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Ines P, Vlasta D, Sanja F, Ana BK, Dubravka H, Fabrice ML, Nikolina UK. Unraveling metabolic flexibility of rhodococci in PCB transformation. CHEMOSPHERE 2021; 282:130975. [PMID: 34111638 DOI: 10.1016/j.chemosphere.2021.130975] [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: 04/01/2021] [Revised: 05/17/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
Even though the genetic attributes suggest presence of multiple degradation pathways, most of rhodococci are known to transform PCBs only via regular biphenyl (bph) pathway. Using GC-MS analysis, we monitored products formed during transformation of 2,4,4'-trichlorobiphenyl (PCB-28), 2,2',5,5'-tetrachlorobiphenyl (PCB-52) and 2,4,3'-trichlorobiphenyl (PCB-25) by previously characterized PCB-degrading rhodococci Z6, T6, R2, and Z57, with the aim to explore their metabolic pleiotropy in PCB transformations. A striking number of different transformation products (TPs) carrying a phenyl ring as a substituent, both those generated as a part of the bph pathway and an array of unexpected TPs, implied a curious transformation ability. We hypothesized that studied rhodococcal isolates, besides the regular one, use at least two alternative pathways for PCB transformation, including the pathway leading to acetophenone formation (via 3,4 (4,5) dioxygenase attack on the molecule), and a third sideway pathway that includes stepwise oxidative decarboxylation of the aliphatic side chain of the 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate. Structure of the identified chlorinated benzoic acids and acetophenones allowed us to hypothesize that the first two pathways were the outcome of a ring-hydroxylating dioxygenase with the ability to attack both the 2,3 (5,6) and the 3,4 (4,5) positions of the biphenyl ring as well as dechlorination activity at both, -ortho and -para positions. We propose that several TPs produced by the bph pathway could have caused the triggering of the third sideway pathway. In conclusion, this study proposed ability of rhodococci to use different strategies in PCB transformation, which allows them to circumvent potential negative aspect of TPs on the overall transformation pathway.
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Affiliation(s)
- Petrić Ines
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Zagreb, Croatia.
| | - Drevenkar Vlasta
- Institute for Medical Research and Occupational Health, Zagreb, Croatia
| | - Fingler Sanja
- Institute for Medical Research and Occupational Health, Zagreb, Croatia
| | | | - Hršak Dubravka
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Zagreb, Croatia
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Garrido-Sanz D, Sansegundo-Lobato P, Redondo-Nieto M, Suman J, Cajthaml T, Blanco-Romero E, Martin M, Uhlik O, Rivilla R. Analysis of the biodegradative and adaptive potential of the novel polychlorinated biphenyl degrader Rhodococcus sp. WAY2 revealed by its complete genome sequence. Microb Genom 2020; 6. [PMID: 32238227 PMCID: PMC7276702 DOI: 10.1099/mgen.0.000363] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The complete genome sequence of Rhodococcus sp. WAY2 (WAY2) consists of a circular chromosome, three linear replicons and a small circular plasmid. The linear replicons contain typical actinobacterial invertron-type telomeres with the central CGTXCGC motif. Comparative phylogenetic analysis of the 16S rRNA gene along with phylogenomic analysis based on the genome-to-genome blast distance phylogeny (GBDP) algorithm and digital DNA–DNA hybridization (dDDH) with other Rhodococcus type strains resulted in a clear differentiation of WAY2, which is likely a new species. The genome of WAY2 contains five distinct clusters of bph, etb and nah genes, putatively involved in the degradation of several aromatic compounds. These clusters are distributed throughout the linear plasmids. The high sequence homology of the ring-hydroxylating subunits of these systems with other known enzymes has allowed us to model the range of aromatic substrates they could degrade. Further functional characterization revealed that WAY2 was able to grow with biphenyl, naphthalene and xylene as sole carbon and energy sources, and could oxidize multiple aromatic compounds, including ethylbenzene, phenanthrene, dibenzofuran and toluene. In addition, WAY2 was able to co-metabolize 23 polychlorinated biphenyl congeners, consistent with the five different ring-hydroxylating systems encoded by its genome. WAY2 could also use n-alkanes of various chain-lengths as a sole carbon source, probably due to the presence of alkB and ladA gene copies, which are only found in its chromosome. These results show that WAY2 has a potential to be used for the biodegradation of multiple organic compounds.
