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Li S, Zhang L, Fang W, Shen Z. Variations in bacterial community succession and assembly mechanisms with mine age across various habitats in coal mining subsidence water areas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174822. [PMID: 39029748 DOI: 10.1016/j.scitotenv.2024.174822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 07/12/2024] [Accepted: 07/13/2024] [Indexed: 07/21/2024]
Abstract
Microorganisms play a pivotal role as catalysts in the biogeochemical cycles of aquatic ecosystems within coal mining subsidence areas. Despite their importance, the succession of microbial communities with increasing mine age, particularly across different habitats, and variations in phylogenetically-based community assembly mechanisms are not well understood. To address this knowledge gap, we collected 72 samples from lake sediments, water, and surrounding topsoil (0-20 cm) at various mining stages (early: 16 years, middle: 31 years, late: 40 years). We analyzed these samples using 16S rRNA gene sequencing and multivariate statistical methods to explore the dynamics and assembly mechanisms of bacterial communities. Our findings reveal that increases in phosphorus and organic matter in sediments, correlating with mining age, significantly enhance bacterial alpha diversity while reducing species richness (P < 0.001). Homogenizing selection (49.9 %) promotes species asynchrony-complementarity, augmenting the bacterial community's ability to metabolize sulfur, phosphorus, and organic matter, resulting in more complex-stable co-occurrence networks. In soil, elevated nitrogen and organic carbon levels markedly influence bacterial community composition (Adonis R2 = 0.761), yet do not significantly alter richness or diversity (P > 0.05). The lake's high connectivity with surrounding soil leads to substantial species drift and organic matter accumulation, thereby increasing bacterial richness in later stages (P < 0.05) and enhancing the ability to metabolize dissolved organic matter, including humic-like substances, fulvic acids, and protein-like materials. The assembly of soil bacterial communities is largely governed by stochastic processes (79.0 %) with species drift (35.8 %) significantly shaping these communities over a broad spatial scale, also affecting water bacterial communities. However, water bacterial community assembly is primarily driven by stochastic processes (51.2 %), with a substantial influence from habitat quality (47.6 %). This study offers comprehensive insights into the evolution of microbial community diversity within coal mining subsidence water areas, with significant implications for enhancing environmental management and protection strategies for these ecosystems.
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Affiliation(s)
- Shuo Li
- School of Earth and Environment, Anhui University of Science and Technology, Huainan, 232001, China
| | - Lei Zhang
- College of Civil and Architecture Engineering, Chuzhou University, Chuzhou, 239000, China.
| | - Wangkai Fang
- School of Earth and Environment, Anhui University of Science and Technology, Huainan, 232001, China
| | - Zhen Shen
- Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
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2
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Shaw DR, Terada A, Saikaly PE. Future directions in microbial nitrogen cycling in wastewater treatment. Curr Opin Biotechnol 2024; 88:103163. [PMID: 38897092 DOI: 10.1016/j.copbio.2024.103163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024]
Abstract
Discoveries in the past decade of novel reactions, processes, and micro-organisms have altered our understanding of microbial nitrogen cycling in wastewater treatment systems. These advancements pave the way for a transition toward more sustainable and energy-efficient wastewater treatment systems that also minimize greenhouse gas emissions. This review highlights these innovative directions in microbial nitrogen cycling within the context of wastewater treatment. Processes such as comammox, Feammox, electro-anammox, and nitrous oxide mitigation offer innovative approaches for sustainable, energy-efficient nitrogen removal. However, while these emerging processes show promise, advancing from laboratory research to practical applications, particularly in decentralized systems, remains a critical next step toward a sustainable and efficient wastewater management.
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Affiliation(s)
- Dario R Shaw
- Water Desalination and Reuse Center (WDRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Akihiko Terada
- Department of Applied Physics and Chemical Engineering, Department of Industrial Technology and Innovation, Tokyo University of Agriculture and Technology, 2-24-16 Building 4-320 Naka, Koganei, Tokyo 184-8588, Japan.
| | - Pascal E Saikaly
- Water Desalination and Reuse Center (WDRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia; Environmental Science & Engineering Program, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia.
