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Li X, Cao X, Zhang Z, Li Y, Zhang Y, Wang C, Fan W. Mechanism of phenanthrene degradation by the halophilic Pelagerythrobacter sp. N7. CHEMOSPHERE 2024; 350:141175. [PMID: 38211788 DOI: 10.1016/j.chemosphere.2024.141175] [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: 08/05/2023] [Revised: 11/19/2023] [Accepted: 01/08/2024] [Indexed: 01/13/2024]
Abstract
PAHs has shown worldwide accumulation and causes a significant environmental problem especially in saline and hypersaline environments. Moderately halophilic bacteria could be useful for the bioremediation of PAH pollution in hypersaline environments. Pelagerythrobacter sp. N7 was isolated from the PAH-degrading consortium 5H, which was enriched from mixed saline soil samples collected in Shanxi Province, China. 16S rRNA in the genomic DNA revealed that strain N7 belonged to Pelagerythrobacter. Strain N7 exhibited a high tolerance to a wide range of salinities (1-10%) and was highly efficient under neutral to weak alkaline conditions (pH 6-9). The whole genome of strain N7 was sequenced and analyzed, revealing an abundance of catabolic genes. Using the whole genome information, we conducted preliminary research on key enzymes and gene clusters involved in the upstream and downstream PAH degradation pathways of strain N7, thereby inferring its degradation pathway for phenanthrene and naphthalene. This study adds to our understanding of PAH degradation in hypersaline environments and, for the first time, identifies a Pelagerythrobacter with PAH-degrading capability. Strain N7, with its high efficiency in phenanthrene degradation, represents a promising resource for the bioremediation of PAHs in hypersaline environments.
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Affiliation(s)
- Xiangjin Li
- Miami College, Henan University, Kaifeng, 475000, Henan, China.
| | - Xinghong Cao
- Miami College, Henan University, Kaifeng, 475000, Henan, China.
| | - Zuotao Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
| | - Yichun Li
- Miami College, Henan University, Kaifeng, 475000, Henan, China.
| | - Yue Zhang
- Miami College, Henan University, Kaifeng, 475000, Henan, China.
| | - Chongyang Wang
- Miami College, Henan University, Kaifeng, 475000, Henan, China.
| | - Weihua Fan
- Miami College, Henan University, Kaifeng, 475000, Henan, China.
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Cao X, Zhang C, Zhang S, Sakamaki T, Wang H, Li XN. Simultaneous removal of sediment and water contaminants in a microbial electrochemical system with embedded active electrode by in-situ utilization of electrons. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130172. [PMID: 36308935 DOI: 10.1016/j.jhazmat.2022.130172] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/01/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023]
Abstract
In the water environment such as lakes, there is a phenomenon that the sediment and overlying water are polluted at the same time. In this study, A microbial electrochemical system with an embedded active electrode was developed for simultaneous removal of polycyclic aromatic hydrocarbons in sediment and antibiotics in overlying water by in-situ utilization of electrons. In the closed-circuit group, the pyrene concentration in sediment decreased from 9.94 to 2.08 mg/L in 96 d, and the sulfamethoxazole concentration in water decreased from 5.12 to 1.12 mg/L in 168 h. These values were 18.71 % and 31.21 % higher, respectively, than those of the open-circuit group. The pyrene degradation pathway may be from polycyclic aromatic substances to low-cyclic aromatic hydrocarbons via successive breakdown of benzene rings. Multiple metabolites produced by reduction verified that SMX or its intermediates were reductively degraded in water. On the active electrode, the relative abundances of Acetobacterium and Piscinibacter, which were genera related to SMX degradation, was promoted, while the electricity-producing genus Pseudomonas was inhibited. ccdA, pksS, torC, and acsE genes related to extracellular electron transport may accelerate electron transport. Electrons could be transferred to SMX under the influence of proteins involved in extracellular electron transport, and SMX could be degraded reductively as an electron acceptor by microbes. Generation of electrons and in-situ utilization for simultaneous removal of solid-liquid two-phase pollutants will provide mechanistic insight into pollutant biodegradation by microbial electrochemistry and promote the development of sustainable bioremediation strategies for surface water.
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Affiliation(s)
- Xian Cao
- School of Energy and Environment, Southeast University, Nanjing 210096, China.
| | - Chong Zhang
- School of Energy and Environment, Southeast University, Nanjing 210096, China.
| | - Shuai Zhang
- School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, China.
| | - Takashi Sakamaki
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba Aramaki 6-6-06, Sendai 980-8579, Japan.
| | - Hui Wang
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China.
| | - Xian-Ning Li
- School of Energy and Environment, Southeast University, Nanjing 210096, China.
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Magdy MM, Gaber Y, Sebak M, Azmy AF, AbdelGhani S. Different metabolic pathways involved in anthracene biodegradation by Brevibacillus, Pseudomonas and Methylocystis Species. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2022. [DOI: 10.1186/s43088-021-00178-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Polycyclic aromatic hydrocarbons (PAHs) such as anthracene are one of the most toxic contaminants to our environment. Microbial biodegradation of these xenobiotics is a cost-effective technological solution. The present study aimed to recover some bacterial isolates from Beni-Suef Governorate in Egypt with high capabilities of anthracene biodegradation. The selected isolates were molecularly characterized by 16S rRNA gene sequencing, the degree of anthracene biodegradation was monitored using optical density (OD) and high-performance liquid chromatography (HPLC), PCR amplification of some selected genes encoding biodegradation of PAHs was monitored, and gas chromatography–mass spectrometry (GC–MS) analysis was applied for detecting the resulted metabolites.
Result
Three bacterial isolates were studied, the 16s rRNA sequences of the isolates showed homology of the first isolate to Brevibacillus sp. (94.58 %), the second isolates showed homology to Pseudomonas sp. (94.53%) and the third isolate showed homology to Methylocystis sp. (99.61 %), all isolates showed the ability to degrade anthracene. PCR amplification of some selected genes encoding biodegradation of PAHs revealed the presence of many biodegrading genes in the selected strains. Gas chromatography-mass spectrometry (GC–MS) analysis of the metabolites resulted from anthracene biodegradation in the present study suggested that more than one biodegradation pathway was followed by the selected isolates.
Conclusions
The selected strains could represent a potential bioremediation tool in solving the PAHs problem in the Egyptian environment with a clean and cost-effective technique.
Graphical Abstract
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Qiu X, Wang W, Zhang L, Guo L, Xu P, Tang H. A thermophile Hydrogenibacillus sp. strain efficiently degrades environmental pollutants polycyclic aromatic hydrocarbons. Environ Microbiol 2021; 24:436-450. [PMID: 34897956 DOI: 10.1111/1462-2920.15869] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 12/06/2021] [Indexed: 11/27/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous pollutants threatening ecosystems and human health. Here, we isolated and characterized a new strain, Hydrogenibacillus sp. N12, which is a thermophilic PAH-degrader. Strain N12 utilizes naphthalene as a sole carbon and energy source above 60°C and co-metabolizes many other PAHs as well. The metabolites were identified in the catabolism of naphthalene by gas chromatography-mass spectrometry (GC-MS) and stable isotopic analysis. Based on the identified metabolites, we proposed two possible metabolic pathways, one via salicylic acid and the other via phthalic acid. Whole-genome sequencing reveals that strain N12 possesses a small chromosome of 2.6 Mb. Combining genetic and transcriptional information, we reveal a new gene cluster for the naphthalene degradation. The genes, designated as narAaAb that are predicted to encode the alpha and beta subunits of naphthalene dioxygenase, were subsequently subcloned into Escherichia coli and the enzyme activity was detected by whole-cell transformation. Capacity to degrade several other tricyclic-PAHs was also characterized, suggesting co-existence of other constitutively expressed enzyme systems in strain N12 in addition to the naphthalene degradation gene cluster. Our study provides insights into the potential of the thermophilic PAH-degrader in biotechnology and environmental management applications.
