and 20.565 ± 1 mg/L correspondingly). Next, total solids removed by BK1 and BK2 2.5 ± 0.3 mg/L and 1.6 ± 0.6 mg/L correspondingly in treated effluent whereas 5.5 ± 0.8 mg/L and 4.6 ± 0.6 mg/L in untreated effluent (initial concentration of treated and untreated effluent 5.6 ± 1.5 mg/L and 9.48 ± 1.2 mg/L correspondingly). Both the strains BK1 and BK2 are highly efficient in the nitrogen and phosphorus removal therefore this strain may be applied for the potential remediation.

Genome Sequence of the Type Strain Azospira restricta SUA2 (DSM 18626)

Azospira restricta SUA2^T (DSM 18626) is a Gram-negative-staining bacterium able to fix nitrogen and accumulate polyhydroxybutyrate storage granules. Here, we report the complete genome sequence (3,975,213 bp with 68.64 mol% G+C content), which may prove useful in future efforts to assess the role of Azospira in nutrient cycling.

Azospira restricta SUA2^T (DSM 18626) is a Gram-negative-staining bacterium able to fix nitrogen and accumulate polyhydroxybutyrate storage granules. Here, we report the complete genome sequence (3,975,213 bp with 68.64 mol% G+C content), which may prove useful in future efforts to assess the role of Azospira in nutrient cycling.

Mechanism of nutrient removal enhancement in low carbon/nitrogen wastewater by a novel high-frequency micro-aeration/anoxic (HMOA) mode

In this study, a novel high-frequency micro-aeration/anoxic (HMOA) mode with a high aeration frequency (15 times/h) and short aeration duration (T_aer = 1 h/cycle) was proposed. Compared with continuous aeration modes, the highest nitrogen and phosphorus removal efficiencies were achieved in the sequencing batch reactor (SBR) under HMOA mode when treating wastewater with carbon/nitrogen (C/N) ratios of 4.5 (85% and 97%, respectively) and 3 (77% and 75%, respectively). Metagenomic analysis was utilized to analyse the microbial metabolic mechanism under the HMOA mode. The results showed that under the HMOA mode, the enhanced transduction and metabolism pathways of nitrate, nitrite, oxygen, phosphorus and acetate provided favourable nutritional conditions for the proliferation of denitrifiers and phosphorus accumulating organisms (PAOs), and simultaneously strengthened the survival capacity of nitrifiers under low dissolved oxygen (DO) conditions. In addition, genes involved in carbon metabolism were upregulated by the HMOA mode, which further increased the utility of carbon sources for denitrifier and PAO metabolism. Consequently, the limited carbon source could be fully utilized in nitrogen and phosphorus removal, which improved the efficiency of treating low C/N wastewater. This study proposed a potential aeration mode for microbial metabolism regulation to enhance nutrient removal in biological wastewater treatment processes.

Heavy metal-immobilizing bacteria combined with calcium polypeptides reduced the uptake of Cd in wheat and shifted the rhizosphere bacterial communities

In situ stabilization techniques for the "remediation" of heavy metal-contaminated soil are a novel and inexpensive technology. However, the mechanisms underlying the interaction of exogenous passivators with the bacterial community in wheat rhizosphere soil remain unclear. Soil static culture and pot experiments were conducted to evaluate the effects and mechanisms of the heavy metal-immobilizing bacterium Enterobacter bugandensis TJ6 and calcium polypeptides (CPPs) and their association with Cd uptake in wheat, soil quality and the rhizobacterial community structure. The results showed that compared with the control treatment (CK), the TJ6, CPP, and TJ6+CPP treatments significantly decreased the diethylenetriaminepentaacetic acid (DTPA)-extractable Cd (25.2%-60.1%) content and increased the pH, organic matter content and urease activity in the wheat rhizosphere soil, which resulted in decreases in the Cd (21.5%-77.8%) content in wheat tissues (grain, straw, and roots). In particular, the TJ6+CPP treatment was more effective at decreasing Cd accumulation in grains. Furthermore, the TJ6+CPP treatment improved the diversity of the soil bacterial community in the wheat rhizosphere, and the relative abundances of Proteobacteria, Firmicutes, Arthrobacter, Microvirga, Ensifer, Brevundimonas, Devosia and Pedobacter were enriched. These results suggest that the TJ6+CPP treatment decreased the uptake of Cd in wheat by i) providing essential elements (N and C sources), ii) increasing the pH and reducing the bioavailable Cd content in wheat rhizosphere soil, iii) allowing colonization to promote plant growth and Cd-resistant bacteria, and iv) increasing the abundance of genes associated with ABC transporters, carbon metabolism and oxidative phosphorylation in the rhizosphere bacterial community. Our results showed that the heavy metal-immobilizing bacterium TJ6 combined with CPPs decreased the Cd content and increased the bacterial community diversity of wheat rhizosphere soil. Our results also highlight the potential of using heavy metal-immobilizing bacteria and CPPs to ensure the safe production of crops growing on heavy metal-polluted soils.

