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Holert J, Borker A, Nübel LL, Daniel R, Poehlein A, Philipp B. Bacteria use a catabolic patchwork pathway of apparently recent origin for degradation of the synthetic buffer compound TRIS. THE ISME JOURNAL 2024; 18:wrad023. [PMID: 38365256 PMCID: PMC10848231 DOI: 10.1093/ismejo/wrad023] [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: 09/07/2023] [Revised: 11/28/2023] [Accepted: 12/06/2023] [Indexed: 02/18/2024]
Abstract
The synthetic buffer compound TRIS (2-amino-2-(hydroxymethyl)propane-1,3-diol) is used in countless applications, and no detailed information on its degradation has been published so far. Herein, we describe the discovery of a complete bacterial degradation pathway for TRIS. By serendipity, a Pseudomonas strain was isolated from sewage sludge that was able to grow with TRIS as only carbon and nitrogen source. Genome and transcriptome analyses revealed two adjacent gene clusters embedded in a mobile genetic element on a conjugative plasmid to be involved in TRIS degradation. Heterologous gene expression revealed cluster I to encode a TRIS uptake protein, a TRIS alcohol dehydrogenase, and a TRIS aldehyde dehydrogenase, catalyzing the oxidation of TRIS into 2-hydroxymethylserine. Gene cluster II encodes a methylserine hydroxymethyltransferase (mSHMT) and a d-serine dehydratase that plausibly catalyze the conversion of 2-hydroxymethylserine into pyruvate. Conjugational plasmid transfer into Pseudomonas putida KT2440 enabled this strain to grow with TRIS and with 2-hydromethylserine, demonstrating that the complete TRIS degradation pathway can be transmitted by horizontal gene transfer. Subsequent enrichments from wastewater purification systems led to the isolation of further TRIS-degrading bacteria from the Pseudomonas and Shinella genera carrying highly similar TRIS degradation gene clusters. Our data indicate that TRIS degradation evolved recently via gene recruitment and enzyme adaptation from multiple independent metabolic pathways, and database searches suggest that the TRIS degradation pathway is now globally distributed. Overall, our study illustrates how engineered environments can enhance the emergence of new microbial metabolic pathways in short evolutionary time scales.
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Affiliation(s)
- Johannes Holert
- Institute for Molecular Microbiology and Biotechnology, Microbial Biotechnology & Ecology Group, University of Münster, Münster, D-48149, Germany
| | - Aron Borker
- Institute for Molecular Microbiology and Biotechnology, Microbial Biotechnology & Ecology Group, University of Münster, Münster, D-48149, Germany
| | - Laura Lucia Nübel
- Institute for Molecular Microbiology and Biotechnology, Microbial Biotechnology & Ecology Group, University of Münster, Münster, D-48149, Germany
| | - Rolf Daniel
- Institute for Microbiology and Genetics, University of Göttingen, Göttingen, D-37077, Germany
| | - Anja Poehlein
- Institute for Microbiology and Genetics, University of Göttingen, Göttingen, D-37077, Germany
| | - Bodo Philipp
- Institute for Molecular Microbiology and Biotechnology, Microbial Biotechnology & Ecology Group, University of Münster, Münster, D-48149, Germany
- Environmental Microbiology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, D-57392, Germany
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Ammeri RW, Kouki S, Hassen W, Oueslati M, Sadfi-Zouaoui N, Hassen A. Bioaugmentation and phytoremediation wastewater treatment process as a viable alternative for pesticides removal: case of pentachlorophenol. JOURNAL OF ENVIRONMENTAL HEALTH SCIENCE & ENGINEERING 2023; 21:373-387. [PMID: 37869599 PMCID: PMC10584799 DOI: 10.1007/s40201-023-00865-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 05/22/2023] [Indexed: 10/24/2023]
Abstract
This study focused on the potential for pentachlorophenol removal by a biological process in secondary treated wastewater (STWW). The proposed process is a combined method of phytoremediation using a native plant, Polypogon maritimus and Lemna minor, and bioaugmentation using a fungus. The bioaugmentation process was performed by a fungal isolate capable of removing PCP, isolated from the compost. The identification of the fungus was performed by morphological, biochemical, and molecular methods. A biological treatment system by bioaugmentation and phytoremediation was set up to estimate the capacity of this process to eliminate a high concentration of PCP. physico-chemical parameters, such as pH, COD, and BOD were tested at experimentation times T0 (initial) and Tf (final). The concentration of PCP is controlled by the HPLC method. Thus, the growth of the fungus was determined by spectrophotometry and enumeration on the agar medium. The results obtained show that the isolated and selected fungus is identified by Penicillium Ilerdanum. The fungal strain used has a significant capacity for tolerance and elimination of PCP. The results of the physico-chemical parameters showed an improvement in the quality of wastewater after the treatment was carried out. The elimination of PCP came with a release of Common law- and an important decrease in the DOC value in the STWW. The results obtained show that the Polypogon treatment shows a significant elimination of PCP by a percentage of the order of 92.01% and 23.58 g. L- 1 chloride concentration. The macrophytes used showed a better ability to tolerate and eliminate PCP with an increase of chlorophyll and its longer sheets. Supplementary Information The online version contains supplementary material available at 10.1007/s40201-023-00865-y.
