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Yang K, Liu W, Lin HM, Chen T, Yang T, Zhang B, Wen X. Ecological and functional differences of abundant and rare sub-communities in wastewater treatment plants across China. ENVIRONMENTAL RESEARCH 2024; 243:117749. [PMID: 38061589 DOI: 10.1016/j.envres.2023.117749] [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: 09/09/2023] [Revised: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 12/17/2023]
Abstract
The microbial community in activated sludge is composed of a small number of abundant sub-community with high abundance and a large number of rare sub-community with limited abundance. Our knowledge regarding the ecological properties of both abundant and rare sub-communities in activated sludge is limited. This article presented an analysis of functional prediction, assembly mechanisms, and biogeographic distribution characteristics of abundant and rare sub-communities in 211 activated sludge samples from 60 wastewater treatment plants across China. Moreover, this study investigated the dominant factors influencing the community structure of these two microbial groups. The results showed that the functions associated with carbon and nitrogen cycling were primarily detected in abundant sub-community, while rare sub-community were primarily involved in sulfur cycling. Both microbial groups were mainly influenced by dispersal limitation, which, to some extent, resulted in a distance-decay relationship in their biogeographic distribution. Moreover, a higher spatial turnover rate of rare sub-communities (0.0887) suggested that spatial differences in microbial community structure among different WWTPs may mainly result from rare sub-community. Moreover, SEM showed that geographic locations affected rare sub-communities greatly, which agreed with their higher dispersal limitation and turnover rate. In contrast, influent characteristics showed stronger correlations with abundant sub-communities, suggesting that abundant sub-community may contribute more to the removal of pollutants. This study enhanced our understanding of abundant and rare microorganisms in activated sludge especially the role of rare species and provided scientific evidence for precise regulation and control of wastewater treatment plants.
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Affiliation(s)
- Kuo Yang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Wei Liu
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China
| | - Hui-Min Lin
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Tan Chen
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; Research Center of Food Environment and Public Health Engineering, Minzu University of China, Beijing 100081, China
| | - Ting Yang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; Research Center of Food Environment and Public Health Engineering, Minzu University of China, Beijing 100081, China
| | - Bing Zhang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; Research Center of Food Environment and Public Health Engineering, Minzu University of China, Beijing 100081, China.
| | - Xianghua Wen
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China.
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2
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Zhang Y, Wu H, Xu R, Wang Y, Chen L, Wei C. Machine learning modeling for the prediction of phosphorus and nitrogen removal efficiency and screening of crucial microorganisms in wastewater treatment plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167730. [PMID: 37852495 DOI: 10.1016/j.scitotenv.2023.167730] [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: 06/12/2023] [Revised: 10/08/2023] [Accepted: 10/08/2023] [Indexed: 10/20/2023]
Abstract
The effectiveness of wastewater treatment plants (WWTPs) is largely determined by the microbial community structure in their activated sludge (AS). Interactions among microbial communities in AS systems and their indirect effects on water quality changes are crucial for WWTP performance. However, there is currently no quantitative method to evaluate the contribution of microorganisms to the operating efficiency of WWTPs. Traditional assessments of WWTP performance are limited by experimental conditions, methods, and other factors, resulting in increased costs and experimental pollutants. Therefore, an effective method is needed to predict WWTP efficiency based on AS community structure and quantitatively evaluate the contribution of microorganisms in the AS system. This study evaluated and compared microbial communities and water quality changes from WWTPs worldwide by meta-analysis of published high-throughput sequencing data. Six machine learning (ML) models were utilized to predict the efficiency of phosphorus and nitrogen removal in WWTPs; among them, XGBoost showed the highest prediction accuracy. Cross-entropy was used to screen the crucial microorganisms related to phosphorus and nitrogen removal efficiency, and the modeling confirmed the reasonableness of the results. Thirteen genera with nitrogen and phosphorus cycling pathways obtained from the screening were considered highly appropriate for the simultaneous removal of phosphorus and nitrogen. The results showed that the microbes Haliangium, Vicinamibacteraceae, Tolumonas, and SWB02 are potentially crucial for phosphorus and nitrogen removal, as they may be involved in the process of phosphorus and nitrogen removal in sewage treatment plants. Overall, these findings have deepened our understanding of the relationship between microbial community structure and performance of WWTPs, indicating that microbial data should play a critical role in the future design of sewage treatment plants. The ML model of this study can efficiently screen crucial microbes associated with WWTP system performance, and it is promising for the discovery of potential microbial metabolic pathways.
