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Sato Y, Jang S, Takeshita K, Itoh H, Koike H, Tago K, Hayatsu M, Hori T, Kikuchi Y. Insecticide resistance by a host-symbiont reciprocal detoxification. Nat Commun 2021; 12:6432. [PMID: 34741016 PMCID: PMC8571283 DOI: 10.1038/s41467-021-26649-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 10/13/2021] [Indexed: 02/03/2023] Open
Abstract
Insecticide resistance is one of the most serious problems in contemporary agriculture and public health. Although recent studies revealed that insect gut symbionts contribute to resistance, the symbiont-mediated detoxification process remains unclear. Here we report the in vivo detoxification process of an organophosphorus insecticide, fenitrothion, in the bean bug Riptortus pedestris. Using transcriptomics and reverse genetics, we reveal that gut symbiotic bacteria degrade this insecticide through a horizontally acquired insecticide-degrading enzyme into the non-insecticidal but bactericidal compound 3-methyl-4-nitrophenol, which is subsequently excreted by the host insect. This integrated "host-symbiont reciprocal detoxification relay" enables the simultaneous maintenance of symbiosis and efficient insecticide degradation. We also find that the symbiont-mediated detoxification process is analogous to the insect genome-encoded fenitrothion detoxification system present in other insects. Our findings highlight the capacity of symbiosis, combined with horizontal gene transfer in the environment, as a powerful strategy for an insect to instantly eliminate a toxic chemical compound, which could play a critical role in the human-pest arms race.
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Affiliation(s)
- Yuya Sato
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Center, 305-8569, Tsukuba, Japan
| | - Seonghan Jang
- Graduate School of Agriculture, Hokkaido University, 060-8589, Sapporo, Japan
| | - Kazutaka Takeshita
- Faculty of Bioresource Sciences, Akita Prefectural University, 010-0195, Akita, Japan
| | - Hideomi Itoh
- Bioproduction Research Institute, AIST, Hokkaido Center, 062-8517, Sapporo, Japan
| | - Hideaki Koike
- Bioproduction Research Institute, AIST, Tsukuba Center, 305-8566, Tsukuba, Japan
| | - Kanako Tago
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305-8604, Tsukuba, Japan
| | - Masahito Hayatsu
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305-8604, Tsukuba, Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Center, 305-8569, Tsukuba, Japan
| | - Yoshitomo Kikuchi
- Graduate School of Agriculture, Hokkaido University, 060-8589, Sapporo, Japan. .,Bioproduction Research Institute, AIST, Hokkaido Center, 062-8517, Sapporo, Japan.
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2
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Ortiz-Hernández ML, Gama-Martínez Y, Fernández-López M, Castrejón-Godínez ML, Encarnación S, Tovar-Sánchez E, Salazar E, Rodríguez A, Mussali-Galante P. Transcriptomic analysis of Burkholderia cenocepacia CEIB S5-2 during methyl parathion degradation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:42414-42431. [PMID: 33813711 DOI: 10.1007/s11356-021-13647-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
Methyl parathion (MP) is a highly toxic organophosphorus pesticide associated with water, soil, and air pollution events. The identification and characterization of microorganisms capable of biodegrading pollutants are an important environmental task for bioremediation of pesticide impacted sites. The strain Burkholderia cenocepacia CEIB S5-2 is a bacterium capable of efficiently hydrolyzing MP and biodegrade p-nitrophenol (PNP), the main MP hydrolysis product. Due to the high PNP toxicity over microbial living forms, the reports on bacterial PNP biodegradation are scarce. According to the genomic data, the MP- and PNP-degrading ability observed in B. cenocepacia CEIB S5-2 is related to the presence of the methyl parathion-degrading gene (mpd) and the gene cluster pnpABA'E1E2FDC, which include the genes implicated in the PNP degradation. In this work, the transcriptomic analysis of the strain in the presence of MP revealed the differential expression of 257 genes, including all genes implicated in the PNP degradation, as well as a set of genes related to the sensing of environmental changes, the response to stress, and the degradation of aromatic compounds, such as translational regulators, membrane transporters, efflux pumps, and oxidative stress response genes. These findings suggest that these genes play an important role in the defense against toxic effects derived from the MP and PNP exposure. Therefore, B. cenocepacia CEIB S5-2 has a great potential for application in pesticide bioremediation approaches due to its biodegradation capabilities and the differential expression of genes for resistance to MP and PNP.