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Affiliation(s)
- Rim Werheni Ammeri
- Laboratory of Treatment and Wastewater Valorization, Water Research and Technology Center (CERTE), Techno Park Borj-Cédria, B.P. 273, Soliman, 8020 Tunisia
- National Bone Marrow Transplant Center, Laboratory Ward, Tunis Rue Djebel Lakhdar 1006, Tunis, Tunisia
| | - Soulwene Kouki
- Laboratory of Treatment and Wastewater Valorization, Water Research and Technology Center (CERTE), Techno Park Borj-Cédria, B.P. 273, Soliman, 8020 Tunisia
| | - Wafa Hassen
- Research Unit of Analysis and Process Applied to the Environmental—APAE Higher Institute of Applied Sciences and Technology Mahdia, the University of Monastir, Monastir, Tunisia
| | - Maroua Oueslati
- Laboratory of Mycology, Pathologies and Biomarkers LR16ES05, Faculty of Sciences of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Najla Sadfi-Zouaoui
- Laboratory of Mycology, Pathologies and Biomarkers LR16ES05, Faculty of Sciences of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Abdennaceur Hassen
- Laboratory of Treatment and Wastewater Valorization, Water Research and Technology Center (CERTE), Techno Park Borj-Cédria, B.P. 273, Soliman, 8020 Tunisia
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3
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Bhatt P, Bhatt K, Huang Y, Li J, Wu S, Chen S. Biofilm formation in xenobiotic-degrading microorganisms. Crit Rev Biotechnol 2023; 43:1129-1149. [PMID: 36170978 DOI: 10.1080/07388551.2022.2106417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/26/2022] [Indexed: 11/03/2022]
Abstract
The increased presence of xenobiotics affects living organisms and the environment at large on a global scale. Microbial degradation is effective for the removal of xenobiotics from the ecosystem. In natural habitats, biofilms are formed by single or multiple populations attached to biotic/abiotic surfaces and interfaces. The attachment of microbial cells to these surfaces is possible via the matrix of extracellular polymeric substances (EPSs). However, the molecular machinery underlying the development of biofilms differs depending on the microbial species. Biofilms act as biocatalysts and degrade xenobiotic compounds, thereby removing them from the environment. Quorum sensing (QS) helps with biofilm formation and is linked to the development of biofilms in natural contaminated sites. To date, scant information is available about the biofilm-mediated degradation of toxic chemicals from the environment. Therefore, we review novel insights into the impact of microbial biofilms in xenobiotic contamination remediation, the regulation of biofilms in contaminated sites, and the implications for large-scale xenobiotic compound treatment.
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Affiliation(s)
- Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, PR China
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, IN, USA
| | - Kalpana Bhatt
- Department of Food Science, Purdue University, West Lafayette, IN, USA
| | - Yaohua Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, PR China
| | - Jiayi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, PR China
| | - Siyi Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, PR China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, PR China
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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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Esikova TZ, Anokhina TO, Suzina NE, Shushkova TV, Wu Y, Solyanikova IP. Characterization of a New Pseudomonas Putida Strain Ch2, a Degrader of Toxic Anthropogenic Compounds Epsilon-Caprolactam and Glyphosate. Microorganisms 2023; 11:microorganisms11030650. [PMID: 36985223 PMCID: PMC10053300 DOI: 10.3390/microorganisms11030650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/24/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
In this work, a new Ch2 strain was isolated from soils polluted by agrochemical production wastes. This strain has a unique ability to utilize toxic synthetic compounds such as epsilon-caprolactam (CAP) as a sole carbon and energy source and the herbicide glyphosate (GP) as a sole source of phosphorus. Analysis of the nucleotide sequence of the 16S rRNA gene of Ch2 revealed that the strain belongs to the species Pseudomonas putida. This strain grew in the mineral medium containing CAP in a concentration range of 0.5 to 5.0 g/L and utilized 6-aminohexanoic acid and adipic acid, which are the intermediate products of CAP catabolism. The ability of strain Ch2 to degrade CAP is determined by a conjugative megaplasmid that is 550 kb in size. When strain Ch2 is cultured in a mineral medium containing GP (500 mg/L), more intensive utilization of the herbicide occurs in the phase of active growth. In the phase of declining growth, there is an accumulation of aminomethylphosphonic acid, which indicates that the C-N bond is the first site cleaved during GP degradation (glyphosate oxidoreductase pathway). Culture growth in the presence of GP during the early step of its degradation is accompanied by unique substrate-dependent changes in the cytoplasm, including the formation of vesicles of cytoplasmic membrane consisting of specific electron-dense content. There is a debate about whether these membrane formations are analogous to metabolosomes, where the primary degradation of the herbicide can take place. The studied strain is notable for its ability to produce polyhydroxyalkanoates (PHAs) when grown in mineral medium containing GP. At the beginning of the stationary growth phase, it was shown that, the amount and size of PHA inclusions in the cells drastically increased; they filled almost the entire volume of cell cytoplasm. The obtained results show that the strain P. putida Ch2 can be successfully used for the PHAs’ production. Moreover, the ability of P. putida Ch2 to degrade CAP and GP determines the prospects of its application for the biological cleanup of CAP production wastes and in situ bioremediation of soil polluted with GP.