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Affiliation(s)
- Yinan Zhang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Haizhen Wu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China.
| | - Rui Xu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Ying Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Liping Chen
- School of Environment and Energy, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou 510006, PR China
| | - Chaohai Wei
- School of Environment and Energy, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou 510006, PR China
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3
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Lin H, Zheng Y, Yang Y, Liu F, Yang K, Zhang B, Wen X. The role of the core microorganisms in the microbial interactions in activated sludge. ENVIRONMENTAL RESEARCH 2023; 235:116660. [PMID: 37451573 DOI: 10.1016/j.envres.2023.116660] [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: 05/08/2023] [Revised: 07/08/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
In order to gain a deeper understanding of the microbial interactions in wastewater treatment plants (WWTPs) in China and clarify the role of the core community in the microbial interactions in activated sludge (AS), this study used a molecular ecological network approach based on random matrix theory to construct co-occurrence networks of the core microorganisms (CoreN), the whole AS community (WholeN) and the microbial communities without the core microorganisms (OtherN), respectively. It was shown that the WholeN had more complex and tighter connections compared with the OtherN, because of its higher total number of nodes, higher average clustering coefficient, and shorter average geodesic distance. The proportions of positive links in the CoreN, WholeN and OtherN were gradually decreased, indicating that the core microorganisms promoted cooperation between AS microorganisms. Moreover, higher robustness after random removal of 50% of the nodes of the WholeN (0.2836 ± 0.0311) was observed than the robustness of the OtherN (0.1152 ± 0.0263). In addition, the vulnerability of OtherN (0.0514) is significantly higher than WholeN (0.0225). Meanwhile, the average ratio of negative/positive cohesion, was significantly decreased when the core microorganisms were removed. These results demonstrated that core community could strengthen the stability of the ecological network in AS. By discerning the key factors affecting ecological network, AS temperature was observed to have a strong correlation with all three networks. Moreover, pollutants in wastewater shown stronger correlations with the CoreN and WholeN, supporting the point that core community play a critical role in pollutant removal in WWTPs to a certain extent.
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Affiliation(s)
- Huimin Lin
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China
| | - Yichen Zheng
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China
| | - Yuankai Yang
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China
| | - Fengyi Liu
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China
| | - Kuo Yang
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China
| | - Bing Zhang
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China; Research Center of Food Environment and Public Health Engineering, Minzu University of China, Beijing, 100081, China.
| | - Xianghua Wen
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing, 100084, China.
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4
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Domańska M, Kuśnierz M, Mackiewicz K. Seasonal prevalence of bacteria in the outflow of two full-scale municipal wastewater treatment plants. Sci Rep 2023; 13:10608. [PMID: 37391517 PMCID: PMC10313732 DOI: 10.1038/s41598-023-37744-3] [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: 04/04/2023] [Accepted: 06/27/2023] [Indexed: 07/02/2023] Open
Abstract
Despite many modern wastewater treatment solutions, the most common is still the use of activated sludge (AS). Studies indicate that the microbial composition of AS is most often influenced by the raw sewage composition (especially influent ammonia), biological oxygen demand, the level of dissolved oxygen, technological solutions, as well as the temperature of wastewater related to seasonality. The available literature mainly refers to the relationship between AS parameters or the technology used and the composition of microorganisms in AS. However, there is a lack of data on the groups of microorganisms leaching into water bodies whose presence is a signal for possible changes in treatment technology. Moreover, sludge flocs in the outflow contain less extracellular substance (EPS) which interferes microbial identification. The novelty of this article concerns the identification and quantification of microorganisms in the AS and in the outflow by fluorescence in situ hybridization (FISH) method from two full-scale wastewater treatment plants (WWTPs) in terms of 4 key groups of microorganisms involved in the wastewater treatment process in the context of their potential technological usefulness. The results of the study showed that Nitrospirae, Chloroflexi and Ca. Accumulibacter phosphatis in treated wastewater reflect the trend in abundance of these bacteria in activated sludge. Increased abundance of betaproteobacterial ammonia-oxidizing bacteria and Nitrospirae in the outflow were observed in winter. Principal component analysis (PCA) showed that loadings obtained from abundance of bacteria in the outflow made larger contributions to the variance in the PC1 factorial axis, than loadings obtained from abundance of bacteria from activated sludge. PCA confirmed the reasonableness of conducting studies not only in the activated sludge, but also in the outflow to find correlations between technological problems and qualitative and quantitative changes in the outflow microorganisms.
