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Ni M, Chen Y, Pan Y, Huang Y, Li DP, Li L, Huang B, Song Z. Study on community structure and metabolic mechanism of dominant polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs) in suspended biofilm based on phosphate recovery. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:152678. [PMID: 34973331 DOI: 10.1016/j.scitotenv.2021.152678] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 05/16/2023]
Abstract
Biofilm sequencing batch reactor (BSBR) can achieve efficient phosphate (P) removal and enrichment, but its process performance and metabolic mechanisms for P removal and enrichment of municipal wastewater remain largely unclear. In the present study, we assessed the P removal and enrichment of municipal wastewater at influent P concentrations of 2.5 mg/L and 10 mg/L. The efficiency of P removal and enzyme activity in polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs) were compared, and the growth and metabolic characteristics of dominant PAOs and GAOs at different influent P concentrations were studied with the macro-sequencing technology. The results showed that the P recovery efficiencies were 70.03% and 76.19% when the influent P concentration was 2.5 mg/L and 10 mg/L in BSBR, respectively, and the maximum P concentration of recovery liquid was 81.29 mg/L and 173.12 mg/L, respectively. There were no phosphate kinase (PPK) and phosphate hydrolase (PPX) in extracellular polymeric substances (EPS). The dominant PAOs were Candidatus_Contendobacter, Dechloromonas, and Flavobacterium, and the dominant GAO was Candidatus_Competibacter. The abundance of Candidatus_Contendobacter was the highest with the most potential contribution to P removal. PAOs had competitive advantages in carbon (C) source uptake, glycogen metabolism, P metabolism, and adenosine triphosphate (ATP) metabolism. HMP was unique to PAOs, EMP had the highest abundance in glycogen metabolism, and ED was contained in PAOs of BSBR. These results indicated that BSBR provided sufficient reducing power and ATP for PAOs through different glycogen decomposition pathways to promote P uptake and obtained competitive advantages in P metabolism, C source uptake, and ATP utilization to achieve efficient P removal and enrichment. Collectively, our current findings provided valuable insights into the P removal and enrichment mechanism of BSBR in municipal sewage.
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Affiliation(s)
- Min Ni
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, China; Jiangsu Key Laboratory of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, China
| | - Yue Chen
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, China
| | - Yang Pan
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, China; National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, Suzhou University of Science and Technology, Suzhou, China.
| | - Yong Huang
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, China; National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, Suzhou University of Science and Technology, Suzhou, China
| | - Da-Peng Li
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, China; National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, Suzhou University of Science and Technology, Suzhou, China
| | - Lu Li
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, China
| | - Bo Huang
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, China
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Ni M, Pan Y, Chen Y, Zhang X, Huang Y, Song Z. Effects of seasonal temperature variations on phosphorus removal, recovery, and key metabolic pathways in the suspended biofilm. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108187] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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3
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Izadi P, Izadi P, Eldyasti A. A review of biochemical diversity and metabolic modeling of EBPR process under specific environmental conditions and carbon source availability. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 288:112362. [PMID: 33831633 DOI: 10.1016/j.jenvman.2021.112362] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/25/2021] [Accepted: 03/09/2021] [Indexed: 05/25/2023]
Abstract
Enhanced biological phosphorus removal (EBPR) is one of the most promising technologies as an economical and environmentally sustainable technique for removal of phosphorus from wastewater (WW). However, with high capacity of EBPR, insufficient P-removal is a major yet common issue of many full-scale wastewater treatment plants (WWTP), due to misinterpreted environmental and microbial disturbance. By developing a rather extensive understanding on biochemical pathways and metabolic models governing the anaerobic and aerobic/anoxic processes; the optimal operational conditions, environmental changes and microbial population interaction are efficiently predicted. Therefore, this paper critically reviews the current knowledge on biochemical pathways and metabolic models of phosphorus accumulating organisms (PAOs) and glycogen accumulating organisms (GAOs) as the most abundant microbial populations in EBPR process with an insight on the effect of available carbon source types in WW on phosphorus removal performance. Moreover, this paper critically assesses the gaps and potential future research in metabolic modeling area. With all the developments on EBPR process in the past few decades, there is still lack of knowledge in this critical sector. This paper hopes to touch on this problem by gathering the existing knowledge and to provide farther insights on the future work onto chemical transformations and metabolic strategies in different conditions to benefit the quantitative model as well as WWTP designs.
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Affiliation(s)
- Parnian Izadi
- Civil engineering, York university, 4700 Keele St, Toronto, M3J 1P3, ON, Canada.
| | - Parin Izadi
- Civil engineering, York university, 4700 Keele St, Toronto, M3J 1P3, ON, Canada.
| | - Ahmed Eldyasti
- Civil engineering, York university, 4700 Keele St, Toronto, M3J 1P3, ON, Canada.
