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Castro-Gutierrez VM, Hassard F, Moir JW. Probe-based qPCR assay enables the rapid and specific detection of bacterial degrading genes for the pesticide metaldehyde in soil. METHODS IN MICROBIOLOGY 2022; 195:106447. [PMID: 35271872 DOI: 10.1016/j.mimet.2022.106447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 03/03/2022] [Accepted: 03/03/2022] [Indexed: 11/30/2022]
Abstract
Metaldehyde, a molluscicide pesticide, has been identified as a pollutant of concern due to its repeated detection in drinking water, thereby generating numerous compliance failures for water utilities. Biological degradation potential for metaldehyde is widespread in soils, occurring at different rates, but to date, no molecular methods for its assessment have been reported. Here, three genes belonging to a shared metaldehyde-degrading gene cluster present in bacteria were used as candidates for development of a quantitative PCR (qPCR) assay for assessing the metaldehyde-degrading potential in soil. Screening of gene targets, primer pairs and optimization of reaction conditions led to the development of a sensitive and specific probe-based qPCR method for quantifying the mahY metaldehyde-degrading gene from soil. The technique was tested across 8 soils with different compositions and origins. The degrading pathway was detected in 4/8 soils, in which a higher number of gene copies correlated with periods of greater metaldehyde removal. Additionally, swift elimination of the pesticide was observed in soils with an elevated initial number of mahY gene copies. The gene cluster was not detected in other soils, even though metaldehyde removal occurred, indicating that other biological degrading pathways are also important in nature. The method described here is the first one available to estimate the microbial metaldehyde degradation potential and activity in soils, and can also be used to detect degrading microorganisms in systems such as sand filters for water purification or to monitor degrading strains in engineered processes.
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Affiliation(s)
- V M Castro-Gutierrez
- Department of Biology, University of York, Heslington, York, UK; Environmental Pollution Research Center (CICA), University of Costa Rica, Montes de Oca 11501, Costa Rica
| | - F Hassard
- Cranfield University, College Road, Cranfield, Bedfordshire MK43 0AL, UK
| | - J W Moir
- Department of Biology, University of York, Heslington, York, UK.
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Complete Genome Sequences of Four Atrazine-Degrading Bacterial Strains, Pseudomonas sp. Strain ADPe, Arthrobacter sp. Strain TES, Variovorax sp. Strain 38R, and Chelatobacter sp. Strain SR38. Microbiol Resour Announc 2021; 10:10/1/e01080-20. [PMID: 33414292 PMCID: PMC8407692 DOI: 10.1128/mra.01080-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We report here the complete genome sequences of four atrazine-degrading bacteria. Their genomes will serve as references for determining the genetic changes that have occurred during an evolution experiment. We report here the complete genome sequences of four atrazine-degrading bacteria. Their genomes will serve as references for determining the genetic changes that have occurred during an evolution experiment.
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Pesce S, Ghiglione JF, Topp E, Martin-Laurent F. Editorial: Microbial Ecotoxicology. Front Microbiol 2020; 11:1342. [PMID: 32676059 PMCID: PMC7333374 DOI: 10.3389/fmicb.2020.01342] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 05/26/2020] [Indexed: 12/12/2022] Open
Affiliation(s)
| | - Jean-François Ghiglione
- CNRS, UMR 7621 Laboratoire d'Océanographie Microbienne, Sorbonne Université, Observatoire Océanologique de Banyuls-sur-Mer, Banyuls-sur-Mer, France
| | - Edward Topp
- Agriculture and Agri-Food Canada, University of Western Ontario, London, ON, Canada
| | - Fabrice Martin-Laurent
- AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Agroécologie, Dijon, France
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Werner J, Nour E, Bunk B, Spröer C, Smalla K, Springael D, Öztürk B. PromA Plasmids Are Instrumental in the Dissemination of Linuron Catabolic Genes Between Different Genera. Front Microbiol 2020; 11:149. [PMID: 32132980 PMCID: PMC7039861 DOI: 10.3389/fmicb.2020.00149] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/22/2020] [Indexed: 01/31/2023] Open
Abstract
PromA plasmids are broad host range (BHR) plasmids, which are often cryptic and hence have an uncertain ecological role. We present three novel PromA γ plasmids which carry genes associated with degradation of the phenylurea herbicide linuron, two of which originated from unrelated Hydrogenophaga hosts isolated from different environments (pPBL-H3-2 and pBPS33-2), and one (pEN1) which was exogenously captured from an on-farm biopurification system (BPS). Hydrogenophaga sp. plasmid pBPS33-2 carries all three necessary gene clusters (hylA, dca, ccd) determining the three main steps for conversion of linuron to Krebs cycle intermediates, while pEN1 only determines the initial linuron hydrolysis step. Hydrogenophaga sp. plasmid pPBL-H3-2 exists as two variants, both containing ccd but with the hylA and dca gene modules interchanged between each other at exactly the same location. Linuron catabolic gene clusters that determine the same step were identical on all plasmids, encompassed in differently arranged constellations and characterized by the presence of multiple IS1071 elements. In all plasmids except pEN1, the insertion spot of the catabolic genes in the PromA γ plasmids was the same. Highly similar PromA plasmids carrying the linuron degrading gene cargo at the same insertion spot were previously identified in linuron degrading Variovorax sp. Interestingly, in both Hydrogenophaga populations not every PromA plasmid copy carries catabolic genes. The results indicate that PromA plasmids are important vehicles of linuron catabolic gene dissemination, rather than being cryptic and only important for the mobilization of other plasmids.