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Affiliation(s)
- Xiaoyu Qiu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Weiwei Wang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lige Zhang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lihua Guo
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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Draft Whole-Genome Sequence of the Anthracene-Degrading Strain Mycolicibacterium frederiksbergense LB501T, Isolated from a Polycyclic Aromatic Hydrocarbon-Contaminated Soil. Microbiol Resour Announc 2020; 9:9/43/e00671-20. [PMID: 33093053 PMCID: PMC7585852 DOI: 10.1128/mra.00671-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we report the draft whole-genome sequence of an anthracene-degrading bacterium, Mycolicibacterium frederiksbergense strain LB501T, using the PacBio and Illumina sequencing platforms. The complete genome sequence of strain LB501T consists of 6,713,618 bp and provides new insights into its metabolic capabilities, including aromatic conversion pathways with promiscuous activities. Here, we report the draft whole-genome sequence of an anthracene-degrading bacterium, Mycolicibacterium frederiksbergense strain LB501T, using the PacBio and Illumina sequencing platforms. The complete genome sequence of strain LB501T consists of 6,713,618 bp and provides new insights into its metabolic capabilities, including aromatic conversion pathways with promiscuous activities.
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Al Farraj DA, Hadibarata T, Yuniarto A, Alkufeidy RM, Alshammari MK, Syafiuddin A. Exploring the potential of halotolerant bacteria for biodegradation of polycyclic aromatic hydrocarbon. Bioprocess Biosyst Eng 2020; 43:2305-2314. [DOI: 10.1007/s00449-020-02415-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 07/22/2020] [Indexed: 12/27/2022]
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Phale PS, Malhotra H, Shah BA. Degradation strategies and associated regulatory mechanisms/features for aromatic compound metabolism in bacteria. ADVANCES IN APPLIED MICROBIOLOGY 2020; 112:1-65. [PMID: 32762865 DOI: 10.1016/bs.aambs.2020.02.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
As a result of anthropogenic activity, large number of recalcitrant aromatic compounds have been released into the environment. Consequently, microbial communities have adapted and evolved to utilize these compounds as sole carbon source, under both aerobic and anaerobic conditions. The constitutive expression of enzymes necessary for metabolism imposes a heavy energy load on the microbe which is overcome by arrangement of degradative genes as operons which are induced by specific inducers. The segmentation of pathways into upper, middle and/or lower operons has allowed microbes to funnel multiple compounds into common key aromatic intermediates which are further metabolized through central carbon pathway. Various proteins belonging to diverse families have evolved to regulate the transcription of individual operons participating in aromatic catabolism. These proteins, complemented with global regulatory mechanisms, carry out the regulation of aromatic compound metabolic pathways in a concerted manner. Additionally, characteristics like chemotaxis, preferential utilization, pathway compartmentalization and biosurfactant production confer an advantage to the microbe, thus making bioremediation of the aromatic pollutants more efficient and effective.
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Affiliation(s)
- Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India.
| | - Harshit Malhotra
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Bhavik A Shah
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
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Anokhina TO, Esikova TZ, Gafarov AB, Polivtseva VN, Baskunov BP, Solyanikova IP. Alternative Naphthalene Metabolic Pathway Includes Formation of ortho-Phthalic Acid and Cinnamic Acid Derivatives in the Rhodococcus opacus Strain 3D. BIOCHEMISTRY (MOSCOW) 2020; 85:355-368. [DOI: 10.1134/s0006297920030116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Bibi N, Hamayun M, Khan SA, Iqbal A, Islam B, Shah F, Khan MA, Lee IJ. Anthracene biodegradation capacity of newly isolated rhizospheric bacteria Bacillus cereus S13. PLoS One 2018; 13:e0201620. [PMID: 30071070 PMCID: PMC6072074 DOI: 10.1371/journal.pone.0201620] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 07/18/2018] [Indexed: 11/24/2022] Open
Abstract
Biodegradation of hazardous pollutants is of immense importance for maintaining a clean environment. However, the concentration of such contaminants/pollutants can be minimized with the help of microorganisms that has the ability to degrade the toxic pollutants into non-toxic metabolites. In the current study, 23 bacterial isolates were purified from the rhizospheric soil of Sysimbrium irio, growing as a wild plant in the vicinity of gas filling stations in Peshawar city. The isolated strains were initially screened on solid nutrient agar and further purified by culturing it on anthracene amended mineral media (PNR). The bacterial growth and anthracene disappearance were observed by calculating optical density (OD). The isolates showed a concentration-dependent growth on anthracene amended PNR media at 30°C and pH7. Also, an increase in bacterial OD from 0.351 to 1.80 with increased shaking speed was noticed. On the contrary, alternate carbon sources (glucose, fructose, sucrose) or nitrogen sources (KNO3, NaNO3, NH4NO3 and CaNO3) posed inhibitory effect on bacterial growth during anthracene degradation. The recorded efficiency of anthracene degradation by the selected bacterial isolate (1.4×1023 CFUmL-1 and 1.80 OD) was 82.29%, after 120 h of incubation. The anthracene was degraded to 9, 10, dihydroxy-anthracene and anthraquinone, detected through GC-MS. The efficient bacterial isolate was identified as S13, a new strain of Bacillus cereus, using 16S rRNA analysis, showing 98% homology. The isolated bacterial strain S13 may be used as a potential tool for bioremediation of toxic hydrocarbons and to keep the environment free from PAH pollutants.
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Affiliation(s)
- Nadia Bibi
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar, Pakistan
| | - Muhammad Hamayun
- Department of Botany, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Sumera Afzal Khan
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar, Pakistan
- * E-mail: (IJL); (SAK)
| | - Amjad Iqbal
- Department of Agriculture, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Badshah Islam
- Department of Agriculture, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Farooq Shah
- Department of Agriculture, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Muhammad Aaqil Khan
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - In-Jung Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- * E-mail: (IJL); (SAK)
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Jauhari N, Mishra S, Kumari B, Singh SN, Chauhan PS, Upreti DK. Bacteria Induced Degradation of Anthracene Mediated by Catabolic Enzymes. Polycycl Aromat Compd 2018. [DOI: 10.1080/10406638.2017.1420667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Nitanshi Jauhari
- Plant Ecology and Environmental Science Division, Plant microbe interaction, Herbarium division, CSIR‐National Botanical Research Institute, Lucknow, U.P., India
| | - Shweta Mishra
- Plant Ecology and Environmental Science Division, Plant microbe interaction, Herbarium division, CSIR‐National Botanical Research Institute, Lucknow, U.P., India
| | - Babita Kumari
- Plant Ecology and Environmental Science Division, Plant microbe interaction, Herbarium division, CSIR‐National Botanical Research Institute, Lucknow, U.P., India
| | - S. N. Singh
- Plant Ecology and Environmental Science Division, Plant microbe interaction, Herbarium division, CSIR‐National Botanical Research Institute, Lucknow, U.P., India
| | - Puneet S. Chauhan
- Plant microbe interaction, CSIR‐National Botanical Research Institute, Lucknow, U.P., India
| | - D. K. Upreti
- Herbarium division, CSIR‐National Botanical Research Institute, Lucknow, U.P., India
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Tian Z, Gold A, Nakamura J, Zhang Z, Vila J, Singleton DR, Collins LB, Aitken MD. Nontarget Analysis Reveals a Bacterial Metabolite of Pyrene Implicated in the Genotoxicity of Contaminated Soil after Bioremediation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:7091-7100. [PMID: 28510420 PMCID: PMC6309544 DOI: 10.1021/acs.est.7b01172] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Bioremediation is an accepted technology for cleanup of soil contaminated with polycyclic aromatic hydrocarbons (PAHs), but it can increase the genotoxicity of the soil despite removal of the regulated PAHs. Although polar biotransformation products have been implicated as causative genotoxic agents, no specific product has been identified. We pursued a nontarget analytical approach combining effect-directed analysis (EDA) and metabolite profiling to compare extracts of PAH-contaminated soil from a former manufactured-gas plant site before and after treatment in a laboratory-scale aerobic bioreactor. A compound with the composition C15H8O2 and four methylated homologues were shown to accumulate as a result of bioreactor treatment, and the C15H8O2 compound purified from soil extracts was determined to be genotoxic. Its structure was established by nuclear magnetic resonance and mass spectroscopy as a heretofore unidentified α,β-unsaturated lactone derived from dioxygenation of pyrene at an apical ring, 2H-naphtho[2,1,8-def]chromen-2-one (NCO), which was confirmed by synthesis. The concentration of NCO in the bioreactor was 11 μg g-1 dry soil, corresponding to 13% of the pyrene removed. It also accumulated in aerobically incubated soil from two additional PAH-contaminated sites and was formed from pyrene by two pyrene-degrading bacterial cultures known to be geographically widespread, underscoring its potential environmental significance.
