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Díaz LKC, Berná A, Boltes K. Bioelectroremediation of a Real Industrial Wastewater: The Role of Electroactive Biofilm and Planktonic Cells through Enzymatic Activities. TOXICS 2024; 12:614. [PMID: 39195716 PMCID: PMC11359648 DOI: 10.3390/toxics12080614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 08/09/2024] [Accepted: 08/13/2024] [Indexed: 08/29/2024]
Abstract
Bioelectrochemical processes are emerging as one of the most efficient and sustainable technologies for wastewater treatment. Their application for industrial wastewater treatment is still low due to the high toxicity and difficulty of biological treatment for industrial effluents. This is especially relevant in pharmaceutical industries, where different solvents, active pharma ingredients (APIs), extreme pH, and salinity usually form a lethal cocktail for the bacterial community in bioreactors. This work evaluates the impact of the anode architecture on the detoxification performance and analyzes, for the first time, the profile of some key bioremediation enzymes (catalase and esterase) and reactive oxygen species (ROS) during the operation of microbial electrochemical cells treating real pharmaceutical wastewater. Our results show the existence of oxidative stress and loss of cell viability in planktonic cells, while the electrogenic bacteria that form the biofilm maintain their biochemical machinery intact, as observed in the bioelectrochemical response. Monitorization of electrical current flowing in the bioelectrochemical system showed how electroactive biofilm, after a short adaptation period, started to degrade the pharma effluent. The electroactive biofilms are responsible for the detoxification of this type of industrial wastewater.
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Affiliation(s)
- Laura Katherin Chaparro Díaz
- Departamento de Química Analítica Química Física e Ingeniería Química, Campus Científico Tecnológico, Universidad de Alcalá, Ctra. A-II km 33.6, 28871 Alcalá de Henares, Madrid, Spain
| | - Antonio Berná
- IMDEA Water, Avda. Punto Com, 2, 28805 Alcalá de Henares, Madrid, Spain;
| | - Karina Boltes
- Departamento de Química Analítica Química Física e Ingeniería Química, Campus Científico Tecnológico, Universidad de Alcalá, Ctra. A-II km 33.6, 28871 Alcalá de Henares, Madrid, Spain
- IMDEA Water, Avda. Punto Com, 2, 28805 Alcalá de Henares, Madrid, Spain;
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2
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Abdelhamid MAA, Khalifa HO, Yoon HJ, Ki MR, Pack SP. Microbial Immobilized Enzyme Biocatalysts for Multipollutant Mitigation: Harnessing Nature's Toolkit for Environmental Sustainability. Int J Mol Sci 2024; 25:8616. [PMID: 39201301 PMCID: PMC11355015 DOI: 10.3390/ijms25168616] [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: 07/08/2024] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 09/02/2024] Open
Abstract
The ever-increasing presence of micropollutants necessitates the development of environmentally friendly bioremediation strategies. Inspired by the remarkable versatility and potent catalytic activities of microbial enzymes, researchers are exploring their application as biocatalysts for innovative environmental cleanup solutions. Microbial enzymes offer remarkable substrate specificity, biodegradability, and the capacity to degrade a wide array of pollutants, positioning them as powerful tools for bioremediation. However, practical applications are often hindered by limitations in enzyme stability and reusability. Enzyme immobilization techniques have emerged as transformative strategies, enhancing enzyme stability and reusability by anchoring them onto inert or activated supports. These improvements lead to more efficient pollutant degradation and cost-effective bioremediation processes. This review delves into the diverse immobilization methods, showcasing their success in degrading various environmental pollutants, including pharmaceuticals, dyes, pesticides, microplastics, and industrial chemicals. By highlighting the transformative potential of microbial immobilized enzyme biocatalysts, this review underscores their significance in achieving a cleaner and more sustainable future through the mitigation of micropollutant contamination. Additionally, future research directions in areas such as enzyme engineering and machine learning hold immense promise for further broadening the capabilities and optimizing the applications of immobilized enzymes in environmental cleanup.
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Affiliation(s)
- Mohamed A. A. Abdelhamid
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-ro 2511, Sejong 30019, Republic of Korea; (M.A.A.A.); (M.-R.K.)
- Department of Botany and Microbiology, Faculty of Science, Minia University, Minia 61519, Egypt
- Faculty of Education and Art, Sohar University, Sohar 311, Oman
| | - Hazim O. Khalifa
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain P.O. Box 1555, United Arab Emirates;
- Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr El-Sheikh 33516, Egypt
| | - Hyo Jik Yoon
- Institute of Natural Science, Korea University, Sejong-ro 2511, Sejong 30019, Republic of Korea;
| | - Mi-Ran Ki
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-ro 2511, Sejong 30019, Republic of Korea; (M.A.A.A.); (M.-R.K.)
- Institute of Industrial Technology, Korea University, Sejong-ro 2511, Sejong 30019, Republic of Korea
| | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-ro 2511, Sejong 30019, Republic of Korea; (M.A.A.A.); (M.-R.K.)
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3
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Ruan Z, Chen K, Cao W, Meng L, Yang B, Xu M, Xing Y, Li P, Freilich S, Chen C, Gao Y, Jiang J, Xu X. Engineering natural microbiomes toward enhanced bioremediation by microbiome modeling. Nat Commun 2024; 15:4694. [PMID: 38824157 PMCID: PMC11144243 DOI: 10.1038/s41467-024-49098-z] [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: 03/26/2022] [Accepted: 05/21/2024] [Indexed: 06/03/2024] Open
Abstract
Engineering natural microbiomes for biotechnological applications remains challenging, as metabolic interactions within microbiomes are largely unknown, and practical principles and tools for microbiome engineering are still lacking. Here, we present a combinatory top-down and bottom-up framework to engineer natural microbiomes for the construction of function-enhanced synthetic microbiomes. We show that application of herbicide and herbicide-degrader inoculation drives a convergent succession of different natural microbiomes toward functional microbiomes (e.g., enhanced bioremediation of herbicide-contaminated soils). We develop a metabolic modeling pipeline, SuperCC, that can be used to document metabolic interactions within microbiomes and to simulate the performances of different microbiomes. Using SuperCC, we construct bioremediation-enhanced synthetic microbiomes based on 18 keystone species identified from natural microbiomes. Our results highlight the importance of metabolic interactions in shaping microbiome functions and provide practical guidance for engineering natural microbiomes.
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Affiliation(s)
- Zhepu Ruan
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Kai Chen
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Weimiao Cao
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Lei Meng
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Bingang Yang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Mengjun Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Youwen Xing
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Pengfa Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Shiri Freilich
- Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay, 30095, Israel
| | - Chen Chen
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Yanzheng Gao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China.
| | - Xihui Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China.
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4
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Yu Y, Trottmann NF, Schärer MR, Fenner K, Robinson SL. Substrate promiscuity of xenobiotic-transforming hydrolases from stream biofilms impacted by treated wastewater. WATER RESEARCH 2024; 256:121593. [PMID: 38631239 DOI: 10.1016/j.watres.2024.121593] [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: 11/27/2023] [Revised: 04/07/2024] [Accepted: 04/08/2024] [Indexed: 04/19/2024]
Abstract
Organic contaminants enter aquatic ecosystems from various sources, including wastewater treatment plant effluent. Freshwater biofilms play a major role in the removal of organic contaminants from receiving water bodies, but knowledge of the molecular mechanisms driving contaminant biotransformations in complex stream biofilm (periphyton) communities remains limited. Previously, we demonstrated that biofilms in experimental flume systems grown at higher ratios of treated wastewater (WW) to stream water displayed an increased biotransformation potential for a number of organic contaminants. We identified a positive correlation between WW percentage and biofilm biotransformation rates for the widely-used insect repellent, N,N-diethyl-meta-toluamide (DEET) and a number of other wastewater-borne contaminants with hydrolyzable moieties. Here, we conducted deep shotgun sequencing of flume biofilms and identified a positive correlation between WW percentage and metagenomic read abundances of DEET hydrolase (DH) homologs. To test the causality of this association, we constructed a targeted metagenomic library of DH homologs from flume biofilms. We screened our complete metagenomic library for activity with four different substrates, including DEET, and a subset thereof with 183 WW-related organic compounds. The majority of active hydrolases in the metagenomic library preferred aliphatic and aromatic ester substrates while, remarkably, only a single reference enzyme was capable of DEET hydrolysis. Of the 626 total enzyme-substrate combinations tested, approximately 5% were active enzyme-substrate pairs. Metagenomic DH family homologs revealed a broad substrate promiscuity spanning 22 different compounds when summed across all enzymes tested. We biochemically characterized the most promiscuous and active enzymes identified based on metagenomic analysis from uncultivated Rhodospirillaceae and Planctomycetaceae. In addition to characterizing new DH family enzymes, we exemplified a framework for linking metagenome-guided hypothesis generation with experimental validation. Overall, this study expands the scope of known enzymatic contaminant biotransformations for metagenomic hydrolases from WW-receiving stream biofilm communities.