Revegetation approach and plant identity unequally affect structure, ecological network and function of soil microbial community in a highly acidified mine tailings pond

Owing to its sustainability and low cost, direct revegetation (DR) has been considered a promising alternative to capped revegetation (CR) for dealing with the serious environmental problem derived from various types of mine wastelands that are widespread in the world. However, a direct comparison of the performance of these two revegetation approaches for reclamation of extremely acidic mine wastelands and the underlying mechanisms is still lacking. To bridge this critical knowledge gap, we established 5000 m² of vegetation on a highly acidified (pH < 3) Pb/Zn mine tailings pond employing both CR and DR schemes (2500 m² for each scheme). We then profiled the structure, ecological network and function of soil microbial communities associated with two dominant plant species of the vegetations via high-throughput sequencing. Our results showed that CR and DR achieved a vegetation coverage of 59.7% and 90.5% within two years, respectively. This pattern was accompanied by higher concentrations of plant nutrients and lower acidification potentials in topsoils of the rhizospheres of the vegetation established by DR compared to those of CR. Revegetation approach, rather than plant identity, mostly affected the structure, ecological network and function of soil microbial community in the mine tailings pond. Rhizosphere soils of the vegetation established by DR generally had higher microbial diversity, higher relative abundances of dominant microbial phyla (e.g. Nitrospirae) that can aid plant uptake of nutrients, more complicated microbial interactive networks and more microbial genes responsible for nutrient cycling than those by CR. As the first report on a direct comparison of CR and DR schemes for reclamation of an extremely acidic mine wasteland, our study has important implications for not only the understanding of microbial ecology in revegetated mine wastelands but also the further development of sustainable revegetation schemes.

Apricot shell- and apple tree-derived biochar affect the fractionation and bioavailability of Zn and Cd as well as the microbial activity in smelter contaminated soil

The aim of this study was to elucidate the effects of apricot shell-derived biochar (ASB) and apple tree-derived biochar (ATB) on soil properties, plant growth, microbial communities, enzymatic activities, and Zn and Cd fractionation and phytoavailability in mining soils. Smelter soil contaminated by Zn (1860.0 mg kg^-1) and Cd (39.9 mg kg^-1) was collected from Fengxian, China, treated with different doses (0 (control), 1, 2.5, 5, and 10% w/w) of both biochars and cultivated by Brassica juncea in a greenhouse pot experiment. The acid-soluble, reducible, oxidizable, and residual fraction and plant tissue concentrations of Zn and Cd were determined. Biochar addition improved plant growth (22.6-29.4%), soil pH (up to 0.94 units), and soil organic matter (up to 4-fold) compared to the control. The ASB and ATB, particularly ATB, reduced the acid-soluble (21-26% for Zn and 15-35% for Cd) and the reducible (9-36% for Zn and 11-19% for Cd) fractions of Zn and Cd and altered these fractions in the organic and residual fractions. Therefore, the biochars decreased the metal concentrations in the roots (36-41% for Zn and 33-37% for Cd) and shoots (25-31% for Zn and 20-29% for Cd), which might be due to the increase in pH, biochar liming effects, and metal sorption by the biochar. The biochars impact on the bacterial community composition was selective. The ASB and ATB decreased the activities of soil β-glucosidase, dehydrogenase, and alkaline phosphatase while increasing the urease activity. The biochars, particularly ATB, can be considered as effective soil amendments for reducing the phytotoxicity of Zn and Cd in contaminated soils, improving plant growth, enhancing the abundance of specific bacterial groups and increasing urease activity; however, more attention should be paid to their negative effects on the activities of β-glucosidase, dehydrogenase, and alkaline phosphatase.