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Li CH, Ye C, Hou XP, Chen MH, Zheng XY, Cai XY. Isolation and characterization of polycyclic aromatic hydrocarbon-degrading bacteria with tolerance to hypoxic environments. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2017; 52:581-589. [PMID: 28281889 DOI: 10.1080/10934529.2017.1293991] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Hypoxic conditions are considerably different from aerobic and anaerobic conditions, and they are widely distributed in natural environments. Many pollutants, including polycyclic aromatic hydrocarbons (PAHs), tend to accumulate in hypoxic environments. However, PAH biodegradation under hypoxic conditions is poorly understood compared with that under obligate aerobic and obligate anaerobic conditions. In the present study, PAH-degrading bacteria were enriched, and their biodegradation rates were tested using a hypoxic station with an 8% oxygen concentration. PAH-degrading bacteria collected from sediments in low-oxygen environments were enriched using phenanthrene (Phe) or pyrene (Pyr) as the sole carbon and energy source. Individual bacterial colonies showing the ability to degrade Phe or Pyr were isolated and identified by 16S rDNA gene sequencing. Morphological and physiological characterizations of the isolated bacterial colonies were performed. The isolated bacteria were observed by scanning electron microscopy (SEM) and were identified as Pseudomonas sp., Klebsiella sp., Bacillus sp., and Comamonas sp. Phylogenetic tree of the isolated PAH-degrading bacteria was also constructed. The biodegradation ability of these bacteria was tested at an initial Phe or Pyr concentration of 50 mg L-1. The biodegradation kinetics were best fit by a first-order rate model and presented regression coefficients (r2) that varied from 0.7728 to 0.9725 (P < 0.05). The half-lives of the PAHs varied from 2.99 to 3.65 d for Phe and increased to 60.3-82.5 d for Pyr. These half-lives were much shorter than those observed under anaerobic conditions but were similar to those observed under aerobic conditions.
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Affiliation(s)
- Chun-Hua Li
- a State Key Laboratory of Environmental Criteria and Risk Assessment , Chinese Research Academy of Environmental Sciences , Beijing , China
| | - Chun Ye
- a State Key Laboratory of Environmental Criteria and Risk Assessment , Chinese Research Academy of Environmental Sciences , Beijing , China
| | - Xiao-Peng Hou
- a State Key Laboratory of Environmental Criteria and Risk Assessment , Chinese Research Academy of Environmental Sciences , Beijing , China
| | - Ming-Hua Chen
- a State Key Laboratory of Environmental Criteria and Risk Assessment , Chinese Research Academy of Environmental Sciences , Beijing , China
| | - Xiang-Yong Zheng
- c Zhejiang Provincial Key Lab for Subtropical Water Environment and Marine Biological Resources Protection, School of Life and Environmental Science, Wenzhou University , Zhejiang , China
| | - Xu-Yi Cai
- b School of Water Resource and Environment, China University of Geosciences , Beijing , China
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Pathak A, Chauhan A, Blom J, Indest KJ, Jung CM, Stothard P, Bera G, Green SJ, Ogram A. Comparative Genomics and Metabolic Analysis Reveals Peculiar Characteristics of Rhodococcus opacus Strain M213 Particularly for Naphthalene Degradation. PLoS One 2016; 11:e0161032. [PMID: 27532207 PMCID: PMC4988695 DOI: 10.1371/journal.pone.0161032] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 07/27/2016] [Indexed: 12/12/2022] Open
Abstract
The genome of Rhodococcus opacus strain M213, isolated from a fuel-oil contaminated soil, was sequenced and annotated which revealed a genome size of 9,194,165 bp encoding 8680 putative genes and a G+C content of 66.72%. Among the protein coding genes, 71.77% were annotated as clusters of orthologous groups of proteins (COGs); 55% of the COGs were present as paralog clusters. Pulsed field gel electrophoresis (PFGE) analysis of M213 revealed the presence of three different sized replicons- a circular chromosome and two megaplasmids (pNUO1 and pNUO2) estimated to be of 750Kb 350Kb in size, respectively. Conversely, using an alternative approach of optical mapping, the plasmid replicons appeared as a circular ~1.2 Mb megaplasmid and a linear, ~0.7 Mb megaplasmid. Genome-wide comparative analysis of M213 with a cohort of sequenced Rhodococcus species revealed low syntenic affiliation with other R. opacus species including strains B4 and PD630. Conversely, a closer affiliation of M213, at the functional (COG) level, was observed with the catabolically versatile R. jostii strain RHA1 and other Rhodococcii such as R. wratislaviensis strain IFP 2016, R. imtechensis strain RKJ300, Rhodococcus sp. strain JVH1, and Rhodococcus sp. strain DK17, respectively. An in-depth, genome-wide comparison between these functional relatives revealed 971 unique genes in M213 representing 11% of its total genome; many associating with catabolic functions. Of major interest was the identification of as many as 154 genomic islands (GEIs), many with duplicated catabolic genes, in particular for PAHs; a trait that was confirmed by PCR-based identification of naphthalene dioxygenase (NDO) as a representative gene, across PFGE-resolved replicons of strain M213. Interestingly, several plasmid/GEI-encoded genes, that likely participate in degrading naphthalene (NAP) via a peculiar pathway, were also identified in strain M213 using a combination of bioinformatics, metabolic analysis and gene expression measurements of selected catabolic genes by RT-PCR. Taken together, this study provides a comprehensive understanding of the genome plasticity and ecological competitiveness of strain M213 likely facilitated by horizontal gene transfer (HGT), bacteriophage attacks and genomic reshuffling- aspects that continue to be understudied and thus poorly understood, in particular for the soil-borne Rhodococcii.
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Affiliation(s)
- Ashish Pathak
- School of the Environment, Florida A&M University, Tallahassee, Florida, United States of America
| | - Ashvini Chauhan
- School of the Environment, Florida A&M University, Tallahassee, Florida, United States of America
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Karl J. Indest
- Environmental Processes Branch, United States Army Engineer Research and Development Center, Vicksburg, Mississippi, United States of America
| | - Carina M. Jung
- Environmental Processes Branch, United States Army Engineer Research and Development Center, Vicksburg, Mississippi, United States of America
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Gopal Bera
- Geochemical and Environmental Research Group, Texas A&M University, College Station, Texas, United States of America
| | - Stefan J. Green
- DNA Services Facility, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Andrew Ogram
- Soil and Water Science Department, University of Florida, Gainesville, Florida, United States of America
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Pleiotropic and epistatic behavior of a ring-hydroxylating oxygenase system in the polycyclic aromatic hydrocarbon metabolic network from Mycobacterium vanbaalenii PYR-1. J Bacteriol 2014; 196:3503-15. [PMID: 25070740 DOI: 10.1128/jb.01945-14] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite the considerable knowledge of bacterial high-molecular-weight (HMW) polycyclic aromatic hydrocarbon (PAH) metabolism, the key enzyme(s) and its pleiotropic and epistatic behavior(s) responsible for low-molecular-weight (LMW) PAHs in HMW PAH-metabolic networks remain poorly understood. In this study, a phenotype-based strategy, coupled with a spray plate method, selected a Mycobacterium vanbaalenii PYR-1 mutant (6G11) that degrades HMW PAHs but not LMW PAHs. Sequence analysis determined that the mutant was defective in pdoA2, encoding an aromatic ring-hydroxylating oxygenase (RHO). A series of metabolic comparisons using high-performance liquid chromatography (HPLC) analysis revealed that the mutant had a lower rate of degradation of fluorene, anthracene, and pyrene. Unlike the wild type, the mutant did not produce a color change in culture media containing fluorene, phenanthrene, and fluoranthene. An Escherichia coli expression experiment confirmed the ability of the Pdo system to oxidize biphenyl, the LMW PAHs naphthalene, phenanthrene, anthracene, and fluorene, and the HMW PAHs pyrene, fluoranthene, and benzo[a]pyrene, with the highest enzymatic activity directed toward three-ring PAHs. Structure analysis and PAH substrate docking simulations of the Pdo substrate-binding pocket rationalized the experimentally observed metabolic versatility on a molecular scale. Using information obtained in this study and from previous work, we constructed an RHO-centric functional map, allowing pleiotropic and epistatic enzymatic explanation of PAH metabolism. Taking the findings together, the Pdo system is an RHO system with the pleiotropic responsibility of LMW PAH-centric hydroxylation, and its epistatic functional contribution is also crucial for the metabolic quality and quantity of the PAH-MN.
