13.5 Conclusions
Evidence is mounting that MGE play an important role in the evolution and adaptability of bacterial species. The rapid accumulation of bacterial genome sequences and the development of powerful tools has allowed, and will continue to allow, new insights into the horizontal gene pool, i.e. the horizontally transferred genetic modules and their mobile genetic vehicles. Identification of the flexible part of bacterial genomes — in contrast to that part which is shared by most strains of a species — will clarify what the cohesive factors forming bacterial species are. The capacity of soil microorganisms to sample the horizontal gene pool provides bacteria with the ability to rapidly adapt to ever-changing environments and is a major driving force of microbial diversity in soil.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Alonso A, Sánchez P, Martínez JL (2001) Environmental selection of antibiotic resistance genes. Environ Microbiol 3:1–9
Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169
Ashelford KE, Day MJ, Fry JC (2003) Elevated abundance of bacteriophage infecting bacteria in soil. Appl Environ Microbiol 69:285–289
Bale MJ, Day MJ, Fry JC (1988) Novel method for studying plasmid transfer in undisturbed river epilithon. Appl Environ Microbiol 54:2756–2758
Beaber JW, Hochhut B, Waldor MK (2004) SOS response promotes horizontal dissemination of antibiotic resistance genes. Nature 427:72–74
Buell CR et al. (2003) The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proc Natl Acad Sci USA 100:10181–10186
Burrus V, Waldor MK (2004) Shaping bacterial genomes with integrative and conjugative elements. Res Microbiol 155:376–386
Canchaya C, Proux C, Fournous G, Bruttin A, Brüssow H (2003) Prophage genomics. Microbiol Mol Biol Rev 67:238–276
Couturier M, Bex F, Berquist PL, Maas WK (1988) Identification and classification of bacterial plasmids. Microbiol Rev 52:375–395
Day T, Young KA (2004) Competitive and facilitative evolutionary diversification. BioScience 54:101–109
De la Cruz F, Davies J (2000) Horizontal gene transfer and the origin of species: lessons from bacteria. Trends Microbiol 8:128–133
Dobrindt U, Hochhut B, Hentschel U, Hacker J (2004) Genomic islands in pathogenic and environmental microorganisms. Nature 2:414–424
Dos Santos VAPM, Heim S, Moore ERB, Strätz M, Timmis KN (2004) Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440. Environ Microbiol 6:1264–1268
Drønen AK, Torsvik V, Goksøyr J, Top EMT (1998) Effect of mercury addition on plasmid incidence and gene mobilising capacity in bulk soil. FEMS Microbiol Ecol 27:381–394
Drønen K, Torsvik V, Top E (1999) Comparison of the plasmid types obtained by two distantly related recipients in biparental exogenous plasmid isolations from soil. FEMS Microbiol Lett 176:105–110
Fry JC (2004) Culture-dependent microbiology. In: Bull AT (ed) Microbial diversity and bioprospecting. ASM Press, Washington, DC, pp 80–87
Galibert F et al. (2001) The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293:668–672
Götz A, Smalla K (1997) Manure enhances plasmid mobilization and survival of Pseudomonas putida introduced into field soil. Appl Environ Microbiol 63:1980–1986
Götz A, Pukall R, Smit E, Tietze E, Prager R, Tschäpe H, Van Elsas JD, Smalla K (1996) Detection and characterization of broad-host-range plasmids in environmental bacteria by PCR. Appl Environ Microbiol 62:2621–2628
Greated A, Thomas CM (1999) A pair of PCR primers for IncP9-plasmids. Microbiology 145:3003–3004
