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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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Wu D, Wang W, Yao Y, Li H, Wang Q, Niu B. Microbial interactions within beneficial consortia promote soil health. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:165801. [PMID: 37499809 DOI: 10.1016/j.scitotenv.2023.165801] [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: 01/31/2022] [Revised: 04/26/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023]
Abstract
By ecologically interacting with various biotic and abiotic agents acting in soil ecosystems, highly diverse soil microorganisms establish complex and stable assemblages and survive in a community context in natural settings. Besides facilitating soil microbiome to maintain great levels of population homeostasis, such microbial interactions drive soil microbes to function as the major engine of terrestrial biogeochemical cycling. It is verified that the regulative effect of microbe-microbe interplay plays an instrumental role in microbial-mediated promotion of soil health, including bioremediation of soil pollutants and biocontrol of soil-borne phytopathogens, which is considered an environmentally friendly strategy for ensuring the healthy condition of soils. Specifically, in microbial consortia, it has been proven that microorganism-microorganism interactions are involved in enhancing the soil health-promoting effectiveness (i.e., efficacies of pollution reduction and disease inhibition) of the beneficial microbes, here defined as soil health-promoting agents. These microbial interactions can positively regulate the soil health-enhancing effect by supporting those soil health-promoting agents utilized in combination, as multi-strain soil health-promoting agents, to overcome three main obstacles: inadequate soil colonization, insufficient soil contaminant eradication and inefficient soil-borne pathogen suppression, all of which can restrict their probiotic functionality. Yet the mechanisms underlying such beneficial interaction-related adjustments and how to efficiently assemble soil health-enhancing consortia with the guidance of microbe-microbe communications remain incompletely understood. In this review, we focus on bacterial and fungal soil health-promoting agents to summarize current research progress on the utilization of multi-strain soil health-promoting agents in the control of soil pollution and soil-borne plant diseases. We discuss potential microbial interaction-relevant mechanisms deployed by the probiotic microorganisms to upgrade their functions in managing soil health. We emphasize the interplay-related factors that should be taken into account when building soil health-promoting consortia, and propose a workflow for assembling them by employing a reductionist synthetic community approach.
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Affiliation(s)
- Di Wu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; The Center for Basic Forestry Research, Northeast Forestry University, Harbin 150040, China; College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Weixiong Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; The Center for Basic Forestry Research, Northeast Forestry University, Harbin 150040, China; College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yanpo Yao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Hongtao Li
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Qi Wang
- Department of Plant Pathology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Ben Niu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; The Center for Basic Forestry Research, Northeast Forestry University, Harbin 150040, China; College of Life Science, Northeast Forestry University, Harbin 150040, China.
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Han Z, Moh ESX, Santos ALS, Barcellos IC, Peng Y, Huang W, Ye J. Dechlorination of wastewater from shell-based glucosamine processing by mangrove wetland-derived fungi. Front Microbiol 2023; 14:1271286. [PMID: 37901808 PMCID: PMC10613029 DOI: 10.3389/fmicb.2023.1271286] [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: 08/04/2023] [Accepted: 09/28/2023] [Indexed: 10/31/2023] Open
Abstract
Wastewater from processing crustacean shell features ultrahigh chloride content. Bioremediation of the wastewater is challenging due to the high chloride ion content, making it inhospitable for most microorganisms to survive and growth. In this study, mangrove wetland-derived fungi were first tested for their salt tolerance, and the highly tolerant isolates were cultured in shrimp processing wastewater and the chloride concentration was monitored. Notably, the filamentous fungal species Aspergillus piperis could remove over 70% of the chloride in the wastewater within 3 days, with the fastest biomass increase (2.01 times heavier) and chloride removal occurring between day one and two. The chloride ions were sequestered into the fungal cells. The genome of this fungal species contained Cl- conversion enzymes, which may have contributed to the ion removal. The fungal strain was found to be of low virulence in larval models and could serve as a starting point for further considerations in bioremediation of shell processing wastewater, promoting the development of green technology in the shell processing industry.
