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Ruan Z, Xu M, Xing Y, Yang K, Xu X, Jiang J, Qiu R. Enhanced growth of wheat in contaminated fields via synthetic microbiome as revealed by genome-scale metabolic modeling. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 953:176047. [PMID: 39241874 DOI: 10.1016/j.scitotenv.2024.176047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 08/08/2024] [Accepted: 09/03/2024] [Indexed: 09/09/2024]
Abstract
The relationship between plants and soil microbial communities is complex and subtle, with microbes playing a crucial role in plant growth. Autochthonous bioaugmentation and nutrient biostimulation are promising bioremediation methods for herbicides in contaminated agricultural soils, but how microbes interact to promote biodegradation and plant growth on barren fields, especially in response to the treatment of the herbicide bromoxynil after wheat seedlings, remains poorly understood. In this study, we explored the microbial community reassembly process from the three-leaf stage to the tillering stage of wheat and put forward the idea of using the overlapping results of three methods (network Zi-Pi analysis, LEfSe analysis, and Random Forest analysis) as keystones for the simplification and optimization of key microbial species in the soil. Then we used genome-scale metabolic models (GSMMs) to design a targeted synthetic microbiome for promoting wheat seedling growing. The results showed that carbon source was more helpful in enriching soil microbial diversity and promoting the role of functional microbial communities, which facilitated the degradation of bromoxynil. Designed a multifunctional synthetic consortium consisting of seven non-degraders which unexpectedly assisted in the degradation of indigenous bacteria, which increased the degradation rate of bromoxynil by 2.05 times, and when adding nutritional supplementation, it increased the degradation rate by 3.65 times. In summary, this study provides important insights for rational fertilization and precise microbial consortium management to improve plant seedling growth in contaminated fields.
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Affiliation(s)
- Zhepu Ruan
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Mengjun Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Youwen Xing
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Kaiqing Yang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Xihui Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China.
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China.
| | - Rongliang Qiu
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China.
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2
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Ruan Z, Chen K, Cao W, Meng L, Yang B, Xu M, Xing Y, Li P, Freilich S, Chen C, Gao Y, Jiang J, Xu X. Engineering natural microbiomes toward enhanced bioremediation by microbiome modeling. Nat Commun 2024; 15:4694. [PMID: 38824157 PMCID: PMC11144243 DOI: 10.1038/s41467-024-49098-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 05/21/2024] [Indexed: 06/03/2024] Open
Abstract
Engineering natural microbiomes for biotechnological applications remains challenging, as metabolic interactions within microbiomes are largely unknown, and practical principles and tools for microbiome engineering are still lacking. Here, we present a combinatory top-down and bottom-up framework to engineer natural microbiomes for the construction of function-enhanced synthetic microbiomes. We show that application of herbicide and herbicide-degrader inoculation drives a convergent succession of different natural microbiomes toward functional microbiomes (e.g., enhanced bioremediation of herbicide-contaminated soils). We develop a metabolic modeling pipeline, SuperCC, that can be used to document metabolic interactions within microbiomes and to simulate the performances of different microbiomes. Using SuperCC, we construct bioremediation-enhanced synthetic microbiomes based on 18 keystone species identified from natural microbiomes. Our results highlight the importance of metabolic interactions in shaping microbiome functions and provide practical guidance for engineering natural microbiomes.
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Affiliation(s)
- Zhepu Ruan
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Kai Chen
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Weimiao Cao
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Lei Meng
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Bingang Yang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Mengjun Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Youwen Xing
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Pengfa Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Shiri Freilich
- Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay, 30095, Israel
| | - Chen Chen
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Yanzheng Gao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China.
| | - Xihui Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China.
