1
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Naveed M, Naveed R, Aziz T, Azeem A, Afzal M, Waseem M, Alharbi M, Alshammari A, Alasmari AF, Albekairi TH. Biodegradation of PVCs through in-vitro identification of Bacillus albus and computational pathway analysis of ABH enzyme. Biodegradation 2024; 35:451-468. [PMID: 38289541 DOI: 10.1007/s10532-023-10064-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 12/13/2023] [Indexed: 06/27/2024]
Abstract
Microplastics pose significant challenges to ecosystems and organisms. They can be ingested by marine and terrestrial species, leading to potential health risks and ecological disruptions. This study aims to address the urgent need for effective remediation strategies by focusing on the biodegradation of microplastics, specifically polyvinyl chloride (PVC) derivatives, using the bacterial strain Bacillus albus. The study provides a comprehensive background on the accumulation of noxious substances in the environment and the importance of harnessing biodegradation as an eco-friendly method for pollutant elimination. The specific objective is to investigate the enzymatic capabilities of Bacillus albus, particularly the alpha/beta hydrolases (ABH), in degrading microplastics. To achieve this, in-silico studies were conducted, including analysis of the ABH protein sequence and its interaction with potential inhibitors targeting PVC derivatives. Docking scores of - 7.2 kcal/mol were obtained to evaluate the efficacy of the interactions. The study demonstrates the promising bioremediation prospects of Bacillus albus for microplastics, highlighting its potential as a key player in addressing microplastic pollution. The findings underscore the urgent need for further experimental validation and practical implementation of Bacillus albus in environmental remediation strategies.
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Affiliation(s)
- Muhammad Naveed
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, 54000, Pakistan.
| | - Rida Naveed
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, 54000, Pakistan
| | - Tariq Aziz
- Department of Agriculture, University of Ioannina, Arta, Greece.
| | - Arooj Azeem
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, 54000, Pakistan
| | - Mahrukh Afzal
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, 54000, Pakistan
| | - Muhammad Waseem
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, 54000, Pakistan
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, 11451, Riyadh, Saudi Arabia
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, 11451, Riyadh, Saudi Arabia
| | - Abdullah F Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, 11451, Riyadh, Saudi Arabia
| | - Thamer H Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, 11451, Riyadh, Saudi Arabia
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2
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Zhou Y, Wang Y, Yao S, Zhao X, Kong Q, Cui L, Zhang H. Driving mechanisms for the adaptation and degradation of petroleum hydrocarbons by native microbiota from seas prone to oil spills. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135060. [PMID: 38943887 DOI: 10.1016/j.jhazmat.2024.135060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 06/15/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Offshore waters have a high incidence of oil pollution, which poses an elevated risk of ecological damage. The microbial community composition and metabolic mechanisms influenced by petroleum hydrocarbons vary across different marine regions. However, research on metabolic strategies for in-situ petroleum degradation and pollution adaptation remains in its nascent stages. This study combines metagenomic techniques with gas chromatography-mass spectrometry (GC-MS) analysis. The data show that the genera Pseudoalteromonas, Hellea, Lentisphaera, and Polaribacter exhibit significant oil-degradation capacity, and that the exertion of their degradation capacity is correlated with nutrient and oil pollution stimuli. Furthermore, tmoA, badA, phdF, nahAc, and fadA were found to be the key genes involved in the degradation of benzene, polycyclic aromatic hydrocarbons, and their intermediates. Key genes (INSR, SLC2A1, and ORC1) regulate microbial adaptation to oil-contaminated seawater, activating oil degradation processes. This process enhances the biological activity of microbial communities and accounts for the geographical variation in their compositional structure. Our results enrich the gene pool for oil pollution adaptation and degradation and provide an application basis for optimizing bioremediation intervention strategies.
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Affiliation(s)
- Yumiao Zhou
- College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Ying Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
| | - Shudi Yao
- College of Geography and Environment, Shandong Normal University, Jinan 250014, China
| | - Xinyu Zhao
- Laoshan Laboratory, Qingdao 266237, China
| | - Qiang Kong
- College of Geography and Environment, Shandong Normal University, Jinan 250014, China
| | - Lihua Cui
- College of Geography and Environment, Shandong Normal University, Jinan 250014, China
| | - Huanxin Zhang
- College of Geography and Environment, Shandong Normal University, Jinan 250014, China.
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3
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Xiong JX, Du LS, Li NN, Wu XT, Xiang Y, Li S, Zou L, Liu D, Huang D, Xie ZF, Wang Y, Li J, Dai J, Yan D, Chao HJ. Pigmentiphaga kullae CHJ604 improved the growth of tobacco by degrading allelochemicals and xenobiotics in continuous cropping obstacles. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133466. [PMID: 38219583 DOI: 10.1016/j.jhazmat.2024.133466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/16/2024]
Abstract
Plant autotoxicity is considered to be one of the important causes of continuous cropping obstacles in modern agriculture, which accumulates a lot of allelochemicals and xenobiotics and is difficult to solve effectively. To overcome tobacco continuous obstacles, a strain Pigmentiphaga kullae CHJ604 isolated from the environment can effectively degrade these compounds in this study. CHJ604 strain can degrade 11 types of autotoxicity allelochemicals and xenobiotics (1646.22 μg/kg) accumulated in the soil of ten-years continuous cropping of tobacco. The 11 allelochemicals and xenobiotics significantly reduced Germination Percentage (GP), Germination Index (GI), and Mean Germination Time (MGT) of tobacco seeds, and inhibited the development of leaves, stems, and roots. These negative disturbances can be eliminated by CHJ604 strain. The degradation pathways of 11 allelochemicals and xenobiotics were obtained by whole genome sequence and annotation of CHJ604 strain. The heterologous expression of a terephthalate 1,2-dioxygenase can catalyze 4-hydroxybenzoic acid, 4-hydroxy-3-methoxybenzoic acid, 4-hydroxybenzaldehyde, and 4-hydroxy-3-methoxy-benzaldehyde, respectively. The phthalate 4,5-dioxygenase can catalyze phthalic acid, diisobutyl phthalate, and dibutyl phthalate. These two enzymes are conducive to the simultaneous degradation of multiple allelochemicals and xenobiotics by strain CHJ604. This study provides new insights into the biodegradation of autotoxicity allelochemicals and xenobiotics as it is the first to describe a degrading bacterium of 11 types of allelochemicals and xenobiotics and their great potential in improving tobacco continuous obstacles.
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Affiliation(s)
- Jia-Xi Xiong
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, PR China
| | - Ling-Shan Du
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, PR China
| | - Na-Na Li
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, PR China
| | - Xiu-Ting Wu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, PR China
| | - Yang Xiang
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, PR China
| | - Sha Li
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, PR China
| | - Lei Zou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Dongqi Liu
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074, PR China
| | - Duo Huang
- Hubei Accurate Inspection & Testing Co., Ltd., Wuhan 430223, PR China
| | - Ze Feng Xie
- Hubei Accurate Inspection & Testing Co., Ltd., Wuhan 430223, PR China
| | - Ying Wang
- Hubei Accurate Inspection & Testing Co., Ltd., Wuhan 430223, PR China
| | - Jinhua Li
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, PR China
| | - Jingcheng Dai
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, PR China
| | - Dazhong Yan
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, PR China
| | - Hong-Jun Chao
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, PR China.
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4
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Palma V, González-Pimentel JL, Jimenez-Morillo NT, Sauro F, Gutiérrez-Patricio S, De la Rosa JM, Tomasi I, Massironi M, Onac BP, Tiago I, González-Pérez JA, Laiz L, Caldeira AT, Cubero B, Miller AZ. Connecting molecular biomarkers, mineralogical composition, and microbial diversity from Mars analog lava tubes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 913:169583. [PMID: 38154629 DOI: 10.1016/j.scitotenv.2023.169583] [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: 08/29/2023] [Revised: 12/13/2023] [Accepted: 12/20/2023] [Indexed: 12/30/2023]
Abstract
Lanzarote (Canary Islands, Spain) is one of the best terrestrial analogs to Martian volcanology. Particularly, Lanzarote lava tubes may offer access to recognizably preserved chemical and morphological biosignatures valuable for astrobiology. By combining microbiological, mineralogical, and organic geochemistry tools, an in-depth characterization of speleothems and associated microbial communities in lava tubes of Lanzarote is provided. The aim is to untangle the underlying factors influencing microbial colonization in Earth's subsurface to gain insight into the possibility of similar subsurface microbial habitats on Mars and to identify biosignatures preserved in lava tubes unequivocally. The microbial communities with relevant representativeness comprise chemoorganotrophic, halophiles, and/or halotolerant bacteria that have evolved as a result of the surrounding oceanic environmental conditions. Many of these bacteria have a fundamental role in reshaping cave deposits due to their carbonatogenic ability, leaving behind an organic record that can provide evidence of past or present life. Based on functional profiling, we infer that Crossiella is involved in fluorapatite precipitation via urea hydrolysis and propose its Ca-rich precipitates as compelling biosignatures valuable for astrobiology. In this sense, analytical pyrolysis, stable isotope analysis, and chemometrics were conducted to characterize the complex organic fraction preserved in the speleothems and find relationships among organic families, microbial taxa, and precipitated minerals. We relate organic compounds with subsurface microbial taxa, showing that organic families drive the microbiota of Lanzarote lava tubes. Our data indicate that bacterial communities are important contributors to biomarker records in volcanic-hosted speleothems. Within them, the lipid fraction primarily consists of low molecular weight n-alkanes, α-alkenes, and branched-alkenes, providing further evidence that microorganisms serve as the origin of organic matter in these formations. The ongoing research in Lanzarote's lava tubes will help develop protocols, routines, and predictive models that could provide guidance on choosing locations and methodologies for searching potential biosignatures on Mars.
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Affiliation(s)
- Vera Palma
- HERCULES Laboratory, University of Évora, Évora, Portugal
| | | | | | - Francesco Sauro
- Department of Earth Sciences and Environmental Geology, University of Bologna, Italy
| | | | - José M De la Rosa
- Instituto de Recursos Naturales y Agrobiologia de Sevilla (IRNAS-CSIC), Sevilla, Spain
| | - Ilaria Tomasi
- Geosciences Department, University of Padova, Padova, Italy
| | | | - Bogdan P Onac
- Karst Research Group, School of Geosciences, University of South Florida, Tampa, FL, USA; Emil G. Racoviță Institute, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Igor Tiago
- CFE-Center for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - José A González-Pérez
- Instituto de Recursos Naturales y Agrobiologia de Sevilla (IRNAS-CSIC), Sevilla, Spain
| | - Leonila Laiz
- Instituto de Recursos Naturales y Agrobiologia de Sevilla (IRNAS-CSIC), Sevilla, Spain
| | - Ana T Caldeira
- HERCULES Laboratory, University of Évora, Évora, Portugal
| | - Beatriz Cubero
- Instituto de Recursos Naturales y Agrobiologia de Sevilla (IRNAS-CSIC), Sevilla, Spain
| | - Ana Z Miller
- HERCULES Laboratory, University of Évora, Évora, Portugal; Instituto de Recursos Naturales y Agrobiologia de Sevilla (IRNAS-CSIC), Sevilla, Spain.
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5
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Salam LB. Diverse hydrocarbon degradation genes, heavy metal resistome, and microbiome of a fluorene-enriched animal-charcoal polluted soil. Folia Microbiol (Praha) 2024; 69:59-80. [PMID: 37450270 DOI: 10.1007/s12223-023-01077-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 07/09/2023] [Indexed: 07/18/2023]
Abstract
Environmental compartments polluted with animal charcoal from the skin and hide cottage industries are rich in toxic heavy metals and diverse hydrocarbon classes, some of which are carcinogenic, mutagenic, and genotoxic, and thus require a bio-based eco-benign decommission strategies. A shotgun metagenomic approach was used to decipher the microbiome, hydrocarbon degradation genes, and heavy metal resistome of a microbial consortium (FN8) from an animal-charcoal polluted site enriched with fluorene. Structurally, the FN8 microbial consortium consists of 26 phyla, 53 classes, 119 orders, 245 families, 620 genera, and 1021 species. The dominant phylum, class, order, family, genus, and species in the consortium are Proteobacteria (51.37%), Gammaproteobacteria (39.01%), Bacillales (18.09%), Microbulbiferaceae (11.65%), Microbulbifer (12.21%), and Microbulbifer sp. A4B17 (19.65%), respectively. The microbial consortium degraded 57.56% (28.78 mg/L) and 87.14% (43.57 mg/L) of the initial fluorene concentration in 14 and 21 days. Functional annotation of the protein sequences (ORFs) of the FN8 metagenome using the KEGG GhostKOALA, KofamKOALA, NCBI's conserved domain database, and BacMet revealed the detection of hydrocarbon degradation genes for benzoate, aminobenzoate, polycyclic aromatic hydrocarbons (PAHs), chlorocyclohexane/chlorobenzene, chloroalkane/chloroalkene, toluene, xylene, styrene, naphthalene, nitrotoluene, and several others. The annotation also revealed putative genes for the transport, uptake, efflux, and regulation of heavy metals such as arsenic, cadmium, chromium, mercury, nickel, copper, zinc, and several others. Findings from this study have established that members of the FN8 consortium are well-adapted and imbued with requisite gene sets and could be a potential bioresource for on-site depuration of animal charcoal polluted sites.
