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Ruiz-Haddad L, Ali M, Pronk M, van Loosdrecht MC, Saikaly PE. Demystifying polyphosphate-accumulating organisms relevant to wastewater treatment: A review of their phylogeny, metabolism, and detection. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 21:100387. [PMID: 38322240 PMCID: PMC10845257 DOI: 10.1016/j.ese.2024.100387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/31/2023] [Accepted: 12/31/2023] [Indexed: 02/08/2024]
Abstract
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.
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Affiliation(s)
- Lucia Ruiz-Haddad
- Environmental Science and Engineering Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Water Desalination and Reuse Center, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Muhammad Ali
- Department of Civil, Structural & Environmental Engineering, Trinity College Dublin, The University of Dublin, Dublin, 2, Ireland
| | - Mario Pronk
- Department of Biotechnology, Delft University of Technology, Delft, 2629 HZ, the Netherlands
| | | | - Pascal E. Saikaly
- Environmental Science and Engineering Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Water Desalination and Reuse Center, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
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2
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Li G, Srinivasan V, Tooker NB, Wang D, Yan Y, Onnis-Hayden A, Gu AZ. Distinct microdiversity of phosphate accumulating organisms (PAOs) between side-stream and conventional enhanced biological phosphorus removal (EBPR) systems with performance implications. WATER RESEARCH 2024; 266:122280. [PMID: 39213686 DOI: 10.1016/j.watres.2024.122280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 07/30/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024]
Abstract
Polyphosphate Accumulating Organisms (PAOs) microdiversity is a key factor to elucidate the mechanisms involved in the side-stream enhanced biological phosphorus removal (S2EBPR) systems, which has been shown to improve the process stability over conventional EBPR. However, fast, effective and cost-efficient methods to resolve PAO microdiversity in real-world activate sludge samples is still in absence. In this study, we applied oligotyping analysis following the regular 16S rRNA gene amplicon sequencing standard operation pipeline (SOP) to resolve subgenus-level PAO oligotypes, which cannot be achieved using traditional 16S rRNA sequencing SOP. The identified oligotype profiles of PAO-containing genera Ca. Accumulibacter, Tetrasphaera and Comamonas showed distinguished community-level differences across 12 water resource recovery facilities (WRRFs), which would not be revealed at the genus level. The WRRF-level differences were observed larger than the temporal differences in the same WRRF, indicating intrinsic sub-genus level microdiversity fingerprint between EBPR/S2EBPR systems. The identified oligotypes can be associated with known PAO clades phylogenetically, suggesting that oligotyping can suffice as a fast and cost-efficient approach for PAO microdiversity profiling. In addition, network analysis can be used to identify coexistence patterns between oligotypes with respect to EBPR/S2EBPR configurations and performance, enabling more detailed analysis between EBPR system performance and PAOs microdiversity. Correlation analyses between oligotype profiles and key EBPR performance parameters revealed potential different biological functional traits among these PAO species with P-removal performance implications.
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Affiliation(s)
- Guangyu Li
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, United States; Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, United States
| | - Varun Srinivasan
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, United States
| | - Nicholas B Tooker
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, United States
| | - Dongqi Wang
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, United States; Department of Municipal and Environmental Engineering, School of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, Shaanxi, China
| | - Yuan Yan
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, United States
| | - Annalisa Onnis-Hayden
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, United States
| | - April Z Gu
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, United States; Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, United States.
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Xie X, Deng X, Chen L, Yuan J, Chen H, Wei C, Liu X, Wuertz S, Qiu G. Integrated genomics provides insights into the evolution of the polyphosphate accumulation trait of Ca. Accumulibacter. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 20:100353. [PMID: 39221073 PMCID: PMC11361876 DOI: 10.1016/j.ese.2023.100353] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 11/18/2023] [Accepted: 11/23/2023] [Indexed: 09/04/2024]
Abstract
Candidatus Accumulibacter, a prominent polyphosphate-accumulating organism (PAO) in wastewater treatment, plays a crucial role in enhanced biological phosphorus removal (EBPR). The genetic underpinnings of its polyphosphate accumulation capabilities, however, remain largely unknown. Here, we conducted a comprehensive genomic analysis of Ca. Accumulibacter-PAOs and their relatives within the Rhodocyclaceae family, identifying 124 core genes acquired via horizontal gene transfer (HGT) at its least common ancestor. Metatranscriptomic analysis of an enrichment culture of Ca. Accumulibacter revealed active transcription of 44 of these genes during an EBPR cycle, notably including the polyphosphate kinase 2 (PPK2) gene instead of the commonly recognized polyphosphate kinase 1 (PPK1) gene. Intriguingly, the phosphate regulon (Pho) genes showed minimal transcriptions, pointing to a distinctive fact of Pho dysregulation, where PhoU, the phosphate signaling complex protein, was not regulating the high-affinity phosphate transport (Pst) system, resulting in continuous phosphate uptake. To prevent phosphate toxicity, Ca. Accumulibacter utilized the laterally acquired PPK2 to condense phosphate into polyphosphate, resulting in the polyphosphate-accumulating feature. This study provides novel insights into the evolutionary emergence of the polyphosphate-accumulating trait in Ca. Accumulibacter, offering potential advancements in understanding the PAO phenotype in the EBPR process.
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Affiliation(s)
- Xiaojing Xie
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Xuhan Deng
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Liping Chen
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Jing Yuan
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Hang Chen
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Chaohai Wei
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Xianghui Liu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Guanglei Qiu
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
- Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou, 510006, China
- The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou, 510006, China
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Stewart RD, Myers KS, Amstadt C, Seib M, McMahon KD, Noguera DR. Refinement of the " Candidatus Accumulibacter" genus based on metagenomic analysis of biological nutrient removal (BNR) pilot-scale plants operated with reduced aeration. mSystems 2024; 9:e0118823. [PMID: 38415636 PMCID: PMC10949500 DOI: 10.1128/msystems.01188-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 01/31/2024] [Indexed: 02/29/2024] Open
Abstract
Members of the "Candidatus Accumulibacter" genus are widely studied as key polyphosphate-accumulating organisms (PAOs) in biological nutrient removal (BNR) facilities performing enhanced biological phosphorus removal (EBPR). This diverse lineage includes 18 "Ca. Accumulibacter" species, which have been proposed based on the phylogenetic divergence of the polyphosphate kinase 1 (ppk1) gene and genome-scale comparisons of metagenome-assembled genomes (MAGs). Phylogenetic classification based on the 16S rRNA genetic marker has been difficult to attain because most "Ca. Accumulibacter" MAGs are incomplete and often do not include the rRNA operon. Here, we investigate the "Ca. Accumulibacter" diversity in pilot-scale treatment trains performing BNR under low dissolved oxygen (DO) conditions using genome-resolved metagenomics. Using long-read sequencing, we recovered medium- and high-quality MAGs for 5 of the 18 "Ca. Accumulibacter" species, all with rRNA operons assembled, which allowed a reassessment of the 16S rRNA-based phylogeny of this genus and an analysis of phylogeny based on the 23S rRNA gene. In addition, we recovered a cluster of MAGs that based on 16S rRNA, 23S rRNA, ppk1, and genome-scale phylogenetic analyses do not belong to any of the currently recognized "Ca. Accumulibacter" species for which we propose the new species designation "Ca. Accumulibacter jenkinsii" sp. nov. Relative abundance evaluations of the genus across all pilot plant operations revealed that regardless of the operational mode, "Ca. A. necessarius" and "Ca. A. propinquus" accounted for more than 40% of the "Ca. Accumulibacter" community, whereas the newly proposed "Ca. A. jenkinsii" accounted for about 5% of the "Ca. Accumulibacter" community.IMPORTANCEOne of the main drivers of energy use and operational costs in activated sludge processes is the amount of oxygen provided to enable biological phosphorus and nitrogen removal. Wastewater treatment facilities are increasingly considering reduced aeration to decrease energy consumption, and whereas successful BNR has been demonstrated in systems with minimal aeration, an adequate understanding of the microbial communities that facilitate nutrient removal under these conditions is still lacking. In this study, we used genome-resolved metagenomics to evaluate the diversity of the "Candidatus Accumulibacter" genus in pilot-scale plants operating with minimal aeration. We identified the "Ca. Accumulibacter" species enriched under these conditions, including one novel species for which we propose "Ca. Accumulibacter jenkinsii" sp. nov. as its designation. Furthermore, the MAGs obtained for five additional "Ca. Accumulibacter" species further refine the phylogeny of the "Ca. Accumulibacter" genus and provide new insight into its diversity within unconventional biological nutrient removal systems.
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Affiliation(s)
- Rachel D. Stewart
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kevin S. Myers
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Carly Amstadt
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Matt Seib
- Madison Metropolitan Sewerage District, Madison, Wisconsin, USA
| | - Katherine D. McMahon
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Daniel R. Noguera
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
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5
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Zhao Y, Zhu Z, Chen X, Li Y. Discovery of a novel potential polyphosphate accumulating organism without denitrifying phosphorus uptake function in an enhanced biological phosphorus removal process. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168952. [PMID: 38043807 DOI: 10.1016/j.scitotenv.2023.168952] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 11/14/2023] [Accepted: 11/25/2023] [Indexed: 12/05/2023]
Abstract
Enhanced biological phosphorus removal (EBPR) is an effective process for phosphorus removal from wastewater. In this study, two lab-scale sequencing batch reactors (SBR) were used to perform EBPR process, in which genus Propioniciclava was unexpectedly accumulated and its relative abundance was over 70 %. A series of tests were conducted to explore the role of Propioniciclava in the two EBPR systems. The two systems performed steadily throughout the study, and the phosphorus removal efficiencies were 96.6 % and 93.5 % for SBR1 and SBR2, respectively. The stoichiometric analysis related to polyphosphate accumulating organisms (PAOs) indicated that polyphosphate accumulating metabolism (PAM) was achieved in the anaerobic phase. It appeared that the Propioniciclava-dominated systems could not perform denitrifying phosphorus removal. Instead, phosphorus was released under anoxic conditions without carbon sources. According to the genomic information from Integrated Microbial Genomes (IMG) database, Propioniciclava owns ppk1, ppk2 and ppx genes that are associated with phosphorus release and uptake functions. By phylogenetic investigation of communities by reconstruction of unobserved states 2 (PICRUSt2) analysis, the abundance of genes related to phosphorus metabolism was much higher than that of genes related to denitrification. Therefore, Propioniciclava was presumed to be a potential PAO without denitrifying phosphorus uptake function. In addition to Propioniciclava, Tessaracoccus and Thiothrix were also enriched in both systems. Overall, this study proposes a novel potential PAO and broadens the understanding of EBPR microbial communities.
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Affiliation(s)
- Yiming Zhao
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Zhengyu Zhu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Xuyang Chen
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Yongmei Li
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
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6
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Xie X, Deng X, Chen J, Chen L, Yuan J, Chen H, Wei C, Liu X, Qiu G. Two new clades recovered at high temperatures provide novel phylogenetic and genomic insights into Candidatus Accumulibacter. ISME COMMUNICATIONS 2024; 4:ycae049. [PMID: 38808122 PMCID: PMC11131965 DOI: 10.1093/ismeco/ycae049] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 05/30/2024]
Abstract
Candidatus Accumulibacter, a key genus of polyphosphate-accumulating organisms, plays key roles in lab- and full-scale enhanced biological phosphorus removal (EBPR) systems. A total of 10 high-quality Ca. Accumulibacter genomes were recovered from EBPR systems operated at high temperatures, providing significantly updated phylogenetic and genomic insights into the Ca. Accumulibacter lineage. Among these genomes, clade IIF members SCELSE-3, SCELSE-4, and SCELSE-6 represent the to-date known genomes encoding a complete denitrification pathway, suggesting that Ca. Accumulibacter alone could achieve complete denitrification. Clade IIC members SSA1, SCUT-1, SCELCE-2, and SCELSE-8 lack the entire set of denitrifying genes, representing to-date known non-denitrifying Ca. Accumulibacter. A pan-genomic analysis with other Ca. Accumulibacter members suggested that all Ca. Accumulibacter likely has the potential to use dicarboxylic amino acids. Ca. Accumulibacter aalborgensis AALB and Ca. Accumulibacter affinis BAT3C720 seemed to be the only two members capable of using glucose for EBPR. A heat shock protein Hsp20 encoding gene was found exclusively in genomes recovered at high temperatures, which was absent in clades IA, IC, IG, IIA, IIB, IID, IIG, and II-I members. High transcription of this gene in clade IIC members SCUT-2 and SCUT-3 suggested its role in surviving high temperatures for Ca. Accumulibacter. Ambiguous clade identity was observed for newly recovered genomes (SCELSE-9 and SCELSE-10). Five machine learning models were developed using orthogroups as input features. Prediction results suggested that they belong to a new clade (IIK). The phylogeny of Ca. Accumulibacter was re-evaluated based on the laterally derived polyphosphokinase 2 gene, showing improved resolution in differentiating different clades.