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Affiliation(s)
- Magdalena Domańska
- Institute of Environmental Engineering, Wroclaw University of Environmental and Life Sciences, pl. Grunwaldzki 24, 50-363, Wrocław, Poland.
| | - Magdalena Kuśnierz
- Institute of Environmental Engineering, Wroclaw University of Environmental and Life Sciences, pl. Grunwaldzki 24, 50-363, Wrocław, Poland
| | - Katarzyna Mackiewicz
- Institute of Environmental Engineering, Wroclaw University of Environmental and Life Sciences, pl. Grunwaldzki 24, 50-363, Wrocław, Poland
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5
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Veloso S, Amouroux D, Lanceleur L, Cagnon C, Monperrus M, Deborde J, Laureau CC, Duran R. Keystone microbial taxa organize micropollutant-related modules shaping the microbial community structure in estuarine sediments. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130858. [PMID: 36706488 DOI: 10.1016/j.jhazmat.2023.130858] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/10/2023] [Accepted: 01/22/2023] [Indexed: 06/18/2023]
Abstract
The fluctuation of environmental conditions drives the structure of microbial communities in estuaries, highly dynamic ecosystems. Microorganisms inhabiting estuarine sediments play a key role in ecosystem functioning. They are well adapted to the changing conditions, also threatened by the presence of pollutants. In order to determine the environmental characteristics driving the organization of the microbial assemblages, we conducted a seasonal survey along the Adour Estuary (Bay of Biscay, France) using 16S rRNA gene Illumina sequencing. Microbial diversity data were combined with a set of chemical analyses targeting metals and pharmaceuticals. Microbial communities were largely dominated by Proteobacteria (41 %) and Bacteroidota (32 %), showing a strong organization according to season, with an important shift in winter. The composition of microbial communities showed spatial distribution according to three main areas (upstream, middle, and downstream estuary) revealing the influence of the Adour River. Further analyses indicated that the microbial community was influenced by biogeochemical parameters (Corg/Norg and δ13C) and micropollutants, including metals (As, Cu, Mn, Sn, Ti, and Zn) and pharmaceuticals (norfloxacin, oxolinic acid and trimethoprim). Network analysis revealed specific modules, organized around keystone taxa, linked to a pollutant type, providing information of paramount importance to understand the microbial ecology in estuarine ecosystems.
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Affiliation(s)
- Sandrine Veloso
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Pau, France
| | - David Amouroux
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Pau, France
| | - Laurent Lanceleur
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Anglet, France
| | - Christine Cagnon
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Pau, France
| | - Mathilde Monperrus
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Anglet, France
| | - Jonathan Deborde
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Anglet, France; Ifremer, LITTORAL, Laboratoire Environnement Ressources des Pertuis Charentais, F-17390 La Tremblade, France
| | - Cristiana Cravo Laureau
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Pau, France
| | - Robert Duran
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Pau, France.
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6
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Yu J, Tang SN, Lee PKH. Universal Dynamics of Microbial Communities in Full-Scale Textile Wastewater Treatment Plants and System Prediction by Machine Learning. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:3345-3356. [PMID: 36795777 DOI: 10.1021/acs.est.2c08116] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The performance of full-scale biological wastewater treatment plants (WWTPs) depends on the operational and environmental conditions of treatment systems. However, we do not know how much these conditions affect microbial community structures and dynamics across systems over time and predictability of the treatment performance. For over a year, the microbial communities of four full-scale WWTPs processing textile wastewater were monitored. During temporal succession, the environmental conditions and system treatment performance were the main drivers, which explained up to 51% of community variations within and between all plants based on the multiple regression models. We identified the universality of community dynamics in all systems using the dissimilarity-overlap curve method, with the significant negative slopes suggesting that the communities containing the same taxa from different plants over time exhibited a similar composition dynamic. The Hubbell neutral theory and the covariance neutrality test indicated that all systems had a dominant niche-based assembly mechanism, supporting that the communities had a similar composition dynamic. Phylogenetically diverse biomarkers for the system conditions and treatment performance were identified by machine learning. Most of the biomarkers (83%) were classified as generalist taxa, and the phylogenetically related biomarkers responded similarly to the system conditions. Many biomarkers for treatment performance perform functions that are crucial for wastewater treatment processes (e.g., carbon and nutrient removal). This study clarifies the relationships between community composition and environmental conditions in full-scale WWTPs over time.
