1
|
Huang Y, Li L, Yin X, Zhang T. Polycyclic aromatic hydrocarbon (PAH) biodegradation capacity revealed by a genome-function relationship approach. ENVIRONMENTAL MICROBIOME 2023; 18:39. [PMID: 37122013 PMCID: PMC10150532 DOI: 10.1186/s40793-023-00497-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/26/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Polycyclic aromatic hydrocarbon (PAH) contamination has been a worldwide environmental issue because of its impact on ecosystems and human health. Biodegradation plays an important role in PAH removal in natural environments. To date, many PAH-degrading strains and degradation genes have been reported. However, a comprehensive PAH-degrading gene database is still lacking, hindering a deep understanding of PAH degraders in the era of big data. Furthermore, the relationships between the PAH-catabolic genotype and phenotype remain unclear. RESULTS Here, we established a bacterial PAH-degrading gene database and explored PAH biodegradation capability via a genome-function relationship approach. The investigation of functional genes in the experimentally verified PAH degraders indicated that genes encoding hydratase-aldolase could serve as a biomarker for preliminarily identifying potential degraders. Additionally, a genome-centric interpretation of PAH-degrading genes was performed in the public genome database, demonstrating that they were ubiquitous in Proteobacteria and Actinobacteria. Meanwhile, the global phylogenetic distribution was generally consistent with the culture-based evidence. Notably, a few strains affiliated with the genera without any previously known PAH degraders (Hyphomonas, Hoeflea, Henriciella, Saccharomonospora, Sciscionella, Tepidiphilus, and Xenophilus) also bore a complete PAH-catabolic gene cluster, implying their potential of PAH biodegradation. Moreover, a random forest analysis was applied to predict the PAH-degrading trait in the complete genome database, revealing 28 newly predicted PAH degraders, of which nine strains encoded a complete PAH-catabolic pathway. CONCLUSIONS Our results established a comprehensive PAH-degrading gene database and a genome-function relationship approach, which revealed several potential novel PAH-degrader lineages. Importantly, this genome-centric and function-oriented approach can overcome the bottleneck of conventional cultivation-based biodegradation research and substantially expand our current knowledge on the potential degraders of environmental pollutants.
Collapse
Affiliation(s)
- Yue Huang
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Liguan Li
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xiaole Yin
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
| |
Collapse
|
2
|
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]
|
3
|
Kosek K, Kozioł K, Luczkiewicz A, Jankowska K, Chmiel S, Polkowska Ż. Environmental characteristics of a tundra river system in Svalbard. Part 2: Chemical stress factors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 653:1585-1596. [PMID: 30446169 DOI: 10.1016/j.scitotenv.2018.11.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/01/2018] [Accepted: 11/01/2018] [Indexed: 06/09/2023]
Abstract
Bacterial communities in the Arctic environment are subject to multiple stress factors, including contaminants, although typically their concentrations are small. The Arctic contamination research has focused on persistent organic pollutants (POPs) because they are bioaccumulative, resistant to degradation and toxic for all organisms. Pollutants have entered the Arctic predominantly by atmospheric and oceanic long-range transport, and this was facilitated by their volatile or semi-volatile properties, while their chemical stability extended their lifetimes following emission. Chemicals present in the Arctic at detectable and quantifiable concentrations testify to their global impact. Chemical contamination may induce serious disorders in the integrity of polar ecosystems influencing the growth of bacterial communities. In this study, the abundance and the types of bacteria in the Arctic freshwater were examined and the microbial characteristics were compared to the amount of potentially harmful chemical compounds in particular elements of the Arctic catchment. The highest concentrations of all determined PAHs were observed in two samples in the vicinity of the estuary both in June and September 2016 and were 1964 ng L-1 (R12) and 3901 ng L-1 (R13) in June, and 2179 ng L-1 (R12) and 1349 ng L-1 (R13) in September. Remarkable concentrations of the sum of phenols and formaldehyde were detected also at the outflow of the Revelva river into the sea (R12) and were 0.24 mg L-1 in June and 0.35 mg L-1 in September 2016. The elevated concentrations of chemical compounds near the estuary suggest a potential impact of the water from the lower tributaries (including the glacier-fed stream measured at R13) or the sea currents and the sea aerosol as pollutant sources. The POPs' degradation at low temperature is not well understood but bacteria capable to degrading such compounds were noted in each sampling point.