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Affiliation(s)
- Daniel Garrido-Sanz
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, C/ Darwin 2, 28049 Madrid, Spain
| | - Paula Sansegundo-Lobato
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, C/ Darwin 2, 28049 Madrid, Spain
| | - Miguel Redondo-Nieto
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, C/ Darwin 2, 28049 Madrid, Spain
| | - Jachym Suman
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technika 3, 16628 Prague, Czech Republic
| | - Tomas Cajthaml
- Laboratory of Environmental Biotechnology, Institute of Microbiology, Czech Academy of Sciences v.v.i., Vídeňská 1083, 14200 Prague, Czech Republic
| | - Esther Blanco-Romero
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, C/ Darwin 2, 28049 Madrid, Spain
| | - Marta Martin
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, C/ Darwin 2, 28049 Madrid, Spain
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technika 3, 16628 Prague, Czech Republic
| | - Rafael Rivilla
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, C/ Darwin 2, 28049 Madrid, Spain
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Steliga T, Wojtowicz K, Kapusta P, Brzeszcz J. Assessment of Biodegradation Efficiency of Polychlorinated Biphenyls (PCBs) and Petroleum Hydrocarbons (TPH) in Soil Using Three Individual Bacterial Strains and Their Mixed Culture. Molecules 2020; 25:E709. [PMID: 32041368 PMCID: PMC7036857 DOI: 10.3390/molecules25030709] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 01/31/2023] Open
Abstract
Biodegradation is one of the most effective and profitable methods for the elimination of toxic polychlorinated biphenyls (PCBs) and total petroleum hydrocarbons (TPH) from the environment. In this study, aerobic degradation of the mentioned pollutants by bacterial strains Mycolicibacterium frederiksbergense IN53, Rhodococcus erythropolis IN129, and Rhodococcus sp. IN306 and mixed culture M1 developed based on those strains at 1:1:1 ratio was analyzed. The effectiveness of individual strains and of the mixed culture was assessed based on carried out respirometric tests and chromatographic analyses. The Rhodococcus sp. IN306 turned out most effective in terms of 18 PCB congeners biodegradation (54.4%). The biodegradation index was decreasing with an increasing number of chlorine atoms in a molecule. Instead, the Mycolicobacterium frederiksbergense IN53 was the best TPH degrader (37.2%). In a sterile soil, contaminated with PCBs and TPH, the highest biodegradation effectiveness was obtained using inoculation with mixed culture M1, which allowed to reduce both the PCBs (51.8%) and TPH (34.6%) content. The PCBs and TPH biodegradation capacity of the defined mixed culture M1 was verified ex-situ with prism method in a non-sterile soil polluted with aged petroleum hydrocarbons (TPH) and spent transformer oil (PCBs). After inoculation with mixed culture M1, the PCBs were reduced during 6 months by 84.5% and TPH by 70.8% as well as soil toxicity was decreased.
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Affiliation(s)
- Teresa Steliga
- Department of Reservoir Fluid Production Technology, Oil and Gas Institute–National Research Institute, ul. Lubicz 25 A, 31-503 Krakow, Poland;
| | - Katarzyna Wojtowicz
- Department of Reservoir Fluid Production Technology, Oil and Gas Institute–National Research Institute, ul. Lubicz 25 A, 31-503 Krakow, Poland;
| | - Piotr Kapusta
- Department of Microbiology, Oil and Gas Institute-National Research Institute, ul. Lubicz 25 A, 31-503 Krakow, Poland; (P.K.); (J.B.)
| | - Joanna Brzeszcz
- Department of Microbiology, Oil and Gas Institute-National Research Institute, ul. Lubicz 25 A, 31-503 Krakow, Poland; (P.K.); (J.B.)