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Affiliation(s)
- Xiaojing Xie
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Xuhan Deng
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Jinling Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Liping Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Jing Yuan
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Hang Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Chaohai Wei
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou 510006, China
| | - Xianghui Liu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore
| | - Guanglei Qiu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou 510006, China
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore
- The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou 510006, China
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Yuan J, Deng X, Xie X, Chen L, Wei C, Feng C, Qiu G. Blind spots of universal primers and specific FISH probes for functional microbe and community characterization in EBPR systems. ISME COMMUNICATIONS 2024; 4:ycae011. [PMID: 38524765 PMCID: PMC10958769 DOI: 10.1093/ismeco/ycae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 03/26/2024]
Abstract
Fluorescence in situ hybridization (FISH) and 16S rRNA gene amplicon sequencing are commonly used for microbial ecological analyses in biological enhanced phosphorus removal (EBPR) systems, the successful application of which was governed by the oligonucleotides used. We performed a systemic evaluation of commonly used probes/primers for known polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs). Most FISH probes showed blind spots and covered nontarget bacterial groups. Ca. Competibacter probes showed promising coverage and specificity. Those for Ca. Accumulibacter are desirable in coverage but targeted out-group bacteria, including Ca. Competibacter, Thauera, Dechlorosoma, and some polyphosphate-accumulating Cyanobacteria. Defluviicoccus probes are good in specificity but poor in coverage. Probes targeting Tetrasphaera or Dechloromonas showed low coverage and specificity. Specifically, DEMEF455, Bet135, and Dech453 for Dechloromonas covered Ca. Accumulibacter. Special attentions are needed when using these probes to resolve the PAO/GAO phenotype of Dechloromonas. Most species-specific probes for Ca. Accumulibacter, Ca. Lutibacillus, Ca. Phosphoribacter, and Tetrasphaera are highly specific. Overall, 1.4% Ca. Accumulibacter, 9.6% Ca. Competibacter, 43.3% Defluviicoccus, and 54.0% Dechloromonas in the MiDAS database were not covered by existing FISH probes. Different 16S rRNA amplicon primer sets showed distinct coverage of known PAOs and GAOs. None of them covered all members. Overall, 520F-802R and 515F-926R showed the most balanced coverage. All primers showed extremely low coverage of Microlunatus (<36.0%), implying their probably overlooked roles in EBPR systems. A clear understanding of the strength and weaknesses of each probe and primer set is a premise for rational evaluation and interpretation of obtained community results.
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Affiliation(s)
- Jing Yuan
- School of Environment and Energy, South China University of Technology, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
| | - Xuhan Deng
- School of Environment and Energy, South China University of Technology, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
| | - Xiaojing Xie
- School of Environment and Energy, South China University of Technology, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
| | - Liping Chen
- School of Environment and Energy, South China University of Technology, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
| | - Chaohai Wei
- School of Environment and Energy, South China University of Technology, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
- Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
- Key Laboratory of Pollution Control and Ecological Restoration in Industrial Clusters, Ministry of Education, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
| | - Chunhua Feng
- School of Environment and Energy, South China University of Technology, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
- Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
- Key Laboratory of Pollution Control and Ecological Restoration in Industrial Clusters, Ministry of Education, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
| | - Guanglei Qiu
- School of Environment and Energy, South China University of Technology, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
- Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
- Key Laboratory of Pollution Control and Ecological Restoration in Industrial Clusters, Ministry of Education, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
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Carvalho VCF, Fradinho JC, Oehmen A, Reis MAM. Long term operation of a phototrophic biological nutrient removal system: Impact of CO 2 concentration and light exposure on process performance. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 334:117490. [PMID: 36801686 DOI: 10.1016/j.jenvman.2023.117490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
The utilization of non-aerated microalgae-bacterial consortia for phototrophic biological nutrient removal (photo-BNR) has emerged as an alternative to conventional wastewater treatment. Photo-BNR systems are operated under transient illumination, with alternating dark-anaerobic, light-aerobic and dark-anoxic conditions. A deep understanding of the impact of operational parameters on the microbial consortium and respective nutrient removal efficiency in photo-BNR systems is required. The present study evaluates, for the first time, the long-term operation (260 days) of a photo-BNR system, fed with a COD:N:P mass ratio of 7.5:1:1, to understand its operational limitations. In particular, different CO2 concentrations in the feed (between 22 and 60 mg C/L of Na2CO3) and variations of light exposure (from 2.75 h to 5.25 h per 8 h cycle) were studied to determine their impact on key parameters, like oxygen production and availability of polyhydroxyalkanoates (PHA), on the performance of anoxic denitrification by polyphosphate accumulating organisms. Results indicate that oxygen production was more dependent on the light availability than on the CO2 concentration. Also, under operational conditions with a COD:Na2CO3 ratio of 8.3 mg COD/mg C and an average light availability of 5.4 ± 1.3 W h/g TSS, no internal PHA limitation was observed, and 95 ± 7%, 92 ± 5% and 86 ± 5% of removal efficiency could be achieved for phosphorus, ammonia and total nitrogen, respectively. 81 ± 1.7% of the ammonia was assimilated into the microbial biomass and 19 ± 1.7% was nitrified, showing that biomass assimilation was the main N removal mechanism taking place in the bioreactor. Overall, the photo-BNR system presented a good settling capacity (SVI ∼60 mL/g TSS) and was able to remove 38 ± 3.3 mg P/L and 33 ± 1.7 mg N/L, highlighting its potential for achieving wastewater treatment without the need of aeration.
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Affiliation(s)
- V C F Carvalho
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University of Lisbon, 2829-516, Caparica, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516, Caparica, Portugal
| | - J C Fradinho
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University of Lisbon, 2829-516, Caparica, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516, Caparica, Portugal.
| | - A Oehmen
- School of Chemical Engineering, University of Queensland, Brisbane, QLD, 4072, Australia
| | - M A M Reis
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University of Lisbon, 2829-516, Caparica, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516, Caparica, Portugal
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9
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Deng X, Yuan J, Chen L, Chen H, Wei C, Nielsen PH, Wuertz S, Qiu G. CRISPR-Cas phage defense systems and prophages in Candidatus Accumulibacter. WATER RESEARCH 2023; 235:119906. [PMID: 37004306 DOI: 10.1016/j.watres.2023.119906] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/27/2023] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
Candidatus Accumulibacter plays a major role in enhanced biological phosphorus removal (EBPR) from wastewater. Although bacteriophages have been shown to represent fatal threats to Ca. Accumulibacter organisms and thus interfere with the stability of the EBPR process, little is known about the ability of different Ca. Accumulibacter strains to resist phage infections. We conducted a systematic analysis of the occurrence and characteristics of clustered regularly interspaced short palindromic repeats and associated proteins (CRISPR-Cas) systems and prophages in Ca. Accumulibacter lineage members (43 in total, including 10 newly recovered genomes). Results indicate that 28 Ca. Accumulibacter genomes encode CRISPR-Cas systems. They were likely acquired via horizontal gene transfer, conveying a distinct adaptivity to phage predation to different Ca. Accumulibacter members. Major differences in the number of spacers show the unique phage resistance of these members. A comparison of the spacers in closely related Ca. Accumulibacter members from distinct geographical locations indicates that habitat isolation may have resulted in the acquisition of resistance to different phages by different Ca. Accumulibacter. Long-term operation of three laboratory-scale EBPR bioreactors revealed high relative abundances of Ca. Accumulibacter with CRISPSR-Cas systems. Their specific resistance to phages in these reactors was indicated by spacer analysis. Metatranscriptomic analyses showed the activation of the CRISPR-Cas system under both anaerobic and aerobic conditions. Additionally, 133 prophage regions were identified in 43 Ca. Accumulibacter genomes. Twenty-seven of them (in 19 genomes) were potentially active. Major differences in the occurrence of CRISPR-Cas systems and prophages in Ca. Accumulibacter will lead to distinct responses to phage predation. This study represents the first systematic analysis of CRISPR-Cas systems and prophages in the Ca. Accumulibacter lineage, providing new perspectives on the potential impacts of phages on Ca. Accumulibacter and EBPR systems.
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Affiliation(s)
- Xuhan Deng
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Jing Yuan
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Liping Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Hang Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Chaohai Wei
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou 510006, China
| | - Per H Nielsen
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; Centre for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg DK-9220, Denmark
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798, Singapore.
| | - Guanglei Qiu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou 510006, China.
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10
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Nguyen P, Marques R, Wang H, Reis MA, Carvalho G, Oehmen A. The impact of pH on the anaerobic and aerobic metabolism of Tetrasphaera-enriched polyphosphate accumulating organisms. WATER RESEARCH X 2023; 19:100177. [PMID: 37008369 PMCID: PMC10063378 DOI: 10.1016/j.wroa.2023.100177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/05/2023] [Accepted: 03/19/2023] [Indexed: 06/19/2023]
Abstract
Members of the genus Tetrasphaera are putative polyphosphate accumulating organisms (PAOs) that have been found in greater abundance than Accumulibacter in many full-scale enhanced biological phosphorus removal (EBPR) wastewater treatment plants worldwide. Nevertheless, previous studies on the effect of environmental conditions, such as pH, on the performance of EBPR have focused mainly on the response of Accumulibacter to pH changes. This study examines the impact of pH on a Tetrasphaera PAO enriched culture, over a pH range from 6.0 to 8.0 under both anaerobic and aerobic conditions, to assess its impact on the stoichiometry and kinetics of Tetrasphaera metabolism. It was discovered that the rates of phosphorus (P) uptake and P release increased with an increase of pH within the tested range, while PHA production, glycogen consumption and substrate uptake rate were less sensitive to pH changes. The results suggest that Tetrasphaera PAOs display kinetic advantages at high pH levels, which is consistent with what has been observed previously for Accumulibacter PAOs. The results of this study show that pH has a substantial impact on the P release and uptake kinetics of PAOs, where the P release rate was >3 times higher and the P uptake rate was >2 times higher at pH 8.0 vs pH 6.0, respectively. Process operational strategies promoting both Tetrasphaera and Accumulibacter activity at high pH do not conflict with each other, but lead to a potentially synergistic impact that can benefit EBPR performance.
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Affiliation(s)
- P.Y. Nguyen
- UCIBIO, REQUIMTE, Department of Chemistry, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, Caparica 2829-516, Portugal
| | - Ricardo Marques
- UCIBIO, REQUIMTE, Department of Chemistry, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, Caparica 2829-516, Portugal
| | - Hongmin Wang
- School of Chemical Engineering, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Maria A.M. Reis
- UCIBIO, REQUIMTE, Department of Chemistry, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, Caparica 2829-516, Portugal
| | - Gilda Carvalho
- UCIBIO, REQUIMTE, Department of Chemistry, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, Caparica 2829-516, Portugal
- School of Chemical Engineering, The University of Queensland, St Lucia, QLD 4072, Australia
- Australian Centre for Water and Environmental Biotechnology (formerly AWMC), The University of Queensland, St Lucia, QLD 4072, Australia
| | - Adrian Oehmen
- UCIBIO, REQUIMTE, Department of Chemistry, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, Caparica 2829-516, Portugal
- School of Chemical Engineering, The University of Queensland, St Lucia, QLD 4072, Australia
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11
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Jia Z, Yuan Q, Roots P, Sabba F, Rosenthal AF, Kozak JA, Wells GF. Partial Nitritation/Anammox and biological phosphorus removal integration in a single bioreactor under mainstream conditions. BIORESOURCE TECHNOLOGY 2023; 373:128714. [PMID: 36754238 DOI: 10.1016/j.biortech.2023.128714] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/03/2023] [Accepted: 02/04/2023] [Indexed: 06/18/2023]
Abstract
Anammox-based nitrogen removal and enhanced biological phosphorus removal (EBPR) are increasingly applied for nutrient removal from wastewater, but are typically operated in separate reactors. Here, a novel process for integrated partial nitritation/anammox (PN/A) and EBPR in a single reactor employing integrated fixed film activated sludge was tested. The reactor was fed with mainstream municipal wastewater (5.4 ± 1.3 g COD/g N) at 20 °C for 243 days. Robust ammonium, total inorganic nitrogen, and orthophosphate removal efficiencies of 94 ± 4 %, 87 ± 7 % and 92 ± 7 % were achieved. Nitrite-oxidizing organisms suppression and ammonia-oxidizing organisms retention were achieved via solids retention time control, intermittent aeration, and suspended versus attached biomass population segregation. The contribution of anammox to nitrogen removal increased from 24 % to 74 %. In parallel, a substantial enrichment of Tetrasphaera polyphosphate accumulating organisms was observed. This work demonstrates a novel intensified bioprocess coupling PN/A and EBPR in the same reactor for efficient nutrient removal from wastewater.