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Affiliation(s)
- Jinjin Yu
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Siang Nee Tang
- Facility Management and Environmental Engineering, TAL Group, Hong Kong SAR, China
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China
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7
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Zhu Y, Liu Y, Chang H, Yang H, Zhang W, Zhang Y, Sun H. Deciphering the microbial community structures and functions of wastewater treatment at high-altitude area. Front Bioeng Biotechnol 2023; 11:1107633. [PMID: 36923457 PMCID: PMC10009103 DOI: 10.3389/fbioe.2023.1107633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 01/30/2023] [Indexed: 03/02/2023] Open
Abstract
Introduction: The proper operation of wastewater treatment plants is a key factor in maintaining a stable river and lake environment. Low purification efficiency in winter is a common problem in high-altitude wastewater treatment plants (WWTPs), and analysis of the microbial community involved in the sewage treatment process at high-altitude can provide valuable references for improving this problem. Methods: In this study, the bacterial communities of high- and low-altitude WWTPs were investigated using Illumina high-throughput sequencing (HTS). The interaction between microbial community and environmental variables were explored by co-occurrence correlation network. Results: At genus level, Thauera (5.2%), unclassified_Rhodocyclaceae (3.0%), Dokdonella (2.5%), and Ferribacterium (2.5%) were the dominant genera in high-altitude group. The abundance of nitrogen and phosphorus removal bacteria were higher in high-altitude group (10.2% and 1.3%, respectively) than in low-altitude group (5.4% and 0.6%, respectively). Redundancy analysis (RDA) and co-occurrence network analysis showed that altitude, ultraviolet index (UVI), pH, dissolved oxygen (DO) and total nitrogen (TN) were the dominated environmental factors (p < 0.05) affecting microbial community assembly, and these five variables explained 21.4%, 20.3%, 16.9%, 11.5%, and 8.2% of the bacterial assembly of AS communities. Discussion: The community diversity of high-altitude group was lower than that of low-altitude group, and WWTPs of high-altitude aeras had a unique microbial community structure. Low temperature and strong UVI are pivotal factors contributing to the reduced diversity of activated sludge microbial communities at high-altitudes.
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Affiliation(s)
- Yuliang Zhu
- School of Environmental and Material Engineering, Yantai University, Yantai, China.,School of Civil Engineering, Yantai University, Yantai, Shandong, China
| | - Yucan Liu
- School of Civil Engineering, Yantai University, Yantai, Shandong, China
| | - Huanhuan Chang
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou, China
| | - Hao Yang
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou, China
| | - Wei Zhang
- School of Environmental and Material Engineering, Yantai University, Yantai, China
| | - Yanxiang Zhang
- School of Environmental and Material Engineering, Yantai University, Yantai, China
| | - Hongwei Sun
- School of Environmental and Material Engineering, Yantai University, Yantai, China
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8
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Wágner DS, Peces M, Nierychlo M, Mielczarek AT, Thornberg D, Nielsen PH. Seasonal microbial community dynamics complicates the evaluation of filamentous bulking mitigation strategies in full-scale WRRFs. WATER RESEARCH 2022; 216:118340. [PMID: 35364352 DOI: 10.1016/j.watres.2022.118340] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/13/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
The activated sludge wastewater treatment process has been thoroughly researched in more than 100 years, yet there are still operational challenges that have not been fully resolved. Such a challenge is the control of filamentous bulking caused by the overgrowth of certain filamentous bacteria. In this study, we tested different mitigation strategies to reduce filamentous bulking, caused by two common filamentous genera found in full-scale water resource recovery facilities (WRRF), Candidatus Microthrix and Candidatus Amarolinea. PAX dosing, ozone addition, hydrocyclone implementation, and the addition of nano-coagulants were tested as mitigation strategies in four parallel treatment lines in a full-scale WRRF over three consecutive years. Unexpectedly, the activated sludge settleability was not affected by any of the mitigation strategies. Some of the strategies appeared to have a strong mitigating effect on the two filamentous species. However, detailed analyses of the microbial communities revealed strong recurrent seasonal variations in all four lines, including the control line which masked the real effect. After removing the effect of the seasonal variation by using a time-series decomposition approach, it was clear that the filamentous bacteria were mostly unaffected by the mitigation strategies. Only PAX dosing had some effect on Ca. Microthrix, but only on one species, Ca. Microthrix subdominans, and not on the most common Ca. Microthrix parvicella. Overall, our study shows the importance of long-term monitoring of microbial communities at species level to understand the normal seasonal pattern to effectively plan and execute full-scale experiments. Moreover, the results highlight the importance of using parallel reference treatment lines when evaluating the effect of mitigation strategies in full-scale treatment plants.
