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Garavaglia M, Muzlera A, Valverde C. Comparative genomics and informational content analysis uncovered internal regions of the core genes rpoD, pepN and gltX for an MLSA with genome-level resolving power within the genus Pseudomonas. Mol Phylogenet Evol 2023; 179:107663. [PMID: 36372354 DOI: 10.1016/j.ympev.2022.107663] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 08/31/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
Abstract
In the field of prokaryotic taxonomy, there has been a recent transition towards phylogenomics as the gold standard approach. However, genome-based phylogenetics is still restrictive for its cost when managing large amounts of isolates. Fast, cheap, and taxonomically competent alternatives, like multilocus sequence analysis (MLSA) are thus recommendable. Nevertheless, the criteria for selecting the conserved genes for MLSA have not been explicit for different bacterial taxa, including the broadly diverse Pseudomonas genus. Here, we have carried out an unbiased and rational workflow to select internal sequence regions of Pseudomonas core genes (CG) for a MLSA with the best phylogenetic power, and with a resolution comparable to the genome-based ANI approach. A computational workflow was established to inspect 126 complete genomes of representatives from over 60 Pseudomonas species and subspecies, in order to identify the most informative CG internal regions and determine which combinations in sets of three partial CG sequences have comparable phylogenetic resolution to that of the current ANI standard. We found that the rpoD346-1196-pepN1711-2571-gltX86-909 concatenated sequences were the best performing in terms of phylogenetic robustness and resulted highly sensitive and specific when contrasted with ANI. The rpoD-pepN-gltX MLSA was validated in silico and in vitro. Altogether, the results presented here supports the proposal of the rpoD-pepN-gltX MLSA as a fast, affordable, and robust phylogenetic tool for members of the Pseudomonas genus.
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Affiliation(s)
- Matías Garavaglia
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
| | - Andrés Muzlera
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
| | - Claudio Valverde
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina.
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Harboul K, Alouiz I, Hammani K, El-Karkouri A. Isotherm and kinetics modeling of biosorption and bioreduction of the Cr(VI) by Brachybacterium paraconglomeratum ER41. Extremophiles 2022; 26:30. [PMID: 36149604 DOI: 10.1007/s00792-022-01278-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/06/2022] [Indexed: 11/04/2022]
Abstract
Chromium is one of the most widely used metals in industry. Hexavalent form [Cr(VI)], which is found in industrial discharges, is very toxic and very soluble in water. From soil taken from an abandoned lead and iron mine, a bacterial strain capable of reducing Cr(VI) was isolated and identified as Brachybacterium paraconglomeratum ER41. Objective of this work was to evaluate the power of this bacterium to reduce Cr(VI). Results obtained showed that this bacterium is capable of eliminating 100 mg/L of Cr(VI) after 48 h (pH 8 and temperature 30 °C). For modeling biosorption kinetics, pseudo-first-order and intraparticle diffusion models gave a better fit. Furthermore, the adsorption mechanism conformed well to Langmuir's isothermal model indicating monolayer type sorption. Biomass analysis of this bacterium before and after contact with chromium by scanning electron microscopy-energy-dispersive X-ray and by Fourier transform infrared spectroscopy showed that the surface ligands of bacterial wall are probably responsible for biosorption and bioreduction process. These results suggest a potential application of B. paraconglomeratum ER41 in bioremediation of polluted discharges.
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Affiliation(s)
- Kaoutar Harboul
- Natural Resources and Environment Laboratory, Polydisciplinary Faculty of Taza, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Imad Alouiz
- Natural Resources and Environment Laboratory, Polydisciplinary Faculty of Taza, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Khalil Hammani
- Natural Resources and Environment Laboratory, Polydisciplinary Faculty of Taza, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Abdenbi El-Karkouri
- Biotechnology, Environment, Agri-Food and Health Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco.