Mechanisms of water regime effects on uptake of cadmium and nitrate by two ecotypes of water spinach (Ipomoea aquatica Forsk.) in contaminated soil

Availability of cadmium (Cd) and nitrate and their transfer to green leafy vegetables is highly dependent on physical, chemical and biochemical conditions of the soil. The phenotypic characteristics, accumulation of hazardous materials and rhizosphere properties of two ecotypes of water spinach in response to water stress were investigated. Flooding significantly enhanced plant growth and decreased Cd and nitrate concentrations in the shoot and root of both ecotypes of water spinach. Flooding extensively changed the physicochemical properties and biological processes in the rhizosphere, including increased pH and activities of urease and acid phosphatase, and decreased availability of Cd and nitrate and activity of nitrate reductase. Furthermore, flooding increased rhizosphere bacteria community diversity (including richness and evenness) and changed their community structure. Denitrifying bacteria (Clostridiales, Azoarcus and Pseudomonas), toxic metal resistant microorganisms (Rhodosporillaceae, Rhizobiales and Geobacter) were enriched in the rhizosphere under flooding conditions, and the plant growth-promoting taxa (Sphingomonadaceae) were preferentially colonized in the high accumulator (HA) rhizosphere region. These results indicated that flooding treatments result in biochemical and microbiological changes in soil, especially in the rhizosphere and reduced the availability of Cd and nitrate to plants, thus decreasing their uptake by water spinach. It is, therefore, possible to promote crop growth and reduce the accumulation of hazardous materials in vegetable crops like water spinach by controlling soil moisture conditions.

Biochar significantly alters rhizobacterial communities and reduces Cd concentration in rice grains grown on Cd-contaminated soils

Cadmium (Cd) contamination poses a serious problem in paddy soils. Biochar is frequently reported to deactivate Cd in soils and reduce Cd accumulation in rice plants, but few studies have addressed whether and how biochar affected the microbial communities in rice rhizosphere, which was an important factor determining the metal bioavailability and plant growth. In this study, biochar was pyrolyzed from bamboo (Phyllostachys heterocycla) chips at 350 °C. By using ICP-MS analysis and 16S rRNA gene sequencing, the impact of the biochar on Cd uptake by rice and on rhizospheric bacterial communities was investigated in both high-accumulating (HA) and low-accumulating (LA) rice cultivars grown in soils artificially contaminated with different Cd levels. Applied biochar significantly reduced Cd contents in rice plants of both cultivars, with substantially lower grain Cd contents for LA grown in highly contaminated soil. Soil pH was slightly increased by the applied biochar. Cd bioavailability was somehow reduced in soils, but not as significant as the reduction of Cd contents in rice plants. More interestingly, biochar application significantly altered the rhizobacterial community: it stimulated growth-promoting bacteria, such as Kaistobacter, Sphingobium (order Sphingomonadales), and Rhizobiaceae (order Rhizobiales); improved natural barrier formation and the transformation of metal mobilization around the rhizosphere mediated by, e.g., Rhodocyclaceae (class Betaproteobacteria) and Geobacter (class Deltaproteobacteria); and enhanced colonization of the LA rhizosphere possibly by taxa involved in Cd immobilization (Desulfovibrionales and Desulfobacterales). These results indicate that biochar application significantly reduces Cd uptake and accumulation by altering the rhizosphere bacterial community in rice grown on Cd-contaminated soils. The baseline data generated in this study provide insights that pave the way toward safer rice production.

Potentials and challenges of phosphorus recovery as vivianite from wastewater: A review

Due to the shortage of phosphorus resources and the limitations of existing phosphorus recovery methods, phosphorus recovery in the form of vivianite has attracted considerable attention with its natural ubiquity, easy accessibility and foreseeable economic value. This review systematically summarizes the chemistry of vivianite, including the characteristics, formation process and influencing factors of the material. Additionally, the potential of phosphorus recovery as vivianite from wastewater has also been comprehensively examined from the prospects of economic value and engineering feasibility. In general, this method is theoretically and practically feasible, and brings some extra benefits in WWTPs. However, the insufficient understanding on vivianite recovery in wastewater/sludge decelerate the development and exploration of such advanced approach. Further researches and cross-field supports would facilitate the improvement of this technique in the future.