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Affiliation(s)
- Dorottya S Wágner
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark; Biofos, Copenhagen, Denmark
| | - Miriam Peces
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Marta Nierychlo
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | | | | | - Per H Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark.
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9
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Petrovski S, Batinovic S, Rose JJ, Seviour RJ. Biological control of problem bacterial populations causing foaming in activated sludge wastewater treatment plants - phage therapy and beyond. Lett Appl Microbiol 2022; 75:776-784. [PMID: 35598184 DOI: 10.1111/lam.13742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 05/17/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022]
Abstract
The production of a stable foam on the surfaces of reactors is a global operating problem in activated sludge plants. In many cases these foams are stabilized by hydrophobic members of the Mycolata, a group of Actinobacteria whose outer membranes contains long chain hydroxylated mycolic acids. There is currently no single strategy which works for all foams. One attractive approach is to use lytic bacteriophages specific for the foam stabilizing Mycolata population. Such phages are present in activated sludge mixed liquor, and can be recovered readily from it. However, no phage has been recovered which lyses Gordonia amarae and Gordonia pseudoamarae, probably the most common foaming Mycolata members. Whole genome sequencing revealed that both G. amarae and G. pseudoamarae from plants around the world are particularly well endowed with genes encoding anti-viral defence mechanisms. However, both these populations were lysed rapidly by a parasitic nanobacterium isolated from a plant in Australia. This organism, a member of the Saccharibacteria was also effective against many other Mycolata, thus providing a potential agent for control of foams stabilized by them.
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Affiliation(s)
- Steve Petrovski
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, 3086, Victoria, Australia
| | - Steven Batinovic
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, 3086, Victoria, Australia
| | - Jayson Ja Rose
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, 3086, Victoria, Australia
| | - Robert J Seviour
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, 3086, Victoria, Australia
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10
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Dueholm MKD, Nierychlo M, Andersen KS, Rudkjøbing V, Knutsson S, Albertsen M, Nielsen PH. MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants. Nat Commun 2022; 13:1908. [PMID: 35393411 PMCID: PMC8989995 DOI: 10.1038/s41467-022-29438-7] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 03/10/2022] [Indexed: 02/07/2023] Open
Abstract
Microbial communities are responsible for biological wastewater treatment, but our knowledge of their diversity and function is still poor. Here, we sequence more than 5 million high-quality, full-length 16S rRNA gene sequences from 740 wastewater treatment plants (WWTPs) across the world and use the sequences to construct the ‘MiDAS 4’ database. MiDAS 4 is an amplicon sequence variant resolved, full-length 16S rRNA gene reference database with a comprehensive taxonomy from domain to species level for all sequences. We use an independent dataset (269 WWTPs) to show that MiDAS 4, compared to commonly used universal reference databases, provides a better coverage for WWTP bacteria and an improved rate of genus and species level classification. Taking advantage of MiDAS 4, we carry out an amplicon-based, global-scale microbial community profiling of activated sludge plants using two common sets of primers targeting regions of the 16S rRNA gene, revealing how environmental conditions and biogeography shape the activated sludge microbiota. We also identify core and conditionally rare or abundant taxa, encompassing 966 genera and 1530 species that represent approximately 80% and 50% of the accumulated read abundance, respectively. Finally, we show that for well-studied functional guilds, such as nitrifiers or polyphosphate-accumulating organisms, the same genera are prevalent worldwide, with only a few abundant species in each genus. Microbial communities are responsible for biological wastewater treatment. Here, Dueholm et al. generate more than 5 million high-quality, full-length 16S rRNA gene sequences from wastewater treatment plants across the world to construct a database with a comprehensive taxonomy, providing insights into diversity and function of these microbial communities.