Collapse
Affiliation(s)
- Klaudia Kosek
- Department of Analytical Chemistry, Faculty of Chemistry, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland
| | - Krystyna Kozioł
- Institute of Geography, Faculty of Geography and Biology, Pedagogical University in Cracow, Podchorążych 2, Cracow 30-084, Poland; Institute of Geophysics, Polish Academy of Sciences, 64 Księcia Janusza St., Warsaw 01-452, Poland
| | - Aneta Luczkiewicz
- Department of Water and Waste-Water Technology, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland
| | - Katarzyna Jankowska
- Department of Water and Waste-Water Technology, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland
| | - Stanisław Chmiel
- Faculty of Earth Sciences and Spatial Management, Maria Curie-Skłodowska University, 2 C-D Kraśnicka Ave., Lublin 20-718, Poland
| | - Żaneta Polkowska
- Department of Analytical Chemistry, Faculty of Chemistry, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland.
| |
Collapse
|
4
|
Muthu M, Ophir Y, Macdonald LJ, Vaidya A, Lloyd-Jones G. Versatile catechol dioxygenases in Sphingobium scionense WP01 T. Antonie van Leeuwenhoek 2018; 111:2293-2301. [PMID: 29959655 DOI: 10.1007/s10482-018-1120-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/22/2018] [Indexed: 11/29/2022]
Abstract
The objective was to understand the roles of multiple catechol dioxygenases in the type strain Sphingobium scionense WP01T (Liang and Lloyd-Jones in Int J Syst Evol Microbiol 60:413-416, 2010a) that was isolated from severely contaminated sawmill soil. The dioxygenases were identified by sequencing, examined by determining the substrate specificities of the recombinant enzymes, and by quantifying gene expression following exposure to model priority pollutants. Catechol dioxygenase genes encoding an extradiol xylE and two intradiol dioxygenases catA and clcA that are highly similar to sequences described in other sphingomonads are described in S. scionense WP01T. The distinct substrate specificities determined for the recombinant enzymes confirm the annotated gene functions and suggest different catabolic roles for each enzyme. The role of the three enzymes was evaluated by analysis of enzyme activity in crude cell extracts from cells grown on meta-toluate, benzoate, biphenyl, naphthalene and phenanthrene which revealed the co-induction of each enzyme by different substrates. This was corroborated by quantifying gene expression when cells were induced by biphenyl, naphthalene and pentachlorophenol. It is concluded that the ClcA and XylE enzymes are recruited in pathways that are involved in the degradation of chlorinated aromatic compounds such as pentachlorophenol, the XylE and ClcA enzymes will also play a role in degradation pathways that produce alkylcatechols, while the three enzymes ClcA, XylE and CatA will be simultaneously involved in pathways that generate catechol as a degradation pathway intermediate.
Collapse
Affiliation(s)
- Muralidharan Muthu
- Scion, Te Papa Tipu Innovation Park, 49 Sala Street, Private Bag 3020, Rotorua, 3046, New Zealand
| | - Yakir Ophir
- Scion, Te Papa Tipu Innovation Park, 49 Sala Street, Private Bag 3020, Rotorua, 3046, New Zealand.,IBR, Ness Ziona, Israel
| | - Lucy J Macdonald
- Scion, Te Papa Tipu Innovation Park, 49 Sala Street, Private Bag 3020, Rotorua, 3046, New Zealand
| | - Alankar Vaidya
- Scion, Te Papa Tipu Innovation Park, 49 Sala Street, Private Bag 3020, Rotorua, 3046, New Zealand
| | - Gareth Lloyd-Jones
- Scion, Te Papa Tipu Innovation Park, 49 Sala Street, Private Bag 3020, Rotorua, 3046, New Zealand.