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3
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Miao L, Sun S, Ma T, Abdelrahman Yousif Abdellah Y, Wang Y, Mi Y, Yan H, Sun G, Hou N, Zhao X, Li C, Zang H. A Novel Estrone Degradation Gene Cluster and Catabolic Mechanism in Microbacterium oxydans ML-6. Appl Environ Microbiol 2023; 89:e0148922. [PMID: 36847539 PMCID: PMC10057884 DOI: 10.1128/aem.01489-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 02/05/2023] [Indexed: 03/01/2023] Open
Abstract
Global-scale estrone (E1) contamination of soil and aquatic environments results from the widespread use of animal manure as fertilizer, threatening both human health and environmental security. A detailed understanding of the degradation of E1 by microorganisms and the associated catabolic mechanism remains a key challenge for the bioremediation of E1-contaminated soil. Here, Microbacterium oxydans ML-6, isolated from estrogen-contaminated soil, was shown to efficiently degrade E1. A complete catabolic pathway for E1 was proposed via liquid chromatography-tandem mass spectrometry (LC-MS/MS), genome sequencing, transcriptomic analysis, and quantitative reverse transcription-PCR (qRT-PCR). In particular, a novel gene cluster (moc) associated with E1 catabolism was predicted. The combination of heterologous expression, gene knockout, and complementation experiments demonstrated that the 3-hydroxybenzoate 4-monooxygenase (MocA; a single-component flavoprotein monooxygenase) encoded by the mocA gene was responsible for the initial hydroxylation of E1. Furthermore, to demonstrate the detoxification of E1 by strain ML-6, phytotoxicity tests were performed. Overall, our findings provide new insight into the molecular mechanism underlying the diversity of E1 catabolism in microorganisms and suggest that M. oxydans ML-6 and its enzymes have potential applications in E1 bioremediation to reduce or eliminate E1-related environmental pollution. IMPORTANCE Steroidal estrogens (SEs) are mainly produced by animals, while bacteria are major consumers of SEs in the biosphere. However, the understanding of the gene clusters that participate in E1 degradation is still limited, and the enzymes involved in the biodegradation of E1 have not been well characterized. The present study reports that M. oxydans ML-6 has effective SE degradation capacity, which facilitates the development of strain ML-6 as a broad-spectrum biocatalyst for the production of certain desired compounds. A novel gene cluster (moc) associated with E1 catabolism was predicted. The 3-hydroxybenzoate 4-monooxygenase (MocA; a single-component flavoprotein monooxygenase) identified in the moc cluster was found to be necessary and specific for the initial hydroxylation of E1 to generate 4-OHE1, providing new insight into the biological role of flavoprotein monooxygenase.
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Affiliation(s)
- Lei Miao
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Shanshan Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Tian Ma
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| | | | - Yue Wang
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Yaozu Mi
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Haohao Yan
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Guanjun Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Ning Hou
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Xinyue Zhao
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Chunyan Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Hailian Zang
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
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Gribble GW. Naturally Occurring Organohalogen Compounds-A Comprehensive Review. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2023; 121:1-546. [PMID: 37488466 DOI: 10.1007/978-3-031-26629-4_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
The present volume is the third in a trilogy that documents naturally occurring organohalogen compounds, bringing the total number-from fewer than 25 in 1968-to approximately 8000 compounds to date. Nearly all of these natural products contain chlorine or bromine, with a few containing iodine and, fewer still, fluorine. Produced by ubiquitous marine (algae, sponges, corals, bryozoa, nudibranchs, fungi, bacteria) and terrestrial organisms (plants, fungi, bacteria, insects, higher animals) and universal abiotic processes (volcanos, forest fires, geothermal events), organohalogens pervade the global ecosystem. Newly identified extraterrestrial sources are also documented. In addition to chemical structures, biological activity, biohalogenation, biodegradation, natural function, and future outlook are presented.
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Affiliation(s)
- Gordon W Gribble
- Department of Chemistry, Dartmouth College, Hanover, NH, 03755, USA.
