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Rolli E, Ghitti E, Mapelli F, Borin S. Polychlorinated biphenyls modify Arabidopsis root exudation pattern to accommodate degrading bacteria, showing strain and functional trait specificity. FRONTIERS IN PLANT SCIENCE 2024; 15:1429096. [PMID: 39036359 PMCID: PMC11258928 DOI: 10.3389/fpls.2024.1429096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/13/2024] [Indexed: 07/23/2024]
Abstract
Introduction The importance of plant rhizodeposition to sustain microbial growth and induce xenobiotic degradation in polluted environments is increasingly recognized. Methods Here the "cry-for-help" hypothesis, consisting in root chemistry remodeling upon stress, was investigated in the presence of polychlorinated biphenyls (PCBs), highly recalcitrant and phytotoxic compounds, highlighting its role in reshaping the nutritional and signaling features of the root niche to accommodate PCB-degrading microorganisms. Results Arabidopsis exposure to 70 µM PCB-18 triggered plant-detrimental effects, stress-related traits, and PCB-responsive gene expression, reproducing PCB phytotoxicity. The root exudates of plantlets exposed for 2 days to the pollutant were collected and characterized through untargeted metabolomics analysis by liquid chromatography-mass spectrometry. Principal component analysis disclosed a different root exudation fingerprint in PCB-18-exposed plants, potentially contributing to the "cry-for-help" event. To investigate this aspect, the five compounds identified in the exudate metabolomic analysis (i.e., scopoletin, N-hydroxyethyl-β-alanine, hypoxanthine, L-arginyl-L-valine, and L-seryl-L-phenylalanine) were assayed for their influence on the physiology and functionality of the PCB-degrading strains Pseudomonas alcaliphila JAB1, Paraburkholderia xenovorans LB400, and Acinetobacter calcoaceticus P320. Scopoletin, whose relative abundance decreased in PCB-18-stressed plant exudates, hampered the growth and proliferation of strains JAB1 and P320, presumably due to its antimicrobial activity, and reduced the beneficial effect of Acinetobacter P320, which showed a higher degree of growth promotion in the scopoletin-depleted mutant f6'h1 compared to Arabidopsis WT plants exposed to PCB. Nevertheless, scopoletin induced the expression of the bph catabolic operon in strains JAB1 and LB400. The primary metabolites hypoxanthine, L-arginyl-L-valine, and L-seryl-L-phenylalanine, which increased in relative abundance upon PCB-18 stress, were preferentially used as nutrients and growth-stimulating factors by the three degrading strains and showed a variable ability to affect rhizocompetence traits like motility and biofilm formation. Discussion These findings expand the knowledge on PCB-triggered "cry-for-help" and its role in steering the PCB-degrading microbiome to boost the holobiont fitness in polluted environments.
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Affiliation(s)
| | | | | | - Sara Borin
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
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Monaco P, Baldoni A, Naclerio G, Scippa GS, Bucci A. Impact of Plant-Microbe Interactions with a Focus on Poorly Investigated Urban Ecosystems-A Review. Microorganisms 2024; 12:1276. [PMID: 39065045 PMCID: PMC11279295 DOI: 10.3390/microorganisms12071276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
The urbanization process, which began with the Industrial Revolution, has undergone a considerable increase over the past few decades. Urbanization strongly affects ecological processes, often deleteriously, because it is associated with a decrease in green spaces (areas of land covered by vegetation), loss of natural habitats, increased rates of species extinction, a greater prevalence of invasive and exotic species, and anthropogenic pollutant accumulation. In urban environments, green spaces play a key role by providing many ecological benefits and contributing to human psychophysical well-being. It is known that interactions between plants and microorganisms that occur in the rhizosphere are of paramount importance for plant health, soil fertility, and the correct functioning of plant ecosystems. The growing diffusion of DNA sequencing technologies and "omics" analyses has provided increasing information about the composition, structure, and function of the rhizomicrobiota. However, despite the considerable amount of data on rhizosphere communities and their interactions with plants in natural/rural contexts, current knowledge on microbial communities associated with plant roots in urban soils is still very scarce. The present review discusses both plant-microbe dynamics and factors that drive the composition of the rhizomicrobiota in poorly investigated urban settings and the potential use of beneficial microbes as an innovative biological tool to face the challenges that anthropized environments and climate change impose. Unravelling urban biodiversity will contribute to green space management, preservation, and development and, ultimately, to public health and safety.
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Affiliation(s)
- Pamela Monaco
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy; (A.B.); (G.N.); (G.S.S.)
| | | | | | | | - Antonio Bucci
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy; (A.B.); (G.N.); (G.S.S.)
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Wu Y, Zhu M, Ouyang X, Qi X, Guo Z, Yuan Y, Dang Z, Yin H. Integrated transcriptomics and metabolomics analyses reveal the aerobic biodegradation and molecular mechanisms of 2,3',4,4',5-pentachlorodiphenyl (PCB 118) in Methylorubrum sp. ZY-1. CHEMOSPHERE 2024; 356:141921. [PMID: 38588902 DOI: 10.1016/j.chemosphere.2024.141921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/18/2024] [Accepted: 04/04/2024] [Indexed: 04/10/2024]
Abstract
2,3',4,4',5-pentachlorodiphenyl (PCB 118), a highly representative PCB congener, has been frequently detected in various environments, garnering much attention across the scientific community. The degradation of highly chlorinated PCBs by aerobic microorganisms is challenging due to their hydrophobicity and persistence. Herein, the biodegradation and adaptation mechanisms of Methylorubrum sp. ZY-1 to PCB 118 were comprehensively investigated using an integrative approach that combined degradation performance, product identification, metabolomic and transcriptomic analyses. The results indicated that the highest degradation efficiency of 0.5 mg L-1 PCB 118 reached 75.66% after seven days of inoculation when the bacteria dosage was 1.0 g L-1 at pH 7.0. A total of eleven products were identified during the degradation process, including low chlorinated PCBs, hydroxylated PCBs, and ring-opening products, suggesting that strain ZY-1 degraded PCB 118 through dechlorination, hydroxylation, and ring-opening pathways. Metabolomic analysis demonstrated that the energy supply and redox metabolism of strain ZY-1 was disturbed with exposure to PCB 118. To counteract this environmental stress, strain ZY-1 adjusted both the fatty acid synthesis and purine metabolism. The analysis of transcriptomics disclosed that multiple intracellular and extracellular oxidoreductases (e.g., monooxygenase, alpha/beta hydrolase and cytochrome P450) participated in the degradation of PCB 118. Besides, active efflux of PCB 118 and its degradation intermediates mediated by multiple transporters (e.g., MFS transporter and ABC transporter ATP-binding protein) might enhance bacterial resistance against these substances. These discoveries provided the inaugural insights into the biotransformation of strain ZY-1 to PCB 118 stress, illustrating its potential in the remediation of contaminated environments.