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Affiliation(s)
- Lateef Babatunde Salam
- Department of Biological Sciences, Microbiology unit, Elizade University, Ilara-Mokin, Ondo State, Nigeria.
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6
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Tsagogiannis E, Asimakoula S, Drainas AP, Marinakos O, Boti VI, Kosma IS, Koukkou AI. Elucidation of 4-Hydroxybenzoic Acid Catabolic Pathways in Pseudarthrobacter phenanthrenivorans Sphe3. Int J Mol Sci 2024; 25:843. [PMID: 38255919 PMCID: PMC10815724 DOI: 10.3390/ijms25020843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
4-hydroxybenzoic acid (4-HBA) is an aromatic compound with high chemical stability, being extensively used in food, pharmaceutical and cosmetic industries and therefore widely distributed in various environments. Bioremediation constitutes the most sustainable approach for the removal of 4-hydroxybenzoate and its derivatives (parabens) from polluted environments. Pseudarthrobacter phenanthrenivorans Sphe3, a strain capable of degrading several aromatic compounds, is able to grow on 4-HBA as the sole carbon and energy source. Here, an attempt is made to clarify the catabolic pathways that are involved in the biodegradation of 4-hydroxybenzoate by Sphe3, applying a metabolomic and transcriptomic analysis of cells grown on 4-HBA. It seems that in Sphe3, 4-hydroxybenzoate is hydroxylated to form protocatechuate, which subsequently is either cleaved in ortho- and/or meta-positions or decarboxylated to form catechol. Protocatechuate and catechol are funneled into the TCA cycle following either the β-ketoadipate or protocatechuate meta-cleavage branches. Our results also suggest the involvement of the oxidative decarboxylation of the protocatechuate peripheral pathway to form hydroxyquinol. As a conclusion, P. phenanthrenivorans Sphe3 seems to be a rather versatile strain considering the 4-hydroxybenzoate biodegradation, as it has the advantage to carry it out effectively following different catabolic pathways concurrently.
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Affiliation(s)
- Epameinondas Tsagogiannis
- Laboratory of Biochemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (E.T.); (S.A.); (A.P.D.); (O.M.)
| | - Stamatia Asimakoula
- Laboratory of Biochemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (E.T.); (S.A.); (A.P.D.); (O.M.)
| | - Alexandros P. Drainas
- Laboratory of Biochemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (E.T.); (S.A.); (A.P.D.); (O.M.)
| | - Orfeas Marinakos
- Laboratory of Biochemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (E.T.); (S.A.); (A.P.D.); (O.M.)
| | - Vasiliki I. Boti
- Unit of Environmental, Organic and Biochemical High-Resolution Analysis-Orbitrap-LC-MS, University of Ioannina, 451110 Ioannina, Greece;
| | - Ioanna S. Kosma
- Laboratory of Food Chemistry, Sector of Industrial Chemistry and Food Chemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece;
| | - Anna-Irini Koukkou
- Laboratory of Biochemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (E.T.); (S.A.); (A.P.D.); (O.M.)
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7
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Ramdass AC, Rampersad SN. Genome features of a novel hydrocarbonoclastic Chryseobacterium oranimense strain and its comparison to bacterial oil-degraders and to other C. oranimense strains. DNA Res 2023; 30:dsad025. [PMID: 37952165 PMCID: PMC10710014 DOI: 10.1093/dnares/dsad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/29/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023] Open
Abstract
For the first time, we report the whole genome sequence of a hydrocarbonoclastic Chryseobacterium oranimense strain isolated from Trinidad and Tobago (COTT) and its genes involved in the biotransformation of hydrocarbons and xenobiotics through functional annotation. The assembly consisted of 11 contigs with 2,794 predicted protein-coding genes which included a diverse group of gene families involved in aliphatic and polycyclic hydrocarbon degradation. Comparative genomic analyses with 18 crude-oil degrading bacteria in addition to two C. oranimense strains not associated with oil were carried out. The data revealed important differences in terms of annotated genes involved in the hydrocarbon degradation process that may explain the molecular mechanisms of hydrocarbon and xenobiotic biotransformation. Notably, many gene families were expanded to explain COTT's competitive ability to manage habitat-specific stressors. Gene-based evidence of the metabolic potential of COTT supports the application of indigenous microbes for the remediation of polluted terrestrial environments and provides a genomic resource for improving our understanding of how to optimize these characteristics for more effective bioremediation.
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Affiliation(s)
- Amanda Christine Ramdass
- Biochemistry Research Lab (Rm216), Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago, West Indies
| | - Sephra Nalini Rampersad
- Biochemistry Research Lab (Rm216), Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago, West Indies
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8
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Mai Z, Wang H, Wang Y, Chen Q, Lyu L, Wei X, Zhou W, Cheng H. Radial Oxygen Loss from the Roots of Mangrove Seedlings Enhances the Removal of Polycyclic Aromatic Hydrocarbons. PLANTS (BASEL, SWITZERLAND) 2023; 12:3711. [PMID: 37960067 PMCID: PMC10647379 DOI: 10.3390/plants12213711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/20/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023]
Abstract
The presence of polycyclic aromatic hydrocarbons (PAHs) in soil poses a significant global environmental concern, particularly in coastal wetlands. Mangrove ecosystems exhibit enormous potential in environmental purification; however, the underlying mechanisms involved in the degradation of pollutants (e.g., PAHs) remain ambiguous. In the present investigation, a soil pot experiment was conducted with the addition of pyrene to evaluate the effect of radial oxygen loss (ROL) from roots on PAH degradation using three mangrove seedlings (Rhizophora stylosa, Aegiceras corniculatum, and Avicennia marina). The results showed that mangrove plantation can significantly promote the efficiency of pyrene removal. As for the three mangrove species studied, the greatest removal rate (90.75%) was observed in the soils associated with A. marina, followed by A. corniculatum (83.83%) and R. stylosa (77.15%). The higher PAH removal efficiency of A. marina can be partially attributed to its distinctive root anatomical structure, characterized by a thin exodermis and high porosity, which facilitates ROL from the roots. The results from qPCR further demonstrate that ROL is beneficial for promoting the abundance of PAH-ring hydroxylating dioxygenase gene, leading to a higher removal efficiency. Additionally, Rhizobiales, Defferrisomatales, and Ardenticatenales may also play important roles in the process of pyrene degradation. In summary, this study provides evidence for elucidating the mechanism of PAH removal from the perspective of ROL, thereby contributing valuable insights for species selection during mangrove restoration and remediation.
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Affiliation(s)
- Zhimao Mai
- State Key Laboratory of Tropical Oceanography, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China (W.Z.)
| | - Hui Wang
- State Key Laboratory of Tropical Oceanography, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China (W.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Youshao Wang
- State Key Laboratory of Tropical Oceanography, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China (W.Z.)
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen 518121, China
| | - Qiqi Chen
- State Key Laboratory of Tropical Oceanography, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China (W.Z.)
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China
| | - Lina Lyu
- State Key Laboratory of Tropical Oceanography, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China (W.Z.)
| | - Xing Wei
- State Key Laboratory of Tropical Oceanography, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China (W.Z.)
| | - Weiwen Zhou
- State Key Laboratory of Tropical Oceanography, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China (W.Z.)
| | - Hao Cheng
- State Key Laboratory of Tropical Oceanography, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China (W.Z.)
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen 518121, China
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9
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Ahmad M, Ling J, Yin J, Chen L, Yang Q, Zhou W, Zhang Y, Huang X, Khan I, Dong J. Evaluation of the Different Nutritional and Environmental Parameters on Microbial Pyrene Degradation by Mangrove Culturable Bacteria. Int J Mol Sci 2023; 24:ijms24098282. [PMID: 37175988 PMCID: PMC10179275 DOI: 10.3390/ijms24098282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/23/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Mangrove ecosystems play curial roles in providing many ecological services and alleviating global climate change. However, they are in decline globally, mainly threatened by human activities and global warming, and organic pollutants, especially PAHs, are among the crucial reasons. Microbial remediation is a cost-effective and environmentally friendly way of alleviating PAH contamination. Therefore, understanding the effects of environmental and nutritional parameters on the biodegradation of polycyclic aromatic hydrocarbons (PAHs) is significant for the bioremediation of PAH contamination. In the present study, five bacterial strains, designated as Bp1 (Genus Rhodococcus), Sp8 (Genus Nitratireductor), Sp13 (Genus Marinobacter), Sp23 (Genus Pseudonocardia), and Sp24 (Genus Mycolicibacterium), have been isolated from mangrove sediment and their ring hydroxylating dioxygenase (RHD) genes have been successfully amplified. Afterward, their degradation abilities were comprehensively evaluated under normal cultural (monoculture and co-culture) and different nutritional (tryptone, yeast extract, peptone, glucose, sucrose, and NPK fertilizer) and environmental (cetyl trimethyl ammonium bromide (CTAB), sodium dodecyl sulfate (SDS)) parameters, as well with different co-contaminants (phenanthrene and naphthalene) and heavy metals (Cd2+, Cu2+, Fe3+, Ni2+, Mg2+, Mn2+, and Co2+). The results showed that strain Sp24 had the highest pyrene degradation rate (85%) in the monoculture experiment after being cultured for 15 days. Adding nitrogen- and carbon-rich sources, including tryptone, peptone, and yeast extract, generally endorsed pyrene degradation. In contrast, the effects of carbon sources (glucose and sucrose) on pyrene degradation were distinct for different bacterial strains. Furthermore, the addition of NPK fertilizer, SDS, Tween-80, phenanthrene, and naphthalene enhanced the bacterial abilities of pyrene removal significantly (p < 0.05). Heavy metals significantly reduced all bacterial isolates' degradation potentials (p < 0.05). The bacterial consortia containing high bio-surfactant-producing strains showed substantially higher pyrene degradation. Moreover, the consortia of three and five bacterial strains showed more degradation efficiency than those of two bacterial strains. These results provide helpful microbial resources for mangrove ecological remediation and insight into optimized culture strategies for the microbial degradation of PAHs.
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Affiliation(s)
- Manzoor Ahmad
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Juan Ling
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China
- Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shantou 515041, China
| | - Jianping Yin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Luxiang Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Qingsong Yang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China
- Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shantou 515041, China
| | - Weiguo Zhou
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China
| | - Yuhang Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China
| | - Xiaofang Huang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China
| | - Imran Khan
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Junde Dong
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China
- Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shantou 515041, China
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10
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Sivapuratharasan V, Lenzen C, Michel C, Muthukrishnan AB, Jayaraman G, Blank LM. Metabolic engineering of Pseudomonas taiwanensis VLB120 for rhamnolipid biosynthesis from biomass-derived aromatics. Metab Eng Commun 2022; 15:e00202. [PMID: 36017490 PMCID: PMC9396041 DOI: 10.1016/j.mec.2022.e00202] [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: 05/13/2022] [Revised: 07/01/2022] [Accepted: 07/27/2022] [Indexed: 12/02/2022] Open
Abstract
Lignin is a ubiquitously available and sustainable feedstock that is underused as its depolymerization yields a range of aromatic monomers that are challenging substrates for microbes. In this study, we investigated the growth of Pseudomonas taiwanensis VLB120 on biomass-derived aromatics, namely, 4-coumarate, ferulate, 4-hydroxybenzoate, and vanillate. The wild type strain was not able to grow on 4-coumarate and ferulate. After integration of catabolic genes for breakdown of 4-coumarate and ferulate, the metabolically engineered strain was able to grow on these aromatics. Further, the specific growth rate of the strain was enhanced up to 3-fold using adaptive laboratory evolution, resulting in increased tolerance towards 4-coumarate and ferulate. Whole-genome sequencing highlighted several different mutations mainly in two genes. The first gene was actP, coding for a cation/acetate symporter, and the other gene was paaA coding for a phenyl acetyl-CoA oxygenase. The evolved strain was further engineered for rhamnolipid production. Among the biomass-derived aromatics investigated, 4-coumarate and ferulate were promising substrates for product synthesis. With 4-coumarate as the sole carbon source, a yield of 0.27 (Cmolrhl/Cmol4-coumarate) was achieved, corresponding to 28% of the theoretical yield. Ferulate enabled a yield of about 0.22 (Cmolrhl/Cmolferulate), representing 42% of the theoretical yield. Overall, this study demonstrates the use of biomass-derived aromatics as novel carbon sources for rhamnolipid biosynthesis. Enabling 4-coumarate and ferulate degradation in Pseudomonas taiwanensis VLB120. The growth rate and tolerance was enhanced towards non-native substrates. Genetic mutations in actP and paaA contributed to the enhanced tolerance. Production of mono-rhamnolipids was established using all the chosen aromatics.