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5
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Precise Regulation of Differential Transcriptions of Various Catabolic Genes by OdcR via a Single Nucleotide Mutation in the Promoter Ensures the Safety of Metabolic Flux. Appl Environ Microbiol 2022; 88:e0118222. [PMID: 36036586 PMCID: PMC9499029 DOI: 10.1128/aem.01182-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Synergistic regulation of the expression of various genes in a catabolic pathway is crucial for the degradation, survival, and adaptation of microorganisms in polluted environments. However, how a single regulator accurately regulates and controls differential transcriptions of various catabolic genes to ensure metabolic safety remains largely unknown. Here, a LysR-type transcriptional regulator (LTTR), OdcR, encoded by the regulator gene odcR, was confirmed to be essential for 3,5-dibromo-4-hydroxybenozate (DBHB) catabolism and simultaneously activated the transcriptions of a gene with unknown function, orf419, and three genes, odcA, odcB, and odcC, involved in the DBHB catabolism in Pigmentiphaga sp. strain H8. OdcB further metabolized the highly toxic intermediate 2,6-dibromohydroquinone, which was produced from DBHB by OdcA. The upregulated transcriptional level of odcB was 7- to 9-fold higher than that of orf419, odcA, or odcC in response to DBHB. Through an electrophoretic mobility shift assay and DNase I footprinting assay, DBHB was found to be the effector and essential for OdcR binding to all four promoters of orf419, odcA, odcB, and odcC. A single nucleotide mutation in the regulatory binding site (RBS) of the promoter of odcB (TAT-N11-ATG), compared to those of odcA/orf419 (CAT-N11-ATG) and odcC (CAT-N11-ATT), was identified and shown to enable the significantly higher transcription of odcB. The precise regulation of these genes by OdcR via a single nucleotide mutation in the promoter avoided the accumulation of 2,6-dibromohydroquinone, ensuring the metabolic safety of DBHB. IMPORTANCE Prokaryotes use various mechanisms, including improvement of the activity of detoxification enzymes, to cope with toxic intermediates produced during catabolism. However, studies on how bacteria accurately regulate differential transcriptions of various catabolic genes via a single regulator to ensure metabolic safety are scarce. This study revealed a LysR-type transcriptional activator, OdcR, which strongly activated odcB transcription for the detoxification of the toxic intermediate 2,6-dibromohydroquinone and slightly activated the transcriptions of other genes (orf419, odcA, and odcC) for 3,5-dibromo-4-hydroxybenozate (DBHB) catabolism in Pigmentiphaga sp. strain H8. Interestingly, the differential transcription/expression of the four genes, which ensured the metabolic safety of DBHB in cells, was determined by a single nucleotide mutation in the regulatory binding sites of the four promoters. This study describes a new and ingenious regulatory mode of ensuring metabolic safety in bacteria, expanding our understanding of synergistic transcriptional regulation in prokaryotes.
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Ruan Z, Xu M, Xing Y, Jiang Q, Yang B, Jiang J, Xu X. Interspecies Metabolic Interactions in a Synergistic Consortium Drive Efficient Degradation of the Herbicide Bromoxynil Octanoate. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:11613-11622. [PMID: 36089742 DOI: 10.1021/acs.jafc.2c03057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Microbial communities play vital roles in biogeochemical cycles, allowing biodegradation of a wide range of pollutants. Although many studies have shown the importance of interspecies interactions on activities of communities, fully elucidating the complex interactions in microbial communities is still challenging. Here, we isolated a consortium containing two bacterial strains (Acinetobacter sp. AG3 and Bacillus sp. R45), which could mineralize bromoxynil octanoate (BO) with higher efficiency than either strain individually. The BO degradation pathway by the synergistic consortium was elucidated, and interspecies interactions in the consortium were explored using genome-scale metabolic models (GSMMs). Modeling showed that growth and degradation enhancements were driven by metabolic interactions, such as syntrophic exchanges of small metabolites in the consortium. Besides, nutritional enhancers were predicted to improve BO degradation, which were tested experimentally. Overall, our results will enhance our understanding of microbial mineralization of BO by consortia and promote the application of microbial communities for bioremediation.
