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Xu N, Qiu C, Yang Q, Zhang Y, Wang M, Ye C, Guo M. Analysis of Phenol Biodegradation in Antibiotic and Heavy Metal Resistant Acinetobacter lwoffii NL1. Front Microbiol 2021; 12:725755. [PMID: 34566929 PMCID: PMC8461059 DOI: 10.3389/fmicb.2021.725755] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/23/2021] [Indexed: 11/30/2022] Open
Abstract
Phenol is a common environmental contaminant. The purpose of this study was to isolate phenol-degrading microorganisms from wastewater in the sections of the Chinese Medicine Manufactory. The phenol-degrading Acinetobacter lwoffii NL1 was identified based on a combination of biochemical characteristics and 16S rRNA genes. To analyze the molecular mechanism, the whole genome of A. lwoffii NL1 was sequenced, yielding 3499 genes on one circular chromosome and three plasmids. Enzyme activity analysis showed that A. lwoffii NL1 degraded phenol via the ortho-cleavage rather than the meta-cleavage pathway. Key genes encoding phenol hydroxylase and catechol 1,2-dioxygenase were located on a megaplasmid (pNL1) and were found to be separated by mobile genetic elements; their function was validated by heterologous expression in Escherichia coli and quantitative real-time PCR. A. lwoffii NL1 could degrade 0.5 g/L phenol within 12 h and tolerate a maximum of 1.1 g/L phenol, and showed resistance against multiple antibiotics and heavy metal ions. Overall, this study shows that A. lwoffii NL1 can be potentially used for efficient phenol degradation in heavy metal wastewater treatment.
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Affiliation(s)
- Nan Xu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Chong Qiu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Qiyuan Yang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Yunzeng Zhang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Mingqi Wang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Minliang Guo
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
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Kalyani DC, Munk L, Mikkelsen JD, Meyer AS. Molecular and biochemical characterization of a new thermostable bacterial laccase from Meiothermus ruber DSM 1279. RSC Adv 2016. [DOI: 10.1039/c5ra24374b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A new bacterial laccase gene (mrlac) fromMeiothermus ruberDSM 1279 was successfully overexpressed to produce a laccase (Mrlac) in soluble form inEscherichia coliduring simultaneous overexpression of a chaperone protein (GroEL/ES).
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Affiliation(s)
- D. C. Kalyani
- Center for BioProcess Engineering
- Dept. of Chemical and Biochemical Engineering
- Technical University of Denmark
- DK-2800 Kgs. Lyngby
- Denmark
| | - L. Munk
- Center for BioProcess Engineering
- Dept. of Chemical and Biochemical Engineering
- Technical University of Denmark
- DK-2800 Kgs. Lyngby
- Denmark
| | - J. D. Mikkelsen
- Center for BioProcess Engineering
- Dept. of Chemical and Biochemical Engineering
- Technical University of Denmark
- DK-2800 Kgs. Lyngby
- Denmark
| | - A. S. Meyer
- Center for BioProcess Engineering
- Dept. of Chemical and Biochemical Engineering
- Technical University of Denmark
- DK-2800 Kgs. Lyngby
- Denmark
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Han L, Liu Y, Li C, Zhao D. Cloning, expression, characterization and mutational analysis of the tfdA gene from Cupriavidus campinensis BJ71. World J Microbiol Biotechnol 2015; 31:1021-30. [PMID: 25850533 DOI: 10.1007/s11274-015-1852-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 04/03/2015] [Indexed: 10/23/2022]
Abstract
2,4-Dichlorophenoxyacetic acid (2,4-D)/α-ketoglutarate (α-KG) dioxygenase (TfdA) is an Fe(II)-dependent enzyme that catalyzes the first step in degradation of the herbicide 2,4-D. Previous studies focused on the tfdA gene in Ralstonia eutropha JMP134 isolated in Australia. In this study, a new tfdA gene was cloned from Cupriavidus campinensis BJ71, an effective degrading bacteria from China, based on the iCOnsensus-DEgenerate Hybrid Oligonucleotide Primers (iCODEHOPs) protocol, combined with high-efficiency Thermal Asymmetric Interlaced PCR (hiTAIL-PCR). The open reading frame of 861 bp encoded a putative 287 amino acid protein with a theoretical molecular mass of 32.32 kDa. The gene was overexpressed in Escherichia coli BL21 (DE3) and the purified TfdA showed optimal activity at pH 6.75 and 30 °C. This enzyme was more thermostable and it could use 3-hydrocinnamic acid as substrate, with a similar enzyme activity compared with 2,4-D. TfdA and its variants were created as maltose-binding protein (MBP) tagged fusion proteins to examine the roles of putative substrate-binding residues. The MBP-N110A, MBP-V198A and MBP-R207K proteins showed decreased k cat and increased Km, and MBP-R278A was inactive, suggesting these residues may affect 2,4-D binding or catalysis.
