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Aso RE, Obuekwe IS. Polycyclic aromatic hydrocarbon: underpinning the contribution of specialist microbial species to contaminant mitigation in the soil. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:654. [PMID: 38913190 DOI: 10.1007/s10661-024-12778-w] [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: 03/04/2024] [Accepted: 06/06/2024] [Indexed: 06/25/2024]
Abstract
The persistence of PAHs poses a significant challenge for conventional remediation approaches, necessitating the exploration of alternative, sustainable strategies for their mitigation. This review underscores the vital role of specialized microbial species (nitrogen-fixing, phosphate-solubilizing, and biosurfactant-producing bacteria) in tackling the environmental impact of polycyclic aromatic hydrocarbons (PAHs). These resistant compounds demand innovative remediation strategies. The study explores microbial metabolic capabilities for converting complex PAHs into less harmful byproducts, ensuring sustainable mitigation. Synthesizing literature from 2016 to 2023, it covers PAH characteristics, sources, and associated risks. Degradation mechanisms by bacteria and fungi, key species, and enzymatic processes are examined. Nitrogen-fixing and phosphate-solubilizing bacteria contributions in symbiotic relationships with plants are highlighted. Biosurfactant-producing bacteria enhance PAH solubility, expanding microbial accessibility for degradation. Cutting-edge trends in omics technologies, synthetic biology, genetic engineering, and nano-remediation offer promising avenues. Recommendations emphasize genetic regulation, field-scale studies, sustainability assessments, interdisciplinary collaboration, and knowledge dissemination. These insights pave the way for innovative, sustainable PAH-contaminated environment restoration.
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Affiliation(s)
- Rufus Emamoge Aso
- Department of Microbiology, Faculty of Life Sciences, University of Benin, Benin, Edo State, Nigeria
| | - Ifeyinwa Sarah Obuekwe
- Department of Microbiology, Faculty of Life Sciences, University of Benin, Benin, Edo State, Nigeria.
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2
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Malhotra H, Dhamale T, Kaur S, Kasarlawar ST, Phale PS. Metabolic engineering of Pseudomonas bharatica CSV86 T to degrade Carbaryl (1-naphthyl- N-methylcarbamate) via the salicylate-catechol route. Microbiol Spectr 2024:e0028424. [PMID: 38869268 DOI: 10.1128/spectrum.00284-24] [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: 02/06/2024] [Accepted: 04/22/2024] [Indexed: 06/14/2024] Open
Abstract
Pseudomonas bharatica CSV86T displays the unique property of preferential utilization of aromatic compounds over simple carbon sources like glucose and glycerol and their co-metabolism with organic acids. Well-characterized growth conditions, aromatic compound metabolic pathways and their regulation, genome sequence, and advantageous eco-physiological traits (indole acetic acid production, alginate production, fusaric acid resistance, organic sulfur utilization, and siderophore production) make it an ideal host for metabolic engineering. Strain CSV86T was engineered for Carbaryl (1-naphthyl-N-methylcarbamate) degradation via salicylate-catechol route by expression of a Carbaryl hydrolase (CH) and a 1-naphthol 2-hydroxylase (1NH). Additionally, the engineered strain exhibited faster growth on Carbaryl upon expression of the McbT protein (encoded by the mcbT gene, a part of Carbaryl degradation upper operon of Pseudomonas sp. C5pp). Bioinformatic analyses predict McbT to be an outer membrane protein, and Carbaryl-dependent expression suggests its probable role in Carbaryl uptake. Enzyme activity and protein analyses suggested periplasmic localization of CH (carrying transmembrane domain plus signal peptide sequence at the N-terminus) and 1NH, enabling compartmentalization of the pathway. Enzyme activity, whole-cell oxygen uptake, spent media analyses, and qPCR results suggest that the engineered strain preferentially utilizes Carbaryl over glucose. The plasmid-encoded degradation property was stable for 75-90 generations even in the absence of selection pressure (kanamycin or Carbaryl). These results indicate the utility of P. bharatica CSV86T as a potential host for engineering various aromatic compound degradation pathways.IMPORTANCEThe current study describes engineering of Carbaryl metabolic pathway in Pseudomonas bharatica CSV86T. Carbaryl, a naphthalene-derived carbamate pesticide, is known to act as an endocrine disruptor, mutagen, cytotoxin, and carcinogen. Removal of xenobiotics from the environment using bioremediation faces challenges, such as slow degradation rates, instability of the degradation phenotype, and presence of simple carbon sources in the environment. The engineered CSV86-MEC2 overcomes these disadvantages as Carbaryl was degraded preferentially over glucose. Furthermore, the plasmid-borne degradation phenotype is stable, and presence of glucose and organic acids does not repress Carbaryl metabolism in the strain. The study suggests the role of outer membrane protein McbT in Carbaryl transport. This work highlights the suitability of P. bharatica CSV86T as an ideal host for engineering aromatic pollutant degradation pathways.
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Affiliation(s)
- Harshit Malhotra
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Tushar Dhamale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Sukhjeet Kaur
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Sravanti T Kasarlawar
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
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Liu Q, Peng Y, Liao J, Liu X, Peng J, Wang JH, Shao Z. Broad-spectrum hydrocarbon-degrading microbes in the global ocean metagenomes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171746. [PMID: 38521276 DOI: 10.1016/j.scitotenv.2024.171746] [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: 12/12/2023] [Revised: 03/14/2024] [Accepted: 03/14/2024] [Indexed: 03/25/2024]
Abstract
Understanding the diversity and functions of hydrocarbon-degrading microorganisms in marine environments is crucial for both advancing knowledge of biogeochemical processes and improving bioremediation methods. In this study, we leveraged nearly 20,000 metagenome-assembled genomes (MAGs), recovered from a wide array of marine samples across the global oceans, to map the diversity of aerobic hydrocarbon-degrading microorganisms. A broad bacterial diversity was uncovered, with a notable preference for degrading aliphatic hydrocarbons over aromatic ones, primarily within Proteobacteria and Actinobacteriota. Three types of broad-spectrum hydrocarbon-degrading bacteria were identified for their ability to degrade various hydrocarbons and possession of multiple copies of hydrocarbon biodegradation genes. These bacteria demonstrate extensive metabolic versatility, aiding their survival and adaptability in diverse environmental conditions. Evidence of gene duplication and horizontal gene transfer in these microbes suggested a potential enhancement in the diversity of hydrocarbon-degrading bacteria. Positive correlations were observed between the abundances of hydrocarbon-degrading genes and environmental parameters such as temperature (-5 to 35 °C) and salinity (20 to 42 PSU). Overall, our findings offer valuable insights into marine hydrocarbon-degrading microorganisms and suggest considerations for selecting microbial strains for oil pollution remediation.
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Affiliation(s)
- Qing Liu
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China
| | - Yongyi Peng
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China
| | - Jing Liao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Xinyue Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Jiaxue Peng
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Jiang-Hai Wang
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China.
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519099, China.
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Li Y, Liu Y, Guo D, Dong H. Differential degradation of petroleum hydrocarbons by Shewanella putrefaciens under aerobic and anaerobic conditions. Front Microbiol 2024; 15:1389954. [PMID: 38659987 PMCID: PMC11040095 DOI: 10.3389/fmicb.2024.1389954] [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: 02/22/2024] [Accepted: 03/27/2024] [Indexed: 04/26/2024] Open
Abstract
The complexity of crude oil composition, combined with the fluctuating oxygen level in contaminated environments, poses challenges for the bioremediation of oil pollutants, because of compound-specific microbial degradation of petroleum hydrocarbons under certain conditions. As a result, facultative bacteria capable of breaking down petroleum hydrocarbons under both aerobic and anaerobic conditions are presumably effective, however, this hypothesis has not been directly tested. In the current investigation, Shewanella putrefaciens CN32, a facultative anaerobic bacterium, was used to degrade petroleum hydrocarbons aerobically (using O2 as an electron acceptor) and anaerobically (using Fe(III) as an electron acceptor). Under aerobic conditions, CN32 degraded more saturates (65.65 ± 0.01%) than aromatics (43.86 ± 0.03%), with the following order of degradation: dibenzofurans > n-alkanes > biphenyls > fluorenes > naphthalenes > alkylcyclohexanes > dibenzothiophenes > phenanthrenes. In contrast, under anaerobic conditions, CN32 exhibited a higher degradation of aromatics (53.94 ± 0.02%) than saturates (23.36 ± 0.01%), with the following order of degradation: dibenzofurans > fluorenes > biphenyls > naphthalenes > dibenzothiophenes > phenanthrenes > n-alkanes > alkylcyclohexanes. The upregulation of 4-hydroxy-3-polyprenylbenzoate decarboxylase (ubiD), which plays a crucial role in breaking down resistant aromatic compounds, was correlated with the anaerobic degradation of aromatics. At the molecular level, CN32 exhibited a higher efficiency in degrading n-alkanes with low and high carbon numbers relative to those with medium carbon chain lengths. In addition, the degradation of polycyclic aromatic hydrocarbons (PAHs) under both aerobic and anaerobic conditions became increasingly difficult with increased numbers of benzene rings and methyl groups. This study offers a potential solution for the development of targeted remediation of pollutants under oscillating redox conditions.
