Genetic population structure of the soil bacterium Myxococcus xanthus at the centimeter scale

Applied and Environmental Microbiology

Volumn 72, Issue 5, 2006, Pages 3615-3625

  Vos, Michiel ^a   Velicer, Gregory J ^a  

^a MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIODIVERSITY; ENVIRONMENTAL ENGINEERING; ENZYMES; GENES; GENETIC ENGINEERING; SOILS;

GENETIC DIVERSITY; GENETIC POPULATION STRUCTURES; SOCIAL PREDATION; SOCIAL SWARMING;

BACTERIA;

EXTRACELLULAR MATRIX ASSOCIATED ZINC METALLOPROTEASE; METALLOPROTEINASE; PILIN; UNCLASSIFIED DRUG;

ABUNDANCE; BACTERIUM; GENE; GENETIC PHENOMENA; GENOTYPE; SOIL MICROORGANISM;

ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM ISOLATE; CLONE; CSGA GENE; FIBA GENE; FRUITING BODY; GENETIC CONSERVATION; GENETIC LINKAGE; GENETIC SELECTION; GENETIC VARIABILITY; GENOTYPE; GERMANY; GRAM NEGATIVE BACTERIUM; MYXOCOCCUS XANTHUS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PILA GENE; POPULATION STRUCTURE; PREDATION; SOIL MICROFLORA; SPECIES HABITAT; UNINDEXED SEQUENCE;

BACTERIAL PROTEINS; BACTERIAL TYPING TECHNIQUES; EVOLUTION, MOLECULAR; GENOTYPE; MOLECULAR SEQUENCE DATA; MYXOCOCCUS XANTHUS; PHYLOGENY; POLYMORPHISM, GENETIC; RECOMBINATION, GENETIC; SELECTION (GENETICS); SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY; VARIATION (GENETICS);

BADEN-WURTTEMBERG; CENTRAL EUROPE; EURASIA; EUROPE; GERMANY; TUBINGEN;

BACTERIA (MICROORGANISMS); MYXOCOCCUS XANTHUS; NEGIBACTERIA; PILA;

EID: 33646586986     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.72.5.3615-3625.2006     Document Type: Article

References (62)

