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Kang WN, Jin L, Ma HY, Li GQ. Integrated Microbiome-Metabolome Analysis Reveals Stage-Dependent Alterations in Bacterial Degradation of Aromatics in Leptinotarsa decemlineata. Front Physiol 2021; 12:739800. [PMID: 34658924 PMCID: PMC8515180 DOI: 10.3389/fphys.2021.739800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/16/2021] [Indexed: 11/16/2022] Open
Abstract
To avoid potential harm during pupation, the Colorado potato beetle Leptinotarsa decemlineata lives in two different habitats throughout its developmental excursion, with the larva and adult settling on potato plants and the pupa in soil. Potato plants and agricultural soil contain a specific subset of aromatics. In the present study, we intended to determine whether the stage-specific bacterial flora plays a role in the catabolism of aromatics in L. decemlineata. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the operational taxonomic units (OTUs) obtained by sequencing of culture-independent 16S rRNA region enriched a group of bacterial genes involved in the elimination of mono- and polycyclic aromatics at the pupal stage compared with those at the larval and adult periods. Consistently, metabolome analysis revealed that dozens of monoaromatics such as styrene, benzoates, and phenols, polycyclic aromatics, for instance, naphthalene and steroids, were more abundant in the pupal sample. Moreover, a total of seven active pathways were uncovered in the pupal specimen. These ways were associated with the biodegradation of benzoate, 4-methoxybenzoate, fluorobenzoates, styrene, vanillin, benzamide, and naphthalene. In addition, the metabolomic profiles and the catabolism abilities were significantly different in the pupae where their bacteria were removed by a mixture of three antibiotics. Therefore, our data suggested the stage-dependent alterations in bacterial breakdown of aromatics in L. decemlineata.
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Affiliation(s)
- Wei-Nan Kang
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Lin Jin
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Hong-Yu Ma
- Public Laboratory Platform, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Guo-Qing Li
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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Alanin KWS, Jørgensen TS, Browne PD, Petersen B, Riber L, Kot W, Hansen LH. An improved direct metamobilome approach increases the detection of larger-sized circular elements across kingdoms. Plasmid 2021; 115:102576. [PMID: 33872684 DOI: 10.1016/j.plasmid.2021.102576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 04/12/2021] [Accepted: 04/12/2021] [Indexed: 10/21/2022]
Abstract
Mobile genetic elements (MGEs) are instrumental in natural prokaryotic genome editing, permitting genome plasticity and allowing microbes to accumulate genetic diversity. MGEs serve as a vast communal gene pool and include DNA elements such as plasmids and bacteriophages (phages) among others. These mobile DNA elements represent a human health risk as they can introduce new traits, such as antibiotic resistance or virulence, to a bacterial strain. Sequencing libraries targeting environmental circular MGEs, referred to as metamobilomes, may broaden our current understanding of the mechanisms behind the mobility, prevalence and content of these elements. However, metamobilomics is affected by a severe bias towards small circular elements, introduced by multiple displacement amplification (MDA). MDA is typically used to overcome limiting DNA quantities after the removal of non-circular DNA during library preparations. By examining the relationship between sequencing coverage and the size of circular MGEs in paired metamobilome datasets with and without MDA, we show that larger circular elements are lost when using MDA. This study is the first to systematically demonstrate that MDA is detrimental to detecting larger-sized plasmids if small plasmids are present. It is also the first to show that MDA can be omitted when using enzyme-based DNA fragmentation and PCR in library preparation kits such as Nextera XT® from Illumina.
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Affiliation(s)
- Katrine Wacenius Skov Alanin
- Department of Environmental Science, Aarhus University, Roskilde, Denmark; Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tue Sparholt Jørgensen
- Department of Environmental Science, Aarhus University, Roskilde, Denmark; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark; Department of Science and Environment, Roskilde University, Denmark
| | - Patrick Denis Browne
- Department of Environmental Science, Aarhus University, Roskilde, Denmark; Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bent Petersen
- Globe Institute, Faculty of Health and Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark; Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Leise Riber
- Department of Biology, Functional Genomics, University of Copenhagen, Copenhagen, Denmark
| | - Witold Kot
- Department of Environmental Science, Aarhus University, Roskilde, Denmark; Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Lars Hestbjerg Hansen
- Department of Environmental Science, Aarhus University, Roskilde, Denmark; Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark.