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Affiliation(s)
- Yaochun Yu
- Department of Environmental Chemistry, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland
| | - Niklas Ferenc Trottmann
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland
| | - Milo R Schärer
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland
| | - Kathrin Fenner
- Department of Environmental Chemistry, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland; Department of Chemistry, University of Zürich, 8057 Zürich, Switzerland
| | - Serina L Robinson
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland.
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5
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Tian R, Posselt M, Miaz LT, Fenner K, McLachlan MS. Influence of Season on Biodegradation Rates in Rivers. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:7144-7153. [PMID: 38527158 PMCID: PMC11044578 DOI: 10.1021/acs.est.3c10541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 03/27/2024]
Abstract
Biodegradation plays a key role in the fate of chemicals in the environment. The variability of biodegradation in time can cause uncertainty in evaluating the environmental persistence and risk of chemicals. However, the seasonality of biodegradation in rivers has not yet been the subject of environmentally relevant testing and systematic investigation for large numbers of chemicals. In this work, we studied the biodegradation of 96 compounds during four seasons at four locations (up- and downstream of WWTPs located on two Swedish rivers). Significant seasonality (ANOVA, p < 0.05) of the first-order rate constant for primary biodegradation was observed for most compounds. Variations in pH and total bacterial cell count were not the major factors explaining the seasonality of biodegradation. Deviation from the classical Arrhenius-type behavior was observed for most of the studied compounds, which calls into question the application of this relationship to correct biodegradation rate constants for differences in environmental temperature. Similarities in magnitude and seasonality of biodegradation rate constants were observed for some groups of chemicals possessing the same functional groups. Moreover, reduced seasonality of biodegradation was observed downstream of WWTPs, while biodegradation rates of most compounds were not significantly different between up- and downstream.
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Affiliation(s)
- Run Tian
- Department
of Environmental Science (ACES), Stockholm
University, Stockholm 10691, Sweden
| | - Malte Posselt
- Department
of Environmental Science (ACES), Stockholm
University, Stockholm 10691, Sweden
| | - Luc T. Miaz
- Department
of Environmental Science (ACES), Stockholm
University, Stockholm 10691, Sweden
| | - Kathrin Fenner
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, Dübendorf 8600, Switzerland
- Department
of Chemistry, University of Zürich, Zürich 8057, Switzerland
| | - Michael S. McLachlan
- Department
of Environmental Science (ACES), Stockholm
University, Stockholm 10691, Sweden
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6
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Liang J, Li C, Mo J, Iwata H, Rehman F, Song J, Guo J. Metatranscriptomic profiles reveal the biotransformation potential of azithromycin in river periphyton. WATER RESEARCH 2024; 251:121140. [PMID: 38246076 DOI: 10.1016/j.watres.2024.121140] [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: 09/12/2023] [Revised: 01/12/2024] [Accepted: 01/14/2024] [Indexed: 01/23/2024]
Abstract
Assessment of the interaction between the biotransformation of chemical contaminants and enzyme activity from aquatic microbial communities is critical for improving the micropollutant degradation in river remediation. Here, association mining based on metatranscriptomic analysis was initially applied to determine the genes encoding enzymes involved in the azithromycin (AZI) transformation process and the corresponding microbial hosts in periphyton, followed by revealing the dynamic variation in the community structure and function. In terms of the biotransformation potential, the highly correlated 15 enzymes were suggested to be primarily involved in AZI biotransformation, energy supply, and antibiotic resistance processes, especially aryl-alcohol dehydrogenases (EC: 1.1.1.90), hydroxylamine dehydrogenase (EC: 1.7.2.6), and monooxygenases (EC: 1.14.11.57) that were involved in the biotransformation of AZI. In the matter of community ecological function, the photosystem II (PSII) reaction center in the periphytic photosynthetic process, as indicated by Fv/Fm, was inhibited after AZI exposure, which may be attributed to the down-regulated genes enriched in the photosynthesis - antenna proteins (ko00196), photosynthesis (ko00195), and two-component system (ko02020) pathways. Furthermore, the periphytic utilization capacity for carbohydrates and phenolic acids was enhanced, which was in accordance with all the increased expression of transcripts involved in the corresponding molecular pathways, including aminobenzoate degradation (ko00627), starch and sucrose metabolism (ko00500), ABC transporters (ko02010), phosphotransferase system (ko02060), galactose metabolism (ko00052), amino sugar and nucleotide sugar metabolism (ko00520). Taken together, this study highlighted the critical role of river periphyton in the micropollutant degradation and unraveled the molecular mechanism of antibiotic biotransformation as well as the structural and functional damage in the periphyton.
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Affiliation(s)
- Jiayi Liang
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China
| | - Chenghao Li
- School of Economics & Management, Northwest University, Xi'an 710127, China
| | - Jiezhang Mo
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou, China
| | - Hisato Iwata
- Center for Marine Environmental Studies, Ehime University, Bunkyo-cho 2-5, Matsuyama, Ehime 790-8577, Japan
| | - Fozia Rehman
- Interdisciplinary Research Center in Biomedical Materials (IRCBM), COMSATS University Islamabad, Campus, Lahore, Pakistan
| | - Jinxi Song
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China
| | - Jiahua Guo
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China.
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7
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Hellal J, Barthelmebs L, Bérard A, Cébron A, Cheloni G, Colas S, Cravo-Laureau C, De Clerck C, Gallois N, Hery M, Martin-Laurent F, Martins J, Morin S, Palacios C, Pesce S, Richaume A, Vuilleumier S. Unlocking secrets of microbial ecotoxicology: recent achievements and future challenges. FEMS Microbiol Ecol 2023; 99:fiad102. [PMID: 37669892 PMCID: PMC10516372 DOI: 10.1093/femsec/fiad102] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/21/2023] [Accepted: 09/04/2023] [Indexed: 09/07/2023] Open
Abstract
Environmental pollution is one of the main challenges faced by humanity. By their ubiquity and vast range of metabolic capabilities, microorganisms are affected by pollution with consequences on their host organisms and on the functioning of their environment. They also play key roles in the fate of pollutants through the degradation, transformation, and transfer of organic or inorganic compounds. Thus, they are crucial for the development of nature-based solutions to reduce pollution and of bio-based solutions for environmental risk assessment of chemicals. At the intersection between microbial ecology, toxicology, and biogeochemistry, microbial ecotoxicology is a fast-expanding research area aiming to decipher the interactions between pollutants and microorganisms. This perspective paper gives an overview of the main research challenges identified by the Ecotoxicomic network within the emerging One Health framework and in the light of ongoing interest in biological approaches to environmental remediation and of the current state of the art in microbial ecology. We highlight prevailing knowledge gaps and pitfalls in exploring complex interactions among microorganisms and their environment in the context of chemical pollution and pinpoint areas of research where future efforts are needed.