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Biodegradation and chemotaxis of polychlorinated biphenyls, biphenyls, and their metabolites by Rhodococcus spp. Biodegradation 2017; 29:1-10. [DOI: 10.1007/s10532-017-9809-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/09/2017] [Indexed: 11/26/2022]
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Papale M, Giannarelli S, Francesconi S, Di Marco G, Mikkonen A, Conte A, Rizzo C, De Domenico E, Michaud L, Giudice AL. Enrichment, isolation and biodegradation potential of psychrotolerant polychlorinated-biphenyl degrading bacteria from the Kongsfjorden (Svalbard Islands, High Arctic Norway). MARINE POLLUTION BULLETIN 2017; 114:849-859. [PMID: 27855955 DOI: 10.1016/j.marpolbul.2016.11.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 11/04/2016] [Accepted: 11/10/2016] [Indexed: 06/06/2023]
Abstract
Persistent organic pollutants (POPs), such as polychlorinated biphenyls (PCBs), have been detected in abiotic Arctic matrices: surface sediments and seawater from coastal areas in the Kongsfjorden were collected and analyzed. Levels of PCBs varied depending on the sampling site. Total PCB concentrations were between 11.63 (site C2W) and 27.69pgl-1 (site AW). These levels were comparable to those reported previously in lake sediments from the northern Svalbard. The occurrence and biodegradation potential of cold-adapted PCB-oxidizing bacteria in seawater and sediment along the fjord was also evaluated. After enrichment with biphenyl, 246 isolates were obtained with 45 of them that were able to grow in the presence of the PCB mixture Aroclor 1242, as the sole carbon source. The catabolic gene bphA was harbored by 17 isolates with affiliates to the genera Algoriphagus, Devosia and Salinibacterium that have been never reported as able to utilize PCBs, thus deserving further investigation. The total removal of Aroclor 1242 and selected PCB congeners was evaluated at 4 and 15°C for eight bphA-harboring isolates and Gelidibacter sp. DS-10. With few exceptions, tested strains showed greater efficiency at 15 than at 4°C. Isolates were able to reduce most chromatographic peaks by >50%, with some di- and trichlorobiphenyls that were quite totally removed (>90%).
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Affiliation(s)
- Maria Papale
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (ChiBioFarAm), University of Messina, Messina, Italy
| | - Stefania Giannarelli
- Department of Chemistry and Industrial Chemistry, University of Pisa, Pisa, Italy
| | - Sandro Francesconi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Pisa, Italy
| | - Gaetano Di Marco
- Istituto per i Processi Chimico Fisici, National Research Council (IPCF-CNR), Messina, Italy
| | - Anu Mikkonen
- Department of Biological and Environmental Sciences, University of Jyvaskyla, Jyvaskyla, Finland
| | - Antonella Conte
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (ChiBioFarAm), University of Messina, Messina, Italy
| | - Carmen Rizzo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (ChiBioFarAm), University of Messina, Messina, Italy
| | - Emilio De Domenico
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (ChiBioFarAm), University of Messina, Messina, Italy
| | - Luigi Michaud
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (ChiBioFarAm), University of Messina, Messina, Italy
| | - Angelina Lo Giudice
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (ChiBioFarAm), University of Messina, Messina, Italy; Institute for the Coastal Marine Environment, National Research Council (IAMC-CNR), Messina, Italy.
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Complete Genome Sequence of the Polychlorinated Biphenyl Degrader Rhodococcus sp. WB1. GENOME ANNOUNCEMENTS 2016; 4:4/5/e00996-16. [PMID: 27738025 PMCID: PMC5064098 DOI: 10.1128/genomea.00996-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Rhodococcus sp. WB1 is a polychlorinated biphenyl degrader which was isolated from contaminated soil in Zhejiang, China. Here, we present the complete genome sequence. The analysis of this genome indicated that a biphenyl-degrading gene cluster and several xenobiotic metabolism pathways are harbored.