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Affiliation(s)
- Vaishnavi Sivapuratharasan
- Institute of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Christoph Lenzen
- Institute of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Carina Michel
- Institute of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Anantha Barathi Muthukrishnan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Guhan Jayaraman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Lars M. Blank
- Institute of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
- Corresponding author.
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11
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Kim SJ, Kim YS, Kim SE, Jung HK, Park J, Yu MJ, Kim KH. Rasiella rasia gen. nov. sp. nov. within the family Flavobacteriaceae isolated from seawater recirculating aquaculture system. J Microbiol 2022; 60:1070-1076. [PMID: 36251119 DOI: 10.1007/s12275-022-2099-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 08/24/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
A novel bacterium designated RR4-40T was isolated from a biofilter of seawater recirculating aquaculture system in Busan, South Korea. Cells are strictly aerobic, Gram-negative, irregular short rod, non-motile, and oxidase- and catalase-negative. Growth was observed at 15-30°C, 0.5-6% NaCl (w/v), and pH 5.0-9.5. The strain grew optimally at 28°C, 3% salinity (w/v), and pH 8.5. The phylogenetic analysis based on 16S rRNA gene sequences showed that strain RR4-40T was most closely related to Marinirhabdus gelatinilytica NH83T (94.16% of 16S rRNA gene similarity) and formed a cluster with genera within the family Flavobacteriaceae. The values of the average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) between genomes of strain RR4-40T and M. gelatinilytica NH83T were 72.91, 18.2, and 76.84%, respectively, and the values against the strains in the other genera were lower than those. The major fatty acids were iso-C15:0 (31.34%), iso-C17:0 3-OH (13.65%), iso-C16:0 3-OH (10.61%), and iso-C15:1 G (10.38%). The polar lipids comprised phosphatidylglycerol, diphosphatidylglycerol, aminophospholipid, aminolipid, glycolipid, and sphingolipid. The major respiratory quinone was menaquinone-6 (MK-6) and the DNA G + C content of strain RR4-40T was 37.4 mol%. According to the polyphasic analysis, strain RR4-40T is considered to represent a novel genus within the family Flavobacteriaceae, for which the name Rasiella rasia gen. nov, sp. nov. is proposed. The type strain is RR4-40T (= KCTC 52650T = MCCC 1K04210T).
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Affiliation(s)
- Seong-Jin Kim
- Department of Microbiology, Pukyong National University, Busan, 48513, Republic of Korea
| | - Young-Sam Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | - Sang-Eon Kim
- Department of Microbiology, Pukyong National University, Busan, 48513, Republic of Korea
- School of Marine and Fisheries Life Science, Pukyong National University, Busan, 48513, Republic of Korea
| | - Hyun-Kyoung Jung
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | - Jeeeun Park
- Department of Microbiology, Pukyong National University, Busan, 48513, Republic of Korea
- School of Marine and Fisheries Life Science, Pukyong National University, Busan, 48513, Republic of Korea
| | - Min-Ju Yu
- Department of Microbiology, Pukyong National University, Busan, 48513, Republic of Korea
| | - Kyoung-Ho Kim
- Department of Microbiology, Pukyong National University, Busan, 48513, Republic of Korea.
- School of Marine and Fisheries Life Science, Pukyong National University, Busan, 48513, Republic of Korea.
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12
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Jiao M, He W, Ouyang Z, Shi Q, Wen Y. Progress in structural and functional study of the bacterial phenylacetic acid catabolic pathway, its role in pathogenicity and antibiotic resistance. Front Microbiol 2022; 13:964019. [PMID: 36160191 PMCID: PMC9493321 DOI: 10.3389/fmicb.2022.964019] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Phenylacetic acid (PAA) is a central intermediate metabolite involved in bacterial degradation of aromatic components. The bacterial PAA pathway mainly contains 12 enzymes and a transcriptional regulator, which are involved in biofilm formation and antimicrobial activity. They are present in approximately 16% of the sequenced bacterial genome. In this review, we have summarized the PAA distribution in microbes, recent structural and functional study progress of the enzyme families of the bacterial PAA pathway, and their role in bacterial pathogenicity and antibiotic resistance. The enzymes of the bacterial PAA pathway have shown potential as an antimicrobial drug target for biotechnological applications in metabolic engineering.
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Affiliation(s)
- Min Jiao
- Department of Critical Care Medicine, Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Wenbo He
- Department of Critical Care Medicine, Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Zhenlin Ouyang
- Department of Critical Care Medicine, Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Qindong Shi
- Department of Critical Care Medicine, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Yurong Wen
- Department of Critical Care Medicine, Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
- Department of Critical Care Medicine, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
- The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education Health Science Center, Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Yurong Wen,
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13
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Stanley M, Palace V, Grosshans R, Levin DB. Floating treatment wetlands for the bioremediation of oil spills: A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 317:115416. [PMID: 35653839 DOI: 10.1016/j.jenvman.2022.115416] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/21/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Conventional oil spill recovery may cause significant damage to shoreline habitats during the removal of oiled material and from human and equipment interaction. In addition, these methods are costly and can leave a significant amount of residual oil in the environment. Biological remediation strategies may be a less invasive option for recovering oil from sensitive regions, with potential to increase recovery. Floating treatment wetlands are a growing area of interest for biodegradation of oil facilitated by plant-bacterial partnerships. Plants are able to stimulate microbial colonization in the rhizosphere, creating greater opportunity for contaminant interaction and degradation. A literature review analysis revealed thirteen articles researching this topic, and found that floating treatment wetlands have high potential to degrade oil contaminants. In some instances, plants and inoculated bacteria exhibited the highest degradation potential, however, plants alone had higher degradation potential than bacteria alone. Research is needed to explore how floating treatment wetlands perform in field-based trials and under variable environmental conditions.
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Affiliation(s)
- Madeline Stanley
- Department of Biosystems Engineering, University of Manitoba, E2-376 EITC, Winnipeg, MB, R3T 5V6, Canada.
| | - Vince Palace
- International Institute for Sustainable Development Experimental Lakes Area, 325-111 Lombard Ave, Winnipeg, MB, R3B 0T4, Canada.
| | - Richard Grosshans
- International Institute for Sustainable Development, 325-111 Lombard Ave, Winnipeg, MB, R3B 0T4, Canada.
| | - David B Levin
- Department of Biosystems Engineering, University of Manitoba, E2-376 EITC, Winnipeg, MB, R3T 5V6, Canada.
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14
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Mechanistic Insight into Phenolic Compounds Toxicity and State-of-the-art Strategies for Enhancing the Tolerance of Escherichia coli to Phenolic Compounds. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-022-0019-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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15
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Jimoh AA, Ikhimiukor OO, Adeleke R. Prospects in the bioremediation of petroleum hydrocarbon contaminants from hypersaline environments: A review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:35615-35642. [PMID: 35247173 DOI: 10.1007/s11356-022-19299-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
Hypersaline environments are underappreciated and are frequently exposed to pollution from petroleum hydrocarbons. Unlike other environs, the high salinity conditions present are a deterrent to various remediation techniques. There is also production of hypersaline waters from oil-polluted ecosystems which contain toxic hydrophobic pollutants that are threat to public health, environmental protection, and sustainability. Currently, innovative advances are being proposed for the remediation of oil-contaminated hypersaline regions. Such advancements include the exploration and stimulation of native microbial communities capable of utilizing and degrading petroleum hydrocarbons. However, prevailing salinity in these environments is unfavourable for the growth of non-halophylic microorganisms, thus limiting effective bioremediation options. An in-depth understanding of the potentials of various remediation technologies of hydrocarbon-polluted hypersaline environments is lacking. Thus, we present an overview of petroleum hydrocarbon pollution in hypersaline ecosystems and discuss the challenges and prospects associated with several technologies that may be employed in remediation of hydrocarbon pollution in the presence of delimiting high salinities. The application of biological remediation technologies including the utilization of halophilic and halotolerant microorganisms is also discussed.
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Affiliation(s)
- Abdullahi Adekilekun Jimoh
- Unit for Environmental Sciences and Management, North-West University (Potchefstroom Campus), Potchefstroom, 2520, South Africa.
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, Bellville, Cape Town, 7535, South Africa.
| | - Odion Osebhahiemen Ikhimiukor
- Environmental Microbiology and Biotechnology Laboratory, Department of Microbiology, University of Ibadan, Ibadan, Nigeria
| | - Rasheed Adeleke
- Unit for Environmental Sciences and Management, North-West University (Potchefstroom Campus), Potchefstroom, 2520, South Africa
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16
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Tang Q, Wu M, Zhang Y, Li J, Liang J, Zhou H, Qu Y, Zhang X. Performance and bacterial community profiles of sequencing batch reactors during long-term exposure to polyethylene terephthalate and polyethylene microplastics. BIORESOURCE TECHNOLOGY 2022; 347:126393. [PMID: 34826561 DOI: 10.1016/j.biortech.2021.126393] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/14/2021] [Accepted: 11/17/2021] [Indexed: 06/13/2023]
Abstract
Microplastics (MPs) are ubiquitous in wastewater treatment plants (WWTPs), but much remains to be learned about their roles in WWTPs. Herein, polyethylene terephthalate (PET) and polyethylene (PE) particles were added into sequencing batch reactors (SBRs), and the sole impacts and co-impacts of MPs with other pollutants (phenol and Cu2+) on wastewater treatment processes were evaluated. Results indicated that MPs did not significantly affect SBR performance, either alone or co-occurrence with phenol, but the co-exposure to MPs and Cu2+ severely suppressed COD removal efficiency by 37.02%-64.70%. The functional groups of activated sludge had no changes after receiving MPs, but the MPs-Cu2+ co-exposure could greatly promote the secretion of extracellular polymeric substances. Furthermore, MPs had no negative impacts on diversity, richness and structure of bacterial communities, and PET and PE showed different preferences for enrichment of bacterial populations. Moreover, the MPs-Cu2+ co-exposure obviously reduced the overall abundances of Cu-related genes in SBRs.
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Affiliation(s)
- Qidong Tang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Dalian University of Technology, Panjin 124221, China
| | - Minghuo Wu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Dalian University of Technology, Panjin 124221, China
| | - Yuelin Zhang
- Panjin QIZHENG Environmental Water Co., Ltd., Panjin 124211, China
| | - Jingzhe Li
- Panjin QIZHENG Environmental Water Co., Ltd., Panjin 124211, China
| | - Jinxuan Liang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Dalian University of Technology, Panjin 124221, China
| | - Hao Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Dalian University of Technology, Panjin 124221, China
| | - Yuanyuan Qu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xuwang Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Dalian University of Technology, Panjin 124221, China.
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17
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Zhang G, Yang X, Zhao Z, Xu T, Jia X. Artificial Consortium of Three E. coli BL21 Strains with Synergistic Functional Modules for Complete Phenanthrene Degradation. ACS Synth Biol 2022; 11:162-175. [PMID: 34914358 DOI: 10.1021/acssynbio.1c00349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are highly toxic and persistent organic pollutions that can accumulate in the environment. In this study, an aromatic ring cleavage module, a salicylic acid synthesis module, and a catechol metabolism module were respectively constructed in three Escherichia coli BL21 strains. Subsequently, the engineered strains were cocultured as an artificial consortium for the biodegradation of phenanthrene, a typical PHA. Single factor experiments and response surface methodology were used to identify the optimal degradation conditions, including an inoculation interval of 6 h, inoculation ratio of 1:1:1, and IPTG concentration of 2 mM. Under these conditions, the 7-day degradation ratio of 100 mg/L phenanthrene reached 72.67%. Moreover, the engineered Escherichia coli BL21 strains showed good phenanthrene degradation ability at substrate concentrations 10 mg/L up to 500 mg/L. Enzyme activity assays combined with gas chromatography-mass spectrometry measurements confirmed that the three engineered strains behaved as a synergistic consortium in the phenanthrene degradation process. Based on the analysis of the key metabolites, the engineered bacteria were supplemented at 7-day intervals in batches so that each engineered strain maintained its optimal degradation ability. The 21-day degradation ratio finally reached 90.66%, which was much higher than what was observed with simultaneous inoculation. These findings suggest that the three engineered strains with separate modules constructed in this study offer an attractive solution for removing PAHs from the environment.