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Affiliation(s)
| | - Lise Barthelmebs
- Université de Perpignan Via Domitia, Biocapteurs – Analyse-Environnement, Perpignan, France
- Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Annette Bérard
- UMR EMMAH INRAE/AU – équipe SWIFT, 228, route de l'Aérodrome, 84914 Avignon Cedex 9, France
| | | | - Giulia Cheloni
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Sète, France
| | - Simon Colas
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | | | - Caroline De Clerck
- AgricultureIsLife, Gembloux Agro-Bio Tech (Liege University), Passage des Déportés 2, 5030 Gembloux, Belgium
| | | | - Marina Hery
- HydroSciences Montpellier, Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Fabrice Martin-Laurent
- Institut Agro Dijon, INRAE, Université de Bourgogne, Université de Bourgogne Franche-Comté, Agroécologie, 21065 Dijon, France
| | - Jean Martins
- IGE, UMR 5001, Université Grenoble Alpes, CNRS, G-INP, INRAE, IRD Grenoble, France
| | | | - Carmen Palacios
- Université de Perpignan Via Domitia, CEFREM, F-66860 Perpignan, France
- CNRS, CEFREM, UMR5110, F-66860 Perpignan, France
| | | | - Agnès Richaume
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5557, Ecologie Microbienne, Villeurbanne, France
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8
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Morin S, Artigas J. Twenty Years of Research in Ecosystem Functions in Aquatic Microbial Ecotoxicology. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2023; 42:1867-1888. [PMID: 37401851 DOI: 10.1002/etc.5708] [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: 11/29/2022] [Revised: 12/20/2022] [Accepted: 06/27/2023] [Indexed: 07/05/2023]
Abstract
One of the major threats to freshwater biodiversity is water pollution including excessive loads of nutrients, pesticides, industrial chemicals, and/or emerging contaminants. The widespread use of organic pesticides for agricultural and nonagricultural (industry, gardening, etc.) purposes has resulted in the presence of their residues in various environments, including surface waters. However, the contribution of pesticides to the deterioration of freshwater ecosystems (i.e., biodiversity decline and ecosystem functions impairment) remains uncertain. Once in the aquatic environment, pesticides and their metabolites can interact with microbial communities, causing undesirable effects. The existing legislation on ecological quality assessment of water bodies in Europe is based on water chemical quality and biological indicator species (Water Framework Directive, Pesticides Directive), while biological functions are not yet included in monitoring programs. In the present literature review, we analyze 20 years (2000-2020) of research on ecological functions provided by microorganisms in aquatic ecosystems. We describe the set of ecosystem functions investigated in these studies and the range of endpoints used to establish causal relationships between pesticide exposure and microbial responses. We focus on studies addressing the effects of pesticides at environmentally realistic concentrations and at the microbial community level to inform the ecological relevance of the ecotoxicological assessment. Our literature review highlights that most studies were performed using benthic freshwater organisms and that autotrophic and heterotrophic communities are most often studied separately, usually testing the pesticides that target the main microbial component (i.e., herbicides for autotrophs and fungicides for heterotrophs). Overall, most studies demonstrate deleterious impacts on the functions studied, but our review points to the following shortcomings: (1) the nonsystematic analysis of microbial functions supporting aquatic ecosystems functioning, (2) the study of ecosystem functions (i.e., nutrient cycling) via proxies (i.e., potential extracellular enzymatic activity measurements) which are sometimes disconnected from the current ecosystem functions, and (3) the lack of consideration of chronic exposures to assess the impact of, adaptations to, or recovery of aquatic microbial communities from pesticides. Environ Toxicol Chem 2023;42:1867-1888. © 2023 SETAC.
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Affiliation(s)
| | - Joan Artigas
- Laboratoire Microorganismes: Génome et Environnement, CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
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9
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Kashyap A, Nishil B, Thatikonda S. Experimental and numerical elucidation of the fate and transport of antibiotics in aquatic environment: A review. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:942. [PMID: 37436551 DOI: 10.1007/s10661-023-11482-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 06/08/2023] [Indexed: 07/13/2023]
Abstract
This review highlights various experimental and mathematical modeling strategies to investigate the fate and transport of antibiotics that elucidate antimicrobial selective pressure in aquatic environments. Globally, the residual antibiotic concentrations in effluents from bulk drug manufacturing industries were 30- and 1500-fold greater than values reported in municipal and hospital effluents, respectively. The antibiotic concentration from different effluents enters the waterbodies that usually get diluted as they go downstream and undergo various abiotic and biotic reactive processes. In aquatic systems, photolysis is the predominant process for antibiotic reduction in the water matrix, while hydrolysis and sorption are frequently reported in the sediment compartment. The rate of antibiotic reduction varies widely with influencing factors such as the chemical properties of the antibiotics and hydrodynamic conditions of river streams. Among all, tetracycline was found to more unstable (log Kow = - 0.62 to - 1.12) that can readily undergo photolysis and hydrolysis; whereas macrolides were more stable (log Kow = 3.06 to 4.02) that are prone to biodegradation. The processes like photolysis, hydrolysis, and biodegradation followed first-order reaction kinetics while the sorption followed a second-order kinetics for most antibiotic classes with reaction rates occurring in the decreasing order of Fluoroquinolones and Sulphonamides. The reports from various experiments on abiotic and biotic processes serve as input parameters for an integrated mathematical modeling to predict the fate of the antibiotics in the aquatic environment. Various mathematical models viz. Fugacity level IV, RSEMM, OTIS, GREAT-ER, SWAT, QWASI, and STREAM-EU are discussed for their potential capabilities. However, these models do not account for microscale interactions of the antibiotics and microbial community under real-field conditions. Also, the seasonal variations for contaminant concentrations that exert selective pressure for antimicrobial resistance has not been accounted. Addressing these aspects collectively is the key to exploring the emergence of antimicrobial resistance. Therefore, a comprehensive model involving antimicrobial resistance parameters like fitness cost, bacterial population dynamics, conjugation transfer efficiency, etc. is required to predict the fate of antibiotics.
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Affiliation(s)
- Arun Kashyap
- Environmental Engineering Division, Department of Civil Engineering, IIT Hyderabad, Kandi, Sangareddy, Telangana, 502285, India
| | - Benita Nishil
- Environmental Engineering Division, Department of Civil Engineering, IIT Hyderabad, Kandi, Sangareddy, Telangana, 502285, India
| | - Shashidhar Thatikonda
- Environmental Engineering Division, Department of Civil Engineering, IIT Hyderabad, Kandi, Sangareddy, Telangana, 502285, India.
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10
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Rios-Miguel AB, Jhm van Bergen T, Zillien C, Mj Ragas A, van Zelm R, Sm Jetten M, Jan Hendriks A, Welte CU. Predicting and improving the microbial removal of organic micropollutants during wastewater treatment: A review. CHEMOSPHERE 2023; 333:138908. [PMID: 37187378 DOI: 10.1016/j.chemosphere.2023.138908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/17/2023]
Abstract
Organic micropollutants (OMPs) consist of widely used chemicals such as pharmaceuticals and pesticides that can persist in surface and groundwaters at low concentrations (ng/L to μg/L) for a long time. The presence of OMPs in water can disrupt aquatic ecosystems and threaten the quality of drinking water sources. Wastewater treatment plants (WWTPs) rely on microorganisms to remove major nutrients from water, but their effectiveness at removing OMPs varies. Low removal efficiency might be the result of low concentrations, inherent stable chemical structures of OMPs, or suboptimal conditions in WWTPs. In this review, we discuss these factors, with special emphasis on the ongoing adaptation of microorganisms to degrade OMPs. Finally, recommendations are drawn to improve the prediction of OMP removal in WWTPs and to optimize the design of new microbial treatment strategies. OMP removal seems to be concentration-, compound-, and process-dependent, which poses a great complexity to develop accurate prediction models and effective microbial processes targeting all OMPs.
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Affiliation(s)
- Ana B Rios-Miguel
- Department of Microbiology, Radboud Institute for Biological and Environmental Science, Radboud University, Nijmegen, the Netherlands.
| | - Tamara Jhm van Bergen
- Department of Environmental Science, Radboud Institute for Biological and Environmental Science, Radboud University, Nijmegen, the Netherlands.
| | - Caterina Zillien
- Department of Environmental Science, Radboud Institute for Biological and Environmental Science, Radboud University, Nijmegen, the Netherlands
| | - Ad Mj Ragas
- Department of Environmental Science, Radboud Institute for Biological and Environmental Science, Radboud University, Nijmegen, the Netherlands
| | - Rosalie van Zelm
- Department of Environmental Science, Radboud Institute for Biological and Environmental Science, Radboud University, Nijmegen, the Netherlands
| | - Mike Sm Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Science, Radboud University, Nijmegen, the Netherlands
| | - A Jan Hendriks
- Department of Environmental Science, Radboud Institute for Biological and Environmental Science, Radboud University, Nijmegen, the Netherlands
| | - Cornelia U Welte
- Department of Microbiology, Radboud Institute for Biological and Environmental Science, Radboud University, Nijmegen, the Netherlands
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11
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Ma Q, Meng N, Su J, Li Y, Gu J, Wang Y, Wang J, Qu Y, Zhao Z, Sun Y. Unraveling the skatole biodegradation process in an enrichment consortium using integrated omics and culture-dependent strategies. J Environ Sci (China) 2023; 127:688-699. [PMID: 36522097 DOI: 10.1016/j.jes.2022.06.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 06/20/2022] [Accepted: 06/20/2022] [Indexed: 06/17/2023]
Abstract
3-Methylindole (skatole) is regarded as one of the most offensive compounds in odor emission. Biodegradation is feasible for skatole removal but the functional species and genes responsible for skatole degradation remain enigmatic. In this study, an efficient aerobic skatole-degrading consortium was obtained. Rhodococcus and Pseudomonas were identified as the two major and active populations by integrated metagenomic and metatranscriptomic analyses. Bioinformatic analyses indicated that the skatole downstream degradation was mainly via the catechol pathway, and upstream degradation was likely catalyzed by the aromatic ring-hydroxylating oxygenase and flavin monooxygenase. Genome binning and gene analyses indicated that Pseudomonas, Pseudoclavibacter, and Raineyella should cooperate with Rhodococcus for the skatole degradation process. Moreover, a pure strain Rhodococcus sp. DMU1 was successfully obtained which could utilize skatole as the sole carbon source. Complete genome sequencing showed that strain DMU1 was the predominant population in the consortium. Further crude enzyme and RT-qPCR assays indicated that strain DMU1 degraded skatole through the catechol ortho-cleavage pathway. Collectively, our results suggested that synergistic degradation of skatole in the consortium should be performed by diverse bacteria with Rhodococcus as the primary degrader, and the degradation mainly proceeded via the catechol pathway.