| |
Collapse
|
5
|
Yan S, Wu G. Reorganization of gene network for degradation of polycyclic aromatic hydrocarbons (PAHs) in Pseudomonas aeruginosa PAO1 under several conditions. J Appl Genet 2017; 58:545-563. [PMID: 28685384 PMCID: PMC5655620 DOI: 10.1007/s13353-017-0402-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 05/22/2017] [Accepted: 06/06/2017] [Indexed: 01/05/2023]
Abstract
Although polycyclic aromatic hydrocarbons (PAHs) are harmful to human health, their elimination from the environment is not easy. Biodegradation of PAHs is promising since many bacteria have the ability to use hydrocarbons as their sole carbon and energy sources for growth. Of various microorganisms that can degrade PAHs, Pseudomonas aeruginosa is particularly important, not only because it causes a series of diseases including infection in cystic fibrosis patients, but also because it is a model bacterium in various studies. The genes that are responsible for degrading PAHs have been identified in P. aeruginosa, however, no gene acts alone as various stresses often initiate different metabolic pathways, quorum sensing, biofilm formation, antibiotic tolerance, etc. Therefore, it is important to study how PAH degradation genes behave under different conditions. In this study, we apply network analysis to investigating how 46 PAH degradation genes reorganized among 5549 genes in P. aeruginosa PAO1 under nine different conditions using publicly available gene coexpression data from GEO. The results provide six aspects of novelties: (i) comparing the number of gene clusters before and after stresses, (ii) comparing the membership in each gene cluster before and after stresses, (iii) defining which gene changed its membership together with PAH degradation genes before and after stresses, (iv) classifying membership-changed-genes in terms of category in Pseudomonas Genome Database, (v) postulating unknown gene’s function, and (vi) proposing new mechanisms for genes of interests. This study can shed light on understanding of cooperative mechanisms of PAH degradation from the level of entire genes in an organism, and paves the way to conduct the similar studies on other genes.
Collapse
Affiliation(s)
- Shaomin Yan
- Bioscience and Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China
| | - Guang Wu
- Bioscience and Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China.
| |
Collapse
|
6
|
Duarte M, Jauregui R, Vilchez-Vargas R, Junca H, Pieper DH. AromaDeg, a novel database for phylogenomics of aerobic bacterial degradation of aromatics. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau118. [PMID: 25468931 PMCID: PMC4250580 DOI: 10.1093/database/bau118] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Understanding prokaryotic transformation of recalcitrant pollutants and the in-situ metabolic nets require the integration of massive amounts of biological data. Decades of biochemical studies together with novel next-generation sequencing data have exponentially increased information on aerobic aromatic degradation pathways. However, the majority of protein sequences in public databases have not been experimentally characterized and homology-based methods are still the most routinely used approach to assign protein function, allowing the propagation of misannotations. AromaDeg is a web-based resource targeting aerobic degradation of aromatics that comprises recently updated (September 2013) and manually curated databases constructed based on a phylogenomic approach. Grounded in phylogenetic analyses of protein sequences of key catabolic protein families and of proteins of documented function, AromaDeg allows query and data mining of novel genomic, metagenomic or metatranscriptomic data sets. Essentially, each query sequence that match a given protein family of AromaDeg is associated to a specific cluster of a given phylogenetic tree and further function annotation and/or substrate specificity may be inferred from the neighboring cluster members with experimentally validated function. This allows a detailed characterization of individual protein superfamilies as well as high-throughput functional classifications. Thus, AromaDeg addresses the deficiencies of homology-based protein function prediction, combining phylogenetic tree construction and integration of experimental data to obtain more accurate annotations of new biological data related to aerobic aromatic biodegradation pathways. We pursue in future the expansion of AromaDeg to other enzyme families involved in aromatic degradation and its regular update. Database URL:http://aromadeg.siona.helmholtz-hzi.de
Collapse
Affiliation(s)
- Márcia Duarte
- Microbial Interactions and Processes Research Group, HZI-Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany, Research Group Microbial Ecology, Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen. Carrera 5 No. 66A-35, Bogotá, Colombia and Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada-UMNG, Campus Cajicá, Bogotá DC, Colombia