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Affiliation(s)
- Yang Li
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
- School of Earth Sciences and Resources, China University of Geosciences, Beijing, China
| | - Yuan Liu
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
- School of Earth Sciences and Resources, China University of Geosciences, Beijing, China
| | - Dongyi Guo
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
| | - Hailiang Dong
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
- School of Earth Sciences and Resources, China University of Geosciences, Beijing, China
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Thimmarayan S, Mohan H, Manasa G, Natesan K, Mahendran S, Muthukumar Sathya P, Oh BT, Ravi Kumar R, Sigamani Gandhimathi R, Jayaprakash A, Seralathan KK. Biodegradation of naphthalene - Ecofriendly approach for soil pollution mitigation. ENVIRONMENTAL RESEARCH 2024; 240:117550. [PMID: 37931735 DOI: 10.1016/j.envres.2023.117550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/08/2023]
Abstract
Naphthalene (NPT), a widely used household pest repellent and insecticide obtained from crude oil, serves as a toxic pollutant to non-target living matter. The stable and resistant nature of NPT makes it difficult to degrade through the physiochemical processes. The present study investigated the bacterial degradation of NPT isolated from crude oil-contaminated soil. Initially, the potent bacteria, Bacillus sp. GN 3.4, were isolated by enrichment culture method and subsequently assessed for NPT biodegradation. The optimum conditions for NPT biodegradation were pH 7.0 at 37 °C, 80 mg/L (initial NPT), 3% v/v (inoculum dose), and 7 days of treatment which showed 100% biodegradation. Furthermore, GC-MS analysis revealed the presence of degradation metabolites, namely, salicylate and hydroquinone indicating potential metabolic pathways. Considering the water-solubility and non-toxic nature of these metabolites, the results imply that Bacillus sp. GN 3.4. could potentially play a role in bioremediation by aiding in eliminating NPT from the soil.
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Affiliation(s)
- Srivalli Thimmarayan
- PG & Research Department of Biochemistry, Sacred Heart College (Autonomous), Tirupattur, 635601, (Affiliated to Thiruvalluvar University, Serkkadu, Vellore-632115, Tamil Nadu, India)
| | - Harshavardhan Mohan
- Division of Biotechnology, Advanced Institute of Environment and Bioscience, College of Environmental and Bioresource Sciences, Jeonbuk National University, Iksan, 54596, Jeonbuk, South Korea
| | - Gaddapara Manasa
- Department of Biochemistry, School of Applied Sciences, REVA University, Bengaluru, Karnataka, 560064, India
| | - Karthi Natesan
- Department of Biochemistry, School of Applied Sciences, REVA University, Bengaluru, Karnataka, 560064, India; Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, 55365, South Korea
| | - Shanmugam Mahendran
- Department of Microbiology, Ayya Nadar Janaki Ammal College, Sivakasi, 626124, Tamil Nadu, India
| | - Pavithra Muthukumar Sathya
- Division of Biotechnology, Advanced Institute of Environment and Bioscience, College of Environmental and Bioresource Sciences, Jeonbuk National University, Iksan, 54596, Jeonbuk, South Korea
| | - Byung-Taek Oh
- Division of Biotechnology, Advanced Institute of Environment and Bioscience, College of Environmental and Bioresource Sciences, Jeonbuk National University, Iksan, 54596, Jeonbuk, South Korea
| | - R Ravi Kumar
- Agro Climate Research Centre, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | | | - Arul Jayaprakash
- PG & Research Department of Biochemistry, Sacred Heart College (Autonomous), Tirupattur, 635601, (Affiliated to Thiruvalluvar University, Serkkadu, Vellore-632115, Tamil Nadu, India).
| | - Kamala-Kannan Seralathan
- Division of Biotechnology, Advanced Institute of Environment and Bioscience, College of Environmental and Bioresource Sciences, Jeonbuk National University, Iksan, 54596, Jeonbuk, South Korea.
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Thacharodi A, Hassan S, Singh T, Mandal R, Chinnadurai J, Khan HA, Hussain MA, Brindhadevi K, Pugazhendhi A. Bioremediation of polycyclic aromatic hydrocarbons: An updated microbiological review. CHEMOSPHERE 2023; 328:138498. [PMID: 36996919 DOI: 10.1016/j.chemosphere.2023.138498] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/08/2023] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
A class of organic priority pollutants known as PAHs is of critical public health and environmental concern due to its carcinogenic properties as well as its genotoxic, mutagenic, and cytotoxic properties. Research to eliminate PAHs from the environment has increased significantly due to awareness about their negative effects on the environment and human health. Various environmental factors, including nutrients, microorganisms present and their abundance, and the nature and chemical properties of the PAH affect the biodegradation of PAHs. A large spectrum of bacteria, fungi, and algae have ability to degrade PAHs with the biodegradation capacity of bacteria and fungi receiving the most attention. A considerable amount of research has been conducted in the last few decades on analyzing microbial communities for their genomic organization, enzymatic and biochemical properties capable of degrading PAH. While it is true that PAH degrading microorganisms offer potential for recovering damaged ecosystems in a cost-efficient way, new advances are needed to make these microbes more robust and successful at eliminating toxic chemicals. By optimizing some factors like adsorption, bioavailability and mass transfer of PAHs, microorganisms in their natural habitat could be greatly improved to biodegrade PAHs. This review aims to comprehensively discuss the latest findings and address the current wealth of knowledge in the microbial bioremediation of PAHs. Additionally, recent breakthroughs in PAH degradation are discussed in order to facilitate a broader understanding of the bioremediation of PAHs in the environment.
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Affiliation(s)
- Aswin Thacharodi
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Saqib Hassan
- Division of Non-Communicable Diseases, Indian Council of Medical Research (ICMR), New Delhi, 110029, India; Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Tripti Singh
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, 201309, India
| | - Ramkrishna Mandal
- Department of Chemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Jeganathan Chinnadurai
- Department of Research and Development, Dr. Thacharodi's Laboratories, No. 24, 5th Cross, Thanthaiperiyar Nagar, Ellapillaichavadi, Puducherry, 605005, India
| | - Hilal Ahmad Khan
- Department of Chemistry, Pondicherry University, Puducherry, 605014, India
| | - Mir Ashiq Hussain
- Department of Chemistry, Pondicherry University, Puducherry, 605014, India
| | - Kathirvel Brindhadevi
- Center for Transdisciplinary Research (CFTR), Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Arivalagan Pugazhendhi
- School of Engineering, Lebanese American University, Byblos, Lebanon; University Centre for Research & Development, Department of Civil Engineering, Chandigarh University, Mohali,140103, India.
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Salvà-Serra F, Pérez-Pantoja D, Donoso RA, Jaén-Luchoro D, Fernández-Juárez V, Engström-Jakobsson H, Moore ERB, Lalucat J, Bennasar-Figueras A. Comparative genomics of Stutzerimonas balearica ( Pseudomonas balearica): diversity, habitats, and biodegradation of aromatic compounds. Front Microbiol 2023; 14:1159176. [PMID: 37275147 PMCID: PMC10234333 DOI: 10.3389/fmicb.2023.1159176] [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: 02/05/2023] [Accepted: 04/13/2023] [Indexed: 06/07/2023] Open
Abstract
Stutzerimonas balearica (Pseudomonas balearica) has been found principally in oil-polluted environments. The capability of S. balearica to thrive from the degradation of pollutant compounds makes it a species of interest for potential bioremediation applications. However, little has been reported about the diversity of S. balearica. In this study, genome sequences of S. balearica strains from different origins were analyzed, revealing that it is a diverse species with an open pan-genome that will continue revealing new genes and functionalities as the genomes of more strains are sequenced. The nucleotide signatures and intra- and inter-species variation of the 16S rRNA genes of S. balearica were reevaluated. A strategy of screening 16S rRNA gene sequences in public databases enabled the detection of 158 additional strains, of which only 23% were described as S. balearica. The species was detected from a wide range of environments, although mostly from aquatic and polluted environments, predominantly related to petroleum oil. Genomic and phenotypic analyses confirmed that S. balearica possesses varied inherent capabilities for aromatic compounds degradation. This study increases the knowledge of the biology and diversity of S. balearica and will serve as a basis for future work with the species.