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Affiliation(s)
- Lizhen Han
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guiyang, 550025, China,
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Tourlousse DM, Kurisu F, Tobino T, Furumai H. Sensitive and substrate-specific detection of metabolically active microorganisms in natural microbial consortia using community isotope arrays. FEMS Microbiol Lett 2013; 342:70-5. [DOI: 10.1111/1574-6968.12112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Revised: 02/20/2013] [Accepted: 02/20/2013] [Indexed: 11/30/2022] Open
Affiliation(s)
- Dieter M. Tourlousse
- Research Center for Water Environment Technology; Graduate School of Engineering; The University of Tokyo; Tokyo; Japan
| | - Futoshi Kurisu
- Research Center for Water Environment Technology; Graduate School of Engineering; The University of Tokyo; Tokyo; Japan
| | - Tomohiro Tobino
- Environmental Science Center; The University of Tokyo; Tokyo; Japan
| | - Hiroaki Furumai
- Research Center for Water Environment Technology; Graduate School of Engineering; The University of Tokyo; Tokyo; Japan
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Wharfe ES, Jarvis RM, Winder CL, Whiteley AS, Goodacre R. Fourier transform infrared spectroscopy as a metabolite fingerprinting tool for monitoring the phenotypic changes in complex bacterial communities capable of degrading phenol. Environ Microbiol 2011; 12:3253-63. [PMID: 20649644 DOI: 10.1111/j.1462-2920.2010.02300.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The coking process produces great volumes of wastewater contaminated with pollutants such as cyanides, sulfides and phenolics. Chemical and physical remediation of this wastewater removes the majority of these pollutants; however, these processes do not remove phenol and thiocyanate. The removal of these compounds has been effected during bioremediation with activated sludge containing a complex microbial community. In this investigation we acquired activated sludge from an industrial bioreactor capable of degrading phenol. The sludge was incubated in our laboratory and monitored for its ability to degrade phenol over a 48 h period. Multiple samples were taken across the time-course and analysed by Fourier transform infrared (FT-IR) spectroscopy. FT-IR was used as a whole-organism fingerprinting approach to monitor biochemical changes in the bacterial cells during the degradation of phenol. We also investigated the ability of the activated sludge to degrade phenol following extended periods (2-131 days) of storage in the absence of phenol. A reduction was observed in the ability of the microbial community to degrade phenol and this was accompanied by a detectable biochemical change in the FT-IR fingerprint related to cellular phenotype of the microbial community. In the absence of phenol a decrease in thiocyanate vibrations was observed, reflecting the ability of these communities to degrade this substrate. Actively degrading communities showed an additional new band in their FT-IR spectra that could be attributed to phenol degradation products from the ortho- and meta-cleavage of the aromatic ring. This study demonstrates that FT-IR spectroscopy when combined with chemometric analysis is a very powerful high throughput screening approach for assessing the metabolic capability of complex microbial communities.
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Affiliation(s)
- Emma S Wharfe
- School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7ND, UK
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Basile LA, Erijman L. Maintenance of phenol hydroxylase genotypes at high diversity in bioreactors exposed to step increases in phenol loading. FEMS Microbiol Ecol 2010; 73:336-48. [PMID: 20500527 DOI: 10.1111/j.1574-6941.2010.00898.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
To better understand how the composition of bacterial communities changes in response to different environmental conditions, we examined the influence of increasing phenol load on the distribution of the protein-coding functional gene of the largest subunit of phenol hydroxylase (LmPH) and of the 16S rRNA gene in lab-scale activated sludge reactors. LmPH diversity was assessed initially from a total of 124 clone sequences retrieved from two reactors exposed to a low (0.25 g L(-1)) and a high (2.5 g L(-1)) phenol concentration. The quantitative changes in the concentration of the eight detected genotypes accompanied changes in the phenol degradation rates, indicating a community structure-function relationship. Nonmetric dimensional analysis showed that LmPH genotypes and the denaturing gradient gel electrophoresis banding patterns clustered together by phenol concentration, rather than by reactor identity. Seven isolates, representing cultivated strains of each of the observed LmPH genotypes, exhibited a rather narrow range of physiological diversity, in terms of the growth rate and the kinetic parameters of the phenol-degrading activity. We suggest that lab-scale reactors support many ecological niches, which allow the maintenance of a high diversity of ecotypes through varying concentrations of phenol, but the ability of particular strains to become dominant members of the community under the different environmental conditions cannot be predicted easily solely from their phenol-degrading properties.