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Pozdnyakova-Filatova I, Petrikov K, Vetrova A, Frolova A, Streletskii R, Zakharova M. The Naphthalene Catabolic Genes of Pseudomonas putida BS3701: Additional Regulatory Control. Front Microbiol 2020; 11:1217. [PMID: 32582120 PMCID: PMC7291925 DOI: 10.3389/fmicb.2020.01217] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/13/2020] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas microorganisms are used for bioremediation of soils contaminated with petroleum hydrocarbons. The overall remediation efficiency is largely dependent on the presence of macro- and micronutrients. Widely varying concentrations of available nitrogen and iron (Fe) in soils were shown to affect residual hydrocarbons in the course of biodegradation. The regulatory mechanisms of expression of hydrocarbon catabolic genes in low nitrogen/low iron conditions remain unclear. The catabolism of naphthalene, a two-ring polycyclic aromatic hydrocarbon, has been well studied in pseudomonads in terms of the involvement of specific transcriptional activators, thus making it useful in revealing additional regulatory control of the adaptation of hydrocarbon destructors to a low level of the essential nutrients. The Pseudomonas putida strain BS3701 is a component of the "MicroBak" preparation for soil remediation. Previously, this strain was shown to contain genes encoding the key enzymes for naphthalene catabolism: naphthalene 1,2-dioxygenase, salicylate hydroxylase, catechol 2,3-dioxygenase, and catechol 1,2-dioxygenase. Our study aimed to clarify whether the naphthalene catabolic gene expression is dependent on the amount of nitrogen and iron in the growth culture medium, and if so, at exactly which stages the expression is regulated. We cultivated the strain in low nitrogen/low iron conditions with the concurrent evaluation of the activity of the key enzymes and the mRNA level of genes encoding these enzymes. We are the first to report that naphthalene catabolic genes are subject not only to transcriptional but also post-transcriptional regulation.
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Affiliation(s)
- Irina Pozdnyakova-Filatova
- Laboratory of Molecular Microbiology, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino, Russia
| | - Kirill Petrikov
- Laboratory of Plasmid Biology, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino, Russia
| | - Anna Vetrova
- Laboratory of Plasmid Biology, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino, Russia
| | - Alina Frolova
- Laboratory of Bacteriophage Biology, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino, Russia
| | - Rostislav Streletskii
- Laboratory of Ecological Soil Science, Lomonosov Moscow State University, Moscow, Russia
| | - Marina Zakharova
- Laboratory of Molecular Microbiology, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino, Russia
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Izmalkova TY, Gafarov AB, Sazonova OI, Sokolov SL, Kosheleva IA, Boronin AM. Diversity of Oil-Degrading Microorganisms in the Gulf of Finland (Baltic Sea) in Spring and in Summer. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718020054] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Leite DCA, Salles JF, Calderon EN, van Elsas JD, Peixoto RS. Specific plasmid patterns and high rates of bacterial co-occurrence within the coral holobiont. Ecol Evol 2018; 8:1818-1832. [PMID: 29435256 PMCID: PMC5792611 DOI: 10.1002/ece3.3717] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/15/2017] [Accepted: 11/16/2017] [Indexed: 12/24/2022] Open
Abstract
Despite the importance of coral microbiomes for holobiont persistence, the interactions among these are not well understood. In particular, knowledge of the co-occurrence and taxonomic importance of specific members of the microbial core, as well as patterns of specific mobile genetic elements (MGEs), is lacking. We used seawater and mucus samples collected from Mussismilia hispida colonies on two reefs located in Bahia, Brazil, to disentangle their associated bacterial communities, intertaxa correlations, and plasmid patterns. Proxies for two broad-host-range (BHR) plasmid groups, IncP-1β and PromA, were screened. Both groups were significantly (up to 252 and 100%, respectively) more abundant in coral mucus than in seawater. Notably, the PromA plasmid group was detected only in coral mucus samples. The core bacteriome of M. hispida mucus was composed primarily of members of the Proteobacteria, followed by those of Firmicutes. Significant host specificity and co-occurrences among different groups of the dominant phyla (e.g., Bacillaceae and Pseudoalteromonadaceae and the genera Pseudomonas, Bacillus, and Vibrio) were detected. These relationships were observed for both the most abundant phyla and the bacteriome core, in which most of the operational taxonomic units showed intertaxa correlations. The observed evidence of host-specific bacteriome and co-occurrence (and potential symbioses or niche space co-dominance) among the most dominant members indicates a taxonomic selection of members of the stable bacterial community. In parallel, host-specific plasmid patterns could also be, independently, related to the assembly of members of the coral microbiome.