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Affiliation(s)
- Zhen Jia
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Quan Yuan
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; School of Ecology and Environment, Beijing Technology and Business University, Beijing 100048, China
| | - Paul Roots
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Fabrizio Sabba
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA; Black & Veatch, KS, USA
| | - Alex F Rosenthal
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Joseph A Kozak
- Metropolitan Water Reclamation District of Greater Chicago, 6001 W Pershing Road, Chicago, IL 60804, USA
| | - George F Wells
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
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12
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Zhao B, Yang Y, Zhao C, Zhang C, Zhang Z, Wang L, Wang S, Wang J. Exploration of the metabolic flexibility of glycogen accumulating organisms through metatranscriptome analysis and metabolic characterization. J Environ Sci (China) 2023; 126:234-248. [PMID: 36503752 DOI: 10.1016/j.jes.2022.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/06/2022] [Accepted: 05/06/2022] [Indexed: 06/17/2023]
Abstract
Glycogen accumulating organisms (GAOs) are closely related to the deterioration of enhanced biological phosphorus removal systems. However, the metabolic mechanisms that drive GAOs remain unclear. Here, the two-thirds supernatant of a reactor were decanted following the anaerobic period to enrich GAOs. Long-term monitoring demonstrated that the system was stable and exhibited typical characteristics of GAOs metabolism. Acetate was completely consumed after 60 min of the anaerobic phase. The level of glycogen decreased from 0.20 to 0.14 g/gSS during the anaerobic phase, whereas the level of glycogen significantly increased to 0.21g/gSS at the end of the aerobic period. Moreover, there was almost no phosphate release and absorption in the complete periods, thus confirming the successful construction of a GAOs enrichment system. Microbial community analysis demonstrated that Ca. Contendobacter was among the core functional genera and showed the highest activity among all of the communities. Furthermore, our study is the first to identify the involvement of the ethyl-malonyl-CoA pathway in the synthesis of polyhydroxyvalerate via croR, ccr, ecm, mcd, mch and mcl genes. The Embden-Meyerhof-Parnas (EMP) pathway was preferentially used via glgP. Furthermore, the glyoxylate cycle was the main source of ATP under anaerobic conditions, whereas the tricarboxylic acid cycle provided ATP under aerobic conditions. aceA and mdh appeared to be major modulators of the glyoxylate pathway for controlling energy flow. Collectively, our findings not only revealed the crucial metabolic mechanisms in a GAOs enrichment system but also provided insights into the potential application of Ca. Contendobacter for wastewater treatment.
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Affiliation(s)
- Bin Zhao
- School of Environmental Science Engineering, Tiangong University, Tianjin 300387, China
| | - Yanping Yang
- School of Environmental Science Engineering, Tiangong University, Tianjin 300387, China; Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300201, China
| | - Chen Zhao
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300201, China
| | - Chunchun Zhang
- School of Environmental Science Engineering, Tiangong University, Tianjin 300387, China; Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300201, China
| | - Zhaohui Zhang
- School of Environmental Science Engineering, Tiangong University, Tianjin 300387, China
| | - Liang Wang
- School of Environmental Science Engineering, Tiangong University, Tianjin 300387, China
| | - Shang Wang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300201, China.
| | - Jingfeng Wang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300201, China.
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13
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Ziliani A, Bovio-Winkler P, Cabezas A, Etchebehere C, Garcia HA, López-Vázquez CM, Brdjanovic D, van Loosdrecht MCM, Rubio-Rincón FJ. Putative metabolism of Ca. Accumulibacter via the utilization of glucose. WATER RESEARCH 2023; 229:119446. [PMID: 36516560 DOI: 10.1016/j.watres.2022.119446] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Ca. Accumulibacter was the predominant microorganism (relative FISH bio-abundance of 67 ± 5%) in a lab-scale sequential batch reactor that accomplished enhanced biological phosphorus removal (EBPR) while using glucose and acetate as the carbon sources (1:1 COD-based ratio). Both organic compounds were completely anaerobically consumed. The reactor's performance in terms of P/C ratio, phosphorous release and uptake, and overall kinetic and stoichiometric parameters were on the high end of the reported spectrum for EBPR systems (100:9.3 net mg phosphate removal per mg COD consumed when using glucose and acetate in a 1:1 ratio). The batch tests showed that, to the best of our knowledge, this is the first time a reactor enriched with Ca. Accumulibacter can putatively utilize glucose as the sole carbon source to biologically remove phosphate (COD:P (mg/mg) removal ratio of 100:6.3 when using only glucose). Thus, this research proposes that Ca. Accumulibacter directly anaerobically stored the fed glucose primarily as glycogen by utilizing the ATP provided via the hydrolysis of poly-P and secondarily as PHA by balancing its ATP utilization (glycogen generation) and formation (PHA storage). Alternative hypotheses are also discussed. The reported findings could challenge the conventional theories of glucose assimilation by Ca. Accumulibacter, and can be of significance for the biological removal of phosphorus from wastewaters with high contents of fermentable compounds or low VFAs.
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Affiliation(s)
- Agustina Ziliani
- Department of Water Supply, Sanitation and Environmental Engineering, IHE Institute for Water Education, Westvest 7, 2611 AX Delft, The Netherlands; Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland.
| | - Patricia Bovio-Winkler
- Laboratorio de Ecología Microbiana, Departamento de Bioquímica y Genómica Microbiana, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Angela Cabezas
- Instituto Tecnológico Regional Centro Sur, Universidad Tecnológica, Durazno, Uruguay
| | - Claudia Etchebehere
- Laboratorio de Ecología Microbiana, Departamento de Bioquímica y Genómica Microbiana, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Hector A Garcia
- Department of Water Supply, Sanitation and Environmental Engineering, IHE Institute for Water Education, Westvest 7, 2611 AX Delft, The Netherlands
| | - Carlos M López-Vázquez
- Department of Water Supply, Sanitation and Environmental Engineering, IHE Institute for Water Education, Westvest 7, 2611 AX Delft, The Netherlands
| | - Damir Brdjanovic
- Department of Water Supply, Sanitation and Environmental Engineering, IHE Institute for Water Education, Westvest 7, 2611 AX Delft, The Netherlands; Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628BC Delft, The Netherlands
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628BC Delft, The Netherlands
| | - Francisco J Rubio-Rincón
- Department of Water Supply, Sanitation and Environmental Engineering, IHE Institute for Water Education, Westvest 7, 2611 AX Delft, The Netherlands
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14
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Zhang C, Guisasola A, Baeza JA. Exploring the stability of an A-stage-EBPR system for simultaneous biological removal of organic matter and phosphorus. CHEMOSPHERE 2023; 313:137576. [PMID: 36529170 DOI: 10.1016/j.chemosphere.2022.137576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 10/27/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
This work evaluates the performance and stability of a continuous anaerobic/aerobic A-stage system with integrated enhanced biological phosphorus removal (A-stage-EBPR) under different operational conditions. Dissolved oxygen (DO) in the aerobic reactor was tested in the 0.2-2 mgDO/L range using real wastewater amended with propionic acid, obtaining almost full simultaneous COD and P removal without nitrification in the range 0.5-1 mgDO/L, but failing at 0.2 mgDO/L. Anaerobic purge was tested to evaluate a possible mainstream P-recovery strategy, generating a P-enriched stream containing 22% of influent P. COD and N mass balances indicated that about 43% of the influent COD could be redirected to the anaerobic digestion for methane production and 66% of influent NH4+-N was discharged in the effluent for the following N-removal B-stage. Finally, when the system was switched to glutamate as sole carbon source, successful EBPR activity and COD removal were maintained for two months, but after this period settleability problems appeared with biomass loss. Microbial community analysis indicated that Propionivibrio, Thiothrix and Lewinella were the most abundant species when propionic acid was the carbon source and Propionivibrio was the most favoured with glutamate. Thiothrix, Hydrogenophaga, Dechloromonas and Desulfobacter appeared as the dominant polyphosphate-accumulating organisms (PAOs) under different operation stages.
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Affiliation(s)
- Congcong Zhang
- GENOCOV. Departament d'Enginyeria Química, Biològica i Ambiental. Escola d'Enginyeria. Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
| | - Albert Guisasola
- GENOCOV. Departament d'Enginyeria Química, Biològica i Ambiental. Escola d'Enginyeria. Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
| | - Juan Antonio Baeza
- GENOCOV. Departament d'Enginyeria Química, Biològica i Ambiental. Escola d'Enginyeria. Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
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15
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Coats ER, Appel FJ, Guho N, Brinkman CK, Mellin J. Interrogating the performance and microbial ecology of an enhanced biological phosphorus removal/post-anoxic denitrification process at bench and pilot scales. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2023; 95:e10852. [PMID: 36987547 DOI: 10.1002/wer.10852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/09/2023] [Accepted: 03/18/2023] [Indexed: 06/19/2023]
Abstract
Research focused on interrogating post-anoxic enhanced biological phosphorus removal (EBPR) at bench and pilot scales. Average bench-scale effluent ranged from 0.33 to 1.4 mgP/L, 0.35 to 3.7 mgNH3 -N/L, and 1.1 to 3.9 mgNOx -N/L. Comparatively, the pilot achieved effluent (50th percentile/average) of 0.13/0.2 mgP/L, 9.7/8.2 mgNH3 -N/L, and 0.38/3.3 mgNOx -N/L under dynamic influent and environmental conditions. For EBPR process monitoring, P:C ratio data indicated that 0.2-0.4 molP/molC will result in stable EBPR; relatedly, a target design influent volatile fatty acid (VFA):P ratio would exceed 15 mgCOD/mgP. Post-anoxic EBPR was enriched for Nitrobacter spp. at 1.70%-20.27%, with Parcubacteria also dominating; the former is putatively associated with nitritation and the latter is a putative fermenting heterotrophic organism. Post-anoxic specific denitrification rates (SDNRs) (20°C) ranged from 0.70 to 3.10 mgN/gVSS/h; there was a strong correlation (R2 = 0.94) between the SDNR and %Parcubacteria for systems operated at a 20-day solids residence time (SRT). These results suggest that carbon substrate potentially generated by this putative fermenter may enhance post-anoxic EBPR. PRACTITIONER POINTS: Post-anoxic EBPR can achieve effluent of <0.2 mgP/L and <12 mgN/L. The P:C and VFA:P ratios can be predictive for EBPR process monitoring. Post-anoxic EBPR was enriched for Nitrobacter spp. over Nitrospira spp. and also for Parcubacteria, which is a putative fermenting heterotrophic organism. Post-anoxic specific denitrification rates (20°C) ranged from 0.70 to 3.10 mgN/gVSS/h. BLASTn analysis of 16S rDNA PAO primer set was shown to be improved to 93.8% for Ca. Accumulibacter phosphatis and 73.2%-94.0% for all potential PAOs.
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Affiliation(s)
- Erik R Coats
- Department of Civil and Environmental Engineering, University of Idaho, Moscow, Idaho, USA
| | - Felicity J Appel
- Department of Civil and Environmental Engineering, University of Idaho, Moscow, Idaho, USA
- Kimley-Horn, Seattle, Washington, USA
| | - Nick Guho
- Department of Civil and Environmental Engineering, University of Idaho, Moscow, Idaho, USA
- Carollo Engineers, Walnut Creek, California, USA
| | - Cynthia K Brinkman
- Department of Civil and Environmental Engineering, University of Idaho, Moscow, Idaho, USA
| | - Jason Mellin
- Department of Civil and Environmental Engineering, University of Idaho, Moscow, Idaho, USA
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16
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Liu H, Zeng W, Meng Q, Fan Z, Peng Y. Phosphorus removal performance, intracellular metabolites and clade-level community structure of Tetrasphaera-dominated polyphosphate accumulating organisms at different temperatures. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 842:156913. [PMID: 35753450 DOI: 10.1016/j.scitotenv.2022.156913] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/17/2022] [Accepted: 06/19/2022] [Indexed: 06/15/2023]
Abstract
Tetrasphaera are polyphosphate accumulating organisms (PAOs) that play an important role in enhanced biological phosphorus removal (EBPR) from wastewater. The effect of a wide range of temperature changes (1-30 °C) on phosphorus removal, metabolism and clade-level community structure of Tetrasphaera-dominated PAOs was investigated. At 10 °C, the bioactivities of Tetrasphaera-dominated communities were obviously inhibited and the EBPR efficiency was only 73 %. Yet at 20-30 °C, EBPR efficiency reached 99 % and the relative abundance of Tetrasphaera was up to 90 %. The temperature variation changed the community distribution of Tetrasphaera clades, which was possibly a main reason for EBPR performance. Amino acids and PHA with different contents were intracellular metabolite of Tetrasphaera-dominated communities during phosphorus release and uptake at different temperatures. Moreover, Tetrasphaera fermented protein and amino acids and released VFAs. The outcomes suggested the great potential of Tetrasphaera-PAOs in the treatment of wastewater with varying temperatures and limited carbon sources.