1. Andrews, T. D., and T. Gojobori. 2004. Strong positive selection and recombination drive the antigenic variation of the PilE protein of the human pathogen Neisseria meningitidis. Genetics 166:25-32.
2. Behmlander, R. M., and M. Dworkin. 1994. Biochemical and structural analyses of the extracellular matrix fibrils of Myxococcus xanthus. J. Bacteriol. 176:6295-6303.
3. Bent, S. J., C. L. Gucker, Y. Oda, and L. J. Forney. 2003. Spatial distribution of Rhodopseudomonas palustris ecotypes on a local scale. Appl. Environ. Microbiol. 69:5192-5197.
4. Breton, A. M., S. Jaoua, and J. Guespin-Michel. 1985. Transfer of plasmid RP4 to Myxococcus xanthus and evidence for its integration into the chromosome. J. Bacteriol. 161:523-528.
5. Buckling, A., and P. B. Rainey. 2002. The role of parasites in sympatric and allopatric host diversification. Nature 420:496-499.
6. 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.
7. Cohan, F. M. 2002. What are bacterial species? Annu. Rev. Microbiol. 56:457-487.
8. Colwell, R. K. 2005. EstimateS: Statistical estimation of species richness and shared species from samples. Version 7.5. User's guide and application. http://purl.oclc.org/estimates.
9. Cooper, J. E., and E. J. Feil. 2004. Multilocus sequence typing-what is resolved? Trends Microbiol. 12:373-377.
10. Craig, L., M. E. Pique, and J. A. Tainer. 2004. Type IV pilus structure and bacterial pathogenicity. Nat. Rev. Microbiol. 2:363-378.
11. Dawid, W. 2000. Biology and global distribution of myxobacteria in soils. FEMS Microbiol. Rev. 24:403-427.
12. Edgar, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
13. Ewens, W. J. 1972. The sampling theory of selectively neutral alleles. Theor. Popul. Biol. 3:87-112.
14. Feil, E. J. 2004. Small change: keeping pace with microevolution. Nat. Rev. Microbiol. 2:483-495.
15. Feil, E. J., B. C. Li, D. M. Aanensen, W. P. Hanage, and B. G. Spratt. 2004. eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. J. Bacteriol. 186:1518-1530.
16. Fenchel, T. 2003. Microbiology. Biogeography for bacteria. Science 301:925-926.
17. Fiegna, F., and G. J. Velicer. 2005. Exploitative and hierarchical antagonism in a cooperative bacterium. PLoS Biol. 3:e370.
18. 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.
19. Hartzell, P. 2002. Genetic tools for dissecting motility and development of Myxococcus xanthus, p. 289-322. In U. N. Streips and R. E. Zasbin (ed.), Modern microbial genetics. Wiley-Liss, Inc., New York, N.Y.
20. Huson, D. H., and D. Bryant. 2005. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23:254-257.
21. Jolley, K. A., E. J. Feil, M. S. Chan, and M. C. Maiden. 2001. Sequence type analysis and recombinational tests (START). Bioinformatics 17:1230-1231.
22. Kaiser, D. 2003. Coupling cell movement to multicellular development in myxobacteria. Nat. Rev. Microbiol. 1:45-54.
23. Karwowski, J. P., G. N. Sunga, S. Kadam, and J. B. McAlpine. 1996. A method for the selective isolation of Myxococcus directly from soil. J. Ind. Microbiol. 16:230-236.
24. Kearns, D. B., P. J. Bonner, D. R. Smith, and L. J. Shimkets. 2002. An extracellular matrix-associated zinc metalloprotease is required for dilauroyl phosphatidylethanolamine chemotactic excitation in Myxococcus xanthus. J. Bacteriol. 184:1678-1684.
25. Kerr, B., M. A. Riley, M. W. Feldman, and B. J. M. Bohannan. 2002. Local dispersal promotes biodiversity in a real-life game of rock-paper-scissors. Nature 418:171-174.
26. Kim, S. K., and D. Kaiser. 1990. Cell motility is required for the transmission of C-factor, an intercellular signal that coordinates fruiting body morphogenesis of Myxococcus xanthus. Genes Dev. 4:896-904.
27. Kumar, S., K. Tamura, and M. Nei. 2004. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 5:150-163.
28. Li, Y., R. Lux, A. E. Pelling, J. K. Gimzewski, and W. Shi. 2005. Analysis of type IV pilus and its associated motility in Myxococcus xanthus using an antibody reactive with native pilin and pili. Microbiology 151:353-360.
29. Lobedanz, S., and L. Sogaard-Andersen. 2003. Identification of the C-signal, a contact-dependent morphogen coordinating multiple developmental responses in Myxococcus xanthus. Genes Dev. 17:2151-2161.
30. Maiden, M. C. J., J. A. Bygraves, E. Feil, G. Morelli, J. E. Russell, R. Urwin, Q. Zhang, J. J. Zhou, K. Zurth, D. A. Caugant, I. M. Feavers, M. Achtman, and B. G. Spratt. 1998. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. USA 95:3140-3145.
31. Martin, S., E. Sodergren, T. Masuda, and D. Kaiser. 1978. Systematic isolation of transducing phages for Myxococcus xanthus. Virology 88:44-53.