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4
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Xu J, Pang H, He J, Nan J. The effect of supporting matrix on sludge granulation under low hydraulic shear force: Performance, microbial community dynamics and microorganisms migration. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 712:136562. [PMID: 32050387 DOI: 10.1016/j.scitotenv.2020.136562] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/12/2019] [Accepted: 01/04/2020] [Indexed: 06/10/2023]
Abstract
Granular sludge usually takes extracellular polymers (EPS) as matrices for colonizing microorganisms and maintaining structural stability. However, the low strength of EPS threatens the disintegration of granules, especially under low hydraulic shear force. To accelerate the formation and enhance the stability of granules, micro-sized melamine (ME) sponges (RA) and polyurethane (PU) sponges (RB) were screened out as matrix substitutes for developing aerobic granular biofilm (AGB) in this study. The superficial gas velocity was 0.8 cm s-1. Both reactors achieved over 95% ammonium nitrogen removal efficiency within 10 days. During stabilization period, the chemical oxygen demand, total nitrogen and total phosphorus removal efficiencies were 90.5%, 70% and 95% in RA and 87.8%, 83% and 88% in RB, respectively. Confocal laser scanning microscopy (CLSM) detection revealed that β-polysaccharide was more concentrated in the outer layer in PU-AGB but uniformly dispersed in ME-AGB. The denitrifying phosphorus accumulating organisms (Flavobacterium) was dominant in RA, while the denitrifying glycogen accumulating organisms (Candidatus_Competibacter) was dominant in RB. Fluorescence in situ hybridization (FISH) analysis indicated that the microbial distribution in ME-AGB was relatively uniform, while there was a significant migration of functional microorganisms in PU-AGB. The super-hydrophilicity of ME and the high hydrophobicity of PU may be the main reasons for these differences. Overall, this study indicated that ME sponge is a more suitable material for supporting AGB than PU sponge.
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Affiliation(s)
- Jie Xu
- School of Environment, Harbin Institute of Technology (HIT), Harbin 150090, China
| | - Heliang Pang
- School of Environment, Harbin Institute of Technology (HIT), Harbin 150090, China.
| | - Junguo He
- Guangzhou University, Guangzhou 510006, China
| | - Jun Nan
- School of Environment, Harbin Institute of Technology (HIT), Harbin 150090, China
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5
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Almuktar SAAAN, Abed SN, Scholz M. Wetlands for wastewater treatment and subsequent recycling of treated effluent: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:23595-23623. [PMID: 29959736 PMCID: PMC6096557 DOI: 10.1007/s11356-018-2629-3] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 06/20/2018] [Indexed: 05/23/2023]
Abstract
Due to water scarcity challenges around the world, it is essential to think about non-conventional water resources to address the increased demand in clean freshwater. Environmental and public health problems may result from insufficient provision of sanitation and wastewater disposal facilities. Because of this, wastewater treatment and recycling methods will be vital to provide sufficient freshwater in the coming decades, since water resources are limited and more than 70% of water are consumed for irrigation purposes. Therefore, the application of treated wastewater for agricultural irrigation has much potential, especially when incorporating the reuse of nutrients like nitrogen and phosphorous, which are essential for plant production. Among the current treatment technologies applied in urban wastewater reuse for irrigation, wetlands were concluded to be the one of the most suitable ones in terms of pollutant removal and have advantages due to both low maintenance costs and required energy. Wetland behavior and efficiency concerning wastewater treatment is mainly linked to macrophyte composition, substrate, hydrology, surface loading rate, influent feeding mode, microorganism availability, and temperature. Constructed wetlands are very effective in removing organics and suspended solids, whereas the removal of nitrogen is relatively low, but could be improved by using a combination of various types of constructed wetlands meeting the irrigation reuse standards. The removal of phosphorus is usually low, unless special media with high sorption capacity are used. Pathogen removal from wetland effluent to meet irrigation reuse standards is a challenge unless supplementary lagoons or hybrid wetland systems are used.
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Affiliation(s)
- Suhad A A A N Almuktar
- Civil Engineering Research Group, School of Computing, Science and Engineering, The University of Salford, Newton Building, Salford, England, M5 4WT, UK
- Department of Architectural Engineering, Faculty of Engineering, The University of Basrah, Al Basrah, Iraq
| | - Suhail N Abed
- Civil Engineering Research Group, School of Computing, Science and Engineering, The University of Salford, Newton Building, Salford, England, M5 4WT, UK
| | - Miklas Scholz
- Civil Engineering Research Group, School of Computing, Science and Engineering, The University of Salford, Newton Building, Salford, England, M5 4WT, UK.
- Division of Water Resources Engineering, Department of Building and Environmental Technology, Faculty of Engineering, Lund University, P.O. Box 118, 221 00, Lund, Sweden.
- Department of Civil Engineering Science, School of Civil Engineering and the Built Environment, University of Johannesburg, Kingsway Campus, Auckland Park, PO Box 524, Johannesburg, 2006, South Africa.
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6
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Nurmiyanto A, Kodera H, Kindaichi T, Ozaki N, Aoi Y, Ohashi A. Dominant Candidatus Accumulibacter phosphatis Enriched in Response to Phosphate Concentrations in EBPR Process. Microbes Environ 2017; 32:260-267. [PMID: 28890468 PMCID: PMC5606696 DOI: 10.1264/jsme2.me17020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
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.