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Affiliation(s)
- Guangbao Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Xiaohui Yang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Zhenhua Zhao
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Tao Xu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Xiaoqiang Jia
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
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18
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Zhang X, Huang Z, Wang D, Zhang Y, Eser BE, Gu Z, Dai R, Gao R, Guo Z. A new thermophilic extradiol dioxygenase promises biodegradation of catecholic pollutants. JOURNAL OF HAZARDOUS MATERIALS 2022; 422:126860. [PMID: 34399224 DOI: 10.1016/j.jhazmat.2021.126860] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 07/22/2021] [Accepted: 08/06/2021] [Indexed: 06/13/2023]
Abstract
Extradiol dioxygenases (EDOs) catalyze the meta cleavage of catechol into 2-hydroxymuconaldehyde, a critical step in the degradation of aromatic compounds in the environment. In the present work, a novel thermophilic extradiol dioxygenase from Thermomonospora curvata DSM43183 was cloned, expressed, and characterized by phylogenetic and biochemical analyses. This enzyme exhibited excellent thermo-tolerance, displaying optimal activity at 50 °C, remaining >40% activity at 70 °C. Structural modeling and molecular docking demonstrated that both active center and pocket-construction loops locate at the C-terminal domain. Site-specific mutants D285A, H205V, F301V based on a rational design were obtained to widen the entrance of substrates; resulting in significantly improved catalytic performance for all the 3 mutants. Compared to the wild-type, the mutant D285A showed remarkably improved activities with respect to the 3,4-dihydroxyphenylacetic acid, catechol, and 3-chlorocatechol, by 17.7, 6.9, and 3.7-fold, respectively. The results thus verified the effectiveness of modeling guided design; and confirmed that the C-terminal loop structure indeed plays a decisive role in determining catalytic ring-opening efficiency and substrate specificity of the enzyme. This study provided a novel thermostable dioxygenase with a broad substrate promiscuity for detoxifying environmental pollutants and provided a new thinking for further enzyme engineering of EDOs.
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Affiliation(s)
- Xiaowen Zhang
- Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of life Science, Jilin University, Changchun 130021, China; Department of Biological and Chemical Engineering, Faculty of Technical Sciences, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Zihao Huang
- Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of life Science, Jilin University, Changchun 130021, China
| | - Dan Wang
- Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of life Science, Jilin University, Changchun 130021, China
| | - Yan Zhang
- Department of Biological and Chemical Engineering, Faculty of Technical Sciences, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Bekir Engin Eser
- Department of Biological and Chemical Engineering, Faculty of Technical Sciences, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Zhenyu Gu
- Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of life Science, Jilin University, Changchun 130021, China
| | - Rongrong Dai
- Department of Biological and Chemical Engineering, Faculty of Technical Sciences, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Renjun Gao
- Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of life Science, Jilin University, Changchun 130021, China.
| | - Zheng Guo
- Department of Biological and Chemical Engineering, Faculty of Technical Sciences, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark.
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19
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Wang X, Teng Y, Ren W, Han Y, Wang X, Li X. Soil bacterial diversity and functionality are driven by plant species for enhancing polycyclic aromatic hydrocarbons dissipation in soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:149204. [PMID: 34346367 DOI: 10.1016/j.scitotenv.2021.149204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 07/13/2021] [Accepted: 07/18/2021] [Indexed: 05/27/2023]
Abstract
Plant-microorganisms symbiosis has been widely used in developing strategies for the rhizoremediation of polycyclic aromatic hydrocarbon (PAHs) contaminated agricultural soils. However, understanding the potential mechanisms for using complex plant-microbe interactions to enhance rhizoremediation in contaminated soils is still limited. In this study, rhizosphere microbiomes were established by cultivating four types of cover crops for 15 months in a PAHs-contaminated field. The results showed that the PAHs removal rates were significantly higher in rhizosphere soils (55.2-82.3%) than the bare soils (20.5%). Of the four cover crops, the rhizosphere soils associated with the alfalfa and clover had higher removal rates for high molecular weight (HMW) PAHs (78.5-87.1%) than the grasses (39.0-46.2%). High-throughput sequencing analysis showed that bacterial community structure between the planted and bare soils, and among four cover crops rhizosphere soils were significantly different. The rhizosphere soils associated with the alfalfa and clover had more abundant degradation-related taxa. Correlation network analysis showed that bacterial communities with high removal rates have stronger interactions. Metagenome analysis indicated that the relative abundance of the key functional genes involved in PAHs degradation and nutrient metabolisms were significantly higher in rhizosphere soils, especially for alfalfa and clover. Overall, this study provides new insights for us to understand the mechanisms by different plants enhancing PAHs dissipation from the viewpoint of microbiology.
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Affiliation(s)
- Xia Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Wenjie Ren
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yujuan Han
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xiaomi Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xiufen Li
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA
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Cárdenas Espinosa MJ, Schmidgall T, Wagner G, Kappelmeyer U, Schreiber S, Heipieper HJ, Eberlein C. An optimized method for RNA extraction from the polyurethane oligomer degrading strain Pseudomonas capeferrum TDA1 growing on aromatic substrates such as phenol and 2,4-diaminotoluene. PLoS One 2021; 16:e0260002. [PMID: 34780548 PMCID: PMC8592408 DOI: 10.1371/journal.pone.0260002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/30/2021] [Indexed: 11/18/2022] Open
Abstract
Bacterial degradation of xenobiotic compounds is an intense field of research already for decades. Lately, this research is complemented by downstream applications including Next Generation Sequencing (NGS), RT-PCR, qPCR, and RNA-seq. For most of these molecular applications, high-quality RNA is a fundamental necessity. However, during the degradation of aromatic substrates, phenolic or polyphenolic compounds such as polycatechols are formed and interact irreversibly with nucleic acids, making RNA extraction from these sources a major challenge. Therefore, we established a method for total RNA extraction from the aromatic degrading Pseudomonas capeferrum TDA1 based on RNAzol® RT, glycogen and a final cleaning step. It yields a high-quality RNA from cells grown on TDA1 and on phenol compared to standard assays conducted in the study. To our knowledge, this is the first report tackling the problem of polyphenolic compound interference with total RNA isolation in bacteria. It might be considered as a guideline to improve total RNA extraction from other bacterial species.
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Affiliation(s)
| | - Tabea Schmidgall
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Georg Wagner
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Uwe Kappelmeyer
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Stephan Schreiber
- Department Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Hermann J. Heipieper
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Christian Eberlein
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
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21
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Latorre-Padilla N, Meynard A, Rivas J, Contreras-Porcia L. Transfer of Pollutants from Macrocystis pyrifera to Tetrapygus niger in a Highly Impacted Coastal Zone of Chile. TOXICS 2021; 9:244. [PMID: 34678940 PMCID: PMC8539136 DOI: 10.3390/toxics9100244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 11/29/2022]
Abstract
PAHs and heavy metals are characteristic pollutants in urbanized coastal areas, especially those with industrial activity. Given this context and the ability of Macrocystis pyrifera to drift when detached and provide trophic subsidy in coastal systems, we analyzed the potential transfer of pollutants to the herbivore Tetrapygus niger, through diet, in an industrialized coastal zone in Central Chile (Caleta Horcón) and characterized the impacted zone using diverse polluted ecotoxicological indices. For this purpose, a culture experiment was conducted where M. pyrifera individuals from Algarrobo (control site) were cultivated in Caleta Horcón and then used as food for T. niger. The contents of both PAHs and heavy metal contents were subsequently determined in algal tissue and sea urchin gonads as well as in the seawater. The results show that algae cultivated in Caleta Horcón had higher concentrations of naphthalene (NAF) compared to those from a low industrial impact zone (Algarrobo) (2.5 and 1.8 mg kg-1, respectively). The concentrations of Cu, As, and Cd were higher in Caleta Horcón than in Algarrobo in both M. pyrifera and T. niger. For all metals, including Pb, higher concentrations were present in T. niger than in M. pyrifera (between 5 and 798 times higher). Additionally, as indicated by the toxicological indices MPI (0.00804) and PLI (10.89), Caleta Horcón is highly contaminated with metals compared to Algarrobo (0.0006 and 0.015, respectively). Finally, the bioconcentration factor (BCF) and trophic transfer factor (TTF) values were greater than one in most cases, with values in Caleta Horcón exceeding those in Algarrobo by one or two orders of magnitude. This study provides evidence that Caleta Horcón is a highly impacted zone (HIZ) compared to Algarrobo, in addition to evidence that the biomagnification of certain pollutants, including the possible responses to contaminants, are apparently not exclusively transferred to T. niger through diet.
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Affiliation(s)
- Nicolás Latorre-Padilla
- Departamento de Ecología y Biodiversidad, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370251, Chile; (N.L.-P.); (A.M.); (J.R.)
- Centro de Investigación Marina Quintay (CIMARQ), Facultad de Ciencias de la Vida, Universidad Andres Bello, Valparaíso, Quintay 2531015, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago 8331150, Chile
- Instituto Milenio en Socio-Ecología Costera (SECOS), Santiago 8370251, Chile
- Programa de Doctorado en Medicina de la Conservación, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370251, Chile
| | - Andrés Meynard
- Departamento de Ecología y Biodiversidad, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370251, Chile; (N.L.-P.); (A.M.); (J.R.)
- Centro de Investigación Marina Quintay (CIMARQ), Facultad de Ciencias de la Vida, Universidad Andres Bello, Valparaíso, Quintay 2531015, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago 8331150, Chile
- Instituto Milenio en Socio-Ecología Costera (SECOS), Santiago 8370251, Chile
| | - Jorge Rivas
- Departamento de Ecología y Biodiversidad, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370251, Chile; (N.L.-P.); (A.M.); (J.R.)
- Centro de Investigación Marina Quintay (CIMARQ), Facultad de Ciencias de la Vida, Universidad Andres Bello, Valparaíso, Quintay 2531015, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago 8331150, Chile
- Instituto Milenio en Socio-Ecología Costera (SECOS), Santiago 8370251, Chile
| | - Loretto Contreras-Porcia
- Departamento de Ecología y Biodiversidad, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370251, Chile; (N.L.-P.); (A.M.); (J.R.)
- Centro de Investigación Marina Quintay (CIMARQ), Facultad de Ciencias de la Vida, Universidad Andres Bello, Valparaíso, Quintay 2531015, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago 8331150, Chile
- Instituto Milenio en Socio-Ecología Costera (SECOS), Santiago 8370251, Chile
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22
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Potential of Variovorax paradoxus isolate BFB1_13 for bioremediation of BTEX contaminated sites. AMB Express 2021; 11:126. [PMID: 34487274 PMCID: PMC8421498 DOI: 10.1186/s13568-021-01289-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 08/29/2021] [Indexed: 12/07/2022] Open
Abstract
Here, we report and discuss the applicability of Variovorax paradoxus strain BFB1_13 in the bioremediation of BTEX contaminated sites. Strain BFB1_13 was capable of degrading all the six BTEX-compounds under both aerobic (O2 conc. 8 mg l−1) and micro-aerobic/oxygen-limited (O2 conc. 0.5 mg l−1) conditions using either individual (8 mg‧l−1) or a mixture of compounds (~ 1.3 mg‧l−1 of each BTEX compound). The BTEX biodegradation capability of SBP-encapsulated cultures (SBP—Small Bioreactor Platform) was also assessed. The fastest degradation rate was observed in the case of aerobic benzene biodegradation (8 mg l−1 per 90 h). Complete biodegradation of other BTEX occurred after at least 168 h of incubation, irrespective of the oxygenation and encapsulation. No statistically significant difference was observed between aerobic and microaerobic BTEX biodegradation. Genes involved in BTEX biodegradation were annotated and degradation pathways were predicted based on whole-genome shotgun sequencing and metabolic analysis. We conclude that V. paradoxus strain BFB1_13 could be used for the development of reactive biobarriers for the containment and in situ decontamination of BTEX contaminated groundwater plumes. Our results suggest that V. paradoxus strain BFB1_13—alone or in co-culture with other BTEX degrading bacterial isolates—can be a new and efficient commercial bioremediation agent for BTEX contaminated sites.