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Affiliation(s)
- Francisco Salvà-Serra
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Danilo Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Santiago, Chile
| | - Raúl A. Donoso
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Víctor Fernández-Juárez
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Hedvig Engström-Jakobsson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Edward R. B. Moore
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jorge Lalucat
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Antoni Bennasar-Figueras
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
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Somee MR, Amoozegar MA, Dastgheib SMM, Shavandi M, Maman LG, Bertilsson S, Mehrshad M. Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea. BMC Genomics 2022; 23:690. [PMID: 36203131 PMCID: PMC9535955 DOI: 10.1186/s12864-022-08906-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/26/2022] [Indexed: 12/04/2022] Open
Abstract
Background Hydrocarbons (HCs) are organic compounds composed solely of carbon and hydrogen that are mainly accumulated in oil reservoirs. As the introduction of all classes of hydrocarbons including crude oil and oil products into the environment has increased significantly, oil pollution has become a global ecological problem. However, our perception of pathways for biotic degradation of major HCs and key enzymes in these bioconversion processes has mainly been based on cultured microbes and is biased by uneven taxonomic representation. Here we used Annotree to provide a gene-centric view of the aerobic degradation ability of aliphatic and aromatic HCs in 23,446 genomes from 123 bacterial and 14 archaeal phyla. Results Apart from the widespread genetic potential for HC degradation in Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes, genomes from an additional 18 bacterial and 3 archaeal phyla also hosted key HC degrading enzymes. Among these, such degradation potential has not been previously reported for representatives in the phyla UBA8248, Tectomicrobia, SAR324, and Eremiobacterota. Genomes containing whole pathways for complete degradation of HCs were only detected in Proteobacteria and Actinobacteriota. Except for several members of Crenarchaeota, Halobacterota, and Nanoarchaeota that have tmoA, ladA, and alkB/M key genes, respectively, representatives of archaeal genomes made a small contribution to HC degradation. None of the screened archaeal genomes coded for complete HC degradation pathways studied here; however, they contribute significantly to peripheral routes of HC degradation with bacteria. Conclusion Phylogeny reconstruction showed that the reservoir of key aerobic hydrocarbon-degrading enzymes in Bacteria and Archaea undergoes extensive diversification via gene duplication and horizontal gene transfer. This diversification could potentially enable microbes to rapidly adapt to novel and manufactured HCs that reach the environment. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08906-w.
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Affiliation(s)
- Maryam Rezaei Somee
- Extremophile Laboratory, Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Mohammad Ali Amoozegar
- Extremophile Laboratory, Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | | | - Mahmoud Shavandi
- Biotechnology Research Group, Research Institute of Petroleum Industry, Tehran, Iran
| | - Leila Ghanbari Maman
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences (SLU), Box 7050, 75007, Uppsala, Sweden
| | - Maliheh Mehrshad
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences (SLU), Box 7050, 75007, Uppsala, Sweden.
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9
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Xiao Q, Lü Z, Zhu Z, Zhang D, Shen J, Huang M, Chen X, Yang J, Huang X, Rao M, Lu S. Exposure to polycyclic aromatic hydrocarbons and the associations with oxidative stress in waste incineration plant workers from South China. CHEMOSPHERE 2022; 303:135251. [PMID: 35688192 DOI: 10.1016/j.chemosphere.2022.135251] [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: 04/11/2022] [Revised: 05/23/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Waste incineration is one of the most common emission sources of polycyclic aromatic hydrocarbons (PAHs), causing potential occupational exposure in waste incineration workers. However, relative investigations among waste incineration plant workers are still very limited, particularly in China. Therefore, we collected urine specimens from 77 workers in a waste incineration plant as the exposed group, and 101 residents as the control group in Shenzhen, China. Nine mono-hydroxylated PAH metabolites (OH-PAHs) and 8-hydroxy-2'-deoxyguanosine (8-OHdG) were measured, and their internal relationships were explored. The urinary levels of most OH-PAHs and 8-OHdG in the exposed group exhibited high levels versus another group (p < 0.05). We found negative associations between OH-PAHs and 8-OHdG in the control group (p < 0.05), while most of OH-PAHs were not associated with 8-OHdG in the exposed group, which indicated that the exposure to waste incineration could enlarge the level of individual oxidative stress damage. Nevertheless, PAHs were less likely to trigger obvious health risks in exposed workers through estimation of human intake and exposure risks. This study provides a reference for occupational PAH exposure and strengthen the need of health monitoring among incineration workers.
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Affiliation(s)
- Qinru Xiao
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Zhanlu Lü
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Zhou Zhu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Duo Zhang
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Junchun Shen
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Min Huang
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Xin Chen
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Jialei Yang
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Xiaoping Huang
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Manting Rao
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Shaoyou Lu
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China.
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Dhamale T, Saha BK, Papade SE, Singh S, Phale PS. A unique global metabolic trait of Pseudomonas bharatica CSV86 T: metabolism of aromatics over simple carbon sources and co-metabolism with organic acids. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35925665 DOI: 10.1099/mic.0.001206] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Hierarchical utilization of substrate by microbes (utilization of simple carbon sources prior to complex ones) poses a major limitation to the efficient remediation of aromatic pollutants. Aromatic compounds, being complex and reduced in nature, appear to be a deferred choice as the carbon source in the presence of a plethora of simple organic compounds in the environment. The soil bacterium Pseudomonas bharatica CSV86T displays a unique carbon source utilization hierarchy. It preferentially utilizes aromatics over glucose and co-metabolizes them with succinate or pyruvate (Basu et al., 2006, Applied and Environmental Microbiology, 72 : 22226-2230). In the present study, the substrate utilization hierarchy for strain CSV86T was tested for additional simple carbon sources such as glycerol, acetate, and tri-carboxylic acid (TCA) cycle intermediates like α-ketoglutarate and fumarate. When grown on a mixture of aromatics (benzoate or naphthalene) plus glycerol, the strain displayed a diauxic growth profile with significantly high activity of aromatic utilization enzymes (catechol 1,2- or 2,3-dioxygenase, respectively) in the first-log phase. This suggests utilization of aromatics in the first-log phase followed by glycerol in the second-log phase. On a mixture of an aromatic plus organic acid (acetate, α-ketoglutarate or fumarate), the strain displayed a monoauxic growth profile, indicating co-metabolism. Interestingly, the presence of glycerol, acetate, α-ketoglutarate or fumarate does not repress metabolism/utilization of the aromatic. Thus, the substrate utilization hierarchy of strain CSV86T is aromatics=organic acids>glucose/glycerol, which is unique as compared to other Pseudomonas species, where degradation of aromatics is repressed by glycerol, glucose, acetate or organic acids, including TCA cycle intermediates. This novel substrate utilization hierarchy appears to be a global metabolic phenomenon in strain CSV86T, thus implying it to be an ideal host for metabolic engineering as well as for its potential application in bioremediation.
