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Nakazawa S, Haramiishi A, Fukuda K, Kanayama Y, Watanabe T, Yuki M, Ohkuma M, Takeda K, Kimbara K, Shintani M. Different transferability of incompatibility (Inc) P-7 plasmid pCAR1 and IncP-1 plasmid pBP136 in stirring liquid conditions. PLoS One 2017; 12:e0186248. [PMID: 29023575 PMCID: PMC5638413 DOI: 10.1371/journal.pone.0186248] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/27/2017] [Indexed: 01/01/2023] Open
Abstract
Self-transmissible plasmids are classified into two types based on their sex pili: short and rigid pili, and long and flexible pili. The transferability of two plasmids with different types of sex pili, pBP136 and pCAR1, was compared in stirring liquid conditions with different cell density. The most probable number method to count transconjugants could detect differences in the transfer frequency with higher resolution in comparison with the conventional CFU counting method. Both plasmids showed higher transfer frequency in high stirring rates than static liquid conditions when the donor and recipient density was 106−107 CFU mL-1. The probability of donor-initiated plasmid transfer was investigated by a single-cell-level analysis using a cell sorter. The probability was >36-fold higher for pBP136 than for pCAR1; thus, the simulated transfer frequency of pBP136 was much higher than that of pCAR1 in stirring liquid conditions. Nevertheless, the transfer frequency of pCAR1 was as high as that of pBP136 when the donor and recipient cell density was 106 CFU mL-1. This fact indicates that the lower probability of the donor pCAR1 to initiate transfer could be overcome by its high tolerance to the shearing force between donor and recipient cells under higher stirring liquid conditions. Our findings can explain the different survival strategies of these two types of plasmids based on their preferences of transfer conditions.
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Affiliation(s)
- Shunsuke Nakazawa
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, Japan
| | - Akira Haramiishi
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, Japan
| | - Kohei Fukuda
- Department of Bioscience, Graduated School of Science and Technology, Shizuoka University, Hamamatsu, Japan
| | - Yukie Kanayama
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, Japan
| | - Toshinori Watanabe
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, Japan
| | - Masahiro Yuki
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, Tsukuba, Japan
| | - Moriya Ohkuma
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, Tsukuba, Japan
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Japan
| | - Kazuhiro Takeda
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, Japan
| | - Kazuhide Kimbara
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, Japan
| | - Masaki Shintani
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, Japan
- Department of Bioscience, Graduated School of Science and Technology, Shizuoka University, Hamamatsu, Japan
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Japan
- * E-mail:
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Yeom J, Lee Y, Noh J, Jung J, Park J, Seo H, Kim J, Han J, Jeon CO, Kim T, Park W. Detection of genetically modified microorganisms in soil using the most-probable-number method with multiplex PCR and DNA dot blot. Res Microbiol 2011; 162:807-16. [PMID: 21810467 DOI: 10.1016/j.resmic.2011.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Accepted: 06/20/2011] [Indexed: 10/17/2022]
Abstract
The principal objective of this study was to detect genetically modified microorganisms (GMMs) that might be accidentally released into the environment from laboratories. Two methods [plate counting and most-probable-number (MPN)] coupled with either multiplex PCR or DNA dot blots were compared using genetically modified Escherichia coli, Pseudomonas putida, and Acinetobacter oleivorans harboring an antibiotic-resistance gene with additional gfp and lacZ genes as markers. Alignments of sequences collected from databases using the Perl scripting language (Perl API) and from denaturing gradient gel electrophoresis analysis revealed that the gfp, lacZ and antibiotic-resistance genes (kanamycin, tetracycline, and ampicillin) in GMMs differed from the counterpart genes in many sequenced genomes and in soil DNA. Thus, specific multiplex PCR primer sets for detection of plasmid-based gfp and lacZ antibiotic-resistance genes could be generated. In the plate counting method, many antibiotic-resistant bacteria from a soil microcosm grew as colonies on antibiotic-containing agar plates. The multiplex PCR verification of randomly selected antibiotic-resistant colonies with specific primers proved ineffective. The MPN-multiplex PCR method and antibiotic-resistant phenotype could be successfully used to detect GMMs, although this method is quite laborious. The MPN-DNA dot blot method screened more cells at a time in a microtiter plate containing the corresponding antibiotics, and was shown to be a more efficient method for the detection of GMMs in soil using specific probes in terms of labor and accuracy.