| | - Ruy Jauregui
- Microbial Interactions and Processes Research Group, HZI-Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany, Research Group Microbial Ecology, Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen. Carrera 5 No. 66A-35, Bogotá, Colombia and Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada-UMNG, Campus Cajicá, Bogotá DC, Colombia Microbial Interactions and Processes Research Group, HZI-Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany, Research Group Microbial Ecology, Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen. Carrera 5 No. 66A-35, Bogotá, Colombia and Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada-UMNG, Campus Cajicá, Bogotá DC, Colombia
| | - Ramiro Vilchez-Vargas
- Microbial Interactions and Processes Research Group, HZI-Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany, Research Group Microbial Ecology, Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen. Carrera 5 No. 66A-35, Bogotá, Colombia and Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada-UMNG, Campus Cajicá, Bogotá DC, Colombia
| | - Howard Junca
- Microbial Interactions and Processes Research Group, HZI-Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany, Research Group Microbial Ecology, Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen. Carrera 5 No. 66A-35, Bogotá, Colombia and Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada-UMNG, Campus Cajicá, Bogotá DC, Colombia Microbial Interactions and Processes Research Group, HZI-Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany, Research Group Microbial Ecology, Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen. Carrera 5 No. 66A-35, Bogotá, Colombia and Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada-UMNG, Campus Cajicá, Bogotá DC, Colombia
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, HZI-Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany, Research Group Microbial Ecology, Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen. Carrera 5 No. 66A-35, Bogotá, Colombia and Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada-UMNG, Campus Cajicá, Bogotá DC, Colombia
| |
Collapse
|
7
|
Izmalkova TY, Sazonova OI, Kosheleva IA, Boronin AM. Phylogenetic analysis of the genes for naphthalene and phenanthrene degradation in Burkholderia sp. strains. RUSS J GENET+ 2013. [DOI: 10.1134/s1022795413060033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
8
|
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.
Collapse
Affiliation(s)
- Somnath Mallick
- Department of Chemistry, Saldiha College, Bankura, West Bengal, India
| | | | | |
Collapse
|
9
|
Brennerova MV, Josefiova J, Brenner V, Pieper DH, Junca H. Metagenomics reveals diversity and abundance of meta-cleavage pathways in microbial communities from soil highly contaminated with jet fuel under air-sparging bioremediation. Environ Microbiol 2009; 11:2216-27. [PMID: 19575758 PMCID: PMC2784041 DOI: 10.1111/j.1462-2920.2009.01943.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The extradiol dioxygenase diversity of a site highly contaminated with aliphatic and aromatic hydrocarbons under air-sparging treatment was assessed by functional screening of a fosmid library in Escherichia coli with catechol as substrate. The 235 positive clones from inserts of DNA extracted from contaminated soil were equivalent to one extradiol dioxygenase-encoding gene per 3.6 Mb of DNA screened, indicating a strong selection for genes encoding this function. Three subfamilies were identified as being predominant, with 72, 55 and 43 fosmid inserts carrying genes, related to those encoding TbuE of Ralstonia pickettii PK01 (EXDO-D), IpbC of Pseudomonas sp. JR1 (EXDO-K2) or DbtC of Burkholderia sp. DBT1 (EXDO-Dbt), respectively, whereas genes encoding enzymes related to XylE of Pseudomonas putida mt-2 were not observed. Genes encoding oxygenases related to isopropylbenzene dioxygenases were usually colocalized with genes encoding EXDO-K2 dioxygenases. Functional analysis of representative proteins indicated a subcluster of EXDO-D proteins to show exceptional high affinity towards different catecholic substrates. Based on Vmax/Km specificity constants, a task-sharing between different extradiol dioxygenases in the community of the contaminated site can be supposed, attaining a complementary and community-balanced catalytic power against diverse catecholic derivatives, as necessary for effective degradation of mixtures of aromatics.
Collapse
Affiliation(s)
- Maria V Brennerova
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic.
| | | | | | | | | |
Collapse
|
10
|
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.
Collapse
|
11
|
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.