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Affiliation(s)
- Tushar Dhamale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India
| | - Braja Kishor Saha
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India
| | - Sandesh E Papade
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India
| | - Srushti Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India.,Present address: Presently affiliated to TCR Therapeutics, Inc., 100 Binney Street, Cambridge, MA 02142, USA
| | - Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India
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Mohapatra B, Malhotra H, Phale PS. Life Within a Contaminated Niche: Comparative Genomic Analyses of an Integrative Conjugative Element ICE nahCSV86 and Two Genomic Islands From Pseudomonas bharatica CSV86 T Suggest Probable Role in Colonization and Adaptation. Front Microbiol 2022; 13:928848. [PMID: 35875527 PMCID: PMC9298801 DOI: 10.3389/fmicb.2022.928848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/08/2022] [Indexed: 11/26/2022] Open
Abstract
Comparative genomic and functional analyses revealed the presence of three genomic islands (GIs, >50 Kb size): ICEnahCSV86, Pseudomonas bharatica genomic island-1 (PBGI-1), and PBGI-2 in the preferentially aromatic-degrading soil bacterium, Pseudomonas bharatica CSV86T. Site-specific genomic integration at or near specific transfer RNAs (tRNAs), near-syntenic structural modules, and phylogenetic relatedness indicated their evolutionary lineage to the type-4 secretion system (T4SS) ICEclc family, thus predicting these elements to be integrative conjugative elements (ICEs). These GIs were found to be present as a single copy in the genome and the encoded phenotypic traits were found to be stable, even in the absence of selection pressure. ICEnahCSV86 harbors naphthalene catabolic (nah-sal) cluster, while PBGI-1 harbors Co-Zn-Cd (czc) efflux genes as cargo modules, whereas PBGI-2 was attributed to as a mixed-function element. The ICEnahCSV86 has been reported to be conjugatively transferred (frequency of 7 × 10–8/donor cell) to Stenotrophomonas maltophilia CSV89. Genome-wide comparative analyses of aromatic-degrading bacteria revealed nah-sal clusters from several Pseudomonas spp. as part of probable ICEs, syntenic to conjugatively transferable ICEnahCSV86 of strain CSV86T, suggesting it to be a prototypical element for naphthalene degradation. It was observed that the plasmids harboring nah-sal clusters were phylogenetically incongruent with predicted ICEs, suggesting genetic divergence of naphthalene metabolic clusters in the Pseudomonas population. Gene synteny, divergence estimates, and codon-based Z-test indicated that ICEnahCSV86 is probably derived from PBGI-2, while multiple recombination events masked the ancestral lineage of PBGI-1. Diversifying selection pressure (dN-dS = 2.27–4.31) imposed by aromatics and heavy metals implied the modular exchange-fusion of various cargo clusters through events like recombination, rearrangement, domain reshuffling, and active site optimization, thus allowing the strain to evolve, adapt, and maximize the metabolic efficiency in a contaminated niche. The promoters (Pnah and Psal) of naphthalene cargo modules (nah, sal) on ICEnahCSV86 were proved to be efficient for heterologous protein expression in Escherichia coli. GI-based genomic plasticity expands the metabolic spectrum and versatility of CSV86T, rendering efficient adaptation to the contaminated niche. Such isolate(s) are of utmost importance for their application in bioremediation and are the probable ideal host(s) for metabolic engineering.
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Affiliation(s)
- Balaram Mohapatra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Harshit Malhotra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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12
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Mohapatra B, Nain S, Sharma R, Phale PS. Functional genome mining and taxono-genomics reveal eco-physiological traits and species distinctiveness of aromatic-degrading Pseudomonas bharatica sp. nov. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:464-474. [PMID: 35388632 DOI: 10.1111/1758-2229.13066] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
Assistive eco-physiological traits are necessary for microbes to adapt and colonize at polluted niches, enabling efficient clean-up. To demarcate species distinctiveness and eco-physiological traits of aromatic compounds metabolizing Pseudomonas sp. CSV86T (earlier identified as Pseudomonas putida), an Indian isolate from a petrol station soil, comparative genome mining, taxono-genomic, and physiological analyses were performed. A 6.79 Mbp genome (62.72 G + C mol%) of CSV86T encodes 6798 CDS and 238 unique genes. Naphthalene metabolism and Co-Zn-Cd resistance gene clusters were part of distinct genomic islands. Abundance of transporters (aromatics, organic acids, amino acids, and metals) and mobile elements (integrases, transposases, conjugative proteins) differentiated CSV86T from its closest relatives. Enhanced siderophore production for Fe-uptake during aromatic metabolism, indole acetic acid production, and fusaric acid resistance wasvalidated by genomic attributes. Full-length 16S-rRNA phylogeny revealed Pseudomonas japonica WLT as a closest relative of CSV86T . However, lower genomic indices (<97% gyrB-rpoB-rpoD homology, <90% ANI, <50% DNA-DNA relatedness) and taxonomic differences (assimilation of organic acids, amino acids, fatty acids composition) substantially differentiated CSV86T from its closest relatives, indicating it to be a novel species as Pseudomonas bharatica. Preferential metabolism of aromatics with advantageous eco-physiological traits renders CSV86T an ideal candidate for bioremediation and host for metabolic engineering.
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Affiliation(s)
- Balaram Mohapatra
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai, Maharashtra, India
| | - Sonam Nain
- Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research (CSIR), Delhi, India
| | - Rakesh Sharma
- Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research (CSIR), Delhi, India
| | - Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai, Maharashtra, India
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13
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Liu J, Liu Y, Dong W, Li J, Yu S, Wang J, Zuo R. Shifts in microbial community structure and function in polycyclic aromatic hydrocarbon contaminated soils at petrochemical landfill sites revealed by metagenomics. CHEMOSPHERE 2022; 293:133509. [PMID: 34995620 DOI: 10.1016/j.chemosphere.2021.133509] [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: 10/19/2021] [Revised: 12/26/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
Investigations of the microbial community structures, potential functions and polycyclic aromatic hydrocarbon (PAH) degradation-related genes in PAH-polluted soils are useful for risk assessments, microbial monitoring, and the potential bioremediation of soils polluted by PAHs. In this study, five soil sampling sites were selected at a petrochemical landfill in Beijing, China, to analyze the contamination characteristics of PAHs and their impact on microorganisms. The concentrations of 16 PAHs were detected by gas chromatography-mass spectrometry. The total concentrations of the PAHs ranged from ND to 3166.52 μg/kg, while phenanthrene, pyrene, fluoranthene and benzo [ghi]perylene were the main components in the soil samples. According to the specific PAH ratios, the PAHs mostly originated from petrochemical wastes in the landfill. The levels of the total toxic benzo [a]pyrene equivalent (1.63-107.73 μg/kg) suggested that PAHs might result in adverse effects on soil ecosystems. The metagenomic analysis showed that the most abundant phyla in the soils were Proteobacteria and Actinobacteria, and Solirubrobacter was the most important genus. At the genus level, Bradyrhizobium, Mycobacterium and Anaeromyxobacter significantly increased under PAH stress. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations, the most abundant category of functions that are involved in adapting to contaminant pressures was identified. Ten PAH degradation-related genes were significantly influenced by PAH pressure and showed correlations with PAH concentrations. All of the results suggested that the PAHs from the petrochemical landfill could be harmful to soil environments and impact the soil microbial community structures, while microorganisms would change their physiological functions to resist pollutant stress.
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Affiliation(s)
- Jiayou Liu
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yun Liu
- South China Institute of Environmental Sciences, Ministry of Environmental Protection of the People's Republic of China, State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, Guangzhou, 510655, China
| | - Weihong Dong
- Key Laboratory of Groundwater Resources and Environments, Ministry of Education, Jilin University, Changchun, Jilin, 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun, Jilin, 130021, China
| | - Jian Li
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing, 100875, China.
| | - Shihang Yu
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Jinsheng Wang
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Rui Zuo
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing, 100875, China
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14
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Dong Y, Wu S, Fan H, Li X, Li Y, Xu S, Bai Z, Zhuang X. Ecological selection of bacterial taxa with larger genome sizes in response to polycyclic aromatic hydrocarbons stress. J Environ Sci (China) 2022; 112:82-93. [PMID: 34955225 DOI: 10.1016/j.jes.2021.04.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 04/24/2021] [Accepted: 04/25/2021] [Indexed: 05/15/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous priority pollutants that cause great damage to the natural environment and health. Average genome size in a community is critical for shedding light on microbiome's functional response to pollution stress within an environment. Here, microcosms under different concentrations were performed to evaluate the selection of PAHs stress on the average genome size in a community. We found the distinct communities of significantly larger genome size with the increase of PAHs concentration gradients in soils, and consistent trends were discovered in soils at different latitudes. The abundance of Proteobacteria and Deinococcus-Thermus with relatively larger genomes increased along with PAHs stress and well adapted to polluted environments. In contrast, the abundance of Patescibacteria with a highly streamlined and smaller genome decreased, implying complex interactions between environmental selection and functional fitness resulted in bacteria with larger genomes becoming more abundant. Moreover, we confirmed the increased capacity for horizontal transfer of degrading genes between communities by showing an increased connection number per node positively related to the nidA gene along the concentration gradients in the co-occurrence network. Our findings suggest PAHs tend to select bacterial taxa with larger genome sizes, with significant consequences for community stability and potential biodegradation strategies.
