Genomics of high molecular weight plasmids isolated from an on-farm biopurification system

Martini MC, Wibberg D, Lozano M, Torres Tejerizo G, Albicoro FJ, Jaenicke S, van Elsas JD, Petroni A, Garcillan-Barcia MP, de la Cruz F, Schlüter A, et al. (2016)
Scientific Reports 6: 28284.

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Abstract / Bemerkung
The use of biopurification systems (BPS) constitutes an efficient strategy to eliminate pesticides from polluted wastewaters from farm activities. BPS environments contain a high microbial density and diversity facilitating the exchange of information among bacteria, mediated by mobile genetic elements (MGEs), which play a key role in bacterial adaptation and evolution in such environments. Here we sequenced and characterized high-molecular-weight plasmids from a bacterial collection of an on-farm BPS. The high-throughput-sequencing of the plasmid pool yielded a total of several Mb sequence information. Assembly of the sequence data resulted in six complete replicons. Using in silico analyses we identified plasmid replication genes whose encoding proteins represent 13 different Pfam families, as well as proteins involved in plasmid conjugation, indicating a large diversity of plasmid replicons and suggesting the occurrence of horizontal gene transfer (HGT) events within the habitat analyzed. In addition, genes conferring resistance to 10 classes of antimicrobial compounds and those encoding enzymes potentially involved in pesticide and aromatic hydrocarbon degradation were found. Global analysis of the plasmid pool suggest that the analyzed BPS represents a key environment for further studies addressing the dissemination of MGEs carrying catabolic genes and pathway assembly regarding degradation capabilities.
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Scientific Reports
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6
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28284
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Martini MC, Wibberg D, Lozano M, et al. Genomics of high molecular weight plasmids isolated from an on-farm biopurification system. Scientific Reports. 2016;6: 28284.
Martini, M. C., Wibberg, D., Lozano, M., Torres Tejerizo, G., Albicoro, F. J., Jaenicke, S., van Elsas, J. D., et al. (2016). Genomics of high molecular weight plasmids isolated from an on-farm biopurification system. Scientific Reports, 6, 28284. doi:10.1038/srep28284
Martini, M. C., Wibberg, D., Lozano, M., Torres Tejerizo, G., Albicoro, F. J., Jaenicke, S., van Elsas, J. D., Petroni, A., Garcillan-Barcia, M. P., de la Cruz, F., et al. (2016). Genomics of high molecular weight plasmids isolated from an on-farm biopurification system. Scientific Reports 6:28284.
Martini, M.C., et al., 2016. Genomics of high molecular weight plasmids isolated from an on-farm biopurification system. Scientific Reports, 6: 28284.
M.C. Martini, et al., “Genomics of high molecular weight plasmids isolated from an on-farm biopurification system”, Scientific Reports, vol. 6, 2016, : 28284.
Martini, M.C., Wibberg, D., Lozano, M., Torres Tejerizo, G., Albicoro, F.J., Jaenicke, S., van Elsas, J.D., Petroni, A., Garcillan-Barcia, M.P., de la Cruz, F., Schlüter, A., Pühler, A., Pistorio, M., Lagares, A., Del Papa, M.F.: Genomics of high molecular weight plasmids isolated from an on-farm biopurification system. Scientific Reports. 6, : 28284 (2016).
Martini, Maria C., Wibberg, Daniel, Lozano, Mauricio, Torres Tejerizo, Gonzalo, Albicoro, Francisco J., Jaenicke, Sebastian, van Elsas, Jan Dirk, Petroni, Alejandro, Garcillan-Barcia, M. Pilar, de la Cruz, Fernando, Schlüter, Andreas, Pühler, Alfred, Pistorio, Mariano, Lagares, Antonio, and Del Papa, Maria F. “Genomics of high molecular weight plasmids isolated from an on-farm biopurification system”. Scientific Reports 6 (2016): 28284.

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Targeted metagenomics demonstrates the ecological role of IS1071 in bacterial community adaptation to pesticide degradation.
Dunon V, Bers K, Lavigne R, Top EM, Springael D., Environ Microbiol 20(11), 2018
PMID: 30207068

73 References

Daten bereitgestellt von Europe PubMed Central.

