1
|
Miri S, Rasooli A, Brar SK, Rouissi T, Martel R. Biodegradation of p-xylene-a comparison of three psychrophilic Pseudomonas strains through the lens of gene expression. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:21465-21479. [PMID: 34762239 DOI: 10.1007/s11356-021-17387-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 11/02/2021] [Indexed: 05/21/2023]
Abstract
p-Xylene is considered a recalcitrant compound despite showing a similar aromatic structure to other BTEXs (benzene, toluene, ethylbenzene, xylene isomers). This study evaluated the p-xylene biodegradation potential of three psychrophilic Pseudomonas strains (Pseudomonas putida S2TR-01, Pseudomonas synxantha S2TR-20, and Pseudomonas azotoformans S2TR-09). The p-xylene metabolism-related catabolic genes (xylM, xylA, and xylE) and the corresponding regulatory genes (xylR and xylS) of the selected strains were investigated. The biodegradation results showed that the P. azotoformans S2TR-09 strain was the only strain that was able to degrade 200 mg/L p-xylene after 60 h at 15 °C. The gene expression study indicated that the xylE (encoding catechol 2,3-dioxygenase) gene represents the bottleneck in p-xylene biodegradation. A lack of xylE expression leads to the accumulation of intermediates and the inhibition of biomass production and complete carbon recovery. The activity of xylene monooxygenase and catechol 2,3-dioxygenase was significantly increased in P. azotoformans S2TR-09 (0.5 and 0.08 U/mg, respectively) in the presence of p-xylene. The expression of the ring cleavage enzyme and its encoding gene (xylE) and activator (xylS) explained the differences in the p-xylene metabolism of the isolated bacteria and can be used as a novel biomarker of efficient p-xylene biodegradation at contaminated sites.
Collapse
Affiliation(s)
- Saba Miri
- Department of Civil Engineering, Lassonde School of Engineering, York University, North York, Toronto, ON, M3J 1P3, Canada
- INRS-ETE, Université du Québec, 490, Rue de la Couronne, Québec, G1K 9A9, Canada
| | - Azadeh Rasooli
- Department of Civil Engineering, Lassonde School of Engineering, York University, North York, Toronto, ON, M3J 1P3, Canada
| | - Satinder Kaur Brar
- Department of Civil Engineering, Lassonde School of Engineering, York University, North York, Toronto, ON, M3J 1P3, Canada.
- INRS-ETE, Université du Québec, 490, Rue de la Couronne, Québec, G1K 9A9, Canada.
| | - Tarek Rouissi
- INRS-ETE, Université du Québec, 490, Rue de la Couronne, Québec, G1K 9A9, Canada
| | - Richard Martel
- INRS-ETE, Université du Québec, 490, Rue de la Couronne, Québec, G1K 9A9, Canada
| |
Collapse
|
2
|
Berthold T, Centler F, Hübschmann T, Remer R, Thullner M, Harms H, Wick LY. Mycelia as a focal point for horizontal gene transfer among soil bacteria. Sci Rep 2016; 6:36390. [PMID: 27811990 PMCID: PMC5095653 DOI: 10.1038/srep36390] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 10/12/2016] [Indexed: 11/09/2022] Open
Abstract
Horizontal gene transfer (HGT) is a main mechanism of bacterial evolution endowing bacteria with new genetic traits. The transfer of mobile genetic elements such as plasmids (conjugation) requires the close proximity of cells. HGT between genetically distinct bacteria largely depends on cell movement in water films, which are typically discontinuous in natural systems like soil. Using laboratory microcosms, a bacterial reporter system and flow cytometry, we here investigated if and to which degree mycelial networks facilitate contact of and HGT between spatially separated bacteria. Our study shows that the network structures of mycelia promote bacterial HGT by providing continuous liquid films in which bacterial migration and contacts are favoured. This finding was confirmed by individual-based simulations, revealing that the tendency of migrating bacteria to concentrate in the liquid film around hyphae is a key factor for improved HGT along mycelial networks. Given their ubiquity, we propose that hyphae can act as focal point for HGT and genetic adaptation in soil.