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Affiliation(s)
- Yuzhu Dong
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanghua Wu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haonan Fan
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianglong Li
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yijing Li
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Sino-Danish Center, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shengjun Xu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhihui Bai
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
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15
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Sharma V, Malla MA, Kori RK, Yadav RS, Azam Z. Applications of Metagenomics for Unrevealing the Extended Horizons of Microbiota Prevalence from Soil to Human Health. Open Microbiol J 2021. [DOI: 10.2174/1874285802115010177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Phylogenetic analysis of different ecosystems has shown that the number of microbial communities in a single sample exceeds their cultured counterparts. Microbes have been found throughout nature and can thrive in adverse conditions. Besides inhabiting diverse environments, they also play a key role in the maintenance of the ecosystem. Most of these microbes are either unculturable or difficult to culture with conventional culturing methods. Metagenomics is an emerging field of science that has been in the light for a decade and offers a potential way to assess microbial diversity. The development of metagenomics opens new ways to study genetic material directly from the environmental samples. DNA sequencing and synthesis technologies are making it possible to read and write entire genomes. The huge amount of data obtained from genome sequencing inevitably requires bioinformatics tools to handle and further process them for analysis. Advances in DNA sequencing and high-performance computing have brought about exemplar improvement in metagenomics, allowing in-depth study of the largely unexplored frontier of microbial life. This culture-independent method provides extensive information regarding the structure, composition, and function of the diverse assemblages of the environmental microbes. The current review presents an overview of the technical aspects of metagenomics along with its diverse applications.
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16
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Aliyu H, de Maayer P, Neumann A. Not All That Glitters Is Gold: The Paradox of CO-dependent Hydrogenogenesis in Parageobacillus thermoglucosidasius. Front Microbiol 2021; 12:784652. [PMID: 34956151 PMCID: PMC8696081 DOI: 10.3389/fmicb.2021.784652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/05/2021] [Indexed: 11/13/2022] Open
Abstract
The thermophilic bacterium Parageobacillus thermoglucosidasius has recently gained interest due to its ability to catalyze the water gas shift reaction, where the oxidation of carbon monoxide (CO) is linked to the evolution of hydrogen (H2) gas. This phenotype is largely predictable based on the presence of a genomic region coding for a carbon monoxide dehydrogenase (CODH—Coo) and hydrogen evolving hydrogenase (Phc). In this work, seven previously uncharacterized strains were cultivated under 50% CO and 50% air atmosphere. Despite the presence of the coo—phc genes in all seven strains, only one strain, Kp1013, oxidizes CO and yields H2. The genomes of the H2 producing strains contain unique genomic regions that code for proteins involved in nickel transport and the detoxification of catechol, a by-product of a siderophore-mediated iron acquisition system. Combined, the presence of these genomic regions could potentially drive biological water gas shift (WGS) reaction in P. thermoglucosidasius.
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Affiliation(s)
- Habibu Aliyu
- Institute of Process Engineering in Life Science 2 - Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Pieter de Maayer
- School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Anke Neumann
- Institute of Process Engineering in Life Science 2 - Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
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17
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Bhatt P, Bhandari G, Bhatt K, Maithani D, Mishra S, Gangola S, Bhatt R, Huang Y, Chen S. Plasmid-mediated catabolism for the removal of xenobiotics from the environment. JOURNAL OF HAZARDOUS MATERIALS 2021; 420:126618. [PMID: 34329102 DOI: 10.1016/j.jhazmat.2021.126618] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 05/27/2021] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
The large-scale application of xenobiotics adversely affects the environment. The genes that are present in the chromosome of the bacteria are considered nonmobile, whereas the genes present on the plasmids are considered mobile genetic elements. Plasmids are considered indispensable for xenobiotic degradation into the contaminated environment. In the contaminated sites, bacteria with plasmids can transfer the mobile genetic element into another strain. This mechanism helps in spreading the catabolic genes into the bacterial population at the contaminated sites. The indigenous microbial strains with such degradative plasmids are important for the bioremediation of xenobiotics. Environmental factors play a critical role in the conjugation efficiency, which is involved in the bioremediation of the xenobiotics at the contaminated sites. However, there is still a need for more research to fill in the gaps regarding plasmids and their impact on bioremediation. This review explores the role of bacterial plasmids in the bioremediation of xenobiotics from contaminated environments.
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Affiliation(s)
- Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Geeta Bhandari
- Department of Biochemistry and Biotechnology, Sardar Bhagwan Singh University, Dehradun 248161, Uttarakhand, India
| | - Kalpana Bhatt
- Department of Botany and Microbiology, Gurukul Kangri University, Haridwar 249404, Uttarakhand, India
| | - Damini Maithani
- Department of Microbiology, G.B Pant University of Agriculture and Technology Pantnagar, U.S Nagar, Uttarakhand, India
| | - Sandhya Mishra
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Saurabh Gangola
- School of Agriculture, Graphic Era Hill University, Bhimtal Campus, 263136, Uttarakhand, India
| | - Rakesh Bhatt
- Department of Civil Engineering, Indian Institute of Technology, Kanpur 208016, Uttar Pradesh, India
| | - Yaohua Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
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18
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Ali SS, Mustafa AM, Sun J. Wood‑feeding termites as an obscure yet promising source of bacteria for biodegradation and detoxification of creosote-treated wood along with methane production enhancement. BIORESOURCE TECHNOLOGY 2021; 338:125521. [PMID: 34273631 DOI: 10.1016/j.biortech.2021.125521] [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: 04/20/2021] [Revised: 07/02/2021] [Accepted: 07/04/2021] [Indexed: 06/13/2023]
Abstract
This study aims to explore distinct bacterial strains from wood-feeding termites and to construct novel bacterial consortium for improving the methane yield during anaerobic digestion by degrading birchwood sawdust (BSD) and removing creosote (CRO) compounds simultaneously. A novel bacterial consortium CTB-4 which stands for the molecularly identified species Burkholderia sp., Xanthomonas sp., Shewanella sp., and Pseudomonas mosselii was successfully developed. The CTB-4 consortium showed high efficiency in the removal of naphthalene and phenol. It also revealed reduction in lignin, hemicellulose, and cellulose by 19.4, 52.5, and 76.8%, respectively. The main metabolites after the CRO degradation were acetic acid, succinate, pyruvate, and acetaldehyde. Pretreatment of treated BSD mixed with CRO enhanced the total methane yield (162 L/kg VS) by 82.7% and biomass reduction by 54.7% compared to the untreated substrate. CRO showed a toxicity decrease of >90%, suggesting the efficiency of constructed bacterial consortia in bioremediation and biofuel production.
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Affiliation(s)
- Sameh S Ali
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Botany Department, Faculty of Science, Tanta University, Tanta 31527, Egypt.
| | - Ahmed M Mustafa
- Department of Agricultural Engineering, Faculty of Agriculture, Suez Canal University, Ismailia 41522, Egypt; State Key Laboratory of Pollution Control and Resourses Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
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19
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Ali SS, Jiao H, Mustafa AM, Koutra E, El-Sapagh S, Kornaros M, Elsamahy T, Khalil M, Bulgariu L, Sun J. Construction of a novel microbial consortium valued for the effective degradation and detoxification of creosote-treated sawdust along with enhanced methane production. JOURNAL OF HAZARDOUS MATERIALS 2021; 418:126091. [PMID: 34118544 DOI: 10.1016/j.jhazmat.2021.126091] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 04/29/2021] [Accepted: 05/10/2021] [Indexed: 06/12/2023]
Abstract
Lignocellulosic biomass represents an unlimited and ubiquitous energy source, which can effectively address current global challenges, including climate change, greenhouse gas emissions, and increased energy demand. However, lignocellulose recalcitrance hinders microbial degradation, especially in case of contaminated materials such as creosote (CRO)-treated wood, which necessitates appropriate processing in order to eliminate pollution. This study might be the first to explore a novel bacterial consortium SST-4, for decomposing birchwood sawdust, capable of concurrently degrading lignocellulose and CRO compounds. Afterwards, SST-4 which stands for molecularly identified bacterial strains Acinetobacter calcoaceticus BSW-11, Shewanella putrefaciens BSW-18, Bacillus cereus BSW-23, and Novosphingobium taihuense BSW-25 was evaluated in terms of biological sawdust pre-treatment, resulting in effective lignocellulose degradation and 100% removal of phenol and naphthalene. Subsequently, the maximum biogas production observed was 18.7 L/kg VS, while cumulative methane production was 162.8 L/kg VS, compared to 88.5 without microbial pre-treatment. The cumulative energy production from AD-I and AD-II through biomethanation was calculated as 3177.1 and 5843.6 KJ/kg, respectively. The pretreatment process exhibited a significant increase in the energy yield by 83.9%. Lastly, effective CRO detoxification was achieved with EC50 values exceeding 90%, showing the potential for an integrated process of effective contaminated wood management and bioenergy production.