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Affiliation(s)
- Ma Laura Ortiz-Hernández
- Misión Sustentabilidad México A.C., Priv. Laureles 6, Col. Chamilpa, C.P 62210, Cuernavaca, Morelos, México
| | - Yitzel Gama-Martínez
- Centro de Investigación en Biotecnología, Laboratorio de Investigaciones Ambientales, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, C.P. 62209, Cuernavaca, Morelos, México
| | - Maikel Fernández-López
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, C.P 62209, Cuernavaca, Morelos, México
| | - María Luisa Castrejón-Godínez
- Facultad de Ciencias Biológicas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, C.P 62209, Cuernavaca, Morelos, México
| | - Sergio Encarnación
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n, Col. Chamilpa, C.P 62210, Cuernavaca, Morelos, México
| | - Efraín Tovar-Sánchez
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, C.P 62209, Cuernavaca, Morelos, México
| | - Emmanuel Salazar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n, Col. Chamilpa, C.P 62210, Cuernavaca, Morelos, México
| | - Alexis Rodríguez
- Centro de Investigación en Biotecnología, Laboratorio de Investigaciones Ambientales, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, C.P. 62209, Cuernavaca, Morelos, México.
| | - Patricia Mussali-Galante
- Centro de Investigación en Biotecnología, Laboratorio de Investigaciones Ambientales, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, C.P. 62209, Cuernavaca, Morelos, México.
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3
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Omics Approaches to Pesticide Biodegradation. Curr Microbiol 2020; 77:545-563. [DOI: 10.1007/s00284-020-01916-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 02/08/2020] [Indexed: 02/08/2023]
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4
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Itoh H, Hori T, Sato Y, Nagayama A, Tago K, Hayatsu M, Kikuchi Y. Infection dynamics of insecticide-degrading symbionts from soil to insects in response to insecticide spraying. THE ISME JOURNAL 2018; 12:909-920. [PMID: 29343832 PMCID: PMC5864243 DOI: 10.1038/s41396-017-0021-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 10/26/2017] [Accepted: 11/11/2017] [Indexed: 11/09/2022]
Abstract
Insecticide resistance is a serious concern in modern agriculture, and an understanding of the underlying evolutionary processes is pivotal to prevent the problem. The bean bug Riptortus pedestris, a notorious pest of leguminous crops, acquires a specific Burkholderia symbiont from the environment every generation, and harbors the symbiont in the midgut crypts. The symbiont's natural role is to promote insect development but the insect host can also obtain resistance against the insecticide fenitrothion (MEP) by acquiring MEP-degrading Burkholderia from the environment. To understand the developing process of the symbiont-mediated MEP resistance in response to the application of the insecticide, we investigated here in parallel the soil bacterial dynamics and the infected gut symbionts under different MEP-spraying conditions by culture-dependent and culture-independent analyses, in conjunction with stinkbug rearing experiments. We demonstrate that MEP application did not affect the total bacterial soil population but significantly decreased its diversity while it dramatically increased the proportion of MEP-degrading bacteria, mostly Burkholderia. Moreover, we found that the infection of stinkbug hosts with MEP-degrading Burkholderia is highly specific and efficient, and is established after only a few times of insecticide spraying at least in a field soil with spraying history, suggesting that insecticide resistance could evolve in a pest bug population more quickly than was thought before.
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Affiliation(s)
- Hideomi Itoh
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Yuya Sato
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Atsushi Nagayama
- Department of Agriculture, Forestry, and Fisheries, Okinawa Prefecture Government Office, Naha, Japan
| | - Kanako Tago
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Masahito Hayatsu
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Yoshitomo Kikuchi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan.
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan.
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5
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Itoh H, Tago K, Hayatsu M, Kikuchi Y. Detoxifying symbiosis: microbe-mediated detoxification of phytotoxins and pesticides in insects. Nat Prod Rep 2018; 35:434-454. [DOI: 10.1039/c7np00051k] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Symbiotic microorganisms degrade natural and artificial toxic compounds, and confer toxin resistance on insect hosts.