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Affiliation(s)
- Hongjun Liu
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, Beijing 100124, PR China
| | - Wei Zeng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, Beijing 100124, PR China.
| | - Qingan Meng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, Beijing 100124, PR China
| | - Zhiwei Fan
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, Beijing 100124, PR China
| | - Yongzhen Peng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, Beijing 100124, PR China
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17
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Pelevina AV, Berestovskaya YY, Grachev VA, Dorofeev AG, Slatinskaya OV, Maksimov GV, Kallistova AY, Nikolaev YA, Grouzdev EV, Ravin NV, Pimenov NV, Mardanov AV. A Phosphate-Accumulating Microbial Community in the Laboratory Bioreactor Predominated by “Candidatus Accumulibacter”. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722800232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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18
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Burzio C, Ekholm J, Modin O, Falås P, Svahn O, Persson F, van Erp T, Gustavsson DJI, Wilén BM. Removal of organic micropollutants from municipal wastewater by aerobic granular sludge and conventional activated sludge. JOURNAL OF HAZARDOUS MATERIALS 2022; 438:129528. [PMID: 35999740 DOI: 10.1016/j.jhazmat.2022.129528] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/02/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Removal performances of organic micropollutants by conventional activated sludge (CAS) and aerobic granular sludge (AGS) were investigated at a full-scale wastewater treatment plant. Lab-scale kinetic experiments were performed to assess the micropollutant transformation rates under oxic and anoxic conditions. Transformation rates were used to model the micropollutant removal in the full-scale processes. Metagenomic sequencing was used to compare the microbial communities and antimicrobial resistance genes of the CAS and AGS systems. Higher transformation ability was observed for CAS compared to AGS for most compounds, both at the full-scale plant and in the complementary batch experiments. Oxic conditions supported the transformation of several micropollutants with faster and/or comparable rates compared to anoxic conditions. The estimated transformation rates from batch experiments adequately predicted the removal for most micropollutants in the full-scale processes. While the compositions in microbial communities differed between AGS and CAS, the full-scale biological reactors shared similar resistome profiles. Even though granular biomass showed lower potential for micropollutant transformation, AGS systems had somewhat higher gene cluster diversity compared to CAS, which could be related to a higher functional diversity. Micropollutant exposure to biomass or mass transfer limitations, therefore played more important roles in the observed differences in OMP removal.
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Affiliation(s)
- Cecilia Burzio
- Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg 41296, Sweden.
| | - Jennifer Ekholm
- Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg 41296, Sweden
| | - Oskar Modin
- Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg 41296, Sweden
| | - Per Falås
- Department of Chemical Engineering, Lund University, PO Box 124, Lund 22100, Sweden
| | - Ola Svahn
- Department of Environmental Science and Bioscience, Kristianstad University, Kristianstad 29139, Sweden
| | - Frank Persson
- Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg 41296, Sweden
| | - Tim van Erp
- Strömstad Municipality, Wastewater Treatment Plant Österröd, Strömstad 45233, Sweden
| | | | - Britt-Marie Wilén
- Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg 41296, Sweden
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19
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Maszenan AM, Bessarab I, Williams RBH, Petrovski S, Seviour RJ. The phylogeny, ecology and ecophysiology of the glycogen accumulating organism (GAO) Defluviicoccus in wastewater treatment plants. WATER RESEARCH 2022; 221:118729. [PMID: 35714465 DOI: 10.1016/j.watres.2022.118729] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/22/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
This comprehensive review looks critically what is known about members of the genus Defluviicoccus, an example of a glycogen accumulating organism (GAO), in wastewater treatment plants, but found also in other habitats. It considers the operating conditions thought to affect its performance in activated sludge plants designed to remove phosphorus microbiologically, including the still controversial view that it competes with the polyphosphate accumulating bacterium Ca. Accumulibacter for readily biodegradable substrates in the anaerobic zone receiving the influent raw sewage. It looks at its present phylogeny and what is known about it's physiology and biochemistry under the highly selective conditions of these plants, where the biomass is recycled continuously through alternative anaerobic (feed); aerobic (famine) conditions encountered there. The impact of whole genome sequence data, which have revealed considerable intra- and interclade genotypic diversity, on our understanding of its in situ behaviour is also addressed. Particular attention is paid to the problems in much of the literature data based on clone library and next generation DNA sequencing data, where Defluviicoccus identification is restricted to genus level only. Equally problematic, in many publications no attempt has been made to distinguish between Defluviicoccus and the other known GAO, especially Ca. Competibacter, which, as shown here, has a very different ecophysiology. The impact this has had and continues to have on our understanding of members of this genus is discussed, as is the present controversy over its taxonomy. It also suggests where research should be directed to answer some of the important research questions raised in this review.
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Affiliation(s)
- Abdul M Maszenan
- E2S2, NUS Environmental Research Institute, National University of Singapore, 117411, Singapore
| | - Irina Bessarab
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, 117456, Singapore
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, 117456, Singapore
| | - Steve Petrovski
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, 3086 Victoria, Australia
| | - Robert J Seviour
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, 3086 Victoria, Australia.
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20
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Reevaluation of the Phylogenetic Diversity and Global Distribution of the Genus " Candidatus Accumulibacter". mSystems 2022; 7:e0001622. [PMID: 35467400 PMCID: PMC9238405 DOI: 10.1128/msystems.00016-22] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
“Candidatus Accumulibacter” was the first microorganism identified as a polyphosphate-accumulating organism (PAO) important for phosphorus removal from wastewater. Members of this genus are diverse, and the current phylogeny and taxonomic framework appear complicated, with most publicly available genomes classified as “Candidatus Accumulibacter phosphatis,” despite notable phylogenetic divergence. The ppk1 marker gene allows for a finer-scale differentiation into different “types” and “clades”; nevertheless, taxonomic assignments remain inconsistent across studies. Therefore, a comprehensive reevaluation is needed to establish a common understanding of this genus, in terms of both naming and basic conserved physiological traits. Here, we provide this reassessment using a comparison of genome, ppk1, and 16S rRNA gene-based approaches from comprehensive data sets. We identified 15 novel species, along with “Candidatus Accumulibacter phosphatis,” “Candidatus Accumulibacter delftensis,” and “Candidatus Accumulibacter aalborgensis.” To compare the species in situ, we designed new species-specific fluorescence in situ hybridization (FISH) probes and revealed their morphology and arrangement in activated sludge. Based on the MiDAS global survey, “Ca. Accumulibacter” species were widespread in wastewater treatment plants (WWTPs) with phosphorus removal, indicating process design as a major driver for their abundance. Genome mining for PAO-related pathways and FISH-Raman microspectroscopy confirmed the potential for PAO metabolism in all “Ca. Accumulibacter” species, with detection in situ of the typical PAO storage polymers. Genome annotation further revealed differences in the nitrate/nitrite reduction pathways. This provides insights into the niche differentiation of these lineages, potentially explaining their coexistence in the same ecosystem while contributing to overall phosphorus and nitrogen removal. IMPORTANCE “Candidatus Accumulibacter” is the most studied PAO, with a primary role in biological nutrient removal. However, the species-level taxonomy of this lineage is convoluted due to the use of different phylogenetic markers or genome sequencing approaches. Here, we redefined the phylogeny of these organisms, proposing a comprehensive approach which could be used to address the classification of other diverse and uncultivated lineages. Using genome-resolved phylogeny, compared to phylogeny based on the 16S rRNA gene and other phylogenetic markers, we obtained a higher-resolution taxonomy and established a common understanding of this genus. Furthermore, genome mining of genes and pathways of interest, validated in situ by application of a new set of FISH probes and Raman microspectroscopy, provided additional high-resolution metabolic insights into these organisms.
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21
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Qiu G, Law Y, Zuniga-Montanez R, Deng X, Lu Y, Roy S, Thi SS, Hoon HY, Nguyen TQN, Eganathan K, Liu X, Nielsen PH, Williams RBH, Wuertz S. Global warming readiness: Feasibility of enhanced biological phosphorus removal at 35 °C. WATER RESEARCH 2022; 216:118301. [PMID: 35364353 DOI: 10.1016/j.watres.2022.118301] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 03/07/2022] [Accepted: 03/12/2022] [Indexed: 06/14/2023]
Abstract
Recent research has shown enhanced biological phosphorus removal (EBPR) from municipal wastewater at warmer temperatures around 30 °C to be achievable in both laboratory-scale reactors and full-scale treatment plants. In the context of a changing climate, the feasibility of EBPR at even higher temperatures is of interest. We operated two lab-scale EBPR sequencing batch reactors for > 300 days at 30 °C and 35 °C, respectively, and followed the dynamics of the communities of polyphosphate accumulating organisms (PAOs) and competing glycogen accumulating organisms (GAOs) using a combination of 16S rRNA gene metabarcoding, quantitative PCR and fluorescence in situ hybridization analyses. Stable and nearly complete phosphorus (P) removal was achieved at 30 °C; similarly, long term P removal was stable at 35 °C with effluent PO43-_P concentrations < 0.5 mg/L on half of all monitored days. Diverse and abundant Candidatus Accumulibacter amplicon sequence variants were closely related to those found in temperate environments, suggesting that EBPR at this temperature does not require a highly specialized PAO community. A slow-feeding strategy effectively limited the carbon uptake rates of GAOs, allowing PAOs to outcompete GAOs at both temperatures. Candidatus Competibacter was the main GAO, along with cluster III Defluviicoccus members. These organisms withstood the slow-feeding regime, suggesting that their bioenergetic characteristics of carbon uptake differ from those of their tetrad-forming relatives. Comparative cycle studies revealed higher carbon and P cycling activity of Ca. Accumulibacter when the temperature was increased from 30 °C to 35 °C, implying that the lowered P removal performance at 35 °C was not a direct effect of temperature, but a result of higher metabolic rates of carbon (and/or P) utilization of PAOs and GAOs, the resultant carbon deficiency, and escalated community competition. An increase in the TOC-to-PO43--P ratio (from 25:1 to 40:1) effectively eased the carbon deficiency and benefited PAOs. In general, a slow-feeding strategy and sufficiently high carbon input benefited a high and stable EBPR at 35 °C, representing basic conditions suitable for full-scale treatment plants experiencing higher water temperatures.
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Affiliation(s)
- Guanglei Qiu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore.
| | - Yingyu Law
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
| | - Rogelio Zuniga-Montanez
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore; Department of Civil and Environmental Engineering, University of California, One Shields Avenue, Davis, CA 95616, United States
| | - Xuhan Deng
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Yang Lu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
| | - Samarpita Roy
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
| | - Sara Swa Thi
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
| | - Hui Yi Hoon
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
| | - Thi Quynh Ngoc Nguyen
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
| | - Kaliyamoorthy Eganathan
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, 119077, Singapore
| | - Xianghui Liu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
| | - Per H Nielsen
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore; Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg DK-9220, Denmark
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, 119077, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore; Department of Civil and Environmental Engineering, University of California, One Shields Avenue, Davis, CA 95616, United States; School of Civil and Environmental Engineering, Nanyang Technological University, 639798, Singapore.
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22
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Chen L, Chen H, Hu Z, Tian Y, Wang C, Xie P, Deng X, Zhang Y, Tang X, Lin X, Li B, Wei C, Qiu G. Carbon uptake bioenergetics of PAOs and GAOs in full-scale enhanced biological phosphorus removal systems. WATER RESEARCH 2022; 216:118258. [PMID: 35320769 DOI: 10.1016/j.watres.2022.118258] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 03/01/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
This work analyzed, for the first time, the bioenergetics of PAOs and GAOs in full-scale wastewater treatment plants (WWTPs) for the uptake of different carbon sources. Fifteen samples were collected from five full-scale WWTPs. Predominance of different PAOs, i.e., Ca. Accumulibacter (0.00-0.49%), Tetrasphaera (0.37-3.94%), Microlunatus phosphovorus (0.01-0.18%), etc., and GAOs, i.e., Ca. Competibacter (0.08-5.39%), Defluviicoccus (0.05-5.34%), Micropruina (0.17-1.87%), etc., were shown by 16S rRNA gene amplicon sequencing. Despite the distinct PAO/GAO community compositions in different samples, proton motive force (PMF) was found as the key driving force (up to 90.1%) for the uptake of volatile fatty acids (VFAs, acetate and propionate) and amino acids (glutamate and aspartate) by both GAOs and PAOs at the community level, contrasting the previous understanding that Defluviicoccus have a low demand of PMF for acetate uptake. For the uptake of acetate or propionate, PAOs rarely activated F1, F0- ATPase (< 11.7%) or fumarate reductase (< 5.3%) for PMF generation; whereas, intensive involvements of these two pathways (up to 49.2% and 61.0%, respectively) were observed for GAOs, highlighting a major and community-level difference in their VFA uptake biogenetics in full-scale systems. However, different from VFAs, the uptake of glutamate and aspartate by both PAOs and GAOs commonly involved fumarate reductase and F1, F0-ATPase activities. Apart from these major and community-level differences, high level fine-scale micro-diversity in carbon uptake bioenergetics was observed within PAO and GAO lineages, probably resulting from their versatilities in employing different pathways for reducing power generation. Ca. Accumulibacter and Halomonas seemed to show higher dependency on the reverse operation of F1, F0-ATPase than other PAOs, likely due to the low involvement of glyoxylate shunt pathway. Unlike Tetrasphaera, but similar to Ca. Accumulibacter, Microlunatus phosphovorus took up glutamate and aspartate via the proton/glutamate-aspartate symporter driven by PMF. This feature was testified using a pure culture of Microlunatus phosphovorus stain NM-1. The major difference between PAOs and GAOs highlights the potential to selectively suppress GAOs for community regulation in EBPR systems. The finer-scale carbon uptake bioenergetics of PAOs or GAOs from different lineages benefits in understanding their interactions in community assembly in complex environment.