Collapse
Affiliation(s)
- Tom Berthold
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Microbiology, Permoserstraße 15, 04318, Leipzig, Germany
| | - Florian Centler
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Microbiology, Permoserstraße 15, 04318, Leipzig, Germany
| | - Thomas Hübschmann
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Microbiology, Permoserstraße 15, 04318, Leipzig, Germany
| | - Rita Remer
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Microbiology, Permoserstraße 15, 04318, Leipzig, Germany
| | - Martin Thullner
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Microbiology, Permoserstraße 15, 04318, Leipzig, Germany
| | - Hauke Harms
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Microbiology, Permoserstraße 15, 04318, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5E, 04103 Leipzig, Germany
| | - Lukas Y. Wick
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Microbiology, Permoserstraße 15, 04318, Leipzig, Germany
| |
Collapse
|
3
|
Merkey BV, Lardon LA, Seoane JM, Kreft JU, Smets BF. Growth dependence of conjugation explains limited plasmid invasion in biofilms: an individual-based modelling study. Environ Microbiol 2011; 13:2435-52. [DOI: 10.1111/j.1462-2920.2011.02535.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
4
|
Seoane J, Yankelevich T, Dechesne A, Merkey B, Sternberg C, Smets BF. An individual-based approach to explain plasmid invasion in bacterial populations. FEMS Microbiol Ecol 2010; 75:17-27. [PMID: 21091520 DOI: 10.1111/j.1574-6941.2010.00994.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
We present an individual-based experimental framework to identify and estimate the main parameters governing bacterial conjugation at the individual cell scale. From this analysis, we have established that transient periods of unregulated plasmid transfer within newly formed transconjugant cells, together with contact mechanics arising from cellular growth and division, are the two main processes determining the emergent inability of the pWW0 TOL plasmid to fully invade spatially structured Pseudomonas putida populations. We have also shown that pWW0 conjugation occurs mainly at advanced stages of the growth cycle and that nongrowing cells, even when exposed to high nutrient concentrations, do not display conjugal activity. These results do not support previous hypotheses relating conjugation decay in the deeper cell layers of bacterial biofilms to nutrient depletion and low physiological activity. We observe, however, that transient periods of elevated plasmid transfer in newly formed transconjugant cells are offset by unfavorable cell-to-cell contact mechanics, which ultimately precludes the pWWO TOL plasmid from fully invading tightly packed multicellular P. putida populations such as microcolonies and biofilms.
Collapse
Affiliation(s)
- Jose Seoane
- Department of Environmental Engineering, Technical University of Denmark, Lyngby, Denmark
| | | | | | | | | | | |
Collapse
|
5
|
Massoudieh A, Crain C, Lambertini E, Nelson KE, Barkouki T, L'amoreaux P, Loge FJ, Ginn TR. Kinetics of conjugative gene transfer on surfaces in granular porous media. JOURNAL OF CONTAMINANT HYDROLOGY 2010; 112:91-102. [PMID: 19969386 DOI: 10.1016/j.jconhyd.2009.10.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Revised: 07/31/2009] [Accepted: 10/23/2009] [Indexed: 05/28/2023]
Abstract
The transfer of genetic material among bacteria in the environment can occur both in the planktonic and attached state. Given the propensity of organisms to exist in sessile microbial communities in oligotrophic subsurface conditions, and that such conditions typify the subsurface, this study focuses on exploratory modeling of horizontal gene transfer among surface-associated Escherichiacoli in the subsurface. The mathematics so far used to describe the kinetics of conjugation in biofilms are developed largely from experimental observations of planktonic gene transfer, and are absent of lags or plasmid stability that appear experimentally. We develop a model and experimental system to quantify bacterial filtration and gene transfer in the attached state, on granular porous media. We include attachment kinetics described in Nelson et al. (2007) using the filtration theory approach of Nelson and Ginn (2001, 2005) with motility of E. coli described according to Biondi et al. (1998).
Collapse
Affiliation(s)
- A Massoudieh
- Dept. of Civil and Environmental Engineering, UC Davis, 1 Shields Avenue, University of California, Davis, CA 95616, United States
| | | | | | | | | | | | | | | |
Collapse
|
6
|
Sørensen SJ, Bailey M, Hansen LH, Kroer N, Wuertz S. Studying plasmid horizontal transfer in situ: a critical review. Nat Rev Microbiol 2005; 3:700-10. [PMID: 16138098 DOI: 10.1038/nrmicro1232] [Citation(s) in RCA: 453] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This review deals with the prospective, experimental documentation of horizontal gene transfer (HGT) and its role in real-time, local adaptation. We have focused on plasmids and their function as an accessory and/or adaptive gene pool. Studies of the extent of HGT in natural environments have identified certain hot spots, and many of these involve biofilms. Biofilms are uniquely suited for HGT, as they sustain high bacterial density and metabolic activity, even in the harshest environments. Single-cell detection of donor, recipient and transconjugant bacteria in various natural environments, combined with individual-based mathematical models, has provided a new platform for HGT studies.