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23
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Remediation of Petroleum-Contaminated Soils with Microbial and Microbial Combined Methods: Advances, Mechanisms, and Challenges. SUSTAINABILITY 2021. [DOI: 10.3390/su13169267] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The petroleum industry’s development has been supported by the demand for petroleum and its by-products. During extraction and transportation, however, oil will leak into the soil, destroying the structure and quality of the soil and even harming the health of plants and humans. Scientists are researching and developing remediation techniques to repair and re-control the afflicted environment due to the health risks and social implications of petroleum hydrocarbon contamination. Remediation of soil contamination produced by petroleum hydrocarbons, on the other hand, is a difficult and time-consuming job. Microbial remediation is a focus for soil remediation because of its convenience of use, lack of secondary contamination, and low cost. This review lists the types and capacities of microorganisms that have been investigated to degrade petroleum hydrocarbons. However, investigations have revealed that a single microbial remediation faces difficulties, such as inconsistent remediation effects and substantial environmental consequences. It is necessary to understand the composition and source of pollutants, the metabolic genes and pathways of microbial degradation of petroleum pollutants, and the internal and external aspects that influence remediation in order to select the optimal remediation treatment strategy. This review compares the degradation abilities of microbial–physical, chemical, and other combination remediation methods, and highlights the degradation capabilities and processes of the greatest microbe-biochar, microbe–nutrition, and microbe–plant technologies. This helps in evaluating and forecasting the chemical behavior of contaminants with both short- and long-term consequences. Although there are integrated remediation strategies for the removal of petroleum hydrocarbons, practical remediation remains difficult. The sources and quantities of petroleum pollutants, as well as their impacts on soil, plants, and humans, are discussed in this article. Following that, the focus shifted to the microbiological technique of degrading petroleum pollutants and the mechanism of the combined microbial method. Finally, the limitations of existing integrated microbiological techniques are highlighted.
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Zan S, Lv J, Li Z, Cai Y, Wang Z, Wang J. Genomic insights into Pseudoalteromonas sp. JSTW coping with petroleum-heavy metals combined pollution. J Basic Microbiol 2021; 61:947-957. [PMID: 34387369 DOI: 10.1002/jobm.202100156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/02/2021] [Accepted: 08/08/2021] [Indexed: 11/05/2022]
Abstract
Worldwide marine compound contamination by petroleum products and heavy metals is a burgeoning environmental concern. Pseudoalteromonas, prevalently distributed in marine environment, has been proven to degrade petroleum and plays an essential role in the fate of oil pollution under the combined pollution. Nevertheless, the research on the reference genes is still incomplete. Therefore, this study aims to thoroughly investigate the reference genes represented by Pseudoalteromonas sp. JSTW via whole-genome sequencing. Next-generation sequencing technology unfolded a genome of 4,026,258 bp, database including Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were utilized to annotate the genes and metabolic pathways conferring to petroleum hydrocarbon degradation. The results show that common alkane and aromatic hydrocarbon degradation genes (alkB, ligB, yqhD, and ladA), chemotaxis gene (MCP, cheA, cheB, pcaY, and pcaR), heavy-metal resistance, and biofilm genes (σ54, merC, pcoA, copB, etc.) were observed in whole-genome sequence (WGS) of JSTW, which indicated that strain JSTW could potentially cope with combined pollution. The degradation efficiency of naphthalene in 60 h by JSTW was 99% without Cu2+ and 67% with 400 mg L-1 Cu2+ . Comparative genome analysis revealed that genomes of Pseudoalteromonas lipolytica strain LEMB 39 and Pseudoalteromonas donghaensis strain HJ51 shared similarity with strain JSTW, suggesting they are also the potential degradater of petroleum hydrocarbons under combined pollution. Therefore, this study provides a WGS annotation and reveals the mechanism of response to combined pollution of Pseudoalteromonas sp. JSTW.
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Affiliation(s)
- Shuaijun Zan
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Jingping Lv
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Zelong Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Yingxue Cai
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Zongcheng Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Jing Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
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25
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Rosas-Díaz J, Escobar-Zepeda A, Adaya L, Rojas-Vargas J, Cuervo-Amaya DH, Sánchez-Reyes A, Pardo-López L. Paenarthrobacter sp. GOM3 Is a Novel Marine Species With Monoaromatic Degradation Relevance. Front Microbiol 2021; 12:713702. [PMID: 34413843 PMCID: PMC8369764 DOI: 10.3389/fmicb.2021.713702] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Paenarthrobacter sp. GOM3, which is a strain that represents a new species-specific context within the genus Paenarthrobacter, is clearly a branched member independent of any group described thus far. This strain was recovered from marine sediments in the Gulf of Mexico, and despite being isolated from a consortium capable of growing with phenanthrene as a sole carbon source, this strain could not grow successfully in the presence of this substrate alone. We hypothesized that the GOM3 strain could participate in the assimilation of intermediate metabolites for the degradation of aromatic compounds. To date, there are no experimental reports of Paenarthrobacter species that degrade polycyclic aromatic hydrocarbons (PAHs) or their intermediate metabolites. In this work, we report genomic and experimental evidence of metabolic benzoate, gentisate, and protocatechuate degradation by Paenarthrobacter sp. GOM3. Gentisate was the preferred substrate with the highest volumetric consumption rate, and genomic analysis revealed that this strain possesses multiple gene copies for the specific transport of gentisate. Furthermore, upon analyzing the GOM3 genome, we found five different dioxygenases involved in the activation of aromatic compounds, suggesting its potential for complete remediation of PAH-contaminated sites in combination with strains capable of assimilating the upper PAH degradation pathway. Additionally, this strain was characterized experimentally for its pathogenic potential and in silico for its antimicrobial resistance. An overview of the potential ecological role of this strain in the context of other members of this taxonomic clade is also reported.
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Affiliation(s)
- Jaime Rosas-Díaz
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autoónoma de México, Cuernavaca, Mexico
| | - Alejandra Escobar-Zepeda
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Libertad Adaya
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autoónoma de México, Cuernavaca, Mexico
| | - Jorge Rojas-Vargas
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autoónoma de México, Cuernavaca, Mexico
| | - Diego Humberto Cuervo-Amaya
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autoónoma de México, Cuernavaca, Mexico
| | - Ayixon Sánchez-Reyes
- Cátedras Conacyt – Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Liliana Pardo-López
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autoónoma de México, Cuernavaca, Mexico
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26
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Liang Y, Ji M, Zhai H, Zhao J. Organic matter composition, BaP biodegradation and microbial communities at sites near and far from the bioanode in a soil microbial fuel cell. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 772:144919. [PMID: 33578157 DOI: 10.1016/j.scitotenv.2020.144919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/28/2020] [Accepted: 12/28/2020] [Indexed: 06/12/2023]
Abstract
Bioanodes in a soil microbial fuel cell (SMFC) can serve as sustainable electron acceptors in microbial metabolism processes; thus, SMFCs are considered a promising in situ bioremediation technology. Most related studies have focused on the removal efficiency of contaminants. Relatively few efforts have been made to comprehensively investigate the organic matter composition and biodegradation metabolites of organic contaminants and microbial communities at various distances from the bioanode. In this study, the level and composition of dissolved organic matter (DOM), biodegradation metabolites of benzo[a]pyrene (BaP), and microbial communities at two sites with different distances (S1cm and S11cm) to the bioanode were investigated in an SMFC. The consumption efficiency of dissolved organic carbon (RDOC) and removal efficiency of BaP (RBaP) at S1cm were slightly higher than those at S11cm after 100 days (RDOC 47.82 ± 5.77% at S1cm and 44.98 ± 10.76% at S11cm; RBaP 72.52 ± 1.88% at S1cm and 68.50 ± 4.34% at S11cm). More fulvic acid-like components and more low-molecular-weight metabolites (indicating a higher biodegradation degree) of BaP were generated at S1cm than at S11cm. The microbial community structures were similar at the two sites. Electroactive bacteria (EAB) and some polycyclic aromatic hydrocarbon degraders were both enriched at the bioanode. Energy metabolism at the bioanode could be upregulated to generate more adenosine triphosphate (ATP). In conclusion, the bioanode could modulate the metabolic pathways in the adjacent soil by strengthening the contact between the EAB and BaP degraders, and providing more ATP to the BaP degraders.
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Affiliation(s)
- Yinxiu Liang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Min Ji
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Hongyan Zhai
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China.
| | - Jun Zhao
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
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Suneel V, Sathish Kumar S, Balaji R, Vethamony P. Formation and weathering assessment of oil-suspended sediment aggregates through a laboratory investigation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:17181-17199. [PMID: 33398743 DOI: 10.1007/s11356-020-11813-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
Formation of oil-suspended sediment aggregates (OSAs) is believed to be one of the natural cleaning processes in the marine environment. In this study, we have investigated the formation processes of OSAs under different mixing periods (continuous mixing and with the addition of sediments in between), oil-sediment ratios (1:1, 1:2 and 2:1) and crude oils (Arabian Light (AL), Kuwait (KW) and Murban (MB)). The results revealed that size of OSAs significantly increased (up to ≈ 1.41 mm) with the addition of sediments. Aggregates (total 36) were extracted for n-alkanes and polycyclic aromatic hydrocarbons to quantify and assess their weathering and toxic levels. The maximum n-alkane depletion was 84% (111-02), 94% (212-02) and 84% (321-02) and PAH depletion was ≈ 72% (111-02), 79% (212-02) and 81% (311-03) for the OSAs of AL, KW and MB crude oils, respectively, for the different samples considered, indicating that n-alkanes were depleted relatively higher than the PAHs. The highest depletion of both n-alkane and PAHs has occurred in OSAs of 10-h continuous mixing. The depletion of both n-alkane and PAHs reduced after the addition of sediments, however, escalated the growth of OSAs, resulting in bigger size OSAs. The concentration of PAHs of all 36 OSAs is greater than 5000 ng/g, indicating very high PAH pollution. Though the formation of OSAs helps in cleaning the spill sites, the carcinogenic threat to the marine ecosystem caused by these OSAs cannot be ignored.
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Affiliation(s)
- V Suneel
- CSIR - National Institute of Oceanography, Dona Paula, Goa, 403 004, India.
| | - S Sathish Kumar
- Indian Institute of Technology Bombay, Powai, Mumbai, 400 076, India
| | - R Balaji
- Indian Institute of Technology Bombay, Powai, Mumbai, 400 076, India
| | - P Vethamony
- Environmental Science Center, Qatar University, P.O Box: 2713, Doha, Qatar
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28
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Filatov DA, Kopytov MA, Ovsyannikova VS, Elchaninova EA. Oxidation of a Mixture of Polyaromatic Hydrocarbons by a Mixed Culture of Hydrocarbon-Oxidizing Microorganisms. EURASIAN CHEMICO-TECHNOLOGICAL JOURNAL 2021. [DOI: 10.18321/ectj1034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The possibility of biochemical oxidation of polyaromatic hydrocarbon mixtures (PAHs) by the mixed culture of hydrocarbon-oxidizing microorganisms (HOM) in a liquid medium and soil was investigated. The mixed HOM culture was represented by Pseudomonas stutzeri, Pseudomonas putida, Bacillus cereus, and Arthrobacter globiformis genera. It was shown that during HOM cultivation of the microorganisms under study in the liquid medium their number increases from 0.25·104 to 11·108 CFU/ml, which is accompanied by an increase in their oxygenase activity. All PAHs identified were subjected to oxidation from 11.3 to 100%. The results of experiments on biodegradation of PAHs under natural conditions have shown that for 60 days the total utilization of oil products in soils was on the average 65% of the initial contamination. This suggests the prospects for the use of the mixed HOM culture under study for effective biodegradation of PAHs polluting soil and waste waters.
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Zakaria NN, Convey P, Gomez-Fuentes C, Zulkharnain A, Sabri S, Shaharuddin NA, Ahmad SA. Oil Bioremediation in the Marine Environment of Antarctica: A Review and Bibliometric Keyword Cluster Analysis. Microorganisms 2021; 9:microorganisms9020419. [PMID: 33671443 PMCID: PMC7922015 DOI: 10.3390/microorganisms9020419] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 02/07/2023] Open
Abstract
Bioremediation of hydrocarbons has received much attention in recent decades, particularly relating to fuel and other oils. While of great relevance globally, there has recently been increasing interest in hydrocarbon bioremediation in the marine environments of Antarctica. To provide an objective assessment of the research interest in this field we used VOSviewer software to analyze publication data obtained from the ScienceDirect database covering the period 1970 to the present, but with a primary focus on the years 2000–2020. A bibliometric analysis of the database allowed identification of the co-occurrence of keywords. There was an increasing trend over time for publications relating to oil bioremediation in maritime Antarctica, including both studies on marine bioremediation and of the metabolic pathways of hydrocarbon degradation. Studies of marine anaerobic degradation remain under-represented compared to those of aerobic degradation. Emerging keywords in recent years included bioprospecting, metagenomic, bioindicator, and giving insight into changing research foci, such as increasing attention to microbial diversity. The study of microbial genomes using metagenomic approaches or whole genome studies is increasing rapidly and is likely to drive emerging fields in future, including rapid expansion of bioprospecting in diverse fields of biotechnology.