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Affiliation(s)
- Liping Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Hang Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Zekun Hu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Yucheng Tian
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Cenchao Wang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Peiran Xie
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Xuhan Deng
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Yushen Zhang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Xia Tang
- Guangzhou Sewage Purification Co., Ltd, Guangzhou 510006, China
| | - Xueran Lin
- Guangzhou Sewage Purification Co., Ltd, Guangzhou 510006, China
| | - Biqing Li
- Guangzhou Sewage Purification Co., Ltd, Guangzhou 510006, China
| | - Chaohai Wei
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; Key Laboratory of Pollution Control and Ecological Restoration in Industrial Clusters, Ministry of Education, Guangzhou 510006, China
| | - Guanglei Qiu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; Key Laboratory of Pollution Control and Ecological Restoration in Industrial Clusters, Ministry of Education, Guangzhou 510006, China.
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23
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Bessarab I, Maszenan AM, Haryono MAS, Arumugam K, Saw NMMT, Seviour RJ, Williams RBH. Comparative Genomics of Members of the Genus Defluviicoccus With Insights Into Their Ecophysiological Importance. Front Microbiol 2022; 13:834906. [PMID: 35495637 PMCID: PMC9041414 DOI: 10.3389/fmicb.2022.834906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/02/2022] [Indexed: 11/23/2022] Open
Abstract
Members of the genus Defluviicoccus occur often at high abundances in activated sludge wastewater treatment plants designed to remove phosphorus, where biomass is subjected to alternating anaerobic feed/aerobic famine conditions, believed to favor the proliferation of organisms like Ca. Accumulibacter and other phosphate-accumulating organisms (PAO), and Defluviicoccus. All have a capacity to assimilate readily metabolizable substrates and store them intracellularly during the anaerobic feed stage so that under the subsequent famine aerobic stage, these can be used to synthesize polyphosphate reserves by the PAO and glycogen by Defluviicoccus. Consequently, Defluviicoccus is described as a glycogen-accumulating organism or GAO. Because they share a similar anaerobic phenotype, it has been proposed that at high Defluviicoccus abundance, the PAO are out-competed for assimilable metabolites anaerobically, and hence aerobic P removal capacity is reduced. Several Defluviicoccus whole genome sequences have been published (Ca. Defluviicoccus tetraformis, Defluviicoccus GAO-HK, and Ca. Defluviicoccus seviourii). The available genomic data of these suggest marked metabolic differences between them, some of which have ecophysiological implications. Here, we describe the whole genome sequence of the type strain Defluviicoccus vanusT, the only cultured member of this genus, and a detailed comparative re-examination of all extant Defluviicoccus genomes. Each, with one exception, which appears not to be a member of this genus, contains the genes expected of GAO members, in possessing multiple copies of those for glycogen biosynthesis and catabolism, and anaerobic polyhydroxyalkanoate (PHA) synthesis. Both 16S rRNA and genome sequence data suggest that the current recognition of four clades is insufficient to embrace their phylogenetic biodiversity, but do not support the view that they should be re-classified into families other than their existing location in the Rhodospirillaceae. As expected, considerable variations were seen in the presence and numbers of genes encoding properties associated with key substrate assimilation and metabolic pathways. Two genomes also carried the pit gene for synthesis of the low-affinity phosphate transport protein, pit, considered by many to distinguish all PAO from GAO. The data re-emphasize the risks associated with extrapolating the data generated from a single Defluviicoccus population to embrace all members of that genus.
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Affiliation(s)
- Irina Bessarab
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Abdul Majid Maszenan
- Nanyang Environment & Water Research Institute (NEWRI), Nanyang Technological University, Singapore, Singapore.,NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
| | - Mindia A S Haryono
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Krithika Arumugam
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Nay Min Min Thaw Saw
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Robert J Seviour
- School of Life Sciences, La Trobe University, Melbourne, VIC, Australia
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
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24
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Adler A, Poirier S, Pagni M, Maillard J, Holliger C. Disentangle genus microdiversity within a complex microbial community by using a multi-distance long-read binning method: example of Candidatus Accumulibacter. Environ Microbiol 2022; 24:2136-2156. [PMID: 35315560 PMCID: PMC9311429 DOI: 10.1111/1462-2920.15947] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 02/19/2022] [Indexed: 11/26/2022]
Abstract
Complete genomes can be recovered from metagenomes by assembling and binning DNA sequences into metagenome assembled genomes (MAGs). Yet, the presence of microdiversity can hamper the assembly and binning processes, possibly yielding chimeric, highly fragmented and incomplete genomes. Here, the metagenomes of four samples of aerobic granular sludge bioreactors containing Candidatus (Ca.) Accumulibacter, a phosphate-accumulating organism of interest for wastewater treatment, were sequenced with both PacBio and Illumina. Different strategies of genome assembly and binning were investigated, including published protocols and a binning procedure adapted to the binning of long contigs (MuLoBiSC). Multiple criteria were considered to select the best strategy for Ca. Accumulibacter, whose multiple strains in every sample represent a challenging microdiversity. In this case, the best strategy relies on long-read only assembly and a custom binning procedure including MuLoBiSC in metaWRAP. Several high-quality Ca. Accumulibacter MAGs, including a novel species, were obtained independently from different samples. Comparative genomic analysis showed that MAGs retrieved in different samples harbour genomic rearrangements in addition to accumulation of point mutations. The microdiversity of Ca. Accumulibacter, likely driven by mobile genetic elements, causes major difficulties in recovering MAGs, but it is also a hallmark of the panmictic lifestyle of these bacteria.
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Affiliation(s)
- Aline Adler
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Simon Poirier
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Marco Pagni
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Julien Maillard
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,IFP Energie nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison Cedex, France
| | - Christof Holliger
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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25
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Chen G, Bai R, Zhang Y, Zhao B, Xiao Y. Application of metagenomics to biological wastewater treatment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150737. [PMID: 34606860 DOI: 10.1016/j.scitotenv.2021.150737] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/20/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
Biological wastewater treatment is a process in which the microbial metabolism of complex communities transforms pollutants into low- or non-toxic products. Due to the absence of an in-depth understanding of the diversity and complexity of microbial communities, it is very likely to ignore the potential mechanisms of microbial community in wastewater treatment. Metagenomics is a technology based on molecular biology, in which massive gene sequences are obtained from environmental samples and analyzed by bioinformatics to determine the composition and function of a microbial community. Metagenomics can identify the state of microbes in their native environments more effectively than traditional molecular methods. This review summarizes the application of metagenomics to assess microbial communities in biological wastewater treatment, such as the biological removal of phosphorus and nitrogen by bacteria, the study of antibiotic resistance genes (ARGs), and the reduction of heavy metals by microbial communities, with an emphasis on the contribution of microbial diversity and metabolic diversity. Technical bottlenecks in the application of metagenomics to biological wastewater treatment are elucidated, and future research directions for metagenomics are proposed, among which the application of multi-omics will be an important research method for future biological wastewater treatment.
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Affiliation(s)
- Geng Chen
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Rui Bai
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yiqing Zhang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Biyi Zhao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yong Xiao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
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26
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Kolakovic S, Salgado R, Freitas EB, Bronze MR, Sekulic MT, Carvalho G, Reis MAM, Oehmen A. Diclofenac biotransformation in the enhanced biological phosphorus removal process. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:151232. [PMID: 34715209 DOI: 10.1016/j.scitotenv.2021.151232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/04/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
Diclofenac is a pharmaceutical active compound frequently detected in wastewater and water bodies, and often reported to be persistent and difficult to biodegrade. While many previous studies have focussed on assessing diclofenac biodegradation in nitrification and denitrification processes, this study focusses on diclofenac biodegradation in the enhanced biological phosphorus removal (EBPR) process, where the efficiency of this process for diclofenac biodegradation as well as the metabolites generated are not well understood. An enrichment of Accumulibacter polyphosphate accumulating organisms (PAOs) was operated in an SBR for over 300 d, and acclimatized to 20 μg/L of diclofenac, which is in a similar range to that observed in domestic wastewater influents. The diclofenac biotransformation was monitored in four periods of stable operation and linked to the microbial community and metabolic behaviour in each period. Nitrification was observed in two of the four periods despite the addition of a nitrification inhibitor, and these periods were positively correlated with increased diclofenac biodegradation. Interestingly, in two periods with excellent phosphorus removal (>99%) and no nitrification, different levels of diclofenac biotransformation were observed. Period 2, enriched in Accumulibacter Type II achieved more significant diclofenac biotransformation (3.4 μg/gX), while period 4, enriched in Accumulibacter Type I achieved lower diclofenac biotransformation (0.4 μg/gX). In total, 23 transformation products were identified, with lower toxicity than the parent compound, enabling the elucidation of multiple metabolic pathways for diclofenac biotransformation. This study showed that PAOs can contribute to diclofenac biotransformation, yielding less toxic transformation products, and can complement the biodegradation carried out by other organisms in activated sludge, particularly nitrifiers.
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Affiliation(s)
- Srdana Kolakovic
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal; University of Novi Sad, Faculty of Technical Sciences, 21000 Novi Sad, Serbia
| | - Ricardo Salgado
- LAQV, REQUIMTE, Department of Chemistry, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; ESTS-IPS-CINEA, Escola Superior de Tecnologia de Setúbal do Instituto Politécnico de Setúbal, Rua Vale de Chaves, Campus do IPS, Estefanilha, 2910-761 Setúbal, Portugal
| | - Elisabete B Freitas
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
| | - Maria R Bronze
- iBET - Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal; Faculdade de Farmácia da Universidade de Lisboa, Lisboa, Portugal
| | - Maja Turk Sekulic
- University of Novi Sad, Faculty of Technical Sciences, 21000 Novi Sad, Serbia
| | - Gilda Carvalho
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal; Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Maria A M Reis
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
| | - Adrian Oehmen
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal; School of Chemical Engineering, The University of Queensland, St Lucia, Queensland 4072, Australia.
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27
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Carvalho VCF, Kessler M, Fradinho JC, Oehmen A, Reis MAM. Achieving nitrogen and phosphorus removal at low C/N ratios without aeration through a novel phototrophic process. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 793:148501. [PMID: 34171805 DOI: 10.1016/j.scitotenv.2021.148501] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/12/2021] [Accepted: 06/13/2021] [Indexed: 06/13/2023]
Abstract
Conventional wastewater treatment technologies for biological nutrient removal (BNR) are highly dependent on aeration for oxygen supply, which represents a major operational cost of the process. Recently, phototrophic enhanced biological phosphorus removal (photo-EBPR) has been suggested as an alternative system for phosphorus removal, based on a consortium of photosynthetic microorganisms and chemotrophic bacteria, eliminating the need for costly aeration. However, wastewater treatment plants must couple nitrogen and phosphorus removal to achieve discharge limits. For this reason, a new microalgae-bacterial based system for phosphorus and nitrogen removal is proposed in this work. The photo-BNR system studied here consists of a sequencing batch reactor operated with dark anaerobic, light aerobic, dark anoxic and idle periods, to allow both N and P removal. Results of the study show that the photo-BNR system was able to remove 100% of the 40 mg N/L of ammonia fed to the reactor and 94 ± 3% of the total nitrogen (Influent COD:N ratio of 300:40, similar to domestic wastewater). Moreover, an average of 25 ± 9.2 mg P/L was simultaneously removed in the photo-BNR tests, representing the P removal capacity of this system, which exceeds the level of P removal required from typical domestic wastewater. Full ammonia removal was achieved during the light phase, with 67 ± 5% of this ammonia being assimilated by the microbial culture and the remaining 33 ± 5% being converted into nitrate. The assimilated P corresponded to 2.8 ± 0.23 mg P/L, which only represented, approximately, 1/9 of the P removal capacity of the system. Half of the nitrified ammonia was subsequently denitrified during the dark anoxic phase (50 ± 24%). Overall, the photo-BNR system represents the first treatment alternative for N and P from domestic wastewater with no need of mechanical aeration or supplemental carbon addition, representing an alternative low-energy technology of interest.
