Chapter 32 : Fitness Traits in Soil Bacteria

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in

Fitness Traits in Soil Bacteria, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817572/9781555813291_Chap32-1.gif /docserver/preview/fulltext/10.1128/9781555817572/9781555813291_Chap32-2.gif


One function of soil bacteria is the structuring of the soil under a principle of reciprocity : while bacteria alter the parent rock and stabilize the aggregates (i.e., the basic units of the structure of soils), soil colonization by bacteria is a function of soil structure. In the bulk soil, the free diffusion of water, soluble nutrients and oxygen in the macropores creates other gradients between macropores and micropores. Studying the fitness traits of in soil, Stuart Levy and colleagues demonstrated the importance of the AdnA transcriptional factor in spreading of the bacterium in soil. Although in vivo expression technology (IVET) studies identify large numbers of sequences, assessing the relative importance of each gene requires more traditional genetic studies. An important example of adaptation by horizontal gene transfer (HGT) is the spread of antibiotic resistance genes, and subsequent selection of bacteria harboring those resistance genes. Soil is likely to be a reservoir of a range of antibiotic resistance genes. The environment is a reservoir of pathogenic bacteria which are capable of living free from a host and is likely to harbor many opportunistic pathogens. A good example is , a species formerly described as a rhizosphere inhabitant and a pathogen of onion, but which has more recently been isolated from patients suffering from cystic fibrosis.

Citation: Gravelat F, Silby M, Strain S. 2005. Fitness Traits in Soil Bacteria, p 425-435. In White D, Alekshun M, McDermott P (ed), Frontiers in Antimicrobial Resistance. ASM Press, Washington, DC. doi: 10.1128/9781555817572.ch32

Key Concept Ranking

Microbial Ecology
Electron Transport System
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


Image of Figure 1
Figure 1

Biofilm formation by the wild-type (a) and an mutant (b) Pf0-1. Strains possessing a GFP-expressing plasmid were incubated for 24 h in the presence of a glass cover-slip. The cover-slip was gently washed with distilled water, and adherent cells were visualized by fluorescence microscopy at 600x magnification. After 24 h wild-type Pf0-1 has formed a thick, structured biofilm, while disruption of profoundly reduced the ability to initiate growth as a biofilm. The importance of biofilms for soil fitness is suggested by the correlation between the biofilm and soil-persistence defects associated with mutants.

Citation: Gravelat F, Silby M, Strain S. 2005. Fitness Traits in Soil Bacteria, p 425-435. In White D, Alekshun M, McDermott P (ed), Frontiers in Antimicrobial Resistance. ASM Press, Washington, DC. doi: 10.1128/9781555817572.ch32
Permissions and Reprints Request Permissions
Download as Powerpoint