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Affiliation(s)
- Deborah C. A. Leite
- Institute of MicrobiologyFederal University of Rio de JaneiroRio de JaneiroBrazil
| | - Joana F. Salles
- Genomics Research in Ecology and Evolution in Nature ‐ Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
| | - Emiliano N. Calderon
- NUPEM/MacaéFederal University of Rio de JaneiroRio de JaneiroBrazil
- Instituto Coral VivoSanta Cruz CabráliaBrazil
| | - Jan D. van Elsas
- Genomics Research in Ecology and Evolution in Nature ‐ Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
| | - Raquel S. Peixoto
- Institute of MicrobiologyFederal University of Rio de JaneiroRio de JaneiroBrazil
- IMAM‐AquaRio – Rio Marine Aquarium Research CenterRio de JaneiroBrazil
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6
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Puntus IF, Vlasova EP, Sokolov AP, Zakharchenko NS, Funtikova TV. Properties of non-homologous salicylate hydroxylases of pseudomonus bacteria. APPL BIOCHEM MICRO+ 2015. [DOI: 10.1134/s0003683815020155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Jørgensen TS, Kiil AS, Hansen MA, Sørensen SJ, Hansen LH. Current strategies for mobilome research. Front Microbiol 2015; 5:750. [PMID: 25657641 PMCID: PMC4302988 DOI: 10.3389/fmicb.2014.00750] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/10/2014] [Indexed: 11/30/2022] Open
Abstract
Mobile genetic elements (MGEs) are pivotal for bacterial evolution and adaptation, allowing shuffling of genes even between distantly related bacterial species. The study of these elements is biologically interesting as the mode of genetic propagation is kaleidoscopic and important, as MGEs are the main vehicles of the increasing bacterial antibiotic resistance that causes thousands of human deaths each year. The study of MGEs has previously focused on plasmids from individual isolates, but the revolution in sequencing technology has allowed the study of mobile genomic elements of entire communities using metagenomic approaches. The problem in using metagenomic sequencing for the study of MGEs is that plasmids and other mobile elements only comprise a small fraction of the total genetic content that are difficult to separate from chromosomal DNA based on sequence alone. The distinction between plasmid and chromosome is important as the mobility and regulation of genes largely depend on their genetic context. Several different approaches have been proposed that specifically enrich plasmid DNA from community samples. Here, we review recent approaches used to study entire plasmid pools from complex environments, and point out possible future developments for and pitfalls of these approaches. Further, we discuss the use of the PacBio long-read sequencing technology for MGE discovery.