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Affiliation(s)
- V C F Carvalho
- UCIBIO-REQUIMTE, Department of Chemistry, Faculty of Sciences and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - M Kessler
- UCIBIO-REQUIMTE, Department of Chemistry, Faculty of Sciences and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - J C Fradinho
- UCIBIO-REQUIMTE, Department of Chemistry, Faculty of Sciences and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal.
| | - A Oehmen
- School of Chemical Engineering, University of Queensland, Brisbane, QLD 4072, Australia
| | - M A M Reis
- UCIBIO-REQUIMTE, Department of Chemistry, Faculty of Sciences and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
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Srinivasan VN, Li G, Wang D, Tooker NB, Dai Z, Onnis-Hayden A, Bott C, Dombrowski P, Schauer P, Pinto A, Gu AZ. Oligotyping and metagenomics reveal distinct Candidatus Accumulibacter communities in side-stream versus conventional full-scale enhanced biological phosphorus removal (EBPR) systems. WATER RESEARCH 2021; 206:117725. [PMID: 34653799 DOI: 10.1016/j.watres.2021.117725] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
Candidatus Accumulibacter phosphatis (CAP) and its clade-level micro-diversity has been associated with and implicated in functional differences in phosphorus removal performance in enhanced biological phosphorus removal (EBPR) systems. Side-stream EBPR (S2EBPR) is an emerging process that has been shown to present a suite of advantages over the conventional EBPR design, however, large knowledge gaps remain in terms of its underlying ecological mechanisms. Here, we compared and revealed the higher-resolution differences in microbial ecology of CAP between a full-scale side-stream EBPR configuration and a conventional A2O EBPR process that were operated in parallel and with the same influent feed. Even though the relative abundance of CAP, revealed by 16S rRNA gene amplicon sequencing, was similar in both treatment trains, a clade-level analysis, using combined 16S rRNA-gene based amplicon sequencing and oligotyping analysis and metagenomics analysis, revealed the distinct CAP microdiversity between the S2EBPR and A2O configurations that likely attributed to the improved performance in S2EBPR in comparison to conventional EBPR. Furthermore, genome-resolved metagenomics enabled extraction of three metagenome-assembled genomes (MAGs) belonging to CAP clades IIB (RCAB4-2), IIC (RC14) and II (RC18), from full-scale EBPR sludge for the first time, including a distinct Ca. Accumulibacter clade that is dominant and associated only with the S2EBPR configuration. The results also revealed the temporally increasing predominance of RC14, which belonged to Clade IIC, during the implementation of the S2EBPR configuration. Finally, we also show the existence of previously uncharacterized diversity of clades of CAP, namely the clades IIB and as yet unidentified clade of type II, in full-scale EBPR communities, highlighting the unknown diversity of CAP communities in full-scale EBPR systems.
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Affiliation(s)
- Varun N Srinivasan
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, United States; Brown and Caldwell, One Tech Drive, Andover, MA 01810, United States
| | - Guangyu Li
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, United States
| | - Dongqi Wang
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, United States; State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, Shaanxi 710048, China
| | - Nicholas B Tooker
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, United States; Department of Civil and Environmental Engineering, University of Massachusetts-Amherst, Amherst, MA 01002, United States
| | - Zihan Dai
- Infrastructure and Environment Division, University of Glasgow, Glasgow G12 8LT, United Kingdom
| | - Annalisa Onnis-Hayden
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, United States
| | - Charles Bott
- Hampton Roads Sanitation District, 1434 Air Rail Avenue, Virginia Beach, VA 23454, United States
| | - Paul Dombrowski
- Woodard & Curran, Inc., 1699 King Street, Enfield, CT 06082, United States
| | - Peter Schauer
- Clean Water Services, 16060 SW 85th Avenue, Tigard, OR 97224, United States
| | - Ameet Pinto
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, United States; Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30318, United States
| | - April Z Gu
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, United States; Civil and Environmental Engineering, Cornell University, Ithaca NY 14853, United States.
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McDaniel EA, Wahl SA, Ishii S, Pinto A, Ziels R, Nielsen PH, McMahon KD, Williams RBH. Prospects for multi-omics in the microbial ecology of water engineering. WATER RESEARCH 2021; 205:117608. [PMID: 34555741 DOI: 10.1016/j.watres.2021.117608] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
Advances in high-throughput sequencing technologies and bioinformatics approaches over almost the last three decades have substantially increased our ability to explore microorganisms and their functions - including those that have yet to be cultivated in pure isolation. Genome-resolved metagenomic approaches have enabled linking powerful functional predictions to specific taxonomical groups with increasing fidelity. Additionally, related developments in both whole community gene expression surveys and metabolite profiling have permitted for direct surveys of community-scale functions in specific environmental settings. These advances have allowed for a shift in microbiome science away from descriptive studies and towards mechanistic and predictive frameworks for designing and harnessing microbial communities for desired beneficial outcomes. Water engineers, microbiologists, and microbial ecologists studying activated sludge, anaerobic digestion, and drinking water distribution systems have applied various (meta)omics techniques for connecting microbial community dynamics and physiologies to overall process parameters and system performance. However, the rapid pace at which new omics-based approaches are developed can appear daunting to those looking to apply these state-of-the-art practices for the first time. Here, we review how modern genome-resolved metagenomic approaches have been applied to a variety of water engineering applications from lab-scale bioreactors to full-scale systems. We describe integrated omics analysis across engineered water systems and the foundations for pairing these insights with modeling approaches. Lastly, we summarize emerging omics-based technologies that we believe will be powerful tools for water engineering applications. Overall, we provide a framework for microbial ecologists specializing in water engineering to apply cutting-edge omics approaches to their research questions to achieve novel functional insights. Successful adoption of predictive frameworks in engineered water systems could enable more economically and environmentally sustainable bioprocesses as demand for water and energy resources increases.
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Affiliation(s)
- Elizabeth A McDaniel
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA.
| | | | - Shun'ichi Ishii
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Yokosuka 237-0061, Japan
| | - Ameet Pinto
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, USA
| | - Ryan Ziels
- Department of Civil Engineering, The University of British Columbia, Vancouver, BC, Canada
| | | | - Katherine D McMahon
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA; Department of Civil and Environmental Engineering, University of Wisconsin - Madison, Madison, WI, USA
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Republic of Singapore.
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Du Z, Behrens SF. Tracking de novo protein synthesis in the activated sludge microbiome using BONCAT-FACS. WATER RESEARCH 2021; 205:117696. [PMID: 34601360 DOI: 10.1016/j.watres.2021.117696] [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: 06/22/2021] [Revised: 08/31/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
In order to ensure stable performance of engineered biotechnologies that rely on mixed microbial community systems, it is important to identify process-specific microbial traits and study their in-situ activity and responses to changing environmental conditions and system operational parameters. We used BioOrthogonal Non-Canonical Amino acid Tagging (BONCAT) in combination with Fluorescence-Activated Cell Sorting (FACS) and 16S rRNA gene amplicon sequencing to identify translationally active cells in activated sludge. We found that only a subset of the activated sludge microbiome is translationally active during the aerobic treatment phase of a full-scale sequencing batch reactor designed to enhance biological phosphorus removal from municipal wastewater. Relative abundance of amplicon sequence variants was not a reliable predictor of species activity. BONCAT-positive and -negative cells revealed a broad range of population-wide and taxa-specific translational heterogeneity. BONCAT-FACS in combination with amplicon sequencing can provide new insights into the ecophysiology of highly dynamic microbiomes in activated sludge systems.
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Affiliation(s)
- Zhe Du
- The BioTechnology Institute, University of Minnesota Twin Cities, St. Paul, MN, 55108, USA
| | - Sebastian F Behrens
- The BioTechnology Institute, University of Minnesota Twin Cities, St. Paul, MN, 55108, USA; Department of Civil, Environmental, and Geo-Engineering, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA.
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Metabolic Differentiation of Co-occurring Accumulibacter Clades Revealed through Genome-Resolved Metatranscriptomics. mSystems 2021; 6:e0047421. [PMID: 34227830 PMCID: PMC8407102 DOI: 10.1128/msystems.00474-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
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.
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Khalil S, Panda P, Ghadamgahi F, Rosberg A, Vetukuri RR. Comparison of two commercial recirculated aquacultural systems and their microbial potential in plant disease suppression. BMC Microbiol 2021; 21:205. [PMID: 34225658 PMCID: PMC8259135 DOI: 10.1186/s12866-021-02273-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 06/25/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Aquaponics are food production systems advocated for food security and health. Their sustainability from a nutritional and plant health perspective is, however, a significant challenge. Recirculated aquaculture systems (RAS) form a major part of aquaponic systems, but knowledge about their microbial potential to benefit plant growth and plant health is limited. The current study tested if the diversity and function of microbial communities in two commercial RAS were specific to the fish species used (Tilapia or Clarias) and sampling site (fish tanks and wastewaters), and whether they confer benefits to plants and have in vitro antagonistic potential towards plant pathogens. RESULTS Microbial diversity and composition was found to be dependent on fish species and sample site. The Tilapia RAS hosted higher bacterial diversity than the Clarias RAS; but the later hosted higher fungal diversity. Both Tilapia and Clarias RAS hosted bacterial and fungal communities that promoted plant growth, inhibited plant pathogens and encouraged biodegradation. The production of extracellular enzymes, related to nutrient availability and pathogen control, by bacterial strains isolated from the Tilapia and Clarias systems, makes them a promising tool in aquaponics and in their system design. CONCLUSIONS This study explored the microbial diversity and potential of the commercial RAS with either Tilapia or Clarias as a tool to benefit the aquaponic system with respect to plant growth promotion and control of plant diseases.
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Affiliation(s)
- Sammar Khalil
- Department of Biosystems and Technology, Swedish University of Agricultural Sciences, Box 103, 230 53, Alnarp, Sweden.
| | - Preeti Panda
- Plant and Food Research, Plant Protection, Lincoln, New Zealand
| | - Farideh Ghadamgahi
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 102, 230 53, Alnarp, Sweden
| | - AnnaKarin Rosberg
- Department of Biosystems and Technology, Swedish University of Agricultural Sciences, Box 103, 230 53, Alnarp, Sweden
| | - Ramesh R Vetukuri
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 102, 230 53, Alnarp, Sweden
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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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Wang Y, Gao H, F Wells G. Integrated omics analyses reveal differential gene expression and potential for cooperation between denitrifying polyphosphate and glycogen accumulating organisms. Environ Microbiol 2021; 23:3274-3293. [PMID: 33769674 DOI: 10.1111/1462-2920.15486] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 03/02/2021] [Accepted: 03/24/2021] [Indexed: 01/06/2023]
Abstract
Unusually high accumulation of the potent greenhouse gas nitrous oxide (N2 O) has previously been documented in denitrifying biological phosphorus (P) removal bioprocesses, but the roles of differential denitrification gene expression patterns and ecological interactions between key functional groups in driving these emissions are not well understood. To address these knowledge gaps, we applied genome-resolved metagenomics and metatranscriptomics to a denitrifying bioprocess enriched in as-yet-uncultivated denitrifying polyphosphate accumulating organisms (PAOs) affiliated with Candidatus Accumulibacter. The six transcriptionally most active populations in the community included three co-occurring Accumulibacter strains affiliated with clades IF (a novel clade identified in this study), IA and IC, a competing glycogen accumulating organism (GAO) affiliated with Competibacteraceae (GAO1), a Gammaproteobacteria PR6 and an Anaerolineae CH7. Strongly elevated expression of nitrite reductase genes compared to nitrous oxide reductase genes was observed in the overall community and in Accumulibacter populations, suggesting a strong role for differential gene expression in driving N2 O accumulation. Surprisingly, while ~90% of the nirS gene transcripts were expressed by the three co-occurring PAO populations, ~93% of the norB gene transcripts were expressed by GAO1 and ~75% of the norZ gene transcripts were mapped to PR6 and several other non-PAO flanking populations. This suggests the potential for cooperation between flanking populations and PAOs in reducing denitrification intermediates. Such cooperation may benefit the community by reducing the accumulation of toxic nitric oxide.
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Affiliation(s)
- Yubo Wang
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - Han Gao
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - George F Wells
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
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Kristensen JM, Singleton C, Clegg LA, Petriglieri F, Nielsen PH. High Diversity and Functional Potential of Undescribed "Acidobacteriota" in Danish Wastewater Treatment Plants. Front Microbiol 2021; 12:643950. [PMID: 33967982 PMCID: PMC8100337 DOI: 10.3389/fmicb.2021.643950] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 03/29/2021] [Indexed: 01/10/2023] Open
Abstract
Microbial communities in water resource recovery facilities encompass a large diversity of poorly characterized lineages that could have undescribed process-critical functions. Recently, it was shown that taxa belonging to "Acidobacteriota" are abundant in Danish full-scale activated sludge wastewater treatment plants (WWTP), and here we investigated their diversity, distribution, and functional potential. "Acidobacteriota" taxa were identified using a comprehensive full-length 16S rRNA gene reference dataset and amplicon sequencing surveys across 37 WWTPs. Members of this phylum were diverse, belonging to 14 families, eight of which are completely uncharacterized and lack type strains. Several lineages were abundant, with relative abundances of up to 5% of the microbial community. Genome annotation and metabolic reconstruction of 50 high-quality "Acidobacteriota" metagenome-assembled genomes (MAGs) from 19 WWTPs showed high metabolic diversity and potential involvement in nitrogen and phosphorus removal and iron reduction. Fluorescence in situ hybridization (FISH) using newly-designed probes revealed cells with diverse morphologies, predominantly located inside activated sludge flocs. FISH in combination with Raman microspectroscopy revealed ecophysiological traits in probe-defined cells from the families Holophagaceae, Thermoanaerobaculaceae, and Vicinamibacteraceae, and families with the placeholder name of midas_f_502, midas_f_973, and midas_f_1548. Members of these lineages had the potential to be polyphosphate-accumulating organisms (PAOs) as intracellular storage was observed for the key compounds polyphosphate and glycogen.