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Affiliation(s)
- Sameh Samir Ali
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Botany Department, Faculty of Science, Tanta University, Tanta 31527, Egypt.
| | - Haixin Jiao
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Ahmed M Mustafa
- State Key Laboratory of Pollution Control and Resourses Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Department of Agricultural Engineering, Faculty of Agriculture, Suez Canal University, Ismailia 41522, Egypt
| | - Eleni Koutra
- Laboratory of Biochemical Engineering & Environmental Technology (LBEET), Department of Chemical Engineering, University of Patras, 1 Karatheodori Str., University Campus, Patras 26504, Greece; INVALOR: Research Infrastructure for Waste Valorization and Sustainable Management, University Campus, Patras 26504, Greece
| | - Shimaa El-Sapagh
- Botany Department, Faculty of Science, Tanta University, Tanta 31527, Egypt
| | - Michael Kornaros
- Laboratory of Biochemical Engineering & Environmental Technology (LBEET), Department of Chemical Engineering, University of Patras, 1 Karatheodori Str., University Campus, Patras 26504, Greece; INVALOR: Research Infrastructure for Waste Valorization and Sustainable Management, University Campus, Patras 26504, Greece
| | - Tamer Elsamahy
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Maha Khalil
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Laura Bulgariu
- Department of Environmental Engineering and Management, Cristofor Simionescu Faculty of Chemical Engineering and Environmental Protection, Gheorghe Asachi Technical University of Iasi, 700050 Iasi, Romania
| | - Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
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20
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Mishra S, Pang S, Zhang W, Lin Z, Bhatt P, Chen S. Insights into the microbial degradation and biochemical mechanisms of carbamates. CHEMOSPHERE 2021; 279:130500. [PMID: 33892453 DOI: 10.1016/j.chemosphere.2021.130500] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 03/01/2021] [Accepted: 04/04/2021] [Indexed: 06/12/2023]
Abstract
Carbamate compounds are commonly applied in agricultural sectors as alternative options to the recalcitrant organochlorine pesticides due to their easier breakdown and less persistent nature. However, the large-scale use of carbamates also leads to toxic environmental residues, causing severe toxicity in various living systems. The toxic effects of carbamates are due to their inhibitor activity against the acetylchlolinesterase enzyme. This enzyme is crucial for neurotransmission signaling in living beings. Hence, from the environmental point of view, the elimination of carbamates is a worldwide concern and priority. Microbial technology can be deliberated as a potential tool that can work efficiently and as an ecofriendly option for the dissipation of carbamate insecticides from contaminated environments by improving biodegradation processes via metabolic activities of microorganisms. A variety of bacterial and fungal species have been isolated and characterized and are capable of degrading a broad range of carbamates in soil and water environments. In addition, microbial carbamate hydrolase genes (mcd, cehA, cahA, cfdJ, and mcbA) were strongly implicated in the evolution of new metabolic functions and carbamate hydrolase enzymes. However, the accurate localization and appropriate functions of carbamate hydrolase enzymes/genes are very limited. To explore the information on the degradation routes of carbamates and promote the application of biodegradation, a study of molecular techniques is required to unlock insights regarding the degradation specific genes and enzymes. Hence, this review discusses the deep understanding of carbamate degradation mechanisms with microbial strains, metabolic pathways, molecular mechanisms, and their genetic basis in degradation.
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Affiliation(s)
- Sandhya Mishra
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Shimei Pang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Wenping Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Ziqiu Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
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A Recently Assembled Degradation Pathway for 2,3-Dichloronitrobenzene in Diaphorobacter sp. Strain JS3051. mBio 2021; 12:e0223121. [PMID: 34425699 PMCID: PMC8406286 DOI: 10.1128/mbio.02231-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Diaphorobacter sp. strain JS3051 utilizes 2,3-dichloronitrobenzene (23DCNB), a toxic anthropogenic compound, as the sole carbon, nitrogen, and energy source for growth, but the metabolic pathway and its origins are unknown. Here, we establish that a gene cluster (dcb), encoding a Nag-like dioxygenase, is responsible for the initial oxidation of the 23DCNB molecule. The 2,3-dichloronitrobenzene dioxygenase system (DcbAaAbAcAd) catalyzes conversion of 23DCNB to 3,4-dichlorocatechol (34DCC). Site-directed mutagenesis studies indicated that residue 204 of DcbAc is crucial for the substrate specificity of 23DCNB dioxygenase. The presence of glutamic acid at position 204 of 23DCNB dioxygenase is unique among Nag-like dioxygenases. Genetic, biochemical, and structural evidence indicate that the 23DCNB dioxygenase is more closely related to 2-nitrotoluene dioxygenase from Acidovorax sp. strain JS42 than to the 34DCNB dioxygenase from Diaphorobacter sp. strain JS3050, which was isolated from the same site as strain JS3051. A gene cluster (dcc) encoding the enzymes for 34DCC catabolism, homologous to a clc operon in Pseudomonas knackmussii strain B13, is also on the chromosome at a distance of 2.5 Mb from the dcb genes. Heterologously expressed DccA catalyzed ring cleavage of 34DCC with high affinity and catalytic efficiency. This work not only establishes the molecular mechanism for 23DCNB mineralization, but also enhances the understanding of the recent evolution of the catabolic pathways for nitroarenes.
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Phale PS, Mohapatra B, Malhotra H, Shah BA. Eco-physiological portrait of a novel Pseudomonas sp. CSV86: an ideal host/candidate for metabolic engineering and bioremediation. Environ Microbiol 2021; 24:2797-2816. [PMID: 34347343 DOI: 10.1111/1462-2920.15694] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 11/30/2022]
Abstract
Pseudomonas sp. CSV86, an Indian soil isolate, degrades wide range of aromatic compounds like naphthalene, benzoate and phenylpropanoids, amongst others. Isolate displays the unique and novel property of preferential utilization of aromatics over glucose and co-metabolizes them with organic acids. Interestingly, as compared to other Pseudomonads, strain CSV86 harbours only high-affinity glucokinase pathway (and absence of low-affinity oxidative route) for glucose metabolism. Such lack of gluconate loop might be responsible for the novel phenotype of preferential utilization of aromatics. The genome analysis and comparative functional mining indicated a large genome (6.79 Mb) with significant enrichment of regulators, transporters as well as presence of various secondary metabolite production clusters, suggesting its eco-physiological and metabolic versatility. Strain harbours various integrative conjugative elements (ICEs) and genomic islands, probably acquired through horizontal gene transfer events, leading to genome mosaicity and plasticity. Naphthalene degradation genes are arranged as regulonic clusters and found to be part of ICECSV86nah . Various eco-physiological properties and absence of major pathogenicity and virulence factors (risk group-1) in CSV86 suggest it to be an ideal candidate for bioremediation. Further, strain can serve as an ideal chassis for metabolic engineering to degrade various xenobiotics preferentially over simple carbon sources for efficient remediation.
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Affiliation(s)
- Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, Maharashtra, 400076, India
| | - Balaram Mohapatra
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, Maharashtra, 400076, India
| | - Harshit Malhotra
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, Maharashtra, 400076, India
| | - Bhavik A Shah
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, Maharashtra, 400076, India
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Malhotra H, Kaur S, Phale PS. Conserved Metabolic and Evolutionary Themes in Microbial Degradation of Carbamate Pesticides. Front Microbiol 2021; 12:648868. [PMID: 34305823 PMCID: PMC8292978 DOI: 10.3389/fmicb.2021.648868] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 06/14/2021] [Indexed: 12/22/2022] Open
Abstract
Carbamate pesticides are widely used as insecticides, nematicides, acaricides, herbicides and fungicides in the agriculture, food and public health sector. However, only a minor fraction of the applied quantity reaches the target organisms. The majority of it persists in the environment, impacting the non-target biota, leading to ecological disturbance. The toxicity of these compounds to biota is mediated through cholinergic and non-cholinergic routes, thereby making their clean-up cardinal. Microbes, specifically bacteria, have adapted to the presence of these compounds by evolving degradation pathways and thus play a major role in their removal from the biosphere. Over the past few decades, various genetic, metabolic and biochemical analyses exploring carbamate degradation in bacteria have revealed certain conserved themes in metabolic pathways like the enzymatic hydrolysis of the carbamate ester or amide linkage, funnelling of aryl carbamates into respective dihydroxy aromatic intermediates, C1 metabolism and nitrogen assimilation. Further, genomic and functional analyses have provided insights on mechanisms like horizontal gene transfer and enzyme promiscuity, which drive the evolution of degradation phenotype. Compartmentalisation of metabolic pathway enzymes serves as an additional strategy that further aids in optimising the degradation efficiency. This review highlights and discusses the conclusions drawn from various analyses over the past few decades; and provides a comprehensive view of the environmental fate, toxicity, metabolic routes, related genes and enzymes as well as evolutionary mechanisms associated with the degradation of widely employed carbamate pesticides. Additionally, various strategies like application of consortia for efficient degradation, metabolic engineering and adaptive laboratory evolution, which aid in improvising remediation efficiency and overcoming the challenges associated with in situ bioremediation are discussed.