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Affiliation(s)
- Yuxuan Wu
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Minghan Zhu
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Xiaofang Ouyang
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Xin Qi
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Zhanyu Guo
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Yibo Yuan
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Zhi Dang
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China; Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou, 510006, China
| | - Hua Yin
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China; Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou, 510006, China.
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Qin G, Jia R, Xue J, Chen L, Li Y, Luo W, Wu X, An T, Fang Z. New Perspectives on the Risks of Hydroxylated Polychlorinated Biphenyl (OH-PCB) Exposure: Intestinal Flora α-Glucosidase Inhibition. TOXICS 2024; 12:237. [PMID: 38668460 PMCID: PMC11053903 DOI: 10.3390/toxics12040237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/14/2024] [Accepted: 03/19/2024] [Indexed: 04/29/2024]
Abstract
Polychlorinated biphenyls (PCBs) are a group of colorless and odorless environmental pollutants with a wide range of toxic effects. Some PCBs, especially less chlorinated ones, will rapidly undergo phase I metabolism after entering the body, and hydroxylated polychlorinated biphenyls (OH-PCBs) are the main metabolites of PCBs. Intestinal flora α-glucosidase is a common carbohydrate-active enzyme which is ubiquitous in human intestinal flora. It can convert complex dietary polysaccharides into monosaccharides, assisting the body in degrading complex carbohydrates and providing energy for the survival and growth of bacterial flora. The present study aims to investigate the inhibition of the activity of intestinal flora α-glucosidase by OH-PCBs. 4-Nitrophenyl-α-D-glucopyranoside (PNPG) was used as a probe substrate for α-glucosidase, and in vitro incubation experiments were conducted to study the inhibition of 26 representative OH-PCBs on α-glucosidase. Preliminary screening of in vitro incubation was performed with 100 μM of OH-PCBs. The results showed that 26 OH-PCBs generally exhibited strong inhibition of α-glucosidase. The concentration-dependent inhibition and half inhibition concentrations (IC50s) of OH-PCBs on α-glucosidase were determined. 4'-OH-PCB 86 and 4'-OH-PCB 106 were chosen as representative OH-PCBs, and the inhibition kinetic parameters (Kis) of inhibitors for α-glucosidase were determined. The inhibition kinetic parameters (Kis) of 4'-OH-PCB 86 and 4'-OH-PCB 106 for α-glucosidase are 1.007 μM and 0.538 μM, respectively. The silico docking method was used to further analyze the interaction mechanism between OH-PCBs and α-glucosidase. All these results will help us to understand the risks of OH-PCB exposure from a new perspective.
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Affiliation(s)
- Guoqiang Qin
- Department of Toxicology and Health Inspection and Quarantine, School of Public Health, Tianjin Medical University, Tianjin 300070, China
| | - Ruoyong Jia
- Department of Toxicology and Health Inspection and Quarantine, School of Public Health, Tianjin Medical University, Tianjin 300070, China
| | - Juntang Xue
- Department of Toxicology and Health Inspection and Quarantine, School of Public Health, Tianjin Medical University, Tianjin 300070, China
| | - Li Chen
- Department of Toxicology and Health Inspection and Quarantine, School of Public Health, Tianjin Medical University, Tianjin 300070, China
| | - Yang Li
- Department of Toxicology and Health Inspection and Quarantine, School of Public Health, Tianjin Medical University, Tianjin 300070, China
| | - Weiming Luo
- Department of Toxicology and Health Inspection and Quarantine, School of Public Health, Tianjin Medical University, Tianjin 300070, China
| | - Xiaomin Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Tianjin Medical University, Tianjin 300070, China
- National Center for Chronic and Noncommunicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100050, China
| | - Tianfeng An
- Department of Toxicology and Health Inspection and Quarantine, School of Public Health, Tianjin Medical University, Tianjin 300070, China
| | - Zhongze Fang
- Department of Toxicology and Health Inspection and Quarantine, School of Public Health, Tianjin Medical University, Tianjin 300070, China
- Tianjin Key Laboratory of Environment, Nutrition and Public Health, Tianjin 300070, China
- National Demonstration Center for Experimental Preventive Medicine Education, Tianjin Medical University, Tianjin 300070, China
- Tianjin Center for International Collaborative Research in Environment, Nutrition and Public Health, Tianjin 300070, China
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Maucourt F, Doumèche B, Nazaret S, Fraissinet-Tachet L. Under explored roles of microbial ligninolytic enzymes in aerobic polychlorinated biphenyl transformation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:19071-19084. [PMID: 38372925 DOI: 10.1007/s11356-024-32291-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/28/2024] [Indexed: 02/20/2024]
Abstract
Polychlorinated biphenyls (PCBs) are persistent organic pollutants in the environment that are responsible for many adverse health effects. Bioremediation appears to be a healthy and cost-effective alternative for remediating PCB-contaminated environments. While some microbial species have been observed to be capable of transforming PCBs, only two different microbial pathways (rdh and bph pathways) have been described to be involved in PCB transformations. Ligninolytic enzymes have been observed or are under suspicion in some microbial PCB transformations. However, the role of these promising PCB-transforming enzymes, which are produced by fungi and some aerobic bacteria, is still unclear. The present review describes their role by identifying microbial PCB-transforming species and their reported ligninolytic enzymes whether proven or suspected to be involved in PCB transformations. There are several lines of evidence that ligninolytic enzymes are responsible for PCB transformations such as (1) the ability of purified laccases from Myceliophthora thermophila, Pycnoporus cinnabarinus, Trametes versicolor, Cladosporium sp, and Coprinus cumatus to transform hydroxy-PCBs; (2) the increased production of laccases and peroxidases by many fungi in the presence of PCBs; and (3) the enhanced PCB transformation by Pseudomonas stutzeri and Sinorhizobium meliloti NM after the addition of ligninolytic enzyme enhancers. However, if the involvement of ligninolytic enzymes in PCB transformation is clearly demonstrated in some fungal species, it does not seem to be implicated in all microbial species suggesting other still unknown metabolic pathways involved in PCB transformation and different from the bph and rdh pathways. Therefore, PCB transformation may involve several metabolic pathways, some involving ligninolytic enzymes, bph or rdh genes, and some still unknown, depending on the microbial species. In addition, current knowledge does not fully clarify the role of ligninolytic enzymes in PCB oxidation and dechlorination. Therefore, further studies focusing on purified ligninolytic enzymes are needed to clearly elucidate their role in PCB transformation.