Collapse
Affiliation(s)
- Ri-He Peng
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | | | | | | | | | | | | | | |
Collapse
|
12
|
Zhao HP, Wang L, Ren JR, Li Z, Li M, Gao HW. Isolation and characterization of phenanthrene-degrading strains Sphingomonas sp. ZP1 and Tistrella sp. ZP5. JOURNAL OF HAZARDOUS MATERIALS 2008; 152:1293-300. [PMID: 17850962 DOI: 10.1016/j.jhazmat.2007.08.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2007] [Revised: 06/19/2007] [Accepted: 08/02/2007] [Indexed: 05/15/2023]
Abstract
Two bacteria strains Sphingomonas sp. strain ZP1 and Tistrella sp. strain ZP5 were identified as phenanthrene-degrading ones, based on Gram staining, oxydase reaction, biochemical tests, FAME analysis, G+C content and 16S rDNA gene sequence analysis. We isolated these two bacteria strains Sphingomonas sp. ZP1 and Tistrella sp. ZP5 from soil samples contaminated with polycyclic aromatic hydrocarbon (PAH)-containing waste from oil refinery field in Shanghai, China. Strain Sphingomonas sp. ZP1 was able to degrade naphthalene, phenanthrene, toluene, methanol and ethanol, salicylic acid and Tween 80. Moreover, it can remove nearly all the phenanthrene at 0.025% concentration in 8 days. Strain Tistrella sp. ZP5 cannot degrade phenanthrene individually but it can increase the speed of phenanthrene degradation together with ZP1. The growth conditions of strain Sphingomonas sp. ZP1 were optimized. The result also indicated that the degradation rate of phenanthrene ranged from 250 to 1000 ppm with strain ZP1 remained nearly the same, i.e., a high concentration of phenanthrene did not inhibit both the growth of microbial strains and the phenanthrene-degradation ability. Besides, the effect of non-ionic surfactants such as Brij 30, Triton X-100 and Tween 80 on the phenanthrene degradation was determined. Such two strains may be useful for bioremediation applications.
Collapse
Affiliation(s)
- He-Ping Zhao
- State Key Laboratory of Pollution Control and Resources Reuse, Tongji University, Shanghai 200092, China
| | | | | | | | | | | |
Collapse
|
13
|
Kasuga I, Nakajima F, Furumai H. Diversity of catechol 2,3-dioxygenase genes of bacteria responding to dissolved organic matter derived from different sources in a eutrophic lake. FEMS Microbiol Ecol 2007; 61:449-58. [PMID: 17645532 DOI: 10.1111/j.1574-6941.2007.00347.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Catechol 2,3-dioxygenase (C23O) is an extradiol dioxygenase that plays an important role in degrading aromatic compounds such as those found at polluted sites. However, little is known about the diversity of C23O genes in unpolluted environments. In such environments, various factors, including the quality and quantity of dissolved organic matter (DOM), could influence the composition and behaviour of bacterial community possessing C230 genes. We investigated C23O genes in bacteria responding to DOM from various sources in a eutrophic lake by PCR and cloning. Six microcosms filled with lake water containing indigenous bacteria and DOM from different sources were incubated for 10 days. After 1 or 2 days of incubation, C23O genes were detected in the microcosms enriched with DOM recovered from inflow river water and humus from reed grass. The sequences were very diverse but had features conserved in extradiol dioxygenases. The clone libraries generated on day 2 showed distinctive compositions among microcosms, indicating that bacteria possessing a variety of C23O genes responded differently to DOM from different sources. After 10 days of incubation, C23O genes in a previously unidentified gene cluster, 'Cluster X', became dominant in the libraries.
Collapse
Affiliation(s)
- Ikuro Kasuga
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.
| | | | | |
Collapse
|
14
|
Lui P, Zhang CK. Detection and quantification of phnE gene from oil-contaminated soil samples by competitive quantitative PCR. Microbiol Res 2006; 162:335-40. [PMID: 16563713 DOI: 10.1016/j.micres.2006.01.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2006] [Indexed: 10/24/2022]
Abstract
The phnE gene encoding catechol 2,3-dioxygenase belonging to the meta-cleavage pathway was selected as the marker gene and was detected and quantified from soil samples by competitive quantitative PCR. A PCR primer pair was designed based on the phnE gene to amplify the target DNA bands and competitor DNA bands. The phnE gene was detected in two samples of three. In samples S1 and S2, the phnE gene copy number was 6.2 x 10(7)/g soil and 5.8 x 10(7)/g soil, respectively. But no phnE gene was detected in sample S3. The target DNA bands were extracted and expressed. The results confirmed that the target DNA bands were the native phnE genes.