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Camacho-Morales RL, Zazueta-Novoa V, Casillas JLG, Ballesteros EA, Bote JAO, Zazueta-Sandoval R. Purification and characteristics of an inducible by polycyclic aromatic hydrocarbons NADP+-dependent naphthalenediol dehydrogenase (NDD) in Mucor circinelloides YR-1. Protein Expr Purif 2014; 97:1-8. [DOI: 10.1016/j.pep.2014.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2013] [Revised: 02/01/2014] [Accepted: 02/06/2014] [Indexed: 10/25/2022]
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16
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Salam LB, Obayori OS, Olatoye NO. Biodegradation of anthracene by a novel actinomycete, Microbacterium sp. isolated from tropical hydrocarbon-contaminated soil. World J Microbiol Biotechnol 2013; 30:335-41. [PMID: 23881542 DOI: 10.1007/s11274-013-1437-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 07/15/2013] [Indexed: 11/30/2022]
Abstract
A novel anthracene-degrading Gram-positive actinomycete, Microbacterium sp. strain SL10 was isolated from a hydrocarbon-contaminated soil at a mechanical engineering workshop in Lagos, Nigeria. The polluted soil had an unusually high total hydrocarbon content of 157 g/kg and presence of various heavy metals. The isolate tolerated salt concentration of more than 4%. It resisted cefotaxime, streptomycin and ciprofloxacin, but susceptible to meropenem, linezolid and vancomycin. The isolate exhibited growth rate and doubling time of 0.82 days(-1) and 0.84 days, respectively on anthracene. It degraded 57.5 and 90.12% of anthracene within 12 and 21 days, respectively while the rate of anthracene utilization by the isolate was 4.79 mg l(-1) d(-1). To the best of our knowledge, this is the first report of isolation and characterization of anthracene-degrading Microbacterium sp.
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Affiliation(s)
- Lateef B Salam
- Department of Microbiology, Faculty of Science, Lagos State University, Ojo, Lagos, Nigeria,
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17
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Benz[a]anthracene biotransformation and production of ring fission products by Sphingobium sp. strain KK22. Appl Environ Microbiol 2013; 79:4410-20. [PMID: 23686261 DOI: 10.1128/aem.01129-13] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A soil bacterium, designated strain KK22, was isolated from a phenanthrene enrichment culture of a bacterial consortium that grew on diesel fuel, and it was found to biotransform the persistent environmental pollutant and high-molecular-weight polycyclic aromatic hydrocarbon (PAH) benz[a]anthracene. Nearly complete sequencing of the 16S rRNA gene of strain KK22 and phylogenetic analysis revealed that this organism is a new member of the genus Sphingobium. An 8-day time course study that consisted of whole-culture extractions followed by high-performance liquid chromatography (HPLC) analyses with fluorescence detection showed that 80 to 90% biodegradation of 2.5 mg liter(-1) benz[a]anthracene had occurred. Biodegradation assays where benz[a]anthracene was supplied in crystalline form (100 mg liter(-1)) confirmed biodegradation and showed that strain KK22 cells precultured on glucose were equally capable of benz[a]anthracene biotransformation when precultured on glucose plus phenanthrene. Analyses of organic extracts from benz[a]anthracene biodegradation by liquid chromatography negative electrospray ionization tandem mass spectrometry [LC/ESI(-)-MS/MS] revealed 10 products, including two o-hydroxypolyaromatic acids and two hydroxy-naphthoic acids. 1-Hydroxy-2- and 2-hydroxy-3-naphthoic acids were unambiguously identified, and this indicated that oxidation of the benz[a]anthracene molecule occurred via both the linear kata and angular kata ends of the molecule. Other two- and single-aromatic-ring metabolites were also documented, including 3-(2-carboxyvinyl)naphthalene-2-carboxylic acid and salicylic acid, and the proposed pathways for benz[a]anthracene biotransformation by a bacterium were extended.
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Ke J, Singh D, Chen S. Metabolism of polycyclic aromatic hydrocarbons by the wood-feeding termite Coptotermes formosanus (Shiraki). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:1788-1797. [PMID: 22280527 DOI: 10.1021/jf204707d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are among the most prevalent and persistent pollutants in the environment. In this study, the wood-feeding termite (WFT) Coptotermes formosanus (Shiraki) was studied regarding the potential ability to degrade two selected low-molecular-weight PAHs, phenanthrene and anthracene. Pyrolysis-gas chromatography/mass spectrometry was employed for analysis of in vivo PAH degradation by three gut segments (fore-, mid-, and hindgut) of the WFT. The results revealed the capability of lower termite for PAH metabolism, which started from the foregut and mainly occurred in the midgut region. Remediation of phenanthrene by the termite has been proposed to be initiated via hydroxylation at the C-10 position. Anthracene metabolism first occurred at the C-3, C-5, and C-12 positions with the addition of aldehyde and carbonyl groups. Ring hydroxylation, methoxylation, esterification, carboxylation, and methylation were detected on both the PAHs for ring fission, suggesting the existence of effective PAH modification activity in the alimentary canal of C. formosanus . This new PAH degradation system of the WFT provides new insights for potential technologies for bioremediation of PAH-contaminated soil and sediment based on the related lingolytic enzymes.
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Affiliation(s)
- Jing Ke
- Department of Biological Systems Engineering, Washington State University, Pullman, Washington 99164-6120, United States
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19
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Megadi VB, Tallur PN, Mulla SI, Ninnekar HZ. Bacterial degradation of fungicide captan. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2010; 58:12863-12868. [PMID: 21121628 DOI: 10.1021/jf1030339] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The phthalimide fungicide captan has been widely used to control plant pathogenic fungi. A strain of Bacillus circulans utilized the fungicide captan as sole source of carbon and energy. The organism degraded captan by a pathway involving its initial hydrolysis to yield cis-1,2,3,6-tetrahydrophthalimide, a compound without fungicidal activity. The formation of this compound was confirmed by HPLC, IR, NMR, and mass spectral analysis. The results also revealed that cis-1,2,3,6-tetrahydrophthalimide was further degraded to o-phthalic acid by a protocatechuate pathway. These findings indicated that there was a complete mineralization of fungicide captan by B. circulans.
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Affiliation(s)
- Veena B Megadi
- Department of Biochemistry, Karnatak University, Dharwad 580 003, Karnataka, India
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20
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Xu Y, Lu M. Bioremediation of crude oil-contaminated soil: comparison of different biostimulation and bioaugmentation treatments. JOURNAL OF HAZARDOUS MATERIALS 2010; 183:395-401. [PMID: 20685037 DOI: 10.1016/j.jhazmat.2010.07.038] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Revised: 07/08/2010] [Accepted: 07/09/2010] [Indexed: 05/27/2023]
Abstract
Biostimulation with inorganic fertilizer and bioaugmentation with hydrocarbon utilizing indigenous bacteria were employed as remedial options for 12 weeks in a crude oil-contaminated soil. To promote oil removal, biocarrier for immobilization of indigenous hydrocarbon-degrading bacteria was developed using peanut hull powder. Biodegradation was enhanced with free-living bacterial culture and biocarrier with a total petroleum hydrocarbon removal ranging from 26% to 61% after a 12-week treatment. Oil removal was also enhanced when peanut hull powder was only used as a bulking agent, which accelerated the mass transfer rate of water, oxygen, nutrients and hydrocarbons, and provided nutrition for the microflora. Dehydrogenase activity in soil was remarkably enhanced by the application of carrier material. Metabolites of polycyclic aromatic hydrocarbons were identified by Fourier transform ion cyclotron resonance mass spectrometry.