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Affiliation(s)
- Morten Kam Dahl Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
| | - 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
| | - Vibeke Rudkjøbing
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Simon Knutsson
- 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
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
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11
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Sun H, Chang H, Tang W, Zhang X, Yang H, Zhang F, Zhang Y. Effects of influent immigration and environmental factors on bacterial assembly of activated sludge microbial communities. ENVIRONMENTAL RESEARCH 2022; 205:112426. [PMID: 34843723 DOI: 10.1016/j.envres.2021.112426] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/17/2021] [Accepted: 11/19/2021] [Indexed: 05/13/2023]
Abstract
The functional mechanism of microbial assembly of activated sludge (AS) in urban wastewater treatment plants (UWTPs) remains unclear. A comprehensive quantitative evaluation of the contribution of influent immigration and environmental factors to AS community composition requires investigation. In this study, the microbial characteristics of six full-scale UWTPs with different influent compositions and environmental factors (altitude, temperature, dissolved oxygen (DO), pH, chemical oxygen demand (COD), total nitrogen (TN), ammonia nitrogen (NH4+-N), and total phosphorus (TP)) were analyzed to determine the main forces affecting the bacterial assembly of AS microbial communities. Abundant and core taxa were screened out based on the abundance and frequency of operational taxonomic units (OTUs) occurrence in all samples. Abundant OTUs (18.7% occurrence) accounted for 87.7% of the total 16S rRNA sequences, while rare OTUs (71.7% occurrence) accounted for only 7.8% of the total 16S rRNA sequences. A total of 135 OTUs were identified as core taxa, accounting for 14.6-26.2% of the total reads, of which 83 OTUs belonged to abundant taxa. The richness and uniformity of the influent community were significantly lower than those of the AS system. The community composition in influent varied from that in AS. Moreover, about 89.7% (86.5% of 16S rRNA sequences) OTUs in AS samples showed positive growth rates, indicating that immigration of influent communities had a limited effect on the microbial composition of AS. Redundancy analysis (RDA) combined with co-occurrence network showed that the bacterial assembly of microbial communities was significantly correlated with altitude, pH, and TN (P < 0.05), and these three parameters could explain 23.3%, 21.1%, and 17.7% of the bacterial assembly of AS microbial communities in UWTPs, respectively.
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Affiliation(s)
- Hongwei Sun
- School of Environmental and Material Engineering, Yantai University, Yantai, 264005, China.
| | - Huanhuan Chang
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, China
| | - Wei Tang
- Yantai City Drainage Service Center, Yantai, 264000, China
| | | | - Hao Yang
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, China
| | - Feng Zhang
- School of Environmental and Material Engineering, Yantai University, Yantai, 264005, China
| | - Yanxiang Zhang
- School of Environmental and Material Engineering, Yantai University, Yantai, 264005, China.
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12
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Peces M, Dottorini G, Nierychlo M, Andersen KS, Dueholm MKD, Nielsen PH. Microbial communities across activated sludge plants show recurring species-level seasonal patterns. ISME COMMUNICATIONS 2022; 2:18. [PMID: 37938743 PMCID: PMC9723569 DOI: 10.1038/s43705-022-00098-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 04/27/2023]
Abstract
Microbial communities in activated sludge (AS) are the core of sanitation in wastewater treatment plants (WWTPs). Microbial communities in AS have shown seasonal changes, however, long-term experiments (>2 years) are rarely conducted, limiting our understanding of the true seasonal dynamics in WWTPs. In this study, we resolved the microbial seasonal dynamics at the species level in four municipal full-scale WWTPs, sampled every 7-10 days, during 3-5 consecutive years. By applying a new time-series analysis approach, we revealed that the seasonal pattern was species-specific, where species belonging to the same functional guild or genus may show different seasonal dynamics. Species could be grouped into cohorts according to their seasonal patterns, where seasonal cohorts showed repeatable annual dynamics across years and plants. Species were also grouped according to their net growth rate in the AS (i.e., growing species and disappearing species). Growing species were more prevailing in spring and autumn cohorts, while disappearing species, which were only present due to the continuous immigration from influent wastewater, were mostly associated with winter and spring cohorts. Most known process-critical species, such as nitrifiers, polyphosphate accumulating organisms and filamentous organisms, showed distinct species-specific patterns. Overall, our study showed that overarching seasonal patterns affected microbial species in full-scale AS plants, with similar seasonal patterns across plants for many dominant species. These recurrent seasonal variations should be taken into account in the operation, understanding and management of the WWTPs.