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Affiliation(s)
- Flavien Maucourt
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-7 69622, Villeurbanne, France
- ENVISOL, 2-4 rue Hector Berlioz, F-38110, La Tour du Pin, France
| | - Bastien Doumèche
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS 5246 ICBMS, F-7 69622, Villeurbanne, France
| | - Sylvie Nazaret
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-7 69622, Villeurbanne, France
| | - Laurence Fraissinet-Tachet
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-7 69622, Villeurbanne, France.
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Matturro B, Di Franca ML, Tonanzi B, Cruz Viggi C, Aulenta F, Di Leo M, Giandomenico S, Rossetti S. Enrichment of Aerobic and Anaerobic Hydrocarbon-Degrading Bacteria from Multicontaminated Marine Sediment in Mar Piccolo Site (Taranto, Italy). Microorganisms 2023; 11:2782. [PMID: 38004793 PMCID: PMC10673493 DOI: 10.3390/microorganisms11112782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Marine sediments act as a sink for the accumulation of various organic contaminants such as polychlorobiphenyls (PCBs). These contaminants affect the composition and activity of microbial communities, particularly favoring those capable of thriving from their biodegradation and biotransformation under favorable conditions. Hence, contaminated environments represent a valuable biological resource for the exploration and cultivation of microorganisms with bioremediation potential. In this study, we successfully cultivated microbial consortia with the capacity for PCB removal under both aerobic and anaerobic conditions. The source of these consortia was a multicontaminated marine sediment collected from the Mar Piccolo (Taranto, Italy), one of Europe's most heavily polluted sites. High-throughput sequencing was employed to investigate the dynamics of the bacterial community of the marine sediment sample, revealing distinct and divergent selection patterns depending on the imposed reductive or oxidative conditions. The aerobic incubation resulted in the rapid selection of bacteria specialized in oxidative pathways for hydrocarbon transformation, leading to the isolation of Marinobacter salinus and Rhodococcus cerastii species, also known for their involvement in aerobic polycyclic aromatic hydrocarbons (PAHs) transformation. On the other hand, anaerobic incubation facilitated the selection of dechlorinating species, including Dehalococcoides mccartyi, involved in PCB reduction. This study significantly contributes to our understanding of the diversity, dynamics, and adaptation of the bacterial community in the hydrocarbon-contaminated marine sediment from one sampling point of the Mar Piccolo basin, particularly in response to stressful conditions. Furthermore, the establishment of consortia with biodegradation and biotransformation capabilities represents a substantial advancement in addressing the challenge of restoring polluted sites, including marine sediments, thus contributing to expanding the toolkit for effective bioremediation strategies.
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Affiliation(s)
- Bruna Matturro
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
- National Biodiversity Future Center, 90133 Palermo, Italy
| | - Maria Letizia Di Franca
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
| | - Barbara Tonanzi
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
- National Biodiversity Future Center, 90133 Palermo, Italy
| | - Carolina Cruz Viggi
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
| | - Federico Aulenta
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
- National Biodiversity Future Center, 90133 Palermo, Italy
| | - Magda Di Leo
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
| | - Santina Giandomenico
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
| | - Simona Rossetti
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
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Zhu DH, Nie FH, Song QL, Wei W, Zhang M, Hu Y, Lin HY, Kang DJ, Chen ZB, Chen JJ. Isolation and genomic characterization of Klebsiella Lw3 with polychlorinated biphenyl degradability. ENVIRONMENTAL TECHNOLOGY 2023; 44:3656-3666. [PMID: 35441572 DOI: 10.1080/09593330.2022.2068381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
Bioremediation of sediment organic pollution has been intensely investigated, but the degradation of complex organic compounds, pesticide residues, and polychlorinated biphenyls (PCBs) remains poorly studied. In this study, sediments were collected from Zhanjiang Mangrove Reserve and inoculated in an inorganic salt medium using only biphenyl (BP) and PCBs as the carbon sources to obtain a PCB-degrading strain. A gram-negative bacterium that metabolized PCBs was isolated and identified as Klebsiella Lw3 by 16S rDNA phylogenetic analysis. Genomic sequencing showed that this bacterium possessed genes related to BP/PCB degradation, and its GC content was 58.2%; we identified 3326 cellular pathways. Gas chromatography-mass spectrometry was employed to test the PCB degrading ability; the results showed that the strain had a good degradation effect on PCB3 at concentrations of 5, 10, 20, 40, and 60 mg/L and that the final degradation rate was higher than 97% after 96 h. Interestingly, this strain showed good biodegradability of PCBs despite having no classical PCB degradation pathway, providing a new direction for Klebsiella research with practical significance for in situ bioremediation of PCB contamination. Overall, this study provides valuable insights into the genetic structure of PCB-degrading strains as well as eco-friendly and low-cost PCB degradation and lays a foundation for the discovery of new degradation pathways.
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Affiliation(s)
- Di-Hua Zhu
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Fang-Hong Nie
- College of Food Science and Technology, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Qing-Lang Song
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Wan Wei
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Min Zhang
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Yao Hu
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Hong-Ying Lin
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Dan-Ju Kang
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Zhi-Bao Chen
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Jin-Jun Chen
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
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Maucourt F, Doumèche B, Chapulliot D, Vallon L, Nazaret S, Fraissinet-Tachet L. Polychlorinated Biphenyl Transformation, Peroxidase and Oxidase Activities of Fungi and Bacteria Isolated from a Historically Contaminated Site. Microorganisms 2023; 11:1887. [PMID: 37630447 PMCID: PMC10457763 DOI: 10.3390/microorganisms11081887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/13/2023] [Accepted: 07/21/2023] [Indexed: 08/27/2023] Open
Abstract
Causing major health and ecological disturbances, polychlorinated biphenyls (PCBs) are persistent organic pollutants still recovered all over the world. Microbial PCB biotransformation is a promising technique for depollution, but the involved molecular mechanisms remain misunderstood. Ligninolytic enzymes are suspected to be involved in many PCB transformations, but their assessments remain scarce. To further inventory the capabilities of microbes to transform PCBs through their ligninolytic enzymes, we investigated the role of oxidase and peroxidase among a set of microorganisms isolated from a historically PCB-contaminated site. Among 29 isolated fungi and 17 bacteria, this work reports for the first time the PCB-transforming capabilities from fungi affiliated to Didymella, Dothiora, Ilyonectria, Naganishia, Rhodoturula, Solicoccozyma, Thelebolus and Truncatella genera and bacteria affiliated to Peribacillus frigotolerans, Peribacillus muralis, Bacillus mycoides, Bacillus cereus, Bacillus toyonensis, Pseudarthrobacter sp., Pseudomonas chlororaphis, Erwinia aphidicola and Chryseobacterium defluvii. In the same way, this is the first report of fungal isolates affiliated to the Dothiora maculans specie and Cladosporium genus that displayed oxidase (putatively laccase) and peroxidase activity, respectively, enhanced in the presence of PCBs (more than 4-fold and 20-fold, respectively, compared to controls). Based on these results, the observed activities are suspected to be involved in PCB transformation.