Collapse
Affiliation(s)
- Peng Lui
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | | |
Collapse
|
15
|
Xia Y, Min H, Rao G, Lv ZM, Liu J, Ye YF, Duan XJ. Isolation and characterization of phenanthrene-degrading Sphingomonas paucimobilis strain ZX4. Biodegradation 2005; 16:393-402. [PMID: 15865153 DOI: 10.1007/s10532-004-2412-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Phenanthrene-degrading bacterium strain ZX4 was isolated from an oil-contaminated soil, and identified as Sphingomonas paucimobilis based on 16S rDNA sequence, cellular fatty acid composition, mol% G + C and Biolog-GN tests. Besides phenanthrene, strain ZX4 could also utilize naphthalene, fluorene and other aromatic compounds. The growth on salicylic acid and catechol showed that the strain degraded phenanthrene via salicylate pathway, while the assay of catechol 2,3-dioxygenase revealed catechol could be metabolized through meta-cleavage pathway. Three genes, including two of meta-cleavage operon genes and one of GST encoding gene were obtained. The order of genes arrangement was similar to S-type metapathway operons. The phylogenetic trees based on 16S rDNA sequence and meta-pathway gene both revealed that strain ZX4 is clustered with strains from genus Sphingomonas.
Collapse
Affiliation(s)
- Ying Xia
- College of Life Sciences, Zhejiang University, 268 Kaixuan Road, Hangzhou, 310029, China
| | | | | | | | | | | | | |
Collapse
|
16
|
Pinyakong O, Habe H, Yoshida T, Nojiri H, Omori T. Identification of three novel salicylate 1-hydroxylases involved in the phenanthrene degradation of Sphingobium sp. strain P2. Biochem Biophys Res Commun 2003; 301:350-7. [PMID: 12565867 DOI: 10.1016/s0006-291x(02)03036-x] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Five sets of large and small subunits of terminal oxygenase (ahdA1[a-e] and ahdA2[a-e]) and a single gene set encoding ferredoxin (ahdA3) and ferredoxin reductase (ahdA4) were found to be scattered through 15.8- and 14-kb DNA fragments of phenanthrene-degrading Sphingobium sp. strain P2. RT-PCR analysis indicated the inducible and specific expression of ahdA3, ahdA4, and three sets of genes for terminal oxygenase (ahdA1[c-e] and ahdA2[c-e]) in this strain grown on phenanthrene. The biotransformation experiments with resting cells of Escherichia coli JM109 harboring recombinant ahd genes revealed that AhdA2cA1c, AhdA1dA2d, and AhdA1eA2e can all function as a salicylate 1-hydroxylase which converts salicylate, a metabolic intermediate of phenanthrene, to catechol in cooperation with the electron transport proteins AhdA3A4. The first two oxygenases exhibited a broad range of substrate specificities such that they also catalyzed the hydroxylation of methyl- and chloro-substituted salicylates to produce their corresponding substituted catechols.
Collapse
Affiliation(s)
- Onruthai Pinyakong
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | | | | | | | | |
Collapse
|
17
|
Kang H, Hwang SY, Kim YM, Kim E, Kim YS, Kim SK, Kim SW, Cerniglia CE, Shuttleworth KL, Zylstra GJ. Degradation of phenanthrene and naphthalene by a Burkholderia species strain. Can J Microbiol 2003; 49:139-44. [PMID: 12718402 DOI: 10.1139/w03-009] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Burkholderia sp. TNFYE-5 was isolated from soil for the ability to grow on phenanthrene as sole carbon and energy source. Unlike most other phenanthrene-degrading bacteria, TNFYE-5 was unable to grow on naphthalene. Growth substrate range experiments coupled with the ring-cleavage enzyme assay data suggest that TNFYE-5 initially metabolizes phenanthrene to 1-hydroxy-2-naphthoate with subsequent degradation through the phthalate and protocatechuate and beta-ketoadipate pathway. A metabolite in the degradation of naphthalene by TNFYE-5 was isolated by high-pressure liquid chromatography (HPLC) and was identified as salicylate by UV-visible spectral and gas chromatography-mass spectrometry analyses. Thus, the inability to degrade salicylate is apparently one major reason for the incapability of TNFYE-5 to grow on naphthalene.