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Affiliation(s)
- Harshit Malhotra
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Sukhjeet Kaur
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
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Zharikova NV, Iasakov TR, Zhurenko EI, Korobov VV, Markusheva TV. Plasmids of the Chlorophenoxyacetic-Acid Degradation of Bacteria of the Genus Raoultella. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821030157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Mohapatra B, Phale PS. Microbial Degradation of Naphthalene and Substituted Naphthalenes: Metabolic Diversity and Genomic Insight for Bioremediation. Front Bioeng Biotechnol 2021; 9:602445. [PMID: 33791281 PMCID: PMC8006333 DOI: 10.3389/fbioe.2021.602445] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/09/2021] [Indexed: 12/21/2022] Open
Abstract
Low molecular weight polycyclic aromatic hydrocarbons (PAHs) like naphthalene and substituted naphthalenes (methylnaphthalene, naphthoic acids, 1-naphthyl N-methylcarbamate, etc.) are used in various industries and exhibit genotoxic, mutagenic, and/or carcinogenic effects on living organisms. These synthetic organic compounds (SOCs) or xenobiotics are considered as priority pollutants that pose a critical environmental and public health concern worldwide. The extent of anthropogenic activities like emissions from coal gasification, petroleum refining, motor vehicle exhaust, and agricultural applications determine the concentration, fate, and transport of these ubiquitous and recalcitrant compounds. Besides physicochemical methods for cleanup/removal, a green and eco-friendly technology like bioremediation, using microbes with the ability to degrade SOCs completely or convert to non-toxic by-products, has been a safe, cost-effective, and promising alternative. Various bacterial species from soil flora belonging to Proteobacteria (Pseudomonas, Pseudoxanthomonas, Comamonas, Burkholderia, and Novosphingobium), Firmicutes (Bacillus and Paenibacillus), and Actinobacteria (Rhodococcus and Arthrobacter) displayed the ability to degrade various SOCs. Metabolic studies, genomic and metagenomics analyses have aided our understanding of the catabolic complexity and diversity present in these simple life forms which can be further applied for efficient biodegradation. The prolonged persistence of PAHs has led to the evolution of new degradative phenotypes through horizontal gene transfer using genetic elements like plasmids, transposons, phages, genomic islands, and integrative conjugative elements. Systems biology and genetic engineering of either specific isolates or mock community (consortia) might achieve complete, rapid, and efficient bioremediation of these PAHs through synergistic actions. In this review, we highlight various metabolic routes and diversity, genetic makeup and diversity, and cellular responses/adaptations by naphthalene and substituted naphthalene-degrading bacteria. This will provide insights into the ecological aspects of field application and strain optimization for efficient bioremediation.
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Affiliation(s)
- Balaram Mohapatra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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Jiang W, Liu Y, Ke Z, Zhang L, Zhang M, Zhou Y, Wang H, Wu C, Qiu J, Hong Q. Substrate preference of carbamate hydrolase CehA reveals its environmental behavior. JOURNAL OF HAZARDOUS MATERIALS 2021; 403:123677. [PMID: 32835992 DOI: 10.1016/j.jhazmat.2020.123677] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/30/2020] [Accepted: 08/06/2020] [Indexed: 06/11/2023]
Abstract
The cehA gene is the earliest reported and most widely found carbaryl hydrolase gene. CehA detoxifies carbaryl and other carbamate pesticides via de-esterification. Currently, there is no systematic research available on substrate preference or the mechanism of CehA action in different hosts. In this study, we found that CehA from different hosts is highly conserved, with more than 99% amino acid sequence similarity, and that transposable elements exist in both the upstream and downstream regions of cehA. By introducing point mutations into the cehA gene of Sphingobium sp. CFD-1, we obtained and heterologously expressed all reported CehA(CehAS) encoding genes. Assays to determine enzymatic properties and substrate profiles of CehAS showed that each CehA has a significant substrate preference for different carbamate insecticides. Specifically, CehA152Phe/Leu determines the catalytic preference for bicyclic carbamate substrates (carbofuran, carbaryl), while CehA494Thr/Ala and 570Thr/Ile determine the preference for monocyclic carbamate substrates (isoprocarb, propoxur) and linear carbamate substrates (oxamyl, aldicarb), respectively. Considering the existence of transposable elements in the flanking regions of cehA, we speculate that the cehA hosts may have acquired the hydrolysis ability, as well as substrate preference for carbamate pesticides, through horizontal gene transfer and genetic copying errors.
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Affiliation(s)
- Wankui Jiang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Yali Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Zhijian Ke
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Lu Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Mingliang Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Yidong Zhou
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Hui Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Chenglong Wu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Jiguo Qiu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Qing Hong
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China.
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Yu Y, Peng M, Liu Y, Ma J, Wang N, Ma S, Feng N, Lu S. Co-exposure to polycyclic aromatic hydrocarbons and phthalates and their associations with oxidative stress damage in school children from South China. JOURNAL OF HAZARDOUS MATERIALS 2021; 401:123390. [PMID: 32659584 DOI: 10.1016/j.jhazmat.2020.123390] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 06/11/2023]
Abstract
Monohydroxylated polycyclic aromatic hydrocarbons (OH-PAHs), phthalate metabolites (mPAEs), and 8-hydroxy-2'-deoxyguanosine (8-OHdG) in the urine of school children aged 8-11 years from Shenzhen, China were measured in order to investigate oxidative stress damage from co-exposure to PAHs and PAEs. The concentrations of OH-PAHs and mPAEs in urine were 0.36-36.5 (median: 3.86) and 9.48-1609 (median: 240) ng/mL respectively. Gender and age did not influence urinary concentrations of ΣOH-PAHs and ΣmPAEs, but geographical variations (i.e., urban versus suburban) were observed. Levels of 8-OHdG were positively correlated with urinary OH-PAHs and mPAEs, with correlation coefficients (r) varying between 0.160 and 0.365 (p < 0.05). OH-PAHs made a greater contribution to oxidative DNA damage than mPAEs when these two types of pollutants were present at the same concentrations. Human health risks were assessed using the hazard quotient and the hazard index for the cumulative risk of a complex of chemicals. The results demonstrated that risks from PAHs could be neglected, but that 29.5 % of school children may be subject to obvious health risks from PAEs, especially diethylhexyl phthalate.
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Affiliation(s)
- Yingxin Yu
- Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, PR China
| | - Mengmeng Peng
- Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, PR China; Institute of Environmental Pollution and Health, School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, PR China
| | - Yanlin Liu
- School of Traffic and Environment, Shenzhen Institute of Information Technology, Shenzhen, 518172, PR China
| | - Jinjing Ma
- Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, PR China; Institute of Environmental Pollution and Health, School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, PR China
| | - Ning Wang
- Institute of Environmental Pollution and Health, School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, PR China
| | - Shengtao Ma
- Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, PR China
| | - Nannan Feng
- School of Public Health, Shanghai Jiao Tong University, Shanghai, 200025, PR China
| | - Shaoyou Lu
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, 510275, PR China.