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Affiliation(s)
- Laura A Basile
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI-CONICET), Buenos Aires, Argentina
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Pandey J, Chauhan A, Jain RK. Integrative approaches for assessing the ecological sustainability ofin situbioremediation. FEMS Microbiol Rev 2009; 33:324-75. [PMID: 19178567 DOI: 10.1111/j.1574-6976.2008.00133.x] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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Sueoka K, Satoh H, Onuki M, Mino T. Microorganisms involved in anaerobic phenol degradation in the treatment of synthetic coke-oven wastewater detected by RNA stable-isotope probing. FEMS Microbiol Lett 2009; 291:169-74. [PMID: 19146573 DOI: 10.1111/j.1574-6968.2008.01448.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
An RNA-based stable-isotope probing method was used to identify anaerobic phenol-assimilating bacteria present in activated sludge and used to treat synthetic coke-oven wastewater. Activated sludge was fed with nitrate and (13)C-labeled or unlabeled phenol under anaerobic conditions. After the incubation period, RNA was extracted from the activated sludge and separated by isopycnic centrifugation. Bacterial rRNA in each density fraction was analyzed by reverse transcription-PCR-mediated terminal restriction fragment length polymorphism and cloning followed by sequencing. A microorganism affiliated with the genus Azoarcus was the first to obviously incorporate (13)C: this microorganism was thought to have utilized phenol directly. The microorganisms affiliated with the genera Microbulbifer, Pelagiobacter, Pseudomonas, and Thauera were the next to incorporate (13)C. Although these microorganisms were involved in phenol degradation, whether they assimilated (13)C-labeled phenol directly or indirectly, could not be determined. Some Azoarcus and Thauera strains have previously been reported to degrade phenol under denitrifying conditions, but no strains of the other three genera have been reported to do so.
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Affiliation(s)
- Kazuo Sueoka
- Institute of Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
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Basile LA, Erijman L. Quantitative assessment of phenol hydroxylase diversity in bioreactors using a functional gene analysis. Appl Microbiol Biotechnol 2008; 78:863-72. [DOI: 10.1007/s00253-008-1351-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Revised: 12/25/2007] [Accepted: 01/03/2008] [Indexed: 11/30/2022]
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Dane F, Shaw JJ. Survival and persistence of bioluminescent Xanthomonas campestris pv. campestris on host and non-host plants in the field environment. ACTA ACUST UNITED AC 2008. [DOI: 10.1111/j.1365-2672.1996.tb03192.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Manefield M, Griffiths RI, Leigh MB, Fisher R, Whiteley AS. Functional and compositional comparison of two activated sludge communities remediating coking effluent. Environ Microbiol 2005; 7:715-22. [PMID: 15819853 DOI: 10.1111/j.1462-2920.2004.00746.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The success of engineered microbiological systems is evident in the global application of activated sludge communities to remediate coking effluent. However, there is a lack of understanding of the microbiology underlying treatment efficiency and stability. In this study, two functionally distinct activated sludge pools, treating the same effluent and operating under the same conditions, were examined to establish a relationship between overall diversity and/or functional diversity with respect to process stability. Molecular profiling, sequencing and RNA-based stable isotope probing were used to examine the bacterial diversity, general composition and functional composition of the most abundant members of the two communities. The inferior process stability in one of the pools could not be explained by reduced total bacterial diversity or evenness. RNA-based stable isotope probing revealed that both pools harboured an abundant phenol-degrading Acidovorax species, and that the pool of inferior stability accommodated an additional closely related phenol-degrading Acidovorax species at high abundance. These results are discussed in the context of deterministic and stochastic models of microbial community assembly.
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Valle A, Bailey MJ, Whiteley AS, Manefield M. N-acyl-l-homoserine lactones (AHLs) affect microbial community composition and function in activated sludge. Environ Microbiol 2004; 6:424-33. [PMID: 15008819 DOI: 10.1111/j.1462-2920.2004.00581.x] [Citation(s) in RCA: 139] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The role of intercellular signalling in the regulation of genes and phenotypes in a broad range of bacterial species is now firmly established. In contrast, the impact of intercellular signalling on microbial community parameters, such as species diversity and function, is less well understood. In this study the role of N-acyl-l-homoserine lactones (AHLs) in microbial community dynamics in an industrial wastewater treatment system is addressed. Seven proteobacterial strains producing compounds with AHL-like activity were isolated from the treatment plant. Three of these belong to genera with no previously identified AHL producing species. Addition of AHLs at 2 micro M to sludge samples generated changes in both community function (phenol degradation) and composition as determined by length heterogeneity PCR and denaturing gradient gel electrophoresis. Phenol degradation was more stable as a result of the AHL augmentation. A dominant functional member of the Thauera genus was transiently supplanted by a member of the Comomonas genus in response to AHL addition. This suggests that AHLs can play a role in mediating microbial community parameters and has implications for ecosystem function and industrial wastewater treatment.