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3
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Ekholm J, Persson F, de Blois M, Modin O, Gustavsson DJI, Pronk M, van Loosdrecht MCM, Wilén BM. Microbiome structure and function in parallel full-scale aerobic granular sludge and activated sludge processes. Appl Microbiol Biotechnol 2024; 108:334. [PMID: 38739161 DOI: 10.1007/s00253-024-13165-8] [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: 02/19/2024] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 05/14/2024]
Abstract
Aerobic granular sludge (AGS) and conventional activated sludge (CAS) are two different biological wastewater treatment processes. AGS consists of self-immobilised microorganisms that are transformed into spherical biofilms, whereas CAS has floccular sludge of lower density. In this study, we investigated the treatment performance and microbiome dynamics of two full-scale AGS reactors and a parallel CAS system at a municipal WWTP in Sweden. Both systems produced low effluent concentrations, with some fluctuations in phosphate and nitrate mainly due to variations in organic substrate availability. The microbial diversity was slightly higher in the AGS, with different dynamics in the microbiome over time. Seasonal periodicity was observed in both sludge types, with a larger shift in the CAS microbiome compared to the AGS. Groups important for reactor function, such as ammonia-oxidising bacteria (AOB), nitrite-oxidising bacteria (NOB), polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs), followed similar trends in both systems, with higher relative abundances of PAOs and GAOs in the AGS. However, microbial composition and dynamics differed between the two systems at the genus level. For instance, among PAOs, Tetrasphaera was more prevalent in the AGS, while Dechloromonas was more common in the CAS. Among NOB, Ca. Nitrotoga had a higher relative abundance in the AGS, while Nitrospira was the main nitrifier in the CAS. Furthermore, network analysis revealed the clustering of the various genera within the guilds to modules with different temporal patterns, suggesting functional redundancy in both AGS and CAS. KEY POINTS: • Microbial community succession in parallel full-scale aerobic granular sludge (AGS) and conventional activated sludge (CAS) processes. • Higher periodicity in microbial community structure in CAS compared to in AGS. • Similar functional groups between AGS and CAS but different composition and dynamics at genus level.
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Affiliation(s)
- Jennifer Ekholm
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Sven Hultins Gata 6, 41296, Gothenburg, Sweden
| | - Frank Persson
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Sven Hultins Gata 6, 41296, Gothenburg, Sweden
| | | | - Oskar Modin
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Sven Hultins Gata 6, 41296, Gothenburg, Sweden
| | - David J I Gustavsson
- Sweden Water Research AB, Ideon Science Park, Scheelevägen 15, 22370, Lund, Sweden
- VA SYD, P.O. Box 191, 20121, Malmö, Sweden
| | - Mario Pronk
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Britt-Marie Wilén
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Sven Hultins Gata 6, 41296, Gothenburg, Sweden.
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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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Farmer M, Rajasabhai R, Tarpeh W, Tyo K, Wells G. Meta-omic profiling reveals ubiquity of genes encoding for the nitrogen-rich biopolymer cyanophycin in activated sludge microbiomes. Front Microbiol 2023; 14:1287491. [PMID: 38033562 PMCID: PMC10687191 DOI: 10.3389/fmicb.2023.1287491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/01/2023] [Indexed: 12/02/2023] Open
Abstract
Recovering nitrogen (N) from municipal wastewater is a promising approach to prevent nutrient pollution, reduce energy use, and transition toward a circular N bioeconomy, but remains a technologically challenging endeavor. Existing N recovery techniques are optimized for high-strength, low-volume wastewater. Therefore, developing methods to concentrate dilute N from mainstream wastewater will bridge the gap between existing technologies and practical implementation. The N-rich biopolymer cyanophycin is a promising candidate for N bioconcentration due to its pH-tunable solubility characteristics and potential for high levels of accumulation. However, the cyanophycin synthesis pathway is poorly explored in engineered microbiomes. In this study, we analyzed over 3,700 publicly available metagenome assembled genomes (MAGs) and found that the cyanophycin synthesis gene cphA was ubiquitous across common activated sludge bacteria. We found that cphA was present in common phosphorus accumulating organisms (PAO) Ca. 'Accumulibacter' and Tetrasphaera, suggesting potential for simultaneous N and P bioconcentration in the same organisms. Using metatranscriptomic data, we confirmed the expression of cphA in lab-scale bioreactors enriched with PAO. Our findings suggest that cyanophycin synthesis is a ubiquitous metabolic activity in activated sludge microbiomes. The possibility of combined N and P bioconcentration could lower barriers to entry for N recovery, since P concentration by PAO is already a widespread biotechnology in municipal wastewater treatment. We anticipate this work to be a starting point for future evaluations of combined N and P bioaccumulation, with the ultimate goal of advancing widespread adoption of N recovery from municipal wastewater.