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Affiliation(s)
- Tue S Jørgensen
- Section of Microbiology, Department of Biology, University of Copenhagen Copenhagen, Denmark
| | - Anne S Kiil
- Section of Microbiology, Department of Biology, University of Copenhagen Copenhagen, Denmark
| | - Martin A Hansen
- Section of Microbiology, Department of Biology, University of Copenhagen Copenhagen, Denmark
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen Copenhagen, Denmark
| | - Lars H Hansen
- Section of Microbiology, Department of Biology, University of Copenhagen Copenhagen, Denmark ; Environmental Microbiology and Biotechnology, Department of Environmental Science, Aarhus University Roskilde, Denmark
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8
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Kosheleva IA, Sazonova OI, Izmalkova TY, Boronin AM. Occurrence of the SAL+ phenotype in soil pseudomonads. Microbiology (Reading) 2014. [DOI: 10.1134/s0026261714060101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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9
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Dealtry S, Ding GC, Weichelt V, Dunon V, Schlüter A, Martini MC, Papa MFD, Lagares A, Amos GCA, Wellington EMH, Gaze WH, Sipkema D, Sjöling S, Springael D, Heuer H, van Elsas JD, Thomas C, Smalla K. Cultivation-independent screening revealed hot spots of IncP-1, IncP-7 and IncP-9 plasmid occurrence in different environmental habitats. PLoS One 2014; 9:e89922. [PMID: 24587126 PMCID: PMC3933701 DOI: 10.1371/journal.pone.0089922] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 01/25/2014] [Indexed: 11/24/2022] Open
Abstract
IncP-1, IncP-7 and IncP-9 plasmids often carry genes encoding enzymes involved in the degradation of man-made and natural contaminants, thus contributing to bacterial survival in polluted environments. However, the lack of suitable molecular tools often limits the detection of these plasmids in the environment. In this study, PCR followed by Southern blot hybridization detected the presence of plasmid-specific sequences in total community (TC-) DNA or fosmid DNA from samples originating from different environments and geographic regions. A novel primer system targeting IncP-9 plasmids was developed and applied along with established primers for IncP-1 and IncP-7. Screening TC-DNA from biopurification systems (BPS) which are used on farms for the purification of pesticide-contaminated water revealed high abundances of IncP-1 plasmids belonging to different subgroups as well as IncP-7 and IncP-9. The novel IncP-9 primer-system targeting the rep gene of nine IncP-9 subgroups allowed the detection of a high diversity of IncP-9 plasmid specific sequences in environments with different sources of pollution. Thus polluted sites are “hot spots” of plasmids potentially carrying catabolic genes.
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Affiliation(s)
- Simone Dealtry
- Julius Kühn-Institut – Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Guo-Chun Ding
- Julius Kühn-Institut – Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Viola Weichelt
- Julius Kühn-Institut – Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Vincent Dunon
- Division of Soil and Water Management, KU Leuven, Heverlee, Belgium
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Bielefeld, Germany
| | - 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, La Plata, 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, 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, La Plata, Argentina
| | | | | | - William Hugo Gaze
- School of Life Sciences, University of Warwick, Warwick, United Kingdom
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Sara Sjöling
- Södertörns högskola (Sodertorn University), Inst. för Naturvetenskap, Miljö och medieteknik (School of Natural Sciences, Environmental Studies and media tech), Huddinge, Sweden
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven, Heverlee, Belgium
| | - Holger Heuer
- Julius Kühn-Institut – Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | | | - Christopher Thomas
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, Warwick, United Kingdom
| | - Kornelia Smalla
- Julius Kühn-Institut – Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
- * E-mail:
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Izmalkova TY, Sazonova OI, Kosheleva IA, Boronin AM. Phylogenetic analysis of the genes for naphthalene and phenanthrene degradation in Burkholderia sp. strains. RUSS J GENET+ 2013. [DOI: 10.1134/s1022795413060033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Panov AV, Esikova TZ, Sokolov SL, Kosheleva IA, Boronin AM. Influence of soil pollution on the composition of a microbial community. Microbiology (Reading) 2013. [DOI: 10.1134/s0026261713010116] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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12
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Volkova OV, Panov AV, Kosheleva IA, Boronin AM. Classification of IncP-7 plasmids based on structural diversity of their basic replicons. Mol Biol 2013. [DOI: 10.1134/s0026893313020167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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13