Hacker J, Blum-Oehler G, Mühldorfer I, Tschäpe H (1997) Pathogenicity islands of virulent bacteria, structure, function and impact on microbial evolution. Mol Microbiol 23:1089–1097
Hacker J, Carniel E (2001) Ecological fitness, genomic islands and bacterial pathogenicity. EMBO J 2:376–381
Hacker J, Hentschel U, Dobrindt U (2003) Prokaryotic chromosomes and disease. Science 301:790–793
Hall RM, Collis CM (1995) Mobile gene cassettes and integrons: capture and spread of genes by site-specific recombination. Mol Microbiol 15:593–600
Heuer H, Krögerrecklenfort E, Egan S, Van Overbeek LS, Guillaume G, Nikolakopoulou TL, Wellington EMH, Van Elsas JD, Collard JM, Karagouni AD, Smalla K (2002) Gentamicin resistance genes in environmental bacteria: prevalence and transfer. FEMS Microbiol Ecol 42:289–302
Hill KE, Weightman AJ, Fry JC (1992) Isolation and screening of plasmids from the epilithon which mobilize recombinant plasmid pD10. Appl Environ Microbiol 58:1292–1300
Holmes AJ, Holley MP, Mahon A, Nield B, Gillings M, Stokes HW (2003) Recombination activity of a distinctive integron-gene cassette system associated with Pseudomonas stutzeri populations in soil. J Bacteriol 185:918–928
Koonin EV, Makarova KS, Aravind L (2001) Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol 55:709–742
Krasowiak R, Smalla K, Sokolov S, Kosheleva I, Sevastyanovich Y, Titok M, Thomas CM (2002) PCR primers for detection and characterisation of IncP-9 plasmids. FEMS Microbiol Ecol 42:217–225
Lan R, Reeves PR (2000) Intraspecies variation in bacterial genomes: the need for a species genome concept. Trends Microbiol 8:396–401
Lilley AK, Bailey MJ (1997a) Impact of plasmid pQBR103 acquisition and carriage on the phytosphere fitness of Pseudomonas fluorescens SBW25: burden and benefit. Appl Environ Microbiol 63:1584–1587
Lilley AK, Bailey MJ (1997b) The acquisition of indigenous plasmids by a genetically marked pseudomonad population colonizing the sugar beet phytosphere is related to local environmental conditions. Appl Environ Microbiol 63:1577–1583
Lilley AK, Fry JC, Day MJ, Bailey MJ (1994) In situ transfer of an exogenously isolated plasmid between Pseudomonas spp. in sugar beet rhizosphere. Microbiology 140:27–33
Lilley AK, Bailey MJ, Day MJ, Fry JC (1996) Diversity of mercury resistance plasmids obtained by exogenous isolation from the bacteria of sugar beet in three successive years. FEMS Microbiol Ecol 20:211–227
Mahillon J, Chandler M (1998) Insertion sequences. Microbiol Mol Biol Rev 62:725–774
Marques MV, da Silva AM, Gomes SL (2001) Genetic organization of plasmid pXF51 from the plant pathogen Xylella fastidiosa. Plasmid 45:184–199
Martinez B, Tomkins J, Wackett LP, Wing R, Sadowsky MJ (2001) Complete nucleotide sequence and organization of the atrazine catabolic plasmid pADP-1 from Pseudomonas sp. strain ADP. J Bacteriol 183:5684–5697
Mazel D, Davies J (1999) Antibiotic resistance in microbes. Cell Mol Life Sci 56:742–754
Nield BS, Holmes AJ, Gillings MR, Recchia GD, Mabbutt BC, Nevalainen KMH, Stokes HW (2001) Recovery of new integron classes from environmental DNA. FEMS Microbiol Lett 195:59–65
Ochman H, Lawrence JG, Groisman EA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405:299–304
Pansegrau W, Lanka E, Barth PT, Figurski DH, Guiney DG, Haas D, Helinski DR, Schwab H, Stanisich VA, Thomas CM (1994) Complete nucleotide sequence of Birmingham IncP alpha plasmids. Compilation and comparative analysis. J Mol Biol 239:623–663