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Affiliation(s)
| | | | | | | | - Per Halkjaer Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
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The community compositions of three nitrogen removal wastewater treatment plants of different configurations in Victoria, Australia, over a 12-month operational period. Appl Microbiol Biotechnol 2020; 104:9839-9852. [DOI: 10.1007/s00253-020-10901-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 08/06/2020] [Accepted: 09/10/2020] [Indexed: 12/23/2022]
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Nierychlo M, Andersen KS, Xu Y, Green N, Jiang C, Albertsen M, Dueholm MS, Nielsen PH. MiDAS 3: An ecosystem-specific reference database, taxonomy and knowledge platform for activated sludge and anaerobic digesters reveals species-level microbiome composition of activated sludge. WATER RESEARCH 2020; 182:115955. [PMID: 32777640 DOI: 10.1016/j.watres.2020.115955] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/13/2020] [Accepted: 05/16/2020] [Indexed: 05/13/2023]
Abstract
The function of the microbiomes in wastewater treatment systems and anaerobic digesters is dictated by the physiological activity of their members and complex interactions between them. Since functional traits are often conserved at low taxonomic ranks (genus, species, strain), high resolution taxonomic classification is crucial to understand the role of microbes in any ecosystem. Here we present MiDAS 3, a comprehensive 16S rRNA gene reference database based on full-length 16S rRNA gene amplicon sequence variants (FL-ASVs) derived from activated sludge and anaerobic digester systems in Denmark. The new database proposes unique provisional names for all unclassified microorganisms down to species level, providing a new and much-needed tool for microbiome research. The MiDAS 3 database was used to analyze the microbiome in 20 Danish wastewater treatment plants with nutrient removal, sampled over 13 years. The 50 most abundant species belonged to 42 genera, including 14 genera with provisional 'midas' name. Of those, 20 have no known function in the system, which highlights the need for more efforts towards elucidating the role of important members of wastewater treatment ecosystems. The new MiDAS 3 database also forms the backbone of the MiDAS Field Guide - an online resource linking the identity of microorganisms in wastewater treatment systems to available data related to their functional importance. The new field guide contains a complete list of genera (>1800) and species (>4200) found in activated sludge and anaerobic digesters in Denmark, but is also relevant to wastewater systems across the world. The identity of the microbes is linked to functional information, where available, and the website provides the possibility to BLAST new sequences against the MiDAS 3 database. The MiDAS Field Guide is a collaborative platform acting as an online knowledge repository, facilitating understanding of wastewater treatment ecosystem function.
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Affiliation(s)
- Marta Nierychlo
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Kasper Skytte Andersen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Yijuan Xu
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Nicholas Green
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Chenjing Jiang
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Morten Simonsen Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
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Oren A, Garrity GM, Parker CT, Chuvochina M, Trujillo ME. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2020; 70:3956-4042. [DOI: 10.1099/ijsem.0.003789] [Citation(s) in RCA: 782] [Impact Index Per Article: 195.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.
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Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M. Garrity
- NamesforLife, LLC, PO Box 769, Okemos MI 48805-0769, USA
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| | | | - Maria Chuvochina
- Australian Centre for Ecogenomics, University of Queensland, St. Lucia QLD 4072, Brisbane, Australia
| | - Martha E. Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, 37007, Salamanca, Spain
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Terashima M, Kamagata Y, Kato S. Rapid Enrichment and Isolation of Polyphosphate-Accumulating Organisms Through 4'6-Diamidino-2-Phenylindole (DAPI) Staining With Fluorescence-Activated Cell Sorting (FACS). Front Microbiol 2020; 11:793. [PMID: 32425914 PMCID: PMC7203516 DOI: 10.3389/fmicb.2020.00793] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 04/02/2020] [Indexed: 12/13/2022] Open
Abstract
Screening for bacteria with abilities to accumulate valuable intracellular compounds from an environmental community is difficult and requires strategic methods. Combining the experimental procedure for phenotyping living cells in a microbial community with the cell recovery necessary for further cultivation will allow for an efficient initial screening process. In this study, we developed a strategy for the isolation of polyphosphate-accumulating organisms (PAOs) by combining (i) nontoxic fluorescence staining of polyphosphate granules in viable microbial cells and (ii) fluorescence-activated cell sorting (FACS) for the rapid detection and collection of target cells. To implement this screening approach, cells from wastewater sludge samples were stained with 4’6-diamidino-2-phenylindole (DAPI) to target cells with high polyphosphate (polyP) accumulation. We found a staining procedure (10 μg/ml of DAPI for 30 min) that can visualize polyP granules while maintaining viability for the majority of the cells (>60%). The polyP positive cells were recovered by FACS, purified by colony isolation and phylogenetically identified by 16S rRNA gene sequencing. Follow-up analysis confirmed that these isolates accumulate polyP, indicating that DAPI can be implemented in staining living cells and FACS can effectively and rapidly screen and isolate individual cells from a complex microbial community.
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Affiliation(s)
- Mia Terashima
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan.,Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan.,Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Souichiro Kato
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan.,Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
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Onnis-Hayden A, Srinivasan V, Tooker NB, Li G, Wang D, Barnard JL, Bott C, Dombrowski P, Schauer P, Menniti A, Shaw A, Stinson B, Stevens G, Dunlap P, Takács I, McQuarrie J, Phillips H, Lambrecht A, Analla H, Russell A, Gu AZ. Survey of full-scale sidestream enhanced biological phosphorus removal (S2EBPR) systems and comparison with conventional EBPRs in North America: Process stability, kinetics, and microbial populations. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2020; 92:403-417. [PMID: 31402530 DOI: 10.1002/wer.1198] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/29/2019] [Accepted: 08/06/2019] [Indexed: 05/25/2023]
Abstract
Sidestream EBPR (S2EBPR) is an emerging alternative process to address common challenges in EBPR related to weak wastewater influent and may improve EBPR process stability. A systematic evaluation and comparison of the process performance and microbial community structure was conducted between conventional and S2EBPR facilities in North America. The statistical analysis suggested higher performance stability in S2EBPR than conventional EBPR, although possible bias associated with other plant-specific factors might have affected the comparison. Variations in stoichiometric values related to EBPR activity and discrepancies between the observed values and current model predictions suggested a varying degree of metabolic versatility of PAOs in S2EBPR systems that warrant further investigation. Microbial community analysis using various techniques suggested comparable known candidate PAO relative abundances in S2EBPR and conventional EBPR systems, whereas the relative abundance of known candidate GAOs seemed to be consistently lower in S2EBPR facilities than conventional EBPR facilities. 16S rRNA gene sequencing analysis revealed differences in the community phylogenetic fingerprints between S2EBPR and conventional facilities and indicated statistically higher microbial diversity index values in S2EBPR facilities than those in conventional EBPRs. PRACTITIONER POINTS: Sidestream EBPR (S2EBPR) can be implemented with varying and flexible configurations, and they offer advantages over conventional configurations for addressing the common challenges in EBPR related to weak wastewater influent and may improve EBPR process stability. Survey of S2EBPR plants in North America suggested statistically more stable phosphorus removal performance in S2EBPR plants than conventional EBPRs, although possible bias might affect the comparison due to other plant-specific factors. The EBPR kinetics and stoichiometry of the S2EBPR facilities seemed to vary and are associated with metabolic versatility of PAOs in S2EBPR systems that warrant further investigation. The abundance of known candidate PAOs in S2EBPR plants was similar to those in conventional EBPRs, and the abundance of known candidate GAOs was generally lower in S2EBPR than conventional EBPR facilities. Further finer-resolution analysis of PAOs and GAOs, as well as identification of other unknown PAOs and GAOs, is needed. Microbial diversity is higher in S2EBPR facilities compared with conventional ones, implying that S2EBPR microbial communities could show better resilience to perturbations due to potential functional redundancy.
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Affiliation(s)
| | - Varun Srinivasan
- Northeastern University, Boston, Massachusetts
- Cornell University, Ithaca, New York
| | - Nicholas B Tooker
- Northeastern University, Boston, Massachusetts
- University of Massachusetts Amherst, Amherst, Massachusetts
| | - Guangyu Li
- Northeastern University, Boston, Massachusetts
| | - Dongqi Wang
- Northeastern University, Boston, Massachusetts
- Xi'an University of Technology, Xi'an, China
| | | | - Charles Bott
- Hampton Roads Sanitation District, Virginia Beach, Virginia
| | | | | | | | | | | | | | | | | | - Jim McQuarrie
- Denver Metro Wastewater Reclamation District, Denver, Colorado
| | | | - Angela Lambrecht
- Regional District of Central Okanagan, West Kelowna, British Columbia, Canada
| | | | | | - April Z Gu
- Northeastern University, Boston, Massachusetts
- Cornell University, Ithaca, New York
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41
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Qiu G, Liu X, Saw NMMT, Law Y, Zuniga-Montanez R, Thi SS, Ngoc Nguyen TQ, Nielsen PH, Williams RBH, Wuertz S. Metabolic Traits of Candidatus Accumulibacter clade IIF Strain SCELSE-1 Using Amino Acids As Carbon Sources for Enhanced Biological Phosphorus Removal. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:2448-2458. [PMID: 31790213 DOI: 10.1021/acs.est.9b02901] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Despite recent evidence from full-scale plants suggesting that Candidatus Accumulibacter may be capable of using amino acids, this metabolic trait has never been confirmed in a bioreactor experiment. Here we show that an enriched culture of Ca. Accumulibacter clade IIF strain SCELSE-1 could metabolize 11 of 20 α-amino acids, with aspartate, glutamate, asparagine, and glutamine resulting in the highest phosphorus removal. The anaerobic uptake of aspartate and glutamate was achieved through a glutamate/aspartate-proton symporter fully powered by the proton motive force (PMF). Under anaerobic conditions aspartate was deaminized and routed into core carbon metabolic pathways to form polyhydroxyalkanoates (PHA). The lack of genes encoding NADH dependent isocitrate dehydrogenase in the Ca. Accumulibacter genome resulted in a kinetic barrier for glutamate to be channelled to the TCA cycle. Glutamate was stored as glutamate polymer. When amino acids (aspartate or glutamate) and acetate were supplied together, Ca. Accumulibacter took up both carbon sources simultaneously, with the uptake rate of each carbon source largely preserved. Overall energy savings (up to 17%) were achieved under mixed carbon scenarios, due to the ability of Ca. Accumulibacter to rearrange its anaerobic carbon metabolism based on the reducing power, PMF and ATP balance.
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Affiliation(s)
- Guanglei Qiu
- Singapore Centre for Environmental Life Sciences Engineering , Nanyang Technological University , Singapore 637551 , Singapore
- School of Environment and Energy , South China University of Technology , Guangzhou 510006 , China
| | - Xianghui Liu
- Singapore Centre for Environmental Life Sciences Engineering , Nanyang Technological University , Singapore 637551 , Singapore
| | - Nay Min Min Thaw Saw
- Singapore Centre for Environmental Life Sciences Engineering , Nanyang Technological University , Singapore 637551 , Singapore
| | - Yingyu Law
- Singapore Centre for Environmental Life Sciences Engineering , Nanyang Technological University , Singapore 637551 , Singapore
| | - Rogelio Zuniga-Montanez
- Singapore Centre for Environmental Life Sciences Engineering , Nanyang Technological University , Singapore 637551 , Singapore
- Department of Civil and Environmental Engineering, One Shields Avenue , University of California , Davis , California 95616 , United States
| | - Sara Swa Thi
- Singapore Centre for Environmental Life Sciences Engineering , Nanyang Technological University , Singapore 637551 , Singapore
| | - Thi Quynh Ngoc Nguyen
- Singapore Centre for Environmental Life Sciences Engineering , Nanyang Technological University , Singapore 637551 , Singapore
| | - Per H Nielsen
- Singapore Centre for Environmental Life Sciences Engineering , Nanyang Technological University , Singapore 637551 , Singapore
- Centre for Microbial Communities, Department of Chemistry and Bioscience , Aalborg University , DK-9220 , Aalborg , Denmark
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering , National University of Singapore , Singapore 119077 , Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering , Nanyang Technological University , Singapore 637551 , Singapore
- Department of Civil and Environmental Engineering, One Shields Avenue , University of California , Davis , California 95616 , United States
- School of Civil and Environmental Engineering , Nanyang Technological University , Singapore 639798 , Singapore
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42
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Optimization of Wastewater Phosphorus Removal in Winter Temperatures Using an Anaerobic–Critical Aerobic Strategy in a Pilot-Scale Sequencing Batch Reactor. WATER 2019. [DOI: 10.3390/w12010110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Biological phosphorus removal using an anaerobic–aerobic sequencing batch reactor (SBR) in a low temperature can be difficult to remove, and aeration always accounts for nearly half of the total electricity costs at many wastewater treatment plants. In this study, a pilot-scale anaerobic–critical aerobic SBR (A–CA SBR) was developed for synthetic domestic wastewater. More importantly, the phase, whose concentration of diffused oxygen was controlled at 1.0–1.5 mg/L, was defined as a critical aerobic phase, which reduced expenses during the operation. To be specific, half of the ammonia was removed within 10 days and no NO3−–N was accumulated during the process. From the SEM and metagenome analysis, Rhodocyclus, Zooglea, Dechloromonas, and Simplicispira had the ability to remove phosphorus and NO3−–N simultaneously, which proved the existence of a potential double-layer sludge structure under an A–CA operational condition. All of the results disclose that the pilot-scale A–CA SBR is a reliable manipulation strategy for phosphorus removal under low temperatures, which can hopefully apply to practical wastewater remediation.