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Panov AV, Volkova OV, Puntus IF, Esikova TZ, Kosheleva IA, Boronin AM. scpA, a new salicylate hydroxylase gene localized in salicylate/caprolactam degradation plasmids. Mol Biol 2013. [DOI: 10.1134/s0026893313010147] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Babin D, Ding GC, Pronk GJ, Heister K, Kögel-Knabner I, Smalla K. Metal oxides, clay minerals and charcoal determine the composition of microbial communities in matured artificial soils and their response to phenanthrene. FEMS Microbiol Ecol 2013; 86:3-14. [DOI: 10.1111/1574-6941.12058] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 12/06/2012] [Accepted: 12/09/2012] [Indexed: 11/30/2022] Open
Affiliation(s)
- Doreen Babin
- Julius Kühn-Institut; Federal Research Centre for Cultivated Plants; Institute for Epidemiology and Pathogen Diagnostics; Braunschweig; Germany
| | - Guo-Chun Ding
- Julius Kühn-Institut; Federal Research Centre for Cultivated Plants; Institute for Epidemiology and Pathogen Diagnostics; Braunschweig; Germany
| | | | - Katja Heister
- Lehrstuhl für Bodenkunde; Technische Universität München; Freising-Weihenstephan; Germany
| | | | - Kornelia Smalla
- Julius Kühn-Institut; Federal Research Centre for Cultivated Plants; Institute for Epidemiology and Pathogen Diagnostics; Braunschweig; Germany
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15
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The organization of naphthalene degradation genes in Pseudomonas putida strain AK5. Res Microbiol 2012; 164:244-53. [PMID: 23266498 DOI: 10.1016/j.resmic.2012.12.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 12/07/2012] [Indexed: 11/21/2022]
Abstract
The Pseudomonas putida АК5 that was isolated from the slime pit of a Nizhnekamsk oil chemical factory can metabolize naphthalene via salicylate and gentisate. Catabolic genes are localized on non-conjugative IncP-7 plasmid pAK5 of about 115 kb in size. The "classical"nah-1 operon and the novel sgp-operon (salicylate-gentisate pathway) are both involved in naphthalene degradation by P. putida АК5, that was first described for Pseudomonas. The sgp-operon includes six open reading frames (ORFs) (sgpAIKGHB). The four ORFs code for the entire salicylate 5-hydroxylase - oxidoreductase component (sgpA), large and small subunits of the oxigenase component (sgpG and sgpH) and 2Fe-2S ferredoxin (sgpB). Genes for gentisate 1, 2-dioxygenase (sgpI) and fumarylpyruvate hydrolase (sgpK) are located in salicylate 5-hydroxylase genes clustering between sgpA and sgpG. The putative positive regulator for the sgp-operon (sgpR) was found upstream of the sgpA gene and oriented in the opposite direction from sgpA. The putative maleylacetoacetate isomerase gene is located apart, directly downstream from the sgp-operon. The sgp-operon organization and phylogenetic analysis of deduced amino acid sequences indicate that this operon has a mosaic structure according to the modular theory of the evolution of modern catabolic pathways.
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16
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Heuer H, Smalla K. Plasmids foster diversification and adaptation of bacterial populations in soil. FEMS Microbiol Rev 2012; 36:1083-104. [DOI: 10.1111/j.1574-6976.2012.00337.x] [Citation(s) in RCA: 194] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Revised: 10/15/2011] [Accepted: 02/24/2012] [Indexed: 11/26/2022] Open
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17
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Miyakoshi M, Shintani M, Inoue K, Terabayashi T, Sai F, Ohkuma M, Nojiri H, Nagata Y, Tsuda M. ParI, an orphan ParA family protein from Pseudomonas putida KT2440-specific genomic island, interferes with the partition system of IncP-7 plasmids. Environ Microbiol 2012; 14:2946-59. [PMID: 22925377 DOI: 10.1111/j.1462-2920.2012.02861.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 07/26/2012] [Accepted: 07/28/2012] [Indexed: 01/09/2023]
Abstract
Pseudomonas putida KT2440 is an ideal soil bacterium for expanding the range of degradable compounds via the recruitment of various catabolic plasmids. In the course of our investigation of the host range of IncP-7 catabolic plasmids pCAR1, pDK1 and pWW53, we found that the IncP-7 miniplasmids composed of replication and partition loci were exceptionally unstable in KT2440, which is the authentic host of the archetypal IncP-9 plasmid pWW0. This study identified ParI, a homologue of ParA family of plasmid partitioning proteins encoded on the KT2440-specific cryptic genomic island, as a negative host factor for the maintenance of IncP-7 plasmids. The miniplasmids were destabilized by ectopic expression of ParI, and the loss rate correlated with the copy number of ParB binding sites in the centromeric parS region. Mutations in the conserved ATPase domains of ParI abolished destabilization of miniplasmids. Furthermore, ParI destabilized miniplasmid derivatives carrying the partition-deficient parA mutations but failed to impact the stability of miniplasmid derivatives with parB mutations in the putative arginine finger. Altogether, these results indicate that ParI interferes with the IncP-7 plasmid partition system. This study extends canonical partition-mediated incompatibility of plasmids beyond heterogeneous mobile genetic elements, namely incompatibility between plasmid and genomic island.
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Affiliation(s)
- Masatoshi Miyakoshi
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan.