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Affiliation(s)
- Zhepu Ruan
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Mengjun Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Youwen Xing
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Qi Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Bingang Yang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Xihui Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
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7
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The Novel Monooxygenase Gene dipD in the dip Gene Cluster of Alcaligenes faecalis JQ135 Is Essential for the Initial Catabolism of Dipicolinic Acid. Appl Environ Microbiol 2022; 88:e0036022. [PMID: 35766505 PMCID: PMC9317849 DOI: 10.1128/aem.00360-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Dipicolinic acid (DPA), an essential pyridine derivative biosynthesized in Bacillus spores, constitutes a major proportion of global biomass carbon pool. Alcaligenes faecalis strain JQ135 could catabolize DPA through the "3HDPA (3-hydroxydipicolinic acid) pathway." However, the genes involved in this 3HDPA pathway are still unknown. In this study, a dip gene cluster responsible for DPA degradation was cloned from strain JQ135. The expression of dip genes was induced by DPA and negatively regulated by DipR. A novel monooxygenase gene, dipD, was crucial for the initial hydroxylation of DPA into 3HDPA and proposed to encode the key catalytic component of the multicomponent DPA monooxygenase. The heme binding protein gene dipF, ferredoxin reductase gene dipG, and ferredoxin genes dipJ/dipK/dipL were also involved in the DPA hydroxylation and proposed to encode other components of the multicomponent DPA monooxygenase. The 18O2 stable isotope labeling experiments confirmed that the oxygen atom in the hydroxyl group of 3HDPA came from dioxygen molecule rather than water. The protein sequence of DipD exhibits no significant sequence similarities with known oxygenases, suggesting that DipD was a new member of oxygenase family. Moreover, bioinformatic survey suggested that the dip gene cluster was widely distributed in many Alpha-, Beta-, and Gammaproteobacteria, including soil bacteria, aquatic bacteria, and pathogens. This study provides new molecular insights into the catabolism of DPA in bacteria. IMPORTANCE Dipicolinic acid (DPA) is a natural pyridine derivative that serves as an essential component of the Bacillus spore. DPA accounts for 5 to 15% of the dry weight of spores. Due to the huge number of spores in the environment, DPA is also considered to be an important component of the global biomass carbon pool. DPA could be decomposed by microorganisms and enter the global carbon cycling; however, the underlying molecular mechanisms are rarely studied. In this study, a DPA catabolic gene cluster (dip) was cloned and found to be widespread in Alpha-, Beta-, and Gammaproteobacteria. The genes responsible for the initial hydroxylation of DPA to 3-hydroxyl-dipicolinic acid were investigated in Alcaligenes faecalis strain JQ135. The present study opens a door to elucidate the mechanism of DPA degradation and its possible role in DPA-based carbon biotransformation on earth.