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Affiliation(s)
- Anna Valle
- DISTAM, MAAE section, University of Milan, Italy. Molecular Microbial Ecology, CEH, Oxford, UK
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Smejkal CW, Seymour FA, Burton SK, Lappin-Scott HM. Characterisation of bacterial cultures enriched on the chlorophenoxyalkanoic acid herbicides 4-(2,4-dichlorophenoxy) butyric acid and 4-(4-chloro-2-methylphenoxy) butyric acid. J Ind Microbiol Biotechnol 2003; 30:561-7. [PMID: 14513383 DOI: 10.1007/s10295-003-0086-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2002] [Accepted: 07/05/2003] [Indexed: 10/26/2022]
Abstract
The aim of this study was to enrich and characterise bacterial consortia from soils around a herbicide production plant through their capability to degrade the herbicides 4-(2,4-dichlorophenoxy) butyric acid (2,4-DB) and 4-(4-chloro-2-methylphenoxy) butyric acid (MCPB). Partial 16S rRNA gene sequencing revealed members of the genera Stenotrophomonas, Brevundimonas, Pseudomonas, and Ochrobactrum in the 2,4-DB- and MCPB-degrading communities. The degradation of 2,4-DB and MCPB was facilitated by the combined activities of the community members. Some of the members were able to utilise other herbicides from the family of chlorophenoxyalkanoic acids. During degradation of 2,4-DB and MCPB, phenol intermediates were detected, indicating ether cleavage of the side chain as the initial step responsible for the breakdown. This was also verified using an indicator medium. Repeated attempts to amplify putatively conserved tfd genes by PCR indicated the absence of tfd genes among the consortia members. First step cleavage of the chlorophenoxybutyric acid herbicides is by ether cleavage in bacteria and is encoded by divergent or different tfd gene types. The isolation of mixed cultures capable of degrading 2,4-DB and MCPB will aid future investigations to determine both the metabolic route for dissimilation and the fate of these herbicides in natural environments.
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Affiliation(s)
- C W Smejkal
- School of Biological Sciences, University of Exeter, Exeter, Devon, EX4 4PS, UK
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Manefield M, Whiteley AS, Griffiths RI, Bailey MJ. RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl Environ Microbiol 2002; 68:5367-73. [PMID: 12406726 PMCID: PMC129944 DOI: 10.1128/aem.68.11.5367-5373.2002] [Citation(s) in RCA: 344] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Identifying microorganisms responsible for recognized environmental processes remains a great challenge in contemporary microbial ecology. Only in the last few years have methodological innovations provided access to the relationship between the function of a microbial community and the phylogeny of the organisms accountable for it. In this study stable-isotope-labeled [13C]phenol was fed into a phenol-degrading community from an aerobic industrial bioreactor, and the 13C-labeled RNA produced was used to identify the bacteria responsible for the process. Stable-isotope-labeled RNA was analyzed by equilibrium density centrifugation in concert with reverse transcription-PCR and denaturing gradient gel electrophoresis. In contradiction with findings from conventional methodologies, this unique approach revealed that phenol degradation in the microbial community under investigation is dominated by a member of the Thauera genus. Our results suggest that this organism is important for the function of this bioreactor.
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Itoh K, Kanda R, Sumita Y, Kim H, Kamagata Y, Suyama K, Yamamoto H, Hausinger RP, Tiedje JM. tfdA-like genes in 2,4-dichlorophenoxyacetic acid-degrading bacteria belonging to the Bradyrhizobium-Agromonas-Nitrobacter-Afipia cluster in alpha-Proteobacteria. Appl Environ Microbiol 2002; 68:3449-54. [PMID: 12089027 PMCID: PMC126798 DOI: 10.1128/aem.68.7.3449-3454.2002] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2001] [Accepted: 04/03/2002] [Indexed: 11/20/2022] Open
Abstract
The 2,4-dichlorophenoxyacetate (2,4-D)/alpha-ketoglutarate dioxygenase gene (tfdA) homolog designated tfdAalpha was cloned and characterized from 2,4-D-degrading bacterial strain RD5-C2. This Japanese upland soil isolate belongs to the Bradyrhizobium-Agromonas-Nitrobacter-Afipia cluster in the alpha subdivision of the class Proteobacteria on the basis of its 16S ribosomal DNA sequence. Sequence analysis showed 56 to 60% identity of tfdAalpha to representative tfdA genes. A MalE-TfdAalpha fusion protein expressed in Escherichia coli exhibited about 10 times greater activity for phenoxyacetate than 2,4-D in an alpha-ketoglutarate- and Fe(II)-dependent reaction. The deduced amino acid sequence of TfdAalpha revealed a conserved His-X-Asp-X(146)-His-X(14)-Arg motif characteristic of the active site of group II alpha-ketoglutarate-dependent dioxygenases. The tfdAalpha genes were also detected in 2,4-D-degrading alpha-Proteobacteria previously isolated from pristine environments in Hawaii and in Saskatchewan, Canada (Y. Kamagata, R. R. Fulthorpe, K. Tamura, H. Takami, L. J. Forney, and J. M. Tiedje, Appl. Environ. Microbiol. 63:2266-2272, 1997). These findings indicate that the tfdA genes in beta- and gamma-Proteobacteria and the tfdAalpha genes in alpha-Proteobacteria arose by divergent evolution from a common ancestor.