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Affiliation(s)
- Miriam Peces
- Department of Chemistry and Bioscience, Section of Biotechnology, Center for Microbial Communities, Aalborg University, Aalborg East, 9220, Denmark
| | - Giulia Dottorini
- Department of Chemistry and Bioscience, Section of Biotechnology, Center for Microbial Communities, Aalborg University, Aalborg East, 9220, Denmark
| | - Marta Nierychlo
- Department of Chemistry and Bioscience, Section of Biotechnology, Center for Microbial Communities, Aalborg University, Aalborg East, 9220, Denmark
| | - Kasper Skytte Andersen
- Department of Chemistry and Bioscience, Section of Biotechnology, Center for Microbial Communities, Aalborg University, Aalborg East, 9220, Denmark
| | - Morten Kam Dahl Dueholm
- Department of Chemistry and Bioscience, Section of Biotechnology, Center for Microbial Communities, Aalborg University, Aalborg East, 9220, Denmark
| | - Per Halkjær Nielsen
- Department of Chemistry and Bioscience, Section of Biotechnology, Center for Microbial Communities, Aalborg University, Aalborg East, 9220, Denmark.
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13
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Chao C, Wang L, Li Y, Yan Z, Liu H, Yu D, Liu C. Response of sediment and water microbial communities to submerged vegetations restoration in a shallow eutrophic lake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 801:149701. [PMID: 34419912 DOI: 10.1016/j.scitotenv.2021.149701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Abstract
Submerged macrophytes are the main primary producers in shallow lakes and play an important role in structuring communities. Aquatic microbes are also an important component of aquatic ecosystems and play important roles in maintaining the health and stability of ecosystems. However, little is known about the interactions between macrophytes and microbes during the reintroduction of submerged vegetation. Here, we chose restored zones dominated by four different submerged vegetations and a bare zone in a shallow eutrophic lake to unveil the microbial diversity, composition and structure changes in sediment and water samples after submerged macrophytes were recovered for one and a half years (July 2019) and two years (April 2020). We found that the recovery of submerged vegetations decreased phosphorus content in water and sediments but increased nitrogen and carbon content in sediments. We observed that the transparency of water in the restored zones was significantly higher than that in the bare zone in July. The recovery of submerged vegetations significantly influenced the alpha diversity of bacterial communities in sediments, with higher values observed in restored zones than in bare zones, whereas no significant influence was found in the water samples. In July, the macrophyte species showed strong effects on the bacterial community composition in water and relatively little effect in sediment. However, a strong effect of the macrophyte species on the composition of bacterial communities in sediments was observed in April, which may be related to the decomposition of plant litter and the decay of detritus. Additionally, the dissimilarity of the sedimentary bacterial community may increase more slowly with environmental changes than the planktonic bacterial community dissimilarity. These results suggest that the large-scale restoration of aquatic macrophytes can not only improve water quality and change sediment characteristics but can also affect the diversity and compositions of bacterial communities, and these effects seem to be very long-lasting.
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Affiliation(s)
- Chuanxin Chao
- The National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Science, Wuhan University, Wuhan, PR China
| | - Ligong Wang
- The National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Science, Wuhan University, Wuhan, PR China
| | - Yang Li
- The National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Science, Wuhan University, Wuhan, PR China
| | - Zhiwei Yan
- The National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Science, Wuhan University, Wuhan, PR China
| | - Huimin Liu
- The National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Science, Wuhan University, Wuhan, PR China
| | - Dan Yu
- The National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Science, Wuhan University, Wuhan, PR China
| | - Chunhua Liu
- The National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Science, Wuhan University, Wuhan, PR China.
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14
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Nittami T, Batinovic S. Recent advances in understanding the ecology of the filamentous bacteria responsible for activated sludge bulking. Lett Appl Microbiol 2021; 75:759-775. [PMID: 34919734 DOI: 10.1111/lam.13634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/26/2021] [Accepted: 12/13/2021] [Indexed: 01/30/2023]
Abstract
Activated sludge bulking caused by filamentous bacteria is still a problem in wastewater treatment plants around the world. Bulking is a microbiological problem, and so its solution on species-specific basis is likely to be reached only after their ecology, physiology and metabolism is better understood. Culture-independent molecular methods have provided much useful information about this group of organisms, and in this review, the methods employed and the information they provide are critically assessed. Their application to understanding bulking caused by the most frequently seen filament in Japan, 'Ca. Kouleothrix', is used here as an example of how these techniques might be used to develop control strategies. Whole genome sequences are now available for some of filamentous bacteria responsible for bulking, and so it is possible to understand why these filaments might thrive in activated sludge plants, and provide clues as to how eventually they might be controlled specifically.