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Affiliation(s)
- Jinki Yeom
- Division of Environmental Science and Ecological Engineering, Korea University, Seoul 136-713, Republic of Korea
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Xia S, Li J, Wang R, Li J, Zhang Z. Tracking composition and dynamics of nitrification and denitrification microbial community in a biofilm reactor by PCR-DGGE and combining FISH with flow cytometry. Biochem Eng J 2010. [DOI: 10.1016/j.bej.2010.01.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Nelson SM, Cooper AAA, Taylor EL, Salisbury VC. Use of bioluminescent Escherichia coli O157:H7 to study intra-protozoan survival of bacteria within Tetrahymena pyriformis. FEMS Microbiol Lett 2003; 223:95-9. [PMID: 12799006 DOI: 10.1016/s0378-1097(03)00349-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
A method was developed that enabled real-time monitoring of the uptake and survival of bioluminescent Escherichia coli O157 within the freshwater ciliate Tetrahymena pyriformis. Constitutively bioluminescent E. coli O157 pLITE27 was cocultured with T. pyriformis in nutrient-deficient (Chalkley's) and in nutrient-rich (proteose peptone, yeast extract) media. Non-internalised bacteria were inactivated by addition of colistin, indicated by a decline in bioluminescence. Protozoa were subsequently lysed with Triton X-100 which lead to a further drop in bioluminescence, consistent with release of live internal bacteria from T. pyriformis into the colistin-containing environment. Bioluminescence measurements for non-lysed cultures indicated that internalised E. coli O157 pLITE27 cells were only slowly digested by T. pyriformis, in both media, over the time period studied. The results suggest that bioluminescent bacteria are useful tools in the study of bacterial intra-protozoan survival.
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Affiliation(s)
- Shona M Nelson
- Centre for Research in Biomedicine, Faculty of Applied Sciences, University of the West of England, Bristol, BS16 1QY, UK.
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Koch B, Jensen LE, Nybroe O. A panel of Tn7-based vectors for insertion of the gfp marker gene or for delivery of cloned DNA into Gram-negative bacteria at a neutral chromosomal site. J Microbiol Methods 2001; 45:187-95. [PMID: 11348676 DOI: 10.1016/s0167-7012(01)00246-9] [Citation(s) in RCA: 199] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The use of Tn7-based systems for site-specific insertion of DNA into the chromosome of Gram-negative bacteria has been limited due to the lack of appropriate vectors. We therefore developed a flexible panel of Tn7 delivery vectors. In one group of vectors, the miniTn7 element, which is inserted into the chromosome, contains a multiple cloning site (MCS) and the kanamycin, streptomycin or gentamicin resistance markers. Another group of vectors intended for tagging with green fluorescent protein (GFP) carries the gfpmut3* gene controlled by the modified lac promoter PA1/04/03, several transcriptional terminators, and various resistance markers. These vectors insert Tn7 into a specific, neutral intergenic region immediately downstream of the gene encoding glucosamine-6-phosphate synthetase (GlmS) in the tested fluorescent Pseudomonas strains. The gfp-tagging vector containing a gentamicin-resistance marker is useful for tagging strains carrying a Tn5 transposon. Tn5 transposons often carry kanamycin-resistance-encoding genes and are frequently used to generate bacterial mutants and to deliver reporter constructions in gene expression studies. To demonstrate the utility of a dual marker/reporter system, the Tn7-gfp marker system was combined with a Tn5-delivered luxAB reporter system in Pseudomonas fluorescens. The system allowed detection of gfp-tagged cells in the barley rhizosphere, while expression of the Tn5-tagged locus could be determined by measuring bioluminescence.
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Affiliation(s)
- B Koch
- Section of Genetics and Microbiology, Department of Ecology, Royal Veterinary and Agricultural University, Thorvaldsensvej 40, 1871 C, Frederiksberg, Denmark.
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Fredslund L, Ekelund F, Jacobsen CS, Johnsen K. Development and application of a most-probable-number-pcr assay to quantify flagellate populations in soil samples. Appl Environ Microbiol 2001; 67:1613-8. [PMID: 11282613 PMCID: PMC92777 DOI: 10.1128/aem.67.4.1613-1618.2001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This paper reports on the first successful molecular detection and quantification of soil protozoa. Quantification of heterotrophic flagellates and naked amoebae in soil has traditionally relied on dilution culturing techniques, followed by most-probable-number (MPN) calculations. Such methods are biased by differences in the culturability of soil protozoa and are unable to quantify specific taxonomic groups, and the results are highly dependent on the choice of media and the skills of the microscopists. Successful detection of protozoa in soil by DNA techniques requires (i) the development and validation of DNA extraction and quantification protocols and (ii) the collection of sufficient sequence data to find specific protozoan 18S ribosomal DNA sequences. This paper describes the development of an MPN-PCR assay for detection of the common soil flagellate Heteromita globosa, using primers targeting a 700-bp sequence of the small-subunit rRNA gene. The method was tested by use of gnotobiotic laboratory microcosms with sterile tar-contaminated soil inoculated with the bacterium Pseudomonas putida OUS82 UCB55 as prey. There was satisfactory overall agreement between H. globosa population estimates obtained by the PCR assay and a conventional MPN assay in the three soils tested.
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Affiliation(s)
- L Fredslund
- Geological Survey of Denmark and Greenland, Department of Geochemistry, Thoravej 8, DK-2400 Copenhagen NV, Denmark
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