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Chen K, Xu X, Yang M, Liu T, Liu B, Zhu J, Wang B, Jiang J. Genetic redundancy of 4-hydroxybenzoate 3-hydroxylase genes ensures the catabolic safety of Pigmentiphaga sp. H8 in 3-bromo-4-hydroxybenzoate-contaminated habitats. Environ Microbiol 2022; 24:5123-5138. [PMID: 35876302 DOI: 10.1111/1462-2920.16141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/17/2022] [Accepted: 07/17/2022] [Indexed: 11/28/2022]
Abstract
Genetic redundancy is prevalent in organisms and plays important roles in the evolution of biodiversity and adaptation to environmental perturbation. However, selective advantages of genetic redundancy in overcoming metabolic disturbance due to structural analogues have received little attention. Here, functional divergence of the three 4-hydroxybenzoate 3-hydroxylase (PHBH) genes (phbh1~3) was found in Pigmentiphaga sp. strain H8. The genes phbh1/phbh2 were responsible for 3-bromo-4-hydroxybenzoate (3-Br-4-HB, an anthropogenic pollutant) catabolism, whereas phbh3 was primarily responsible for 4-hydroxybenzoate (4-HB, a natural intermediate of lignin) catabolism. 3-Br-4-HB inhibited 4-HB catabolism by competitively binding PHBH3, and was toxic to strain H8 cells especially at high concentrations. The existence of phbh1/phbh2 not only enabled strain H8 to utilize 3-Br-4-HB, but also ensured the catabolic safety of 4-HB. Molecular docking and site-directed mutagenesis analyses revealed that Val199 and Phe384 of PHBH1/PHBH2 were required for the hydroxylation activity towards 3-Br-4-HB. Phylogenetic analysis indicated that phbh1 and phbh2 originated from a common ancestor and evolved specifically in strain H8 to adapt to 3-Br-4-HB-contaminated habitats, whereas phbh3 evolved independently. This study deepens our understanding of selective advantages of genetic redundancy in prokaryote's metabolic robustness and reveals the factors driving the divergent evolution of redundant genes in adaptation to environmental perturbation. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Kai Chen
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Xihui Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Muji Yang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Tairong Liu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Bin Liu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Jianchun Zhu
- Laboratory Centre of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Baozhan Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
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9
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Cheng M, Chen D, Parales RE, Jiang J. Oxygenases as Powerful Weapons in the Microbial Degradation of Pesticides. Annu Rev Microbiol 2022; 76:325-348. [PMID: 35650666 DOI: 10.1146/annurev-micro-041320-091758] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Oxygenases, which catalyze the reductive activation of O2 and incorporation of oxygen atoms into substrates, are widely distributed in aerobes. They function by switching the redox states of essential cofactors that include flavin, heme iron, Rieske non-heme iron, and Fe(II)/α-ketoglutarate. This review summarizes the catalytic features of flavin-dependent monooxygenases, heme iron-dependent cytochrome P450 monooxygenases, Rieske non-heme iron-dependent oxygenases, Fe(II)/α-ketoglutarate-dependent dioxygenases, and ring-cleavage dioxygenases, which are commonly involved in pesticide degradation. Heteroatom release (hydroxylation-coupled hetero group release), aromatic/heterocyclic ring hydroxylation to form ring-cleavage substrates, and ring cleavage are the main chemical fates of pesticides catalyzed by these oxygenases. The diversity of oxygenases, specificities for electron transport components, and potential applications of oxygenases are also discussed. This article summarizes our current understanding of the catalytic mechanisms of oxygenases and a framework for distinguishing the roles of oxygenases in pesticide degradation. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Minggen Cheng
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs and Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China;
| | - Dian Chen
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Rebecca E Parales
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, California, USA
| | - Jiandong Jiang
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs and Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China;
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10
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Min J, Fang S, Peng J, Lv X, Xu L, Li Y, Hu X. Microbial detoxification of 2,4,6-tribromophenol via a novel process with consecutive oxidative and hydrolytic debromination: Biochemical, genetic and evolutionary characterization. ENVIRONMENTAL RESEARCH 2022; 205:112494. [PMID: 34890595 DOI: 10.1016/j.envres.2021.112494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/26/2021] [Accepted: 12/01/2021] [Indexed: 06/13/2023]
Abstract
As a typical brominated flame retardants (BFRs), 2,4,6-tribromophenol (TBP) has serious hazard to the environmental health and its environmental fate has attracted considerable attention. Dehalogenation reaction plays key role in microbial TBP degradation and detoxification. So far, several halophenols-degrading enzymes have been reported to transform their substrate by oxidative dehalogenation; however, the molecular and biochemistry characterization of microbial hydrolytic dehalogenation is limited. In this study, Cupriavidus sp. CNP-8 with high TBP degradation activity was found to degrade TBP via an obviously differnet pathway as compared to other reported TBP-degraders. The transcription of hnp genes were significantly upregulated with TBP stimulation, indicating their involvment in TBP degradation. Enzymatic assays with 18O-labeling experiments showed that HnpAB, a two-component FAD-dependent monooxygenase, transformed TBP via consecutive oxidative and hydrolytic debromination reactions with the formation of 6-bromo-1,2,4-benzenetriol (BBT) as the ring-cleavage substrate. The function of the BBT ring-cleavage enzyme (HnpC) was also characterized both in vitro and in vivo. This finding provides new molecular mechanism of microbial detoxification of TBP and novel information of the environmental fate of this BFRs. Furthermore, to investigate the frequency of this novel dehalogenation mechanism in microbes, we also analyzed the distribution as well as the genetic structure of the hnpABC cluster by comparative genomics. Although hnpA homolog is distributed in several bacterial genera including Cupriavidus, Paraburkholderia, Variovorax and Streptomyces, the complete hnpABC cluster is only retrieved from Cupriavidus and strictly conservative in the genomes. This indicated that Cupriavidus have unique evolutionary pattern in acquiring the hnpABC to degrade TBP and its analogs, enhancing our understanding of the microbial adaptive evolution in halophenols-contaminated environment.