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Affiliation(s)
- Hideomi Itoh
- Bioproduction Research Institute
- National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido
- Sapporo 062-8517
- Japan
| | - Kanako Tago
- Institute for Agro-Environmental Sciences
- National Agriculture and Food Research Organization (NARO)
- Tsukuba 305-8604
- Japan
| | - Masahito Hayatsu
- Institute for Agro-Environmental Sciences
- National Agriculture and Food Research Organization (NARO)
- Tsukuba 305-8604
- Japan
| | - Yoshitomo Kikuchi
- Bioproduction Research Institute
- National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido
- Sapporo 062-8517
- Japan
- Graduate School of Agriculture
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6
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Characterization of methyl parathion degradation by a Burkholderia zhejiangensis strain, CEIB S4-3, isolated from agricultural soils. Biodegradation 2017; 28:351-367. [DOI: 10.1007/s10532-017-9801-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 07/04/2017] [Indexed: 11/27/2022]
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7
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Riptortus pedestris and Burkholderia symbiont: an ideal model system for insect–microbe symbiotic associations. Res Microbiol 2017; 168:175-187. [DOI: 10.1016/j.resmic.2016.11.005] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 11/28/2016] [Indexed: 01/06/2023]
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8
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Pinto-Carbó M, Sieber S, Dessein S, Wicker T, Verstraete B, Gademann K, Eberl L, Carlier A. Evidence of horizontal gene transfer between obligate leaf nodule symbionts. THE ISME JOURNAL 2016; 10:2092-105. [PMID: 26978165 PMCID: PMC4989318 DOI: 10.1038/ismej.2016.27] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 12/29/2015] [Accepted: 01/12/2016] [Indexed: 01/06/2023]
Abstract
Bacteria of the genus Burkholderia establish an obligate symbiosis with plant species of the Rubiaceae and Primulaceae families. The bacteria, housed within the leaves, are transmitted hereditarily and have not yet been cultured. We have sequenced and compared the genomes of eight bacterial leaf nodule symbionts of the Rubiaceae plant family. All of the genomes exhibit features consistent with genome erosion. Genes potentially involved in the biosynthesis of kirkamide, an insecticidal C7N aminocyclitol, are conserved in most Rubiaceae symbionts. However, some have partially lost the kirkamide pathway due to genome erosion and are unable to synthesize the compound. Kirkamide synthesis is therefore not responsible for the obligate nature of the symbiosis. More importantly, we find evidence of intra-clade horizontal gene transfer (HGT) events affecting genes of the secondary metabolism. This indicates that substantial gene flow can occur at the early stages following host restriction in leaf nodule symbioses. We propose that host-switching events and plasmid conjugative transfers could have promoted these HGTs. This genomic analysis of leaf nodule symbionts gives, for the first time, new insights in the genome evolution of obligate symbionts in their early stages of the association with plants.
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Affiliation(s)
- Marta Pinto-Carbó
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Simon Sieber
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Steven Dessein
- Plant Conservation and Population Biology, KU Leuven, Leuven, Belgium
- Botanic Garden, Meise, Belgium
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Brecht Verstraete
- Plant Conservation and Population Biology, KU Leuven, Leuven, Belgium
- Botanic Garden, Meise, Belgium
| | - Karl Gademann
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Aurelien Carlier
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
- Laboratory of Microbiology, Ghent University, 9000 Belgium, Switzerland
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9
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Peeters C, Meier-Kolthoff JP, Verheyde B, De Brandt E, Cooper VS, Vandamme P. Phylogenomic Study of Burkholderia glathei-like Organisms, Proposal of 13 Novel Burkholderia Species and Emended Descriptions of Burkholderia sordidicola, Burkholderia zhejiangensis, and Burkholderia grimmiae. Front Microbiol 2016; 7:877. [PMID: 27375597 PMCID: PMC4896955 DOI: 10.3389/fmicb.2016.00877] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 05/24/2016] [Indexed: 11/14/2022] Open
Abstract
Partial gyrB gene sequence analysis of 17 isolates from human and environmental sources revealed 13 clusters of strains and identified them as Burkholderia glathei clade (BGC) bacteria. The taxonomic status of these clusters was examined by whole-genome sequence analysis, determination of the G+C content, whole-cell fatty acid analysis and biochemical characterization. The whole-genome sequence-based phylogeny was assessed using the Genome Blast Distance Phylogeny (GBDP) method and an extended multilocus sequence analysis (MLSA) approach. The results demonstrated that these 17 BGC isolates represented 13 novel Burkholderia species that could be distinguished by both genotypic and phenotypic characteristics. BGC strains exhibited a broad metabolic versatility and developed beneficial, symbiotic, and pathogenic interactions with different hosts. Our data also confirmed that there is no phylogenetic subdivision in the genus Burkholderia that distinguishes beneficial from pathogenic strains. We therefore propose to formally classify the 13 novel BGC Burkholderia species as Burkholderia arvi sp. nov. (type strain LMG 29317T = CCUG 68412T), Burkholderia hypogeia sp. nov. (type strain LMG 29322T = CCUG 68407T), Burkholderia ptereochthonis sp. nov. (type strain LMG 29326T = CCUG 68403T), Burkholderia glebae sp. nov. (type strain LMG 29325T = CCUG 68404T), Burkholderia pedi sp. nov. (type strain LMG 29323T = CCUG 68406T), Burkholderia arationis sp. nov. (type strain LMG 29324T = CCUG 68405T), Burkholderia fortuita sp. nov. (type strain LMG 29320T = CCUG 68409T), Burkholderia temeraria sp. nov. (type strain LMG 29319T = CCUG 68410T), Burkholderia calidae sp. nov. (type strain LMG 29321T = CCUG 68408T), Burkholderia concitans sp. nov. (type strain LMG 29315T = CCUG 68414T), Burkholderia turbans sp. nov. (type strain LMG 29316T = CCUG 68413T), Burkholderia catudaia sp. nov. (type strain LMG 29318T = CCUG 68411T) and Burkholderia peredens sp. nov. (type strain LMG 29314T = CCUG 68415T). Furthermore, we present emended descriptions of the species Burkholderia sordidicola, Burkholderia zhejiangensis and Burkholderia grimmiae. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA and gyrB gene sequences determined in this study are LT158612-LT158624 and LT158625-LT158641, respectively.