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Affiliation(s)
- Nur Nadhirah Zakaria
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (N.N.Z.); (N.A.S.)
| | - Peter Convey
- British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge CB3 0ET, UK;
| | - Claudio Gomez-Fuentes
- Department of Chemical Engineering, Universidad de Magallanes, Avda, Bulnes 01855, Chile;
- Center for Research and Antarctic Environmental Monitoring (CIMAA), Universidad de Magallanes, Avda, Bulnes 01855, Chile
| | - Azham Zulkharnain
- Department of Bioscience and Engineering, College of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan;
| | - Suriana Sabri
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia;
| | - Noor Azmi Shaharuddin
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (N.N.Z.); (N.A.S.)
| | - Siti Aqlima Ahmad
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (N.N.Z.); (N.A.S.)
- Center for Research and Antarctic Environmental Monitoring (CIMAA), Universidad de Magallanes, Avda, Bulnes 01855, Chile
- National Antarctic Research Centre, B303 Level 3, Block B, IPS Building, Universiti Malaya, Kuala Lumpur 50603, Malaysia
- Correspondence:
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30
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Verasoundarapandian G, Wong CY, Shaharuddin NA, Gomez-Fuentes C, Zulkharnain A, Ahmad SA. A Review and Bibliometric Analysis on Applications of Microbial Degradation of Hydrocarbon Contaminants in Arctic Marine Environment at Metagenomic and Enzymatic Levels. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18041671. [PMID: 33572432 PMCID: PMC7916232 DOI: 10.3390/ijerph18041671] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 12/20/2022]
Abstract
The globe is presently reliant on natural resources, fossil fuels, and crude oil to support the world’s energy requirements. Human exploration for oil resources is always associated with irreversible effects. Primary sources of hydrocarbon pollution are instigated through oil exploration, extraction, and transportation in the Arctic region. To address the state of pollution, it is necessary to understand the mechanisms and processes of the bioremediation of hydrocarbons. The application of various microbial communities originated from the Arctic can provide a better interpretation on the mechanisms of specific microbes in the biodegradation process. The composition of oil and consequences of hydrocarbon pollutants to the various marine environments are also discussed in this paper. An overview of emerging trends on literature or research publications published in the last decade was compiled via bibliometric analysis in relation to the topic of interest, which is the microbial community present in the Arctic and Antarctic marine environments. This review also presents the hydrocarbon-degrading microbial community present in the Arctic, biodegradation metabolic pathways (enzymatic level), and capacity of microbial degradation from the perspective of metagenomics. The limitations are stated and recommendations are proposed for future research prospects on biodegradation of oil contaminants by microbial community at the low temperature regions of the Arctic.
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Affiliation(s)
| | - Chiew-Yen Wong
- School of Health Sciences, International Medical University, Kuala Lumpur 57000, Malaysia;
- National Antarctic Research Center, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Noor Azmi Shaharuddin
- Department of Biochemistry, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (G.V.); (N.A.S.)
| | - Claudio Gomez-Fuentes
- Department of Chemical Engineering, Universidad de Magallanes, Avda. Bulnes 01855, Punta Arenas, Chile;
- Center for Research and Antarctic Environmental Monitoring (CIMAA), Universidad de Magallanes, Avda. Bulnes 01855, Punta Arenas, Chile
| | - Azham Zulkharnain
- Department of Bioscience and Engineering, Shibaura Institute of Technology, Saitama-shi 337-8570, Saitama, Japan;
| | - Siti Aqlima Ahmad
- Department of Biochemistry, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (G.V.); (N.A.S.)
- National Antarctic Research Center, Universiti Malaya, Kuala Lumpur 50603, Malaysia
- Center for Research and Antarctic Environmental Monitoring (CIMAA), Universidad de Magallanes, Avda. Bulnes 01855, Punta Arenas, Chile
- Correspondence:
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Assessing the bioremediation potential of indigenously isolated Klebsiella sp. WAH1 for diclofenac sodium: optimization, toxicity and metabolic pathway studies. World J Microbiol Biotechnol 2021; 37:33. [PMID: 33469843 DOI: 10.1007/s11274-021-02998-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 01/08/2021] [Indexed: 10/22/2022]
Abstract
Among the various pharmaceutical pollutants, diclofenac sodium (DFS), a widely prescribed non-steroid anti-inflammatory drug is detected in the aquatic environment at concentrations which can be harmful to living organisms. Present study illustrates the isolation and characterization of strain Klebsiella pneumoniae WAH1 from activated sludge and its ability to degrade DFS as sole source of carbon and energy. The growth and degradation capacity of K. pneumoniae WAH1 under different conditions of pH, temperature, rotation speed, and inoculum age were evaluated using optical density and liquid chromatography-mass spectroscopy (LCMS). The results show that K. pneumoniae WAH1 can grow well with DFS as its sole source of carbon and degrade 79.14% of DFS (10 mg L-1) within 72 h. Based on chemical structure of intermediates detected through LCMS, it is inferred that degradation pathway advanced by hydroxylation, decarboxylation, and dechlorination reactions. Toxicity studies revealed the non-toxic nature of the end-products of DFS degradation after 72 h. The findings suggest that K. pneumoniae WAH1 has an excellent potential for bioremediation of DFS in industrial wastewaters.
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32
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Metagenome Analysis of a Hydrocarbon-Degrading Bacterial Consortium Reveals the Specific Roles of BTEX Biodegraders. Genes (Basel) 2021; 12:genes12010098. [PMID: 33466668 PMCID: PMC7828808 DOI: 10.3390/genes12010098] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 11/17/2022] Open
Abstract
Environmental contamination by petroleum hydrocarbons is of concern due to the carcinogenicity and neurotoxicity of these compounds. Successful bioremediation of organic contaminants requires bacterial populations with degradative capacity for these contaminants. Through successive enrichment of microorganisms from a petroleum-contaminated soil using diesel fuel as the sole carbon and energy source, we successfully isolated a bacterial consortium that can degrade diesel fuel hydrocarbons. Metagenome analysis revealed the specific roles of different microbial populations involved in the degradation of benzene, toluene, ethylbenzene and xylene (BTEX), and the metabolic pathways involved in these reactions. One hundred and five putative coding DNA sequences were identified as responsible for both the activation of BTEX and central metabolism (ring-cleavage) of catechol and alkylcatechols during BTEX degradation. The majority of the Coding DNA sequences (CDSs) were affiliated to Acidocella, which was also the dominant bacterial genus in the consortium. The inoculation of diesel fuel contaminated soils with the consortium resulted in approximately 70% hydrocarbon biodegradation, indicating the potential of the consortium for environmental remediation of petroleum hydrocarbons.
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Wang B, Gao F, Xu J, Gao J, Li Z, Wang L, Zhang F, Wang Y, Tian Y, Peng R, Yao Q. Optimization, reconstruction and heterologous expression of the gene cluster encoding toluene/ o-xylene monooxygenase from Pseudomonas stutzeri in Escherichia coli and its successive hydroxylation of toluene and benzene. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1996267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Bo Wang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, PR China
| | - Feng Gao
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Jing Xu
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Jianjie Gao
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Zhenjun Li
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Lijuan Wang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Fujian Zhang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Yu Wang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Yongsheng Tian
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Rihe Peng
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Quanhong Yao
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
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Praveen P, Vaidya A, Tutt K, Andrews J. Assessing the potential of purple phototrophic microbial community for nitrogen recycling from ammonia-rich medium and anaerobic digestate. BIORESOURCE TECHNOLOGY 2021; 320:124436. [PMID: 33248813 DOI: 10.1016/j.biortech.2020.124436] [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: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 06/12/2023]
Abstract
Purple phototrophic bacteria (PPB) community, enriched from municipal wastewater, was characterized to assess their growth, tolerance, composition and potential for resource recovery from NH4+-rich medium. Batch experiments were conducted in tissue culture flasks and glass bottles under anaerobic conditions with infra-red lights. PPBs showed remarkable tolerance to high concentrations of NH4+-N and acetate. Below 1.5 g/L, growth was unaffected by NH4+-N with optical density at 590 nm (OD590) reaching 2.6-2.9, while they could tolerate 4.5 g/L NH4+-N. Similarly, PPB growth was unaffected at acetate concentrations below 4 g/L and they could tolerate >20 g/L acetate. Taxonomic characterization showed that the community comprised of 37-52% PPBs (with 15-20% proteins) under different conditions, with Rhodobacter sp. over Rhodopseudomonas sp. dominating at higher NH4+-N concentrations. PPBs showed growth and removal rates in anaerobic digestate and accumulated 26% proteins. These results indicated the potential of PPBs in resource recovery from NH4+-rich wastewater.
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Affiliation(s)
| | - Alankar Vaidya
- Scion, Te Papa Tipu Innovation Park, 49 Sala Street, Rotorua, New Zealand
| | - Keryn Tutt
- Scion, Te Papa Tipu Innovation Park, 49 Sala Street, Rotorua, New Zealand
| | - John Andrews
- Scion, Te Papa Tipu Innovation Park, 49 Sala Street, Rotorua, New Zealand
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35
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Kazemzadeh S, Naghavi NS, Emami-Karvani Z, Emtiazi G, Fouladgar M. Production of glycolipid biosurfactant during crude oil degradation by the novel indigenous isolated Achromobacter kerstersii LMG3441. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2020; 82:2134-2147. [PMID: 33263590 DOI: 10.2166/wst.2020.474] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
This study aimed to find biosurfactant producing and crude oil-degrading bacteria able to decontaminate crude oil from wastewater. The bacteria that were isolated from contaminated sites in an oil refinery plant in Isfahan, Iran, were identified by 16S rDNA sequencing as Achromobacter kerstersii strain LMG3441, Klebsiella pneumonia strain SKBA6, and Klebsiella variicola strain SKV2. According to the results obtained from different tests for the production of biosurfactant among three strains, only Achromobacter kerstersii strain LMG3441 was selected for further study. The pattern of residual hydrocarbons was analyzed by high-resolution gas chromatography-mass spectrometry (GC-MS). This novel and indigenous strain was capable of producing the highest amount of a glycolipid biosurfactant (7.81 g/L) in MSM (mineral salt medium) with 1% (v/v) crude oil as the only source of carbon and energy. The compound showed high surface activation capacity with reduction of surface tension from 40 mN m-1 in the control to 23.3 mN m-1 by the bacterium. The results of GC-MS for assessment of residual hydrocarbons in the MSM and comparison with crude oil as a control showed that 53% of the hydrocarbons in the crude oil were consumed by this novel strain.
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Affiliation(s)
- Somayeh Kazemzadeh
- Department of Microbiology, Falavarjan Branch, Islamic Azad University, Isfahan, Iran E-mail:
| | - Nafiseh Sadat Naghavi
- Department of Microbiology, Falavarjan Branch, Islamic Azad University, Isfahan, Iran E-mail:
| | | | - Giti Emtiazi
- Department of Biotechnology, Faculty of Biological Science and Technology, Shahid Ashrafi Esfahani University, Isfahan, Iran
| | - Masoud Fouladgar
- Department of Basic Sciences, Falavarjan Branch, Islamic Azad University, Isfahan, Iran
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36
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Keshavarzifard M, Vazirzadeh A, Sharifinia M. Implications of anthropogenic effects on the coastal environment of Northern Persian Gulf, using jinga shrimp (Metapenaeus affinis) as indicator. MARINE POLLUTION BULLETIN 2020; 159:111463. [PMID: 32892912 DOI: 10.1016/j.marpolbul.2020.111463] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/07/2020] [Accepted: 07/08/2020] [Indexed: 06/11/2023]
Abstract
The distribution and sources of PAHs in jinga shrimp (Metapenaeus affinis), and human health risks due to consumption was evaluated in collected samples from the Musa Bay, Persian Gulf. The total concentration of PAHs (∑16PAHs) ranged from 10 to 144 μg kg-1 dry weight, indicating low to moderate level of pollution. The PAHs were dominated by three- (41%) and two-ring (38%) compounds. Source identification analyses indicated the PAH pollution mostly originated from petroleum inputs. A preliminary evaluation of human health risk using chronic daily intake, hazard index, benzo[a]pyrene-equivalent (BaPeq) concentration (PEC) as well as the incremental life cancer risk and non-cancer risk assessment suggest low potential health risk for consumers of the Metapenaeus affinis. However, the results indicate minimal risks associated with the intake of PAHs via shrimp consumption, but long-term monitoring is required to evaluate the changes in ecological and human health impacts of contaminants in the region. MAIN FINDING: PAHs in Metapenaeus affinis from Musa bay, which influenced by anthropogenic activities were low to moderate level of pollution. Human health risk indicates low potential health risk for consumers.