1. Alexandre, G.,, S. E. Greer,, and I. B. Zhulin. 2000. Energy taxis is the dominant behavior in Azospirillum brasilense. J. Bacteriol. 182:60426048.
2. Alexandre, G.,, S. Greer-Phillips,, and I. B. Zhulin. 2004. Ecological role of energy taxis in microorganisms. FEMS Microbiol. Rev. 28:113126.
3. Andrén, O.,, and J. Balandreau. 1999. Biodiversity and soil functioning - from black box to can of worms? Appl. Soil Ecol. 13:105108.
4. Arora, S. K.,, B. W. Ritchings,, E. C. Almira,, S. Lory,, and R. Ramphal. 1997. A transcriptional activator, FleQ, regulates mucin adhesion and flagellar gene expression in Pseudomonas aeruginosa in a cascade manner. J. Bacteriol. 179:55745581.
5. Atlas, R. M.,, and R. Bartha. 1998. Microbial ecology: fundamentals and applications. Benjamin Cummings Publishing Company, Inc., Menlo Park, Calif.
6. Bevivino, A.,, S. Tabacchioni,, L. Chiarini,, M. V. Carusi,, M. Del Gallo,, and P. Visca. 1994. Phenotypic comparison between rhizosphere and clinical isolates of Burkholderia cepacia. Microbiology 140:10691077.
7. Bjedov, I.,, O. Tenaillon,, B. Gerard,, V. Souza,, E. Denamur,, M. Radman,, F. Taddei,, and I. Matic. 2003. Stress-induced mutagenesis in bacteria. Science 300:14041409.
8. Bourret, R. B.,, and A. M. Stock. 2002. Molecular information processing: lessons from bacterial chemotaxis. J. Biol. Chem. 277:96259628.
9. Bull, H. J.,, G. J. McKenzie,, P. J. Hastings,, and S. M. Rosenberg. 2000. Evidence that stationary-phase hypermutation in the Escherichia coli chromosome is promoted by recombination. Genetics 154:14271437.
10. Clark, I. M.,, T. A. Mendum,, and P. R. Hirsch. 2002. The influence of the symbiotic plasmid pRL1JI on the distribution of GM rhizobia in soil and crop rhizospheres, and implications for gene flow. Antonie van Leeuwenhoek 81:607616.
11. Compeau, G.,, B. J. Al-Achi,, E. Platsouka,, and S. B. Levy. 1988. Survival of rifampin-resistant mutants of Pseudomonas fluorescens and Pseudomonas putida in soil systems. Appl. Environ. Microbiol. 54:24322438.
12. Dance, D. A. 2000. Ecology of Burkholderia pseudomallei and the interactions between environmental Burkholderia spp. and human-animal hosts. Acta Trop. 74:159168.
13. Danese, P. N.,, L. A. Pratt,, and R. Kolter. 2000. Exopolysaccharide production is required for development of Escherichia coli K-12 biofilm architecture. J. Bacteriol. 182:35933596.
14. Davison, J. 1999. Genetic exchange between bacteria in the environment. Plasmid 42:7391.
15. de la Cruz, F.,, and J. Davies. 2000. Horizontal gene transfer and the origin of species: lessons from bacteria. Trends Microbiol. 8:128133.
16. de Weger, L. A.,, A. J. van der Bij,, L. C. Dekkers,, M. Simons,, C. A. Wijffelman,, and B. J. J. Lugtenberg. 1995. Colonization of the rhizosphere of crop plants by plant-beneficial pseudomonads. FEMS Microbiol. Ecol. 17:221227.
17. DeFlaun, M.,, B. Marshall,, E. Kulle,, and S. Levy. 1994. Tn5 insertion mutants of Pseudomonas fluorescens defective in adhesion to soil and seeds. Appl. Environ. Microbiol. 60:26372642.
18. DeFlaun, M.,, A. Tanzer,, A. McAteer,, B. Marshall,, and S. Levy. 1990. Development of an adhesion assay and characterization of an adhesion-deficient mutant of Pseudomonas fluorescens. Appl. Environ. Microbiol. 56:112119.
19. Dekkers, L. C.,, C. C. Phoelich,, L. van der Fits,, and B. J. Lugtenberg. 1998. A site-specific recombinase is required for competitive root colonization by Pseudomonas fluorescens WCS365. Proc. Natl. Acad. Sci. USA 95:70517056.