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Zhang L, Long B, Wu J, Cheng Y, Zhang B, Zeng Y, Huang S, Zeng M. Evolution of microbial community during dry storage and recovery of aerobic granular sludge. Heliyon 2019; 5:e03023. [PMID: 31890963 PMCID: PMC6926229 DOI: 10.1016/j.heliyon.2019.e03023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/18/2019] [Accepted: 12/06/2019] [Indexed: 12/15/2022] Open
Abstract
Aerobic granular sludge (AGS) was imbedded in agar and stored at 4 °C for 30 days, and then the stored granules were recovered in a sequencing batch reactor fed real wastewater within 11 days. Variations in microbial community compositions were investigated during dry storage and recovery of AGS, aiming to elucidate the mechanism of granular stability loss and recovery. The storage and recovery of AGS involved microbial community evolution. The dominant bacterial genera of the mature AGS were Zoogloea (relative abundance of 22.39%), Thauera (16.03%) and Clostridium_sensu_stricto (11.17%), and those of the stored granules were Acidovorax (26.79%), Macellibacteroides (12.83%) and Pseudoxanthomonas (5.69%), respectively. However, the dominant genera were Streptococcus (43.64%), Clostridium_sensu_stricto (12.3.6%) and Lactococcus (11.47%) in the recovered AGS. Methanogens were always the dominant archaeal species in mature AGS (93.01%), stored granules (99.99%) and the recovered AGS (94.84%). Facultative anaerobes and anaerobes proliferated and dominated in the stored granules, and their metabolic activities gradually led to granular structure destruction and property deterioration. However, the stored granules served as carriers for the microbes originated from the real septic tank wastewater during recovery. They proliferated rapidly and secreted a large number of extracellular polymeric substances which helped to recover the granular structure in 11 days.
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Affiliation(s)
- Linan Zhang
- School of Architectural and Surveying & Mapping Engineering, Jiangxi University of Science and Technology, Hongqi Ave. 86, Ganzhou, 341000, Jiangxi, China
| | - Bei Long
- School of Architectural and Surveying & Mapping Engineering, Jiangxi University of Science and Technology, Hongqi Ave. 86, Ganzhou, 341000, Jiangxi, China
| | - Junfeng Wu
- Henan Province Key Laboratory of Water Pollution Control and Rehabilitation Technology, Mingyue Road, Pingdingshan, 467036, Henan, China
| | - Yuanyuan Cheng
- School of Architectural and Surveying & Mapping Engineering, Jiangxi University of Science and Technology, Hongqi Ave. 86, Ganzhou, 341000, Jiangxi, China
| | - Binchao Zhang
- School of Architectural and Surveying & Mapping Engineering, Jiangxi University of Science and Technology, Hongqi Ave. 86, Ganzhou, 341000, Jiangxi, China
| | - Yu Zeng
- School of Architectural and Surveying & Mapping Engineering, Jiangxi University of Science and Technology, Hongqi Ave. 86, Ganzhou, 341000, Jiangxi, China
| | - Sinong Huang
- School of Architectural and Surveying & Mapping Engineering, Jiangxi University of Science and Technology, Hongqi Ave. 86, Ganzhou, 341000, Jiangxi, China
| | - Mingjing Zeng
- School of Architectural and Surveying & Mapping Engineering, Jiangxi University of Science and Technology, Hongqi Ave. 86, Ganzhou, 341000, Jiangxi, China
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Profiling population-level diversity and dynamics of Accumulibacter via high throughput sequencing of ppk1. Appl Microbiol Biotechnol 2019; 103:9711-9722. [DOI: 10.1007/s00253-019-10183-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 09/09/2019] [Accepted: 10/07/2019] [Indexed: 12/13/2022]
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Nguyen Quang M, Rogers T, Hofman J, Lanham AB. Global Sensitivity Analysis of Metabolic Models for Phosphorus Accumulating Organisms in Enhanced Biological Phosphorus Removal. Front Bioeng Biotechnol 2019; 7:234. [PMID: 31637235 PMCID: PMC6787149 DOI: 10.3389/fbioe.2019.00234] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 09/09/2019] [Indexed: 11/23/2022] Open
Abstract
The aim of this study was to identify, quantify and prioritize for the first time the sources of uncertainty in a mechanistic model describing the anaerobic-aerobic metabolism of phosphorus accumulating organisms (PAO) in enhanced biological phosphorus removal (EBPR) systems. These wastewater treatment systems play an important role in preventing eutrophication and metabolic models provide an advanced tool for improving their stability via system design, monitoring and prediction. To this end, a global sensitivity analysis was conducted using standard regression coefficients and Sobol sensitivity indices, taking into account the effect of 39 input parameters on 10 output variables. Input uncertainty was characterized with data in the literature and propagated to the output using the Monte Carlo method. The low degree of linearity between input parameters and model outputs showed that model simplification by linearization can be pursued only in very well defined circumstances. Differences between first and total-order sensitivity indices showed that variance in model predictions was due to interactions between combinations of inputs, as opposed to the direct effect of individual inputs. The major sources of uncertainty affecting the prediction of liquid phase concentrations, as well as intra-cellular glycogen and poly-phosphate was due to 64% of the input parameters. In contrast, the contribution to variance in intra-cellular PHA constituents was uniformly distributed among all inputs. In addition to the intra-cellular biomass constituents, notably PHB, PH2MV and glycogen, uncertainty with respect to input parameters directly related to anaerobic propionate uptake, aerobic poly-phosphate formation, glycogen formation and temperature contributed most to the variance of all model outputs. Based on the distribution of total-order sensitivities, characterization of the influent stream and intra-cellular fractions of PHA can be expected to significantly improve model reliability. The variance of EBPR metabolic model predictions was quantified. The means to account for this variance, with respect to each quantity of interest, given knowledge of the corresponding input uncertainties, was prescribed. On this basis, possible avenues and pre-requisite requirements to simplify EBPR metabolic models for PAO, both structurally via linearization, as well as by reduction of the number of non-influential variables were outlined.
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Affiliation(s)
- Minh Nguyen Quang
- Department of Chemical Engineering, Water Innovation and Research Centre, University of Bath, Bath, United Kingdom
| | - Tim Rogers
- Department of Mathematical Sciences, Centre for Networks and Collective Behaviour, University of Bath, Bath, United Kingdom
| | - Jan Hofman
- Department of Chemical Engineering, Water Innovation and Research Centre, University of Bath, Bath, United Kingdom
| | - Ana B Lanham
- Department of Chemical Engineering, Water Innovation and Research Centre, University of Bath, Bath, United Kingdom
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Dorofeev AG, Nikolaev YA, Mardanov AV, Pimenov NV. Cyclic Metabolism as a Mode of Microbial Existence. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719040052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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47
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Li C, Liu S, Ma T, Zheng M, Ni J. Simultaneous nitrification, denitrification and phosphorus removal in a sequencing batch reactor (SBR) under low temperature. CHEMOSPHERE 2019; 229:132-141. [PMID: 31078028 DOI: 10.1016/j.chemosphere.2019.04.185] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 04/23/2019] [Accepted: 04/24/2019] [Indexed: 05/14/2023]
Abstract
Simultaneous nitrogen and phosphorus removal in winter is one of the great challenges in wastewater treatment processes due to the poor bioactivity of microbial communities. In this study, excellent performance of simultaneous nitrification, denitrification and phosphorus removal (SNDPR) was achieved at low temperature of 10 °C and COD/N ratio of 6 in a lab-scale sequencing batch reactor. Total nitrogen (TN) and phosphorus (TP) removal efficiency reached 89.6% and 97.5%, respectively, accompanied with N2O emission of 7.46% TN due to the primary contribution (70%) of nitrifier denitrification. It was further confirmed that polyphosphate accumulating organisms (PAOs) were dominant in microbial communities revealed by fluorescence in situ hybridization and 16S rRNA amplicon sequencing. Moreover, denitrifying phosphorus removal by PAOs through nitrite pathway was found to be the main reason for the high efficiency of this SNDPR process. Denitrifying PAOs, especially the subgroup PAOII capable of utilizing nitrite to take up phosphorus, played a significant role in highly efficient TN and TP removal at low temperature. Furthermore, genus Propionivibrio was enriched (48.9%) in the bacterial community based on the 16S rRNA analysis, which was proposed to be a crucial member involved in the nitrogen and phosphorus removal simultaneously at low temperature in this system.
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Affiliation(s)
- Can Li
- Department of Environmental Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, China
| | - Shufeng Liu
- Department of Environmental Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, China
| | - Tao Ma
- Department of Environmental Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, China
| | - Maosheng Zheng
- Key Laboratory of Regional Energy Systems Optimization, North China Electric Power University, Beijing, 102206, China.
| | - Jinren Ni
- Department of Environmental Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, China.
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48
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Zhang AN, Mao Y, Wang Y, Zhang T. Mining traits for the enrichment and isolation of not-yet-cultured populations. MICROBIOME 2019; 7:96. [PMID: 31238973 PMCID: PMC6593511 DOI: 10.1186/s40168-019-0708-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 06/05/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND The lack of pure cultures limits our understanding into 99% of bacteria. Proper interpretation of the genetic and the transcriptional datasets can reveal clues for the enrichment and even isolation of the not-yet-cultured populations. Unraveling such information requires a proper mining method. RESULTS Here, we present a method to infer the hidden traits for the enrichment of not-yet-cultured populations. We demonstrate this method using Candidatus Accumulibacter. Our method constructs a whole picture of the carbon, electron, and energy flows in the not-yet-cultured populations from the genomic datasets. Then, it decodes the coordination across three flows from the transcriptional datasets. Based on it, our method diagnoses the status of the not-yet-cultured populations and provides strategy to optimize the enrichment systems. CONCLUSION Our method could shed light to the exploration into the bacterial dark matter in the environments.
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Affiliation(s)
- An-Ni Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Hong Kong, China
| | - Yanping Mao
- Environmental Biotechnology Laboratory, The University of Hong Kong, Hong Kong, China
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, China
| | - Yubo Wang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Hong Kong, China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Hong Kong, China.
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Re-evaluating the microbiology of the enhanced biological phosphorus removal process. Curr Opin Biotechnol 2019; 57:111-118. [PMID: 30959426 DOI: 10.1016/j.copbio.2019.03.008] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 02/01/2019] [Accepted: 03/03/2019] [Indexed: 10/27/2022]
Abstract
We have critically assessed some of the dogmas in the microbiology of enhanced biological phosphorus removal (EBPR) and argue that the genus Tetrasphaera can be as important as Ca. Accumulibacter for phosphorus removal; and that proliferation of their competitors, the glycogen accumulating organisms, does not appear to be a practical problem for EBPR efficiency even under tropical conditions. An increasing number of EBPR-related genomes are changing our understanding of their physiology, for example, their potential to participate in denitrification. Rather than trying to identify organisms that adhere to strict phenotype metabolic models, we advocate for broader analyses of the whole microbial communities in EBPR plants by iterative studies with isolates, lab enrichments, and full-scale systems.
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50
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Resolving the individual contribution of key microbial populations to enhanced biological phosphorus removal with Raman-FISH. ISME JOURNAL 2019; 13:1933-1946. [PMID: 30894691 PMCID: PMC6776032 DOI: 10.1038/s41396-019-0399-7] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 02/02/2019] [Accepted: 02/28/2019] [Indexed: 02/05/2023]
Abstract
Enhanced biological phosphorus removal (EBPR) is a globally important biotechnological process and relies on the massive accumulation of phosphate within special microorganisms. Candidatus Accumulibacter conform to the classical physiology model for polyphosphate accumulating organisms and are widely believed to be the most important player for the process in full-scale EBPR systems. However, it was impossible till now to quantify the contribution of specific microbial clades to EBPR. In this study, we have developed a new tool to directly link the identity of microbial cells to the absolute quantification of intracellular poly-P and other polymers under in situ conditions, and applied it to eight full-scale EBPR plants. Besides Ca. Accumulibacter, members of the genus Tetrasphaera were found to be important microbes for P accumulation, and in six plants they were the most important. As these Tetrasphaera cells did not exhibit the classical phenotype of poly-P accumulating microbes, our entire understanding of the microbiology of the EBPR process has to be revised. Furthermore, our new single-cell approach can now also be applied to quantify storage polymer dynamics in individual populations in situ in other ecosystems and might become a valuable tool for many environmental microbiologists.
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