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Affiliation(s)
- McKenna Farmer
- Civil and Environmental Engineering, Northwestern University, Evanston, IL, United States
| | - Rashmi Rajasabhai
- Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States
| | - William Tarpeh
- Chemical Engineering, Stanford University, Stanford, CA, United States
| | - Keith Tyo
- Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States
| | - George Wells
- Civil and Environmental Engineering, Northwestern University, Evanston, IL, United States
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Wang Z, Song W, Zhang X, Zheng M, Li H, Yu K, Guo F. Expanding the Diversity of Accumulibacter with a Novel Type and Deciphering the Transcriptional and Morphological Features among Co-Occurring Strains. Appl Environ Microbiol 2023; 89:e0077123. [PMID: 37466435 PMCID: PMC10467341 DOI: 10.1128/aem.00771-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/25/2023] [Indexed: 07/20/2023] Open
Abstract
"Candidatus Accumulibacter" is the major polyphosphate-accumulating organism (PAO) in global wastewater treatment systems, and its phylogenetic and functional diversity have expanded in recent years. In addition to the widely recognized type I and II sublineages, we discovered a novel type enriched in laboratory bioreactors. Core gene and machine learning-based gene feature profiling supported the assertion that type III "Ca. Accumulibacter" is a potential PAO with the unique function of using dimethyl sulfoxide as an electron acceptor. Based on the correlation between ppk1 and genome similarity, the species-level richness of Accumulibacter was estimated to be over 100, suggesting that the currently recognized species are only the tip of the iceberg. Meanwhile, the interstrain transcriptional and morphological features of multiple "Ca. Accumulibacter" strains co-occurring in a bioreactor were investigated. Metatranscriptomics of seven co-occurring strains indicated that the expression level and interphasic dynamics of PAO phenotype-related genes had minimal correlation with their phylogeny. In particular, the expression of denitrifying and polyphosphate (poly-P) metabolism genes exhibited higher interstrain and interphasic divergence than expression of glycogen and polyhydroxyalkanoate metabolic genes. A strategy of cloning rRNA genes from different strains based on similar genomic synteny was successfully applied to differentiate their morphology via fluorescence in situ hybridization. Our study further expands the phylogenetic and functional diversity of "Ca. Accumulibacter" and proposes that deciphering the function and capability of certain "Ca. Accumulibacter" should be tailored to the environment and population in question. IMPORTANCE In the last 2 decades, "Ca. Accumulibacter" has garnered significant attention as the core functional but uncultured taxon for enhanced biological phosphorus removal due to its phylogenetic and functional diversity and intragenus niche differentiation. Since 2002, it has been widely known that this genus has two sublineages (type I and II). However, in this study, a metagenomic approach led to the discovery of a novel type (type III) with proposed novel functional features. By comparing the average nucleotide identity of "Ca. Accumulibacter" genomes and the similarity of ppk1, a phylogenetic biomarker largely deposited in databases, the global species-level richness of "Ca. Accumulibacter" was estimated for the first time to be over 100. Furthermore, we observed the co-occurrence of multiple "Ca. Accumulibacter" strains in a single bioreactor and found the simultaneous transcriptional divergence of these strains intriguing with regard to their niche differentiation within a single community. Our results indicated a decoupling feature between transcriptional pattern and phylogeny for co-occurring strains.