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Affiliation(s)
- Qiao Ma
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China.
| | - Nan Meng
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Jiancheng Su
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Yujie Li
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Jiazheng Gu
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Yidi Wang
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Jingwei Wang
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Yuanyuan Qu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Zelong Zhao
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China.
| | - Yeqing Sun
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
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12
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Gabrielli M, Delli Compagni R, Gusmaroli L, Malpei F, Polesel F, Buttiglieri G, Antonelli M, Turolla A. Modelling and prediction of the effect of operational parameters on the fate of contaminants of emerging concern in WWTPs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159200. [PMID: 36202354 DOI: 10.1016/j.scitotenv.2022.159200] [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: 04/05/2022] [Revised: 09/08/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Wastewater treatment plants (WWTPs) provide a barrier against the discharge of contaminants of emerging concern (CECs) into the environment. The removal of CECs is highly WWTP-specific and the underlying mechanisms are still poorly understood, hampering the optimization of biological treatment steps for their removal. To fill this knowledge gap, we assessed the influence of four operational parameters of activated sludge biological treatment, namely total suspended solids, temperature, pH and redox conditions, on the sorption and biodegradation of four CECs under controlled laboratory conditions. Design of Experiments was used to better address the factors influencing CECs removal and interactions among operational parameters. The derived statistical models showed results in concordance with previous studies and indicated how sorption and biodegradation of the investigated CECs depend on most tested parameters and few of their interactions. The predictions of the developed models have been compared with literature values, indicating how the tested parameters are responsible for most of the variability of sorption, while they could not reliably generalize biodegradation rates. The developed models were also implemented as an extension of a mechanistic biological treatment model, successfully describing the dynamic behaviour of a large-scale WWTP, which was observed during a three-day continuous monitoring campaign. Compared to a traditional modelling approach, the one including the developed models showed on average almost a three-fold uncertainty reduction, favouring its use to aid WWTP managers and regulators for improved assessment of CEC fate and removal. Finally, the models highlighted that, while higher temperatures and solids concentrations generically favoured CECs removal, removal efficiency vary significantly due to operational parameters and no globally optimum conditions for CECs removal exist. The use of these models opens the door to the combined dynamic management of both traditional contaminants and CECs in WWTPs.
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Affiliation(s)
- Marco Gabrielli
- Politecnico di Milano, Department of Civil and Environmental Engineering (DICA), Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Riccardo Delli Compagni
- Politecnico di Milano, Department of Civil and Environmental Engineering (DICA), Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Lucia Gusmaroli
- Catalan Institute for Water Research (ICRA-CERCA), C. Emili Grahit 101, 17003 Girona, Spain; Universitat de Girona, Plaça de Sant Domènec, 3, 17004 Girona, Spain
| | - Francesca Malpei
- Politecnico di Milano, Department of Civil and Environmental Engineering (DICA), Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | | | - Gianluigi Buttiglieri
- Catalan Institute for Water Research (ICRA-CERCA), C. Emili Grahit 101, 17003 Girona, Spain; Universitat de Girona, Plaça de Sant Domènec, 3, 17004 Girona, Spain
| | - Manuela Antonelli
- Politecnico di Milano, Department of Civil and Environmental Engineering (DICA), Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Andrea Turolla
- Politecnico di Milano, Department of Civil and Environmental Engineering (DICA), Piazza Leonardo da Vinci 32, 20133 Milano, Italy.
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13
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Davenport R, Curtis‐Jackson P, Dalkmann P, Davies J, Fenner K, Hand L, McDonough K, Ott A, Ortega‐Calvo JJ, Parsons JR, Schäffer A, Sweetlove C, Trapp S, Wang N, Redman A. Scientific concepts and methods for moving persistence assessments into the 21st century. INTEGRATED ENVIRONMENTAL ASSESSMENT AND MANAGEMENT 2022; 18:1454-1487. [PMID: 34989108 PMCID: PMC9790601 DOI: 10.1002/ieam.4575] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 09/29/2021] [Accepted: 12/06/2021] [Indexed: 05/19/2023]
Abstract
The evaluation of a chemical substance's persistence is key to understanding its environmental fate, exposure concentration, and, ultimately, environmental risk. Traditional biodegradation test methods were developed many years ago for soluble, nonvolatile, single-constituent test substances, which do not represent the wide range of manufactured chemical substances. In addition, the Organisation for Economic Co-operation and Development (OECD) screening and simulation test methods do not fully reflect the environmental conditions into which substances are released and, therefore, estimates of chemical degradation half-lives can be very uncertain and may misrepresent real environmental processes. In this paper, we address the challenges and limitations facing current test methods and the scientific advances that are helping to both understand and provide solutions to them. Some of these advancements include the following: (1) robust methods that provide a deeper understanding of microbial composition, diversity, and abundance to ensure consistency and/or interpret variability between tests; (2) benchmarking tools and reference substances that aid in persistence evaluations through comparison against substances with well-quantified degradation profiles; (3) analytical methods that allow quantification for parent and metabolites at environmentally relevant concentrations, and inform on test substance bioavailability, biochemical pathways, rates of primary versus overall degradation, and rates of metabolite formation and decay; (4) modeling tools that predict the likelihood of microbial biotransformation, as well as biochemical pathways; and (5) modeling approaches that allow for derivation of more generally applicable biotransformation rate constants, by accounting for physical and/or chemical processes and test system design when evaluating test data. We also identify that, while such advancements could improve the certainty and accuracy of persistence assessments, the mechanisms and processes by which they are translated into regulatory practice and development of new OECD test guidelines need improving and accelerating. Where uncertainty remains, holistic weight of evidence approaches may be required to accurately assess the persistence of chemicals. Integr Environ Assess Manag 2022;18:1454-1487. © 2022 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).
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Affiliation(s)
| | | | - Philipp Dalkmann
- Bayer AG, Crop Science Division, Environmental SafetyMonheimGermany
| | | | - Kathrin Fenner
- Eawag, Swiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
- Department of ChemistryUniversity of ZürichZürichSwitzerland
| | - Laurence Hand
- Syngenta, Product Safety, Jealott's Hill International Research CentreBracknellUK
| | | | - Amelie Ott
- School of EngineeringNewcastle UniversityNewcastle upon TyneUK
- European Centre for Ecotoxicology and Toxicology of Chemicals (ECETOC)BrusselsBelgium
| | - Jose Julio Ortega‐Calvo
- Instituto de Recursos Naturales y Agrobiología de SevillaConsejo Superior de Investigaciones CientíficasSevillaSpain
| | - John R. Parsons
- Institute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
| | - Andreas Schäffer
- RWTH Aachen University, Institute for Environmental ResearchAachenGermany
| | - Cyril Sweetlove
- L'Oréal Research & InnovationEnvironmental Research DepartmentAulnay‐sous‐BoisFrance
| | - Stefan Trapp
- Department of Environmental EngineeringTechnical University of DenmarkBygningstorvetLyngbyDenmark
| | - Neil Wang
- Total Marketing & ServicesParis la DéfenseFrance
| | - Aaron Redman
- ExxonMobil Petroleum and ChemicalMachelenBelgium
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14
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Ruan Z, Xu M, Xing Y, Jiang Q, Yang B, Jiang J, Xu X. Interspecies Metabolic Interactions in a Synergistic Consortium Drive Efficient Degradation of the Herbicide Bromoxynil Octanoate. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:11613-11622. [PMID: 36089742 DOI: 10.1021/acs.jafc.2c03057] [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] [Indexed: 06/15/2023]
Abstract
Microbial communities play vital roles in biogeochemical cycles, allowing biodegradation of a wide range of pollutants. Although many studies have shown the importance of interspecies interactions on activities of communities, fully elucidating the complex interactions in microbial communities is still challenging. Here, we isolated a consortium containing two bacterial strains (Acinetobacter sp. AG3 and Bacillus sp. R45), which could mineralize bromoxynil octanoate (BO) with higher efficiency than either strain individually. The BO degradation pathway by the synergistic consortium was elucidated, and interspecies interactions in the consortium were explored using genome-scale metabolic models (GSMMs). Modeling showed that growth and degradation enhancements were driven by metabolic interactions, such as syntrophic exchanges of small metabolites in the consortium. Besides, nutritional enhancers were predicted to improve BO degradation, which were tested experimentally. Overall, our results will enhance our understanding of microbial mineralization of BO by consortia and promote the application of microbial communities for bioremediation.