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Affiliation(s)
- Mehrzad Keshavarzifard
- Shrimp Research Center, Iranian Fisheries Science Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Bushehr, Iran; Department of Natural Resources and Environmental Engineering, School of Agriculture, Shiraz University, Shiraz, Iran.
| | - Arya Vazirzadeh
- Department of Natural Resources and Environmental Engineering, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Moslem Sharifinia
- Shrimp Research Center, Iranian Fisheries Science Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Bushehr, Iran.
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37
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Puyol D, Hülsen T, Padrino B, Batstone DJ, Martinez F, Melero JA. Exploring the inhibition boundaries of mixed cultures of purple phototrophic bacteria for wastewater treatment in anaerobic conditions. WATER RESEARCH 2020; 183:116057. [PMID: 32623241 DOI: 10.1016/j.watres.2020.116057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 04/26/2020] [Accepted: 06/13/2020] [Indexed: 06/11/2023]
Abstract
The development of novel wastewater platforms should include the analysis of the most critical functional factors including the effects of toxic or inhibitory substances. Due to the novelty of purple phototrophic bacteria (PPB)-based wastewater treatment systems, this analysis has not been done yet in mixed cultures. In this work, various relevant chemical compounds, including aromatic (phenol, 2,4,6-trichlorophenol or 246TCP, 4-nitrophenol or 4CP, sulfathiazole) and aliphatic organics (methanol, trichlorethylene or TCE, oleic acid, ethanol, propionic acid), inorganic salts (ammonium, ClO3-, Na+), and metals (Fe3+, Fe2+, Cu2+, Zn2+, Ni2+, Al3+), as well as pH, are analyzed for their effect on mixed PPB cultures in anaerobic photoheterotrophic conditions using acetate as the model organic substrate. The most toxic substances detected were 246TCP, 4NP, Cu2+, Fe2+ and Ni2+, (Ki for activity: 23 ± 2, 97 ± 12, 3.1 ± 0.4, 13 ± 3, 13 ± 1 mg/L, and Ki (or toxicity threshold) for growth: 17 ± 2, (119), 3.5 ± 0.4, (4.8), (22.9) mg/L, respectively). Some substances inhibited the activity more than the growth (sulfathiazole, Ni2+ and Fe3+), or the growth more than the activity (TCE, 4NP and Fe2+). In addition, some organic substrates, such as phenol, ethanol and propionate, specifically inhibited the acetate uptake, being noncompetitive in the case of phenol and ethanol, and most likely competitive in the case of propionate. These findings are relevant for the wastewater treatment and resource recovery applications of the PPB technology, as well as for the upgrading of current models (Photo-Anaerobic Model). In addition, the data will open possibilities to promote the production of specific compounds (as PHA or single-cell proteins) by selectively inhibiting some parts of the PPB metabolism.
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Affiliation(s)
- D Puyol
- Department of Chemical and Environmental Engineering, University Rey Juan Carlos, Móstoles, Madrid, Spain.
| | - T Hülsen
- Advanced Water Management Centre, University of Queensland, Brisbane, QLD, Australia
| | - B Padrino
- Department of Chemical and Environmental Engineering, University Rey Juan Carlos, Móstoles, Madrid, Spain
| | - D J Batstone
- Advanced Water Management Centre, University of Queensland, Brisbane, QLD, Australia
| | - F Martinez
- Department of Chemical and Environmental Engineering, University Rey Juan Carlos, Móstoles, Madrid, Spain
| | - J A Melero
- Department of Chemical and Environmental Engineering, University Rey Juan Carlos, Móstoles, Madrid, Spain
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38
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Functional Gene Diversity of Selected Indigenous Hydrocarbon-Degrading Bacteria in Aged Crude Oil. Int J Microbiol 2020; 2020:2141209. [PMID: 32802067 PMCID: PMC7414327 DOI: 10.1155/2020/2141209] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 06/02/2020] [Indexed: 12/05/2022] Open
Abstract
Crude oil pollution has consistently deteriorated all environmental compartments through the cycle of activities of the oil and gas industries. However, there is a growing need to identify microbes with catabolic potentials to degrade these pollutants. This research was conducted to identify bacteria with functional degradative genes. A crude oil-polluted soil sample was obtained from an aged spill site at Imo River, Ebubu, Komkom community, Nigeria. Bacteria isolates were obtained and screened for hydrocarbon degradation potential by turbidometry assay. Plasmid and chromosomal DNA of the potential degraders were further screened for the presence of selected catabolic genes (C230, Alma, Alkb, nahAC, and PAHRHD(GP)) and identified by molecular typing. Sixteen (16) out of the fifty (50) isolates obtained showed biodegradation activity in a liquid broth medium at varying levels. Bacillus cereus showed highest potential for this assay with an optical density of 2.450 @ 600 nm wavelength. Diverse catabolic genes resident in plasmids and chromosomes of the isolates and, in some cases, both plasmid and chromosomes of the same organism were observed. The C230 gene was resident in >50% of the microbial population tested, while other genes occurred in lower proportions with the least observed in nahAC and PAHRHD. These organisms can serve as potential bioremediation agents.
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39
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Sakshi, Haritash AK. A comprehensive review of metabolic and genomic aspects of PAH-degradation. Arch Microbiol 2020; 202:2033-2058. [DOI: 10.1007/s00203-020-01929-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/14/2020] [Accepted: 05/26/2020] [Indexed: 01/01/2023]
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40
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Gafni A, Siebner H, Bernstein A. Potential for co-metabolic oxidation of TCE and evidence for its occurrence in a large-scale aquifer survey. WATER RESEARCH 2020; 171:115431. [PMID: 31893553 DOI: 10.1016/j.watres.2019.115431] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 11/30/2019] [Accepted: 12/20/2019] [Indexed: 06/10/2023]
Abstract
Trichloroethylene (TCE) is a groundwater pollutant that is prevalent worldwide. In contaminated groundwater, TCE can be biodegraded following either reductive dechlorination or aerobic co-metabolic oxidation. However, since the co-metabolic process is not accompanied by indicative and easily detectable transformation products, little is known about its prominence in the environment. To estimate the environmental importance of the oxidative process, a regional groundwater survey was conducted. In this survey, polluted water from 100 wells along the Israeli Coastal Aquifer was sampled. Geochemical data indicated oxic conditions prevailing in most sites. The sampled groundwater was used for microcosm experiments, functional gene analysis, and TCE compound-specific isotope analysis (δ13C and δ37Cl). Enrichments of methane and toluene oxidizers in microcosms indicated the high potential of the indigenous microbial community to co-metabolically oxidize TCE. This was further reinforced by the high abundance of mmoX and PHE functional genes quantified in some of the sites (yet lower abundance of TOD functional gene was found). Finally, compound-specific isotope analysis was used to assess the magnitude of TCE oxidation in practice. Applying the isotopic tool for scattered points on a regional scale demanded the consideration of a wide δ13C range of source TCE, hampering the ability to detect small shifts of a single permil. Thus, despite the high potential for the oxidation process, no evidence was attained for the natural occurrence of the process, and significant isotopic shifts were restricted to actively treated sites only. This limitation should be considered in future regional scale studies, in which no single source is defined.
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Affiliation(s)
- Almog Gafni
- Zuckerberg Institute for Water Research, Department of Environmental Hydrology and Microbiology, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Hagar Siebner
- Zuckerberg Institute for Water Research, Department of Environmental Hydrology and Microbiology, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Anat Bernstein
- Zuckerberg Institute for Water Research, Department of Environmental Hydrology and Microbiology, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel.
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41
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Bao H, Wang J, Zhang H, Li J, Li H, Wu F. Effects of biochar and organic substrates on biodegradation of polycyclic aromatic hydrocarbons and microbial community structure in PAHs-contaminated soils. JOURNAL OF HAZARDOUS MATERIALS 2020; 385:121595. [PMID: 31744730 DOI: 10.1016/j.jhazmat.2019.121595] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 10/19/2019] [Accepted: 11/01/2019] [Indexed: 06/10/2023]
Abstract
A incubation experiment was conducted to investigate whether combined amendment of biochar (B) and compost (CP), mushroom residue (M) and corn straw (Y) could enhance biodegradation of polycyclic aromatic hydrocarbons (PAHs) in contaminated soils. After 77 days of incubation, both B + M and B + Y significantly (p < 0.01) increased removal rate of PAHs compared with amendment of biochar alone. However, B+CP resulted in a significant (p < 0.01) decreasing of PAHs removal. Compared with no biochar and no organic substrates addition (CK) and B, both B+M and B+Y significantly (p < 0.01) enhanced concentrations of dissolved organic carbon (DOC) and were favorable for the microbial growth reflected by microbial biomass carbons (MBC) and emission of carbon dioxide. Redundancy analysis (RDA) indicated that B + CP, B + M and B + Y separated the bacterial community compared with CK and B. However, the community composition structure in B + CP was different from that of B + M and B + Y. Moreover, the abundance of some PAHs degraders and PAH degradation genes predicted by PICRUSt software was promoted by B + M or B + Y, whereas that was inhibited under B + CP. The present study suggested that both B + M and B + Y could accelerate biodegradation of PAHs mainly through increasing the concentration of DOC and the abundances of microbial PAH degraders in soils.
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Affiliation(s)
- Huanyu Bao
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agricultureand Rural Affairs, Yangling 712100, Shaanxi, PR China; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin 150090, PR China
| | - Jinfeng Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agricultureand Rural Affairs, Yangling 712100, Shaanxi, PR China
| | - He Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agricultureand Rural Affairs, Yangling 712100, Shaanxi, PR China
| | - Jiao Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agricultureand Rural Affairs, Yangling 712100, Shaanxi, PR China
| | - Hui Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, Department of Ecology, College of Life Science and Technology, Jinan University, Guangzhou 510632, PR China.
| | - Fuyong Wu
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agricultureand Rural Affairs, Yangling 712100, Shaanxi, PR China.
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42
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Gafni A, Gelman F, Ronen Z, Bernstein A. Variable carbon and chlorine isotope fractionation in TCE co-metabolic oxidation. CHEMOSPHERE 2020; 242:125130. [PMID: 31669996 DOI: 10.1016/j.chemosphere.2019.125130] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/12/2019] [Accepted: 10/14/2019] [Indexed: 06/10/2023]
Abstract
Identifying co-metabolic TCE oxidation in polluted groundwater is challenging due to lack of indicative by-products. This challenge may theoretically be resolved if the oxidation process can be characterized by a distinct dual isotope enrichment. In this work, we aimed to explore the carbon and chlorine isotope effects associated with TCE oxidation by a variety of oxygenases. These included pure strains and enrichment cultures of methane, toluene and ammonia oxidizers, as well as experiments with crude extracts. Isotope effects determined for TCE oxidation by toluene and ammonia oxidizers were mostly in line with expected values for epoxidation mechanism (ϵ13C -11.0 ± 0.7 to -24.8 ± 0.2‰ and ϵ37Cl +0.9 ± 0.5 to +1.0 ± 0.4‰), whereas, the methanotrophs resulted in distinctively different isotope effects (ϵ13C -2.4 ± 0.4 to -3.4 ± 0.8‰ and ϵ37Cl -1.8 ± 0.2 to -2.9 ± 0.9‰). It is suggested that in TCE oxidation by methanotrophs, substrate binding rather than bond cleavage is rate limiting, leading to this unexpected isotope effect. On the environmental level, our results imply that the oxidative process can be differentiated if catalyzed by toluene and ammonia oxidizers or by methanotrophs. Additionally, the oxidative process can be distinguished from the reductive one. However, using dual isotope analysis in the field may result in an under-estimation of the overall co-metabolic process if methanotrophs are to be excluded due to low isotope effects.
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Affiliation(s)
- Almog Gafni
- Zuckerberg Institute for Water Research, Department of Environmental Hydrology and Microbiology, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Faina Gelman
- Geological Survey of Israel, 32 Yesha'ayahu Leibowitz St, Jerusalem, 9692100, Israel
| | - Zeev Ronen
- Zuckerberg Institute for Water Research, Department of Environmental Hydrology and Microbiology, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Anat Bernstein
- Zuckerberg Institute for Water Research, Department of Environmental Hydrology and Microbiology, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel.