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Affiliation(s)
- Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University Ghent, Belgium
| | - Jan P Meier-Kolthoff
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH Braunschweig, Germany
| | - Bart Verheyde
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University Ghent, Belgium
| | - Evie De Brandt
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University Ghent, Belgium
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine Pittsburgh, PA, USA
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent UniversityGhent, Belgium; BCCM/LMG Bacteria Collection, Department of Biochemistry and Microbiology, Ghent UniversityGhent, Belgium
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10
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Xu Y, Buss EA, Boucias DG. Culturing and Characterization of Gut Symbiont Burkholderia spp. from the Southern Chinch Bug, Blissus insularis (Hemiptera: Blissidae). Appl Environ Microbiol 2016; 82:3319-30. [PMID: 27016568 PMCID: PMC4959241 DOI: 10.1128/aem.00367-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 03/20/2016] [Indexed: 12/30/2022] Open
Abstract
UNLABELLED The phloem-feeding Southern chinch bug, Blissus insularis, harbors a high density of the exocellular bacterial symbiont Burkholderia in the lumen of specialized midgut crypts. Here we developed an organ culture method that initially involved incubating the B. insularis crypts in osmotically balanced insect cell culture medium. This approach enabled the crypt-inhabiting Burkholderia spp. to make a transition to an in vitro environment and to be subsequently cultured in standard bacteriological media. Examinations using ribotyping and BOX-PCR fingerprinting techniques demonstrated that most in vitro-produced bacterial cultures were identical to their crypt-inhabiting Burkholderia counterparts. Genomic and physiological analyses of gut-symbiotic Burkholderia spp. that were isolated individually from two separate B. insularis laboratory colonies revealed that the majority of individual insects harbored a single Burkholderia ribotype in their midgut crypts, resulting in a diverse Burkholderia community within each colony. The diversity was also exhibited by the phenotypic and genotypic characteristics of these Burkholderia cultures. Access to cultures of crypt-inhabiting bacteria provides an opportunity to investigate the interaction between symbiotic Burkholderia spp. and the B. insularis host. Furthermore, the culturing method provides an alternative strategy for establishing in vitro cultures of other fastidious insect-associated bacterial symbionts. IMPORTANCE An organ culture method was developed to establish in vitro cultures of a fastidious Burkholderia symbiont associated with the midgut crypts of the Southern chinch bug, Blissus insularis The identities of the resulting cultures were confirmed using the genomic and physiological features of Burkholderia cultures isolated from B. insularis crypts, showing that host insects maintained the diversity of Burkholderia spp. over multiple generations. The availability of characterized gut-symbiotic Burkholderia cultures provides a resource for genetic manipulation of these bacteria and for examination of the mechanisms underlying insect-bacterium symbiosis.
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Affiliation(s)
- Yao Xu
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, USAWageningen University
| | - Eileen A Buss
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, USAWageningen University
| | - Drion G Boucias
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, USAWageningen University
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11
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Abstract
The survival capacity of microorganisms in a contaminated environment is limited by the concentration and/or toxicity of the pollutant. Through evolutionary processes, some bacteria have developed or acquired mechanisms to cope with the deleterious effects of toxic compounds, a phenomenon known as tolerance. Common mechanisms of tolerance include the extrusion of contaminants to the outer media and, when concentrations of pollutants are low, the degradation of the toxic compound. For both of these approaches, plasmids that encode genes for the degradation of contaminants such as toluene, naphthalene, phenol, nitrobenzene, and triazine or are involved in tolerance toward organic solvents and heavy metals, play an important role in the evolution and dissemination of these catabolic pathways and efflux pumps. Environmental plasmids are often conjugative and can transfer their genes between different strains; furthermore, many catabolic or efflux pump genes are often associated with transposable elements, making them one of the major players in bacterial evolution. In this review, we will briefly describe catabolic and tolerance plasmids and advances in the knowledge and biotechnological applications of these plasmids.
