Relationship between spatial and genetic distance in Agrobacterium spp. in 1 cubic centimeter of soil

Applied and Environmental Microbiology

Volumn 69, Issue 3, 2003, Pages 1482-1487

  Vogel, J ^c   Normand, P ^a   Thioulouse, J ^b   Nesme, X ^a   Grundmann, G L ^a  

^a University of Lyon   (France)

^b UNIVERSITÉ LYON 1   (France)

^c SA Sugar Assoc Experiment Station   (South Africa)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; CELL CULTURE; CLONING; DNA; SOILS;

GENETIC UNITS;

BACTERIOLOGY;

BACTERIUM; GENETIC ANALYSIS; POPULATION STRUCTURE; SOIL MICROORGANISM;

AMPLIFIED RIBOSOMAL DNA RESTRICTION ANALYSIS; ARTICLE; GENETIC DISTANCE; GENETIC VARIABILITY; GENOME; MOLECULAR CLONING; NONHUMAN; RHIZOBIUM; RIBOTYPING; SAMPLING; SOIL;

AGRICULTURE; ECOSYSTEM; POPULATION DYNAMICS; RHIZOBIUM; RIBOTYPING; SOIL MICROBIOLOGY; VARIATION (GENETICS); ZEA MAYS;

AGROBACTERIUM; BACTERIA (MICROORGANISMS); NEGIBACTERIA;

EID: 0242586014     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.69.3.1482-1487.2003     Document Type: Article

References (34)