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.

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.

Elucidating functional microorganisms and metabolic mechanisms in a novel engineered ecosystem integrating C, N, P and S biotransformation by metagenomics

Denitrifying sulfur conversion-associated enhanced biological phosphorous removal (DS-EBPR) system is not only a novel wastewater treatment process, but also an ideal model for microbial ecology in a community context. However, it exists the knowledge gap on the roles and interactions of functional microorganisms in the DS-EBPR system for carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) bioconversions. We use genome-resolved metagenomics to build up an ecological model of microbial communities in a lab-scale DS-EBPR system with stable operation for more than 400 days. Our results yield 11 near-complete draft genomes that represent a substantial portion of the microbial community (39.4%). Sulfate-reducing bacteria (SRB) and sulfide-oxidizing bacteria (SOB) promote complex metabolic processes and interactions for C, N, P and S conversions. Bins 1-4 and 10 are considered as new potential polyphosphate-accumulating organisms (PAOs), in which Bins 1-4 can be considered as S-related PAOs (S-PAOs) with no previously cultivated or reported members. Our findings give an insight into a new ecological system with C, N, P and S simultaneous bioconversions and improve the understanding of interactions among SRB, SOB, denitrifiers and PAOs within a community context.

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.

Dominant Candidatus Accumulibacter phosphatis Enriched in Response to Phosphate Concentrations in EBPR Process

Candidatus Accumulibacter phosphatis (Accumulibacter), which plays an important role in enhanced biological phosphorus removal in wastewater treatment plants, is phylogenetically classified into two major types (Types I and II). Phosphate concentrations affect the Accumulibacter community of the biomass enriched in treatment plants. Therefore, in the present study, Accumulibacter enrichments were conducted using a down-flow hanging sponge reactor under five conditions and a wide range of controlled phosphate concentrations in order to investigate how phosphate governs the community. We found that excessive phosphate levels inhibited Accumulibacter activity, that this inhibitory effect was greater for Type II. In addition, the affinity of Type II for phosphate was higher than that of Type I. Type IIA-B dominated at a phosphate concentration less than 5 mg P L^-1, while Type IA was dominant at 50 and 500 mg P L^-1. These patterns of enrichment may be explained by an inhibition kinetics model.

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

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

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.

Characterisation of Phosphate Accumulating Organisms and Techniques for Polyphosphate Detection: A Review

Phosphate minerals have long been used for the production of phosphorus-based chemicals used in many economic sectors. However, these resources are not renewable and the natural phosphate stocks are decreasing. In this context, the research of new phosphate sources has become necessary. Many types of wastes contain non-negligible phosphate concentrations, such as wastewater. In wastewater treatment plants, phosphorus is eliminated by physicochemical and/or biological techniques. In this latter case, a specific microbiota, phosphate accumulating organisms (PAOs), accumulates phosphate as polyphosphate. This molecule can be considered as an alternative phosphate source, and is directly extracted from wastewater generated by human activities. This review focuses on the techniques which can be applied to enrich and try to isolate these PAOs, and to detect the presence of polyphosphate in microbial cells.

Roles of extracellular polymeric substances in enhanced biological phosphorus removal process

Enhanced biological phosphorus removal (EBPR) process is known to mainly rely on the ability of phosphorus-accumulating organisms to take up, transform and store excess amount of phosphorus (P) inside the cells. However, recent studies have revealed considerable accumulation of P also in the extracellular polymeric substances (EPS) of sludge, implying a non-negligible role of EPS in P removal by EBPR sludge. However, the contribution of EPS to P uptake and the forms of accumulated extracellular P vary substantially in different studies, and the underlying mechanism of P transformation and transportation in EPS remains poorly understood. This review provides a new recognition into the P removal process in EBPR system by incorporating the role of EPS. It overviews on the characteristics of P accumulation in EPS, explores the mechanism of P transformation and transportation in EBPR sludge and EPS, summarizes the main influential factors for the P-accumulation properties of EPS, and discusses the remaining knowledge gaps and needed future efforts that may lead to better understanding and use of such an EPS role for maximizing P recovery from wastewater.