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12
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Freas N, Newton P, Perozich J. Analysis of nucleotide diphosphate sugar dehydrogenases reveals family and group-specific relationships. FEBS Open Bio 2016; 6:77-89. [PMID: 27047744 PMCID: PMC4794789 DOI: 10.1002/2211-5463.12022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/03/2015] [Accepted: 12/14/2015] [Indexed: 12/02/2022] Open
Abstract
UDP‐glucose dehydrogenase (UDPGDH), UDP‐N‐acetyl‐mannosamine dehydrogenase (UDPNAMDH) and GDP‐mannose dehydrogenase (GDPMDH) belong to a family of NAD+‐linked 4‐electron‐transfering oxidoreductases called nucleotide diphosphate sugar dehydrogenases (NDP‐SDHs). UDPGDH is an enzyme responsible for converting UDP‐d‐glucose to UDP‐d‐glucuronic acid, a product that has different roles depending on the organism in which it is found. UDPNAMDH and GDPMDH convert UDP‐N‐acetyl‐mannosamine to UDP‐N‐acetyl‐mannosaminuronic acid and GDP‐mannose to GDP‐mannuronic acid, respectively, by a similar mechanism to UDPGDH. Their products are used as essential building blocks for the exopolysaccharides found in organisms like Pseudomonas aeruginosa and Staphylococcus aureus. Few studies have investigated the relationships between these enzymes. This study reveals the relationships between the three enzymes by analysing 229 amino acid sequences. Eighteen invariant and several other highly conserved residues were identified, each serving critical roles in maintaining enzyme structure, coenzyme binding or catalytic function. Also, 10 conserved motifs that included most of the conserved residues were identified and their roles proposed. A phylogenetic tree demonstrated relationships between each group and verified group assignment. Finally, group entropy analysis identified novel conservations unique to each NDP‐SDH group, including residue positions critical to NDP‐sugar substrate interaction, enzyme structure and intersubunit contact. These positions may serve as targets for future research. Enzymes UDP‐glucose dehydrogenase (UDPGDH, EC 1.1.1.22).
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Affiliation(s)
- Nicholas Freas
- Department of Biology Franciscan University of Steubenville OH USA
| | - Peter Newton
- Department of Biology Franciscan University of Steubenville OH USA
| | - John Perozich
- Department of Biology Franciscan University of Steubenville OH USA
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13
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Draft Genome Sequence of Burkholderia cordobensis Type Strain LMG 27620, Isolated from Agricultural Soils in Argentina. GENOME ANNOUNCEMENTS 2015; 3:3/5/e01238-15. [PMID: 26494680 PMCID: PMC4616187 DOI: 10.1128/genomea.01238-15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Bacteria of the genus
Burkholderia
are commonly found in diverse ecological niches in nature. We report here the draft genome sequence of
Burkholderia cordobensis
type strain LMG 27620, isolated from agricultural soil in Córdoba, Argentina. This strain harbors several genes involved in chitin utilization and phenol degradation, which make it an interesting candidate for biocontrol purposes and xenobiotic degradation in polluted environments.
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14
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Tago K, Kikuchi Y, Nakaoka S, Katsuyama C, Hayatsu M. Insecticide applications to soil contribute to the development of Burkholderia mediating insecticide resistance in stinkbugs. Mol Ecol 2015; 24:3766-78. [PMID: 26059639 DOI: 10.1111/mec.13265] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 06/03/2015] [Accepted: 06/04/2015] [Indexed: 11/30/2022]
Abstract
Some soil Burkholderia strains are capable of degrading the organophosphorus insecticide, fenitrothion, and establish symbiosis with stinkbugs, making the host insects fenitrothion-resistant. However, the ecology of the symbiotic degrading Burkholderia adapting to fenitrothion in the free-living environment is unknown. We hypothesized that fenitrothion applications affect the dynamics of fenitrothion-degrading Burkholderia, thereby controlling the transmission of symbiotic degrading Burkholderia from the soil to stinkbugs. We investigated changes in the density and diversity of culturable Burkholderia (i.e. symbiotic and nonsymbiotic fenitrothion degraders and nondegraders) in fenitrothion-treated soil using microcosms. During the incubation with five applications of pesticide, the density of the degraders increased from less than the detection limit to around 10(6)/g of soil. The number of dominant species among the degraders declined with the increasing density of degraders; eventually, one species predominated. This process can be explained according to the competitive exclusion principle using V(max) and K(m) values for fenitrothion metabolism by the degraders. We performed a phylogenetic analysis of representative strains isolated from the microcosms and evaluated their ability to establish symbiosis with the stinkbug Riptortus pedestris. The strains that established symbiosis with R. pedestris were assigned to a cluster including symbionts commonly isolated from stinkbugs. The strains outside the cluster could not necessarily associate with the host. The degraders in the cluster predominated during the initial phase of degrader dynamics in the soil. Therefore, only a few applications of fenitrothion could allow symbiotic degraders to associate with their hosts and may cause the emergence of symbiont-mediated insecticide resistance.