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Affiliation(s)
- Kazuhito Itoh
- Faculty of Life and Environmental Science, Shimane University, Matsue, Shimane 690-8504, Japan.
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George SE, Nelson GM. Effectiveness of Chromosomal and Plasmid-linked Genes for Enumerating Biotechnology Agents In Vivo. MICROBIAL ECOLOGY IN HEALTH AND DISEASE 2002. [DOI: 10.1080/089106002760002711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- S. Elizabeth George
- From the Of. ce of Research and Development, National Health and Environmental Effects Research Laboratory, Environmental Carcinogenesis Division, US Environmental Protection Agency, Research Triangle Park, NC 27711, USA
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Smejkal CW, Vallaeys T, Burton SK, Lappin-Scott HM. A rapid method to screen degradation ability in chlorophenoxyalkanoic acid herbicide-degrading bacteria. Lett Appl Microbiol 2001; 32:273-7. [PMID: 11298940 DOI: 10.1046/j.1472-765x.2001.00900.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS An agar medium containing a range of related chlorophenoxyalkanoic acid herbicides, 2,4-dichlorophenoxyacetic acid (2,4-D), 2-methyl-4-chlorophenoxyacetic acid (MCPA), racemic mecoprop, (R)-mecoprop and racemic 2,4-DP (2-(2,4-dichlorophenoxy) propionic acid) was developed to assess the catabolic activity of a range of degradative strains. METHODS AND RESULTS The medium was previously developed containing 2,4-D as a carbon source to visualise degradation by the production of dark violet bacterial colonies. Strains isolated on mecoprop were able to degrade 2,4-D, MCPA, racemic mecoprop, (R)-mecoprop and racemic 2,4-DP, whereas the 2,4-D-enriched strains were limited to 2,4-D and MCPA as carbon sources. Sphingomonas sp. TFD44 solely degraded the dichlorinated compounds, 2,4-D, racemic 2,4-DP and 2,4-DB (2,4-dichlorophenoxybutyric acid). However, Sphingomonas sp. AW5, originally isolated on 2,4,5-T, was the only strain to degrade the phenoxybutyric compound MCPB (4-chloro-2-methylphenoxybutyric acid). CONCLUSION This medium has proved to be a very effective and rapid method for screening herbicide degradation by bacterial strains. SIGNIFICANCE AND IMPACT OF THE STUDY This method reduces the problem of assessing the biodegradability of this family of compounds to an achievable level.
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Affiliation(s)
- C W Smejkal
- School of Biological Sciences, University of Exeter, UK.
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el-Deeb BA, Soltan SM, Ali AM, Ali KA. Detoxication of the herbicide diuron by Pseudomonas sp. Folia Microbiol (Praha) 2000; 45:211-6. [PMID: 11271802 DOI: 10.1007/bf02908946] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A strain of bacteria able to detoxicate the herbicide diuron in pure culture was isolated from sites contaminated with different urea herbicides. Diuron was used as a sole source of carbon and energy by this isolate which is a Gram-negative, aerobic, rod-shaped bacterium with a single polar flagellum, and grows at 40 degrees C. The strain has been identified as Pseudomonas sp.
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Affiliation(s)
- B A el-Deeb
- Botany Department, Faculty of Science, Sohag, Egypt
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Errampalli D, Leung K, Cassidy MB, Kostrzynska M, Blears M, Lee H, Trevors JT. Applications of the green fluorescent protein as a molecular marker in environmental microorganisms. J Microbiol Methods 1999; 35:187-99. [PMID: 10333070 DOI: 10.1016/s0167-7012(99)00024-x] [Citation(s) in RCA: 155] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In this review, we examine numerous applications of the green fluorescent protein (GFP) marker gene in environmental microbiology research. The GFP and its variants are reviewed and applications in plant-microbe interactions, biofilms, biodegradation, bacterial-protozoan interactions, gene transfer, and biosensors are discussed. Methods for detecting GFP-marked cells are also examined. The GFP is a useful marker in environmental microorganisms, allowing new research that will increase our understanding of microorganisms in the environment.