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Affiliation(s)
- Awaluddin Nurmiyanto
- Graduate School of Engineering, Hiroshima University.,Department of Environmental Engineering, Islamic University of Indonesia (UII)
| | - Hiroya Kodera
- Graduate School of Engineering, Hiroshima University
| | | | | | - Yoshiteru Aoi
- Graduated School of Advanced Sciences of Matter, Department of Molecular Biotechnology, Hiroshima University
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7
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Zeng W, Wang A, Li C, Guo Y, Peng Y. Population dynamics of “ Candidatus Accumulibacter phosphatis” under the modes of complete nitrification and partial nitrification (nitritation) in domestic wastewater treatment system. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2017.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Camejo PY, Owen BR, Martirano J, Ma J, Kapoor V, Santo Domingo J, McMahon KD, Noguera DR. Candidatus Accumulibacter phosphatis clades enriched under cyclic anaerobic and microaerobic conditions simultaneously use different electron acceptors. WATER RESEARCH 2016; 102:125-137. [PMID: 27340814 PMCID: PMC7323474 DOI: 10.1016/j.watres.2016.06.033] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 05/26/2016] [Accepted: 06/13/2016] [Indexed: 05/05/2023]
Abstract
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.
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Affiliation(s)
- Pamela Y Camejo
- Department of Civil and Environmental Engineering, University of Wisconsin - Madison, Madison, WI, USA.
| | - Brian R Owen
- Department of Civil and Environmental Engineering, University of Wisconsin - Madison, Madison, WI, USA.
| | - Joseph Martirano
- Department of Civil and Environmental Engineering, University of Wisconsin - Madison, Madison, WI, USA.
| | - Juan Ma
- School of Environmental & Municipal Engineering, Lanzhou Jiaotong University, China.
| | - Vikram Kapoor
- Environmental Protection Agency, Cincinnati, OH, USA.
| | | | - Katherine D McMahon
- Department of Civil and Environmental Engineering, University of Wisconsin - Madison, Madison, WI, USA; Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA.
| | - Daniel R Noguera
- Department of Civil and Environmental Engineering, University of Wisconsin - Madison, Madison, WI, USA.
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9
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Mao Y, Wang Z, Li L, Jiang X, Zhang X, Ren H, Zhang T. Exploring the Shift in Structure and Function of Microbial Communities Performing Biological Phosphorus Removal. PLoS One 2016; 11:e0161506. [PMID: 27547976 PMCID: PMC4993488 DOI: 10.1371/journal.pone.0161506] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 08/05/2016] [Indexed: 01/26/2023] Open
Abstract
A sequencing batch reactor fed mainly by acetate was operated to perform enhanced biological phosphorus removal (EBPR). A short-term pH shock from 7.0 to 6.0 led to a complete loss of phosphate-removing capability and a drastic change of microbial communities. 16S rRNA gene pyrosequencing showed that large proportions of glycogen accumulating organisms (GAOs) (accounted for 16% of bacteria) bloomed, including Candidatus Competibacter phosphatis and Defluviicoccus-related tetrad-forming organism, causing deteriorated EBPR performance. The EBPR performance recovered with time and the dominant Candidatus Accumulibacter (Accumulibacter) clades shifted from Clade IIC to IIA while GAOs populations shrank significantly. The Accumulibacter population variation provided a good opportunity for genome binning using a bi-dimensional coverage method, and a genome of Accumulibacter Clade IIC was well retrieved with over 90% completeness. Comparative genomic analysis demonstrated that Accumulibacter clades had different abilities in nitrogen metabolism and carbon fixation, which shed light on enriching different Accumulibacter populations selectively.
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Affiliation(s)
- Yanping Mao
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, China
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zhiping Wang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Liguan Li
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xiaotao Jiang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xuxiang Zhang
- School of Environment, Nanjing University, Nanjing, China
| | - Hongqiang Ren
- School of Environment, Nanjing University, Nanjing, China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- * E-mail:
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Barr JJ, Dutilh BE, Skennerton CT, Fukushima T, Hastie ML, Gorman JJ, Tyson GW, Bond PL. Metagenomic and metaproteomic analyses of Accumulibacter phosphatis-enriched floccular and granular biofilm. Environ Microbiol 2015; 18:273-87. [PMID: 26279094 DOI: 10.1111/1462-2920.13019] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 06/30/2015] [Accepted: 08/11/2015] [Indexed: 11/30/2022]
Abstract
Biofilms are ubiquitous in nature, forming diverse adherent microbial communities that perform a plethora of functions. Here we operated two laboratory-scale sequencing batch reactors enriched with Candidatus Accumulibacter phosphatis (Accumulibacter) performing enhanced biological phosphorus removal. Reactors formed two distinct biofilms, one floccular biofilm, consisting of small, loose, microbial aggregates, and one granular biofilm, forming larger, dense, spherical aggregates. Using metagenomic and metaproteomic methods, we investigated the proteomic differences between these two biofilm communities, identifying a total of 2022 unique proteins. To understand biofilm differences, we compared protein abundances that were statistically enriched in both biofilm states. Floccular biofilms were enriched with pathogenic secretion systems suggesting a highly competitive microbial community. Comparatively, granular biofilms revealed a high-stress environment with evidence of nutrient starvation, phage predation pressure, and increased extracellular polymeric substance and cell lysis. Granular biofilms were enriched in outer membrane transport proteins to scavenge the extracellular milieu for amino acids and other metabolites, likely released through cell lysis, to supplement metabolic pathways. This study provides the first detailed proteomic comparison between Accumulibacter-enriched floccular and granular biofilm communities, proposes a conceptual model for the granule biofilm, and offers novel insights into granule biofilm formation and stability.