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Affiliation(s)
- Kanako Tago
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences (NIAES), 3-1-3 Kannondai, Tsukuba, Ibaraki, 305-8604, Japan
| | - Yoshitomo Kikuchi
- Bioproduction Research Institute, Hokkaido Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-higashi, Toyohira-ku, Sapporo, Hokkaido, 062-8517, Japan.,Graduate School of Agriculture, Hokkaido University, Kita 8, Nishi 5, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan
| | - Sinji Nakaoka
- Laboratory for Mathematical Modeling of Immune System, RIKEN Center for Integrative Medical Science Center (IMS-RCAI), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Chie Katsuyama
- Graduate School of Integrated Arts and Sciences, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8521, Japan
| | - Masahito Hayatsu
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences (NIAES), 3-1-3 Kannondai, Tsukuba, Ibaraki, 305-8604, Japan
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15
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Sawana A, Adeolu M, Gupta RS. Molecular signatures and phylogenomic analysis of the genus Burkholderia: proposal for division of this genus into the emended genus Burkholderia containing pathogenic organisms and a new genus Paraburkholderia gen. nov. harboring environmental species. Front Genet 2014; 5:429. [PMID: 25566316 PMCID: PMC4271702 DOI: 10.3389/fgene.2014.00429] [Citation(s) in RCA: 294] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 11/21/2014] [Indexed: 01/22/2023] Open
Abstract
The genus Burkholderia contains large number of diverse species which include many clinically important organisms, phytopathogens, as well as environmental species. However, currently, there is a paucity of biochemical or molecular characteristics which can reliably distinguish different groups of Burkholderia species. We report here the results of detailed phylogenetic and comparative genomic analyses of 45 sequenced species of the genus Burkholderia. In phylogenetic trees based upon concatenated sequences for 21 conserved proteins as well as 16S rRNA gene sequence based trees, members of the genus Burkholderia grouped into two major clades. Within these main clades a number of smaller clades including those corresponding to the clinically important Burkholderia cepacia complex (BCC) and the Burkholderia pseudomallei groups were also clearly distinguished. Our comparative analysis of protein sequences from Burkholderia spp. has identified 42 highly specific molecular markers in the form of conserved sequence indels (CSIs) that are uniquely found in a number of well-defined groups of Burkholderia spp. Six of these CSIs are specific for a group of Burkholderia spp. (referred to as Clade I in this work) which contains all clinically relevant members of the genus (viz. the BCC and the B. pseudomallei group) as well as the phytopathogenic Burkholderia spp. The second main clade (Clade II), which is composed of environmental Burkholderia species, is also distinguished by 2 identified CSIs that are specific for this group. Additionally, our work has also identified multiple CSIs that serve to clearly demarcate a number of smaller groups of Burkholderia spp. including 3 CSIs that are specific for the B. cepacia complex, 4 CSIs that are uniquely found in the B. pseudomallei group, 5 CSIs that are specific for the phytopathogenic Burkholderia spp. and 22 other CSI that distinguish two groups within Clade II. The described molecular markers provide highly specific means for the demarcation of different groups of Burkholderia spp. and they also offer novel and useful targets for the development of diagnostic assays for the clinically important members of the BCC or the pseudomallei groups. Based upon the results of phylogenetic analyses, the identified CSIs and the pathogenicity profile of Burkholderia species, we are proposing a division of the genus Burkholderia into two genera. In this new proposal, the emended genus Burkholderia will correspond to the Clade I and it will contain only the clinically relevant and phytopathogenic Burkholderia species. All other Burkholderia spp., which are primarily environmental, will be transferred to a new genus Paraburkholderia gen. nov.
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Affiliation(s)
| | | | - Radhey S. Gupta
- Department of Biochemistry and Biomedical Sciences, Health Sciences Center, McMaster UniversityHamilton, ON, Canada
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16
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Draft Genome Sequence of the Organophosphorus Compound-Degrading Burkholderia zhejiangensis Strain CEIB S4-3. GENOME ANNOUNCEMENTS 2014; 2:2/6/e01323-14. [PMID: 25523778 PMCID: PMC4271168 DOI: 10.1128/genomea.01323-14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Burkholderia species are widely distributed in the environment. A Burkholderia zhejiangensis strain was isolated from pesticide-contaminated soil from an agricultural field in Mexico and identified as an organophosphorus compound-degrading bacterium. In this study, we report the draft genome sequence of Burkholderia zhejiangensis strain CEIB S4-3.