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Affiliation(s)
- Flavien Maucourt
- Université de Lyon, Universite Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
- ENVISOL, 2-4 Rue Hector Berlioz, F-38110 La Tour du Pin, France
| | - Bastien Doumèche
- Université de Lyon, Universite Claude Bernard Lyon 1, CNRS 5246 ICBMS, F-69622 Villeurbanne, France
| | - David Chapulliot
- Université de Lyon, Universite Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Laurent Vallon
- Université de Lyon, Universite Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Sylvie Nazaret
- Université de Lyon, Universite Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Laurence Fraissinet-Tachet
- Université de Lyon, Universite Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
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9
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Hirose J. Diversity and Evolution of Integrative and Conjugative Elements Involved in Bacterial Aromatic Compound Degradation and Their Utility in Environmental Remediation. Microorganisms 2023; 11:microorganisms11020438. [PMID: 36838403 PMCID: PMC9960961 DOI: 10.3390/microorganisms11020438] [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: 12/29/2022] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/12/2023] Open
Abstract
Integrative and conjugative elements (ICEs) are mobile DNA molecules that can be transferred through excision, conjugation, and integration into chromosomes. They contribute to the horizontal transfer of genomic islands across bacterial species. ICEs carrying genes encoding aromatic compound degradation pathways are of interest because of their contribution to environmental remediation. Recent advances in DNA sequencing technology have increased the number of newly discovered ICEs in bacterial genomes and have enabled comparative analysis of their evolution. The two different families of ICEs carry various aromatic compound degradation pathway genes. ICEclc and its related ICEs contain a number of members with diverse catabolic capabilities. In addition, the Tn4371 family, which includes ICEs that carry the chlorinated biphenyl catabolic pathway, has been identified. It is apparent that they underwent evolution through the acquisition, deletion, or exchange of modules to adapt to an environmental niche. ICEs have the property of both stability and mobility in the chromosome. Perspectives on the use of ICEs in environmental remediation are also discussed.
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Affiliation(s)
- Jun Hirose
- Department of Applied Chemistry, Faculty of Engineering, University of Miyazaki, Miyazaki 889-2192, Japan
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10
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Keil-Stietz K, Lein PJ. Gene×environment interactions in autism spectrum disorders. Curr Top Dev Biol 2022; 152:221-284. [PMID: 36707213 PMCID: PMC10496028 DOI: 10.1016/bs.ctdb.2022.11.001] [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] [Indexed: 12/24/2022]
Abstract
There is credible evidence that environmental factors influence individual risk and/or severity of autism spectrum disorders (hereafter referred to as autism). While it is likely that environmental chemicals contribute to the etiology of autism via multiple mechanisms, identifying specific environmental factors that confer risk for autism and understanding how they contribute to the etiology of autism has been challenging, in part because the influence of environmental chemicals likely varies depending on the genetic substrate of the exposed individual. Current research efforts are focused on elucidating the mechanisms by which environmental chemicals interact with autism genetic susceptibilities to adversely impact neurodevelopment. The goal is to not only generate insights regarding the pathophysiology of autism, but also inform the development of screening platforms to identify specific environmental factors and gene×environment (G×E) interactions that modify autism risk. Data from such studies are needed to support development of intervention strategies for mitigating the burden of this neurodevelopmental condition on individuals, their families and society. In this review, we discuss environmental chemicals identified as putative autism risk factors and proposed mechanisms by which G×E interactions influence autism risk and/or severity using polychlorinated biphenyls (PCBs) as an example.
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Affiliation(s)
- Kimberly Keil-Stietz
- Department of Comparative Biosciences, University of Wisconsin-Madison, School of Veterinary Medicine, Madison, WI, United States
| | - Pamela J Lein
- Department of Molecular Biosciences, University of California, Davis, School of Veterinary Medicine, Davis, CA, United States.
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11
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Rosato A, Barone M, Negroni A, Brigidi P, Fava F, Biagi E, Candela M, Zanaroli G. Bacterial colonization dynamics of different microplastic types in an anoxic salt marsh sediment and impact of adsorbed polychlorinated biphenyls on the plastisphere. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 315:120411. [PMID: 36240963 DOI: 10.1016/j.envpol.2022.120411] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/14/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Plastic debris dispersed into the environment provide a substrate for microbial colonization, constituting a new human-made ecosystem called "plastisphere", and altering the microbial species distribution in aquatic, coastal and benthic ecosystems. The study aims at exploring the interaction among microplastics (MPs) made of different polymers, a persistent organic contaminant (polychlorinated biphenyls, PCBs), and the environmental microbial communities, in an anoxic marine sediment. Plastic pellets were incubated in the field in a salt marsh anoxic sediment, to observe the stages of plastisphere formation, by quantitative PCR and 16S rRNA gene sequencing, and PCB dechlorination activity on the MPs surface. Microbes from the sediment rapidly colonized the different microplastics types, with PVC recruiting a peculiar community enriched in sulfate-reducing bacteria. The composition of the plastisphere varied along the 1-year incubation possibly in response either to warmer temperatures in spring-summer or to microhabitat's changes due to the progressive plastic surface weathering. Even if PCB contaminated MPs were able to recruit potentially dehalogenating taxa, actual dechlorination was not detectable after 1 year. This suggests that the concentration of potentially dehalorespiring bacteria in the natural environment could be too low for the onset of the dechlorination process on MP-sorbed contaminants. Our study, which is among very few available longitudinally exploring the plastisphere composition in an anoxic sediment context, is the first exploring the fate and possible biodegradation of persistent organic pollutants sorbed on MPs reaching the seafloor.
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Affiliation(s)
- Antonella Rosato
- Dept. of Civil, Chemical, Environmental and Materials Engineering (DICAM), Alma Mater Studiorum University of Bologna, Via Terracini 28, 40131, Bologna, Italy
| | - Monica Barone
- Dept. of Pharmacy and Biotechnology (FaBit), Alma Mater Studiorum University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy; Dept. of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum University of Bologna, Via Massarenti 9, 40138, Bologna, Italy
| | - Andrea Negroni
- Dept. of Civil, Chemical, Environmental and Materials Engineering (DICAM), Alma Mater Studiorum University of Bologna, Via Terracini 28, 40131, Bologna, Italy
| | - Patrizia Brigidi
- Dept. of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum University of Bologna, Via Massarenti 9, 40138, Bologna, Italy
| | - Fabio Fava
- Dept. of Civil, Chemical, Environmental and Materials Engineering (DICAM), Alma Mater Studiorum University of Bologna, Via Terracini 28, 40131, Bologna, Italy
| | - Elena Biagi
- Dept. of Civil, Chemical, Environmental and Materials Engineering (DICAM), Alma Mater Studiorum University of Bologna, Via Terracini 28, 40131, Bologna, Italy
| | - Marco Candela
- Dept. of Pharmacy and Biotechnology (FaBit), Alma Mater Studiorum University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Giulio Zanaroli
- Dept. of Civil, Chemical, Environmental and Materials Engineering (DICAM), Alma Mater Studiorum University of Bologna, Via Terracini 28, 40131, Bologna, Italy.