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18
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Volkova OV, Kosheleva IA, Boronin AM. Structure of replication initiation region in Pseudomonas IncP-7 streptomycin resistance plasmid Rms148. Mol Biol 2012. [DOI: 10.1134/s0026893312030120] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Li L, Norman A, Hansen L, Sorensen S. Metamobilomics – expanding our knowledge on the pool of plasmid encoded traits in natural environments using high-throughput sequencing. Clin Microbiol Infect 2012; 18 Suppl 4:5-7. [DOI: 10.1111/j.1469-0691.2012.03862.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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20
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Ding GC, Heuer H, He Z, Xie J, Zhou J, Smalla K. More functional genes and convergent overall functional patterns detected by geochip in phenanthrene-spiked soils. FEMS Microbiol Ecol 2012; 82:148-56. [DOI: 10.1111/j.1574-6941.2012.01413.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 05/02/2012] [Accepted: 05/08/2012] [Indexed: 11/30/2022] Open
Affiliation(s)
- Guo-Chun Ding
- Julius Kühn-Institut; Federal Research Centre for Cultivated Plants (JKI); Institute for Epidemiology and Pathogen Diagnostics; Braunschweig; Germany
| | - Holger Heuer
- Julius Kühn-Institut; Federal Research Centre for Cultivated Plants (JKI); Institute for Epidemiology and Pathogen Diagnostics; Braunschweig; Germany
| | - Zhili He
- Institute for Environmental Genomics and Department of Botany and Microbiology; University of Oklahoma; Norman; OK; USA
| | - Jianping Xie
- Institute for Environmental Genomics and Department of Botany and Microbiology; University of Oklahoma; Norman; OK; USA
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Botany and Microbiology; University of Oklahoma; Norman; OK; USA
| | - Kornelia Smalla
- Julius Kühn-Institut; Federal Research Centre for Cultivated Plants (JKI); Institute for Epidemiology and Pathogen Diagnostics; Braunschweig; Germany
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21
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Occurrence of plasmids in the aromatic degrading bacterioplankton of the baltic sea. Genes (Basel) 2011; 2:853-68. [PMID: 24710296 PMCID: PMC3927600 DOI: 10.3390/genes2040853] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 09/23/2011] [Accepted: 10/20/2011] [Indexed: 11/21/2022] Open
Abstract
Plasmids are mobile genetic elements that provide their hosts with many beneficial traits including in some cases the ability to degrade different aromatic compounds. To fulfill the knowledge gap regarding catabolic plasmids of the Baltic Sea water, a total of 209 biodegrading bacterial strains were isolated and screened for the presence of these mobile genetic elements. We found that both large and small plasmids are common in the cultivable Baltic Sea bacterioplankton and are particularly prevalent among bacterial genera Pseudomonas and Acinetobacter. Out of 61 plasmid-containing strains (29% of all isolates), 34 strains were found to carry large plasmids, which could be associated with the biodegradative capabilities of the host bacterial strains. Focusing on the diversity of IncP-9 plasmids, self-transmissible m-toluate (TOL) and salicylate (SAL) plasmids were detected. Sequencing the repA gene of IncP-9 carrying isolates revealed a high diversity within IncP-9 plasmid family, as well as extended the assumed bacterial host species range of the IncP-9 representatives. This study is the first insight into the genetic pool of the IncP-9 catabolic plasmids in the Baltic Sea bacterioplankton.