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Affiliation(s)
- Johannes Werner
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research, Rostock, Germany
| | - Eman Nour
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Braunschweig, Germany
- Faculty of Organic Agriculture, Heliopolis University for Sustainable Development, Cairo, Egypt
| | - Boyke Bunk
- Bioinformatics Department, Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Central Services, Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Braunschweig, Germany
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven, Leuven, Belgium
| | - Başak Öztürk
- Division of Soil and Water Management, KU Leuven, Leuven, Belgium
- Junior Research Group Microbial Biotechnology, Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Labour sharing promotes coexistence in atrazine degrading bacterial communities. Sci Rep 2019; 9:18363. [PMID: 31798012 PMCID: PMC6892810 DOI: 10.1038/s41598-019-54978-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 11/22/2019] [Indexed: 12/13/2022] Open
Abstract
Microbial communities are pivotal in the biodegradation of xenobiotics including pesticides. In the case of atrazine, multiple studies have shown that its degradation involved a consortia rather than a single species, but little is known about how interdependency between the species composing the consortium is set up. The Black Queen Hypothesis (BQH) formalized theoretically the conditions leading to the evolution of dependency between species: members of the community called ‘helpers’ provide publicly common goods obtained from the costly degradation of a compound, while others called ‘beneficiaries’ take advantage of the public goods, but lose access to the primary resource through adaptive degrading gene loss. Here, we test whether liquid media supplemented with the herbicide atrazine could support coexistence of bacterial species through BQH mechanisms. We observed the establishment of dependencies between species through atrazine degrading gene loss. Labour sharing between members of the consortium led to coexistence of multiple species on a single resource and improved atrazine degradation potential. Until now, pesticide degradation has not been approached from an evolutionary perspective under the BQH framework. We provide here an evolutionary explanation that might invite researchers to consider microbial consortia, rather than single isolated species, as an optimal strategy for isolation of xenobiotics degraders.
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Lazarini-Martínez A, Pérez-Valdespino A, Martínez FH, Ordaz NR, Galíndez-Mayer J, Juárez-Ramírez C, Curiel-Quesada E. Assembly of an atrazine catabolic operon and its introduction to Gram-negative hosts for robust and stable degradation of triazine herbicides. FEMS Microbiol Lett 2019; 366:5634263. [DOI: 10.1093/femsle/fnz233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/19/2019] [Indexed: 01/24/2023] Open
Abstract
ABSTRACTIn 1995, Pseudomonas sp. ADP, capable of metabolizing atrazine, was isolated from contaminated soil. Genes responsible for atrazine mineralization were found scattered in the 108.8 kb pADP-1 plasmid carried by this strain, some of them flanked by insertion sequences rendering them unstable. The goal of this work was to construct a transcriptional unit containing the atz operon in an easy to transfer manner, to be introduced and inherited stably by Gram-negative bacteria. atz genes were PCR amplified, joined into an operon and inserted onto the mobilizable plasmid pBAMD1–2. Primers were designed to add efficient transcription and translation signals. Plasmid bearing the atz operon was transferred to different Gram-negative strains by conjugation, which resulted in Tn5 transposase-mediated chromosomal insertion of the atz operon. To test the operon activity, atrazine degradation by transposants was assessed both colorimetrically and by high-performance liquid chromatography (HPLC). Transposants mineralized atrazine more efficiently than wild-type Pseudomonas sp. ADP and did not accumulate cyanuric acid. Atrazine degradation was not repressed by simple nitrogen sources. Genes conferring atrazine-mineralizing capacities were stable and had little or null effect on the fitness of different transposants. Introduction of catabolic operons in a stable fashion could be used to develop bacteria with better degrading capabilities useful in bioremediation.