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12
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Tufail MA, Iltaf J, Zaheer T, Tariq L, Amir MB, Fatima R, Asbat A, Kabeer T, Fahad M, Naeem H, Shoukat U, Noor H, Awais M, Umar W, Ayyub M. Recent advances in bioremediation of heavy metals and persistent organic pollutants: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 850:157961. [PMID: 35963399 DOI: 10.1016/j.scitotenv.2022.157961] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 08/02/2022] [Accepted: 08/06/2022] [Indexed: 06/15/2023]
Abstract
Heavy metals and persistent organic pollutants are causing detrimental effects on the environment. The seepage of heavy metals through untreated industrial waste destroys the crops and lands. Moreover, incineration and combustion of several products are responsible for primary and secondary emissions of pollutants. This review has gathered the remediation strategies, current bioremediation technologies, and their primary use in both in situ and ex situ methods, followed by a detailed explanation for bioremediation over other techniques. However, an amalgam of bioremediation techniques and nanotechnology could be a breakthrough in cleaning the environment by degrading heavy metals and persistant organic pollutants.
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Affiliation(s)
| | - Jawaria Iltaf
- Institute of Chemistry, University of Sargodha, 40100, Pakistan
| | - Tahreem Zaheer
- Department of Biological Physics, Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Leeza Tariq
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan
| | - Muhammad Bilal Amir
- Key Laboratory of Insect Ecology and Molecular Biology, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Rida Fatima
- School of Science, Department of Chemistry, University of Management and Technology, Lahore, Pakistan
| | - Ayesha Asbat
- Department of Pharmacy, The University of Lahore, Lahore, Pakistan
| | - Tahira Kabeer
- Center of Agriculture Biochemistry and Biotechnology CABB, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Fahad
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan, Pakistan
| | - Hamna Naeem
- Department of Environmental Sciences, Fatima Jinnah Women University, The Mall, 46000 Rawalpindi, Pakistan
| | - Usama Shoukat
- Integrated Genomics Cellular Development Biology Lab, Department of Entomology, University of Agriculture, Faisalabad, Pakistan
| | - Hazrat Noor
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Muhammad Awais
- International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Wajid Umar
- Institute of Environmental Science, Hungarian University of Agriculture and Life Sciences, Gödöllő 2100, Hungary
| | - Muhaimen Ayyub
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad, Pakistan
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13
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Xiang Z, Huang S, Zhao LL, Zhang Z, Chen K, Cao W, Zheng K, Yan X. Base-catalyzed H/D exchange of polychlorinated biphenyls. Tetrahedron Lett 2022. [DOI: 10.1016/j.tetlet.2022.154200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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14
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Qin R, Zhu Y, Ai M, Jia X. Reconstruction and optimization of a Pseudomonas putida-Escherichia coli microbial consortium for mcl-PHA production from lignocellulosic biomass. Front Bioeng Biotechnol 2022; 10:1023325. [PMID: 36338139 PMCID: PMC9626825 DOI: 10.3389/fbioe.2022.1023325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/10/2022] [Indexed: 11/18/2022] Open
Abstract
The demand for non-petroleum-based, especially biodegradable plastics has been on the rise in the last decades. Medium-chain-length polyhydroxyalkanoate (mcl-PHA) is a biopolymer composed of 6–14 carbon atoms produced from renewable feedstocks and has become the focus of research. In recent years, researchers aimed to overcome the disadvantages of single strains, and artificial microbial consortia have been developed into efficient platforms. In this work, we reconstructed the previously developed microbial consortium composed of engineered Pseudomonas putida KT∆ABZF (p2-a-J) and Escherichia coli ∆4D (ACP-SCLAC). The maximum titer of mcl-PHA reached 3.98 g/L using 10 g/L glucose, 5 g/L octanoic acid as substrates by the engineered P. putida KT∆ABZF (p2-a-J). On the other hand, the maximum synthesis capacity of the engineered E. coli ∆4D (ACP-SCLAC) was enhanced to 3.38 g/L acetic acid and 0.67 g/L free fatty acids (FFAs) using 10 g/L xylose as substrate. Based on the concept of “nutrient supply-detoxification,” the engineered E. coli ∆4D (ACP-SCLAC) provided nutrient for the engineered P. putida KT∆ABZF (p2-a-J) and it acted to detoxify the substrates. Through this functional division and rational design of the metabolic pathways, the engineered P. putida-E. coli microbial consortium could produce 1.30 g/L of mcl-PHA from 10 g/L glucose and xylose. Finally, the consortium produced 1.02 g/L of mcl-PHA using lignocellulosic hydrolysate containing 10.50 g/L glucose and 10.21 g/L xylose as the substrate. The consortium developed in this study has good potential for mcl-PHA production and provides a valuable reference for the production of high-value biological products using inexpensive carbon sources.
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Affiliation(s)
- Ruolin Qin
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Yinzhuang Zhu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Mingmei Ai
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
| | - Xiaoqiang Jia
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- *Correspondence: Xiaoqiang Jia,
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15
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Wu R, Zhang S, Wang S. Development and microbial characterization of Bio-RD-PAOP for effective remediation of polychlorinated biphenyls. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129190. [PMID: 35739720 DOI: 10.1016/j.jhazmat.2022.129190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 05/02/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
Polychlorinated biphenyls (PCBs) as typical halogenated persistent organic pollutants are widely distributed in natural environments, and can be enriched and magnified in organisms via food webs. It is consequently urgent and necessary to develop techniques to completely remove these persistent organohalides. In this study, we developed a process (Bio-RD-PAOP) by integrating microbial reductive dechlorination (Bio-RD) with subsequent persulfate activation and oxidation process (PAOP) for effective remediation of PCBs. Results showed the synergistic combination of advantages of Bio-RD and PAOP in dechlorination of higher-chlorinated PCBs and of PAOP in degradation/mineralization of lower-chlorinated PCBs, respectively. For the PAOP, both experimental evidences and theoretical calculations suggested that degradation rate and efficiency decreased with the increased PCB chlorine numbers. Relative to the Bio-RD and PAOP, Bio-RD-PAOP had significantly higher PCB removal efficiencies, of which values were PCB congener-specific. For example, removal efficiency of Bio-RD-PAOP in removing PCB88 is 2.50 and 1.86 times of that of Bio-RD and PAOP, respectively. In contrast, the efficiency is 1.66 and 3.35 times of Bio-RD and PAOP, respectively, for PCB180 removal. The PAOP-derived oxidizing species (mainly sulfate free radical) significantly decreased microbial abundance, particularly of the organohalide-respiring Dehalococcoides. Notably, co-existence of other microorganisms alleviated the inhibitive effect of oxidizing species on the Dehalococcoides, possibly due to formation of microbial flocs or biofilm. This study provided a promising strategy for extensive remediation of organohalide-contaminated sites, as well as new insight into impact of PAOP-derived oxidizing species on the organohalide-respiring community.