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Affiliation(s)
- Yaohui Xu
- Department of Geochemistry, Yangtze University, Nanhuan Road, Jingzhou 434023, China.
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Mallick S, Chakraborty J, Dutta TK. Role of oxygenases in guiding diverse metabolic pathways in the bacterial degradation of low-molecular-weight polycyclic aromatic hydrocarbons: a review. Crit Rev Microbiol 2010; 37:64-90. [PMID: 20846026 DOI: 10.3109/1040841x.2010.512268] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Widespread environmental pollution by polycyclic aromatic hydrocarbons (PAHs) poses an immense risk to the environment. Bacteria-mediated attenuation has a great potential for the restoration of PAH-contaminated environment in an ecologically accepted manner. Bacterial degradation of PAHs has been extensively studied and mining of biodiversity is ever expanding the biodegradative potentials with intelligent manipulation of catabolic genes and adaptive evolution to generate multiple catabolic pathways. The present review of bacterial degradation of low-molecular-weight (LMW) PAHs describes the current knowledge about the diverse metabolic pathways depicting novel metabolites, enzyme-substrate/metabolite relationships, the role of oxygenases and their distribution in phylogenetically diverse bacterial species.
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Affiliation(s)
- Somnath Mallick
- Department of Chemistry, Saldiha College, Bankura, West Bengal, India
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22
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Ding JY, Lai MC. The biotechnological potential of the extreme halophilic archaea Haloterrigena sp. H13 in xenobiotic metabolism using a comparative genomics approach. ENVIRONMENTAL TECHNOLOGY 2010; 31:905-914. [PMID: 20662380 DOI: 10.1080/09593331003734210] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Extreme halophilic archaea are thriving and dominant populations within hypersaline environments. Because of the extreme properties of the enzymes of halophilic archaea and similar metabolic abilities to their bacterial counterparts, our interests focus on their potential biotechnological applications. In this study, the partial genome of a newly isolated extreme halophilic archaeon, Haloterrigena sp. H13, was investigated. The genome size was estimated to be about 3.9 MB, and a genomic shotgun library was constructed. A total of 1479 clones from the library were sequenced once, and 1186 contigs were obtained. From these contigs, 580 open reading frames (ORFs) were identified, and 394 ORFs were annotated. From the partial genome of strain H13, we identified genes that may be involved in 1,2-dichloroethane degradation, naphthalene/anthracene degradation, gamma-hexachlorocyclohexane degradation, 1-/2-methylnaphthalene degradation and benzoate degradation via CoA ligation. Among the identified ORFs, gene homologs of (S)-2-haloacid dehalogenase (EC 3.8.1.2) and salicylate hydroxylase (EC 1.14.13.1), which might be involved in the degradation of dichloroethane, gamma-hexachlorocyclohexane and naphthalene, were found in the partial genome sequence of strain H13. According to the current genome annotation of peripheral metabolic pathways and the putative xenobiotic-degrading enzymes, the potential of extreme haloarchaea in bioremediation applications is proposed.
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Affiliation(s)
- Jiun-Yan Ding
- Department of Life Sciences, National Chung Hsing University, Taichung, 40227 Taiwan, ROC
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23
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Biodegradation of aromatic compounds: current status and opportunities for biomolecular approaches. Appl Microbiol Biotechnol 2010; 85:207-28. [PMID: 19730850 DOI: 10.1007/s00253-009-2192-4] [Citation(s) in RCA: 147] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Revised: 08/05/2009] [Accepted: 08/05/2009] [Indexed: 02/03/2023]
Abstract
Biodegradation can achieve complete and cost-effective elimination of aromatic pollutants through harnessing diverse microbial metabolic processes. Aromatics biodegradation plays an important role in environmental cleanup and has been extensively studied since the inception of biodegradation. These studies, however, are diverse and scattered; there is an imperative need to consolidate, summarize, and review the current status of aromatics biodegradation. The first part of this review briefly discusses the catabolic mechanisms and describes the current status of aromatics biodegradation. Emphasis is placed on monocyclic, polycyclic, and chlorinated aromatic hydrocarbons because they are the most prevalent aromatic contaminants in the environment. Among monocyclic aromatic hydrocarbons, benzene, toluene, ethylbenzene, and xylene; phenylacetic acid; and structurally related aromatic compounds are highlighted. In addition, biofilms and their applications in biodegradation of aromatic compounds are briefly discussed. In recent years, various biomolecular approaches have been applied to design and understand microorganisms for enhanced biodegradation. In the second part of this review, biomolecular approaches, their applications in aromatics biodegradation, and associated biosafety issues are discussed. Particular attention is given to the applications of metabolic engineering, protein engineering, and "omics" technologies in aromatics biodegradation.
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24
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Kanaly RA, Harayama S. Advances in the field of high-molecular-weight polycyclic aromatic hydrocarbon biodegradation by bacteria. Microb Biotechnol 2010; 3:136-64. [PMID: 21255317 PMCID: PMC3836582 DOI: 10.1111/j.1751-7915.2009.00130.x] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Revised: 05/22/2009] [Accepted: 05/26/2009] [Indexed: 11/26/2022] Open
Abstract
Interest in understanding prokaryotic biotransformation of high-molecular-weight polycyclic aromatic hydrocarbons (HMW PAHs) has continued to grow and the scientific literature shows that studies in this field are originating from research groups from many different locations throughout the world. In the last 10 years, research in regard to HMW PAH biodegradation by bacteria has been further advanced through the documentation of new isolates that represent diverse bacterial types that have been isolated from different environments and that possess different metabolic capabilities. This has occurred in addition to the continuation of in-depth comprehensive characterizations of previously isolated organisms, such as Mycobacterium vanbaalenii PYR-1. New metabolites derived from prokaryotic biodegradation of four- and five-ring PAHs have been characterized, our knowledge of the enzymes involved in these transformations has been advanced and HMW PAH biodegradation pathways have been further developed, expanded upon and refined. At the same time, investigation of prokaryotic consortia has furthered our understanding of the capabilities of microorganisms functioning as communities during HMW PAH biodegradation.
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Affiliation(s)
- Robert A Kanaly
- Department of Genome Systems, Faculty of Bionanoscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Kanagawa-ken, Yokohama 236-0027, Japan.
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25
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Abstract
Microorganisms provide a wealth of biodegradative potential in the reduction and elimination of xenobiotic compounds in the environment. One useful metric to evaluate potential biodegradation pathways is thermodynamic feasibility. However, experimental data for the thermodynamic properties of xenobiotics is scarce. The present work uses a group contribution method to study the thermodynamic properties of the University of Minnesota Biocatalysis/Biodegradation Database. The Gibbs free energies of formation and reaction are estimated for 914 compounds (81%) and 902 reactions (75%), respectively, in the database. The reactions are classified based on the minimum and maximum Gibbs free energy values, which accounts for uncertainty in the free energy estimates and a feasible concentration range relevant to biodegradation. Using the free energy estimates, the cumulative free energy change of 89 biodegradation pathways (51%) in the database could be estimated. A comparison of the likelihood of the biotransformation rules in the Pathway Prediction System and their thermodynamic feasibility was then carried out. This analysis revealed that when evaluating the feasibility of biodegradation pathways, it is important to consider the thermodynamic topology of the reactions in the context of the complete pathway. Group contribution is shown to be a viable tool for estimating, a priori, the thermodynamic feasibility and the relative likelihood of alternative biodegradation reactions. This work offers a useful tool to a broad range of researchers interested in estimating the feasibility of the reactions in existing or novel biodegradation pathways.