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Xu L, Chen X, Li H, Hu F, Liang M. Characterization of the biosorption and biodegradation properties of Ensifer adhaerens: A potential agent to remove polychlorinated biphenyls from contaminated water. JOURNAL OF HAZARDOUS MATERIALS 2016; 302:314-322. [PMID: 26476319 DOI: 10.1016/j.jhazmat.2015.09.066] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/23/2015] [Accepted: 09/29/2015] [Indexed: 06/05/2023]
Abstract
Ensifer adhaerens is a soil bacterium known for its potential to remove pollutants from the environment. We investigated the contributions of biosorption and biodegradation to the process of polychlorinated biphenyl (PCB) removal from water by living or heat-killed E. adhaerens with different incubation times. We examined the physicochemical properties of E. adhaerens, including its membrane surface moieties, extracellular polymeric substances, and defense-related enzyme activities. In addition, we measured the biosorption and biodegradation of different PCB congeners. We found that removal of PCBs by heat-killed E. adhaerens was attributed to biosorption only, while both biosorption and biodegradation were responsible for the dissipation of PCBs by live E. adhaerens. Biosorption initially plays a major role in PCB removal, but biodegradation becomes increasingly important with increased incubation time. The results of infrared spectroscopy analysis showed that bacterial lipids, proteins, and polysaccharides, which offer abundant binding sites, are responsible for the biosorption of PCBs. Biodegradation was correlated with loosely bound polysaccharides and defense-related enzyme activities that could increase the pollutant's solubility and facilitate further degradation. The PCB congeners exhibited different biosorption and biodegradation patterns, and the patterns were correlated with the octanol-water partition coefficients (Kow) of the congeners. The more hydrophobic organic compounds tended to have higher biosorption, but lower biodegradation capacities. These results indicate that E. adhaerens-mediated biosorption and biodegradation of PCBs are dependent on the status of the strain, the incubation time, and the PCB congener present, and suggest guidelines for PCB removal from water.
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Affiliation(s)
- Li Xu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095, PR China
| | - Xiong Chen
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095, PR China
| | - Huixin Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095, PR China
| | - Feng Hu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095, PR China
| | - Mingxiang Liang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095, PR China.
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Hu J, Qian M, Zhang Q, Cui J, Yu C, Su X, Shen C, Hashmi MZ, Shi J. Sphingobium fuliginis HC3: a novel and robust isolated biphenyl- and polychlorinated biphenyls-degrading bacterium without dead-end intermediates accumulation. PLoS One 2015; 10:e0122740. [PMID: 25875180 PMCID: PMC4395236 DOI: 10.1371/journal.pone.0122740] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 02/12/2015] [Indexed: 11/19/2022] Open
Abstract
Biphenyl and polychlorinated biphenyls (PCBs) are typical environmental pollutants. However, these pollutants are hard to be totally mineralized by environmental microorganisms. One reason for this is the accumulation of dead-end intermediates during biphenyl and PCBs biodegradation, especially benzoate and chlorobenzoates (CBAs). Until now, only a few microorganisms have been reported to have the ability to completely mineralize biphenyl and PCBs. In this research, a novel bacterium HC3, which could degrade biphenyl and PCBs without dead-end intermediates accumulation, was isolated from PCBs-contaminated soil and identified as Sphingobium fuliginis. Benzoate and 3-chlorobenzoate (3-CBA) transformed from biphenyl and 3-chlorobiphenyl (3-CB) could be rapidly degraded by HC3. This strain has strong degradation ability of biphenyl, lower chlorinated (mono-, di- and tri-) PCBs as well as mono-CBAs, and the biphenyl/PCBs catabolic genes of HC3 are cloned on its plasmid. It could degrade 80.7% of 100 mg L -1 biphenyl within 24 h and its biphenyl degradation ability could be enhanced by adding readily available carbon sources such as tryptone and yeast extract. As far as we know, HC3 is the first reported that can degrade biphenyl and 3-CB without accumulation of benzoate and 3-CBA in the genus Sphingobium, which indicates the bacterium has the potential to totally mineralize biphenyl/PCBs and might be a good candidate for restoring biphenyl/PCBs-polluted environments.