20. Dighton, J.,, H. E. Jones,, C. H. Robinson,, and J. Beckett. 1997. The role of abiotic factors, cultivation practices and soil fauna in the dispersal of genetically modified microorganisms in soils. Appl. Soil Ecol. 5:109131.
21. Dixon, J. B. 1991. Roles of clays in soils. Applied Clay Science 5:489503.
22. Fenchel, T. 2002. Microbial behavior in a heterogeneous world. Science 296:10681071.
23. Finan, T. M. 2002. Evolving insights: symbiosis islands and horizontal gene transfer. J. Bacteriol. 184:28552856.
24. Finelli, A.,, C. V. Gallant,, K. Jarvi,, and L. L. Burrows. 2003. Use of in-biofilm expression technology to identify genes involved in Pseudomonas aeruginosa biofilm development. J. Bacteriol. 185:27002710.
25. Gal, M.,, G. M. Preston,, R. C. Massey,, A. J. Spiers,, and P. B. Rainey. 2003. Genes encoding a cellulosic polymer contribute toward the ecological success of Pseudomonas fluorescens SBW25 on plant surfaces. Mol. Ecol. 12:31093121.
26. Garrett, E. S.,, D. Perlegas,, and D. J. Wozniak. 1999. Negative control of flagellum synthesis in Pseudomonas aeruginosa is modulated by the alternative sigma factor AlgT (AlgU). J. Bacteriol. 181:74017404.
27. Gogarten, J. P.,, W. F. Doolittle,, and J. G. Lawrence. 2002. Prokaryotic evolution in light of gene transfer. Mol. Biol. Evol. 19:22262238.
28. Goodman, M. F. 2002. Error-prone repair DNA polymerases in Prokaryotes and Eukaryotes. Annu. Rev. Biochem. 71:1750.
29. Göttfert, M.,, S. Röthlisberger,, C. Kündig,, C. Beck,, R. Marty,, and H. Hennecke. 2001. Potential symbiosis-specific genes uncovered by sequencing a 410-kilobase DNA region of the Bradyrhizobium japonicum chromosome. J. Bacteriol. 183: 14051412.
30. Hassink, J.,, L. A. Bouwman,, K. B. Zwart,, and L. Brussaard. 1993. Relationships between habitable pore space, soil biota and mineralization rates in grassland soils. Soil Biol. Biochem. 25:4755.
31. Heinemann, J. A.,, and G. F. Sprague, Jr. 1989. Bacterial conjugative plasmids mobilize DNA transfer between bacteria and yeast. Nature 340:205209.
32. Hinsa, S. M.,, M. Espinosa-Urgel,, J. L. Ramos,, and G. A. O’Toole. 2003. Transition from reversible to irreversible attachment during biofilm formation by Pseudomonas fluorescens WCS365 requires an ABC transporter and a large secreted protein. Mol. Microbiol. 49:905918.
33. Hirsch, P. R.,, and J. D. Spokes. 1994. Survival and dispersion of genetically modified rhizobia in the field and genetic interactions with native strains. FEMS Microbiol. Ecol. 15:147160.
34. Jyot, J.,, N. Dasgupta,, and R. Ramphal. 2002. FleQ, the major flagellar gene regulator in Pseudomonas aeruginosa, binds to enhancer sites located either upstream or atypically downstream of the RpoN binding site. J. Bacteriol. 184:52515260.
35. Lugtenberg, B. J.,, L. Dekkers,, and G. V. Bloemberg. 2001. Molecular determinants of rhizosphere colonization by Pseudomonas. Annu. Rev. Phytopathol. 39:461490.
36. Mahan, M. J.,, J. M. Slauch,, and J. J. Mekalanos. 1993. Selection of bacterial virulence genes that are specifically induced in host tissues. Science 259:686688.
37. Marshall, B.,, E. A. Robleto,, R. Wetzler,, P. Kulle,, P. Casaz,, and S. B. Levy. 2001. The adnA transcriptional factor affects persistence and spread of Pseudomonas fluorescens under natural field conditions. Appl. Environ. Microbiol. 67:852857.