Microbiological study of bacteriophage induction in the presence of chemical stress factors in enhanced biological phosphorus removal (EBPR)

Polyphosphate accumulating organisms (PAOs) are responsible for carrying the enhanced biological phosphorus removal (EBPR). Although the EBPR process is well studied, the failure of EBPR performance at both laboratory and full-scale plants has revealed a lack of knowledge about the ecological and microbiological aspects of EBPR processes. Bacteriophages are viruses that infect bacteria as their sole host. Bacteriophage infection of polyphosphate accumulating organisms (PAOs) has not been considered as a main contributor to biological phosphorus removal upsets. This study examined the effects of different stress factors on the dynamics of bacteriophages and the corresponding effects on the phosphorus removal performance in a lab-scale EBPR system. The results showed that copper (heavy metal), cyanide (toxic chemical), and ciprofloxacin (antibiotic), as three different anthropogenic stress factors, can induce phages integrated onto bacterial genomes (i.e. prophages) in an enriched EBPR sequencing batch reactor, resulting in a decrease in the polyphosphate kinase gene ppk1 clades copy number, phosphorus accumulation capacity, and phosphorus removal performance. This study opens opportunities for further research on the effects of bacteriophages in nutrient cycles both in controlled systems such as wastewater treatment plants and natural ecosystems.

Effect of sludge age on methanogenic and glycogen accumulating organisms in an aerobic granular sludge process fed with methanol and acetate

The influence of sludge age on granular sludge formation and microbial population dynamics in a methanol- and acetate-fed aerobic granular sludge system operated at 35°C was investigated. During anaerobic feeding of the reactor, methanol was initially converted to methane by methylotrophic methanogens. These methanogens were able to withstand the relatively long aeration periods. Lowering the anaerobic solid retention time (SRT) from 17 to 8 days enabled selective removal of the methanogens and prevented unwanted methane formation. In absence of methanogens, methanol was converted aerobically, while granule formation remained stable. At high SRT values (51 days), γ-Proteobacteria were responsible for acetate removal through anaerobic uptake and subsequent aerobic growth on storage polymers formed [so called metabolism of glycogen-accumulating organisms (GAO)]. When lowering the SRT (24 days), Defluviicoccus-related organisms (cluster II) belonging to the α-Proteobacteria outcompeted acetate consuming γ-Proteobacteria at 35°C. DNA from the Defluviicoccus-related organisms in cluster II was not extracted by the standard DNA extraction method but with liquid nitrogen, which showed to be more effective. Remarkably, the two GAO types of organisms grew separately in two clearly different types of granules. This work further highlights the potential of aerobic granular sludge systems to effectively influence the microbial communities through sludge age control in order to optimize the wastewater treatment processes.

Available nitrogen is the key factor influencing soil microbial functional gene diversity in tropical rainforest

Background

Tropical rainforests cover over 50 % of all known plant and animal species and provide a variety of key resources and ecosystem services to humans, largely mediated by metabolic activities of soil microbial communities. A deep analysis of soil microbial communities and their roles in ecological processes would improve our understanding on biogeochemical elemental cycles. However, soil microbial functional gene diversity in tropical rainforests and causative factors remain unclear. GeoChip, contained almost all of the key functional genes related to biogeochemical cycles, could be used as a specific and sensitive tool for studying microbial gene diversity and metabolic potential. In this study, soil microbial functional gene diversity in tropical rainforest was analyzed by using GeoChip technology.

Results

Gene categories detected in the tropical rainforest soils were related to different biogeochemical processes, such as carbon (C), nitrogen (N) and phosphorus (P) cycling. The relative abundance of genes related to C and P cycling detected mostly derived from the cultured bacteria. C degradation gene categories for substrates ranging from labile C to recalcitrant C were all detected, and gene abundances involved in many recalcitrant C degradation gene categories were significantly (P < 0.05) different among three sampling sites. The relative abundance of genes related to N cycling detected was significantly (P < 0.05) different, mostly derived from the uncultured bacteria. The gene categories related to ammonification had a high relative abundance. Both canonical correspondence analysis and multivariate regression tree analysis showed that soil available N was the most correlated with soil microbial functional gene structure.