Overview of on-farm bioremediation systems to reduce the occurrence of point source contamination.
De Wilde T, Spanoghe P, Debaer C, Ryckeboer J, Springael D, Jaeken P., Pest Manag. Sci. 63(2), 2007
PMID: 17199234
Improvement of pesticide mineralization in on-farm biopurification systems by bioaugmentation with pesticide-primed soil.
Sniegowski K, Bers K, Van Goetem K, Ryckeboer J, Jaeken P, Spanoghe P, Springael D., FEMS Microbiol. Ecol. 76(1), 2011
PMID: 21231937
Mobile genetic elements: the agents of open source evolution.
Frost LS, Leplae R, Summers AO, Toussaint A., Nat. Rev. Microbiol. 3(9), 2005
PMID: 16138100
Biased biological functions of horizontally transferred genes in prokaryotic genomes.
Nakamura Y, Itoh T, Matsuda H, Gojobori T., Nat. Genet. 36(7), 2004
PMID: 15208628
Community-wide plasmid gene mobilization and selection.
Sentchilo V, Mayer AP, Guy L, Miyazaki R, Green Tringe S, Barry K, Malfatti S, Goessmann A, Robinson-Rechavi M, van der Meer JR., ISME J 7(6), 2013
PMID: 23407308
Analysis of two marine metagenomes reveals the diversity of plasmids in oceanic environments.
Ma Y, Paulsen IT, Palenik B., Environ. Microbiol. 14(2), 2011
PMID: 22059529
An improved method for including upper size range plasmids in metamobilomes.
Norman A, Riber L, Luo W, Li LL, Hansen LH, Sorensen SJ., PLoS ONE 9(8), 2014
PMID: 25116381
Hundreds of circular novel plasmids and DNA elements identified in a rat cecum metamobilome.
Jorgensen TS, Xu Z, Hansen MA, Sorensen SJ, Hansen LH., PLoS ONE 9(2), 2014
PMID: 24503942
Current strategies for mobilome research.
Jorgensen TS, Kiil AS, Hansen MA, Sorensen SJ, Hansen LH., Front Microbiol 5(), 2014
PMID: 25657641
Plasmid detection, characterization, and ecology
AUTHOR UNKNOWN, 2015
Characterization of a collection of plasmid-containing bacteria isolated from an on-farm biopurification system used for pesticide removal.
Martini MC, Albicoro FJ, Nour E, Schluter A, van Elsas JD, Springael D, Smalla K, Pistorio M, Lagares A, Del Papa MF., Plasmid 80(), 2015
PMID: 25957823
High prevalence of IncP-1 plasmids and IS1071 insertion sequences in on-farm biopurification systems and other pesticide-polluted environments.
Dunon V, Sniegowski K, Bers K, Lavigne R, Smalla K, Springael D., FEMS Microbiol. Ecol. 86(3), 2013
PMID: 23802695
Shifts in abundance and diversity of mobile genetic elements after the introduction of diverse pesticides into an on-farm biopurification system over the course of a year.
Dealtry S, Holmsgaard PN, Dunon V, Jechalke S, Ding GC, Krogerrecklenfort E, Heuer H, Hansen LH, Springael D, Zuhlke S, Sorensen SJ, Smalla K., Appl. Environ. Microbiol. 80(13), 2014
PMID: 24771027
GenDB--an open source genome annotation system for prokaryote genomes.
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A., Nucleic Acids Res. 31(8), 2003
PMID: 12682369