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Sazonova OI, Izmalkova TY, Kosheleva IA, Boronin AM. Salicylate degradation by Pseudomonas putida strains not involving the “Classical” nah2 operon. Microbiology (Reading) 2008. [DOI: 10.1134/s002626170806009x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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23
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Sevastsyanovich YR, Krasowiak R, Bingle LEH, Haines AS, Sokolov SL, Kosheleva IA, Leuchuk AA, Titok MA, Smalla K, Thomas CM. Diversity of IncP-9 plasmids of Pseudomonas. MICROBIOLOGY (READING, ENGLAND) 2008; 154:2929-2941. [PMID: 18832300 PMCID: PMC2885752 DOI: 10.1099/mic.0.2008/017939-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2008] [Revised: 04/30/2008] [Accepted: 06/30/2008] [Indexed: 11/18/2022]
Abstract
IncP-9 plasmids are important vehicles for degradation and resistance genes that contribute to the adaptability of Pseudomonas species in a variety of natural habitats. The three completely sequenced IncP-9 plasmids, pWW0, pDTG1 and NAH7, show extensive homology in replication, partitioning and transfer loci (an approximately 25 kb region) and to a lesser extent in the remaining backbone segments. We used PCR, DNA sequencing, hybridization and phylogenetic analyses to investigate the genetic diversity of 30 IncP-9 plasmids as well as the possibility of recombination between plasmids belonging to this family. Phylogenetic analysis of rep and oriV sequences revealed nine plasmid subgroups with 7-35 % divergence between them. Only one phenotypic character was normally associated with each subgroup, except for the IncP-9beta cluster, which included naphthalene- and toluene-degradation plasmids. The PCR and hybridization analysis using pWW0- and pDTG1-specific primers and probes targeting selected backbone loci showed that members of different IncP-9 subgroups have considerable similarity in their overall organization, supporting the existence of a conserved ancestral IncP-9 sequence. The results suggested that some IncP-9 plasmids are the product of recombination between plasmids of different IncP-9 subgroups but demonstrated clearly that insertion of degradative transposons has occurred on multiple occasions, indicating that association of this phenotype with these plasmids is not simply the result of divergent evolution from a single successful ancestral degradative plasmid.
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Affiliation(s)
| | - Renata Krasowiak
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Lewis E. H. Bingle
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Anthony S. Haines
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Sergey L. Sokolov
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Irina A. Kosheleva
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Anastassia A. Leuchuk
- Genetics Department, Biology Faculty, Belarus State University, 6 Kurchatova St, Minsk 220064, Belarus
| | - Marina A. Titok
- Genetics Department, Biology Faculty, Belarus State University, 6 Kurchatova St, Minsk 220064, Belarus
| | - Kornelia Smalla
- Julius Kühn Institute – Federal Research Centre for Cultivated Plants (JKI), Messeweg 11/12, 38104 Braunschweig, Germany
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24
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Huang WE, Stoecker K, Griffiths R, Newbold L, Daims H, Whiteley AS, Wagner M. Raman-FISH: combining stable-isotope Raman spectroscopy and fluorescence in situ hybridization for the single cell analysis of identity and function. Environ Microbiol 2007; 9:1878-89. [PMID: 17635536 DOI: 10.1111/j.1462-2920.2007.01352.x] [Citation(s) in RCA: 217] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have coupled fluorescence in situ hybridization (FISH) with Raman microscopy for simultaneous cultivation-independent identification and determination of (13)C incorporation into microbial cells. Highly resolved Raman confocal spectra were generated for individual cells which were grown in minimal medium where the ratio of (13)C to (12)C content of the sole carbon source was incrementally varied. Cells which were (13)C-labelled through anabolic incorporation of the isotope exhibited key red-shifted spectral peaks, the calculated 'red shift ratio' (RSR) being highly correlated with the (13)C-content of the cells. Subsequently, Raman instrumentation and FISH protocols were optimized to allow combined epifluorescence and Raman imaging of Fluos, Cy3 and Cy5-labelled microbial populations at the single cell level. Cellular (13)C-content determinations exhibited good congruence between fresh cells and FISH hybridized cells indicating that spectral peaks, including phenylalanine resonance, which were used to determine (13)C-labelling, were preserved during fixation and hybridization. In order to demonstrate the suitability of this technology for structure-function analyses in complex microbial communities, Raman-FISH was deployed to show the importance of Pseudomonas populations during naphthalene degradation in groundwater microcosms. Raman-FISH extends and complements current technologies such as FISH-microautoradiography and stable isotope probing in that it can be applied at the resolution of single cells in complex communities, is quantitative if suitable calibrations are performed, can be used with stable isotopes and has analysis times of typically 1 min per cell.