1. fr 1. Cho, J. C., and J. M. Tiedje. 2000. Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil. Appl. Environ. Microbiol. 66:5448-5456.
2. Cohan, F. M. 2002. What are bacterial species? Annu. Rev. Microbiol. 56:457-487.
3. Dijkshoorn, L., B. M. Ursing, and J. B. Ursing. 2000. Strain, clone, and species: comments on three basic concepts of bacteriology. J. Med. Microbiol. 49:397-401.
4. Diniz-Filho, J. A. F., and M. Pires de Campos Telles. 2000. Spatial pattern and genetic diversity estimates are linked in stochastic models of population differentiation. Genet. Mol. Biol. 23:541-544.
5. Dunbar, J., S. White, and L. Forney. 1997. Genetic diversity through the looking glass: effect of enrichment bias. Appl. Environ. Microbiol. 63:1326-1331.
6. Felske, A., and A. D. L. Akkermans. 1998. Spatial homogeneity of abundant bacterial 16S rRNA molecules in grassland soils. Microb. Ecol. 36:31-36.
7. Franck, S. A., and P. Amarasekare. 1998. Increasing resource specialization among competitors shifts control of diversity from local to spatial processes. Ecol. Lett. 1:3-12.
8. Gower, J. C. 1966. Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika 53:325-338.
9. Grundmann, G. L., A. Dechesne, F. Bartoli, J. L. Chassé, J. P. Flandrois, and R. Kizungu. 2001. Spatial modeling of nitrifier micro habitats in soil. Soil Sci. Soc. Am. J. 65:1709-1716.
10. Grundmann, G. L., and P. Normand. 2000. Microscale diversity of the genus Nitrobacter in soil on the basis of analysis of genes encoding rRNA. Appl. Environ. Microbiol. 66:4543-4546.
11. Hattori, T. 1988. Soil aggregates as microhabitats of microorganisms. Institute of Agricultural Research, Tohoku University, Tohoku, Japan.
12. Haubold, B., M. Travisano, P. B. Rainey, and R. R. Hudson. 1998. Detecting linkage disequilibrium in bacterial populations. Genetics 150:1341-1348.
13. Heljnen, C. E., and J. A. Van Veen. 1991. A determination of protective microhabitats for bacteria introduced into soil. FEMS Microbiol. Ecol. 85:73-80.
14. Istock, C. A., K. E. Duncan, N. Ferguson, and X. Zhou. 1992. Sexuality in a natural population of bacteria: Bacillus subtilis challenges the clonal paradigm. Mol. Ecol. 1:95-103.
15. Krimi, Z., A. Petit, C. Mougel, Y. Dessaux, and X. Nesme. 2002. Seasonal fluctuations and long-term persistence of pathogenic populations of Agrobacterium spp. in soils. Appl. Environ. Microbiol. 68:3358-3365.
16. Lenski, R. E. 1993. Assessing the genetic structure of microbial populations. Proc. Natl. Acad. Sci. USA 90:4334-4336.
17. Maynard-Smith, J., N. H. Smith, M. O'Rourke, and B. G. Spratt. 1993. How clonal are bacteria? Proc. Natl. Acad. Sci. USA 90:4384-4388.
18. McArthur, J. V., D. A. Kovacic, and M. H. Smith. 1988. Genetic diversity in natural populations of a soil bacterium across a landscape gradient. Proc. Natl. Acad. Sci. USA 85:9621-9624.
19. McArthur, J. V., L. G. Leff, and M. H. Smith. 1992. Genetic diversity of bacteria along a stream continuum. J. N. Am. Benthol. Soc. 11:269-277.
20. Moore, L. W., C. I. Kado, and H. Bouzar. 1988. Agrobacterium, p. 16-36. In N. W. Shaad (ed.), Laboratory guide for identification of plant pathogenic bacteria, 2nd ed. APS Press, St. Paul, Minn.
21. Mougel, C., B. Cournoyer, and X. Nesme. 2001. Novel tellurite-amended media and specific chromosomal and Ti plasmid probes for direct analysis of soil populations of Agrobacterium biovars 1 and 2. Appl. Environ. Microbiol. 67:65-74.
22. Mougel, C., J. Thioulouse, G. Perriere, and X. Nesme. 2002. A mathematical method for determining genome divergence and species delineation using AFLP. Int. J. Syst. Evol. Microbiol. 52:573-586.
23. Nei, M., and W.-H. Li. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA 76:5269-5273.
24. Ponsonnet, C., and X. Nesme. 1994. Identification of Agrobacterium strains by PCR-RFLP analysis of pTi and chromosomal regions. Arch. Microbiol. 161:300-309.
25. Popoff, M. Y., K. Kersters, M. Kiredjian, I. Miras, and C. Coynault. 1984. Position taxonomique de souches de Agrobacterium d'origine hospitalière. Ann. Microbiol. 135A:427-442.
26. Rainey, P. B., and M. Travisano. 1998. Adaptive radiation in a heterogeneous environment. Nature 394:69-72.
27. Souza, V., L. Eguiarte, G. Avila, R. Cappello, C. Gallardo, J. Montoya, and D. Pinero. 1994. Genetic structure of Rhizobium etli biovar phaseoli associated with wild and cultivated bean plants (Phaseolus vulgaris and Phaseolus coccineus) in Morelos, Mexico. Appl. Environ. Microbiol. 60:1260-1268.
28. Tenover, F. C., R. D. Arbeit, R. V. Goering, P. A. Mickelsen, B. E. Murray, D. H. Persing, and B. Swaminathan. 1995. Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. J. Clin. Microbiol. 33:2233-2239.
29. Thioulouse, J., D. Chessel, S. Dolédec, and J. M. Oliver. 1997. ADE-4: a multivariate analysis and graphical display software. Statistics Comput. 7:75-83.
30. Tibayrenc, M., F. Kjellberg, J. Arnaud, B. Oury, S. F. Breniere, M. L. Darde, and F. J. Ayala. 1991. Are eukaryotic microorganisms clonal or sexual? A population genetics vantage. Proc. Natl. Acad. Sci. USA 88:5129-5133.
31. Tilmann, D. 1994. Competition and biodiversity in spatially structured habitats. Ecology 75:2-16.
32. Torsvik, V., J. Goksoyr, and F. L. Daae. 1990. High diversity in DNA of soil bacteria. Appl. Environ. Microbiol. 56:782-787.
33. Vilas-Boas, G., V. Sanchis, D. Lereclus, M. V. Lemos, and D. Bourguet. 2002. Genetic differentiation between sympatric populations of Bacillus cereus and Bacillus thuringiensis. Appl. Environ. Microbiol. 68:1414-1424.
34. Wise, M. G., L. J. Shimkets, and J. V. McArthur. 1995. Genetic structure of a lotic population of Burkolderia (Pseudomonas) cepacia. Appl. Environ. Microbiol. 61:1791-1798.