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Affiliation(s)
- Rifeng Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Shangwei Zhang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China.
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16
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Ullah R, Zhu B, Kakar KU, Nawaz Z, Mushtaq M, Durrani TS, Islam ZU, Nawaz F. Micro-synteny conservation analysis revealed the evolutionary history of bacterial biphenyl degradation pathway. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:494-505. [PMID: 35560986 DOI: 10.1111/1758-2229.13081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 06/15/2023]
Abstract
Phenolic compounds have been enlisted by the United States Environmental Protection Agency (USEPA) and the European Union (EU) as pollutants of priority concern. The biphenyl degradation pathway plays an essential role in prokaryote polychlorinated biphenyls degradation. Our understanding of prokaryotic pathways and their evolution has dramatically increased in recent years with the advancements in prokaryotic genome sequencing and analysis tools. In this work, we applied bioinformatics tools to study the evolution of the biphenyl degradation pathway focusing on the phylogeny and initiation of four representative species (Burkholderia xenovorans LB400, Polaromonas naphthalenivorans CJ2, Pseudomonas putida F1 and Rhodococcus jostii RHA1). These species contained partial or full concatenated genes from bph gene cluster (i.e. bphRbphA1A2A3A4BCKHJID). The aim was to establish this pathway's origin and development mode in the prokaryotic world. Genomic screening revealed that many bacterial species possess genes for the biphenyl degradation pathway. However, the micro-synteny conservation analysis indicated that massive gene recruitment events might have occurred during the evolution of the biphenyl degradation pathway. Combining with the phylogenetic positions, this work points to the evolutionary process of acquiring the biphenyl degradation pathway by different fragments through horizontal gene transfer in these bacterial groups. This study reports the first-ever evidence of the birth of this pathway in the represented species.
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Affiliation(s)
- Raqeeb Ullah
- Department of Environmental Science, Faculty of Life Sciences and Informatics, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, 87300, Pakistan
| | - Bo Zhu
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Kaleem U Kakar
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, 87300, Pakistan
| | - Zarqa Nawaz
- Department of Botany, University of Central Punjab, Rawalpindi, Pakistan
| | - Muhammd Mushtaq
- Department of Biotechnology, Faculty of Life Sciences and Informatics, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, 87300, Pakistan
| | - Taimoor Shah Durrani
- Department of Environmental Science, Faculty of Life Sciences and Informatics, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, 87300, Pakistan
| | - Zia Ul Islam
- Department of Civil and Environmental Engineering, The University of Toledo, Toledo, OH, USA
| | - Faheem Nawaz
- Department of Environmental Science, Faculty of Life Sciences and Informatics, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, 87300, Pakistan
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17
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Chen J, Xu F, Yang K, Chen C, Wan J, Shen C. The amendment of Organic matters enhances the anaerobic dechlorination of Polychlorinated Biphenyls in Paddy Soil. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2022; 109:393-400. [PMID: 35687131 DOI: 10.1007/s00128-022-03563-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
The toxicity of high-chlorinated polychlorinated biphenyls (PCBs) can be efficiently reduced through anaerobic dechlorination. However, this approach suffers a lot in face of in situ microbial remediations, like a shortage of biomass. In this study, we showed that the amendment of organic matters could help microbiota in paddy soil with anaerobic dechlorination and greatly shortened the lag period. The presence of organic matters offered a better environment for dechlorinating bacteria. They provided not only a more strictly anaerobic milieu but also copious carbon sources. By using high-throughput 16S rRNA gene sequencing, genera Dehalobacter, Dehalobacterium, and Desulfitobacterium capable of dechlorination were identified in enriched cultures. Taken together, this study proved that extra organic matters can promote anaerobic dechlorination in paddy soil slurry microcosm systems, which provides new insights into the bioremediation of PCB-contaminated soils.
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Affiliation(s)
- Jingwen Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Fengjun Xu
- Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Kai Yang
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Chen Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, China
- Department of Civil and Environmental Engineering, National University of Singapore, Queenstown, Singapore
| | - Jixing Wan
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Chaofeng Shen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, China.
- Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, 310058, Hangzhou, China.
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Biostimulation and Bioaugmentation of Soils Contaminated with Decachlorobiphenyl (PCB-209) Using Native Bacterial Strains Individually and in Consortia. SUSTAINABILITY 2022. [DOI: 10.3390/su14159068] [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
Historically, microorganisms have proven to be efficient alternatives for the removal of PCBs, since these contaminants continue to be a major problem for human health and the environment. In this work, the removal of decachlorobiphenyl (PCB-209) was evaluated using native bacterial strains individually and in consortia through biostimulation and bioaugmentation processes. Bacillus sp. DCB13, Staphylococcus sp. DCB28, and Acinetobacter sp. DCB104 were biostimulated in a minimal medium that initially contained biphenyl and later PCB-209 for adaptation as a carbon source. The removal potential of PCB-209 by bacterial strains was evaluated in a bioaugmentation process under aerobic conditions. Using a completely randomized design, ten different treatments were evaluated. Finally, the bacterial growth (CFU/g of soil) and the chemical characteristics of the bioaugmented soil were determined, as was the content of PCB-209 removed by gas chromatography–mass spectrometry. Strains DCB13, DCB28, and DCB104 showed cell growth (>3.4 × 105 CFU/mL) during 120 h of biostimulation, with a marked difference between treatments with biphenyl compared with those where PCB-209 was added. Strains DCB13 and DCB104 (3.4 × 105 CFU/mL and 2.0 × 106 CFU/mL, respectively) grew better with PCB-209, while DCB28 grew better with biphenyl (4.5 × 106 CFU/mL). In bioaugmented soils contaminated with PCB-209, the strains showed maximum growth when inoculated in a consortium (>2.0 × 104 CFU/g). The results showe that the range of the bacterial elimination of PCB-209 in the treatments was from 9.58 to 17.33 mg/kg. The highest elimination potential of PCB-209 was obtained when the bacterial strains were inoculated in a consortium. These findings open a wide perspective for the use of native bacteria for the cleaning and restoration of soils contaminated by toxic chemicals.