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Affiliation(s)
- Zhepu Ruan
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Mengjun Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Youwen Xing
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Qi Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Bingang Yang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Xihui Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
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15
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The Geochemical Drivers of Bacterial Community Diversity in the Watershed Sediments of the Heihe River (Northern China). WATER 2022. [DOI: 10.3390/w14121948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The city of Zhangye (Gansu Region, China) has been subjected to several changes related to the development of new profitable human activities. Unfortunately, this growth has led to a general decrease in water quality due to the release of several toxic wastes and pollutants (e.g., heavy metals) into the Heihe River. In order to assess the environmental exposure and the potential threat to human health, microbiological diversity for the monitoring of water pollution by biotic and abiotic impact factors was investigated. In particular, we analysed samples collected on different sites using 454 pyrotag sequencing of the 16S ribosomal genes. Then, we focused on alpha-diversity indices to test the hypothesis that communities featuring lower diversity show higher resistance to the disturbance events. The findings report that a wide range of environmental factors such as pH, nutrients and chemicals (heavy metals (HMs)), affected microbial diversity by stimulating mutualistic relationships among bacteria. Furthermore, a selection in bacterial taxa related to the different concentrations of polluting compounds was highlighted. Supporting the hypothesis, our investigation highlights the importance of microbial communities as sentinels for ecological status diagnosis.
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16
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Nolte TM, Peijnenburg WJGM, Miguel ABR, Zhang YN, Hendriks AJ. Stoichiometric ratios for biotics and xenobiotics capture effective metabolic coupling to re(de)fine biodegradation. WATER RESEARCH 2022; 217:118333. [PMID: 35421691 DOI: 10.1016/j.watres.2022.118333] [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: 01/15/2022] [Revised: 03/07/2022] [Accepted: 03/19/2022] [Indexed: 06/14/2023]
Abstract
Preserving human and environmental health requires anthropogenic pollutants to be biologically degradable. Depending on concentration, both nutrients and pollutants induce and activate metabolic capacity in the endemic bacterial consortium, which in turn aids their degradation. Knowledge on such 'acclimation' is rarely implemented in risk assessment cost-effectively. As a result, an accurate description of the mechanisms and kinetics of biodegradation remains problematic. In this study, we defined a yield 'effectivity', comprising the effectiveness at which a pollutant (substrate) enhances its own degradation by inducing (biomass) cofactors involved therein. Our architecture for calculation represents the interplay between concentration and metabolism via both stoichiometric and thermodynamic concepts. The calculus for yield 'effectivity' is biochemically intuitive, implicitly embeds co-metabolism and distinguishes 'endogenic' from 'exogenic' substances' reflecting various phenomena in biodegradation and bio-transformation studies. We combined data on half-lives of pollutants/nutrients in wastewater and surface water with transition-state rate theory to obtain also experimental values for effective yields. These quantify the state of acclimation: the portion of biodegradation kinetics attributable to (contributed by) 'natural metabolism', in view of similarity to natural substances. Calculated and experimental values showed statistically significant correspondence. Particularly, carbohydrate metabolism and nucleic acid metabolism appeared relevant for acclimation (R2 = 0.11-0.42), affecting rates up to 104.9(±0.7) times: under steady-state acclimation, a compound stoichiometrically identical to carbohydrates or nucleic acids, is 103.2 to 104.9 times faster aerobically degraded than a compound marginally similar. Our new method, simulating (contribution by) the state of acclimation, supplements existing structure-biodegradation and kinetic models for predicting biodegradation in wastewater and surface water. The accuracy of prediction may increase when characterizing nutrients/co-metabolites in terms of, e.g., elemental analysis. We discuss strengths and limitations of our approach by comparison to empirical and mechanism-based methods.
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Affiliation(s)
- Tom M Nolte
- Radboud University Nijmegen, Department of Environmental Science, Institute for Water and Wetland Research, 6500 GL Nijmegen, the Netherlands.
| | - Willie J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, the Netherlands; National Institute of Public Health and the Environment, PO Box 1, 3720 BA Bilthoven, the Netherlands
| | - Ana B Rios- Miguel
- Radboud University Nijmegen, Department of Microbiology, Institute for Water and Wetland Research, 6500 GL Nijmegen, the Netherlands
| | - Ya-Nan Zhang
- School of Environment, Northeast Normal University, NO. 2555 Jingyue Street, Changchun, Jilin 130117, China
| | - A Jan Hendriks
- Radboud University Nijmegen, Department of Environmental Science, Institute for Water and Wetland Research, 6500 GL Nijmegen, the Netherlands
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17
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Pawlowski J, Bruce K, Panksep K, Aguirre FI, Amalfitano S, Apothéloz-Perret-Gentil L, Baussant T, Bouchez A, Carugati L, Cermakova K, Cordier T, Corinaldesi C, Costa FO, Danovaro R, Dell'Anno A, Duarte S, Eisendle U, Ferrari BJD, Frontalini F, Frühe L, Haegerbaeumer A, Kisand V, Krolicka A, Lanzén A, Leese F, Lejzerowicz F, Lyautey E, Maček I, Sagova-Marečková M, Pearman JK, Pochon X, Stoeck T, Vivien R, Weigand A, Fazi S. Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151783. [PMID: 34801504 DOI: 10.1016/j.scitotenv.2021.151783] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/06/2021] [Accepted: 11/14/2021] [Indexed: 06/13/2023]
Abstract
Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, the eDNA metabarcoding has also been applied to soft sediment samples, mainly for assessing microbial or meiofaunal biota. Compared to classical methodologies based on manual sorting and morphological identification of benthic taxa, eDNA metabarcoding offers potentially important advantages for assessing the environmental quality of sediments. The methods and protocols utilized for sediment eDNA metabarcoding can vary considerably among studies, and standardization efforts are needed to improve their robustness, comparability and use within regulatory frameworks. Here, we review the available information on eDNA metabarcoding applied to sediment samples, with a focus on sampling, preservation, and DNA extraction steps. We discuss challenges specific to sediment eDNA analysis, including the variety of different sources and states of eDNA and its persistence in the sediment. This paper aims to identify good-practice strategies and facilitate method harmonization for routine use of sediment eDNA in future benthic monitoring.
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Affiliation(s)
- J Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland; ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - K Bruce
- NatureMetrics Ltd, CABI Site, Bakeham Lane, Egham TW20 9TY, UK
| | - K Panksep
- Institute of Technology, University of Tartu, Tartu 50411, Estonia; Chair of Hydrobiology and Fishery, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia; Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Estonia
| | - F I Aguirre
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy
| | - S Amalfitano
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy
| | - L Apothéloz-Perret-Gentil
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - T Baussant
- Norwegian Research Center AS, NORCE Environment, Marine Ecology Group, Mekjarvik 12, 4070 Randaberg, Norway
| | - A Bouchez
- INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| | - L Carugati
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - K Cermakova
- ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - T Cordier
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; NORCE Climate, NORCE Norwegian Research Centre AS, Bjerknes Centre for Climate Research, Jahnebakken 5, 5007 Bergen, Norway
| | - C Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - F O Costa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - R Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - A Dell'Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - S Duarte
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - U Eisendle
- University of Salzburg, Dept. of Biosciences, 5020 Salzburg, Austria
| | - B J D Ferrari
- Swiss Centre for Applied Ecotoxicology (Ecotox Centre), EPFL ENAC IIE-GE, 1015 Lausanne, Switzerland
| | - F Frontalini
- Department of Pure and Applied Sciences, Urbino University, Urbino, Italy
| | - L Frühe
- Technische Universität Kaiserslautern, Ecology Group, D-67663 Kaiserslautern, Germany
| | - A Haegerbaeumer
- Bielefeld University, Animal Ecology, 33615 Bielefeld, Germany
| | - V Kisand
- Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - A Krolicka
- Norwegian Research Center AS, NORCE Environment, Marine Ecology Group, Mekjarvik 12, 4070 Randaberg, Norway
| | - A Lanzén
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia, Spain
| | - F Leese
- University of Duisburg-Essen, Faculty of Biology, Aquatic Ecosystem Research, Germany
| | - F Lejzerowicz
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - E Lyautey
- Univ. Savoie Mont Blanc, INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| | - I Maček
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia; Faculty of Mathematics, Natural Sciences and Information Technologies (FAMNIT), University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia
| | - M Sagova-Marečková
- Czech University of Life Sciences, Dept. of Microbiology, Nutrition and Dietetics, Prague, Czech Republic
| | - J K Pearman
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - X Pochon
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Science, University of Auckland, Warkworth 0941, New Zealand
| | - T Stoeck
- Technische Universität Kaiserslautern, Ecology Group, D-67663 Kaiserslautern, Germany
| | - R Vivien
- Swiss Centre for Applied Ecotoxicology (Ecotox Centre), EPFL ENAC IIE-GE, 1015 Lausanne, Switzerland
| | - A Weigand
- National Museum of Natural History Luxembourg, 25 Rue Münster, L-2160 Luxembourg, Luxembourg
| | - S Fazi
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy.