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Affiliation(s)
- Stacey D. Finley
- Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208
| | - Linda J. Broadbelt
- Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208
| | - Vassily Hatzimanikatis
- Laboratory of Computational Systems Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics (SIB), CH H4 625, Station 6, CH-1015 Lausanne, Switzerland; telephone: +41-21-693-98-70; fax: +41-21-693-98-75
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Leneva NA, Kolomytseva MP, Baskunov BP, Golovleva LA. Phenanthrene and anthracene degradation by microorganisms of the genus Rhodococcus. APPL BIOCHEM MICRO+ 2009. [DOI: 10.1134/s0003683809020094] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Fan L, Ni J, Wu Y, Zhang Y. Treatment of bromoamine acid wastewater using combined process of micro-electrolysis and biological aerobic filter. JOURNAL OF HAZARDOUS MATERIALS 2009; 162:1204-1210. [PMID: 18621476 DOI: 10.1016/j.jhazmat.2008.06.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Revised: 06/01/2008] [Accepted: 06/03/2008] [Indexed: 05/26/2023]
Abstract
The wastewater originated from the production of bromoamine acid was treated in a sequential system of micro-electrolysis (ME) and biological aerobic filter (BAF). Decolorization and COD(Cr) removal rate of the proposed system was investigated with full consideration of the influence of two major controlling factors such as organic loading rate (OLR) and hydraulic retention time (HRT). The removal rate of COD(Cr) was 81.2% and that of chrominance could be up to 96.6% at an OLR of 0.56 kg m(-3)d(-1) when the total HRT was 43.4h. Most of the chrominance was removed by the ME treatment, however, the BAF process was more effective for COD(Cr) removal. The GC-MS and HPLC-MS analysis of the contaminants revealed that 1-aminoanthraquinone, bromoamine acid and mono-sulfonated 1,2-dichlorobenzene were the main organic components in the wastewater. The reductive transformation of the anthraquinone derivatives in the ME reactor improved the biodegradability of the wastewater, and rendered the decolorization. After long-term of operation, it was observed that the predominant microorganisms immobilized on the BAF carriers were rod-shaped and globular. Four bacterial strains with apparent 16S rDNA fragments in the Denaturing Gradient Gel Electrophoresis (DGGE) profiles of BAF samples were identified as Variovorax sp., Sphingomonas sp., Mycobacterium sp., and Microbacterium sp.
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Affiliation(s)
- Li Fan
- Shenzhen Graduate School, Peking University, The Key Laboratory for Environmental and Urban Sciences, Guang Dong 518055, China
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Bacterial degradation of aromatic compounds. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2009; 6:278-309. [PMID: 19440284 PMCID: PMC2672333 DOI: 10.3390/ijerph6010278] [Citation(s) in RCA: 468] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Accepted: 01/06/2009] [Indexed: 11/21/2022]
Abstract
Aromatic compounds are among the most prevalent and persistent pollutants in the environment. Petroleum-contaminated soil and sediment commonly contain a mixture of polycyclic aromatic hydrocarbons (PAHs) and heterocyclic aromatics. Aromatics derived from industrial activities often have functional groups such as alkyls, halogens and nitro groups. Biodegradation is a major mechanism of removal of organic pollutants from a contaminated site. This review focuses on bacterial degradation pathways of selected aromatic compounds. Catabolic pathways of naphthalene, fluorene, phenanthrene, fluoranthene, pyrene, and benzo[a]pyrene are described in detail. Bacterial catabolism of the heterocycles dibenzofuran, carbazole, dibenzothiophene, and dibenzodioxin is discussed. Bacterial catabolism of alkylated PAHs is summarized, followed by a brief discussion of proteomics and metabolomics as powerful tools for elucidation of biodegradation mechanisms.
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Zeinali M, Vossoughi M, Ardestani S. Degradation of phenanthrene and anthracene byNocardia otitidiscaviarumstrain TSH1, a moderately thermophilic bacterium. J Appl Microbiol 2008; 105:398-406. [DOI: 10.1111/j.1365-2672.2008.03753.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Peng RH, Xiong AS, Xue Y, Fu XY, Gao F, Zhao W, Tian YS, Yao QH. Microbial biodegradation of polyaromatic hydrocarbons. FEMS Microbiol Rev 2008; 32:927-55. [PMID: 18662317 DOI: 10.1111/j.1574-6976.2008.00127.x] [Citation(s) in RCA: 393] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are widespread in various ecosystems and are pollutants of great concern due to their potential toxicity, mutagenicity and carcinogenicity. Because of their hydrophobic nature, most PAHs bind to particulates in soil and sediments, rendering them less available for biological uptake. Microbial degradation represents the major mechanism responsible for the ecological recovery of PAH-contaminated sites. The goal of this review is to provide an outline of the current knowledge of microbial PAH catabolism. In the past decade, the genetic regulation of the pathway involved in naphthalene degradation by different gram-negative and gram-positive bacteria was studied in great detail. Based on both genomic and proteomic data, a deeper understanding of some high-molecular-weight PAH degradation pathways in bacteria was provided. The ability of nonligninolytic and ligninolytic fungi to transform or metabolize PAH pollutants has received considerable attention, and the biochemical principles underlying the degradation of PAHs were examined. In addition, this review summarizes the information known about the biochemical processes that determine the fate of the individual components of PAH mixtures in polluted ecosystems. A deeper understanding of the microorganism-mediated mechanisms of catalysis of PAHs will facilitate the development of new methods to enhance the bioremediation of PAH-contaminated sites.
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Affiliation(s)
- Ri-He Peng
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
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31
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Zeinali M, Vossoughi M, Ardestani SK. Naphthalene metabolism in Nocardia otitidiscaviarum strain TSH1, a moderately thermophilic microorganism. CHEMOSPHERE 2008; 72:905-909. [PMID: 18471862 DOI: 10.1016/j.chemosphere.2008.03.038] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Revised: 03/11/2008] [Accepted: 03/18/2008] [Indexed: 05/26/2023]
Abstract
The thermophilic bacterium Nocardia otitidiscaviarum strain TSH1, originally isolated in our laboratory from a petroindustrial wastewater contaminated soil in Iran, grows at 50 degrees C on a broad range of hydrocarbons. Transformation of naphthalene by strain TSH1 which is able to use this two ring-polycyclic aromatic hydrocarbon (PAH) as a sole source of carbon and energy was investigated. The metabolic pathway was elucidated by identifying metabolites, biotransformation studies and monitoring enzyme activities in cell-free extracts. The identification of metabolites suggests that strain TSH1 initiates its attack on naphthalene by dioxygenation at its C-1 and C-2 positions to give 1,2-dihydro-1,2-dihydroxynaphthalene. The intermediate 2-hydroxycinnamic acid, characteristic of the meta-cleavage of the resulting diol was identified in the acidic extract. Apart from typical metabolites of naphthalene degradation known from mesophiles, benzoic acid was identified as an intermediate for the naphthalene pathway of this Nocardia strain. Neither phthalic acid nor salicylic acid metabolites were detected in culture extracts. Enzymatic experiments with cell extract showed the catechol 1,2-dioxygenase activity while transformation of phthalic acid and protocatechuic acid was not observed. The results of enzyme activity assays and identification of benzoic acid in culture extract provide strong indications that further degradation goes through benzoate and beta-ketoadipate pathway. Our results indicate that naphthalene degradation by thermophilic N. otitidiscaviarum strain TSH1 differs from the known pathways found for the thermophilic Bacillus thermoleovorans Hamburg 2 and mesophilic bacteria.
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Affiliation(s)
- Majid Zeinali
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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Microbial metabolism of 1-aminoanthracene by Beauveria bassiana. Bioorg Med Chem 2008; 16:5085-9. [PMID: 18378148 DOI: 10.1016/j.bmc.2008.03.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2008] [Revised: 03/05/2008] [Accepted: 03/10/2008] [Indexed: 11/24/2022]
Abstract
The carcinogen and mutagen, 1-aminoanthracene, was efficiently metabolized by the fungal strain Beauveria bassiana ATCC 7159 to yield three new metabolites identified as 1-acetamido-5-[(4'-O-methyl-beta-d-glucopyranosyl)oxy]anthracene, 1-acetamido-8-[(4'-O-methyl-beta-d-glucopyranosyl)oxy]anthraquinone, and 1-acetamido-6-[(4'-O-methyl-beta-d-glucopyranosyl)oxy]anthraquinone, together with 1-acetamidoanthracene and 1-acetamidoanthraquinone. Formation of these metabolites suggests that the metabolic pathways of 1-aminoanthracene in B. bassiana ATCC 7159 involve acetylation, oxidation, hydroxylation, and O-methylglucosylation.