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Affiliation(s)
- D Errampalli
- Agriculture and Agri-Food Canada, Charlottetown, PEI
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Nickel K, Suter MJ, Kohler HP. Involvement of two alpha-ketoglutarate-dependent dioxygenases in enantioselective degradation of (R)- and (S)-mecoprop by Sphingomonas herbicidovorans MH. J Bacteriol 1997; 179:6674-9. [PMID: 9352915 PMCID: PMC179594 DOI: 10.1128/jb.179.21.6674-6679.1997] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Cell extracts of Sphingomonas herbicidovorans MH grown on (R)-mecoprop contained an enzyme activity that selectively converted (R)-mecoprop to 4-chloro-2-methylphenol, whereas extracts of cells grown on (S)-mecoprop contained an enzyme activity selective for the S enantiomer. Both reactions were dependent on alpha-ketoglutarate and ferrous ions. Besides 4-chloro-2-methylphenol, pyruvate and succinate were detected as products of the reactions. Labeling experiments with (18)O2 revealed that both enzyme activities catalyzed a dioxygenation reaction. One of the oxygen atoms of pyruvate and one of the oxygen atoms of succinate were derived from molecular oxygen. Analysis of cell extracts obtained from cells grown on different substrates by sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed that growth on (R)-mecoprop and (S)-mecoprop caused the appearance of prominent protein bands at 34 and 32 kDa, respectively. Both protein bands were present when cells grew on the racemic mixture. The results demonstrate that S. herbicidovorans initiated the degradation of each enantiomer of mecoprop by a specific alpha-ketoglutarate-dependent dioxygenase. By comparing conversion rates of various phenoxy herbicides, we confirmed that the two enzyme activities were distinct from that of TfdA, which catalyzes the first step in the degradation of 2,4-dichlorophenoxyacetic acid in Ralstonia eutropha JMP134.
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Affiliation(s)
- K Nickel
- Swiss Federal Institute for Environmental Science and Technology (EAWAG), Dübendorf, Switzerland
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Sassanella TM, Fukumori F, Bagdasarian M, Hausinger RP. Use of 4-Nitrophenoxyacetic Acid for Detection and Quantification of 2,4-Dichlorophenoxyacetic Acid (2,4-D)/(alpha)-Ketoglutarate Dioxygenase Activity in 2,4-D-Degrading Microorganisms. Appl Environ Microbiol 1997; 63:1189-91. [PMID: 16535548 PMCID: PMC1389142 DOI: 10.1128/aem.63.3.1189-1191.1997] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Purified 2,4-dichlorophenoxyacetic acid (2,4-D)/(alpha)-ketoglutarate dioxygenase (TfdA) was shown to use 4-nitrophenoxyacetic acid (K(infm) = 0.89 (plusmn) 0.04 mM, k(infcat) [catalytic constant] = 540 (plusmn) 10 min(sup-1)), producing intensely yellow 4-nitrophenol. This reagent was used to develop a rapid, continuous, colorimetric assay for the detection of TfdA and analogous activities in 2,4-D-degrading bacterial cells and extracts.
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Danganan CE, Shankar S, Ye RW, Chakrabarty AM. Substrate diversity and expression of the 2,4,5-trichlorophenoxyacetic acid oxygenase from Burkholderia cepacia AC1100. Appl Environ Microbiol 1995; 61:4500-4. [PMID: 8534119 PMCID: PMC167763 DOI: 10.1128/aem.61.12.4500-4504.1995] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Burkholderia cepacia AC1100 uses the chlorinated aromatic compound 2,4,5-trichlorophenoxyacetic acid as a sole source of carbon and energy. The genes encoding the proteins involved in the first step (tftA and tftB [previously designated tftA1 and tftA2, respectively]) have been cloned and sequenced. The oxygenase, TftAB, is capable of converting not only 2,4,5-trichlorophenoxyacetic acid to 2,4,5-trichlorophenol but also a wide range of chlorinated aromatic phenoxyacetates to their corresponding phenolic derivatives, as shown by whole-cell and cell-free assays. The rate of substrate utilization by TftAB depends upon the extent of chlorination of the substrate, the positions of the chlorines, and the phenoxy group. These results indicate a mechanistic similarity between TftAB and the 2,4-dichlorophenoxyacetic acid/alpha-ketoglutarate-dependent dioxygenase, TfdA, from Alcaligenes eutrophus JMP134. The promoter of the oxygenase genes was localized by promoter-probe analysis, and the transcriptional start site was identified by primer extension. The beta-galactosidase activity of the construct containing the promoter region cloned upstream of the beta-galactosidase gene in the promoter-probe vector pKRZ-1 showed that this construct is constitutively expressed in Escherichia coli and in AC1100. The -35 and -10 regions of the oxygenase genes show significant sequence identity to typical Escherichia coli sigma 70 promoters.