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Affiliation(s)
- Jinxing Hu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Mingrong Qian
- Institute of Quality and Standard on Agricultural Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Qian Zhang
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Jinglan Cui
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Chunna Yu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xiaomei Su
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Chaofeng Shen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Muhammad Z. Hashmi
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Jiyan Shi
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
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Isolation and characterization of marine diesel oil-degrading Acinetobacter sp. strain Y2. ANN MICROBIOL 2012. [DOI: 10.1007/s13213-012-0513-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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10
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Plant exudates promote PCB degradation by a rhodococcal rhizobacteria. Appl Microbiol Biotechnol 2011; 95:1589-603. [PMID: 22202970 DOI: 10.1007/s00253-011-3824-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 12/04/2011] [Accepted: 12/07/2011] [Indexed: 10/14/2022]
Abstract
Rhodococcus erythropolis U23A is a polychlorinated biphenyl (PCB)-degrading bacterium isolated from the rhizosphere of plants grown on a PCB-contaminated soil. Strain U23A bphA exhibited 99% identity with bphA1 of Rhodococcus globerulus P6. We grew Arabidopsis thaliana in a hydroponic axenic system, collected, and concentrated the plant secondary metabolite-containing root exudates. Strain U23A exhibited a chemotactic response toward these root exudates. In a root colonizing assay, the number of cells of strain U23A associated to the plant roots (5.7 × 10⁵ CFU g⁻¹) was greater than the number remaining in the surrounding sand (4.5 × 10⁴ CFU g⁻¹). Furthermore, the exudates could support the growth of strain U23A. In a resting cell suspension assay, cells grown in a minimal medium containing Arabidopsis root exudates as sole growth substrate were able to metabolize 2,3,4'- and 2,3',4-trichlorobiphenyl. However, no significant degradation of any of congeners was observed for control cells grown on Luria-Bertani medium. Although strain U23A was unable to grow on any of the flavonoids identified in root exudates, biphenyl-induced cells metabolized flavanone, one of the major root exudate components. In addition, when used as co-substrate with sodium acetate, flavanone was as efficient as biphenyl to induce the biphenyl catabolic pathway of strain U23A. Together, these data provide supporting evidence that some rhodococci can live in soil in close association with plant roots and that root exudates can support their growth and trigger their PCB-degrading ability. This suggests that, like the flagellated Gram-negative bacteria, non-flagellated rhodococci may also play a key role in the degradation of persistent pollutants.
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Genome sequence of Rhodococcus sp. strain R04, a polychlorinated-biphenyl biodegrader. J Bacteriol 2011; 193:5032-3. [PMID: 21742862 DOI: 10.1128/jb.05635-11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genus Rhodococcus has proved to be a promising option for the cleanup of polluted sites and application of a microbial biocatalyst. Rhodococcus sp. strain R04, isolated from oil-contaminated soil, can biodegrade polychlorinated biphenyls. Here we report the draft genome sequence of Rhodococcus sp. strain R04, which could be used to predict genes for xenobiotic biodegradation and provide important insights into the applications of this strain.