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Affiliation(s)
- Jeremy J Barr
- Department of Biology, San Diego State University, San Diego, CA, USA.,Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Qld, Australia.,Environmental Biotechnology Cooperative Research Centre (EBCRC), Sydney, NSW, Australia
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands.,Centre for Molecular and Biomedical Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.,Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Connor T Skennerton
- Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Qld, Australia.,Australian Centre for Ecogenomics, School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia.,Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Toshikazu Fukushima
- Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Qld, Australia.,Division of Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Marcus L Hastie
- Protein Discovery Centre, Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Herston, Qld, Australia
| | - Jeffrey J Gorman
- Protein Discovery Centre, Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Herston, Qld, Australia
| | - Gene W Tyson
- Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Qld, Australia.,Australian Centre for Ecogenomics, School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
| | - Philip L Bond
- Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Qld, Australia.,Environmental Biotechnology Cooperative Research Centre (EBCRC), Sydney, NSW, Australia
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11
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Wong DHJ, Beiko RG. Transfer of energy pathway genes in microbial enhanced biological phosphorus removal communities. BMC Genomics 2015; 16:526. [PMID: 26173980 PMCID: PMC4502571 DOI: 10.1186/s12864-015-1752-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 07/06/2015] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Lateral gene transfer (LGT) is an important evolutionary process in microbial evolution. In sewage treatment plants, LGT of antibiotic resistance and xenobiotic degradation-related proteins has been suggested, but the role of LGT outside these processes is unknown. Microbial communities involved in Enhanced Biological Phosphorus Removal (EBPR) have been used to treat wastewater in the last 50 years and may provide insights into adaptation to an engineered environment. We introduce two different types of analysis to identify LGT in EBPR sewage communities, based on identifying assembled sequences with more than one strong taxonomic match, and on unusual phylogenetic patterns. We applied these methods to investigate the role of LGT in six energy-related metabolic pathways. RESULTS The analyses identified overlapping but non-identical sets of transferred enzymes. All of these were homologous with sequences from known mobile genetic elements, and many were also in close proximity to transposases and integrases in the EBPR data set. The taxonomic method had higher sensitivity than the phylogenetic method, identifying more potential LGTs. Both analyses identified the putative transfer of five enzymes within an Australian community, two in a Danish community, and none in a US-derived culture. CONCLUSIONS Our methods were able to identify sequences with unusual phylogenetic or compositional properties as candidate LGT events. The association of these candidates with known mobile elements supports the hypothesis of transfer. The results of our analysis strongly suggest that LGT has influenced the development of functionally important energy-related pathways in EBPR systems, but transfers may be unique to each community due to different operating conditions or taxonomic composition.
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Affiliation(s)
- Dennis H-J Wong
- Faculty of Graduate Studies, Dalhousie University, Halifax, Nova Scotia, Canada.
| | - Robert G Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada.
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12
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From macro to lab-scale: Changes in bacterial community led to deterioration of EBPR in lab reactor. Open Life Sci 2013. [DOI: 10.2478/s11535-013-0116-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AbstractA laboratory scale sequencing batch reactor (SBR), fed with synthetic wastewater containing a mixture of organic compounds, was operated for nearly six months. Despite maintaining the same operational conditions, a deterioration of enhanced biological phosphorus removal (EBPR) occurred after 40 days of SBR operation. The Prel/Cupt ratio decreased from 0.28 to 0.06 P-mol C-mol−1, and C requirements increased from 11 to 32 mg C h−1 g−1 of mixed liquor suspended solids. A FISH analysis showed that the percentage of Accumulibacter in an overall community of polyphosphate accumulating organisms (PAOs) and glycogen accumulating organisms (GAOs) dropped from 93% to 13%. An increase in abundance of Gammaproteobacteria (from 2.6% to 22%) and Alphaproteobacteria (from 1.8% to 10%) was observed. The number of Competibacter increased from 0.5% to nearly 9%. Clusters 1 and 2 of Defluviicoccus-related GAOs, not detected before deterioration, constituted 35% and 27% of Alphaproteobacteria, respectively. We concluded that lab-scale experiments should not be extended implicitly to full-scale EBPR systems because some bacterial groups are detected mainlyin lab-scale reactors. Well-defined, lab-scale operational conditions reduce the number of ecological niches available to bacteria.
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13
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Characterization of the denitrification-associated phosphorus uptake properties of "Candidatus Accumulibacter phosphatis" clades in sludge subjected to enhanced biological phosphorus removal. Appl Environ Microbiol 2013; 79:1969-79. [PMID: 23335771 DOI: 10.1128/aem.03464-12] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
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."