Pukall R, Tschäpe H, Smalla K (1996) Monitoring the spread of broad host and narrow host range plasmids in soil microcosms. FEMS Microbiol Ecol 20:53–66
Salanoubat M, Genin S, Artiguenave F, Gouzy J, Mangenot S, Arlat M, Billault A, Brottier P, Camus JC, Cattolico L, Chandler M, Choisne N, Claudel-Renard C, Cunnac S, Demange N, Gaspin C, Lavie M, Moisan A, Robert C, Saurin W, Schiex T, Siguier P, Thebault P, Whalen M, Wincker P, Levy M, Weissenbach J, Boucher CA (2002) Genome sequence of the plant pathogen Ralstonia solanacearum. Nature 415:497–502
Schlosser PD, Handelsman J (2003) Biotechnological prospects from metagenomics. Curr Opin Biotechnol 14:303–310
Schneiker S, Keller M, Dröge M, Lanka E, Pühler A (2001) The genetic organization and evolution of the broad-host-range mercury resistance plasmid pSB102 isolated from a microbial population residing in the rhizosphere of alfalfa. Nucleic Acids Res 29:5169–5181
Simpson AJ, Reinach FC, Arruda P, Abreu FA et al. (2000) The genome sequence of the plant pathogen Xylella fastidiosa. The Xylella fastidiosa Consortium of the Organization for Nucleotide Sequencing and Analysis. Nature 406:151–157
Smalla K (2004) Culture-independent microbiology. In: Bull AT (ed) Microbial diversity and bioprospecting. ASM Press, Washington, DC, pp 88–99
Smalla K, Sobecky P (2002) The prevalence and diversity of mobile genetic elements in environmental bacteria assessed with new tools. FEMS Microbiol Ecol 42:165–175
Smalla K, Cresswell N, Mendonça-Hagler LC, Wolters A, Van Elsas JD (1993) Rapid DNA extraction protocol from soil for polymerase chain reaction-mediated amplification. J Appl Bacteriol 74:78–85
Smalla K, Heuer H, Götz A, Niemeyer D, Krögerrecklenfort E, Tietze E (2000a) 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
Smalla K, Krögerrecklenfort E, Heuer H et al. (2000b) PCR-based detection of mobile genetic elements in total community DNA. Microbiology 146:1256–1257
Smalla K, Osborn M, Wellington EMH (2000c) Isolation and characterisation of plasmids from bacteria. In: Thomas CM (ed) The horizontal gene pool — bacterial plasmids and gene spread. Harwood Academic Publishers, London, pp 207–248
Smit E, Wolters A, Van Elsas JD (1998) Self-transmissible mercury resistance plasmids with gene-mobilizing capacity in soil bacterial populations: Influence of wheat roots and mercury addition. Appl Environ Microbiol 64:1210–1219
Staley JT, Konopka A (1985) Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu Rev Microbiol 39:321–346
Stokes HW, Holmes AJ, Nield BS, Holley MP, Nevalainen KMH, Mabbutt BC, Gillings MR (2001) Gene cassette PCR: sequence-independent recovery of entire genes from environmental DNA. Appl Environ Microbiol 67:5240–5246
Szpirer C, Top E, Couturier M, Mergeay M (1999) Retrotransfer or gene capture: a feature of conjugative plasmids, with ecological and evolutionary significance. Microbiology 145:3321–3329
Tauch A, Schneiker S, Selbitschka W, Pühler A, Van Overbeek LS, Smalla K, Thomas CM, Bailey MJ, Forney LJ, Weightman A, Ceglowski P, Pembroke T, Tietze E, Schröder G, Lanka E, Van Elsas JD (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
Thomas CM (2001) Paradigms of plasmid organization. Mol Microbiol 37:485–491
Thorsted PB, Macartney DP, Akhtar P, Haines AS, Ali N, Davidson P, Stafford T, Pocklington MJ, Pansegrau W, Wilkins BM, Lanka E, Thomas CM (1998) Complete sequence of the IncPβ plasmid R751: implications for evolution and organisation of the IncP backbone. J Mol Biol 282:969–990