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17
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Transcriptional activation of multiple operons involved in para-nitrophenol degradation by Pseudomonas sp. Strain WBC-3. Appl Environ Microbiol 2014; 81:220-30. [PMID: 25326309 DOI: 10.1128/aem.02720-14] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas sp. strain WBC-3 utilizes para-nitrophenol (PNP) as a sole carbon and energy source. The genes involved in PNP degradation are organized in the following three operons: pnpA, pnpB, and pnpCDEFG. How the expression of the genes is regulated is unknown. In this study, an LysR-type transcriptional regulator (LTTR) is identified to activate the expression of the genes in response to the specific inducer PNP. While the LTTR coding gene pnpR was found to be not physically linked to any of the three catabolic operons, it was shown to be essential for the growth of strain WBC-3 on PNP. Furthermore, PnpR positively regulated its own expression, which is different from the function of classical LTTRs. A regulatory binding site (RBS) with a 17-bp imperfect palindromic sequence (GTT-N11-AAC) was identified in all pnpA, pnpB, pnpC, and pnpR promoters. Through electrophoretic mobility shift assays and mutagenic analyses, this motif was proven to be necessary for PnpR binding. This consensus motif is centered at positions approximately -55 bp relative to the four transcriptional start sites (TSSs). RBS integrity was required for both high-affinity PnpR binding and transcriptional activation of pnpA, pnpB, and pnpR. However, this integrity was essential only for high-affinity PnpR binding to the promoter of pnpCDEFG and not for its activation. Intriguingly, unlike other LTTRs studied, no changes in lengths of the PnpR binding regions of the pnpA and pnpB promoters were observed after the addition of the inducer PNP in DNase I footprinting.
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18
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Draghi WO, Peeters C, Cnockaert M, Snauwaert C, Wall LG, Zorreguieta A, Vandamme P. Burkholderia cordobensis sp. nov., from agricultural soils. Int J Syst Evol Microbiol 2014; 64:2003-2008. [PMID: 24623656 DOI: 10.1099/ijs.0.059667-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-negative, rod-shaped bacteria were isolated from agricultural soils in Córdoba province in central Argentina. Their 16S rRNA gene sequences demonstrated that they belong to the genus Burkholderia, with Burkholderia zhejiangensis as most closely related formally named species; this relationship was confirmed through comparative gyrB sequence analysis. Whole-cell fatty acid analysis supported their assignment to the genus Burkholderia. Burkholderia sp. strain YI23, for which a whole-genome sequence is available, represents the same taxon, as demonstrated by its highly similar 16S rRNA (100% similarity) and gyrB (99.1-99.7%) gene sequences. The results of DNA-DNA hybridization experiments and physiological and biochemical characterization further substantiated the genotypic and phenotypic distinctiveness of the Argentinian soil isolates, for which the name Burkholderia cordobensis sp. nov. is proposed, with strain MMP81(T) ( = LMG 27620(T) = CCUG 64368(T)) as the type strain.
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Affiliation(s)
- Walter O Draghi
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
- Fundación Instituto Leloir and IIBA - Consejo Nacional de Investigaciones Científicas y Tecnológicas, Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Cindy Snauwaert
- BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Luis G Wall
- Science and Technology Department, National University of Quilmes, Roque Sáenz Peña 352, Bernal, B1876BXD Buenos Aires, Argentina
| | - Angeles Zorreguieta
- Fundación Instituto Leloir and IIBA - Consejo Nacional de Investigaciones Científicas y Tecnológicas, Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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19
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Sakai Y, Ogawa N, Shimomura Y, Fujii T. A 2,4-dichlorophenoxyacetic acid degradation plasmid pM7012 discloses distribution of an unclassified megaplasmid group across bacterial species. MICROBIOLOGY-SGM 2014; 160:525-536. [PMID: 24440834 DOI: 10.1099/mic.0.074369-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Analysis of the complete nucleotide sequence of plasmid pM7012 from 2,4-dichlorophenoxyacetic-acid (2,4-D)-degrading bacterium Burkholderia sp. M701 revealed that the plasmid had 582 142 bp, with 541 putative protein-coding sequences and 39 putative tRNA genes for the transport of the standard 20 aa. pM7012 contains sequences homologous to the regions involved in conjugal transfer and plasmid maintenance found in plasmids byi_2p from Burkholderia sp. YI23 and pBVIE01 from Burkholderia sp. G4. No relaxase gene was found in any of these plasmids, although genes for a type IV secretion system and type IV coupling proteins were identified. Plasmids with no relaxase gene have been classified as non-mobile plasmids. However, nucleotide sequences with a high level of similarity to the genes for plasmid transfer, plasmid maintenance, 2,4-D degradation and arsenic resistance contained on pM7012 were also detected in eight other megaplasmids (~600 or 900 kb) found in seven Burkholderia strains and a strain of Cupriavidus, which were isolated as 2,4-D-degrading bacteria in Japan and the United States. These results suggested that the 2,4-D degradation megaplasmids related to pM7012 are mobile and distributed across various bacterial species worldwide, and that the plasmid group could be distinguished from known mobile plasmid groups.