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12
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Yin Y, Guo J, Zheng L, Tian L, Wang X. Capability of polychlorinated biophenyl (PCBs) degrading fungi segregated from sediments. World J Microbiol Biotechnol 2011. [DOI: 10.1007/s11274-011-0728-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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13
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Egorova DO, Shumkova ES, Demakov VA, Plotnikova EG. Degradation of chlorinated biphenyls and products of their bioconversion by Rhodococcus sp. B7a strain. APPL BIOCHEM MICRO+ 2010. [DOI: 10.1134/s0003683810060062] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Congener Selectivity During Polychlorinated Biphenyls Degradation by Enterobacter sp. LY402. Curr Microbiol 2010; 62:784-9. [DOI: 10.1007/s00284-010-9792-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2010] [Accepted: 10/01/2010] [Indexed: 10/18/2022]
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15
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Puglisi E, Cahill MJ, Lessard PA, Capri E, Sinskey AJ, Archer JAC, Boccazzi P. Transcriptional response of Rhodococcus aetherivorans I24 to polychlorinated biphenyl-contaminated sediments. MICROBIAL ECOLOGY 2010; 60:505-515. [PMID: 20369357 DOI: 10.1007/s00248-010-9650-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Accepted: 02/22/2010] [Indexed: 05/29/2023]
Abstract
We used a microarray targeting 3,524 genes to assess the transcriptional response of the actinomycete Rhodococcus aetherivorans I24 in minimal medium supplemented with various substrates (e.g., PCBs) and in both PCB-contaminated and non-contaminated sediment slurries. Relative to the reference condition (minimal medium supplemented with glucose), 408 genes were upregulated in the various treatments. In medium and in sediment, PCBs elicited the upregulation of a common set of 100 genes, including gene-encoding chaperones (groEL), a superoxide dismutase (sodA), alkyl hydroperoxide reductase protein C (ahpC), and a catalase/peroxidase (katG). Analysis of the R. aetherivorans I24 genome sequence identified orthologs of many of the genes in the canonical biphenyl pathway, but very few of these genes were upregulated in response to PCBs or biphenyl. This study is one of the first to use microarrays to assess the transcriptional response of a soil bacterium to a pollutant under conditions that more closely resemble the natural environment. Our results indicate that the transcriptional response of R. aetherivorans I24 to PCBs, in both medium and sediment, is primarily directed towards reducing oxidative stress, rather than catabolism.
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Affiliation(s)
- Edoardo Puglisi
- Istituto di Chimica Agraria ed Ambientale, Università Cattolica del Sacro Cuore, Piacenza, Italy
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16
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Xie F, Chao Y, Xue Z, Yang X, Zhang G, Shi J, Qian S. Stereoselective epoxidation of cis-propenylphosphonic acid to fosfomycin by a newly isolated bacterium Bacillus simplex strain S101. J Ind Microbiol Biotechnol 2009; 36:739-46. [DOI: 10.1007/s10295-009-0546-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Accepted: 02/06/2009] [Indexed: 10/21/2022]
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17
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Cometabolic degradation of mono-chloro benzoic acids by Rhodococcus sp. R04 grown on organic carbon sources. World J Microbiol Biotechnol 2009. [DOI: 10.1007/s11274-009-9996-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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18
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Purification, characterization, and substrate specificity of two 2,3-dihydroxybiphenyl 1,2-dioxygenase from Rhodococcus sp. R04, showing their distinct stability at various temperature. Biochimie 2008; 90:1530-8. [PMID: 18585431 DOI: 10.1016/j.biochi.2008.05.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2007] [Accepted: 05/29/2008] [Indexed: 11/20/2022]
Abstract
The genes of two 2,3-dihydroxybiphenyl 1,2-dioxygenases (BphC1 and BphC2) were obtained from the gene library of Rhodococcus sp. R04. The enzymes have been purified to apparent electrophoretic homogeneity from the cell extracts of the recombinant harboring bphC1 and bphC2. Both BphC1 and BphC2 were hexamers, consisting of six subunits of 35 and 33 kDa as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, respectively. The enzymes had similar optimal pH (pH 9.0), but different temperatures for their maximum activity (30 degrees C for BphC1, 80 degrees C for BphC2). In addition, they exhibited distinct stability at various temperatures. The enzymes could cleave a wide range of catechols, with 2,3-dihydroxybiphenyl being the optimum substrate for BphC1 and BphC2. BphC1 was inhibited by 2,3-dihydroxybiphenyl, catechol and 3-chlorocatechol, whereas BphC2 showed strong substrate inhibition for all the given substrates. BphC2 exhibited a half-life of 15 min at 80 degrees C and 50 min at 70 degrees C, making it the most thermostable extradiol dioxygenase studied in mesophilic bacteria. After disruption of bphC1 and bphC2 genes, R04DeltaC1 (bphC1 mutant) delayed the time of their completely eliminating biphenyl another 15 h compared with its parent strain R04, but R04DeltaC2 (bphC2 mutant) lost the ability to grow on biphenyl, suggesting that BphC1 plays an assistant role in the degrading of biphenyl by strain R04, while BphC2 is essential for the growth of strain R04 on biphenyl.