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Affiliation(s)
- Tatiana Z. Esikova
- Laboratory of Plasmid Biology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Center for Biological Research of the Russian Academy of Sciences, Prosp. Nauki 5, Pushchino, 142290 Pushchino, Russia
| | - Tatiana O. Anokhina
- Laboratory of Plasmid Biology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Center for Biological Research of the Russian Academy of Sciences, Prosp. Nauki 5, Pushchino, 142290 Pushchino, Russia
| | - Nataliya E. Suzina
- Laboratory of Cytology of Microorganisms, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Prosp. Nauki 5, Pushchino, 142290 Pushchino, Russia
| | - Tatiana V. Shushkova
- Laboratory of Microbial Enzymology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Center for Biological Research of the Russian Academy of Sciences, Prosp. Nauki 5, Pushchino, 142290 Pushchino, Russia
| | - Yonghong Wu
- Zigui Ecological Station for Three Gorges Dam Project, State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China
| | - Inna P. Solyanikova
- Laboratory of Microbial Enzymology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Center for Biological Research of the Russian Academy of Sciences, Prosp. Nauki 5, Pushchino, 142290 Pushchino, Russia
- Regional Microbiological Center, Institute of Pharmacy, Chemistry and Biology, Belgorod National Research University, 308015 Belgorod, Russia
- Correspondence:
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6
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Lu Q, Zhao R, Li Q, Ma Y, Chen J, Yu Q, Zhao D, An S. Elemental composition and microbial community differences between wastewater treatment plant effluent and local natural surface water: A Zhengzhou city study. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 325:116398. [PMID: 36244289 DOI: 10.1016/j.jenvman.2022.116398] [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: 07/07/2022] [Revised: 09/06/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Wastewater treatment plant (WWTP) effluent is discharged into rivers as supplemental water, which may result in ecological risk. This study compares the element composition and microbial community of WWTP effluent and natural surface water (NSW) and reveals the potential ecological risk of WWTP effluent discharge. Twenty recently upgraded WWTPs and three relatively large reservoirs in Zhengzhou city, China, were selected. The contents of N, P, S, K, Ca, Mg, B, Si, Na, Fe, Mn, Co, Ni and Sn were significantly higher in WWTP effluent than in NSW, while those of Mo, V, Pb and Cd were significantly lower. There was no significant difference between WWTP effluent and NSW in terms of the element imbalance index (IMI) (representing the extent of imbalance of element proportions) relative to the class IV surface water quality standard (the control standard for most Chinese rivers). The macronutrient IMI relative to the Hoagland formula was significantly lower in WWTP effluent than in NSW, and WWTP effluent discharge could significantly lower this index in NSW; this may be an important cause of primary productivity explosion. The microbial diversity was significantly higher in WWTP effluent than in NSW. The predicted relative abundances of mobile genetic elements and oxidative-stress-tolerant phenotypes were significantly higher in WWTP effluent than in NSW, whereas the abundance of gram-negative phenotypes was significantly lower, and that of potential pathogenic phenotypes was slightly lower. The effluent from upgraded WWTPs exhibited a low risk of pathogen diffusion but a high risk of antibiotic resistance gene diffusion. The element composition and microbial community should be considered when evaluating the ecological risk of WWTP effluent discharge.
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Affiliation(s)
- Qianqian Lu
- Department of Biological Science and Technology, Nanjing University, Nanjing, 210093, PR China
| | - Ran Zhao
- Department of Biological Science and Technology, Nanjing University, Nanjing, 210093, PR China
| | - Qiming Li
- Department of Biological Science and Technology, Nanjing University, Nanjing, 210093, PR China
| | - Yu Ma
- Department of Biological Science and Technology, Nanjing University, Nanjing, 210093, PR China
| | - Jing Chen
- Department of Biological Science and Technology, Nanjing University, Nanjing, 210093, PR China
| | - Qi Yu
- Department of Biological Science and Technology, Nanjing University, Nanjing, 210093, PR China
| | - Dehua Zhao
- Department of Biological Science and Technology, Nanjing University, Nanjing, 210093, PR China.
| | - Shuqing An
- Department of Biological Science and Technology, Nanjing University, Nanjing, 210093, PR China
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7
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Zhao W, You J, Yin S, Yang H, He S, Feng L, Li J, Zhao Q, Wei L. Extracellular polymeric substances-antibiotics interaction in activated sludge: A review. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2023; 13:100212. [PMID: 36425126 PMCID: PMC9678949 DOI: 10.1016/j.ese.2022.100212] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 05/09/2023]
Abstract
Antibiotics, the most frequently prescribed drugs, have been widely applied to prevent or cure human and veterinary diseases and have undoubtedly led to massive releases into sewer networks and wastewater treatment systems, a hotspot where the occurrence and transformation of antibiotic resistance take place. Extracellular polymeric substances (EPS), biopolymers secreted via microbial activity, play an important role in cell adhesion, nutrient retention, and toxicity resistance. However, the potential roles of sludge EPS related to the resistance and removal of antibiotics are still unclear. This work summarizes the composition and physicochemical characteristics of state-of-the-art microbial EPS, highlights the critical role of EPS in antibiotics removal, evaluates their defense performances under different antibiotics exposures, and analyzes the typical factors that could affect the sorption and biotransformation behavior of antibiotics. Next, interactions between microbial EPS and antibiotic resistance genes are analyzed. Future perspectives, especially the engineering application of microbial EPS for antibiotics toxicity detection and defense, are also emphatically stressed.
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8
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Li J, Wang Y, Guo F, Chen J, Wang J, Fan X, Li B, Verma SK, Wei Q, Yan L, Wu J. Efficient catalytic degradation of methylene blue by a novel Fe 3+-TiO 2@CGS three-dimensional photoelectric system. Front Chem 2022; 10:1065003. [PMID: 36561145 PMCID: PMC9763565 DOI: 10.3389/fchem.2022.1065003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
In this study, a novel three-dimensional photoelectric system was designed and constructed for the degradation of methylene blue (MB) via photocatalysis, electrocatalysis, and photoelectric catalysis. To this end, a Ti/RuO2-IrO2-SnO2-CeO2 electrode was prepared via a thermal oxidation coating method and used as a dimensionally-stable anode (DSA). The cathode was made of a titanium sheet with Fe3+-doped TiO2 loaded on coal gasification slag (CGS) (Fe3+-TiO2@CGS) as a photocatalyst. The factors affecting the degradation efficiency, such as the supporting electrolyte, current density, and initial pH were systematically investigated. The results revealed Fe3+-TiO2@CGS three-dimensional photoelectric system exhibiting efficient synergistic performance of photocatalysis and electrocatalysis with a synergistic factor of 1.11. Photo-generated holes (h+) were generated by light irradiation and direct anodic oxidation. Furthermore, hydroxyl radicals (HO·) radicals were induced via other pathways. Such active species showed highly-oxidizing abilities, beneficial to the degradation of methylene blue (MB). The representative Fe3+-TiO2@CGS three-dimensional photoelectric system showed super high degradation efficiency at pH 11 and current density of 18.76 mA cm-2. Using NaCl as a supporting electrolyte, the degradation yield reached 99.98% after 60 min of photoelectrical treatment. Overall, the novel Fe3+-TiO2@CGS three-dimensional photoelectrical system looks very promising for the highly efficient catalytic degradation of organic contaminants.