32. Martiny, J. B., B. J. Bohannan, J. H. Brown, R. K. Colwell, J. A. Fuhrman, J. L. Green, M. C. Horner-Devine, M. Kane, J. A. Krumins, C. R. Kuske, P. J. Morin, S. Naeem, L. Ovreas, A. L. Reysenbach, V. H. Smith, and J. T. Staley. 2006. Microbial biogeography: putting microorganisms on the map. Nat. Rev. Microbiol. 4:102-112.
33. Milne, I., F. Wright, G. Rowe, D. F. Marshall, D. Husmeier, and G. McGuire. 2004. TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments. Bioinformatics 20:1806-1807.
34. Nei, M., and N. A. Kumar. 2000. Molecular evolution and phylogenetics. Oxford University Press, New York, N.Y.
35. Neilan, B. A., M. L. Saker, J. Fastner, A. Torokne, and B. P. Burns. 2003. Phylogeography of the invasive cyanobacterium Cylindrospermopsis raciborskii. Mol. Ecol. 12:133-140.
36. O'Connor, K. A., and D. R. Zusman. 1988. Reexamination of the role of autolysis in the development of Myxococcus xanthus. J. Bacteriol. 170:4103-4112.
37. Oda, Y., B. Star, L. A. Huisman, J. C. Gottschal, and L. J. Forney. 2003. Biogeography of the purple nonsulfur bacterium Rhodopseudomonas palustris. Appl. Environ. Microbiol. 69:5186-5191.
38. Papke, R. T., and D. M. Ward. 2004. The importance of physical isolation to microbial diversification. FEMS Microbiol. Ecol. 48:293-303.
39. 38a. Papke, R. T., J. E. Koenig, F. Rodriguez-Valera, and W. F. Doolittle. 2004. Frequent recombination in a saltern population of Halorubrum. Science 306:1928-1929.
40. Posada, D. 2002. Evaluation of methods for detecting recombination from DNA sequences: empirical data. Mol. Biol. Evol. 19:708-717.
41. Rainey, P. B., and M. Travisano. 1998. Adaptive radiation in a heterogeneous environment. Nature 394:69-72.
42. Reichenbach, H. 1984. Myxobacteria: a most peculiar group of social prokaryotes, p. 1-50. In E. Rosenberg (ed.), Myxobacteria: development and cell interactions. Springer Verlag, New York, N.Y.
43. Rocha, E. P., J. M. Smith, L. D. Hurst, M. T. Holden, J. E. Cooper, N. H. Smith, and E. J. Feil. 2005. Comparisons of dN/dS are time dependent for closely related bacterial genomes. J. Theor. Biol. 239:226-235.
44. Rosenberg, E., K. H. Keller, and M. Dworkin. 1977. Cell density-dependent growth of Myxococcus xanthm on casein. J. Bacteriol. 129:770-777.
45. Rosenberg, E., and M. Varon. 1984. Antibiotics and lytic enzymes, p. 109-125. In E. Rosenberg (ed.), Myxobacteria: development and cell interactions. Springer Verlag, New York, N.Y.
46. Rozas, J., and R. Rozas. 1999. DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15:174-175.
47. Sarkar, S. F., and D. S. Guttman. 2004. Evolution of the core genome of Pseudomonas syringae, a highly clonal, endemic plant pathogen. Appl. Environ. Microbiol. 70:1999-2012.
48. Sawyer, S. 1989. Statistical tests for detecting gene conversion. Mol. Biol. Evol. 6:526-538.
49. Schneider, S., D. Roessli, and L. Excoffier. 2000. Arlequin: a software for population genetics data analysis. Ver 2.000. Genetics and Biometry Laboratory, Department of Anthropology, University of Geneva, Geneva, Switzerland.
50. Shimkets, L., and C. R. Woese. 1992. A phylogenetic analysis of the myxobacteria-basis for their classification. Proc. Natl. Acad. Sci. USA 89:9459-9463.
51. Shimkets, L. J. 1999. Intercellular signaling during fruiting-body development of Myxococcus xanthus. Annu. Rev. Microbiol. 53:525-549.
52. Shimkets, L. J. 1990. Social and developmental biology of the myxobacteria. Microbiol. Rev. 54:473-501.
53. Smith, J. M. 1992. Analyzing the mosaic structure of genes. J. Mol. Evol. 34:126-129.
54. Smith, J. M., N. H. Smith, M. O'Rourke, and B. G. Spratt. 1993. How clonal are bacteria? Proc. Natl. Acad. Sci. USA 90:4384-4388.
55. Spangenberg, C., R. Fislage, U. Romling, and B. Tummler. 1997. Disrespectful type IV pilins. Mol. Microbiol. 25:203-204.
56. Stackebrandt, E., and O. Pauker. 2005. Gene sequence heterogeneity of Corallococcus coralloides strains isolated from geographically diverse locations. Environ. Microbiol. 7:1017-1023.
57. Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
58. Thompson, J. R., S. Pacocha, C. Pharino, V. Klepac-Ceraj, D. E. Hunt, J. Benoit, R. Sarma-Rupavtarm, D. L. Distel, and M. F. Polz. 2005. Genotypic diversity within a natural coastal bacterioplankton population. Science 307:1311-1313.
59. Travisano, M., and G. J. Velicer. 2004. Strategies of microbial cheater control. Trends Microbiol. 12:72-78.
60. Vogel, J., P. Normand, J. Thioulouse, X. Nesme, and G. L. Grundmann. 2003. Relationship between spatial and genetic distance in Agrobacterium spp. in 1 cubic centimeter of soil. Appl. Environ. Microbiol. 69:1482-1487.
61. Watterson, G. A. 1978. Homozygosity test of neutrality. Genetics 88:405-417.
62. Whitaker, R. J., D. W. Grogan, and J. W. Taylor. 2003. Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 301:976-978.