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33
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Degradation of naphthalene by thermophilic bacteria via a pathway, through protocatechuic acid. Open Life Sci 2008. [DOI: 10.2478/s11535-007-0042-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AbstractA number of thermophilic bacteria capable of utilizing naphthalene as a sole source of carbon were isolated from a high-temperature oilfield in Lithuania. These isolates were able to utilize several other aromatic compounds, such as anthracene, benzene, phenol, benzene-1, 3-diol, protocatechuic acid as well. Thermophilic isolate G27 ascribed to Geobacillus genus was found to have a high aromatic compound degrading capacity. Spectrophotometric determination of enzyme activities in cell-free extracts revealed that the last aromatic ring fission enzyme in naphthalene biotransformation by Geobacillus sp. G27 was inducible via protocatechuate 3, 4-dioxygenase; no protocatechuate 4, 5-dioxygenase, protocatechuate 2, 3-dioxygenase activities were detected. Intermediates such as o-phthalic and protocatechuic acids detected in culture supernatant confirmed that the metabolism of naphthalene by Geobacillus sp. G27 can proceed through protocatechuic acid via ortho-cleavage pathway and thus differs from the pathways known for mesophilic bacteria.
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Husain S. Literature overview: Microbial metabolism of high molecular weight polycyclic aromatic hydrocarbons. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/rem.20165] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Singleton DR, Richardson SD, Aitken MD. Effects of enrichment with phthalate on polycyclic aromatic hydrocarbon biodegradation in contaminated soil. Biodegradation 2007; 19:577-87. [PMID: 17990065 DOI: 10.1007/s10532-007-9163-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2007] [Accepted: 10/29/2007] [Indexed: 11/26/2022]
Abstract
The effect of enrichment with phthalate on the biodegradation of polycyclic aromatic hydrocarbons (PAH) was tested with bioreactor-treated and untreated contaminated soil from a former manufactured gas plant (MGP) site. Soil samples that had been treated in a bioreactor and enriched with phthalate mineralized (14)C-labeled phenanthrene and pyrene to a greater extent than unenriched samples over a 22.5-h incubation, but did not stimulate benzo[a]pyrene mineralization. In contrast to the positive effects on (14)C-labeled phenanthrene and pyrene, no significant differences were found in the extent of biodegradation of native PAH when untreated contaminated soil was incubated with and without phthalate amendment. Denaturing-gradient gel electrophoresis (DGGE) profiles of bacterial 16S rRNA genes from unenriched and phthalate-enriched soil samples were substantially different, and clonal sequences matched to prominent DGGE bands revealed that beta-Proteobacteria related to Ralstonia were most highly enriched by phthalate addition. Quantitative real-time PCR analyses confirmed that, of previously determined PAH-degraders in the bioreactor, only Ralstonia-type organisms increased in response to enrichment, accounting for 89% of the additional bacterial 16S rRNA genes resulting from phthalate enrichment. These findings indicate that phthalate amendment of this particular PAH-contaminated soil did not significantly enrich for organisms associated with high molecular weight PAH degradation or have any significant effect on overall degradation of native PAH in the soil.
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Affiliation(s)
- David R Singleton
- Department of Environmental Sciences and Engineering, School of Public Health, University of North Carolina, Chapel Hill, NC 27599, USA.
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Günther S, Geyer W, Harms H, Müller S. Fluorogenic surrogate substrates for toluene-degrading bacteria—Are they useful for activity analysis? J Microbiol Methods 2007; 70:272-83. [PMID: 17559957 DOI: 10.1016/j.mimet.2007.04.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2007] [Revised: 04/25/2007] [Accepted: 04/25/2007] [Indexed: 11/19/2022]
Abstract
Cultivated bacterial toluene degraders use one or several of four described pathways for the aerobic degradation of this priority groundwater contaminant. To be able to identify un-cultivated toluene-degrading bacteria within enriched or natural consortia, we attempted to develop a set of staining techniques that invariably label toluene-degrading bacteria while differentiating between the different degradation pathways. In the literature, we found suggestions for pathway-specific labels of individual cells that rely on the conversion of toluene surrogates into specific colored and fluorescent products. These surrogate substrates were phenylacetylene (PA), cinnamonitrile, 3-hydroxyphenylacetylene (3-HPA), and indole. We were able to confirm that the chromogenic reactions reliably verified the pathway-specific reactions of well-characterized toluene-degrading bacterial species. However, it was most surprising to find out that three (PA, 3-HPA and cinnamonitrile) of the four supplied surrogate substrates did not lead to any product fluorescence above the cultures' autofluorescence, neither inside of cells nor in supernatants. More disturbingly, the original surrogate compound 3-HPA was inherently fluorescent and found to stain cells at intensities that depended on their states in the cell cycle. Indoxyl originating from the surrogate substrate indole was the only fluorescent product that was formed. It was detected intracellularly when the cells were sealed with para-formaldehyde, but its appearance was unrelated to the presence of expressed toluene degradation pathways. These findings were scrutinized by fluorescence spectroscopy, fluorescence microscopy, and flow cytometry. Activity and growth of the test bacteria were determined by analyzing chromosome numbers and membrane integrity. Our results contradict literature reports that propose the surrogate fluorogenic substrates for the identification of toluene degraders and the identification of specific pathways used by them.
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Affiliation(s)
- Susanne Günther
- UFZ, Helmholtz-Centre for Environmental Research, Department of Environmental Microbiology, Permoserstrasse 15, 04318 Leipzig, Germany
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van Herwijnen R, Joffe B, Ryngaert A, Hausner M, Springael D, Govers HAJ, Wuertz S, Parsons JR. Effect of bioaugmentation and supplementary carbon sources on degradation of polycyclic aromatic hydrocarbons by a soil-derived culture. FEMS Microbiol Ecol 2006; 55:122-35. [PMID: 16420621 DOI: 10.1111/j.1574-6941.2005.00001.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The degradation of polycyclic aromatic hydrocarbons (PAHs) by an undefined culture obtained from a PAH-polluted soil and the same culture bioaugmented with three PAH-degrading strains was studied in carbon-limited chemostat cultures. The PAHs were degraded efficiently by the soil culture and bioaugmentation did not significantly improve the PAH degrading performance. The presence of PAHs did, however, influence the bacterial composition of the bioaugmented and non-bioaugmented soil cultures, resulting in the increase in cell concentration of sphingomonad strains. the initial enhancement of the degradation of the PAHs by biostimulation gradually disappeared and only the presence of salicylate in the additional carbon sources had a lasting slightly stimulating effect on the degradation of phenanthrene. The results suggest that bioaugmentation and biostimulation have limited potential to enhance PAH bioremediation by culture already proficient in the degradation of such contaminants.
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Affiliation(s)
- René van Herwijnen
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
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Vacca DJ, Bleam WF, Hickey WJ. Isolation of soil bacteria adapted to degrade humic acid-sorbed phenanthrene. Appl Environ Microbiol 2005; 71:3797-805. [PMID: 16000791 PMCID: PMC1169045 DOI: 10.1128/aem.71.7.3797-3805.2005] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The goal of these studies was to determine how sorption by humic acids affected the bioavailability of polynuclear aromatic hydrocarbons (PAHs) to PAH-degrading microbes. Micellar solutions of humic acid were used as sorbents, and phenanthrene was used as a model PAH. Enrichments from PAH-contaminated soils established with nonsorbed phenanthrene yielded a total of 25 different isolates representing a diversity of bacterial phylotypes. In contrast, only three strains of Burkholderia spp. and one strain each of Delftia sp. and Sphingomonas sp. were isolated from enrichments with humic acid-sorbed phenanthrene (HASP). Using [14C]phenanthrene as a radiotracer, we verified that only HASP isolates were capable of mineralizing HASP, a phenotype hence termed "competence." Competence was an all-or-nothing phenotype: noncompetent strains showed no detectable phenanthrene mineralization in HASP cultures, but levels of phenanthrene mineralization effected by competent strains in HASP and NSP cultures were not significantly different. Levels and rates of phenanthrene mineralization exceeded those predicted to be supported solely by the metabolism of phenanthrene in the aqueous phase of HASP cultures. Thus, competent strains were able to directly access phenanthrene sorbed by the humic acids and did not rely on desorption for substrate uptake. To the best of our knowledge, this is the first report of (i) a selective interaction between aerobic bacteria and humic acid molecules and (ii) differential bioavailability to bacteria of PAHs sorbed to a natural biogeopolymer.