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Affiliation(s)
- Jian Li
- School of Chemical Engineering and Technology, National Engineering Research Center of Coal Preparation and Purification, China University of Mining and Technology, Xuzhou, China,School of Chemistry and Chemical Engineering, Yulin University, Yulin, China
| | - Yufei Wang
- School of Chemical Engineering and Technology, National Engineering Research Center of Coal Preparation and Purification, China University of Mining and Technology, Xuzhou, China,School of Chemistry and Chemical Engineering, Yulin University, Yulin, China
| | - Fanhui Guo
- School of Chemical Engineering and Technology, National Engineering Research Center of Coal Preparation and Purification, China University of Mining and Technology, Xuzhou, China
| | - Juan Chen
- School of Chemical Engineering and Technology, National Engineering Research Center of Coal Preparation and Purification, China University of Mining and Technology, Xuzhou, China,School of Chemistry and Chemical Engineering, Yulin University, Yulin, China
| | - Jinxi Wang
- School of Chemical Engineering and Technology, National Engineering Research Center of Coal Preparation and Purification, China University of Mining and Technology, Xuzhou, China,School of Chemistry and Chemical Engineering, Yulin University, Yulin, China
| | - Xiaoyong Fan
- School of Chemistry and Chemical Engineering, Yulin University, Yulin, China
| | - Baoning Li
- School of Chemistry and Chemical Engineering, Yulin University, Yulin, China
| | - Santosh Kumar Verma
- School of Chemistry and Chemical Engineering, Yulin University, Yulin, China
| | - Qingbo Wei
- School of Chemistry and Chemical Engineering, Yan’an University, Yan’an, China
| | - Long Yan
- School of Chemistry and Chemical Engineering, Yulin University, Yulin, China,*Correspondence: Long Yan, ; Jianjun Wu,
| | - Jianjun Wu
- School of Chemical Engineering and Technology, National Engineering Research Center of Coal Preparation and Purification, China University of Mining and Technology, Xuzhou, China,*Correspondence: Long Yan, ; Jianjun Wu,
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9
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Insights into the toxicity and biodegradation of fipronil in contaminated environment. Microbiol Res 2022; 266:127247. [DOI: 10.1016/j.micres.2022.127247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 10/21/2022] [Accepted: 10/26/2022] [Indexed: 11/05/2022]
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10
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Yaashikaa PR, Devi MK, Kumar PS. Engineering microbes for enhancing the degradation of environmental pollutants: A detailed review on synthetic biology. ENVIRONMENTAL RESEARCH 2022; 214:113868. [PMID: 35835162 DOI: 10.1016/j.envres.2022.113868] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/28/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Anthropogenic activities resulted in the deposition of huge quantities of contaminants such as heavy metals, dyes, hydrocarbons, etc into an ecosystem. The serious ill effects caused by these pollutants to all living organisms forced in advancement of technology for degrading or removing these pollutants. This degrading activity is mostly depending on microorganisms owing to their ability to survive in harsh adverse conditions. Though native strains possess the capability to degrade these pollutants the development of genetic engineering and molecular biology resulted in engineering approaches that enhanced the efficiency of microbes in degrading pollutants at faster rate. Many bioinformatics tools have been developed for altering/modifying genetic content in microbes to increase their degrading potency. This review provides a detailed note on engineered microbes - their significant importance in degrading environmental contaminants and the approaches utilized for modifying microbes. The genes responsible for degrading the pollutants have been identified and modified fir increasing the potential for quick degradation. The methods for increasing the tolerance in engineered microbes have also been discussed. Thus engineered microbes prove to be effective alternate compared to native strains for degrading pollutants.
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Affiliation(s)
- P R Yaashikaa
- Department of Biotechnology, Saveetha School of Engineering, SIMATS, Chennai, 602105, India
| | - M Keerthana Devi
- Department of Biotechnology, Saveetha School of Engineering, SIMATS, Chennai, 602105, India
| | - P Senthil Kumar
- Department of Chemical Engineering, Sri Sivasubramaniya Nadar College of Engineering, Chennai, 603110, India; Centre of Excellence in Water Research (CEWAR), Sri Sivasubramaniya Nadar College of Engineering, Chennai, 603110, India.
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11
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Bhatt P, Bhandari G, Bhatt K, Simsek H. Microalgae-based removal of pollutants from wastewaters: Occurrence, toxicity and circular economy. CHEMOSPHERE 2022; 306:135576. [PMID: 35803375 DOI: 10.1016/j.chemosphere.2022.135576] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/06/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
The natural and anthropogenic sources of water bodies are contaminated with diverse categories of pollutants such as antibiotics, pharmaceuticals, pesticides, heavy metals, organic compounds, and other industrial chemicals. Depending on the type and the origin of the pollutants, the degree of contamination can be categorized into lower to higher concentrations. Therefore, the removal of hazardous chemicals from the environment is an important aspect. The physical, chemical and biological approaches have been developed and implemented to treat wastewaters. The microbial and algal treatment methods have emerged as a growing field due to their eco-friendly and sustainable approach. Particularly, microalgae emerged as a potential organism for the treatment of contaminated water bodies. The microalgae of the genera Chlorella, Anabaena, Ankistrodesmus, Aphanizomenon, Arthrospira, Botryococcus, Chlamydomonas, Chlorogloeopsis, Dunaliella, Haematococcus, Isochrysis, Nannochloropsis, Porphyridium, Synechococcus, Scenedesmus, and Spirulina reported for the wastewater treatment and biomass production. Microalgae have the potential for adsorption, bioaccumulation, and biodegradation. The microalgal strains can mitigate the hazardous chemicals via their diverse cellular mechanisms. Applications of the microalgae strains were found to be effective for sustainable developments and circular economy due to the production of biomass with the utilization of pollutants.