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18
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Rich SL, Zumstein MT, Helbling DE. Identifying Functional Groups that Determine Rates of Micropollutant Biotransformations Performed by Wastewater Microbial Communities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:984-994. [PMID: 34939795 DOI: 10.1021/acs.est.1c06429] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The goal of this research was to identify functional groups that determine rates of micropollutant (MP) biotransformations performed by wastewater microbial communities. To meet this goal, we performed a series of incubation experiments seeded with four independent wastewater microbial communities and spiked them with a mixture of 40 structurally diverse MPs. We collected samples over time and used high-resolution mass spectrometry to estimate biotransformation rate constants for each MP in each experiment and to propose structures of 46 biotransformation products. We then developed random forest models to classify the biotransformation rate constants based on the presence of specific functional groups or observed biotransformations. We extracted classification importance metrics from each random forest model and compared them across wastewater microbial communities. Our analysis revealed 30 functional groups that we define as either biotransformation promoters, biotransformation inhibitors, structural features that can be biotransformed based on uncharacterized features of the wastewater microbial community, or structural features that are not rate-determining. Our experimental data and analysis provide novel insights into MP biotransformations that can be used to more accurately predict MP biotransformations or to inform the design of new chemical products that may be more readily biodegradable during wastewater treatment.
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Affiliation(s)
- Stephanie L Rich
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Michael T Zumstein
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
- Division of Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, University of Vienna, Wien 1090 Austria
| | - Damian E Helbling
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
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19
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Kennes-Veiga DM, Gónzalez-Gil L, Carballa M, Lema JM. Enzymatic cometabolic biotransformation of organic micropollutants in wastewater treatment plants: A review. BIORESOURCE TECHNOLOGY 2022; 344:126291. [PMID: 34752884 DOI: 10.1016/j.biortech.2021.126291] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/28/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
Biotransformation of trace-level organic micropollutants (OMPs) by complex microbial communities in wastewater treatment facilities is a key process for their detoxification and environmental impact reduction. Therefore, understanding the metabolic activities and mechanisms that contribute to their biotransformation is essential when developing approaches aiming to minimize their discharge. This review addresses the relevance of cometabolic processes and discusses the main enzymatic activities currently known to take part in OMPs removal under different redox environments in the compartments of wastewater treatment plants. Furthermore, the most common methodologies to decipher such enzymes are discussed, including the use of in vitro enzyme assays, enzymatic inhibitors, the analysis of transformation products and the application of several -omic techniques. Finally, perspectives on major challenges and future research requirements to improve OMPs biotransformation are proposed.
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Affiliation(s)
- David M Kennes-Veiga
- CRETUS, Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - Lorena Gónzalez-Gil
- Defence University Centre, Spanish Naval Academy, Plaza de España, 36920 Marín, Spain
| | - Marta Carballa
- CRETUS, Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Juan M Lema
- CRETUS, Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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20
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Fenner K, Men Y. Comment on "Role of Ammonia Oxidation in Organic Micropollutant Transformation during Wastewater Treatment": Overlooked Evidence to the Contrary. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:12128-12129. [PMID: 34405990 DOI: 10.1021/acs.est.1c04178] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- Kathrin Fenner
- Department of Environmental Chemistry, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 Zürich, Switzerland
- Department of Chemistry, University of Zürich, 8057 Zürich, Switzerland
| | - Yujie Men
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside California 92521, United States
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21
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Kennes-Veiga DM, Vogler B, Fenner K, Carballa M, Lema JM. Heterotrophic enzymatic biotransformations of organic micropollutants in activated sludge. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 780:146564. [PMID: 33774287 DOI: 10.1016/j.scitotenv.2021.146564] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/16/2021] [Accepted: 03/14/2021] [Indexed: 06/12/2023]
Abstract
While heterotrophic microorganisms constitute the major fraction of activated sludge biomass, the role of heterotrophs in the biotransformation of organic micropollutants (OMPs) has not been fully elucidated. Yet, such knowledge is essential, particularly when conceiving novel wastewater treatment plants based on a two-stage process including an A-stage under heterotrophic conditions and a B-stage based on anammox activity. Biotransformation of OMPs in activated sludge is thought to mostly occur cometabolically thanks to the action of low specificity enzymes involved in the metabolism of the primary substrates. For a better understanding of the process, it is important to determine such enzymatic activities and the underlying mechanisms involved in OMPs biotransformation. This task has proven to be difficult due to the lack of information about the enzymatic processes and the complexity of the biological systems present in activated sludge. In this paper, a continuous aerobic heterotrophic reactor following 20 OMPs at environmental concentrations was operated to (i) assess the potential of heterotrophs during the cometabolic biotransformation of OMPs, (ii) identify biotransformation reactions catalyzed by aerobic heterotrophs and (iii) predict possible heterotrophic enzymatic activities responsible for such biotransformations. Contradicting previous reports on the dominant role of nitrifiers in OMPs removal during activated sludge treatment, the heterotrophic population proved its capacity to biotransform the OMPs to extents equivalent to reported values in nitrifying activated sludge plants. Besides, 12 transformation products potentially formed through the activity of several enzymes present in heterotrophs, including monooxygenases, dioxygenases, hydrolases and transferases, were identified.
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Affiliation(s)
- David M Kennes-Veiga
- Cretus Institute, Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Galicia, Spain.
| | - Bernadette Vogler
- Swiss Federal Institute of Aquatic Science and Technology, Eawag, 8600 Dübendorf, Switzerland
| | - Kathrin Fenner
- Swiss Federal Institute of Aquatic Science and Technology, Eawag, 8600 Dübendorf, Switzerland; Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 Zürich, Switzerland; Department of Chemistry, University of Zürich, 8057 Zürich, Switzerland
| | - Marta Carballa
- Cretus Institute, Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Galicia, Spain
| | - Juan M Lema
- Cretus Institute, Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Galicia, Spain
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22
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Fenner K, Elsner M, Lueders T, McLachlan MS, Wackett LP, Zimmermann M, Drewes JE. Methodological Advances to Study Contaminant Biotransformation: New Prospects for Understanding and Reducing Environmental Persistence? ACS ES&T WATER 2021; 1:1541-1554. [PMID: 34278380 PMCID: PMC8276273 DOI: 10.1021/acsestwater.1c00025] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 06/11/2021] [Accepted: 06/11/2021] [Indexed: 05/14/2023]
Abstract
Complex microbial communities in environmental systems play a key role in the detoxification of chemical contaminants by transforming them into less active metabolites or by complete mineralization. Biotransformation, i.e., transformation by microbes, is well understood for a number of priority pollutants, but a similar level of understanding is lacking for many emerging contaminants encountered at low concentrations and in complex mixtures across natural and engineered systems. Any advanced approaches aiming to reduce environmental exposure to such contaminants (e.g., novel engineered biological water treatment systems, design of readily degradable chemicals, or improved regulatory assessment strategies to determine contaminant persistence a priori) will depend on understanding the causal links among contaminant removal, the key driving agents of biotransformation at low concentrations (i.e., relevant microbes and their metabolic activities), and how their presence and activity depend on environmental conditions. In this Perspective, we present the current understanding and recent methodological advances that can help to identify such links, even in complex environmental microbiomes and for contaminants present at low concentrations in complex chemical mixtures. We discuss the ensuing insights into contaminant biotransformation across varying environments and conditions and ask how much closer we have come to designing improved approaches to reducing environmental exposure to contaminants.