Conclusions

Overall high microbial functional gene diversity and different soil microbial metabolic potential for different biogeochemical processes were considered to exist in tropical rainforest. Soil available N could be the key factor in shaping the soil microbial functional gene structure and metabolic potential.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-015-0491-8) contains supplementary material, which is available to authorized users.

Enhancement of post-anoxic denitrification for biological nutrient removal: effect of different carbon sources

Previous research has demonstrated that post-anoxic denitrification and biological nutrient removal could be achieved in the oxic/anoxic/extended-idle wastewater treatment regime. This study further investigated the effect of different carbon sources on post-anoxic denitrification and biological nutrient removal. Acetate, propionate (volatile fatty acids (VFAs)), glucose (carbohydrate), methanol, and ethanol (alcohol) were used as the sole carbon source, respectively. The experimental results showed that VFA substrates led to an improvement in nitrogen and phosphorus removal. The total nitrogen and phosphorus removal efficiency values driven by acetate achieved 93 and 99%, respectively. In contrast, glucose present in mixed liquor deteriorated total nitrogen and phosphorus removal efficiency values to 72 and 54%. In the reactors cultured with methanol and ethanol, 66 and 63% of the total nitrogen were removed, and phosphorus removal efficiency values were 78 and 71%, respectively. The mechanism studies revealed that different carbon sources affected the transformations of intracellular polyhydroxyalkanoates (PHAs) and glycogen. PHAs are the dominant storages for microorganisms cultured with VFA substrates. Though glycogen is not the favorable energy and carbon source for polyphosphate-accumulating organisms, it can be consumed by microorganisms related to biological nitrogen removal and is able to serve as the electron donor for post-anoxic denitrification.

Phosphorus sequestration in the form of polyphosphate by microbial symbionts in marine sponges

Marine sponges are major habitat-forming organisms in coastal benthic communities and have an ancient origin in evolution history. Here, we report significant accumulation of polyphosphate (polyP) granules in three common sponge species of the Caribbean coral reef. The identity of the polyP granules was confirmed by energy-dispersive spectroscopy (EDS) and by the fluorescence properties of the granules. Microscopy images revealed that a large proportion of microbial cells associated with sponge hosts contained intracellular polyP granules. Cyanobacterial symbionts cultured from sponges were shown to accumulate polyP. We also amplified polyphosphate kinase (ppk) genes from sponge DNA and confirmed that the gene was expressed. Based on these findings, we propose here a potentially important phosphorus (P) sequestration pathway through symbiotic microorganisms of marine sponges. Considering the widespread sponge population and abundant microbial cells associated with them, this pathway is likely to have a significant impact on the P cycle in benthic ecosystems.

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.

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.

Isolation and identification of an iopromide-degrading strain and its application in an A2/O system

An iopromide (IOPr)-degrading bacterium was isolated from activated sludge of a wastewater treatment plant in Shanghai. Based on its morphology, physiological-biochemical characteristics and a phylogenetic analysis of its 16S rRNA sequence, the bacterium was identified and named as Pseudomonas sp. I-24. The optimum condition for degrading IOPr was at 30°C and pH 7.0. After 5 days, strain I-24 could degrade 30 mg/L IOPr by 99% in a basal salts medium with a 5% (V/V) inoculum and 200 mg/L starch as the primary substrate. When applied to an Anaerobic-Anoxic/Aerobic (A2/O) process, with the coexistence of other bacteria, the strain I-24 got lower (61.3%) IOPr removal, but in two A2/O systems (with and without I-24 inoculation), the CODcr removal were both approximately 95%. The trial dosed with strain I-24 showed better IOPr removal than the un-dosed one. I-24 sustained its abundance in the A2/O system during the experiment.

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".