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Affiliation(s)
- Jun Min
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Suyun Fang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Jian Peng
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Xin Lv
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Lingxue Xu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Yan Li
- College of Life Science of Yantai University, Yantai, China
| | - Xiaoke Hu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.
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11
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Westphal AH, Tischler D, van Berkel WJH. Natural diversity of FAD-dependent 4-hydroxybenzoate hydroxylases. Arch Biochem Biophys 2021; 702:108820. [PMID: 33684360 DOI: 10.1016/j.abb.2021.108820] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/19/2021] [Accepted: 02/21/2021] [Indexed: 01/05/2023]
Abstract
4-Hydroxybenzoate 3-hydroxylase (PHBH) is the most extensively studied group A flavoprotein monooxygenase (FPMO). PHBH is almost exclusively found in prokaryotes, where its induction, usually as a consequence of lignin degradation, results in the regioselective formation of protocatechuate, one of the central intermediates in the global carbon cycle. In this contribution we introduce several less known FAD-dependent 4-hydroxybenzoate hydroxylases. Phylogenetic analysis showed that the enzymes discussed here reside in distinct clades of the group A FPMO family, indicating their separate divergence from a common ancestor. Protein homology modelling revealed that the fungal 4-hydroxybenzoate 3-hydroxylase PhhA is structurally related to phenol hydroxylase (PHHY) and 3-hydroxybenzoate 4-hydroxylase (3HB4H). 4-Hydroxybenzoate 1-hydroxylase (4HB1H) from yeast catalyzes an oxidative decarboxylation reaction and is structurally similar to 3-hydroxybenzoate 6-hydroxylase (3HB6H), salicylate hydroxylase (SALH) and 6-hydroxynicotinate 3-monooxygenase (6HNMO). Genome mining suggests that the 4HB1H activity is widespread in the fungal kingdom and might be responsible for the oxidative decarboxylation of vanillate, an import intermediate in lignin degradation. 4-Hydroxybenzoyl-CoA 1-hydroxylase (PhgA) catalyzes an intramolecular migration reaction (NIH shift) during the three-step conversion of 4-hydroxybenzoate to gentisate in certain Bacillus species. PhgA is phylogenetically related to 4-hydroxyphenylacetate 1-hydroxylase (4HPA1H). In summary, this paper shines light on the natural diversity of group A FPMOs that are involved in the aerobic microbial catabolism of 4-hydroxybenzoate.
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Affiliation(s)
- Adrie H Westphal
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands.
| | - Dirk Tischler
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Germany.
| | - Willem J H van Berkel
- Laboratory of Food Chemistry, Wageningen University & Research, Wageningen, the Netherlands.