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Affiliation(s)
- Pankaj Bhatt
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, IN, 47906, USA.
| | - Geeta Bhandari
- Department of Biosciences, Swami Rama Himalayan University, Dehradun, 248016, India
| | - Kalpana Bhatt
- Department of Food Science, Purdue University, West Lafayette, IN, USA
| | - Halis Simsek
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, IN, 47906, USA.
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Castro-Gutierrez V, Fuller E, Garcillán-Barcia MP, Helgason T, Hassard F, Moir J. Dissemination of metaldehyde catabolic pathways is driven by mobile genetic elements in Proteobacteria. Microb Genom 2022; 8. [DOI: 10.1099/mgen.0.000881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bioremediation of metaldehyde from drinking water using metaldehyde-degrading strains has recently emerged as a promising alternative. Whole-genome sequencing was used to obtain full genomes for metaldehyde degraders
Acinetobacter calcoaceticus
E1 and
Sphingobium
CMET-H. For the former, the genetic context of the metaldehyde-degrading genes had not been explored, while for the latter, none of the degrading genes themselves had been identified. In
A. calcoaceticus
E1, IS91 and IS6-family insertion sequences (ISs) were found surrounding the metaldehyde-degrading gene cluster located in plasmid pAME76. This cluster was located in closely-related plasmids and associated to identical ISs in most metaldehyde-degrading β- and γ-Proteobacteria, indicating horizontal gene transfer (HGT). For
Sphingobium
CMET-H, sequence analysis suggested a phytanoyl-CoA family oxygenase as a metaldehyde-degrading gene candidate due to its close homology to a previously identified metaldehyde-degrading gene known as mahX. Heterologous gene expression in
Escherichia coli
alongside degradation tests verified its functional significance and the degrading gene homolog was henceforth called mahS. It was found that mahS is hosted within the conjugative plasmid pSM1 and its genetic context suggested a crossover between the metaldehyde and acetoin degradation pathways. Here, specific replicons and ISs responsible for maintaining and dispersing metaldehyde-degrading genes in α, β and γ-Proteobacteria through HGT were identified and described. In addition, a homologous gene implicated in the first step of metaldehyde utilisation in an α-Proteobacteria was uncovered. Insights into specific steps of this possible degradation pathway are provided.
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Affiliation(s)
- Víctor Castro-Gutierrez
- Environmental Pollution Research Center (CICA), University of Costa Rica, Montes de Oca, 11501, Costa Rica
- Cranfield University, College Road, Cranfield, Bedfordshire, MK43 0AL, UK
- Department of Biology, University of York, Heslington, York, UK
| | - Edward Fuller
- Department of Biology, University of York, Heslington, York, UK
| | - María Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Consejo Superior de Investigaciones Científicas, Santander, Cantabria, Spain
| | | | - Francis Hassard
- Cranfield University, College Road, Cranfield, Bedfordshire, MK43 0AL, UK
| | - James Moir
- Department of Biology, University of York, Heslington, York, UK
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Wang D, Meng Y, Meng F. Genome-centric metagenomics insights into functional divergence and horizontal gene transfer of denitrifying bacteria in anammox consortia. WATER RESEARCH 2022; 224:119062. [PMID: 36116192 DOI: 10.1016/j.watres.2022.119062] [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: 05/09/2022] [Revised: 08/21/2022] [Accepted: 09/03/2022] [Indexed: 06/15/2023]
Abstract
Denitrifying bacteria with high abundances in anammox communities play crucial roles in achieving stable anammox-based systems. Despite the relative constant composition of denitrifying bacteria, their functional diversity remains to be explored in anammox communities. Herein, a total of 77 high-quality metagenome-assembled genomes (MAGs) of denitrifying bacteria were recovered from the anammox community in a full-scale swine wastewater treatment plant. Among these microbes, a total of 26 MAGs were affiliated with the seven dominant denitrifying genera that have total abundances higher than 1%. A meta-analysis of these species suggested that external organics reduced the abundances of genus Ignavibacterium and species MAG.305 of UTPRO2 in anammox communities. Comparative genome analysis revealed functional divergence across different denitrifying bacteria, largely owing to their distinct capabilities for carbohydrate (including endogenous and exogenous) utilization and vitamin (e.g., pantothenate and thiamine) biosynthesis. Serval microbes in this system contained fewer genes encoding biotin, pantothenate and methionine biosynthesis compared with their related species from other habitats. In addition, the genes encoding energy production and conversion (73 genes) and inorganic ion transport (53 genes) putatively transferred from other species to denitrifying bacteria, while these denitrifying bacteria (especially genera UTPRO2 and SCN-69-89) likely donated the genes encoding nutrients (e.g., inorganic ion and amino acid) transporter (64 genes) for other members to utilize new metabolites. Collectively, these findings highlighted the functional divergence of these denitrifying bacteria and speculated that the genetic interactions within anammox communities through horizontal gene transfer may be one of the reasons for their functional divergence.
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Affiliation(s)
- Depeng Wang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, Hunan 410125, PR China
| | - Yabing Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, Hunan 410125, PR China
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, Hunan 410125, PR China.