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Salam LB, Obayori OS. Remarkable shift in structural and functional properties of an animal charcoal-polluted soil accentuated by inorganic nutrient amendment. J Genet Eng Biotechnol 2020; 18:70. [PMID: 33175233 PMCID: PMC7658278 DOI: 10.1186/s43141-020-00089-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/02/2020] [Indexed: 12/02/2022]
Abstract
Background Soils polluted with animal charcoal from skin and hide cottage industries harbour extremely toxic and carcinogenic hydrocarbon pollutants and thus require a bio-based eco-friendly strategy for their depuration. The effects of carbon-free mineral medium (CFMM) amendment on hydrocarbon degradation and microbial community structure and function in an animal charcoal-polluted soil was monitored for 6 weeks in field moist microcosms consisting of CFMM-treated soil (FN4) and an untreated control (FN1). Hydrocarbon degradation was monitored using gas chromatography-flame ionization detector (GC-FID), and changes in microbial community structure were monitored using Kraken, while functional annotation of putative open reading frames (ORFs) was done using KEGG KofamKOALA and NCBI’s conserved domain database (CDD). Results Gas chromatographic analysis of hydrocarbon fractions revealed the removal of 84.02% and 82.38% aliphatic and 70.09% and 70.14% aromatic fractions in FN4 and FN1 microcosms in 42 days. Shotgun metagenomic analysis of the two metagenomes revealed a remarkable shift in the microbial community structure. In the FN4 metagenome, 92.97% of the population belong to the phylum Firmicutes and its dominant representative genera Anoxybacillus (64.58%), Bacillus (21.47%) and Solibacillus (2.39%). In untreated FN1 metagenome, the phyla Proteobacteria (56.12%), Actinobacteria (23.79%) and Firmicutes (11.20%), and the genera Xanthobacter (9.73%), Rhizobium (7.49%) and Corynebacterium (7.35%), were preponderant. Functional annotation of putative ORFs from the two metagenomes revealed the detection of degradation genes for aromatic hydrocarbons, benzoate, xylene, chlorocyclohexane/chlorobenzene, toluene and several others in FN1 metagenome. In the FN4 metagenome, only seven hydrocarbon degradation genes were detected. Conclusion This study revealed that though CFMM amendment slightly increases the rate of hydrocarbon degradation, it negatively impacts the structural and functional properties of the animal charcoal-polluted soil. It also revealed that intrinsic bioremediation of the polluted soil could be enhanced via addition of water and aeration. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-020-00089-9.
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Affiliation(s)
- Lateef Babatunde Salam
- Department of Biological Sciences, Microbiology unit, Summit University, Offa, Kwara, Nigeria.
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Podell S, Blanton JM, Oliver A, Schorn MA, Agarwal V, Biggs JS, Moore BS, Allen EE. A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes. MICROBIOME 2020; 8:97. [PMID: 32576248 PMCID: PMC7313196 DOI: 10.1186/s40168-020-00877-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 05/28/2020] [Indexed: 05/09/2023]
Abstract
BACKGROUND Marine sponges and their microbiomes contribute significantly to carbon and nutrient cycling in global reefs, processing and remineralizing dissolved and particulate organic matter. Lamellodysidea herbacea sponges obtain additional energy from abundant photosynthetic Hormoscilla cyanobacterial symbionts, which also produce polybrominated diphenyl ethers (PBDEs) chemically similar to anthropogenic pollutants of environmental concern. Potential contributions of non-Hormoscilla bacteria to Lamellodysidea microbiome metabolism and the synthesis and degradation of additional secondary metabolites are currently unknown. RESULTS This study has determined relative abundance, taxonomic novelty, metabolic capacities, and secondary metabolite potential in 21 previously uncharacterized, uncultured Lamellodysidea-associated microbial populations by reconstructing near-complete metagenome-assembled genomes (MAGs) to complement 16S rRNA gene amplicon studies. Microbial community compositions aligned with sponge host subgroup phylogeny in 16 samples from four host clades collected from multiple sites in Guam over a 3-year period, including representatives of Alphaproteobacteria, Gammaproteobacteria, Oligoflexia, and Bacteroidetes as well as Cyanobacteria (Hormoscilla). Unexpectedly, microbiomes from one host clade also included Cyanobacteria from the prolific secondary metabolite-producer genus Prochloron, a common tunicate symbiont. Two novel Alphaproteobacteria MAGs encoded pathways diagnostic for methylotrophic metabolism as well as type III secretion systems, and have been provisionally assigned to a new order, designated Candidatus Methylospongiales. MAGs from other taxonomic groups encoded light-driven energy production pathways using not only chlorophyll, but also bacteriochlorophyll and proteorhodopsin. Diverse heterotrophic capabilities favoring aerobic versus anaerobic conditions included pathways for degrading chitin, eukaryotic extracellular matrix polymers, phosphonates, dimethylsulfoniopropionate, trimethylamine, and benzoate. Genetic evidence identified an aerobic catabolic pathway for halogenated aromatics that may enable endogenous PBDEs to be used as a carbon and energy source. CONCLUSIONS The reconstruction of high-quality MAGs from all microbial taxa comprising greater than 0.1% of the sponge microbiome enabled species-specific assignment of unique metabolic features that could not have been predicted from taxonomic data alone. This information will promote more representative models of marine invertebrate microbiome contributions to host bioenergetics, the identification of potential new sponge parasites and pathogens based on conserved metabolic and physiological markers, and a better understanding of biosynthetic and degradative pathways for secondary metabolites and halogenated compounds in sponge-associated microbiota. Video Abstract.
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Affiliation(s)
- Sheila Podell
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Jessica M Blanton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Aaron Oliver
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Michelle A Schorn
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jason S Biggs
- University of Guam Marine Laboratory, UoG Station, Mangilao, GU, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Eric E Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
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Special Issue: Genetics of Biodegradation and Bioremediation. Genes (Basel) 2020; 11:genes11040441. [PMID: 32316688 PMCID: PMC7230606 DOI: 10.3390/genes11040441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 01/03/2023] Open
Abstract
Many different biodegradation pathways, both aerobic and anaerobic, have already been characterised, and the phylogenetic relationships among catabolic genes within the different types of pathways have been studied. However, new biodegradation activities and their coding genes are continuously being reported, including those involved in the catabolism of emerging contaminants or those generally regarded as non-biodegradable. Gene regulation is also an important issue for the efficient biodegradation of contaminants. Specific induction by the substrate and over-imposed global regulatory networks adjust the expression of the biodegradation genes to the bacterial physiological needs. New biodegradation pathways can be assembled in a particular strain or in a bacterial consortium by recruiting biodegradation genes from different origins through horizontal gene transfer. The abundance and diversity of biodegradation genes, analysed by either genomic or metagenomic approaches, constitute valuable indicators of the biodegradation potential of a particular environmental niche. This knowledge paves the way to systems metabolic engineering approaches to valorise biowaste for the production of value-added products.
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Phale PS, Malhotra H, Shah BA. Degradation strategies and associated regulatory mechanisms/features for aromatic compound metabolism in bacteria. ADVANCES IN APPLIED MICROBIOLOGY 2020; 112:1-65. [PMID: 32762865 DOI: 10.1016/bs.aambs.2020.02.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
As a result of anthropogenic activity, large number of recalcitrant aromatic compounds have been released into the environment. Consequently, microbial communities have adapted and evolved to utilize these compounds as sole carbon source, under both aerobic and anaerobic conditions. The constitutive expression of enzymes necessary for metabolism imposes a heavy energy load on the microbe which is overcome by arrangement of degradative genes as operons which are induced by specific inducers. The segmentation of pathways into upper, middle and/or lower operons has allowed microbes to funnel multiple compounds into common key aromatic intermediates which are further metabolized through central carbon pathway. Various proteins belonging to diverse families have evolved to regulate the transcription of individual operons participating in aromatic catabolism. These proteins, complemented with global regulatory mechanisms, carry out the regulation of aromatic compound metabolic pathways in a concerted manner. Additionally, characteristics like chemotaxis, preferential utilization, pathway compartmentalization and biosurfactant production confer an advantage to the microbe, thus making bioremediation of the aromatic pollutants more efficient and effective.
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Affiliation(s)
- Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India.
| | - Harshit Malhotra
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Bhavik A Shah
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
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Abstract
Since Barbara McClintock’s groundbreaking discovery of mobile DNA sequences some 70 years ago, transposable elements have come to be recognized as important mutagenic agents impacting genome composition, genome evolution, and human health. Transposable elements are a major constituent of prokaryotic and eukaryotic genomes, and the transposition mechanisms enabling transposon proliferation over evolutionary time remain engaging topics for study, suggesting complex interactions with the host, both antagonistic and mutualistic. The impact of transposition is profound, as over 100 human heritable diseases have been attributed to transposon insertions. Transposition can be highly mutagenic, perturbing genome integrity and gene expression in a wide range of organisms. This mutagenic potential has been exploited in the laboratory, where transposons have long been utilized for phenotypic screening and the generation of defined mutant libraries. More recently, barcoding applications and methods for RNA-directed transposition are being used towards new phenotypic screens and studies relevant for gene therapy. Thus, transposable elements are significant in affecting biology both
in vivo and in the laboratory, and this review will survey advances in understanding the biological role of transposons and relevant laboratory applications of these powerful molecular tools.
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Affiliation(s)
- Anuj Kumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.,Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA
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