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12
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Maucourt B, Vuilleumier S, Bringel F. Transcriptional regulation of organohalide pollutant utilisation in bacteria. FEMS Microbiol Rev 2020; 44:189-207. [PMID: 32011697 DOI: 10.1093/femsre/fuaa002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 01/31/2020] [Indexed: 12/13/2022] Open
Abstract
Organohalides are organic molecules formed biotically and abiotically, both naturally and through industrial production. They are usually toxic and represent a health risk for living organisms, including humans. Bacteria capable of degrading organohalides for growth express dehalogenase genes encoding enzymes that cleave carbon-halogen bonds. Such bacteria are of potential high interest for bioremediation of contaminated sites. Dehalogenase genes are often part of gene clusters that may include regulators, accessory genes and genes for transporters and other enzymes of organohalide degradation pathways. Organohalides and their degradation products affect the activity of regulatory factors, and extensive genome-wide modulation of gene expression helps dehalogenating bacteria to cope with stresses associated with dehalogenation, such as intracellular increase of halides, dehalogenase-dependent acid production, organohalide toxicity and misrouting and bottlenecks in metabolic fluxes. This review focuses on transcriptional regulation of gene clusters for dehalogenation in bacteria, as studied in laboratory experiments and in situ. The diversity in gene content, organization and regulation of such gene clusters is highlighted for representative organohalide-degrading bacteria. Selected examples illustrate a key, overlooked role of regulatory processes, often strain-specific, for efficient dehalogenation and productive growth in presence of organohalides.
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Affiliation(s)
- Bruno Maucourt
- Université de Strasbourg, UMR 7156 CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Stéphane Vuilleumier
- Université de Strasbourg, UMR 7156 CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Françoise Bringel
- Université de Strasbourg, UMR 7156 CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
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13
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Yun H, Liang B, Kong D, Li X, Wang A. Fate, risk and removal of triclocarban: A critical review. JOURNAL OF HAZARDOUS MATERIALS 2020; 387:121944. [PMID: 31901847 DOI: 10.1016/j.jhazmat.2019.121944] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 12/01/2019] [Accepted: 12/19/2019] [Indexed: 06/10/2023]
Abstract
The halogenated antimicrobial triclocarban (TCC) has large production and consumption over last decades. Its extensive utilization in personal care products and insufficient treatment in conventional wastewater treatment plants (WWTPs) has led to its listing as one of emerging organic contaminants (EOCs). Due to the hydrophobicity and chemical stability of TCC, it has been omnipresent detected in terrestrial and aquatic environments, and its prolonged exposure has thrown potential pernicious threat to ecosystem and human health. Considering its recalcitrance, especially under anoxic conditions, both biological and non-biological methods have been exploited for its removal. The efficiency of advanced oxidation processes was optimistic, but complete removal can rarely be realized through a single method. The biodegradation of TCC either with microbial community or pure culture is feasible but efficient bacterial degraders and the molecular mechanism of degradation need to be further explored. This review provides comprehensive information of the occurrence, potential ecological and health effects, and biological and non-biological removal of TCC, and outlines future prospects for the risk evaluation and enhanced bioremediation of TCC in various environments.