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Zhao Y, Gao J, Wang Z, Cui Y, Zhang Y, Dai H, Li D. Distinct bacterial communities and resistance genes enriched by triclocarban-contaminated polyethylene microplastics in antibiotics and heavy metals polluted sewage environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 839:156330. [PMID: 35640752 DOI: 10.1016/j.scitotenv.2022.156330] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Knowledge gaps still surround the question of what biofilms form on contaminated microplastics (MPs) in the antibiotics and (or) heavy metals polluted sewage. In this work, the clean polyethylene microplastics (PE MPs) and triclocarban (TCC)-contaminated PE MPs were cultured in the sewage containing only ampicillin (AMP), only copper (Cu) and both AMP and Cu for 28 days. The results showed that the TCC on PE MPs (with concentration of 2.48 mg/g PE MPs) did not impede the adhesion of the bacteria and the formation of biofilm. Moreover, many potential pathogenic bacteria (Aquabacterium and Pseudoxanthomonas) and potential resistant bacteria (Stenotrophomonas) were more likely to attach on TCC-contaminated PE MPs compared with clean PE MPs. In addition, biofilms of TCC-contaminated PE MPs had highest potential pathogenic functions. TCC-contaminated PE MPs also caused the increases of various resistance genes in both biofilm and sewage. The co-occurrence of TCC, AMP and Cu might exert a stronger selective pressure on bacterial communities and promote the co-selection of resistance genes. In addition, TCC-contaminated PE MPs resulted in higher abundance of five mobile genetic elements (MGEs) (intI1, intI3, tnpA-04, IS613 and trb-C) in sewage, which might further promote the transmission of resistance genes.
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Affiliation(s)
- Yifan Zhao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Jingfeng Gao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China.
| | - Zhiqi Wang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Yingchao Cui
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Yi Zhang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Huihui Dai
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Dingchang Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
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15
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Rios-Miguel AB, Smith GJ, Cremers G, van Alen T, Jetten MS, Op den Camp HJ, Welte CU. Microbial paracetamol degradation involves a high diversity of novel amidase enzyme candidates. WATER RESEARCH X 2022; 16:100152. [PMID: 36042984 PMCID: PMC9420511 DOI: 10.1016/j.wroa.2022.100152] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/13/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Pharmaceuticals are relatively new to nature and often not completely removed in wastewater treatment plants (WWTPs). Consequently, these micropollutants end up in water bodies all around the world posing a great environmental risk. One exception to this recalcitrant conversion is paracetamol, whose full degradation has been linked to several microorganisms. However, the genes and corresponding proteins involved in microbial paracetamol degradation are still elusive. In order to improve our knowledge of the microbial paracetamol degradation pathway, we inoculated a bioreactor with sludge of a hospital WWTP (Pharmafilter, Delft, NL) and fed it with paracetamol as the sole carbon source. Paracetamol was fully degraded without any lag phase and the enriched microbial community was investigated by metagenomic and metatranscriptomic analyses, which demonstrated that the microbial community was very diverse. Dilution and plating on paracetamol-amended agar plates yielded two Pseudomonas sp. isolates: a fast-growing Pseudomonas sp. that degraded 200 mg/L of paracetamol in approximately 10 h while excreting 4-aminophenol, and a slow-growing Pseudomonas sp. that degraded paracetamol without obvious intermediates in more than 90 days. Each Pseudomonas sp. contained a different highly-expressed amidase (31% identity to each other). These amidase genes were not detected in the bioreactor metagenome suggesting that other as-yet uncharacterized amidases may be responsible for the first biodegradation step of paracetamol. Uncharacterized deaminase genes and genes encoding dioxygenase enzymes involved in the catabolism of aromatic compounds and amino acids were the most likely candidates responsible for the degradation of paracetamol intermediates based on their high expression levels in the bioreactor metagenome and the Pseudomonas spp. genomes. Furthermore, cross-feeding between different community members might have occurred to efficiently degrade paracetamol and its intermediates in the bioreactor. This study increases our knowledge about the ongoing microbial evolution towards biodegradation of pharmaceuticals and points to a large diversity of (amidase) enzymes that are likely involved in paracetamol metabolism in WWTPs.
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Key Words
- 4-AP, 4-aminophenol
- APAP, N-acetyl-p-aminophenol or paracetamol
- Amidase evolution
- Deaminase
- Dioxygenase
- GAC, granular activated carbon
- HGT, horizontal gene transfer
- HQ, hydroquinone
- HRT, hydraulic retention time
- MAG, metagenome-assembled genome
- MBR, membrane bioreactor
- Metagenomics
- Mobile genetic elements
- Pfast, Pseudomonas sp. isolate growing fast on APAP as sole carbon source
- Pseudomonas
- Pslow, Pseudomonas sp. isolate growing slow on APAP as sole carbon source
- SRT, solid retention time
- TPM, transcripts per million
- WWTP, wastewater treatment plant
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Affiliation(s)
- Ana B. Rios-Miguel
- Department of Microbiology, Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
| | - Garrett J. Smith
- Department of Microbiology, Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
| | - Geert Cremers
- Department of Microbiology, Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
| | - Theo van Alen
- Department of Microbiology, Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
| | - Mike S.M. Jetten
- Department of Microbiology, Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
| | - Huub J.M. Op den Camp
- Department of Microbiology, Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
| | - Cornelia U. Welte
- Department of Microbiology, Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
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16
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Athanasakoglou A, Fenner K. Toward Characterizing the Genetic Basis of Trace Organic Contaminant Biotransformation in Activated Sludge: The Role of Multicopper Oxidases as a Case Study. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:313-324. [PMID: 34932304 DOI: 10.1021/acs.est.1c05803] [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: 06/14/2023]
Abstract
Activated sludge treatment leverages the ability of microbes to uptake and (co)-metabolize chemicals and has shown promise in eliminating trace organic contaminants (TrOCs) during wastewater treatment. However, targeted interventions to optimize the process are limited as the fundamental drivers of the observed reactions remain elusive. In this work, we present a comprehensive workflow for the identification and characterization of key enzymes involved in TrOCs biotransformation pathways in complex microbial communities. To demonstrate the applicability of the workflow, we investigated the role of the enzymatic group of multicopper oxidases (MCOs) as one putatively relevant driver of TrOCs biotransformation. To this end, we analyzed activated sludge metatranscriptomic data and selected, synthesized, and heterologously expressed three phylogenetically distinct MCO-encoding genes expressed in communities with different TrOCs oxidation potentials. Following the purification of the encoded enzymes, we screened their activities against different substrates. We saw that MCOs exhibit significant activities against selected TrOCs in the presence of the mediator compound 2,2'-azino-bis-3-ethylbenzthiazoline-6-sulfonic acid and, in some cases, also in the presence of the wastewater contaminant 4'-hydroxy-benzotriazole. In the first case, we identified oxidation products previously reported from activated sludge communities and concluded that in the presence of appropriate mediators, bacterial MCOs could contribute to the biological removal of TrOCs. Similar investigations of other key enzyme systems may significantly advance our understanding of TrOCs biodegradation and assist the rational design of biology-based water treatment strategies in the future.
