IncP-1 and PromA Group Plasmids Are Major Providers of Horizontal Gene Transfer Capacities Across Bacteria in the Mycosphere of Different Soil Fungi

Microbial Ecology

Volumn 69, Issue 1, 2015, Pages 169-179

  Zhang, Miaozhi ^a   Visser, Sander ^a   Pereira e Silva, Michele C ^b   van Elsas, Jan Dirk ^a  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

AMPULLOCLITOCYBE; BASIDIOMYCOTA; FUNGI; GALERINA; INOCYBE; PSEUDOMONAS FLUORESCENS; RUSSULA;

BACTERIUM; FUNGUS; GENETICS; HORIZONTAL GENE TRANSFER; MICROBIOLOGY; PLASMID;

BACTERIA; FUNGI; GENE TRANSFER, HORIZONTAL; PLASMIDS; SOIL MICROBIOLOGY;

EID: 84920821639     PISSN: 00953628     EISSN: 1432184X     Source Type: Journal    
DOI: 10.1007/s00248-014-0482-6     Document Type: Article

References (34)

1. Alvarado A, Garcillán-Barcia MP, de la Cruz F (2012) A degenerate primer MOB typing (DPMT) method to classify Gamma-proteobacterial plasmids in clinical and environmental settings. PLoS ONE 7(7):e40438
2. Atkinson GF (1918) Some new species of Inocybe. Am J Bot 5(4):210–218
3. Bach HJ et al (2002) Enumeration of total bacteria and bacteria with genes for proteolytic activity in pure cultures and in environmental samples by quantitative PCR mediated amplification. J Microbiol Meth 49:235–245
4. Bale MJ et al (1988) Novel method for studying plasmid transfer in undisturbed river epilithon. Appl Environ Microbiol 54:2756–2758
5. Bergstrom CT, Llipsitch M, Levin BR (2000) National selection, infectious transfer and the existence conditions for bacterial plasmids. Genetics 155:1505–1519
6. Birnboim HC, Doly J (1979) A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res 7:1513–1523
7. Boersma FGH (2009) Mechanisms of bacterial selection in the mycosphere of tricholomataceous fungi. PhD Thesis University of Groningen
8. Clarke KR, Gorley RN (2006) PRIMER v6: user manual/tutorial. PRIMER-E, Plymouth
9. Dennis JJ (2005) The evolution of IncP catabolic plasmids. Curr Opin Biotechnol 16:291–298
10. Earle FS (1909) The genera of North American gill fungi. Bull N Y Bot Gard 5:373–451
11. Folman LB et al (2008) Impact of white-rot fungi on numbers and community composition of bacteria colonizing beech wood from forest soil. FEMS Microbiol Ecol 63:181–191
12. Frost LS, Leplae R, Summers AO, Toussaint A (2005) Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol 3:722–732
13. Götz A et al (1996) Detection and characterization of broad-host-range plasmids in environmental bacteria by PCR. Appl Environ Microbiol 62:2621–2628
14. Hammer Ø, Harper DAT, Ryan PD (2001) PAST: paleontological statistics software package for education and data analysis. Palaeontol Electron 4:9
15. Heuer H, Smalla K (2012) Plasmids foster diversification and adaptation of bacterial populations in soil. FEMS Microbiol Rev 36:1083–1104
16. Mela F et al (2008) Comparative genomics of the pIPO2/pSB102 family of environmental plasmids: sequence, evolution, and ecology of pTer331 isolated from Collimonas fungivorans Ter331. FEMS Microbiol Ecol 66:45–62
17. Melzer A, Zvára A (1927) Russula exalbicans (Pers.). Arch Prírodov Výzk Cech 17(4):97
18. Redhead SA, Lutzoni F, Moncalvo JM, Vilgalys R (2002) Phylogeny of agarics: partial systematics solutions for core omphalinoid genera in the Agaricales (euagarics). Mycotaxon 83:19–57
19. Sambrook J, Russel DW (2001) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, New York
20. Sarand I, Haario H, Jörgensen KS, Romantschuk M (2000) Effect of inoculation of a TOL plasmid containing mycorrhizosphere bacterium on development of Scots pine seedlings, their mycorrhizosphere and the microbial flora in m-toluate-amended soil. FEMS Microbiol Ecol 31:127–141
21. Schlüter A, Szczepanowski R, Pühler A, Top EM (2007) Genomics of IncP-1 antibiotic resistance plasmids isolated from wastewater treatment plants provides evidence for a widely accessible drug resistance gene pool. FEMS Microbiol Rev 31:449–477
22. Smalla K, Heuer H, Götz A, Niemeyer D, Krögerrecklenfort E, Tietze E (2000) Exogenous isolation of antibiotic resistance plasmids from piggery manure slurries reveals a high prevalence and diversity of IncQ-like plasmids. Appl Environ Microbiol 66:4854–4862
23. Smit E et al (1999) Analysis of fungal diversity in the wheat rhizosphere by sequencing of cloned PCR-amplified genes encoding 18S rRNA and temperature gradient gel electrophoresis. Appl Environ Microbiol 65:2612–2621
24. Sota M, Top EM (2008) Horizontal gene transfer mediated by plasmids. In: Lipps G (ed) Plasmids: current research and future trends. Caister Academic Press, Norfolk, UK, pp 111–181
25. Tauch A, Schneiker S, Selbitschka W, Puhler A, Van Overbeek LS, Smalla K (2002) The complete nucleotide sequence and environmental distribution of the cryptic, conjugative, broad-host-range plasmid pIPO2 isolated from bacteria of the wheat rhizosphere. Microbiology 148:1637–1653
26. Thomas CM (2000) The horizontal gene pool: bacterial plasmids and gene spread. Harwood Academic Publishers, Amsterdam
27. Valášková V et al (2009) Phylogenetic composition and properties of bacteria coexisting with the fungus Hypholoma fasciculare in decaying wood. ISME J 3:1218–1221
28. Van der Auwera GA et al (2009) Plasmids captured in C. metallidurans CH34: defining the PromA family of broad-host-range plasmids. Antonie van Leeuwenhoek 96:193–204
29. Van Elsas JD, Gardener BBM, Wolters AC, Smit E (1998) Isolation, characterization, and transfer of cryptic genemobilizing plasmids in the wheat rhizosphere. Appl Environ Microbiol 64:880–889
30. Van Elsas JD, Turner S, Bailey MJ (2003) Horizontal gene transfer in the phytosphere. New Phytol 157:525–537
31. Versalovic J, Schneider M, de Bruijn FJ, Lupski JR (1994) Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods Mol Cell Biol 5:25–40
32. Warmink JA, van Elsas JD (2008) Selection of bacterial populations in the mycosphere of Laccaria proxima: is type III secretion involved? ISME J 2:887–900
33. Warmink JA, Nazir R, van Elsas JD (2009) Universal and species-specific bacterial ‘fungiphiles’ in the mycospheres of different basidiomycetous fungi. Environ Microbiol 11:300–312
34. Zhang M, Pereira e Silva MC, Chaib de Mares M, van Elsas JD (2014) The mycosphere constitutes an arena for horizontal gene transfer with strong evolutionary implications for bacterial–fungal interactions. FEMS Microbiol Ecol. doi: 10.1111/1574-6941.12350