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Prekrasna I, Pavlovska M, Oleinik I, Dykyi E, Slobodnik J, Alygizakis N, Solomenko L, Stoica E. Bacterial communities of the Black Sea exhibit activity against persistent organic pollutants in the water column and sediments. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 234:113367. [PMID: 35272192 DOI: 10.1016/j.ecoenv.2022.113367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 02/23/2022] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
The ability of bacteria to degrade organic pollutants influences their fate in the environment, impact on the other biota and accumulation in the food web. The aim of this study was to evaluate abundance and expression activity of the catabolic genes targeting widespread pollutants, such as polyaromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and hexachloro-cyclohexane (HCH) in the Black Sea water column and sediments. Concentrations of PAHs, PCBs and HCH were determined by gas chromatography (GC) coupled to mass spectrometry (MS) and electron capture (ECD) detectors. bphA1, PAH-RHDα, nahAc, linA and linB that encode biphenyl 2,3 dioxygenase, α-subunits of ring hydroxylating dioxygenases, naphthalene dioxygenase, dehydrochlorinase and halidohydrolase correspondently were quantified by quantitative PCR. More recalcitrant PAHs, PCBs and HCH tended to accumulate in the Black Sea environments. In water samples, 3- and 4-ringed PAHs outnumbered naphthalene, while PAHs with > 4 rings prevailed in the sediments. Congeners with 4-8 chlorines with ortho-position of the substituents were the most abundant among the PCBs. β-HCH was determined at highest concentration in water samples, and total amount of HCH exceeded its legacy Environmental Quality Standard value. bphA1, was the most numerous gene in water layers (105 copies/mL) and sediments (105 copies/mg), followed by linB and PAH-RHDα genes (103 copies/mL; 105 copies/mg). The least abundant genes were linA (103 copies/mL; 104 copies/mg) and nahAc (102 copies/mL; 104 copies/mg). The most widely distributed gene bphА1 was one of the least expressed (10-3-10-2 copies/mL; 10-1 copies/mg). The most actively expressed genes were linB (101-102 copies/mL; 103 copies/mg), PAH-RHDα (101 copies/mL; 102 copies/mg) and linA (10-1-100 copies/mL; 100 copies/mg). Interaction of bacteria with PAHs, PCBs and HCH is evidenced by high copy numbers of the catabolic genes that initiate their degradation. More persistent compounds, such as high-molecular weight PAHs or β-HCH are accumulating in the Black Sea water and sediments, albeit microbial activity is directed against them.
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Affiliation(s)
- Ievgeniia Prekrasna
- State Institution National Antarctic Scientific Center, Taras Shevchenko Blvd., 16, 01601 Kyiv, Ukraine
| | - Mariia Pavlovska
- State Institution National Antarctic Scientific Center, Taras Shevchenko Blvd., 16, 01601 Kyiv, Ukraine; National University of Life and Environmental Sciences of Ukraine, 15, Heroiv Oborony Str., 03041 Kyiv, Ukraine
| | - Iurii Oleinik
- Ukrainian Scientific Center of Ecology of the Sea, 89 Frantsuzsky Blvd., 65009 Odessa, Ukraine
| | - Evgen Dykyi
- State Institution National Antarctic Scientific Center, Taras Shevchenko Blvd., 16, 01601 Kyiv, Ukraine
| | | | - Nikiforos Alygizakis
- Environmental Institute, Okruzna 784/42, 97241 Kos, Slovak Republic; Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens Greece
| | - Liudmyla Solomenko
- National University of Life and Environmental Sciences of Ukraine, 15, Heroiv Oborony Str., 03041 Kyiv, Ukraine
| | - Elena Stoica
- National Institute for Marine Research and Development "Grigore Antipa", Blvd. Mamaia no. 300, RO-900581 Constanţa 3, Romania.
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A New ICE clc Subfamily Integrative and Conjugative Element Responsible for Horizontal Transfer of Biphenyl and Salicylic Acid Catabolic Pathway in the PCB-Degrading Strain Pseudomonas stutzeri KF716. Microorganisms 2021; 9:microorganisms9122462. [PMID: 34946064 PMCID: PMC8704644 DOI: 10.3390/microorganisms9122462] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 11/23/2022] Open
Abstract
Integrative and conjugative elements (ICEs) are chromosomally integrated self-transmissible mobile genetic elements. Although some ICEs are known to carry genes for the degradation of aromatic compounds, information on their genetic features is limited. We identified a new member of the ICEclc family carrying biphenyl catabolic bph genes and salicylic acid catabolic sal genes from the PCB-degrading strain Pseudomonas stutzeri KF716. The 117-kb ICEbph-salKF716 contains common core regions exhibiting homology with those of degradative ICEclc from P. knackmussii B13 and ICEXTD from Azoarcus sp. CIB. A comparison of the gene loci collected from the public database revealed that several putative ICEs from P. putida B6-2, P, alcaliphila JAB1, P. stutzeri AN10, and P. stutzeri 2A20 had highly conserved core regions with those of ICEbph-salKF716, along with the variable region that encodes the catabolic genes for biphenyl, naphthalene, toluene, or phenol. These data indicate that this type of ICE subfamily is ubiquitously distributed within aromatic compound-degrading bacteria. ICEbph-salKF716 was transferred from P. stutzeri KF716 to P. aeruginosa PAO1 via a circular extrachromosomal intermediate form. In this study, we describe the structure and genetic features of ICEbph-salKF716 compared to other catabolic ICEs.