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Affiliation(s)
- T Nittami
- Division of Materials Science and Chemical Engineering, Faculty of Engineering, Yokohama National University, Yokohama, Japan
| | - S Batinovic
- Department of Physiology, Anatomy, and Microbiology, La Trobe University, Bundoora, Vic., Australia
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15
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Spieck E, Wegen S, Keuter S. Relevance of Candidatus Nitrotoga for nitrite oxidation in technical nitrogen removal systems. Appl Microbiol Biotechnol 2021; 105:7123-7139. [PMID: 34508283 PMCID: PMC8494671 DOI: 10.1007/s00253-021-11487-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/29/2021] [Accepted: 07/31/2021] [Indexed: 01/10/2023]
Abstract
Abstract Many biotechnological applications deal with nitrification, one of the main steps of the global nitrogen cycle. The biological oxidation of ammonia to nitrite and further to nitrate is critical to avoid environmental damage and its functioning has to be retained even under adverse conditions. Bacteria performing the second reaction, oxidation of nitrite to nitrate, are fastidious microorganisms that are highly sensitive against disturbances. One important finding with relevance for nitrogen removal systems was the discovery of the mainly cold-adapted Cand. Nitrotoga, whose activity seems to be essential for the recovery of nitrite oxidation in wastewater treatment plants at low temperatures, e.g., during cold seasons. Several new strains of this genus have been recently described and ecophysiologically characterized including genome analyses. With increasing diversity, also mesophilic Cand. Nitrotoga representatives have been detected in activated sludge. This review summarizes the natural distribution and driving forces defining niche separation in artificial nitrification systems. Further critical aspects for the competition with Nitrospira and Nitrobacter are discussed. Knowledge about the physiological capacities and limits of Cand. Nitrotoga can help to define physico-chemical parameters for example in reactor systems that need to be run at low temperatures. Key points • Characterization of the psychrotolerant nitrite oxidizer Cand. Nitrotoga • Comparison of the physiological features of Cand. Nitrotoga with those of other NOB • Identification of beneficial environmental/operational parameters for proliferation Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11487-5.
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Affiliation(s)
- Eva Spieck
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany.
| | - Simone Wegen
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
| | - Sabine Keuter
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
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16
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Sun C, Zhang B, Ning D, Zhang Y, Dai T, Wu L, Li T, Liu W, Zhou J, Wen X. Seasonal dynamics of the microbial community in two full-scale wastewater treatment plants: Diversity, composition, phylogenetic group based assembly and co-occurrence pattern. WATER RESEARCH 2021; 200:117295. [PMID: 34091223 DOI: 10.1016/j.watres.2021.117295] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
The optimal operation and functional stability of a wastewater treatment plant (WWTP) strongly depend on the properties of its microbial community. However, a knowledge gap remains regarding the seasonal dynamics of microbial community properties, especially phylogenetic group based assembly and co-occurrence patterns. Accordingly, in this study, influent and activated sludge (AS) samples were weekly collected from 2 full-scale WWTPs for one year (89 influent and 103 AS samples in total) and examined by high-throughput Illumina-MiSeq sequencing. The results suggested that the microbial community diversity and composition in the influent fluctuated substantially with season, while those in the AS had a relatively more stable pattern throughout the year. The phylogenetic group based assembly mechanisms of AS community were identified by using "Infer Community Assembly Mechanisms by Phylogenetic-bin-based null model (iCAMP)". The results showed that drift accounted for the largest proportion (52.8%), while homogeneous selection (18.2%) was the most important deterministic process. Deterministic processes dominated in 47 microbial groups (bins), which were also found (~40%) in the AS core taxa dataset. Moreover, the results suggested that Nitrospira were more susceptible to stochastic processes in winter, which may provide a possible explanation for nitrification failure in winter. Network analysis results suggested that the network structure of the AS community could be more stable in summer and autumn. In addition, there were no identical keystone taxa found in different networks (constructed from different plants, sources, and seasons), which supported the context dependency theory. The results of this study deepened our understanding of the microbial ecology in AS systems and provided a foundation for further studies on the community regulation strategy of WWTPs.
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Affiliation(s)
- Chenxiang Sun
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China; Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK, 73019, USA
| | - Bing Zhang
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China
| | - Daliang Ning
- Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK, 73019, USA
| | - Ya Zhang
- Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK, 73019, USA
| | - Tianjiao Dai
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China
| | - Linwei Wu
- Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK, 73019, USA
| | - Tianle Li
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China
| | - Wei Liu
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jizhong Zhou
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China; Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK, 73019, USA; Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Xianghua Wen
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China.
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