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43
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Esikova TZ, Gafarov AB, Anokhina TO. Genetic Control of Degradation of epsilon-Caprolactam, Toluene, and meta-Xylene in Pseudomonas putida Strain CT3. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720020046] [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] Open
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44
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Stiborova H, Strejcek M, Musilova L, Demnerova K, Uhlik O. Diversity and phylogenetic composition of bacterial communities and their association with anthropogenic pollutants in sewage sludge. CHEMOSPHERE 2020; 238:124629. [PMID: 31524607 DOI: 10.1016/j.chemosphere.2019.124629] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/31/2019] [Accepted: 08/19/2019] [Indexed: 05/23/2023]
Abstract
Despite wastewater treatment, sewage sludge is often contaminated with multiple pollutants. Their impact on the phylogenetic composition and diversity of prokaryotic communities in sludge samples remains largely unknown. In this study, we analyzed the phylogenetic structure of bacterial communities and diversity in sludge from six waste water treatment plants (WWTPs) and linked this information with the pollutants identified in these samples: eight potentially toxic metals (PTMs) and four groups of organic pollutants [polychlorinated biphenyls (PCBs), polyromantic hydrocarbons (PAHs), brominated flame retardants (BFRs) and organochlorine pesticides (OCPs)]. Alpha diversity measures and the distribution of dominant phyla varied among the samples, with the community from the thermophilic anaerobic digestion (TAD)-stabilized sample from Prague being the least rich and the least diverse and containing on average 36% of 16S rRNA gene sequence reads of the thermotolerant genus Coprothermobacter of the class Clostridia (phylum Firmicutes). Using weighted UniFrac distance-based redundancy analysis (dbRDA), we found that a collection of 5 PTMs: Cr, Cu, Ni, Pb, Zn, and a pair of BFRs: hexabromocyclododecane (HBCD) and tribromodiphenyl ethers (triBDEs) were significantly associated with the bacterial community structure in mesophilic anaerobic digestion (MAD)-stabilized samples, whereas PCBs were observed to be marginally significant. Altogether, 85% of the variance in bacterial community structure could be ascribed to these pollutants. The data presented here contribute to a greater understanding of the ecological effects of combined pollution on the composition and diversity of bacterial communities, hence have the potential to aid in predicting ecosystem functions and/or disruptions associated with pollution.
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Affiliation(s)
- Hana Stiborova
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic.
| | - Michal Strejcek
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Lucie Musilova
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Katerina Demnerova
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Ondrej Uhlik
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
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Hong H, Seo H, Park W, Kim KJ. Sequence, structure and function-based classification of the broadly conserved FAH superfamily reveals two distinct fumarylpyruvate hydrolase subfamilies. Environ Microbiol 2019; 22:270-285. [PMID: 31657110 DOI: 10.1111/1462-2920.14844] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/21/2019] [Accepted: 10/23/2019] [Indexed: 11/30/2022]
Abstract
Fumarylacetoacetate hydrolase (FAH) superfamily proteins are found ubiquitously in microbial pathways involved in the catabolism of aromatic substances. Although extensive bioinformatic data on these proteins have been acquired, confusion caused by problems with the annotation of these proteins hinders research into determining their physiological functions. Here we classify 606 FAH superfamily proteins using a maximum likelihood (ML) phylogenetic tree, comparative gene-neighbourhood patterns and in vitro enzyme assays. The FAH superfamily proteins used for the analyses are divided into five distinct subfamilies, and two of them, FPH-A and FPH-B, contain the majority of the proteins of undefined function. These subfamilies include clusters designated FPH-I and FPH-II, respectively, which include two distinct types of fumarylpyruvate hydrolase (FPH), an enzyme involved in the final step of the gentisate pathway. We determined the crystal structures of these FPH enzymes at 2.0 Å resolutions and investigate the substrate binding mode by which these types of enzymes can accommodate fumarylpyruvate as a substrate. Consequentially, we identify the molecular signatures of the two types of FPH enzymes among the broadly conserved FAH superfamily proteins. Our studies allowed us to predict the relationship of unknown FAH superfamily proteins using their sequence information.
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Affiliation(s)
- Hwaseok Hong
- Structural and Molecular Biology Laboratory, School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 702701, Republic of Korea.,KNU Institute for Microorganisms, Kyungpook National University, Daegu, 702701, Republic of Korea
| | - Hogyun Seo
- Structural and Molecular Biology Laboratory, School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 702701, Republic of Korea.,KNU Institute for Microorganisms, Kyungpook National University, Daegu, 702701, Republic of Korea
| | - Woojin Park
- Structural and Molecular Biology Laboratory, School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 702701, Republic of Korea.,KNU Institute for Microorganisms, Kyungpook National University, Daegu, 702701, Republic of Korea
| | - Kyung-Jin Kim
- Structural and Molecular Biology Laboratory, School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 702701, Republic of Korea.,KNU Institute for Microorganisms, Kyungpook National University, Daegu, 702701, Republic of Korea
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Truskewycz A, Gundry TD, Khudur LS, Kolobaric A, Taha M, Aburto-Medina A, Ball AS, Shahsavari E. Petroleum Hydrocarbon Contamination in Terrestrial Ecosystems-Fate and Microbial Responses. Molecules 2019; 24:molecules24183400. [PMID: 31546774 PMCID: PMC6767264 DOI: 10.3390/molecules24183400] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 09/06/2019] [Accepted: 09/11/2019] [Indexed: 11/18/2022] Open
Abstract
Petroleum hydrocarbons represent the most frequent environmental contaminant. The introduction of petroleum hydrocarbons into a pristine environment immediately changes the nature of that environment, resulting in reduced ecosystem functionality. Natural attenuation represents the single, most important biological process which removes petroleum hydrocarbons from the environment. It is a process where microorganisms present at the site degrade the organic contaminants without the input of external bioremediation enhancers (i.e., electron donors, electron acceptors, other microorganisms or nutrients). So successful is this natural attenuation process that in environmental biotechnology, bioremediation has developed steadily over the past 50 years based on this natural biodegradation process. Bioremediation is recognized as the most environmentally friendly remediation approach for the removal of petroleum hydrocarbons from an environment as it does not require intensive chemical, mechanical, and costly interventions. However, it is under-utilized as a commercial remediation strategy due to incomplete hydrocarbon catabolism and lengthy remediation times when compared with rival technologies. This review aims to describe the fate of petroleum hydrocarbons in the environment and discuss their interactions with abiotic and biotic components of the environment under both aerobic and anaerobic conditions. Furthermore, the mechanisms for dealing with petroleum hydrocarbon contamination in the environment will be examined. When petroleum hydrocarbons contaminate land, they start to interact with its surrounding, including physical (dispersion), physiochemical (evaporation, dissolution, sorption), chemical (photo-oxidation, auto-oxidation), and biological (plant and microbial catabolism of hydrocarbons) interactions. As microorganism (including bacteria and fungi) play an important role in the degradation of petroleum hydrocarbons, investigations into the microbial communities within contaminated soils is essential for any bioremediation project. This review highlights the fate of petroleum hydrocarbons in tertial environments, as well as the contributions of different microbial consortia for optimum petroleum hydrocarbon bioremediation potential. The impact of high-throughput metagenomic sequencing in determining the underlying degradation mechanisms is also discussed. This knowledge will aid the development of more efficient, cost-effective commercial bioremediation technologies.
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Affiliation(s)
- Adam Truskewycz
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC 3083, Australia.
| | - Taylor D Gundry
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC 3083, Australia.
| | - Leadin S Khudur
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC 3083, Australia.
| | - Adam Kolobaric
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC 3083, Australia.
| | - Mohamed Taha
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC 3083, Australia.
- Department of Biochemistry, Faculty of Agriculture, Benha University, Moshtohor, Toukh, Qaliuobia 13736, Egypt.
| | - Arturo Aburto-Medina
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC 3083, Australia.
| | - Andrew S Ball
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC 3083, Australia.
| | - Esmaeil Shahsavari
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC 3083, Australia.
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Imam A, Suman SK, Ghosh D, Kanaujia PK. Analytical approaches used in monitoring the bioremediation of hydrocarbons in petroleum-contaminated soil and sludge. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.05.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Construction and analysis of an engineered Escherichia coli-Pseudomonas aeruginosa co-culture consortium for phenanthrene bioremoval. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.05.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Xie X, Müller N. Enhanced aniline degradation by Desulfatiglans anilini in a synthetic microbial community with the phototrophic purple sulfur bacterium Thiocapsa roseopersicina. Syst Appl Microbiol 2019; 42:125998. [PMID: 31345671 DOI: 10.1016/j.syapm.2019.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 06/23/2019] [Accepted: 06/26/2019] [Indexed: 11/30/2022]
Abstract
Desulfatiglans anilini is a sulfate-reducing bacterium (SRB) capable of oxidizing aniline, although growth and aniline turnover rates are slow, making it difficult to analyze the metabolism of the strain. Therefore, this study was designed to investigate the effect of sulfide on growth of D. anilini cultures, in order to improve its growth and aniline turnover rates, and study the biochemical mechanisms of sulfide inhibition. Hydrogen sulfide was found to inhibit growth of D. anilini, regardless of whether the strain was grown with aniline or phenol, and complete inhibition was observed at 20mM hydrogen sulfide. For improving the growth of D. anilini with aniline, the sulfide-consuming phototrophic bacterium Thiocapsa roseopersicina was co-cultured in a synthetic microbial community with D. anilini using a co-cultivation device that continuously removed hydrogen sulfide from the culture. The doubling time of D. anilini with aniline was 15 days in the co-cultivation device, compared to 26 days in the absence of a sulfide-oxidizing partner. Moreover, the aniline degradation rate was significantly increased by a factor of 2.66 during co-cultivation of D. anilini with T. roseopersicina. The initial carboxylation reaction during aniline degradation was measured in cell-free extracts of D. anilini with carbon dioxide (CO2) as a co-substrate in the presence of aniline and ATP. The effects of hydrogen sulfide on this aniline carboxylating system and on phenylphosphate synthase activity for phenol activation were studied, and it was concluded that hydrogen sulfide severely inhibited these enzyme activities.
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Affiliation(s)
- Xiaoman Xie
- Department of Biology, University of Konstanz, Constance, Germany; Konstanz Research School Chemical Biology, Constance, Germany
| | - Nicolai Müller
- Department of Biology, University of Konstanz, Constance, Germany.
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Stable-Isotope Probing-Enabled Cultivation of the Indigenous Bacterium Ralstonia sp. Strain M1, Capable of Degrading Phenanthrene and Biphenyl in Industrial Wastewater. Appl Environ Microbiol 2019; 85:AEM.00511-19. [PMID: 31053587 DOI: 10.1128/aem.00511-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 04/26/2019] [Indexed: 02/06/2023] Open
Abstract
To identify and obtain the indigenous degraders metabolizing phenanthrene (PHE) and biphenyl (BP) from the complex microbial community within industrial wastewater, DNA-based stable-isotope probing (DNA-SIP) and cultivation-based methods were applied in the present study. DNA-SIP results showed that two bacterial taxa (Vogesella and Alicyclobacillus) were considered the key biodegraders responsible for PHE biodegradation only, whereas Bacillus and Cupriavidus were involved in BP degradation. Vogesella and Alicyclobacillus have not been linked with PHE degradation previously. Additionally, DNA-SIP helped reveal the taxonomic identity of Ralstonia-like degraders involved in both PHE and BP degradation. To target the separation of functional Ralstonia-like degraders from the wastewater, we modified the traditional cultivation medium and culture conditions. Finally, an indigenous PHE- and BP-degrading strain, Ralstonia pickettii M1, was isolated via a cultivation-dependent method, and its role in PHE and BP degradation was confirmed by enrichment of the 16S rRNA gene and distinctive dioxygenase genes in the DNA-SIP experiment. Our study has successfully established a program for the application of DNA-SIP in the isolation of the active functional degraders from an environment. It also deepens our insight into the diversity of indigenous PHE- and BP-degrading communities.IMPORTANCE The comprehensive treatment of wastewater in industrial parks suffers from the presence of multiple persistent organic pollutants (POPs), such as polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs), which reduce the activity of activated sludge and are difficult to eliminate. Characterizing and applying active bacterial degraders metabolizing multiple POPs therefore helps to reveal the mechanisms of synergistic metabolism and to improve wastewater treatment efficiency in industrial parks. To date, SIP studies have successfully investigated the biodegradation of PAHs or PCBs in real-world habitats. DNA-SIP facilitates the isolation of target microorganisms that pose environmental concerns. Here, an indigenous phenanthrene (PHE)- and biphenyl (BP)-degrading strain in wastewater, Ralstonia pickettii M1, was isolated via a cultivation-dependent method, and its role in PHE and BP degradation was confirmed by DNA-SIP. Our study provides a routine protocol for the application of DNA-SIP in the isolation of the active functional degraders from an environment.
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