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21
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Ines P, Vlasta D, Sanja F, Ana BK, Dubravka H, Fabrice ML, Nikolina UK. Unraveling metabolic flexibility of rhodococci in PCB transformation. CHEMOSPHERE 2021; 282:130975. [PMID: 34111638 DOI: 10.1016/j.chemosphere.2021.130975] [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: 04/01/2021] [Revised: 05/17/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
Even though the genetic attributes suggest presence of multiple degradation pathways, most of rhodococci are known to transform PCBs only via regular biphenyl (bph) pathway. Using GC-MS analysis, we monitored products formed during transformation of 2,4,4'-trichlorobiphenyl (PCB-28), 2,2',5,5'-tetrachlorobiphenyl (PCB-52) and 2,4,3'-trichlorobiphenyl (PCB-25) by previously characterized PCB-degrading rhodococci Z6, T6, R2, and Z57, with the aim to explore their metabolic pleiotropy in PCB transformations. A striking number of different transformation products (TPs) carrying a phenyl ring as a substituent, both those generated as a part of the bph pathway and an array of unexpected TPs, implied a curious transformation ability. We hypothesized that studied rhodococcal isolates, besides the regular one, use at least two alternative pathways for PCB transformation, including the pathway leading to acetophenone formation (via 3,4 (4,5) dioxygenase attack on the molecule), and a third sideway pathway that includes stepwise oxidative decarboxylation of the aliphatic side chain of the 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate. Structure of the identified chlorinated benzoic acids and acetophenones allowed us to hypothesize that the first two pathways were the outcome of a ring-hydroxylating dioxygenase with the ability to attack both the 2,3 (5,6) and the 3,4 (4,5) positions of the biphenyl ring as well as dechlorination activity at both, -ortho and -para positions. We propose that several TPs produced by the bph pathway could have caused the triggering of the third sideway pathway. In conclusion, this study proposed ability of rhodococci to use different strategies in PCB transformation, which allows them to circumvent potential negative aspect of TPs on the overall transformation pathway.
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Affiliation(s)
- Petrić Ines
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Zagreb, Croatia.
| | - Drevenkar Vlasta
- Institute for Medical Research and Occupational Health, Zagreb, Croatia
| | - Fingler Sanja
- Institute for Medical Research and Occupational Health, Zagreb, Croatia
| | | | - Hršak Dubravka
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Zagreb, Croatia
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22
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Rolli E, Vergani L, Ghitti E, Patania G, Mapelli F, Borin S. 'Cry-for-help' in contaminated soil: a dialogue among plants and soil microbiome to survive in hostile conditions. Environ Microbiol 2021; 23:5690-5703. [PMID: 34139059 PMCID: PMC8596516 DOI: 10.1111/1462-2920.15647] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/25/2021] [Accepted: 06/16/2021] [Indexed: 12/20/2022]
Abstract
An open question in environmental ecology regards the mechanisms triggered by root chemistry to drive the assembly and functionality of a beneficial microbiome to rapidly adapt to stress conditions. This phenomenon, originally described in plant defence against pathogens and predators, is encompassed in the ‘cry‐for‐help’ hypothesis. Evidence suggests that this mechanism may be part of the adaptation strategy to ensure the holobiont fitness in polluted environments. Polychlorinated biphenyls (PCBs) were considered as model pollutants due to their toxicity, recalcitrance and poor phyto‐extraction potential, which lead to a plethora of phytotoxic effects and rise environmental safety concerns. Plants have inefficient detoxification processes to catabolize PCBs, even leading to by‐products with a higher toxicity. We propose that the ‘cry‐for‐help’ mechanism could drive the exudation‐mediated recruitment and sustainment of the microbial services for PCBs removal, exerted by an array of anaerobic and aerobic microbial degrading populations working in a complex metabolic network. Through this synergistic interaction, the holobiont copes with the soil contamination, releasing the plant from the pollutant stress by the ecological services provided by the boosted metabolism of PCBs microbial degraders. Improving knowledge of root chemistry under PCBs stress is, therefore, advocated to design rhizoremediation strategies based on plant microbiome engineering.
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Affiliation(s)
- Eleonora Rolli
- Department of Food, Environmental and Nutritional Sciences, DeFENS, University of Milan, Via Celoria 2, Milan, 20133, Italy
| | - Lorenzo Vergani
- Department of Food, Environmental and Nutritional Sciences, DeFENS, University of Milan, Via Celoria 2, Milan, 20133, Italy
| | - Elisa Ghitti
- Department of Food, Environmental and Nutritional Sciences, DeFENS, University of Milan, Via Celoria 2, Milan, 20133, Italy
| | - Giovanni Patania
- Department of Food, Environmental and Nutritional Sciences, DeFENS, University of Milan, Via Celoria 2, Milan, 20133, Italy
| | - Francesca Mapelli
- Department of Food, Environmental and Nutritional Sciences, DeFENS, University of Milan, Via Celoria 2, Milan, 20133, Italy
| | - Sara Borin
- Department of Food, Environmental and Nutritional Sciences, DeFENS, University of Milan, Via Celoria 2, Milan, 20133, Italy
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23
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Khalid F, Hashmi MZ, Jamil N, Qadir A, Ali MI. Microbial and enzymatic degradation of PCBs from e-waste-contaminated sites: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:10474-10487. [PMID: 33411303 DOI: 10.1007/s11356-020-11996-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 12/07/2020] [Indexed: 05/21/2023]
Abstract
Electronic waste is termed as e-waste and on recycling it produces environmental pollution. Among these e-waste pollutants, polychlorinated biphenyls (PCBs) are significantly important due to ubiquitous, organic in nature and serious health and environmental hazards. PCBs are used in different electrical equipment such as in transformers and capacitors for the purposes of exchange of heat and hydraulic fluids. Bioremediation is a reassuring technology for the elimination of the PCBs from the environment. In spite of their chemical stability, there are several microbes which can bio-transform or mineralize the PCBs aerobically or anaerobically. In this review paper, our objective was to summarize the information regarding PCB-degrading enzymes and microbes. The review suggested that the most proficient PCB degraders during anaerobic condition are Dehalobacter, Dehalococcoides, and Desulfitobacterium and in aerobic condition are Burkholderia, Achromobacter, Comamonas, Ralstonia, Pseudomonas, Bacillus, and Alcaligenes etc., showing the broadest substrate among bacterial strains. Enzymes found in soil such as dehydrogenases and fluorescein diacetate (FDA) esterases have the capability to breakdown PCBs. Biphenyl upper pathway involves four enzymes: dehydrogenase (bphB), multicomponent dioxygenase (bphA, E, F, and G), second dioxygenase (bphC), hydrolase, and (bphD). Biphenyl dioxygenase is considered as the foremost enzyme used for aerobic degradation of PCBs in metabolic pathway. It has been proved that several micro-organisms are responsible for the PCB metabolization. The review provides novel strategies for e-waste-contaminated soil management.
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Affiliation(s)
- Foqia Khalid
- College of Earth and Environmental Science, University of the Punjab, Lahore, Pakistan
| | - Muhammad Zaffar Hashmi
- Department of Chemistry, COMSATS University Islamabad, Islamabad, 44000, Pakistan.
- Pakistan Academy of Science, 3-Constitution Avenue Sector G-5/2, Islamabad, Pakistan.
| | - Nadia Jamil
- College of Earth and Environmental Science, University of the Punjab, Lahore, Pakistan
| | - Abdul Qadir
- College of Earth and Environmental Science, University of the Punjab, Lahore, Pakistan
| | - Muhammad Ishtiaq Ali
- Department of Microbiology, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
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