Collapse
Affiliation(s)
- H Kang
- Department of Biology and Institute of Life Science, Yonsei University, Seoul 120-749, Korea
| | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Pinyakong O, Habe H, Omori T. The unique aromatic catabolic genes in sphingomonads degrading polycyclic aromatic hydrocarbons (PAHs). J GEN APPL MICROBIOL 2003; 49:1-19. [PMID: 12682862 DOI: 10.2323/jgam.49.1] [Citation(s) in RCA: 135] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Many members of the sphingomonad genus isolated from different geological areas can degrade a wide variety of polycyclic aromatic hydrocarbons (PAHs) and related compounds. These sphingomonads such as Sphingobium yanoikuyae strain B1, Novosphingobium aromaticivorans strain F199, and Sphingobium sp. strain P2 have been found to possess a unique group of genes for aromatic degradation, which are distantly related with those in pseudomonads and other genera reported so far both in sequence homology and gene organization. Genes for aromatics degradation in these sphingomonads are complexly arranged; the genes necessary for one degradation pathway are scattered through several clusters. These aromatic catabolic gene clusters seem to be conserved among many other sphingomonads such as Sphingobium yanoikuyae strain Q1, Sphingomonas paucimobilis strain TNE12, S. paucimobilis strain EPA505, Sphingobium agrestis strain HV3, and Sphingomonas chungbukensis strain DJ77. Furthermore, some genes for naphthalenesulfonate degradation found in Sphingomonas xenophaga strain BN6 also share a high sequence homology with their homologues found in these sphingomonads. On the other hand, protocatechuic catabolic gene clusters found in fluorene-degrading Sphingomonas sp. strain LB126 appear to be more closely related with those previously found in lignin-degrading S. paucimobilis SYK-6 than the genes in this group of sphingomonads. This review summarizes the information on the distribution of these strains and relationships among their aromatic catabolic genes.
Collapse
Affiliation(s)
- Onruthai Pinyakong
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | | | | |
Collapse
|
19
|
Walia S, Shi L, Khan AA, Joshi B, Chaudry GR. Sequence analysis and molecular characterization of a nitrocatechol dioxygenase gene from Pseudomonas putida. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2002; 37:379-391. [PMID: 12081029 DOI: 10.1081/pfc-120004478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A Pseudomonas putida capable of degrading polychlorinated biphenyl was also found to transform 4-nitrocatechol to 3-nitro-2-hydroxy-6-oxohexa-2,4-dienoic acid (NHODA). Crude cell extract of this bacterium exhibited an enzyme (nitrocatechol dioxygenase, Ndo) activity catalyzing this transformation. The gene encoding Ndo was cloned in E. coli. The cloned gene (ndo) expressed in E. coli had enzyme activity that degraded not only 4-nitrocatechol but also 4-chlorocatechol, 4-methylcatechol, 2,3-dihydroxybiphenyl, and 4'-chloro-2,3-dihydroxybiphenyl. Nucleotide sequence analysis of the cloned ndo exhibited an open reading frame of 939 base pairs. This sequence can encode a 313 amino acids protein of approximately molecular weight of 35 kd, which was confirmed by in vitro transcription and translation assay and SDS-PAGE analysis. A putative ribosomal binding site (GAGGAGA) was present 7 base pairs upstream from the AUG start codon and a promotor site homologous to E. coli '-10' and '-35' regulatory region was located at '-123' and '-174' area of our clone with sequences of TTGAAG and GTGACA, respectively. The deduced amino acid sequence showed 69% homology with Cdo from Burkholderia cepacia AAI. A unique insertion of 21 amino acids was found towards the N-terminal of the Ndo. Expression of ndo in strain OU83 was repressed in presence of 3-chlorobenzoic acid as judged by the decrease in the expression of ndo specific transcript.
Collapse
Affiliation(s)
- Satish Walia
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA
| | | | | | | | | |
Collapse
|