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Affiliation(s)
- Zhiping Han
- College of Food Science and Engineering, Lingnan Normal University, Zhanjiang, Guangdong, China
| | - Edward S. X. Moh
- ARC Centre of Excellence for Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | - André L. S. Santos
- Department of General Microbiology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), and Rede Micologia RJ – FAPERJ, Rio de Janeiro, Brazil
| | - Iuri C. Barcellos
- Department of General Microbiology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), and Rede Micologia RJ – FAPERJ, Rio de Janeiro, Brazil
| | - Yuanhuai Peng
- College of Food Science and Engineering, Lingnan Normal University, Zhanjiang, Guangdong, China
| | - Weicong Huang
- College of Food Science and Engineering, Lingnan Normal University, Zhanjiang, Guangdong, China
| | - Jianzhi Ye
- Agricultural Products Processing Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, China
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Jiang L, Zhang J, Fang M, Qin Y, Huang Y, Tao R. Analysis of subgingival micro-organisms based on multi-omics and Treg/Th17 balance in type 2 diabetes with/without periodontitis. Front Microbiol 2022; 13:939608. [PMID: 36519166 PMCID: PMC9743466 DOI: 10.3389/fmicb.2022.939608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 10/10/2022] [Indexed: 01/02/2024] Open
Abstract
Type 2 diabetes mellitus (T2DM) and periodontitis are common and interrelated diseases, resulting in altered host response microbiota. The subgingival micro-organisms play a key role in periodontitis pathogenesis. To assess the shift of subgingival microbiome and metabolome in T2DM, we performed an analysis of the subgingival microbiome in patients with T2DM (n = 20) compared with non-diabetes (ND) subjects (n = 21). Furthermore, patients were subdivided into 10 T2DM with periodontitis (DP), 10 T2DM without periodontitis (DNP), 10 periodontitis (P), and 11 healthy control (H) groups. 16SrRNA gene sequencing combined with ultra high-performance liquid chromatography-mass spectrometry (UHPLC-MS) based metabolomics was performed in all participants. T lymphocyte immunity was analyzed by flow cytometry. Furthermore, the network relationship among subgingival micro-organisms, metabolites, blood glucose level, and T lymphocyte immunity were analyzed. The results showed that the difference of the subgingival microbiome from healthy to periodontitis status was less prominent in T2DM compared with ND, though the clinical signs of disease were similar. The bacteria Eubacterium nodatum group, Filifactor, Fretibacterium, Peptostreptococcus, and Desulfovibrio, amongst others, may be important in the pathopoiesia of periodontitis in the T2DM state. In addition, some dominant bacteria showed network relationships. The Treg/Th17 ratio was lower in the DP and DNP groups than in the P and H groups-though that of P was lower than for H. The percentage of CD4+/CD8+ PD1 and CD8+ PDL1 was higher in the DP and DNP groups than in the H group; the percentage of CD8+ PDL1 was higher in the DP than P groups. Subgingival micro-organisms in periodontitis had a significant metabolic shift in terms of their signature metabolites. Butyrate metabolism and phenylalanine metabolism may play a role in the pathogenesis of periodontitis with/without T2DM. Specifically, biphenyl degradation, tryptophan metabolism, and the two-component system may play important roles in periodontitis with T2DM. Lastly, the network relationship among subgingival micro-organisms, metabolites, blood glucose level, and T lymphocyte immunity were unbalanced. This study identified the changes in the subgingival microbiome associated with periodontitis in T2DM, as well as the associated network between bacterial flora, metabolism dysbiosis, and immune regulation.