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Affiliation(s)
- Kathrin Fenner
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 Zürich, Switzerland
- Department of Chemistry, University of Zürich, 8057 Zürich, Switzerland
| | - Martin Elsner
- Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Tillmann Lueders
- Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, 95448 Bayreuth, Germany
| | - Michael S McLachlan
- Department of Environmental Science (ACES), Stockholm University, 106 91 Stockholm, Sweden
| | - Lawrence P Wackett
- Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota 55108, United States
| | - Michael Zimmermann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jörg E Drewes
- Chair of Urban Water Systems Engineering, Technical University of Munich, 85748 Garching, Germany
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23
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Störiko A, Pagel H, Mellage A, Cirpka OA. Does It Pay Off to Explicitly Link Functional Gene Expression to Denitrification Rates in Reaction Models? Front Microbiol 2021; 12:684146. [PMID: 34220770 PMCID: PMC8250433 DOI: 10.3389/fmicb.2021.684146] [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] [Received: 03/22/2021] [Accepted: 04/29/2021] [Indexed: 11/13/2022] Open
Abstract
Environmental omics and molecular-biological data have been proposed to yield improved quantitative predictions of biogeochemical processes. The abundances of functional genes and transcripts relate to the number of cells and activity of microorganisms. However, whether molecular-biological data can be quantitatively linked to reaction rates remains an open question. We present an enzyme-based denitrification model that simulates concentrations of transcription factors, functional-gene transcripts, enzymes, and solutes. We calibrated the model using experimental data from a well-controlled batch experiment with the denitrifier Paracoccous denitrificans. The model accurately predicts denitrification rates and measured transcript dynamics. The relationship between simulated transcript concentrations and reaction rates exhibits strong non-linearity and hysteresis related to the faster dynamics of gene transcription and substrate consumption, relative to enzyme production and decay. Hence, assuming a unique relationship between transcript-to-gene ratios and reaction rates, as frequently suggested, may be an erroneous simplification. Comparing model results of our enzyme-based model to those of a classical Monod-type model reveals that both formulations perform equally well with respect to nitrogen species, indicating only a low benefit of integrating molecular-biological data for estimating denitrification rates. Nonetheless, the enzyme-based model is a valuable tool to improve our mechanistic understanding of the relationship between biomolecular quantities and reaction rates. Furthermore, our results highlight that both enzyme kinetics (i.e., substrate limitation and inhibition) and gene expression or enzyme dynamics are important controls on denitrification rates.
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Affiliation(s)
- Anna Störiko
- Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
| | - Holger Pagel
- Biogeophysics, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Adrian Mellage
- Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
| | - Olaf A. Cirpka
- Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
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24
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Sagova-Mareckova M, Boenigk J, Bouchez A, Cermakova K, Chonova T, Cordier T, Eisendle U, Elersek T, Fazi S, Fleituch T, Frühe L, Gajdosova M, Graupner N, Haegerbaeumer A, Kelly AM, Kopecky J, Leese F, Nõges P, Orlic S, Panksep K, Pawlowski J, Petrusek A, Piggott JJ, Rusch JC, Salis R, Schenk J, Simek K, Stovicek A, Strand DA, Vasquez MI, Vrålstad T, Zlatkovic S, Zupancic M, Stoeck T. Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring. WATER RESEARCH 2021; 191:116767. [PMID: 33418487 DOI: 10.1016/j.watres.2020.116767] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/14/2020] [Accepted: 12/19/2020] [Indexed: 06/12/2023]
Abstract
Bioindication has become an indispensable part of water quality monitoring in most countries of the world, with the presence and abundance of bioindicator taxa, mostly multicellular eukaryotes, used for biotic indices. In contrast, microbes (bacteria, archaea and protists) are seldom used as bioindicators in routine assessments, although they have been recognized for their importance in environmental processes. Recently, the use of molecular methods has revealed unexpected diversity within known functional groups and novel metabolic pathways that are particularly important in energy and nutrient cycling. In various habitats, microbial communities respond to eutrophication, metals, and natural or anthropogenic organic pollutants through changes in diversity and function. In this review, we evaluated the common trends in these changes, documenting that they have value as bioindicators and can be used not only for monitoring but also for improving our understanding of the major processes in lotic and lentic environments. Current knowledge provides a solid foundation for exploiting microbial taxa, community structures and diversity, as well as functional genes, in novel monitoring programs. These microbial community measures can also be combined into biotic indices, improving the resolution of individual bioindicators. Here, we assess particular molecular approaches complemented by advanced bioinformatic analysis, as these are the most promising with respect to detailed bioindication value. We conclude that microbial community dynamics are a missing link important for our understanding of rapid changes in the structure and function of aquatic ecosystems, and should be addressed in the future environmental monitoring of freshwater ecosystems.
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Affiliation(s)
- M Sagova-Mareckova
- Dept. of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamýcká 129, Prague 6, 16500, Czechia.
| | - J Boenigk
- Biodiversity, University of Duisburg-Essen, Universitaetsstraße 5, 45141 Essen, Germany
| | - A Bouchez
- UMR CARRTEL, INRAE, UMR Carrtel, 75 av. de Corzent, FR-74203 Thonon les Bains cedex, France; University Savoie Mont-Blanc, UMR CARRTEL, FR-73370 Le Bourget du Lac, France
| | - K Cermakova
- ID-Gene Ecodiagnostics, Campus Biotech Innovation Park, 15, av. Sécheron, 1202 Geneva, Switzerland
| | - T Chonova
- UMR CARRTEL, INRAE, UMR Carrtel, 75 av. de Corzent, FR-74203 Thonon les Bains cedex, France; University Savoie Mont-Blanc, UMR CARRTEL, FR-73370 Le Bourget du Lac, France
| | - T Cordier
- Department of Genetics and Evolution, University of Geneva, Science III, 4 Boulevard d'Yvoy, 1205 Geneva, Switzerland
| | - U Eisendle
- University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria
| | - T Elersek
- National Institute of Biology, Vecna pot 111, SI-1000 Ljubljana, Slovenia
| | - S Fazi
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Via Salaria km 29,300 - C.P. 10, 00015 Monterotondo St., Rome, Italy
| | - T Fleituch
- Institute of Nature Conservation, Polish Academy of Sciences, ul. Adama Mickiewicza 33, 31-120 Krakow, Poland
| | - L Frühe
- Ecology Group, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - M Gajdosova
- Dept. of Ecology, Faculty of Science, Charles University, Viničná 7, 12844 Prague, Czechia
| | - N Graupner
- Biodiversity, University of Duisburg-Essen, Universitaetsstraße 5, 45141 Essen, Germany
| | - A Haegerbaeumer
- Dept. of Animal Ecology, Bielefeld University, Konsequenz 45, 33615 Bielefeld, Germany
| | - A-M Kelly
- School of Natural Sciences, Trinity College Dublin, University of Dublin, College Green, Dublin 2, D02 PN40, Ireland
| | - J Kopecky
- Epidemiology and Ecology of Microoganisms, Crop Research Institute, Drnovská 507, 16106 Prague 6, Czechia
| | - F Leese
- Biodiversity, University of Duisburg-Essen, Universitaetsstraße 5, 45141 Essen, Germany; Aquatic Ecosystem Resarch, University of Duisburg-Essen, Universitaetsstrasse 5 D-45141 Essen, Germany
| | - P Nõges
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5, Tartu 51006, Estonia
| | - S Orlic
- Institute Ruđer Bošković, Bijenička 54, 10000 Zagreb, Croatia; Center of Excellence for Science and Technology Integrating Mediterranean, Bijenička 54,10 000 Zagreb, Croatia
| | - K Panksep
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5, Tartu 51006, Estonia
| | - J Pawlowski
- ID-Gene Ecodiagnostics, Campus Biotech Innovation Park, 15, av. Sécheron, 1202 Geneva, Switzerland; Department of Genetics and Evolution, University of Geneva, Science III, 4 Boulevard d'Yvoy, 1205 Geneva, Switzerland; Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
| | - A Petrusek
- Dept. of Ecology, Faculty of Science, Charles University, Viničná 7, 12844 Prague, Czechia
| | - J J Piggott
- School of Natural Sciences, Trinity College Dublin, University of Dublin, College Green, Dublin 2, D02 PN40, Ireland
| | - J C Rusch
- Norwegian Veterinary Institute, P.O. Box 750, Sentrum, NO-0106 Oslo, Norway; Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway
| | - R Salis
- Department of Biology, Faculty of Science, Lund University, Sölvegatan 37, 223 62 Lund, Sweden
| | - J Schenk
- Dept. of Animal Ecology, Bielefeld University, Konsequenz 45, 33615 Bielefeld, Germany
| | - K Simek
- Institute of Hydrobiology, Biology Centre CAS, Branišovská 31, 370 05 České Budějovice, Czechia
| | - A Stovicek
- Dept. of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamýcká 129, Prague 6, 16500, Czechia
| | - D A Strand
- Norwegian Veterinary Institute, P.O. Box 750, Sentrum, NO-0106 Oslo, Norway
| | - M I Vasquez