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Affiliation(s)
- Yoriko Sakai
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Tsukuba, Ibaraki 305-8604, Japan
| | - Naoto Ogawa
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Surugaku, Shizuoka 422-8529, Japan
| | - Yumi Shimomura
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Tsukuba, Ibaraki 305-8604, Japan
| | - Takeshi Fujii
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Tsukuba, Ibaraki 305-8604, Japan
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20
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Kumar S, Vikram S, Raghava GPS. Genome annotation of Burkholderia sp. SJ98 with special focus on chemotaxis genes. PLoS One 2013; 8:e70624. [PMID: 23940608 PMCID: PMC3734258 DOI: 10.1371/journal.pone.0070624] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 06/20/2013] [Indexed: 11/18/2022] Open
Abstract
Burkholderia sp. strain SJ98 has the chemotactic activity towards nitroaromatic and chloronitroaromatic compounds. Recently our group published draft genome of strain SJ98. In this study, we further sequence and annotate the genome of stain SJ98 to exploit the potential of this bacterium. We specifically annotate its chemotaxis genes and methyl accepting chemotaxis proteins. Genome of Burkholderia sp. SJ98 was annotated using PGAAP pipeline that predicts 7,268 CDSs, 52 tRNAs and 3 rRNAs. Our analysis based on phylogenetic and comparative genomics suggest that Burkholderia sp. YI23 is closest neighbor of the strain SJ98. The genes involved in the chemotaxis of strain SJ98 were compared with genes of closely related Burkholderia strains (i.e. YI23, CCGE 1001, CCGE 1002, CCGE 1003) and with well characterized bacterium E. coli K12. It was found that strain SJ98 has 37 che genes including 19 methyl accepting chemotaxis proteins that involved in sensing of different attractants. Chemotaxis genes have been found in a cluster along with the flagellar motor proteins. We also developed a web resource that provides comprehensive information on strain SJ98 that includes all analysis data (http://crdd.osdd.net/raghava/genomesrs/burkholderia/).
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Affiliation(s)
- Shailesh Kumar
- Bioinformatics Centre, Council of Scientific and Industrial Research - Institute of Microbial Technology, Sector 39-A, Chandigarh, India
| | - Surendra Vikram
- Bioinformatics Centre, Council of Scientific and Industrial Research - Institute of Microbial Technology, Sector 39-A, Chandigarh, India
| | - Gajendra Pal Singh Raghava
- Bioinformatics Centre, Council of Scientific and Industrial Research - Institute of Microbial Technology, Sector 39-A, Chandigarh, India
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21
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Dunon V, Sniegowski K, Bers K, Lavigne R, Smalla K, Springael D. High prevalence of IncP-1 plasmids and IS1071 insertion sequences in on-farm biopurification systems and other pesticide-polluted environments. FEMS Microbiol Ecol 2013; 86:415-31. [PMID: 23802695 DOI: 10.1111/1574-6941.12173] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 04/22/2013] [Accepted: 06/18/2013] [Indexed: 11/26/2022] Open
Abstract
Mobile genetic elements (MGEs) are considered as key players in the adaptation of bacteria to degrade organic xenobiotic recalcitrant compounds such as pesticides. We examined the prevalence and abundance of IncP-1 plasmids and IS1071, two MGEs that are frequently linked with organic xenobiotic degradation, in laboratory and field ecosystems with and without pesticide pollution history. The ecosystems included on-farm biopurification systems (BPS) processing pesticide-contaminated wastewater and soil. Comparison of IncP-1/IS1071 prevalence between pesticide-treated and nontreated soil and BPS microcosms suggested that both IncP-1 and IS1071 proliferated as a response to pesticide treatment. The increased prevalence of IncP-1 plasmids and IS1071-specific sequences in treated systems was accompanied by an increase in the capacity to mineralize the applied pesticides. Both elements were also encountered in high abundance in field BPS ecosystems that were in operation at farmyards and that showed the capacity to degrade/mineralize a wide range of chlorinated aromatics and pesticides. In contrast, IS1071 and especially IncP-1, MGE were less abundant in field ecosystems without pesticide history although some of them still showed a high IS1071 abundance. Our data suggest that MGE-containing organisms were enriched in pesticide-contaminated environments like BPS where they might contribute to spreading of catabolic genes and to pathway assembly.
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Affiliation(s)
- Vincent Dunon
- Division of Soil and Water Management, KU Leuven, Heverlee, Belgium
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22
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Nelson OW, Garrity GM. Genome sequences published outside of Standards in Genomic Sciences, January-March 2012. Stand Genomic Sci 2012. [DOI: 10.4056/sigs.1756022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Oranmiyan W. Nelson
- 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA
| | - George M. Garrity
- 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA
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