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Affiliation(s)
- Wei E Huang
- Biodiversity and Ecosystem Function Group, Molecular Microbial Ecology Section, Centre for Ecology and Hydrology Oxford, Mansfield Road, Oxford, OX1 3SR, UK
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25
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Yano H, Garruto CE, Sota M, Ohtsubo Y, Nagata Y, Zylstra GJ, Williams PA, Tsuda M. Complete Sequence Determination Combined with Analysis of Transposition/Site-specific Recombination Events to Explain Genetic Organization of IncP-7 TOL Plasmid pWW53 and Related Mobile Genetic Elements. J Mol Biol 2007; 369:11-26. [PMID: 17408691 DOI: 10.1016/j.jmb.2007.02.098] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2006] [Revised: 02/22/2007] [Accepted: 02/26/2007] [Indexed: 11/19/2022]
Abstract
Recent studies have indicated that the evolutionarily common catabolic gene clusters are loaded on structurally diverse toluene-catabolic (TOL) plasmids and their residing transposons. To elucidate the mechanisms supporting the diversification of catabolic plasmids and transposons, we determined here the complete 107,929 bp sequence of pWW53, a TOL plasmid from Pseudomonas putida MT53. pWW53 was found to belong to the IncP-7 incompatibility group that play important roles in the catabolism of several xenobiotics. pWW53 carried two distinct transposase-resolvase gene clusters (tnpAR modules), five short terminal inverted repeats (IRs), and three site-specific resolution (res) sites that are all typical of class II transposons. This organization of pWW53 suggested the four possible transposable regions, Tn4657 to Tn4660. The largest 86 kb region (Tn4657) spanned the three other regions, and Tn4657 and Tn4660 (62 kb) covered all of the 36 xyl genes for toluene catabolism. Our subsequent transposition experiments clarified that the three transposons, Tn4657 to Tn4659, indeed exhibit their transposability, and that pWW53 also generated another 37 kb toluene-catabolic transposon, Tn4656, which carried the two separated and inversely oriented segments of pWW53: the tnpRA-IR module of Tn4658 and a part of xyl gene clusters on Tn4657. The Tn4658 transposase was able to mediate the transposition of Tn4658, Tn4657, and Tn4656, while the Tn4659 transposase catalyzed only the transposition of Tn4659. Tn4656 was formed by the Tn4658 resolvase-mediated site-specific inversion between the two inversely oriented res sites on pWW53. These findings and comparison with other catabolic plasmids clearly indicate multiple copies of transposition-related genes and sites on one plasmid and their recombination activities contribute greatly to the diversification of plasmid structures as well as wide dissemination of the evolutionary common gene clusters in various plasmids.
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Affiliation(s)
- Hirokazu Yano
- Graduate School of Life Sciences, Tohoku University, Katahira, Sendai 980-8577, Japan
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26
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Ono A, Miyazaki R, Sota M, Ohtsubo Y, Nagata Y, Tsuda M. Isolation and characterization of naphthalene-catabolic genes and plasmids from oil-contaminated soil by using two cultivation-independent approaches. Appl Microbiol Biotechnol 2006; 74:501-10. [PMID: 17096121 DOI: 10.1007/s00253-006-0671-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2006] [Revised: 09/06/2006] [Accepted: 09/10/2006] [Indexed: 10/23/2022]
Abstract
Two different cultivation-independent approaches were applied to isolate genes for naphthalene dioxygenase (NDO) from oil-contaminated soil in Japan. One approach was the construction of a broad-host-range cosmid-based metagenomic DNA library, and the other was the so-called exogenous plasmid isolation technique. Our screening of NDO genes in both approaches was based on the functional complementation of Pseudomonas putida strains which contained Tn4655K, a transposon carrying the entire set of naphthalene-catabolic (nah) genes but lacking the NDO-encoding gene. We obtained in the former approach a cosmid clone (pSLX928-6) that carried an nah upper pathway operon for conversion of naphthalene to salicylate, and this operon showed a significantly high level of similarity to the corresponding operon on an IncP-9 naphthalene-catabolic plasmid, pDTG1. In the latter approach, the microbial fraction from the soil was mated with a plasmid-free P. putida strain containing a chromosomal copy of Tn4655K, and transconjugants were obtained that received either a 200- or 80-kb plasmid containing all the nah genes for the complete degradation of naphthalene. Subsequent analysis revealed that (1) both plasmids belong to the IncP-9 incompatibility group; (2) their nah upper pathway operons are significantly similar, but not completely identical, to those of pDTG1 and pSLX928-6; and (3) these plasmids carried genes for the salicylate metabolism by the meta-cleavage pathway.
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Affiliation(s)
- Akira Ono
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan
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