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Cafiero JH, Martini MC, Lozano MJ, Vacca C, Lagares A, Tomatis PE, Del Papa MF. BioF is a novel B2 metallo-β-lactamase from Pseudomonas sp. isolated from an on-farm biopurification system. Environ Microbiol 2021; 24:1247-1262. [PMID: 34725905 DOI: 10.1111/1462-2920.15822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/13/2021] [Accepted: 10/13/2021] [Indexed: 11/30/2022]
Abstract
Antimicrobial resistance represents a major global health concern and environmental bacteria are considered a source of resistance genes. Carbapenems are often used as the last antibiotic option to treat multidrug-resistant bacteria. Metallo-β-lactamases (MBLs) are able to render resistance to almost all β-lactam antibiotics, including carbapenems. Unfortunately, there are no inhibitors against MBLs for clinical use. Subclass B2 MBLs are the only enzymes working as strict carbapenemases, under-represented, encoded in chromosome genes and only functional as mono-zinc enzymes. Despite current efforts in MBLs inhibitor development, B2 carbapenemase activity is especially difficult to suppress, even in vitro. In this study we characterized BioF, a novel subclass B2 MBL identified in a new environmental Pseudomonas sp. strain isolated from an on-farm biopurification system (BPS). Although blaBioF is most likely a chromosomal gene, it is found in a genomic island and may represent a step previous to the horizontal transmission of B2 genes. The new B2 MBL is active as a mono-zinc enzyme and is a potent carbapenemase with incipient activity against some cephalosporins. BioF activity is not affected by excess zinc and is only inhibited at high metal chelator concentrations. The discovery and characterization of B2 MBL BioF as a potent carbapenemase in a BPS bacterial isolate emphasizes the importance of exploring antibiotic resistances existing in the environmental microbiota under the influence of human activities before they could emerge clinically.
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Affiliation(s)
- Juan Hilario Cafiero
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular (IBBM, CCT-CONICET-La Plata), Universidad Nacional de La Plata, Calle 115 entre 49 y 50, La Plata, 1900, Argentina
| | - María Carla Martini
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular (IBBM, CCT-CONICET-La Plata), Universidad Nacional de La Plata, Calle 115 entre 49 y 50, La Plata, 1900, Argentina
| | - Mauricio Javier Lozano
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular (IBBM, CCT-CONICET-La Plata), Universidad Nacional de La Plata, Calle 115 entre 49 y 50, La Plata, 1900, Argentina
| | - Carolina Vacca
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular (IBBM, CCT-CONICET-La Plata), Universidad Nacional de La Plata, Calle 115 entre 49 y 50, La Plata, 1900, Argentina
| | - Antonio Lagares
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular (IBBM, CCT-CONICET-La Plata), Universidad Nacional de La Plata, Calle 115 entre 49 y 50, La Plata, 1900, Argentina
| | - Pablo Emiliano Tomatis
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Ocampo y Esmeralda, Rosario, 2000, Argentina.,Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, 2000, Argentina
| | - María Florencia Del Papa
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular (IBBM, CCT-CONICET-La Plata), Universidad Nacional de La Plata, Calle 115 entre 49 y 50, La Plata, 1900, Argentina
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4
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Bhatt P, Bhandari G, Bhatt K, Maithani D, Mishra S, Gangola S, Bhatt R, Huang Y, Chen S. Plasmid-mediated catabolism for the removal of xenobiotics from the environment. JOURNAL OF HAZARDOUS MATERIALS 2021; 420:126618. [PMID: 34329102 DOI: 10.1016/j.jhazmat.2021.126618] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 05/27/2021] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
The large-scale application of xenobiotics adversely affects the environment. The genes that are present in the chromosome of the bacteria are considered nonmobile, whereas the genes present on the plasmids are considered mobile genetic elements. Plasmids are considered indispensable for xenobiotic degradation into the contaminated environment. In the contaminated sites, bacteria with plasmids can transfer the mobile genetic element into another strain. This mechanism helps in spreading the catabolic genes into the bacterial population at the contaminated sites. The indigenous microbial strains with such degradative plasmids are important for the bioremediation of xenobiotics. Environmental factors play a critical role in the conjugation efficiency, which is involved in the bioremediation of the xenobiotics at the contaminated sites. However, there is still a need for more research to fill in the gaps regarding plasmids and their impact on bioremediation. This review explores the role of bacterial plasmids in the bioremediation of xenobiotics from contaminated environments.