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14
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Comparison between aerobic and anoxic metabolism of denitrifying-EBPR sludge: effect of biomass poly-hydroxyalkanoates content. N Biotechnol 2013; 30:227-37. [DOI: 10.1016/j.nbt.2012.05.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2011] [Revised: 05/22/2012] [Accepted: 05/28/2012] [Indexed: 11/23/2022]
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15
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Bassin JP, Kleerebezem R, Dezotti M, van Loosdrecht MCM. Simultaneous nitrogen and phosphate removal in aerobic granular sludge reactors operated at different temperatures. WATER RESEARCH 2012; 46:3805-3816. [PMID: 22591819 DOI: 10.1016/j.watres.2012.04.015] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Revised: 04/05/2012] [Accepted: 04/07/2012] [Indexed: 05/31/2023]
Abstract
The main biological conversions taking place in two lab-scale aerobic granular sludge sequencing batch reactors were evaluated. Reactors were operated at different temperatures (20 and 30 °C) and accomplished simultaneous COD, nitrogen and phosphate removal. Nitrogen and phosphate conversions were linked to the microbial community structure as assessed by fluorescent in situ hybridization (FISH) analysis. Anoxic tests were performed to evaluate the contribution of anoxic phosphate uptake to the overall phosphate removal and to clarify the denitrification pathway. Complete nitrification/denitrification and phosphate removal were achieved in both systems. A considerable fraction of the phosphate removal was coupled to denitrification (denitrifying dephosphatation). From the results obtained in anoxic batch experiments dosing either nitrite or nitrate, denitrification was proposed to proceed mainly via the nitrate pathway. Denitrifying glycogen-accumulating organisms (DGAOs) were observed to be the main organisms responsible for the reduction of nitrate to nitrite. A significant fraction of the nitrite was further reduced to nitrogen gas while being used as electron acceptor by denitrifying polyphosphate-accumulating organisms (PAO clade II) for anoxic phosphate uptake.
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Affiliation(s)
- J P Bassin
- Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
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16
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Abstract
‘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.
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Affiliation(s)
- Shaomei He
- Department of Civil and Environmental Engineering Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
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'Candidatus Accumulibacter' gene expression in response to dynamic EBPR conditions. ISME JOURNAL 2010; 5:329-40. [PMID: 20703317 DOI: 10.1038/ismej.2010.127] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Enhanced biological phosphorus removal (EBPR) activated sludge communities enriched in 'Candidatus Accumulibacter' relatives are widely used in wastewater treatment, but much remains to be learned about molecular-level controls on the EBPR process. The expression of genes found in the carbon and polyphosphate metabolic pathways in Accumulibacter was investigated using reverse transcription quantitative PCR. During a normal anaerobic/aerobic EBPR cycle, gene expression exhibited a dynamic change in response to external acetate, oxygen, phosphate concentrations and probably internal chemical pools. Anaerobic acetate addition induced expression of genes associated with the methylmalonyl-CoA pathway enabling the split mode of the tricarboxylic acid (TCA) cycle. Components of the full TCA cycle were induced after the switch to aerobic conditions. The induction of a key gene in the glyoxylate shunt pathway was observed under both anaerobic and aerobic conditions, with a higher induction by aeration. Polyphosphate kinase 1 from Accumulibacter was expressed, but did not appear to be regulated by phosphate limitation. To understand how Accumulibacter responds to disturbed electron donor and acceptor conditions, we perturbed the process by adding acetate aerobically. When high concentrations of oxygen were present simultaneously with acetate, phosphate-release was almost completely inhibited, and polyphosphate kinase 1 transcript abundance decreased. Genes associated with the methylmalonyl-CoA pathway were repressed and genes associated with the aerobic TCA cycle exhibited higher expression under this perturbation, suggesting that more acetyl-CoA was metabolized through the TCA cycle. These findings suggest that several genes involved in EBPR are tightly regulated at the transcriptional level.
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Bacterial community and "Candidatus Accumulibacter" population dynamics in laboratory-scale enhanced biological phosphorus removal reactors. Appl Environ Microbiol 2010; 76:5479-87. [PMID: 20601516 DOI: 10.1128/aem.00370-10] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
"Candidatus Accumulibacter" and total bacterial community dynamics were studied in two lab-scale enhanced biological phosphorus removal (EBPR) reactors by using a community fingerprint technique, automated ribosomal intergenic spacer analysis (ARISA). We first evaluated the quantitative capability of ARISA compared to quantitative real-time PCR (qPCR). ARISA and qPCR provided comparable relative quantification of the two dominant "Ca. Accumulibacter" clades (IA and IIA) detected in our reactors. The quantification of total "Ca. Accumulibacter" 16S rRNA genes relative to that from the total bacterial community was highly correlated, with ARISA systematically underestimating "Ca. Accumulibacter" abundance, probably due to the different normalization techniques applied. During 6 months of normal (undisturbed) operation, the distribution of the two clades within the total "Ca. Accumulibacter" population was quite stable in one reactor while comparatively dynamic in the other reactor. However, the variance in the clade distribution did not appear to affect reactor performance. Instead, good EBPR activity was positively associated with the abundance of total "Ca. Accumulibacter." Therefore, we concluded that the different clades in the system provided functional redundancy. We disturbed the reactor operation by adding nitrate together with acetate feeding in the anaerobic phase to reach initial reactor concentrations of 10 mg/liter NO(3)-N for 35 days. The reactor performance deteriorated with a concomitant decrease in the total "Ca. Accumulibacter" population, suggesting that a population shift was the cause of performance upset after a long exposure to nitrate in the anaerobic phase.