- Department of Chemical Engineering, Cyprus University of Technology, 30 Arch. Kyprianos Str., 3036 Limassol, Cyprus
| | - T Vrålstad
- Norwegian Veterinary Institute, P.O. Box 750, Sentrum, NO-0106 Oslo, Norway
| | - S Zlatkovic
- Ministry of Environmental Protection, Omladinskih brigada 1, 11070 Belgrade, Serbia; Agency "Akvatorija", 11. krajiške divizije 49, 11090 Belgrade, Serbia
| | - M Zupancic
- National Institute of Biology, Vecna pot 111, SI-1000 Ljubljana, Slovenia
| | - T Stoeck
- Ecology Group, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany
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25
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Su Q, Schittich AR, Jensen MM, Ng H, Smets BF. Role of Ammonia Oxidation in Organic Micropollutant Transformation during Wastewater Treatment: Insights from Molecular, Cellular, and Community Level Observations. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:2173-2188. [PMID: 33543927 DOI: 10.1021/acs.est.0c06466] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Organic micropollutants (OMPs) are a threat to aquatic environments, and wastewater treatment plants may act as a source or a barrier of OMPs entering the environment. Understanding the fate of OMPs in wastewater treatment processes is needed to establish efficient OMP removal strategies. Enhanced OMP biotransformation has been documented during biological nitrogen removal and has been attributed to the cometabolic activity of ammonia-oxidizing bacteria (AOB) and, specifically, to the ammonia monooxygenase (AMO) enzyme. Yet, the exact mechanisms of OMP biotransformation are often unknown. This critical review aims to fundamentally and quantitatively evaluate the role of ammonia oxidation in OMP biotransformation during wastewater treatment processes. OMPs can be transformed by AOB via direct and indirect enzymatic reactions: AMO directly transforms OMPs primarily via hydroxylation, while biologically produced reactive nitrogen species (hydroxylamine (NH2OH), nitrite (NO2-), and nitric oxide (NO)) can chemically transform OMPs through nitration, hydroxylation, and deamination and can contribute significantly to the observed OMP transformations. OMPs containing alkyl, aliphatic hydroxyl, ether, and sulfide functional groups as well as substituted aromatic rings and aromatic primary amines can be biotransformed by AMO, while OMPs containing alkyl groups, phenols, secondary amines, and aromatic primary amines can undergo abiotic transformations mediated by reactive nitrogen species. Higher OMP biotransformation efficiencies and rates are obtained in AOB-dominant microbial communities, especially in autotrophic reactors performing nitrification or nitritation, than in non-AOB-dominant microbial communities. The biotransformations of OMPs in wastewater treatment systems can often be linked to ammonium (NH4+) removal following two central lines of evidence: (i) Similar transformation products (i.e., hydroxylated, nitrated, and desaminated TPs) are detected in wastewater treatment systems as in AOB pure cultures. (ii) Consistency in OMP biotransformation (rbio, μmol/g VSS/d) to NH4+ removal (rNH4+, mol/g VSS/d) rate ratios (rbio/rNH4+) is observed for individual OMPs across different systems with similar rNH4+ and AOB abundances. In this review, we conclude that AOB are the main drivers of OMP biotransformation during wastewater treatment processes. The importance of biologically driven abiotic OMP transformation is quantitatively assessed, and functional groups susceptible to transformations by AMO and reactive nitrogen species are systematically classified. This critical review will improve the prediction of OMP transformation and facilitate the design of efficient OMP removal strategies during wastewater treatment.
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Affiliation(s)
- Qingxian Su
- National University of Singapore Environmental Research Institute, 5A Engineering Drive 1, 117411 Singapore, Singapore
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark
| | - Anna-Ricarda Schittich
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark
| | - Marlene Mark Jensen
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark
| | - Howyong Ng
- National University of Singapore Environmental Research Institute, 5A Engineering Drive 1, 117411 Singapore, Singapore
- Centre for Water Research, Department of Civil & Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, 117576 Singapore, Singapore
| | - Barth F Smets
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark
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26
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Wu G, Geng J, Xu K, Ren H. Removal of pharmaceuticals by ammonia oxidizers during nitrification. Appl Microbiol Biotechnol 2021; 105:909-921. [PMID: 33415368 DOI: 10.1007/s00253-020-11032-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 11/16/2020] [Accepted: 11/23/2020] [Indexed: 01/25/2023]
Abstract
The adverse effect of pharmaceuticals on ecosystem and human health raises great interest for the removal of pharmaceuticals in wastewater treatment plants (WWTPs). Enhanced removal of pharmaceuticals by ammonia oxidizers (AOs) has been observed during nitrification. This review provides a comprehensive summary on the removal of pharmaceuticals by AOs-ammonia oxidizing bacteria (AOB), ammonia oxidizing archaea (AOA), and complete ammonia oxidizer (comammox) during nitrification in pure ammonia oxidizing culture and mixed microbes systems. The superior removal of pharmaceuticals by AOs in conditions with nitrifying activity compared with the conditions without nitrifying activity was proposed. The contribution of AOs on pharmaceuticals removal in pure and mixed microbe systems was discussed and activated sludge modeling was suggested as the proper measure on assessing the contribution of AOs on the removal of pharmaceuticals in mixed microbe culture. Three transformation processes and the involved reaction types of pharmaceuticals transformation during nitrification were reviewed. The present paper provides a systematical summary on pharmaceuticals removal by different AOs across pure and mixed microbes culture during nitrification, which opens up the opportunity to optimize the wastewater biological treatment systems for enhanced removal of pharmaceuticals. KEY POINTS: • The superior removal of pharmaceuticals by ammonia oxidizers (AOs) was summarized. • The removal contribution of pharmaceuticals attributed by AOs was elucidated. • The transformation processes and reaction types of pharmaceuticals were discussed.
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Affiliation(s)
- Gang Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, Jiangsu, People's Republic of China
| | - Jinju Geng
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, Jiangsu, People's Republic of China.
| | - Ke Xu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, Jiangsu, People's Republic of China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, Jiangsu, People's Republic of China
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27
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Nguyen PY, Carvalho G, Reis MAM, Oehmen A. A review of the biotransformations of priority pharmaceuticals in biological wastewater treatment processes. WATER RESEARCH 2021; 188:116446. [PMID: 33038717 DOI: 10.1016/j.watres.2020.116446] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 08/19/2020] [Accepted: 09/22/2020] [Indexed: 05/18/2023]
Abstract
Wastewater effluent discharges have been considered as one of the main sources of synthetic chemicals entering into the aquatic environment. Even though they occur at low concentrations, pharmaceutically active compounds (PhACs) can have an impact on ecological toxicity that affects aquatic organisms. Moreover, new regulations in development toward preserving water quality reinforces the increasing need to monitor and abate some PhACs in wastewater treatment plants (WWTPs), where they are typically only partially eliminated. Unlike most previous reviews, we have focussed on how the main biological and chemical molecular factors impact the biotransformations of key PhACs in biological WWTP processes. Biotransformations have been found to be an important contributor towards the removal of PhACs from WWTP effluents. This review paper critically assesses these aspects and the recent advances that have been achieved in wastewater treatment processes for biodegradation of 7 PhACs; namely the non-steroidal anti-inflammatory drug (NSAID) diclofenac (DCF); the macrolide antibiotics azithromycin (AZM), erythromycin (ERY) and clarithromycin (CLR); the two natural estrogens estrone (E1) and 17β-estradiol (E2), and the synthetic estrogen 17α-ethinylesradiol (EE2). These represent the micropollutants of the EU Watch list in Decision 2015/495/EU that are most relevant to WWTPs due to their frequent detection. The metabolic pathways, transformation products and impact of relevant factors to biological WWTP processes is addressed in this review. The biokinetics of PhAC biodegradation in different engineered bioprocesses is also discussed. Promising technologies and operational strategies that are likely to have a high impact on controlling PhAC releases are highlighted and future research needs are also proposed.
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Affiliation(s)
- P Y Nguyen
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
| | - Gilda Carvalho
- Advanced Water Management Centre, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Maria A M Reis
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Adrian Oehmen
- School of Chemical Engineering, The University of Queensland, Brisbane, QLD, 4072, Australia.
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