38. Martínez-Romero, E.,, and J. Caballero-Mellado. 1996. Rhizobium phylogenies and bacterial genetic diversity. Crit. Rev. Plant Sci. 15:113140.
39. Mirleau, P.,, S. Delorme,, L. Philippot,, J. Meyer,, S. Mazurier,, and P. Lemanceau. 2000. Fitness in soil and rhizosphere of Pseudomonas fluorescens C7R12 compared with a C7R12 mutant affected in pyoverdine synthesis and uptake. FEMS Microbiol. Ecol. 34:3544.
40. Monds, R. D.,, M. W. Silby,, and H. K. Mahanty. 2001. Expression of the Pho regulon negatively regulates biofilm formation by Pseudomonas aureofaciens PA147-2. Mol. Microbiol. 42:415426.
41. Moorthy, S.,, and P. I. Watnick. 2004. Genetic evidence that the Vibrio cholerae monolayer is a distinct stage in biofilm development. Mol. Microbiol. 52:573587.
42. Moulin, L.,, A. Munive,, B. Dreyfus,, and C. Boivin-Masson. 2001. Nodulation of legumes by members of the beta-subclass of Proteobacteria. Nature 411:948950.
43. Nunan, N.,, K. Wu,, I. M. Young,, J. W. Crawford,, and K. Ritz. 2003. Spatial distribution of bacterial communities and their relationships with the micro-architecture of soil. FEMS Microbiol. Ecol. 44:203215.
44. O’Toole, G.,, H. B. Kaplan,, and R. Kolter. 2000. Biofilm formation as microbial development. Annu. Rev. Microbiol. 54: 4979.
45. O’Toole, G. A.,, K. A. Gibbs,, P. W. Hager,, P. V. Phibbs, Jr.,, and R. Kolter. 2000. The global carbon metabolism regulator Crc is a component of a signal transduction pathway required for biofilm development by Pseudomonas aeruginosa. J. Bacteriol. 182:425431.
46. O’Toole, G. A.,, and R. Kolter. 1998. Initiation of biofilm formation in Pseudomonas fluorescens WCS365 proceeds via multiple, convergent signalling pathways: a genetic analysis. Mol. Microbiol. 28:449461.
47. Parke, J. L.,, and D. Gurian-Sherman. 2001. Diversity of the Burkholderia cepacia complex and implications for risk assessment of biological control strains. Annu. Rev. Phytopathol. 39:225258.
48. Perret, X.,, C. Staehelin,, and W. J. Broughton. 2000. Molecular basis of symbiotic promiscuity. Microbiol. Mol. Biol. Rev. 64:180201.
49. Rahme, L. G.,, F. M. Ausubel,, H. Cao,, E. Drenkard,, B. C. Goumnerov,, G. W. Lau,, S. Mahajan-Miklos,, J. Plotnikova,, M. W. Tan,, J. Tsongalis,, C. L. Walendziewicz,, and R. G. Tompkins. 2000. Plants and animals share functionally common bacterial virulence factors. Proc. Natl. Acad. Sci. USA 97:88158821.
50. Ramey, B. E.,, A. G. Matthysse,, and C. Fuqua. 2004. The FNRtype transcriptional regulator SinR controls maturation of Agrobacterium tumefaciens biofilms. Mol. Microbiol. 52:14951511.
51. Ranjard, L.,, and A. Richaume. 2001. Quantitative and qualitative microscale distribution of bacteria in soil. Research Microbiol. 152:707716.
52. Rao, C. V.,, J. R. Kirby,, and A. P. Arkin. 2004. Design and diversity in bacterial chemotaxis: a comparative study in Escherichia coli and Bacillus subtilis. PLoS Biol. 2:E49. Epub 2004 Feb 17.
53. Robleto, E. A.,, I. Lopez-Hernandez,, M. W. Silby,, and S. B. Levy. 2003. Genetic analysis of the AdnA regulon in Pseudomonas fluorescens: nonessential role of flagella in adhesion to sand and biofilm formation. J. Bacteriol. 185:453460.
54. Sanchez-Contreras, M.,, M. Martin,, M. Villacieros,, F. O’Gara,, I. Bonilla,, and R. Rivilla. 2002. Phenotypic selection and phase variation occur during alfalfa root colonization by Pseudomonas fluorescens F113. J. Bacteriol. 184:15871596.