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Monclús H, Sipma J, Ferrero G, Rodriguez-Roda I, Comas J. Biological nutrient removal in an MBR treating municipal wastewater with special focus on biological phosphorus removal. BIORESOURCE TECHNOLOGY 2010; 101:3984-3991. [PMID: 20137918 DOI: 10.1016/j.biortech.2010.01.038] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Revised: 12/29/2009] [Accepted: 01/10/2010] [Indexed: 05/28/2023]
Abstract
The performance of an MBR pilot plant for biological nutrient removal was evaluated during 210days of operation. The set point values for the internal recycles were determined in advance with the use of an optimisation spreadsheet based on the ASM2d model to optimise the simultaneous removal of C, N and P. The biological nutrient removal (BNR) efficiencies were high from the start of operation with COD and N removal efficiencies of 92+/-6% and 89+/-7, respectively. During the course of the experiment P removal efficiencies increased and finally a P-removal efficiency of 92% was achieved. The activity of poly-phosphate accumulating organisms (PAOs) and denitrifying poly-phosphate accumulating organisms (DPAOs) increased and the specific phosphate accumulation rates after 150days of operation amounted to 13.6mgPg(-1)VSSh(-1) and 5.6mgPg(-1)VSSh(-1), for PAOs and DPAOs, respectively.
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Affiliation(s)
- Hector Monclús
- Laboratory of Chemical and Environmental Engineering (LEQUiA), Institute of the Environment, University of Girona, E17071 Girona, Spain
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20
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Flowers JJ, He S, Yilmaz S, Noguera DR, McMahon KD. Denitrification capabilities of two biological phosphorus removal sludges dominated by different "Candidatus Accumulibacter" clades. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:583-588. [PMID: 20808723 PMCID: PMC2929836 DOI: 10.1111/j.1758-2229.2009.00090.x] [Citation(s) in RCA: 158] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The capability of "Candidatus Accumulibacter" to use nitrate as an electron acceptor for phosphorus uptake was investigated using two activated sludge communities. The two communities were enriched in Accumulibacter clade IA and clade IIA, respectively. By performing a series of batch experiments, we found that clade IA was able to couple nitrate reduction with phosphorus uptake, but clade IIA could not. These results agree with a previously proposed hypothesis that different populations of Accumulibacter have different nitrate reduction capabilities, and they will help to understand the ecological roles that these two clades provide.
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Affiliation(s)
- Jason J. Flowers
- Department of Civil and Environmental Engineering, University of Wisconsin at Madison, Madison, WI, 53706, USA
| | - Shaomei He
- Department of Civil and Environmental Engineering, University of Wisconsin at Madison, Madison, WI, 53706, USA
| | - Safak Yilmaz
- Department of Civil and Environmental Engineering, University of Wisconsin at Madison, Madison, WI, 53706, USA
| | - Daniel R. Noguera
- Department of Civil and Environmental Engineering, University of Wisconsin at Madison, Madison, WI, 53706, USA
| | - Katherine D. McMahon
- Department of Civil and Environmental Engineering, University of Wisconsin at Madison, Madison, WI, 53706, USA
- Department of Bacteriology, University of Wisconsin at Madison, Madison, WI, 53706, USA
- corresponding author: Address: 5525 Microbial Science Building, 1550 Linden Dr., Madison, WI 53925, Tel: (608) 263-3137, Fax: (608) 262-5199,
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Forbes CM, O'Leary ND, Dobson AD, Marchesi JR. The contribution of âomicâ-based approaches to the study of enhanced biological phosphorus removal microbiology. FEMS Microbiol Ecol 2009; 69:1-15. [DOI: 10.1111/j.1574-6941.2009.00698.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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22
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Wilmes P, Simmons SL, Denef VJ, Banfield JF. The dynamic genetic repertoire of microbial communities. FEMS Microbiol Rev 2008; 33:109-32. [PMID: 19054116 PMCID: PMC2704941 DOI: 10.1111/j.1574-6976.2008.00144.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Community genomic data have revealed multiple levels of variation between and within microbial consortia. This variation includes large-scale differences in gene content between ecosystems as well as within-population sequence heterogeneity. In the present review, we focus specifically on how fine-scale variation within microbial and viral populations is apparent from community genomic data. A major unresolved question is how much of the observed variation is due to neutral vs. adaptive processes. Limited experimental data hint that some of this fine-scale variation may be in part functionally relevant, whereas sequence-based and modeling analyses suggest that much of it may be neutral. While methods for interpreting population genomic data are still in their infancy, we discuss current interpretations of existing datasets in the light of evolutionary processes and models. Finally, we highlight the importance of virus–host dynamics in generating and shaping within-population diversity.
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Affiliation(s)
- Paul Wilmes
- Department of Earth and Planetary Science, University of California at Berkeley, Berkeley, CA 94720, USA
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23
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Lopez-Vazquez CM, Brdjanovic D, van Loosdrecht MCM. Comment on "Could polyphosphate-accumulating organisms (PAOs) be glycogen-accumulating organisms (GAOs)?" by Zhou, Y., Pijuan, M., Zeng, R., Lu, Huabing and Yuan Z. Water Res. (2008) doi:10.1016/j.waterres.2008.01.003. WATER RESEARCH 2008; 42:3561-3562. [PMID: 18490044 DOI: 10.1016/j.watres.2008.03.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Accepted: 03/29/2008] [Indexed: 05/26/2023]
Affiliation(s)
- Carlos M Lopez-Vazquez
- Department of Environmental Resources, UNESCO-IHE Institute for Water Education, Westvest 7, 2611 AX, Delft, The Netherlands
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The microbiology of phosphorus removal in activated sludge processes-the current state of play. J Microbiol 2008; 46:115-24. [PMID: 18545960 DOI: 10.1007/s12275-008-0051-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2008] [Accepted: 03/18/2008] [Indexed: 10/22/2022]
Abstract
This review discusses critically what we know and would like to know about the microbiology of phosphorus (P) removal in activated sludge systems. In particular, the description of the genome sequences of two strains of the polyphosphate accumulating organism found in these processes, Candidatus 'Accumulibacter phosphatis', allows us to address many of the previously unanswered questions relating to how these processes behave, and to raise new questions about the microbiology of P removal. This article attempts to be deliberately speculative, and inevitably subjective, but hopefully at the same time useful to those who have an active interest in these environmentally very important processes.