Collapse
Affiliation(s)
- Søren J Sørensen
- Department of Microbiology, Institute of Biology, University of Copenhagen, Sølvgade 83H, 1307 Copenhagen K, Denmark.
| | | | | | | | | |
Collapse
|
7
|
Pinedo CA, Smets BF. Conjugal TOL transfer from Pseudomonas putida to Pseudomonas aeruginosa: effects of restriction proficiency, toxicant exposure, cell density ratios, and conjugation detection method on observed transfer efficiencies. Appl Environ Microbiol 2005; 71:51-7. [PMID: 15640169 PMCID: PMC544212 DOI: 10.1128/aem.71.1.51-57.2005] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The effects of restriction proficiency and premating exposure to toxicants on conjugal transfer of the TOL plasmid between Pseudomonas spp. was investigated by examinations of filter matings. A Pseudomonas putida KT2442-derived strain carrying a gfp-tagged variant of the TOL plasmid was used as a donor, and both restriction-deficient (PAO1162N) and -proficient (PAO2002N) Pseudomonas aeruginosa strains were used as recipients. The in situ enumeration of conjugation events allowed us to obtain frequency estimates that were unbiased by transconjugant growth or plasmid retransfer. We observed a strong dependence of the plasmid transfer frequency on the initial donor-to-recipient ratio of surface matings, which invalidated the use of mass action-based plasmid transfer kinetic estimators. Careful control of the initial parental cell densities permitted evaluations of the true effects of restriction proficiency and toxicant exposure on TOL transfer. At standard donor-to-recipient ratios (10(-3) for PAO1162N and 2 x 10(1) for PAO2002N) and total cell densities (10(5) cells/mm(2) for PAO1162N and 10(6) cells/mm(2) for PAO2002N), plasmid transfer frequencies without toxicant exposure were approximately 10(-7) (events/mm(2))(-1) for PAO1162N and 10(-11) (events/mm(2))(-1) for PAO2002N based on in situ observations of conjugation events. The enumeration of transconjugants via selective plating yielded transfer frequencies that were up to 1 order of magnitude lower. Premating exposure to sodium dodecyl sulfate (1 to 10 mM) significantly increased the transfer frequency for the restriction-proficient strain PAO2002N (P < 0.05) but not for the restriction-deficient strain PAO1162N. On the other hand, premating exposure to ethanol, toluene, or phenol had no positive effect on the plasmid transfer frequency. Clearly, restriction proficiency provides a strong barrier to interspecific transfer of the TOL plasmid, and this barrier was only marginally attenuated by recipient exposure to toxicants within the ranges examined.
Collapse
Affiliation(s)
- Catalina Arango Pinedo
- Environmental Engineering Program, Department of Civil and Environmental Engineering, University of Connecticut, Storrs, Connecticut, USA
| | | |
Collapse
|
8
|
Lilley A, Bailey M. The transfer dynamics of Pseudomonas sp. plasmid pQBR11 in biofilms. FEMS Microbiol Ecol 2002; 42:243-50. [DOI: 10.1111/j.1574-6941.2002.tb01014.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
|
9
|
Smets BF, Rittmann BE, Stahl DA. Quantification of the effect of substrate concentration on the conjugal transfer rate of the TOL plasmid in short-term batch mating experiments. Lett Appl Microbiol 1995; 21:167-72. [PMID: 7576502 DOI: 10.1111/j.1472-765x.1995.tb01033.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Batch mating experiments with Pseudomonas putida PAW 1 (TOL) as a donor and Pseudomonas aeruginosa PAO 1162 as a recipient strain were performed to quantify the effect of the substrate concentration in the mating medium on the observed plasmid transfer rate coefficient. The impact of the substrate concentration in the mating medium was highly correlated with the growth history of the donor strain. When the donor strain was harvested in exponential growth phase, no impact was observed; when the donor strain was taken from the stationary phase, however, a strong impact of the substrate concentration was measured: a 10-fold reduction in the substrate concentration decreased the observed plasmid transfer rate by 55%.
Collapse
Affiliation(s)
- B F Smets
- Department of Civil and Environmental Engineering, University of Connecticut, Storrs 06269-2037, USA
| | | | | |
Collapse
|