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Affiliation(s)
- Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Geeta Bhandari
- Department of Biochemistry and Biotechnology, Sardar Bhagwan Singh University, Dehradun 248161, Uttarakhand, India
| | - Kalpana Bhatt
- Department of Botany and Microbiology, Gurukul Kangri University, Haridwar 249404, Uttarakhand, India
| | - Damini Maithani
- Department of Microbiology, G.B Pant University of Agriculture and Technology Pantnagar, U.S Nagar, Uttarakhand, India
| | - Sandhya Mishra
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Saurabh Gangola
- School of Agriculture, Graphic Era Hill University, Bhimtal Campus, 263136, Uttarakhand, India
| | - Rakesh Bhatt
- Department of Civil Engineering, Indian Institute of Technology, Kanpur 208016, Uttar Pradesh, India
| | - Yaohua Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
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Rios Miguel AB, Jetten MS, Welte CU. The role of mobile genetic elements in organic micropollutant degradation during biological wastewater treatment. WATER RESEARCH X 2020; 9:100065. [PMID: 32984801 PMCID: PMC7494797 DOI: 10.1016/j.wroa.2020.100065] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/19/2020] [Accepted: 08/28/2020] [Indexed: 05/24/2023]
Abstract
Wastewater treatment plants (WWTPs) are crucial for producing clean effluents from polluting sources such as hospitals, industries, and municipalities. In recent decades, many new organic compounds have ended up in surface waters in concentrations that, while very low, cause (chronic) toxicity to countless organisms. These organic micropollutants (OMPs) are usually quite recalcitrant and not sufficiently removed during wastewater treatment. Microbial degradation plays a pivotal role in OMP conversion. Microorganisms can adapt their metabolism to the use of novel molecules via mutations and rearrangements of existing genes in new clusters. Many catabolic genes have been found adjacent to mobile genetic elements (MGEs), which provide a stable scaffold to host new catabolic pathways and spread these genes in the microbial community. These mobile systems could be engineered to enhance OMP degradation in WWTPs, and this review aims to summarize and better understand the role that MGEs might play in the degradation and wastewater treatment process. Available data about the presence of catabolic MGEs in WWTPs are reviewed, and current methods used to identify and measure MGEs in environmental samples are critically evaluated. Finally, examples of how these MGEs could be used to improve micropollutant degradation in WWTPs are outlined. In the near future, advances in the use of MGEs will hopefully enable us to apply selective augmentation strategies to improve OMP conversion in WWTPs.
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Affiliation(s)
- Ana B. Rios Miguel
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525, AJ Nijmegen, the Netherlands
| | - Mike S.M. Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525, AJ Nijmegen, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525, AJ Nijmegen, the Netherlands
| | - Cornelia U. Welte
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525, AJ Nijmegen, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525, AJ Nijmegen, the Netherlands
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Conjugative Transfer of IncP-9 Catabolic Plasmids Requires a Previously Uncharacterized Gene, mpfK, Whose Homologs Are Conserved in Various MPF T-Type Plasmids. Appl Environ Microbiol 2019; 85:AEM.01850-19. [PMID: 31604768 DOI: 10.1128/aem.01850-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/02/2019] [Indexed: 11/20/2022] Open
Abstract
Conjugative transfer of bacterial plasmids to recipient cells is often mediated by type IV secretion machinery. Experimental investigations into the minimal gene sets required for efficient conjugative transfer suggest that such gene sets are variable, depending on plasmids. We have been analyzing the conjugative transfer of Pseudomonas-derived and IncP-9 plasmids, NAH7 and pWW0, whose conjugation systems belong to the MPFT type. Our deletion analysis and synthetic biology analysis in this study showed that these plasmids require previously uncharacterized genes, mpfK (formerly orf34) and its functional homolog, kikA, respectively, for their efficient conjugative transfer. MpfK was localized in periplasm and had four cysteine residues whose intramolecular or intermolecular disulfide bond formation was suggested to be important for efficient conjugative transfer. The mpfK homologs were specifically carried by many MPFT-type plasmids, including non-IncP-9 plasmids, such as R388 and R751. Intriguingly, the mpfK homologs from the two non-IncP-9 plasmids were not required for conjugation of their plasmids, but were able to complement efficiently the transfer defect of the NAH7 mpfK mutant. Our results suggested the importance of the mpfK homologs for conjugative transfer of MPFT-type plasmids.IMPORTANCE IncP-9 plasmids are important mobile genetic elements for the degradation of various aromatic hydrocarbons. Elucidation of conjugative transfer of such plasmids is expected to greatly contribute to our understanding of its role in the bioremediation of polluted environments. The present study mainly focused on the conjugation system of NAH7, a well-studied and naphthalene-catabolic IncP-9 plasmid. Our analysis showed that the NAH7 conjugation system uniquely requires, in addition to the conserved components of the type IV secretion system (T4SS), a previously uncharacterized periplasmic protein, MpfK, for successful conjugation. Our findings collectively revealed a unique type of T4SS-associated conjugation system in the IncP-9 plasmids.