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Affiliation(s)
- C E Danganan
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago 60612, USA
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25
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Danganan CE, Ye RW, Daubaras DL, Xun L, Chakrabarty AM. Nucleotide sequence and functional analysis of the genes encoding 2,4,5-trichlorophenoxyacetic acid oxygenase in Pseudomonas cepacia AC1100. Appl Environ Microbiol 1994; 60:4100-6. [PMID: 7527626 PMCID: PMC201942 DOI: 10.1128/aem.60.11.4100-4106.1994] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Pseudomonas cepacia AC1100 is able to use the chlorinated aromatic compound 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) as the sole source of carbon and energy. One of the early steps in this pathway is the conversion of 2,4,5-T to 2,4,5-trichlorophenol (2,4,5-TCP). 2,4,5-TCP accumulates in the culture medium when AC1100 is grown in the presence of 2,4,5-T. A DNA region from the AC1100 genome has been subcloned as a 2.7-kb SstI-XbaI DNA fragment, which on transfer to Pseudomonas aeruginosa PAO1 allows the conversion of 2,4,5-T to 2,4,5-TCP. We have determined the directions of transcription of these genes as well as the complete nucleotide sequences of the genes and the number and sizes of the polypeptides synthesized by pulse-labeling experiments. This 2.7-kb DNA fragment encodes two polypeptides with calculated molecular masses of 51 and 18 kDa. Proteins of similar sizes were seen in the T7 pulse-labeling experiment in Escherichia coli. We have designated the genes for these proteins tftA1 (which encodes the 51-kDa protein) and tftA2 (which encodes the 18-kDa protein). TftA1 and TftA2 have strong amino acid sequence homology to BenA and BenB from the benzoate 1,2-dioxygenase system of Acinetobacter calcoaceticus, as well as to XylX and XylY from the toluate 1,2-dioxygenase system of Pseudomonas putida. The Pseudomonas aeruginosa PAO1 strain containing the 2.7-kb SstI-XbaI fragment was able to convert not only 2,4,5-T to 2,4,5-TCP but also 2,4-dichlorophenoxyacetic acid to 2,4-dichlorophenol and phenoxyacetate to phenol.
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Affiliation(s)
- C E Danganan
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago 60612
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26
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Akkermans AD, Mirza M, Harmsen HJ, Blok HJ, Herron PR, Sessitsch A, Akkermans WM. Molecular ecology of microbes: A review of promises, pitfalls and true progress. FEMS Microbiol Rev 1994. [DOI: 10.1111/j.1574-6976.1994.tb00134.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Short KA, King RJ, Seidler RJ, Olsen RH. Biodegradation of phenoxyacetic acid in soil by Pseudomonas putida PP0301(pR0103), a constitutive degrader of 2,4-dichlorophenoxyacetate. Mol Ecol 1994; 1:89-94. [PMID: 1344988 DOI: 10.1111/j.1365-294x.1992.tb00160.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The efficacy of using genetically engineered microbes (GEMs) to degrade recalcitrant environmental toxicants was demonstrated by the application of Pseudomonas putida PP0301(pR0103) to an Oregon agricultural soil amended with 500 micrograms/g of a model xenobiotic, phenoxyacetic acid (PAA). P. putida PP0301(pR0103) is a constitutive degrader of 2,4-dichlorophenoxyacetate (2,4-D) and is also active on the non-inducing substrate, PAA. PAA is the parental compound of 2,4-dichlorophenoxyacetic acid (2,4-D) and whilst the indigenous soil microbiota degraded 500 micrograms/g 2,4-D to less than 10 micrograms/g, PAA degradation was insignificant during a 40-day period. No significant degradation of PAA occurred in soil inoculated with the parental strain P. putida PP0301 or the inducible 2,4-D degrader P. putida PP0301(pR0101). Moreover, co-amendment of soil with 2,4-D and PAA induced the microbiota to degrade 2,4-D; PAA was not degraded. P. putida PP0301-(pR0103) mineralized 500-micrograms/g PAA to trace levels within 13 days and relieved phytotoxicity of PAA to Raphanus sativus (radish) seeds with 100% germination in the presence of the GEM and 7% germination in its absence. In unamended soil, survival of the plasmid-free parental strain P. putida PP0301 was similar to the survival of the GEM strain P. putida PP0301(pR0103). However, in PAA amended soil, survival of the parent strain was over 10,000-fold lower (< 3 colony forming units per gram of soil) than survival of the GEM strain after 39 days.