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Affiliation(s)
- Zhongjie Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Wei Song
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Xue Zhang
- School of Environment and Energy, Peking University Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Minjia Zheng
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Hao Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Ke Yu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Feng Guo
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
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7
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Wang H, Zhang L, Dan Q, Zhang Y, Wang S, Zhang Q, Li X, Wang C, Peng Y. Ultra-high nitrogen removal from real municipal wastewater using selective enhancement of glycogen accumulating organisms (GAOs) in a partial nitrification-anammox (PNA) system. WATER RESEARCH 2023; 230:119594. [PMID: 36638736 DOI: 10.1016/j.watres.2023.119594] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/22/2022] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
Integrating endogenous denitrification (ED) into partial nitrification-anammox (PNA) systems by adequately utilizing organics in municipal wastewater is a promising approach to improve nitrogen removal efficiency (NRE). In this study, a novel strategy to inhibit phosphorus-accumulating organisms (PAOs) by inducing phosphorus release and exclusion was adopted intermittently, optimizing organics allocation between PAOs and glycogen-accumulating organisms (GAOs). Enhanced ED-synergized anammox was established to treat real municipal wastewater, achieving an NRE of 97.5±2.2% and effluent total inorganic nitrogen (TIN) of less than 2.0 mg/L. With low poly-phosphorus (poly-P) levels (poly-P/VSS below 0.01 (w/w)), glycogen accumulating metabolism (GAM) acquired organics exceeded that of phosphorus accumulating metabolism (PAM) and dominated endogenous metabolism. Ca. Competibacter (GAO) dominated the community following phosphorus-rich supernatant exclusion, with abundance increasing from 3.4% to 5.7%, accompanied by enhanced ED capacity (0.2 to 1.4 mg N/g VSS /h). The enriched subgroups (GB4, GB5) of Ca. Competibcater established a consistent nitrate cycle with anammox bacteria (AnAOB) through endogenous partial denitrification (EPD) at a ∆NO2--N/∆NH4+-N of 0.91±0.11, guaranteeing the maintenance of AnAOB abundance and performance. These results provide new insights into the flexibility of PNA for the energy-efficient treatment of low-strength ammonium wastewater.
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Affiliation(s)
- Hanbin Wang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
| | - Liang Zhang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
| | - Qiongpeng Dan
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
| | - Yingxin Zhang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
| | - Shuying Wang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
| | - Qiong Zhang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
| | - Xiyao Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
| | - Chuanxin Wang
- Guangdong Shouhui Lantian Engineering and Technology Co. Ltd, Guangdong 510075, PR China
| | - Yongzhen Peng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China.
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8
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McDaniel EA, van Steenbrugge JJM, Noguera DR, McMahon KD, Raaijmakers JM, Medema MH, Oyserman BO. TbasCO: trait-based comparative 'omics identifies ecosystem-level and niche-differentiating adaptations of an engineered microbiome. ISME COMMUNICATIONS 2022; 2:111. [PMID: 37938301 PMCID: PMC9723799 DOI: 10.1038/s43705-022-00189-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 09/29/2022] [Accepted: 10/10/2022] [Indexed: 11/09/2023]
Abstract
A grand challenge in microbial ecology is disentangling the traits of individual populations within complex communities. Various cultivation-independent approaches have been used to infer traits based on the presence of marker genes. However, marker genes are not linked to traits with complete fidelity, nor do they capture important attributes, such as the timing of gene expression or coordination among traits. To address this, we present an approach for assessing the trait landscape of microbial communities by statistically defining a trait attribute as a shared transcriptional pattern across multiple organisms. Leveraging the KEGG pathway database as a trait library and the Enhanced Biological Phosphorus Removal (EBPR) model microbial ecosystem, we demonstrate that a majority (65%) of traits present in 10 or more genomes have niche-differentiating expression attributes. For example, while many genomes containing high-affinity phosphorus transporter pstABCS display a canonical attribute (e.g. up-regulation under phosphorus starvation), we identified another attribute shared by many genomes where transcription was highest under high phosphorus conditions. Taken together, we provide a novel framework for unravelling the functional dynamics of uncultivated microorganisms by assigning trait-attributes through genome-resolved time-series metatranscriptomics.
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Affiliation(s)
- E A McDaniel
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA.
| | - J J M van Steenbrugge
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands.
- Microbial Ecology, Netherlands Institute of Ecological Research, Wageningen, The Netherlands.
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands.
| | - D R Noguera
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - K 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
| | - J M Raaijmakers
- Microbial Ecology, Netherlands Institute of Ecological Research, Wageningen, The Netherlands
- Institute of Biology, Leiden University, Leiden, Netherlands
| | - M H Medema
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
- Institute of Biology, Leiden University, Leiden, Netherlands
| | - B O Oyserman
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands.
- Microbial Ecology, Netherlands Institute of Ecological Research, Wageningen, The Netherlands.