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Solyanikova IP, Travkin VM, Rybkina DO, Plotnikova EG, Golovleva LA. Variability of enzyme system of Nocardioform bacteria as a basis of their metabolic activity. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2008; 43:241-252. [PMID: 18368545 DOI: 10.1080/03601230701771180] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The present review describes some aspects of organization of biodegradative pathways of Nocardioform microorganisms, first of all, with respect to their ability to degrade aromatic compounds, mostly methylbenzoate, chlorosubstituted phenols, and chlorinated biphenyls and the intermediates of their transformation: 4-chlorobenzoate and para-hydroxybenzoate. Various enzyme systems induced during degradation processes are defined. The ability of microorganisms to induce a few key enzymes under the influence of xenobiotics is described. This ability may increase the biodegradative potential of strains allowing them to survive in the changing environment or demonstrate to some extent the unspecific response of microorganisms to the effect of toxicants. Nocardioform microorganisms responsible for degradation of such persistent compounds as polychlorinated biphenyls, polyaromatic hydrocarbons, chlorinated benzoates and phenols and other xenobiotics are characterized. The possibility of using Nocardioform microorganisms in some aspects of biotechnology due to their ability to produce some compounds important for industry is also estimated.
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Affiliation(s)
- Inna P Solyanikova
- Skryabin' Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow, Russia
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Michaud L, Di Marco G, Bruni V, Lo Giudice A. Biodegradative potential and characterization of psychrotolerant polychlorinated biphenyl-degrading marine bacteria isolated from a coastal station in the Terra Nova Bay (Ross Sea, Antarctica). MARINE POLLUTION BULLETIN 2007; 54:1754-61. [PMID: 17854841 DOI: 10.1016/j.marpolbul.2007.07.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2007] [Revised: 07/18/2007] [Accepted: 07/20/2007] [Indexed: 05/17/2023]
Abstract
Antarctic marine bacteria were screened for their ability to degrade polychlorinated biphenyls (PCB) as the sole carbon and energy source at both 4 degrees C and 15 degrees C. PCB-degrading isolates (7.1%) were identified by sequencing their 16S rDNA as Pseudoalteromonas, Psychrobacter and Arthrobacter members. One representative isolate per genera was selected for evaluating the biodegradative potential under laboratory scale and phenotypically characterized. Removal of individual PCB congeners was between 35.6% and 79.8% at 4 degrees C and between 0.4% and 82.8% at 15 degrees C. Differences in the removal patterns of PCB congeners were observed in relation to the phylogenetic affiliation: Arthrobacter isolate showed similar biodegradation efficiencies when growing at 4 degrees C and 15 degrees C, while Pseudoalteromonas better degraded PCBs at 15 degrees C. No biodegradation was detected for Psychrobacter isolate at 4 degrees C. Results obtained highlight the occurrence of PCB-degrading bacteria in Antarctic seawater and suggest the potential exploitation of autochthonous bacteria for PCB bioremediation in cold marine environments.
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Affiliation(s)
- Luigi Michaud
- Dipartimento di Biologia Animale ed Ecologia Marina (DBAEM), Università di Messina, Salita Sperone 31, 98166 Messina, Italy.
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Yang X, Liu X, Song L, Xie F, Zhang G, Qian S. Characterization and functional analysis of a novel gene cluster involved in biphenyl degradation in Rhodococcus sp. strain R04. J Appl Microbiol 2007; 103:2214-24. [DOI: 10.1111/j.1365-2672.2007.03461.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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