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Affiliation(s)
- Lanlan Jiang
- Department of Periodontics and Oral Medicine, College of Stomatology, Guangxi Medical University, Nanning, China
- Guangxi Health Commission Key Laboratory of Prevention and Treatment for Oral Infectious Diseases, Nanning, China
- Guangxi Key Laboratory of the Rehabilitation and Reconstruction for Oral and Maxillofacial Research, Nanning, China
| | - Jiaming Zhang
- Guangxi Health Commission Key Laboratory of Prevention and Treatment for Oral Infectious Diseases, Nanning, China
| | - Meifei Fang
- Department of Periodontics and Oral Medicine, College of Stomatology, Guangxi Medical University, Nanning, China
| | - Yingfen Qin
- Department of Endocrinology, The First Affiliated Hospital, Guangxi Medical University, Nanning, China
| | - Yuxiao Huang
- Department of Periodontics and Oral Medicine, College of Stomatology, Guangxi Medical University, Nanning, China
| | - Renchuan Tao
- Department of Periodontics and Oral Medicine, College of Stomatology, Guangxi Medical University, Nanning, China
- Guangxi Health Commission Key Laboratory of Prevention and Treatment for Oral Infectious Diseases, Nanning, China
- Guangxi Key Laboratory of the Rehabilitation and Reconstruction for Oral and Maxillofacial Research, Nanning, China
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Dutta N, Usman M, Ashraf MA, Luo G, Zhang S. A critical review of recent advances in the bio-remediation of chlorinated substances by microbial dechlorinators. CHEMICAL ENGINEERING JOURNAL ADVANCES 2022. [DOI: 10.1016/j.ceja.2022.100359] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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Malik G, Arora R, Chaturvedi R, Paul MS. Implementation of Genetic Engineering and Novel Omics Approaches to Enhance Bioremediation: A Focused Review. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2022; 108:443-450. [PMID: 33837794 DOI: 10.1007/s00128-021-03218-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 03/25/2021] [Indexed: 06/12/2023]
Abstract
Bioremediation itself is considered to be a cost effective soil clean-up technique and preferred over invasive physical and chemical treatments. Besides increasing efficiency, application of genetic engineering has led to reduction in the time duration required to achieve remediation, overcoming the so called 'Achilles heel' of Bioremediation. Omics technologies, namely genomics, transcriptomics, proteomics, and metabolomics, are being employed extensively to gain insights at genetic level. A wise synchronised application of these approaches can help scrutinize complex metabolic pathways, and molecular changes in response to heavy metal stress, and also its fate i.e., uptake, transport, sequestration and detoxification. In the present review, an account of some latest achievements made in the field is presented.
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Affiliation(s)
| | - Rahul Arora
- The Francis Crick Institute, London, United Kingdom
- Division of Biosciences, University College London, London, United Kingdom
| | | | - Manoj S Paul
- Department of Botany, St. John's College, Agra, U.P, India
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Li R, Ren W, Teng Y, Sun Y, Xu Y, Zhao L, Wang X, Christie P, Luo Y. The inhibitory mechanism of natural soil colloids on the biodegradation of polychlorinated biphenyls by a degrading bacterium. JOURNAL OF HAZARDOUS MATERIALS 2021; 415:125687. [PMID: 34088185 DOI: 10.1016/j.jhazmat.2021.125687] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 03/05/2021] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
In spite of extensive studies of soil model components, the role of natural soil colloids in the biodegradation of organic pollutants remain poorly understood. Accordingly, the present study selected Mollisol colloids (MCs) and Ultisol colloids (UCs) to investigate their effects on the biodegradation of 3, 3', 4, 4'-tetrachlorobiphenyl (PCB77) by Bradyrhizobium diazoefficiens USDA 110. Results demonstrated that both natural soil colloids significantly decreased the biodegradation of PCB77, which partly resulted from the significant decrease in the bioaccessibility of PCB77. Furthermore, the activity of Bradyrhizobium diazoefficiens USDA 110 was remarkably inhibited under the exposure to the two types of soil colloids, which was mainly ascribed to the inhibition of cell reproduction but not the lethal effect of reactive oxygen species. The calculated results from Ex-DLVO theory further indicated that the repulsion between UCs and biodegrading bacteria retarded the effective contact of cells with adsorbed PCB77 from UCs, resulting in the decline of the rate of cell reproduction. In general, the inhibition of MCs was limited to PCB77 bioaccessibility, whereas the negative effect of UCs was controlled by PCB77 bioaccessibility and the effective contact of cells with colloids. This study could provide implication for the enhancement of microbial remediation in contaminated soil.