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Affiliation(s)
- Anastasia Athanasakoglou
- Department of Environmental Chemistry, 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
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 Zürich, Switzerland
- Department of Chemistry, University of Zürich, 8057 Zürich, Switzerland
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17
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Long range PCR reveals the genetic cargo of IncP-1 plasmids in the complex microbial community of an on-farm biopurification system treating pesticide contaminated wastewater. Appl Environ Microbiol 2021; 88:e0164821. [PMID: 34878814 DOI: 10.1128/aem.01648-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Promiscuous plasmids like IncP-1 plasmids play an important role in the bacterial adaptation to pollution by acquiring and distributing xenobiotic catabolic genes. However, most information comes from isolates and the role of plasmids in governing community-wide bacterial adaptation to xenobiotics and other adaptive forces is not fully understood. Current information on the contribution of IncP-1 plasmids in community adaptation is limited because methods are lacking that directly isolate and identify the plasmid borne adaptive functions in whole-community DNA. In this study, we optimized long range PCR to directly access and identify the cargo carried by IncP-1 plasmids in environmental DNA. The DNA between the IncP-1 backbone genes trbP and traC, a main insertion site of adaptive trait determinants, is amplified and its content analysed by high-throughput sequencing. The method was applied to DNA of an on-farm biopurification system (BPS), treating pesticide contaminated wastewater, to examine whether horizontal gene exchange of catabolic functions by IncP-1 plasmids is a main driver of community adaptation in BPS. The cargo recovered from BPS community DNA, encoded catabolic but also resistance traits and various other (un)known functions. Unexpectedly, catabolic traits composed only a minor fraction of the cargo, indicating that the IncP-1 region between trbP and traC is not a major contributor to catabolic adaptation of the BPS microbiome. Instead, it contains a functionally diverse set of genes which either may assist biodegradation functions, be remnants of random gene recruitment, or confer other crucial functions for proliferation in the BPS environment. IMPORTANCE This study presents a long range PCR for direct and cultivation-independent access to the identity of the cargo of a major insertion hot spot of adaptive genes in IncP-1 plasmids and hence a new mobilome tool for understanding the role of IncP-1 plasmids in complex communities. The method was applied to DNA of an on-farm biopurification system (BPS) treating pesticide-contaminated wastewater, aiming at new insights on whether horizontal exchange of catabolic functions by IncP-1 plasmids is a main driver of community adaptation in BPS. Unexpectedly, catabolic functions represented a small fraction of the cargo genes while multiple other gene functions were recovered. These results show that the cargo of the target insertion hot spot in IncP-1 plasmids in a community, not necessarily relates to the main selective trait imposed on that community. Instead these functions might contribute to adaptation to unknown selective forces or represent remnants of random gene recruitment.
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Bhatt P, Bhandari G, Bhatt K, Maithani D, Mishra S, Gangola S, Bhatt R, Huang Y, Chen S. Plasmid-mediated catabolism for the removal of xenobiotics from the environment. JOURNAL OF HAZARDOUS MATERIALS 2021; 420:126618. [PMID: 34329102 DOI: 10.1016/j.jhazmat.2021.126618] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 05/27/2021] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
The large-scale application of xenobiotics adversely affects the environment. The genes that are present in the chromosome of the bacteria are considered nonmobile, whereas the genes present on the plasmids are considered mobile genetic elements. Plasmids are considered indispensable for xenobiotic degradation into the contaminated environment. In the contaminated sites, bacteria with plasmids can transfer the mobile genetic element into another strain. This mechanism helps in spreading the catabolic genes into the bacterial population at the contaminated sites. The indigenous microbial strains with such degradative plasmids are important for the bioremediation of xenobiotics. Environmental factors play a critical role in the conjugation efficiency, which is involved in the bioremediation of the xenobiotics at the contaminated sites. However, there is still a need for more research to fill in the gaps regarding plasmids and their impact on bioremediation. This review explores the role of bacterial plasmids in the bioremediation of xenobiotics from contaminated environments.
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Affiliation(s)
- Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Geeta Bhandari
- Department of Biochemistry and Biotechnology, Sardar Bhagwan Singh University, Dehradun 248161, Uttarakhand, India
| | - Kalpana Bhatt
- Department of Botany and Microbiology, Gurukul Kangri University, Haridwar 249404, Uttarakhand, India
| | - Damini Maithani
- Department of Microbiology, G.B Pant University of Agriculture and Technology Pantnagar, U.S Nagar, Uttarakhand, India
| | - Sandhya Mishra
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Saurabh Gangola
- School of Agriculture, Graphic Era Hill University, Bhimtal Campus, 263136, Uttarakhand, India
| | - Rakesh Bhatt
- Department of Civil Engineering, Indian Institute of Technology, Kanpur 208016, Uttar Pradesh, India
| | - Yaohua Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
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Biodegradation of aromatic pollutants meets synthetic biology. Synth Syst Biotechnol 2021; 6:153-162. [PMID: 34278013 PMCID: PMC8260767 DOI: 10.1016/j.synbio.2021.06.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 05/24/2021] [Accepted: 06/03/2021] [Indexed: 02/02/2023] Open
Abstract
Ubiquitously distributed microorganisms are natural decomposers of environmental pollutants. However, because of continuous generation of novel recalcitrant pollutants due to human activities, it is difficult, if not impossible, for microbes to acquire novel degradation mechanisms through natural evolution. Synthetic biology provides tools to engineer, transform or even re-synthesize an organism purposefully, accelerating transition from unable to able, inefficient to efficient degradation of given pollutants, and therefore, providing new solutions for environmental bioremediation. In this review, we described the pipeline to build chassis cells for the treatment of aromatic pollutants, and presented a proposal to design microbes with emphasis on the strategies applied to modify the target organism at different level. Finally, we discussed challenges and opportunities for future research in this field.