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Martini MC, Quiroga MP, Pistorio M, Lagares A, Centrón D, Del Papa MF. Novel environmental class 1 integrons and cassette arrays recovered from an on-farm bio-purification plant. FEMS Microbiol Ecol 2017; 94:4781311. [DOI: 10.1093/femsec/fix190] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 12/27/2017] [Indexed: 11/12/2022] Open
Affiliation(s)
- María Carla Martini
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 115 entre 49 y 50, 1900, La Plata, Argentina
| | - María Paula Quiroga
- Instituto de Microbiología y Parasitología Médica, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Paraguay 2155, 1121, Ciudad Autónoma de Buenos Aires, Argentina
| | - Mariano Pistorio
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 115 entre 49 y 50, 1900, La Plata, Argentina
| | - Antonio Lagares
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 115 entre 49 y 50, 1900, La Plata, Argentina
| | - Daniela Centrón
- Instituto de Microbiología y Parasitología Médica, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Paraguay 2155, 1121, Ciudad Autónoma de Buenos Aires, Argentina
| | - María Florencia Del Papa
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 115 entre 49 y 50, 1900, La Plata, Argentina
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Groundwater contamination with 2,6-dichlorobenzamide (BAM) and perspectives for its microbial removal. Appl Microbiol Biotechnol 2017; 101:5235-5245. [PMID: 28616645 DOI: 10.1007/s00253-017-8362-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/23/2017] [Accepted: 05/25/2017] [Indexed: 01/26/2023]
Abstract
The pesticide metabolite 2,6-dichlorobenzamide (BAM) is very persistent in both soil and groundwater and has become one of the most frequently detected groundwater micropollutants. BAM is not removed by the physico-chemical treatment techniques currently used in drinking water treatment plants (DWTP); therefore, if concentrations exceed the legal threshold limit, it represents a sizeable problem for the stability and quality of drinking water production, especially in places that depend on groundwater for drinking water. Bioremediation is suggested as a valuable strategy for removing BAM from groundwater by deploying dedicated BAM-degrading bacteria in DWTP sand filters. Only a few bacterial strains with the capability to degrade BAM have been isolated, and of these, only three isolates belonging to the Aminobacter genus are able to mineralise BAM. Considerable effort has been made to elucidate degradation pathways, kinetics and degrader genes, and research has recently been presented on the application of strain Aminobacter sp. MSH1 for the purification of BAM-contaminated water. The aim of the present review was to provide insight into the issue of BAM contamination and to report on the current status and knowledge with regard to the application of microorganisms for purification of BAM-contaminated water resources. This paper discusses the prospects and challenges for bioaugmentation of DWTP sand filters with specific BAM-degrading bacteria and identifies relevant perspectives for future research.
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Isolation of Viable but Non-culturable Bacteria from Printing and Dyeing Wastewater Bioreactor Based on Resuscitation Promoting Factor. Curr Microbiol 2017; 74:787-797. [DOI: 10.1007/s00284-017-1240-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 03/21/2017] [Indexed: 12/22/2022]
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Kishida K, Inoue K, Ohtsubo Y, Nagata Y, Tsuda M. Host Range of the Conjugative Transfer System of IncP-9 Naphthalene-Catabolic Plasmid NAH7 and Characterization of Its oriT Region and Relaxase. Appl Environ Microbiol 2017; 83:e02359-16. [PMID: 27742684 PMCID: PMC5165122 DOI: 10.1128/aem.02359-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/06/2016] [Indexed: 12/21/2022] Open
Abstract
NAH7 and pWW0 from gammaproteobacterial Pseudomonas putida strains are IncP-9 conjugative plasmids that carry the genes for degradation of naphthalene and toluene, respectively. Although such genes on these plasmids are well-characterized, experimental investigation of their conjugation systems remains at a primitive level. To clarify these conjugation systems, in this study, we investigated the NAH7-encoded conjugation system by (i) analyzing the origin of its conjugative transfer (oriT)-containing region and its relaxase, which specifically nicks within the oriT region for initiation of transfer, and (ii) comparing the conjugation systems between NAH7 and pWW0. The NAH7 oriT (oriTN) region was located within a 430-bp fragment, and the strand-specific nicking (nic) site and its upstream sequences that were important for efficient conjugation in the oriTN region were identified. Unlike many other relaxases, the NAH7 relaxase exhibited unique features in its ability to catalyze, in a conjugation-independent manner, the site-specific intramolecular recombination between two copies of the oriTN region, between two copies of the pWW0 oriT (oriTW) region (which is clearly different from the oriTN region), and between the oriTN and oriTW regions. The pWW0 relaxase, which is also clearly different from the NAH7 relaxase, was strongly suggested to have the ability to conjugatively and efficiently mobilize the oriTN-containing plasmid. Such a plasmid was, in the presence of the NAH7Δnic derivative, conjugatively transferable to alphaproteobacterial and betaproteobacterial strains in which the NAH7 replication machinery is nonfunctional, indicating that the NAH7 conjugation system has a broader host range than its replication system. IMPORTANCE Various studies have strongly suggested an important contribution of conjugative transfer of catabolic plasmids to the rapid and wide dissemination of the plasmid-loaded degradation genes to microbial populations. Degradation genes on such plasmids are often loaded on transposons, which can be inserted into the genomes of the recipient bacterial strains where the transferred plasmids cannot replicate. The aim was to advance detailed molecular knowledge of the determinants of host range for plasmids. This aim is expected to be easily and comprehensively achieved using an experimental strategy in which the oriT region is connected with a plasmid that has a broad host range of replication. Using such a strategy in this study, we showed that (i) the NAH7 oriT-relaxase system has unique properties that are significantly different from other well-studied systems and (ii) the host range of the NAH7 conjugation system is broader than previously thought.