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Affiliation(s)
- K A Short
- USEPA Environmental Research Laboratory, Corvallis, OR 97333
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28
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Purification and characterization of 2,4-dichlorophenoxyacetate/alpha-ketoglutarate dioxygenase. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(20)80527-4] [Citation(s) in RCA: 131] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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29
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Fukumori F, Hausinger RP. Alcaligenes eutrophus JMP134 "2,4-dichlorophenoxyacetate monooxygenase" is an alpha-ketoglutarate-dependent dioxygenase. J Bacteriol 1993; 175:2083-6. [PMID: 8458850 PMCID: PMC204309 DOI: 10.1128/jb.175.7.2083-2086.1993] [Citation(s) in RCA: 137] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The Alcaligenes eutrophus JMP134 tfdA gene, encoding the enzyme responsible for the first step in 2,4-dichlorophenoxyacetic acid (2,4-D) biodegradation, was overexpressed in Escherichia coli, and several enzymatic properties of the partially purified gene product were examined. Although the tfdA-encoded enzyme is typically referred to as 2,4-D monooxygenase, we were unable to observe any reductant-dependent activity. Rather, we demonstrate that this enzyme is a ferrous ion-dependent dioxygenase that uses alpha-ketoglutarate as a cosubstrate. The alpha-ketoglutarate is converted to succinate concomitant with 2,4-D conversion to 2,4-dichlorophenol. By using [1-14C]alpha-ketoglutarate, we established that carbon dioxide is the second product derived from alpha-ketoglutarate. Finally, we verified the proposal that glyoxylate is the second product derived from 2,4-D.
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Affiliation(s)
- F Fukumori
- Center for Microbial Ecology, Michigan State University, East Lansing 48824
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30
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AMIN-HANJANI S, MEIKLE A, GLOVER LA, PROSSER JI, KILLHAM K. Plasmid and chromosomally encoded luminescence marker systems for detection of Pseudomonas fluorescens in soil. Mol Ecol 1993. [DOI: 10.1111/j.1365-294x.1993.tb00098.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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31
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Atlas RM. Molecular methods for environmental monitoring and containment of genetically engineered microorganisms. Biodegradation 1992; 3:137-46. [PMID: 1369233 DOI: 10.1007/bf00129079] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Plans to introduce genetically engineered microorganisms into the environment has led to concerns over safety and has raised questions about how to detect and to contain such microorganisms. Specific gene sequences, such as lacZ, have been inserted into genetically engineered microorganisms to permit their phenotypic detection. Molecular methods have been developed based upon recovery of DNA from environmental samples and gene probe hybridization to specific diagnostic gene sequences for the specific detection of genetically engineered microorganisms. DNA amplification using the polymerase chain reaction has been applied to enhance detection sensitivity so that single gene targets can be detected. Detection of messenger RNA has permitted the monitoring of gene expression in the environment. The use of reporter genes, such as the lux gene for bioluminescence, likewise has permitted the observation of gene expression. Conditional lethal constructs have been developed as models for containment of genetically engineered microorganisms. Suicide vectors, based upon the hok gene have been developed as model containment systems.
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Affiliation(s)
- R M Atlas
- Department of Biology, University of Louisville, KY 40292
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32
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Turner JT, Lampel JS, Stearman RS, Sundin GW, Gunyuzlu P, Anderson JJ. Stability of the delta-endotoxin gene from Bacillus thuringiensis subsp. kurstaki in a recombinant strain of Clavibacter xyli subsp. cynodontis. Appl Environ Microbiol 1991; 57:3522-8. [PMID: 1664710 PMCID: PMC184006 DOI: 10.1128/aem.57.12.3522-3528.1991] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Deletion of chromosomally inserted gene sequences from Clavibacter xyli subsp. cynodontis, a xylem-inhabiting endophyte, was studied in vitro and in planta. We found that nonreplicating plasmid pCG610, which conferred resistance to kanamycin and tetracycline and contained segments of C. xyli subsp. cynodontis genomic DNA, integrated into a homologous sequence in the bacterial chromosome. In addition, pCG610 contains two copies of the gene encoding the CryIA(c) insecticidal protein of Bacillus thuringiensis subsp. kurstaki HD73. Using drug resistance phenotypes and specific DNA probes, we found that the loss of all three genes arose both in vitro under nonselective conditions and in planta. The resulting segregants are probably formed by recombination between the repeated DNA sequences flanking pCG610 that resulted from the integration event into the chromosome. Eventually, segregants predominated in the bacterial population. The loss of the integrated plasmid from C. xyli subsp. cynodontis revealed a possible approach for decreasing the environmental consequences of recombinant bacteria for agricultural use.
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Affiliation(s)
- J T Turner
- Microbial Ecology Group, Crop Genetics International, Hanover, Maryland 21076
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