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Affiliation(s)
- Alfredo Lazarini-Martínez
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás. CP11340 Mexico City, Mexico
| | - Abigail Pérez-Valdespino
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás. CP11340 Mexico City, Mexico
| | - Fernando Hernández Martínez
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás. CP11340 Mexico City, Mexico
| | - Nora Ruiz Ordaz
- Department of Biochemical Engineering, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional. Av. Wilfrido Massieu 399, Unidad Adolfo López Mateos, CP07738 Mexico City, Mexico
| | - Juvencio Galíndez-Mayer
- Department of Biochemical Engineering, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional. Av. Wilfrido Massieu 399, Unidad Adolfo López Mateos, CP07738 Mexico City, Mexico
| | - Cleotilde Juárez-Ramírez
- Department of Biochemical Engineering, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional. Av. Wilfrido Massieu 399, Unidad Adolfo López Mateos, CP07738 Mexico City, Mexico
| | - Everardo Curiel-Quesada
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás. CP11340 Mexico City, Mexico
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Silva VP, Moreira-Santos M, Mateus C, Teixeira T, Ribeiro R, Viegas CA. Evaluation of Arthrobacter aurescens Strain TC1 as Bioaugmentation Bacterium in Soils Contaminated with the Herbicidal Substance Terbuthylazine. PLoS One 2015; 10:e0144978. [PMID: 26662024 PMCID: PMC4684385 DOI: 10.1371/journal.pone.0144978] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 11/25/2015] [Indexed: 11/17/2022] Open
Abstract
In the last years the chloro-s-triazine active substance terbuthylazine has been increasingly used as an herbicide and may leave residues in the environment which can be of concern. The present study aimed at developing a bioaugmentation tool based on the soil bacterium Arthrobacter aurescens strain TC1 for the remediation of terbuthylazine contaminated soils and at examining its efficacy for both soil and aquatic compartments. First, the feasibility of growing the bioaugmentation bacterium inocula on simple sole nitrogen sources (ammonium and nitrate) instead of atrazine, while still maintaining its efficiency to biodegrade terbuthylazine was shown. In sequence, the successful and quick (3 days) bioremediation efficacy of ammonium-grown A. aurescens TC1 cells was proven in a natural soil freshly spiked or four-months aged with commercial terbuthylazine at a dose 10× higher than the recommended in corn cultivation, to mimic spill situations. Ecotoxicity assessment of the soil eluates towards a freshwater microalga supported the effectiveness of the bioaugmentation tool. Obtained results highlight the potential to decontaminate soil while minimizing terbuthylazine from reaching aquatic compartments via the soil-water pathway. The usefulness of this bioaugmentation tool to provide rapid environment decontamination is particularly relevant in the event of accidental high herbicide contamination. Its limitations and advantages are discussed.
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Affiliation(s)
- Vera P Silva
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico (IST), Universidade de Lisboa (UL), Lisboa, Portugal
| | - Matilde Moreira-Santos
- CFE-Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Carla Mateus
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico (IST), Universidade de Lisboa (UL), Lisboa, Portugal
| | - Tânia Teixeira
- CFE-Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Rui Ribeiro
- CFE-Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Cristina A Viegas
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico (IST), Universidade de Lisboa (UL), Lisboa, Portugal.,Department of Bioengineering, IST, UL, Lisboa, Portugal
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Platero AI, Santero E, Govantes F. Genetic evidence of a high-affinity cyanuric acid transport system in Pseudomonas sp. ADP. FEMS Microbiol Lett 2014; 352:150-6. [PMID: 24484197 DOI: 10.1111/1574-6968.12392] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 01/24/2014] [Accepted: 01/27/2014] [Indexed: 11/28/2022] Open
Abstract
The Pseudomonas sp. ADP plasmid pADP-1 encodes the activities involved in the hydrolytic degradation of the s-triazine herbicide atrazine. Here, we explore the presence of a specific transport system for the central intermediate of the atrazine utilization pathway, cyanuric acid, in Pseudomonas sp. ADP. Growth in fed-batch cultures containing limiting cyanuric acid concentrations is consistent with high-affinity transport of this substrate. Acquisition of the ability to grow at low cyanuric acid concentrations upon conjugal transfer of pADP1 to the nondegrading host Pseudomonas putida KT2442 suggests that all activities required for this phenotype are encoded in this plasmid. Co-expression of the pADP1-borne atzDEF and atzTUVW genes, encoding the cyanuric acid utilization pathway and the subunits of an ABC-type solute transport system, in P. putida KT2442 was sufficient to promote growth at cyanuric acid concentrations as low as 50 μM in batch culture. Taken together, our results strongly suggest that the atzTUVW gene products are involved in high-affinity transport of cyanuric acid.
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Affiliation(s)
- Ana I Platero
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Sevilla, Spain; Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Sevilla, Spain
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Udiković-Kolić N, Scott C, Martin-Laurent F. Evolution of atrazine-degrading capabilities in the environment. Appl Microbiol Biotechnol 2012; 96:1175-89. [DOI: 10.1007/s00253-012-4495-0] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 10/02/2012] [Accepted: 10/03/2012] [Indexed: 11/30/2022]
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