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Affiliation(s)
- Ran Li
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjie Ren
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China.
| | - Yi Sun
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yongfeng Xu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Ling Zhao
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaomi Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Peter Christie
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yongming Luo
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
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The Operon Encoding Hydrolytic Dehalogenation of 4-Chlorobenzoate Is Transcriptionally Regulated by the TetR-Type Repressor FcbR and Its Ligand 4-Chlorobenzoyl Coenzyme A. Appl Environ Microbiol 2021; 87:AEM.02652-20. [PMID: 33397703 DOI: 10.1128/aem.02652-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/22/2020] [Indexed: 12/24/2022] Open
Abstract
The bacterial hydrolytic dehalogenation of 4-chlorobenzoate (4CBA) is a coenzyme A (CoA)-activation-type catabolic pathway that is usually a common part of the microbial mineralization of chlorinated aromatic compounds. Previous studies have shown that the transport and dehalogenation genes for 4CBA are typically clustered as an fcbBAT1T2T3C operon and inducibly expressed in response to 4CBA. However, the associated molecular mechanism remains unknown. In this study, a gene (fcbR) adjacent to the fcb operon was predicted to encode a TetR-type transcriptional regulator in Comamonas sediminis strain CD-2. The fcbR knockout strain exhibited constitutive expression of the fcb cluster. In the host Escherichia coli, the expression of the Pfcb -fused green fluorescent protein (gfp) reporter was repressed by the introduction of the fcbR gene, and genetic studies combining various catabolic genes suggest that the ligand for FcbR may be an intermediate metabolite. Purified FcbR could bind to the Pfcb DNA probe in vitro, and the metabolite 4-chlorobenzyl-CoA (4CBA-CoA) prevented FcbR binding to the P fcb DNA probe. Isothermal titration calorimetry (ITC) measurements showed that 4CBA-CoA could bind to FcbR at a 1:1 molar ratio. DNase I footprinting showed that FcbR protected a 42-bp DNA motif (5'-GGAAATCAATAGGTCCATAGAAAATCTATTGACTAATCGAAT-3') that consists of two sequence repeats containing four pseudopalindromic sequences (5'-TCNATNGA-3'). This binding motif overlaps with the -35 box of Pfcb and was proposed to prevent the binding of RNA polymerase. This study characterizes a transcriptional repressor of the fcb operon, together with its ligand, thus identifying halogenated benzoyl-CoA as belonging to the class of ligands of transcriptional regulators.IMPORTANCE The bacterial hydrolytic dehalogenation of 4CBA is a special CoA-activation-type catabolic pathway that plays an important role in the biodegradation of polychlorinated biphenyls and some herbicides. With genetic and biochemical approaches, the present study identified the transcriptional repressor and its cognate effector of a 4CBA hydrolytic dehalogenation operon. This work extends halogenated benzoyl-CoA as a new member of CoA-derived effector compounds that mediate allosteric regulation of transcriptional regulators.
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Recent advances in the biodegradation of polychlorinated biphenyls. World J Microbiol Biotechnol 2020; 36:145. [PMID: 32862310 DOI: 10.1007/s11274-020-02922-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/22/2020] [Indexed: 12/22/2022]
Abstract
Polychlorinated biphenyls (PCBs) are typical lasting organic pollutants. Persistence and recalcitrance to biodegradation of PCBs have hampered the transformation of PCB congeners from the environment. Biological transformation of polychlorinated biphenyls could take place through anaerobic dechlorination, aerobic microbial degradation, and a combination of transformation of anaerobic dechlorination and aerobic degradation. Under anaerobic conditions, microbial dechlorination is an important degradation mode for PCBs, especially high-chlorinated congeners. The low-chlorinated compounds formed after reductive dechlorination could be further aerobically degraded and completely mineralized. This paper reviews the recent advances in biological degradation of PCBs, introduces the functional bacteria and enzymes involved in the anaerobic and aerobic degradation of PCBs, and discusses the synergistic action of anaerobic reduction and aerobic degradation. In addition, the different ways to the microbial remediation of PCBs-contaminated environments are discussed. This review provides a theoretical foundation and practical basis to use PCBs-degrading microorganisms for bioremediation.
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