AUTHOR UNKNOWN, 2004
Complete genome sequence of Pseudomonas sp. strain VLB120 a solvent tolerant, styrene degrading bacterium, isolated from forest soil.
Kohler KA, Ruckert C, Schatschneider S, Vorholter FJ, Szczepanowski R, Blank LM, Niehaus K, Goesmann A, Puhler A, Kalinowski J, Schmid A., J. Biotechnol. 168(4), 2013
PMID: 24161918
Klebsiella pneumoniae multiresistance plasmid pMET1: similarity with the Yersinia pestis plasmid pCRY and integrative conjugative elements.
Soler Bistue AJ, Birshan D, Tomaras AP, Dandekar M, Tran T, Newmark J, Bui D, Gupta N, Hernandez K, Sarno R, Zorreguieta A, Actis LA, Tolmasky ME., PLoS ONE 3(3), 2008
PMID: 18350140
Complete nucleotide sequence of Birmingham IncP alpha plasmids. Compilation and comparative analysis.
Pansegrau W, Lanka E, Barth PT, Figurski DH, Guiney DG, Haas D, Helinski DR, Schwab H, Stanisich VA, Thomas CM., J. Mol. Biol. 239(5), 1994
PMID: 8014987
Prevalence of tet gene and complete genome sequencing of tet gene-encoded plasmid (pAHH01) isolated from Aeromonas species in South Korea.
Han JE, Kim JH, Choresca CH Jr, Shin SP, Jun JW, Chai JY, Park SC., J. Appl. Microbiol. 112(4), 2012
PMID: 22309714
Detection and characterization of broad-host-range plasmids in environmental bacteria by PCR.
Gotz A, Pukall R, Smit E, Tietze E, Prager R, Tschape H, van Elsas JD, Smalla K., Appl. Environ. Microbiol. 62(7), 1996
PMID: 8779598
Horizontal gene transfer and the origin of species: lessons from bacteria.
de la Cruz F, Davies J., Trends Microbiol. 8(3), 2000
PMID: 10707066
Ordering the bestiary of genetic elements transmissible by conjugation.
Garcillan-Barcia MP, de la Cruz F., Mob Genet Elements 3(1), 2013
PMID: 23734300
A classification scheme for mobilization regions of bacterial plasmids.
Francia MV, Varsaki A, Garcillan-Barcia MP, Latorre A, Drainas C, de la Cruz F., FEMS Microbiol. Rev. 28(1), 2004
PMID: 14975531
The diversity of conjugative relaxases and its application in plasmid classification.
Garcillan-Barcia MP, Francia MV, de la Cruz F., FEMS Microbiol. Rev. 33(3), 2009
PMID: 19396961
The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation.
Guglielmini J, Quintais L, Garcillan-Barcia MP, de la Cruz F, Rocha EP., PLoS Genet. 7(8), 2011
PMID: 21876676
Mobility of plasmids.
Smillie C, Garcillan-Barcia MP, Francia MV, Rocha EP, de la Cruz F., Microbiol. Mol. Biol. Rev. 74(3), 2010
PMID: 20805406
Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion.
Guglielmini J, Neron B, Abby SS, Garcillan-Barcia MP, de la Cruz F, Rocha EP., Nucleic Acids Res. 42(9), 2014
PMID: 24623814
Identification of bacterial plasmids based on mobility and plasmid population biology.
Garcillan-Barcia MP, Alvarado A, de la Cruz F., FEMS Microbiol. Rev. 35(5), 2011
PMID: 21711366
Towards an integrated model of bacterial conjugation.
Cabezon E, Ripoll-Rozada J, Pena A, de la Cruz F, Arechaga I., FEMS Microbiol. Rev. 39(1), 2014
PMID: 25154632
Recent advances in the structural and molecular biology of type IV secretion systems.
Trokter M, Felisberto-Rodrigues C, Christie PJ, Waksman G., Curr. Opin. Struct. Biol. 27(), 2014
PMID: 24709394
Cultivation-independent screening revealed hot spots of IncP-1, IncP-7 and IncP-9 plasmid occurrence in different environmental habitats.
Dealtry S, Ding GC, Weichelt V, Dunon V, Schluter A, Martini MC, Del Papa MF, Lagares A, Amos GC, Wellington EM, Gaze WH, Sipkema D, Sjoling S, Springael D, Heuer H, van Elsas JD, Thomas C, Smalla K., PLoS ONE 9(2), 2014
PMID: 24587126
PCR primers for detection and characterisation of IncP-9 plasmids.
Krasowiak R, Smalla K, Sokolov S, Kosheleva I, Sevastyanovich Y, Titok M, Thomas CM., FEMS Microbiol. Ecol. 42(2), 2002
PMID: 19709281
Dynamics of the IncW genetic backbone imply general trends in conjugative plasmid evolution.
Fernandez-Lopez R, Garcillan-Barcia MP, Revilla C, Lazaro M, Vielva L, de la Cruz F., FEMS Microbiol. Rev. 30(6), 2006
PMID: 17026718
Bringing them together: plasmid pMV158 rolling circle replication and conjugation under an evolutionary perspective.
Lorenzo-Diaz F, Fernandez-Lopez C, Garcillan-Barcia MP, Espinosa M., Plasmid 74(), 2014
PMID: 24942190
Quantification of IncP-1 plasmid prevalence in environmental samples.
Jechalke S, Dealtry S, Smalla K, Heuer H., Appl. Environ. Microbiol. 79(4), 2012
PMID: 23241977
Plasmid diversity and adaptation analyzed by massive sequencing of Escherichia coli plasmids
AUTHOR UNKNOWN, 2015
Barnase and barstar: two small proteins to fold and fit together.
Hartley RW., Trends Biochem. Sci. 14(11), 1989
PMID: 2696173
ARDB--Antibiotic Resistance Genes Database.
Liu B, Pop M., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18832362
Active efflux, a common mechanism for biocide and antibiotic resistance.
Levy SB., J. Appl. Microbiol. 92 Suppl(), 2002
PMID: 12000614
Characterization of ESBL disseminating plasmids
AUTHOR UNKNOWN, 2015
Aminoglycosides: activity and resistance.
Mingeot-Leclercq MP, Glupczynski Y, Tulkens PM., Antimicrob. Agents Chemother. 43(4), 1999
PMID: 10103173
Characterization of ermB gene transposition by Tn1545 and Tn917 in macrolide-resistant Streptococcus pneumoniae isolates.
Okitsu N, Kaieda S, Yano H, Nakano R, Hosaka Y, Okamoto R, Kobayashi T, Inoue M., J. Clin. Microbiol. 43(1), 2005
PMID: 15634967
The multifaceted roles of antibiotics and antibiotic resistance in nature.
Sengupta S, Chattopadhyay MK, Grossart HP., Front Microbiol 4(), 2013
PMID: 23487476
Outwitting multidrug resistance to antifungals.
Monk BC, Goffeau A., Science 321(5887), 2008
PMID: 18635793
Mercury resistance transposons of gram-negative environmental bacteria and their classification.
Mindlin S, Kholodii G, Gorlenko Z, Minakhina S, Minakhin L, Kalyaeva E, Kopteva A, Petrova M, Yurieva O, Nikiforov V., Res. Microbiol. 152(9), 2001
PMID: 11763242
The TOL plasmids: determinants of the catabolism of toluene and the xylenes.
Assinder SJ, Williams PA., Adv. Microb. Physiol. 31(), 1990
PMID: 2264522
ISfinder: the reference centre for bacterial insertion sequences.
Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M., Nucleic Acids Res. 34(Database issue), 2006
PMID: 16381877
Horizontal gene transfer: perspectives at a crossroads of scientific disciplines.
Smets BF, Barkay T., Nat. Rev. Microbiol. 3(9), 2005
PMID: 16145755
Paradigms of plasmid organization.
Thomas CM., Mol. Microbiol. 37(3), 2000
PMID: 10931342
The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds.
Top EM, Springael D., Curr. Opin. Biotechnol. 14(3), 2003
PMID: 12849778
Divergence of mobile genetic elements involved in the distribution of xenobiotic-catabolic capacity.
Nojiri H, Shintani M, Omori T., Appl. Microbiol. Biotechnol. 64(2), 2003
PMID: 14689248