Top E, De Smet I, Verstraete W, Dijkmans R, Mergeay M (1994) Exogenous isolation of mobilizing plasmids from polluted soils and sludges. Appl Environ Microbiol 60:831–839
Top EM, Holben WE, Forney LJ (1995) Characterization of diverse 2,4-dichlorophenoxy-acetic acid-degradative plasmids isolated from soil by complementation. Appl Environ Microbiol 61:1691–1698
Top EM, Maltseva OV, Forney LJ (1996) Capture of a catabolic plasmid that encodes only 2,4-dichlorophenoxyacetic acid: α-ketoglutaric acid dioxygenase (TfdA) by genetic complementation. Appl Environ Microbiol 62:2470–2476
Top EM, Springael D (2003) The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds. Curr Opin Biotechnol 14:262–269
Toussaint A, Merlin C (2002) Mobile elements as a combination of functional modules. Plasmid 47:26–35
Tralau T, Cook AM, Ruff J (2001) Map of the IncP1β plasmid pTSA encoding the widespread genes (tsa) for p-toluenesulfonate degradation in Comamonas testosteroni T-2. Appl Environ Microbiol 67:1508–1516
Trefault N, De la Iglesia R, Molina AM, Manzano M, Ledger T, Pérez-Pantoja D, Sánchez MA, Stuardo M, González B (2004) Genetic organization of the catabolic plasmid pJP4 from Ralstonia eutropha JMP (pJP4) reveals mechanisms of adaptation to chloroaromatic pollutants and evolution of specialized chloroaromatic degradation pathways. Environ Microbiol 6:655–668
Tschäpe H (1994) The spread of plasmids as a function of bacterial adaptability. FEMS Microbiol Ecol 15:23–32
Turner SL, Rigottier-Gois L, Power RS, Amarger N, Young JPW (1996) Diversity of repC plasmid replication sequences of Rhizobium leguminosarum. Microbiology 142:1705–1723
Van der Meer JR, Sentchilo V (2003) Genomic islands and the evolution of catabolic pathways in bacteria. Curr Opin Biotechnol 14:248–254
Van Elsas JD, Fry J, Hirsch P, Molin S (2000) Ecology of plasmid transfer and spread. In: Thomas CM (ed) The horizontal gene pool — bacterial plasmids and gene spread. Harwood Academic Publishers, London, pp 175–206
Van Elsas JD, Bailey MJ (2002) The ecology of transfer of mobile genetic elements. FEMS Microbiol Ecol 42:187–197
Van Elsas JD, McSpadden-Gardener BB, Wolters AC, Smit E (1998) Isolation, characterization, and transfer of cryptic gene-mobilizing plasmids in the wheat rhizosphere. Appl Environ Microbiol 64:880–889
Van Overbeek LS, Wellington EMH, Egan S, Smalla K, Heuer H, Collard JM, Guillaume G, Karagouni AD, Nikolakopoulou TL, Van Elsas JD (2002) Prevalence of streptomycin resistance genes in bacterial populations in European habitats. FEMS Microbiol Ecol 42:277–288
Vedler E, Vahter M, Heinaru A (2004) The completely sequenced plasmid pEST4011 contains a novel IncP1 backbone and a catabolic transposon harboring tfd genes for 2,4-dichlorophenoxyacetic acid degradation. J Bacteriol 186:7161–7174
Witte W (1998) Medical consequences of antibiotic use in agriculture. Science 279:996–997
Wood DW et al. (2001) The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science 294:2317–2323
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2006 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Smalla, K., Heuer, H. (2006). How to Assess the Abundance and Diversity of Mobile Genetic Elements in Soil Bacterial Communities?. In: Nannipieri, P., Smalla, K. (eds) Nucleic Acids and Proteins in Soil. Soil Biology, vol 8. Springer, Berlin, Heidelberg . https://doi.org/10.1007/3-540-29449-X_13
Download citation
DOI: https://doi.org/10.1007/3-540-29449-X_13
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-29448-1
Online ISBN: 978-3-540-29449-8
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)