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Wilmes P, Wexler M, Bond PL. Metaproteomics provides functional insight into activated sludge wastewater treatment. PLoS One 2008; 3:e1778. [PMID: 18392150 PMCID: PMC2289847 DOI: 10.1371/journal.pone.0001778] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2007] [Accepted: 01/31/2008] [Indexed: 11/21/2022] Open
Abstract
Background Through identification of highly expressed proteins from a mixed culture activated sludge system this study provides functional evidence of microbial transformations important for enhanced biological phosphorus removal (EBPR). Methodology/Principal Findings A laboratory-scale sequencing batch reactor was successfully operated for different levels of EBPR, removing around 25, 40 and 55 mg/l P. The microbial communities were dominated by the uncultured polyphosphate-accumulating organism “Candidatus Accumulibacter phosphatis”. When EBPR failed, the sludge was dominated by tetrad-forming α-Proteobacteria. Representative and reproducible 2D gel protein separations were obtained for all sludge samples. 638 protein spots were matched across gels generated from the phosphate removing sludges. 111 of these were excised and 46 proteins were identified using recently available sludge metagenomic sequences. Many of these closely match proteins from “Candidatus Accumulibacter phosphatis” and could be directly linked to the EBPR process. They included enzymes involved in energy generation, polyhydroxyalkanoate synthesis, glycolysis, gluconeogenesis, glycogen synthesis, glyoxylate/TCA cycle, fatty acid β oxidation, fatty acid synthesis and phosphate transport. Several proteins involved in cellular stress response were detected. Conclusions/Significance Importantly, this study provides direct evidence linking the metabolic activities of “Accumulibacter” to the chemical transformations observed in EBPR. Finally, the results are discussed in relation to current EBPR metabolic models.
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Affiliation(s)
- Paul Wilmes
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | - Margaret Wexler
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Philip L. Bond
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
- * E-mail:
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Carvalho G, Lemos PC, Oehmen A, Reis MAM. Denitrifying phosphorus removal: linking the process performance with the microbial community structure. WATER RESEARCH 2007; 41:4383-96. [PMID: 17669460 DOI: 10.1016/j.watres.2007.06.065] [Citation(s) in RCA: 196] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2007] [Revised: 06/26/2007] [Accepted: 06/29/2007] [Indexed: 05/16/2023]
Abstract
This study investigated the link between the process performance of two denitrifying phosphorus (P) removal systems and their microbial community structure. Two sequencing batch reactors (SBRs) were operated with either acetate or propionate as the sole carbon source, and were gradually acclimatised from anaerobic-aerobic to anaerobic-anoxic conditions. It was found that the propionate SBR was able to sustain denitrifying P removal after acclimatisation, while the enhanced biological phosphorus removal (EBPR) activity in the acetate reactor collapsed after the aerobic phase was eliminated. The results suggested that the anoxic glycogen production rate in the acetate SBR was insufficient to support the anaerobic glycogen demand for acetate uptake. The chemical transformations in each SBR suggested that different types of polyphosphate-accumulating organisms (PAOs) were present in each system, possessing different affinities for nitrate. Microbial characterisation with fluorescence in situ hybridisation (FISH) revealed that Accumulibacter was the dominant organism in each reactor, although different cell morphotypes were observed. A coccus morphotype was predominant in the acetate SBR while the propionate SBR was enriched in a rod morphotype. It is hypothesised that the coccus morphotype corresponds to an Accumulibacter strain that is unable to use nitrate as electron acceptor but is able to use oxygen, and possibly nitrite. The rod morphotype is proposed to be a PAO able to use nitrate, nitrite and oxygen. This hypothesis is in agreement with literature studies focussed on the identity of denitrifying PAOs (DPAOs), as well as a recent metagenomic study on Accumulibacter.
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Affiliation(s)
- Gilda Carvalho
- REQUIMTE/CQFB, Chemistry Department, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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27
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He S, Gall DL, McMahon KD. "Candidatus Accumulibacter" population structure in enhanced biological phosphorus removal sludges as revealed by polyphosphate kinase genes. Appl Environ Microbiol 2007; 73:5865-74. [PMID: 17675445 PMCID: PMC2074919 DOI: 10.1128/aem.01207-07] [Citation(s) in RCA: 193] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We investigated the fine-scale population structure of the "Candidatus Accumulibacter" lineage in enhanced biological phosphorus removal (EBPR) systems using the polyphosphate kinase 1 gene (ppk1) as a genetic marker. We retrieved fragments of "Candidatus Accumulibacter" 16S rRNA and ppk1 genes from one laboratory-scale and several full-scale EBPR systems. Phylogenies reconstructed using 16S rRNA genes and ppk1 were largely congruent, with ppk1 granting higher phylogenetic resolution and clearer tree topology and thus serving as a better genetic marker than 16S rRNA for revealing population structure within the "Candidatus Accumulibacter" lineage. Sequences from at least five clades of "Candidatus Accumulibacter" were recovered by ppk1-targeted PCR, and subsequently, specific primer sets were designed to target the ppk1 gene for each clade. Quantitative real-time PCR (qPCR) assays using "Candidatus Accumulibacter"-specific 16S rRNA and "Candidatus Accumulibacter" clade-specific ppk1 primers were developed and conducted on three laboratory-scale and nine full-scale EBPR samples and two full-scale non-EBPR samples to determine the abundance of the total "Candidatus Accumulibacter" lineage and the relative distributions and abundances of the five "Candidatus Accumulibacter" clades. The qPCR-based estimation of the total "Candidatus Accumulibacter" fraction as a proportion of the bacterial community as measured using 16S rRNA genes was not significantly different from the estimation measured using ppk1, demonstrating the power of ppk1 as a genetic marker for detection of all currently defined "Candidatus Accumulibacter" clades. The relative distributions of "Candidatus Accumulibacter" clades varied among different EBPR systems and also temporally within a system. Our results suggest that the "Candidatus Accumulibacter" lineage is more diverse than previously realized and that different clades within the lineage are ecologically distinct.