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Affiliation(s)
- D J Vacca
- Department of Soil Science, University of Wisconsin-Madison, Madison, WI 53706-1299, USA.
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López Z, Vila J, Minguillón C, Grifoll M. Metabolism of fluoranthene by Mycobacterium sp. strain AP1. Appl Microbiol Biotechnol 2005; 70:747-56. [PMID: 16133330 DOI: 10.1007/s00253-005-0120-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2005] [Revised: 07/19/2005] [Accepted: 07/25/2005] [Indexed: 10/25/2022]
Abstract
The pyrene-degrading Mycobacterium strain AP1 was found to utilize fluoranthene as a sole source of carbon and energy. Identification of metabolites formed from fluoranthene (by growing cells and washed-cell suspensions), the kinetics of metabolite accumulation, and metabolite-feeding studies all indicated that strain AP1 oxidizes fluoranthene using three alternative routes. The first route is initiated by dioxygenation at C-7 and C-8 and, following meta cleavage and pyruvate release, produces a hydroxyacenaphthoic acid that is decarboxylated to acenaphthenone (V). Monooxygenation of this ketone to the quinone and subsequent hydrolysis generates naphthalene-1,8-dicarboxylic acid (IV), which is further degraded via benzene-1,2,3-tricarboxylic acid (III). A second route involves dioxygenation at C-1 and C-2, followed by dehydrogenation and meta cleavage of the resulting diol. A two-carbon fragment excision of the meta cleavage product yields 9-fluorenone-1-carboxylic acid (II), which appears to undergo angular dioxygenation and further degradation to produce benzene-1,2,3-tricarboxylic acid (III), merging this route with the 7,8-dioxygenation route. Decarboxylation of benzene-1,2,3-tricarboxylic acid to phthalate (VIII), as well as further oxidation of the latter, would connect both routes with the central metabolism. The identification of Z-9-carboxymethylenefluorene-1-carboxylic acid (I) suggests a third route for fluoranthene degradation involving dioxygenation at C-2, C-3, and ortho cleavage. There is no evidence of any further degradation of this compound.
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Affiliation(s)
- Zaira López
- Departament de Microbiologia, Universitat de Barcelona, Diagonal 645, 08028, Barcelona, Spain
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Pieper DH, Martins dos Santos VAP, Golyshin PN. Genomic and mechanistic insights into the biodegradation of organic pollutants. Curr Opin Biotechnol 2005; 15:215-24. [PMID: 15193329 DOI: 10.1016/j.copbio.2004.03.008] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Several new methodologies have enabled recent studies on the microbial biodegradation mechanisms of organic pollutants. Culture-independent techniques for analysis of the genetic and metabolic potential of natural and model microbial communities that degrade organic pollutants have identified new metabolic pathways and enzymes for aerobic and anaerobic degradation. Furthermore, structural studies of the enzymes involved have revealed the specificities and activities of key catabolic enzymes, such as dioxygenases. Genome sequencing of several biodegradation-relevant microorganisms have provided the first whole-genome insights into the genetic background of the metabolic capability and biodegradation versatility of these organisms. Systems biology approaches are still in their infancy, but are becoming increasingly helpful to unravel, predict and quantify metabolic abilities within particular organisms or microbial consortia.
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Affiliation(s)
- Dietmar H Pieper
- Division of Microbiology, German Research Centre for Biotechnology, Mascheroder Weg 1, Braunschweig, Germany
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Foght J. Chapter 5 Whole-cell bio-processing of aromatic compounds in crude oil and fuels. STUDIES IN SURFACE SCIENCE AND CATALYSIS 2004. [DOI: 10.1016/s0167-2991(04)80146-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
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Aitken MD, Long TC. Biotransformation, Biodegradation, and Bioremediation of Polycyclic Aromatic Hydrocarbons. SOIL BIOLOGY 2004. [DOI: 10.1007/978-3-662-06066-7_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Herwijnen R, Sande BF, Wielen FW, Springael D, Govers HA, Parsons JR. Influence of phenanthrene and fluoranthene on the degradation of fluorene and glucose by Sphingomonas sp. strain LB126 in chemostat cultures. FEMS Microbiol Ecol 2003; 46:105-11. [DOI: 10.1016/s0168-6496(03)00202-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Wick LY, Pelz O, Bernasconi SM, Andersen N, Harms H. Influence of the growth substrate on ester-linked phospho- and glycolipid fatty acids of PAH-degrading Mycobacterium sp. LB501T. Environ Microbiol 2003; 5:672-80. [PMID: 12871234 DOI: 10.1046/j.1462-2920.2003.00455.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The influences of poorly water-soluble anthracene on ester-linked phospholipid fatty acid (PLFA) and glycolipid fatty acid (GLFA) profiles of Mycobacterium sp. LB501T were studied. Bacteria were cultivated on either anthracene or glucose (one culture with successively amended small doses of this substrate and one with excess concentrations) to distinguish between influences of the chemical structure and the bioavailability of the growth substrate. Results revealed that GLFA and PLFA profiles of M. sp. LB501T depended on the availability and the structure of the carbon source. Fatty acid profiles obtained with anthracene differed from those obtained with excess glucose. They were interpreted as a specific adaptation to this poorly bioavailable polycyclic aromatic hydrocarbon (PAH). In contrast, profiles obtained with low glucose concentrations showed clear signs of starvation stress. Stable carbon isotopic ratios (delta13C) of GLFA and PLFA of M. sp. LB501T were analysed to characterize the 13C-fractionation during the biosynthesis of individual fatty acids and to evaluate their value as markers for substrate usage. Although the delta13C values of PLFA and GLFA showed differential isotope fractionation during anthracene- and glucose-degradation, they were sufficiently distinct to be used as signatures of bacterial substrate usage.
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Affiliation(s)
- Lukas Y Wick
- Swiss Federal Institute of Technology Lausanne (EPFL), ENAC/ISTE-Laboratory of Soil Science, CH-1015 Lausanne, Switzerland.
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van Herwijnen R, Wattiau P, Bastiaens L, Daal L, Jonker L, Springael D, Govers HAJ, Parsons JR. Elucidation of the metabolic pathway of fluorene and cometabolic pathways of phenanthrene, fluoranthene, anthracene and dibenzothiophene by Sphingomonas sp. LB126. Res Microbiol 2003; 154:199-206. [PMID: 12706509 DOI: 10.1016/s0923-2508(03)00039-1] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The metabolic pathway of the PAH fluorene and the cometabolic pathway of the PAHs phenanthrene, fluoranthene, anthracene and dibenzothiophene in Sphingomonas sp. LB126 were examined. To our knowledge this is the first study on the cometabolic degradation of the three-ring PAHs phenanthrene, anthracene and the four-ring PAH fluoranthene by a fluorene-utilizing species. Metabolism of fluorene was shown to proceed via the 9-fluorenone pathway to form o-phthalic acid and protocatechuic acid. The cometabolic mono-hydroxylation found for phenanthrene, fluoranthene and anthracene shows similarity with the hydroxylation of fluorene. Several mono- and dihydroxy products and ring-cleavage products were identified for phenanthrene, fluoranthene and anthracene. It appeared that the cometabolism of those three compounds is a non-specific process, in contrast to the metabolism of fluorene. For dibenzothiophene the metabolites dibenzothiophene-5-oxide and dibenzothiophene-5,5-dioxide were identified; these compounds appeared to be the products of a dead-end pathway. Since apart from dibenzothiophene no metabolites were found in very high concentrations for any of the other substrates, complete degradation is suggested, even for the cometabolic degradation of phenanthrene, fluoranthene and anthracene.
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Affiliation(s)
- René van Herwijnen
- University of Amsterdam, Department of Environmental and Toxicological Chemistry (IBED-MTC), Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands
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