Characterization of the denitrification-associated phosphorus uptake properties of "Candidatus Accumulibacter phosphatis" clades in sludge subjected to enhanced biological phosphorus removal

To characterize the denitrifying phosphorus (P) uptake properties of "Candidatus Accumulibacter phosphatis," a sequencing batch reactor (SBR) was operated with acetate. The SBR operation was gradually acclimated from anaerobic-oxic (AO) to anaerobic-anoxic-oxic (A2O) conditions by stepwise increases of nitrate concentration and the anoxic time. The communities of "Ca. Accumulibacter" and associated bacteria at the initial (AO) and final (A2O) stages were compared using 16S rRNA and polyphosphate kinase genes and using fluorescence in situ hybridization (FISH). The acclimation process led to a clear shift in the relative abundances of recognized "Ca. Accumulibacter" subpopulations from clades IIA > IA > IIF to clades IIC > IA > IIF, as well as to increases in the abundance of other associated bacteria (Dechloromonas [from 1.2% to 19.2%] and "Candidatus Competibacter phosphatis" [from 16.4% to 20.0%]), while the overall "Ca. Accumulibacter" abundance decreased (from 55.1% to 29.2%). A series of batch experiments combined with FISH/microautoradiography (MAR) analyses was performed to characterize the denitrifying P uptake properties of the "Ca. Accumulibacter" clades. In FISH/MAR experiments using slightly diluted sludge (∼0.5 g/liter), all "Ca. Accumulibacter" clades successfully took up phosphorus in the presence of nitrate. However, the "Ca. Accumulibacter" clades showed no P uptake in the presence of nitrate when the sludge was highly diluted (∼0.005 g/liter); under these conditions, reduction of nitrate to nitrite did not occur, whereas P uptake by "Ca. Accumulibacter" clades occurred when nitrite was added. These results suggest that the "Ca. Accumulibacter" cells lack nitrate reduction capabilities and that P uptake by "Ca. Accumulibacter" is dependent upon nitrite generated by associated nitrate-reducing bacteria such as Dechloromonas and "Ca. Competibacter."

Enzymes of inorganic polyphosphate metabolism

Inorganic polyphosphate (PolyP) is a linear polymer containing a few to several hundred orthophosphate residues linked by energy-rich phosphoanhydride bonds. Investigation of PolyP-metabolizing enzymes is important for medicine, because PolyPs perform numerous functions in the cells. In human organism, PolyPs are involved in the regulation of Ca(2+) uptake in mitochondria, bone tissue development, and blood coagulation. The essentiality of polyphosphate kinases in the virulence of pathogenic bacteria is a basis for the discovery of new antibiotics. The properties of the major enzymes of PolyP metabolism, first of all polyphosphate kinases and exopolyphosphatases, are described in the review. The main differences between the enzymes of PolyP biosynthesis and utilization of prokaryotic and eukaryotic cells, as well as the multiple functions of some enzymes of PolyP metabolism, are considered.

GeoChip-based analysis of the functional gene diversity and metabolic potential of soil microbial communities of mangroves

Mangroves are unique and highly productive ecosystems and harbor very special microbial communities. Although the phylogenetic diversity of sediment microbial communities of mangrove habitats has been examined extensively, little is known regarding their functional gene diversity and metabolic potential. In this study, a high-throughput functional gene array (GeoChip 4.0) was used to analyze the functional diversity, composition, structure, and metabolic potential of microbial communities in mangrove habitats from mangrove national nature reserves in China. GeoChip data indicated that these microbial communities were functionally diverse as measured by the number of genes detected, unique genes, and various diversity indices. Almost all key functional gene categories targeted by GeoChip 4.0 were detected in the mangrove microbial communities, including carbon (C) fixation, C degradation, methane generation, nitrogen (N) fixation, nitrification, denitrification, ammonification, N reduction, sulfur (S) metabolism, metal resistance, antibiotic resistance, and organic contaminant degradation. Detrended correspondence analysis (DCA) of all detected genes showed that Spartina alterniflora (HH), an invasive species, did not harbor significantly different microbial communities from Aegiceras corniculatum (THY), a native species, but did differ from other species, Kenaelia candel (QQ), Aricennia marina (BGR), and mangrove-free mud flat (GT). Canonical correspondence analysis (CCA) results indicated the microbial community structure was largely shaped by surrounding environmental variables, such as total nitrogen (TN), total carbon (TC), pH, C/N ratio, and especially salinity. This study presents a comprehensive survey of functional gene diversity of soil microbial communities from different mangrove habitats/species and provides new insights into our understanding of the functional potential of microbial communities in mangrove ecosystems.

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.