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9
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Valk LC, Peces M, Singleton CM, Laursen MD, Andersen MH, Mielczarek AT, Nielsen PH. Exploring the microbial influence on seasonal nitrous oxide concentration in a full-scale wastewater treatment plant using metagenome assembled genomes. WATER RESEARCH 2022; 219:118563. [PMID: 35594748 DOI: 10.1016/j.watres.2022.118563] [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: 02/11/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
Nitrous oxide is a highly potent greenhouse gas and one of the main contributors to the greenhouse gas footprint of wastewater treatment plants (WWTP). Although nitrous oxide can be produced by abiotic reactions in these systems, biological N2O production resulting from the imbalance of nitrous oxide production and reduction by microbial populations is the dominant cause. The microbial populations responsible for the imbalance have not been clearly identified, yet they are likely responsible for strong seasonal nitrous oxide patterns. Here, we examined the seasonal nitrous oxide concentration pattern in Avedøre WWTP alongside abiotic parameters, the microbial community composition based on 16S rRNA gene sequencing and already available metagenome-assembled genomes (MAGs). We found that the WWTP parameters could not explain the observed pattern. While no distinct community changes between periods of high and low dissolved nitrous oxide concentrations were determined, we found 26 and 28 species with positive and negative correlations to the seasonal N2O concentrations, respectively. MAGs were identified for 124 species (approximately 31% mean relative abundance of the community), and analysis of their genomic nitrogen transformation potential could explain this correlation for four of the negatively correlated species. Other abundant species were also analysed for their nitrogen transformation potential. Interestingly, only one full-denitrifier (Candidatus Dechloromonas phosphorivorans) was identified. 59 species had a nosZ gene predicted, with the majority identified as a clade II nosZ gene, mainly from the phylum Bacteroidota. A correlation of MAG-derived functional guilds with the N2O concentration pattern showed that there was a small but significant negative correlation with nitrite oxidizing bacteria and species with a nosZ gene (N2O reducers (DEN)). More research is required, specifically long-term activity measurements in relation to the N2O concentration to increase the resolution of these findings.
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Affiliation(s)
- Laura Christina Valk
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Miriam Peces
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Caitlin Margaret Singleton
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Mads Dyring Laursen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | | | | | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark.
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10
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Li Y, Zhao J, Li Y, Jin B, Wang L, Li Y. Effects of combined 4-chlorophenol and Cu 2+ on functional genes for nitrogen and phosphorus removal and heavy metal resistance genes in sequencing batch bioreactors. BIORESOURCE TECHNOLOGY 2022; 346:126666. [PMID: 34990861 DOI: 10.1016/j.biortech.2021.126666] [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: 11/22/2021] [Revised: 12/25/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
The effects of combined 4-chlorophenol (4-CP) and Cu2+ on microbial community structures, functional genes for nitrogen and phosphorus removal, and heavy metal resistance genes (HMRGs) were explored in wastewater treatment using sequencing batch bioreactors (SBRs). Compared to influent 4-CP (2.3-4.5 mg/L), the removal of pollutants including chemical oxygen demands (COD), NH4+-N, PO43--P, and 4-CP was inhibited under Cu2+ stress (5 mg/L). The effects of Cu2+ on microbial community structures were more significant than those of 4-CP with respect to operational time, while the dominant function from gene information was not affected with or without influent 4-CP and Cu2+ via sequencing analysis. The influent 4-CP and Cu2+ largely influenced the dynamic changes of functional genes and HMRGs, and the abundance of partial HMRGs was correlated to the functional genes and dominant genera. This study provides insights into the treatment of combined chlorophenols and Cu2+ in wastewater.
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Affiliation(s)
- Yahe Li
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Jianguo Zhao
- Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, School of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou 450001, China
| | - Yu Li
- Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, School of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou 450001, China
| | - Baodan Jin
- Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, School of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou 450001, China
| | - Lan Wang
- Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, School of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou 450001, China
| | - Yanfei Li
- Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201318, China.
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Dockx L, Caluwé M, Dobbeleers T, Dries J. Nitrous oxide formation during simultaneous phosphorus and nitrogen removal in aerobic granular sludge treating different carbon substrates. BIORESOURCE TECHNOLOGY 2022; 345:126542. [PMID: 34906707 DOI: 10.1016/j.biortech.2021.126542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/05/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
The impact of different substrates on N2O dynamics and gene expression of marker enzymes (nirS, nirK and nosZ) involved in denitrifying enhanced biological phosphorus removal (d-EBPR) was investigated. Aerobic granular sludge fed with VFAs led to an anoxic P-uptake (27.7 ± 1.2 mg PO43--P.gVSS-1) and N2O emissions up to 80.7 ± 3.4% N2O-N. A decisive role of Accumulibacter in N2O formation was observed. Dosage of amino acids (12.0 ± 1.2 mg PO43--P.gVSS-1) and glucose (1.5 ± 0.9 mg PO43--P.gVSS-1) as sole substrate did not support d-EBPR activity. Presence of NO2- resulted in higher N2O formation in comparison to nitrate and a nosZ/(nirS + nirK) ratio lower than 0.3. A linear correlation (R2 > 0.95) between the nosZ/(nirS + nirK) ratio and the N2O reductase rate was found only when dosing the same type of substrate. This suggests an interplay between the microbial community composition and different polyhydroxyalkanoates derivatives, when dosing different substrates.