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Rios‐Miguel AB, Jetten MSM, Welte CU. Effect of concentration and hydraulic reaction time on the removal of pharmaceutical compounds in a membrane bioreactor inoculated with activated sludge. Microb Biotechnol 2021; 14:1707-1721. [PMID: 34132479 PMCID: PMC8313272 DOI: 10.1111/1751-7915.13837] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/16/2021] [Accepted: 05/10/2021] [Indexed: 01/04/2023] Open
Abstract
Pharmaceuticals are often not fully removed in wastewater treatment plants (WWTPs) and are thus being detected at trace levels in water bodies all over the world posing a risk to numerous organisms. These organic micropollutants (OMPs) reach WWTPs at concentrations sometimes too low to serve as growth substrate for microorganisms; thus, co-metabolism is thought to be the main conversion mechanism. In this study, the microbial removal of six pharmaceuticals was investigated in a membrane bioreactor at increasing concentrations (4-800 nM) of the compounds and using three different hydraulic retention times (HRT; 1, 3.5 and 5 days). The bioreactor was inoculated with activated sludge from a municipal WWTP and fed with ammonium, acetate and methanol as main growth substrates to mimic co-metabolism. Each pharmaceutical had a different average removal efficiency: acetaminophen (100%) > fluoxetine (50%) > metoprolol (25%) > diclofenac (20%) > metformin (15%) > carbamazepine (10%). Higher pharmaceutical influent concentrations proportionally increased the removal rate of each compound, but surprisingly not the removal percentage. Furthermore, only metformin removal improved to 80-100% when HRT or biomass concentration was increased. Microbial community changes were followed with 16S rRNA gene amplicon sequencing in response to the increment of pharmaceutical concentration: Nitrospirae and Planctomycetes 16S rRNA relative gene abundance decreased, whereas Acidobacteria and Bacteroidetes increased. Remarkably, the Dokdonella genus, previously implicated in acetaminophen metabolism, showed a 30-fold increase in abundance at the highest concentration of pharmaceuticals applied. Taken together, these results suggest that the incomplete removal of most pharmaceutical compounds in WWTPs is dependent on neither concentration nor reaction time. Accordingly, we propose a chemical equilibrium or a growth substrate limitation as the responsible mechanisms of the incomplete removal. Finally, Dokdonella could be the main acetaminophen degrader under activated sludge conditions, and non-antibiotic pharmaceuticals might still be toxic to relevant WWTP bacteria.
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Affiliation(s)
- Ana B. Rios‐Miguel
- Department of MicrobiologyInstitute for Water and Wetland ResearchRadboud UniversityHeyendaalseweg 135Nijmegen6525 AJThe Netherlands
| | - Mike S. M. Jetten
- Department of MicrobiologyInstitute for Water and Wetland ResearchRadboud UniversityHeyendaalseweg 135Nijmegen6525 AJThe Netherlands
- Soehngen Institute of Anaerobic MicrobiologyRadboud UniversityHeyendaalseweg 135Nijmegen6525 AJThe Netherlands
| | - Cornelia U. Welte
- Department of MicrobiologyInstitute for Water and Wetland ResearchRadboud UniversityHeyendaalseweg 135Nijmegen6525 AJThe Netherlands
- Soehngen Institute of Anaerobic MicrobiologyRadboud UniversityHeyendaalseweg 135Nijmegen6525 AJThe Netherlands
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21
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Ku YS, Wang Z, Duan S, Lam HM. Rhizospheric Communication through Mobile Genetic Element Transfers for the Regulation of Microbe-Plant Interactions. BIOLOGY 2021; 10:biology10060477. [PMID: 34071379 PMCID: PMC8227670 DOI: 10.3390/biology10060477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 05/24/2021] [Accepted: 05/24/2021] [Indexed: 12/25/2022]
Abstract
Simple Summary Rhizosphere, where microbes and plants coexist, is a hotspot of mobile genetic element (MGE) transfers. It was suggested that ancient MGE transfers drove the evolution of both microbes and plants. On the other hand, recurrent MGE transfers regulate microbe-plant interaction and the adaptation of microbes and plants to the environment. The studies of MGE transfers in the rhizosphere provide useful information for the research on pathogenic/ beneficial microbe-plant interaction. In addition, MGE transfers between microbes and the influence by plant root exudates on such transfers provide useful information for the research on bioremediation. Abstract The transfer of mobile genetic elements (MGEs) has been known as a strategy adopted by organisms for survival and adaptation to the environment. The rhizosphere, where microbes and plants coexist, is a hotspot of MGE transfers. In this review, we discuss the classic mechanisms as well as novel mechanisms of MGE transfers in the rhizosphere. Both intra-kingdom and cross-kingdom MGE transfers will be addressed. MGE transfers could be ancient events which drove evolution or recurrent events which regulate adaptations. Recent findings on MGE transfers between plant and its interacting microbes suggest gene regulations brought forth by such transfers for symbiosis or defense mechanisms. In the natural environment, factors such as temperature and soil composition constantly influence the interactions among different parties in the rhizosphere. In this review, we will also address the effects of various environmental factors on MGE transfers in the rhizosphere. Besides environmental factors, plant root exudates also play a role in the regulation of MGE transfer among microbes in the rhizosphere. The potential use of microbes and plants for bioremediation will be discussed.
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