55. Silby, M. W.,, P. B. Rainey,, and S. B. Levy. 2004. IVET experiments in Pseudomonas fluorescens reveal cryptic promoters at loci associated with recognizable overlapping genes. Microbiology 150:518520.
56. Silby, M. W.,, and S. B. Levy. 2004. Use of in vivo expression technology to identify genes important in growth and survival of Pseudomonas fluorescens Pf0-1 in soil: discovery of expressed sequences with novel genetic organization. J. Bacteriol. 186:74117419.
57. Spiers, A. J.,, J. Bohannon,, S. M. Gehrig,, and P. B. Rainey. 2003. Biofilm formation at the air-liquid interface by the Pseudomonas fluorescens SBW25 wrinkly spreader requires an acetylated form of cellulose. Mol. Microbiol. 50:1527.
58. Sullivan, J. T.,, H. N. Patrick,, W. L. Lowther,, D. B. Scott,, and C. W. Ronson. 1995. Nodulating strains of Rhizobium loti arise through chromosomal symbiotic gene transfer in the environment. Proc. Natl. Acad. Sci. USA 92:89858989.
59. Sullivan, J. T.,, and C. W. Ronson. 1998. Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. Proc. Natl. Acad. Sci. USA 95:51455149.
60. Sullivan, J. T.,, J. R. Trzebiatowski,, R. W. Cruickshank,, J. Gouzy,, S. D. Brown,, R. M. Elliot,, D. J. Fleetwood,, N. G. Mc- Callum,, U. Rossbach,, G. S. Stuart,, J. E. Weaver,, R. J. Webby,, F. J. de Bruijn,, and C. W. Ronson. 2002. Comparative sequence analysis of the symbiosis island of Mesorhizobium loti strain R7A. J. Bacteriol. 184:30863095.
61. Tenaillon, O.,, H. Le Nagard,, B. Godelle,, and F. Taddei. 2000. Mutators and sex in bacteria: conflict between adaptive strategies. Proc. Natl. Acad. Sci. USA 97:1046510470.
62. Tenaillon, O.,, F. Taddei,, M. Radman,, and I. Matic. 2001. Second- order selection in bacterial evolution: selection acting on mutation and recombination rates in the course of adaptation. Res. Microbiol. 152:1116.
63. van Berkum, P.,, Z. Terefework,, L. Paulin,, S. Suomalainen,, K. Lindström,, and B. D. Eardly. 2003. Discordant phylogenies within the rrn loci of rhizobia. J. Bacteriol. 185:29882998.
64. van Veen, J. A.,, L. S. van Overbeek,, and J. D. van Elsas. 1997. Fate and activity of microorganisms introduced into soil. Microbiol. Mol. Biol. Rev. 61:121135.
65. Whiteley, M.,, M. G. Bangera,, R. E. Bumgarner,, M. R. Parsek,, G. M. Teitzel,, S. Lory,, and E. P. Greenberg. 2001. Gene expression in Pseudomonas aeruginosa biofilms. Nature 413:860864.
66. Williams, V.,, and M. Fletcher. 1996. Pseudomonas fluorescens adhesion and transport through porous media are affected by lipopolysaccharide composition. Appl. Environ. Microbiol. 62: 100104.
67. Wozniak, D. J.,, T. J. Wyckoff,, M. Starkey,, R. Keyser,, P. Azadi,, G. A. O’Toole,, and M. R. Parsek. 2003. Alginate is not a significant component of the extracellular polysaccharide matrix of PA14 and PAO1 Pseudomonas aeruginosa biofilms. Proc. Natl. Acad. Sci. USA 100:79077912.
68. Yeiser, B.,, E. D. Pepper,, M. F. Goodman,, and S. E. Finkel. 2002. SOS-induced DNA polymerases enhance long-term survival and evolutionary fitness. Proc. Natl. Acad. Sci. USA 99:87378741. Epub 2002 Jun 11.
69. Zambrano, M. M.,, D. A. Siegele,, M. Almiron,, A. Tormo,, and R. Kolter. 1993. Microbial competition: Escherichia coli mutants that take over stationary phase cultures. Science 259:17571760.

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error