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Affiliation(s)
- Shaomei He
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
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McMahon KD, Yilmaz S, He S, Gall DL, Jenkins D, Keasling JD. Polyphosphate kinase genes from full-scale activated sludge plants. Appl Microbiol Biotechnol 2007; 77:167-73. [PMID: 17671784 DOI: 10.1007/s00253-007-1122-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2007] [Revised: 07/05/2007] [Accepted: 07/09/2007] [Indexed: 10/23/2022]
Abstract
The performance of enhanced biological phosphorus removal (EBPR) wastewater treatment processes depends on the presence of bacteria that accumulate large quantities of polyphosphate. One such group of bacteria has been identified and named Candidatus Accumulibacter phosphatis. Accumulibacter-like bacteria are abundant in many EBPR plants, but not much is known about their community or population ecology. In this study, we used the polyphosphate kinase gene (ppk1) as a high-resolution genetic marker to study population structure in activated sludge. Ppk1 genes were amplified from samples collected from full-scale wastewater treatment plants of different configurations. Clone libraries were constructed using primers targeting highly conserved regions of ppk1, to retrieve these genes from activated sludge plants that did, and did not, perform EBPR. Comparative sequence analysis revealed that ppk1 fragments were retrieved from organisms affiliated with the Accumulibacter cluster from EBPR plants but not from a plant that did not perform EBPR. A new set of more specific primers was designed and validated to amplify a 1,100 bp ppk1 fragment from Accumulibacter-like bacteria. Our results suggest that the Accumulibacter cluster has finer-scale architecture than previously revealed by 16S ribosomal RNA-based analyses.
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Affiliation(s)
- Katherine D McMahon
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA.
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29
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McMahon KD, Martin HG, Hugenholtz P. Integrating ecology into biotechnology. Curr Opin Biotechnol 2007; 18:287-92. [PMID: 17509863 DOI: 10.1016/j.copbio.2007.04.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2007] [Revised: 04/09/2007] [Accepted: 04/19/2007] [Indexed: 01/08/2023]
Abstract
New high-throughput culture-independent molecular tools are allowing the scientific community to characterize and understand the microbial communities underpinning environmental biotechnology processes in unprecedented ways. By creatively leveraging these new data sources, microbial ecology has the potential to transition from a purely descriptive to a predictive framework, in which ecological principles are integrated and exploited to engineer systems that are biologically optimized for the desired goal. But to achieve this goal, ecology, engineering and microbiology curricula need to be changed from the very root to better promote interdisciplinarity.
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Affiliation(s)
- Katherine D McMahon
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI, USA.
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30
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García Martín H, Ivanova N, Kunin V, Warnecke F, Barry KW, McHardy AC, Yeates C, He S, Salamov AA, Szeto E, Dalin E, Putnam NH, Shapiro HJ, Pangilinan JL, Rigoutsos I, Kyrpides NC, Blackall LL, McMahon KD, Hugenholtz P. Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat Biotechnol 2006; 24:1263-9. [PMID: 16998472 DOI: 10.1038/nbt1247] [Citation(s) in RCA: 459] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2006] [Accepted: 07/26/2006] [Indexed: 11/08/2022]
Abstract
Enhanced biological phosphorus removal (EBPR) is one of the best-studied microbially mediated industrial processes because of its ecological and economic relevance. Despite this, it is not well understood at the metabolic level. Here we present a metagenomic analysis of two lab-scale EBPR sludges dominated by the uncultured bacterium, "Candidatus Accumulibacter phosphatis." The analysis sheds light on several controversies in EBPR metabolic models and provides hypotheses explaining the dominance of A. phosphatis in this habitat, its lifestyle outside EBPR and probable cultivation requirements. Comparison of the same species from different EBPR sludges highlights recent evolutionary dynamics in the A. phosphatis genome that could be linked to mechanisms for environmental adaptation. In spite of an apparent lack of phylogenetic overlap in the flanking communities of the two sludges studied, common functional themes were found, at least one of them complementary to the inferred metabolism of the dominant organism. The present study provides a much needed blueprint for a systems-level understanding of EBPR and illustrates that metagenomics enables detailed, often novel, insights into even well-studied biological systems.
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Affiliation(s)
- Héctor García Martín
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
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