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Affiliation(s)
- Hui Yun
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshui South Road #222, Lanzhou, 730000, Gansu, China; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshui South Road #222, Lanzhou, 730000, Gansu, China; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Bin Liang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| | - Deyong Kong
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Shenyang Academy of Environmental Sciences, Shenyang, 110167, China
| | - Xiangkai Li
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshui South Road #222, Lanzhou, 730000, Gansu, China; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshui South Road #222, Lanzhou, 730000, Gansu, China
| | - Aijie Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
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14
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Ma Q, Qu H, Meng N, Li S, Wang J, Liu S, Qu Y, Sun Y. Biodegradation of skatole by Burkholderia sp. IDO3 and its successful bioaugmentation in activated sludge systems. ENVIRONMENTAL RESEARCH 2020; 182:109123. [PMID: 32069749 DOI: 10.1016/j.envres.2020.109123] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/03/2020] [Accepted: 01/06/2020] [Indexed: 06/10/2023]
Abstract
Skatole is the key malodorous compound in livestock and poultry waste and wastewater with a low odor threshold. It not only causes serious nuisance to residents and workers, but also poses threat to the environment and human health due to its biotoxicity and recalcitrant nature. Biological treatment is an eco-friendly and cost-effective approach for skatole removal, while the bacterial resources are scarce. Herein, the Burkholderia strain was reported to efficiently degrade skatole for the first time. Results showed that strain IDO3 maintained high skatole-degrading performance under the conditions of pH 4.0-9.0, rotate speed 0-250 rpm, and temperature 30-35 °C. RNA-seq analysis indicated that skatole activated the oxidative phosphorylation and ATP production levels in strain IDO3. The oxidoreductase activity item which contained 373 differently expressed genes was significantly impacted by Gene Ontology analysis. Furthermore, the bioaugmentation experiment demonstrated that strain IDO3 could notably increase the removal of skatole in activated sludge systems. High-throughput 16S rRNA gene sequencing data indicated that the alpha-diversity and bacterial community tended to be stable in the bioaugmented group after 8 days operation. PICRUSt analysis indicated that xenobiotics biodegradation and metabolism, and membrane transport categories significantly increased, consistent with the improved skatole removal performance in the bioaugmented group. Burkholderia was survived and colonized to be the predominant population during the whole operation process (34.19-64.00%), confirming the feasibility of Burkholderia sp. IDO3 as the bioaugmentation agent in complex systems.
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Affiliation(s)
- Qiao Ma
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, China.
| | - Hui Qu
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, China
| | - Nan Meng
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, China
| | - Shuzhen Li
- School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Jingwei Wang
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, China
| | - Shengwei Liu
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, China
| | - Yuanyuan Qu
- School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yeqing Sun
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, China.
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Min J, Chen W, Hu X. Biodegradation of 2,6-dibromo-4-nitrophenol by Cupriavidus sp. strain CNP-8: Kinetics, pathway, genetic and biochemical characterization. JOURNAL OF HAZARDOUS MATERIALS 2019; 361:10-18. [PMID: 30176407 DOI: 10.1016/j.jhazmat.2018.08.063] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 08/18/2018] [Accepted: 08/20/2018] [Indexed: 06/08/2023]
Abstract
Compound 2,6-dibromo-4-nitrophenol (2,6-DBNP) with high cytotoxicity and genotoxicity has been recently identified as an emerging brominated disinfection by-product during chloramination and chlorination of water, and its environmental fate is of great concern. To date, the biodegradation process of 2,6-DBNP is unknown. Herein, Cupriavidus sp. strain CNP-8 was reported to be able to utilize 2,6-DBNP as a sole source of carbon, nitrogen and energy. It degraded 2,6-DBNP in concentrations up to 0.7 mM, and the degradation of 2,6-DBNP conformed to Haldane inhibition model with μmax of 0.096 h-1, Ks of 0.05 mM and Ki of 0.31 mM. Comparative transcriptome and real-time quantitative PCR analyses suggested that the hnp gene cluster was likely responsible for 2,6-DBNP catabolism. Three Hnp proteins were purified and functionally verified. HnpA, a FADH2-dependent monooxygenase, was found to catalyze the sequential denitration and debromination of 2,6-DBNP to 6-bromohydroxyquinol (6-BHQ) in the presence of the flavin reductase HnpB. Gene knockout and complementation revealed that hnpA is essential for strain CNP-8 to utiluze 2,6-DBNP. HnpC, a 6-BHQ 1,2-dioxygenase was proposed to catalyze the ring-cleavage of 6-BHQ during 2,6-DBNP catabolism. These results fill a gap in the understanding of the microbial degradation process and mechanism of 2,6-DBNP.
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Affiliation(s)
- Jun Min
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Weiwei Chen
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Xiaoke Hu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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