AUTHOR UNKNOWN, 0
DNA sequence homology in Rhizobium meliloti plasmids.
Jouanin L, De Lajudie P, Bazetoux S, Huguet T., Mol. Gen. Genet. 182(2), 1981
PMID: 6270502
InterPro and InterProScan: tools for protein sequence classification and comparison.
Mulder N, Apweiler R., Methods Mol. Biol. 396(), 2007
PMID: 18025686
Consed: a graphical tool for sequence finishing.
Gordon D, Abajian C, Green P., Genome Res. 8(3), 1998
PMID: 9521923
Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid.
Wibberg D, Blom J, Jaenicke S, Kollin F, Rupp O, Scharf B, Schneiker-Bekel S, Sczcepanowski R, Goesmann A, Setubal JC, Schmitt R, Puhler A, Schluter A., J. Biotechnol. 155(1), 2011
PMID: 21329740
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ., Nucleic Acids Res. 25(17), 1997
PMID: 9254694
FastTree 2--approximately maximum-likelihood trees for large alignments.
Price MN, Dehal PS, Arkin AP., PLoS ONE 5(3), 2010
PMID: 20224823
Metagenomic analysis reveals potential biodegradation pathways of persistent pesticides in freshwater and marine sediments.
Fang H, Cai L, Yang Y, Ju F, Li X, Yu Y, Zhang T., Sci. Total Environ. 470-471(), 2013
PMID: 24239819

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