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Affiliation(s)
- Lennert Dockx
- BioWAVE, Biochemical Wastewater Valorization and Engineering, Faculty of Applied Engineering, University of Antwerp, Groenenborgerlaan 171, Antwerp 2020, Belgium
| | - Michel Caluwé
- BioWAVE, Biochemical Wastewater Valorization and Engineering, Faculty of Applied Engineering, University of Antwerp, Groenenborgerlaan 171, Antwerp 2020, Belgium
| | - Thomas Dobbeleers
- BioWAVE, Biochemical Wastewater Valorization and Engineering, Faculty of Applied Engineering, University of Antwerp, Groenenborgerlaan 171, Antwerp 2020, Belgium
| | - Jan Dries
- BioWAVE, Biochemical Wastewater Valorization and Engineering, Faculty of Applied Engineering, University of Antwerp, Groenenborgerlaan 171, Antwerp 2020, Belgium.
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Exploring the Meta-regulon of the CRP/FNR Family of Global Transcriptional Regulators in a Partial-Nitritation Anammox Microbiome. mSystems 2021; 6:e0090621. [PMID: 34636676 PMCID: PMC8510549 DOI: 10.1128/msystems.00906-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microorganisms must respond to environmental changes to survive, often by controlling transcription initiation. Intermittent aeration during wastewater treatment presents a cyclically changing environment to which microorganisms must react. We used an intermittently aerated bioreactor performing partial nitritation and anammox (PNA) to investigate how the microbiome responds to recurring change. Meta-transcriptomic analysis revealed a dramatic disconnect between the relative DNA abundance and gene expression within the metagenome-assembled genomes (MAGs) of community members, suggesting the importance of transcriptional regulation in this microbiome. To explore how community members responded to cyclic aeration via transcriptional regulation, we searched for homologs of the catabolite repressor protein/fumarate and nitrate reductase regulatory protein (CRP/FNR) family of transcription factors (TFs) within the MAGs. Using phylogenetic analyses, evaluation of sequence conservation in important amino acid residues, and prediction of genes regulated by TFs in the MAGs, we identified homologs of the oxygen-sensing FNR in Nitrosomonas and Rhodocyclaceae, nitrogen-sensing dissimilative nitrate respiration regulator that responds to nitrogen species (DNR) in Rhodocyclaceae, and nitrogen-sensing nitrite and nitric oxide reductase regulator that responds to nitrogen species (NnrR) in Nitrospira MAGs. Our data also predict that CRP/FNR homologs in Ignavibacteria, Flavobacteriales, and Saprospiraceae MAGs sense carbon availability. In addition, a CRP/FNR homolog in a Brocadia MAG was most closely related to CRP TFs known to sense carbon sources in well-studied organisms. However, we predict that in autotrophic Brocadia, this TF most likely regulates a diverse set of functions, including a response to stress during the cyclic aerobic/anoxic conditions. Overall, this analysis allowed us to define a meta-regulon of the PNA microbiome that explains functions and interactions of the most active community members. IMPORTANCE Microbiomes are important contributors to many ecosystems, including ones where nutrient cycling is stimulated by aeration control. Optimizing cyclic aeration helps reduce energy needs and maximize microbiome performance during wastewater treatment; however, little is known about how most microbial community members respond to these alternating conditions. We defined the meta-regulon of a PNA microbiome by combining existing knowledge of how the CRP/FNR family of bacterial TFs respond to stimuli, with metatranscriptomic analyses to characterize gene expression changes during aeration cycles. Our results indicated that, for some members of the community, prior knowledge is sufficient for high-confidence assignments of TF function, whereas other community members have CRP/FNR TFs for which inferences of function are limited by lack of prior knowledge. This study provides a framework to begin elucidating meta-regulons in microbiomes, where pure cultures are not available for traditional transcriptional regulation studies. Defining the meta-regulon can help in optimizing microbiome performance.
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