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Affiliation(s)
- Kouhei Kishida
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Kei Inoue
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Yoshiyuki Ohtsubo
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Yuji Nagata
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Masataka Tsuda
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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11
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Martini MC, Wibberg D, Lozano M, Torres Tejerizo G, Albicoro FJ, Jaenicke S, van Elsas JD, Petroni A, Garcillán-Barcia MP, de la Cruz F, Schlüter A, Pühler A, Pistorio M, Lagares A, Del Papa MF. Genomics of high molecular weight plasmids isolated from an on-farm biopurification system. Sci Rep 2016; 6:28284. [PMID: 27321040 PMCID: PMC4913263 DOI: 10.1038/srep28284] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/31/2016] [Indexed: 12/02/2022] Open
Abstract
The use of biopurification systems (BPS) constitutes an efficient strategy to eliminate pesticides from polluted wastewaters from farm activities. BPS environments contain a high microbial density and diversity facilitating the exchange of information among bacteria, mediated by mobile genetic elements (MGEs), which play a key role in bacterial adaptation and evolution in such environments. Here we sequenced and characterized high-molecular-weight plasmids from a bacterial collection of an on-farm BPS. The high-throughput-sequencing of the plasmid pool yielded a total of several Mb sequence information. Assembly of the sequence data resulted in six complete replicons. Using in silico analyses we identified plasmid replication genes whose encoding proteins represent 13 different Pfam families, as well as proteins involved in plasmid conjugation, indicating a large diversity of plasmid replicons and suggesting the occurrence of horizontal gene transfer (HGT) events within the habitat analyzed. In addition, genes conferring resistance to 10 classes of antimicrobial compounds and those encoding enzymes potentially involved in pesticide and aromatic hydrocarbon degradation were found. Global analysis of the plasmid pool suggest that the analyzed BPS represents a key environment for further studies addressing the dissemination of MGEs carrying catabolic genes and pathway assembly regarding degradation capabilities.
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Affiliation(s)
- María C Martini
- Instituto de Biotecnología y Biología Molecular (IBBM), CONICET- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, Institute for Genome Research and Systems Biology, D-33615 Bielefeld, Germany
| | - Mauricio Lozano
- Instituto de Biotecnología y Biología Molecular (IBBM), CONICET- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - Gonzalo Torres Tejerizo
- Instituto de Biotecnología y Biología Molecular (IBBM), CONICET- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - Francisco J Albicoro
- Instituto de Biotecnología y Biología Molecular (IBBM), CONICET- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - Sebastian Jaenicke
- Center for Biotechnology (CeBiTec), Bielefeld University, Institute for Genome Research and Systems Biology, D-33615 Bielefeld, Germany
| | | | - Alejandro Petroni
- Servicio Antimicrobianos, Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas-ANLIS Dr. Carlos G. Malbrán, Buenos Aires, Argentina
| | - M Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-Consejo Superior de Investigaciones Científicas (CSIC), 39011 Santander, Spain
| | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-Consejo Superior de Investigaciones Científicas (CSIC), 39011 Santander, Spain
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Institute for Genome Research and Systems Biology, D-33615 Bielefeld, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Bielefeld University, Institute for Genome Research and Systems Biology, D-33615 Bielefeld, Germany
| | - Mariano Pistorio
- Instituto de Biotecnología y Biología Molecular (IBBM), CONICET- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - Antonio Lagares
- Instituto de Biotecnología y Biología Molecular (IBBM), CONICET- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - María F Del Papa
- Instituto de Biotecnología y Biología Molecular (IBBM), CONICET- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
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