Effects of plant genotype and growth stage on the betaproteobacterial communities associated with different potato cultivars in two fields

Applied and Environmental Microbiology

Volumn 76, Issue 11, 2010, Pages 3675-3684

  Inceoǧlu, Özgül ^a   Salles, Joana Falcão ^a   Van Overbeek, Leo ^b   Van Elsas, Jan Dirk ^a  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL COMMUNITY; BETAPROTEOBACTERIA; BULK SOILS; CLONE LIBRARY; COMMUNITY STRUCTURES; DENATURING GRADIENT GEL ELECTROPHORESIS; FUNCTIONAL GENES; GROWTH STAGES; IN-PLANTS; NUTRIENT CYCLING; PLANT CULTIVARS; PLANT GENOTYPE; PLANT GROWTH PROMOTION; PLANT GROWTH STAGES; POTATO CULTIVARS; QUANTITATIVE PCR; RHIZOSPHERE EFFECTS; ROOT DEVELOPMENT; SANDY SOILS; SOIL TYPES; TUBER STARCH; VARIOVORAX PARADOXUS;

BACTERIOLOGY; CLONING; ELECTROPHORESIS; GELS; ORGANIC COMPOUNDS; PLANT LIFE EXTENSION; PLANTS (BOTANY); SOCIAL SCIENCES; STARCH;

SOILS;

BACTERIAL DNA; RIBOSOME DNA; RNA 16S;

BACTERIUM; CULTIVAR; ELECTROKINESIS; GENOTYPE; GROWTH RATE; MICROBIAL COMMUNITY; NUTRIENT CYCLING; POLYMERASE CHAIN REACTION; POTATO; RHIZOSPHERE; SOIL MICROORGANISM; SOIL TYPE; STARCH;

ARTICLE; BETAPROTEOBACTERIA; BIODIVERSITY; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; DNA DENATURATION; DNA FINGERPRINTING; DNA SEQUENCE; GENETICS; GROWTH, DEVELOPMENT AND AGING; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT ROOT; POLYACRYLAMIDE GEL ELECTROPHORESIS; POTATO;

BETAPROTEOBACTERIA; BIODIVERSITY; CLUSTER ANALYSIS; DNA FINGERPRINTING; DNA, BACTERIAL; DNA, RIBOSOMAL; ELECTROPHORESIS, POLYACRYLAMIDE GEL; MOLECULAR SEQUENCE DATA; NUCLEIC ACID DENATURATION; PHYLOGENY; PLANT ROOTS; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY; SOLANUM TUBEROSUM;

ACHROMOBACTER; BACTERIA (MICROORGANISMS); BETAPROTEOBACTERIA; SOLANUM TUBEROSUM; TUBER (TRUFFLE); VARIOVORAX; VARIOVORAX PARADOXUS;

EID: 77953068888     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.00040-10     Document Type: Article

References (55)

1. Becker, S., P. Böger, R. Oehlmann, and A. Ernst. 2000. PCR bias in ecological analysis: a case study for quantitative Taq nuclease assays in analyses of microbial communities. Appl. Environ. Microbiol. 66:4945-4953.
2. Brimecombe, M., F. de Leij, and J. Lynch. 2006. The effect of root exudates on rhizosphere microbial populations, p. 95-140. In R. Pinton, Z. Varanini, and P. Nannipieri (ed.), The rhizosphere-biochemistry and organic substances at the soil-plant interface. CRC Press, Boca Raton, FL.
3. Chen, W., L. Moulin, C. Bontemps, P. Vandamme, G. Bena, and C. BoivinMasson. 2003. Legume symbiotic nitrogen fixation by beta-proteobacteria is widespread in nature. J. Bacteriol. 185:7266-7272. (Pubitemid 37509844)
4. Cole, J., B. Chai, R. Farris, Q. Wang, A. Kulam-Syed-Mohideen, D. McGarrell, A. Bandeia, and J. Tiedje. 2007. The Ribosomal Database Project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res. 35:169-172. (Pubitemid 46056192)
5. Cunliffe, M., and M. Kertesz. 2006. Effect of Sphingobium yanoikuyae B1 inoculation on bacterial community dynamics and polycyclic aromatic hydrocarbon degradation in aged and freshly FAH-contaminated soils. Environ. Pollut. 144:228-237.
6. Dalmastri, C., L. Chiarini, C. Cantale, A. Bevivino, and S. Tabacchioni. 1999. Soil type and maize cultivar affect the genetic diversity of maize root-associated Burkholderia cepacia populations. Microb. Ecol. 38:273-284.
7. de Vetten, N., A. Wolters, K. Raemakers, I. van der Meer, R. ter Stege, E. Heeres, P. Heeres, and R. Visser. 2003. A transformation method for obtaining marker-free plants of a cross-pollinating and vegetatively propagated crop. Nat. Biotechnol. 21:439-442.
8. Dobbelaere, S., J. Vanderleyden, and Y. Okon. 2003. Plant growth promoting effects of diazotrophs in rhizosphere. Crit. Rev. Plant Sci. 22:107-149.
9. Duineveld, B., A. Rosado, J. D. van Elsas, and J. A. van Veen. 1998. Analysis of dynamics of bacterial communities in the rhizosphere of chrysanthemum via denaturing gradient gel electrophoresis and substrate utilization patterns. Appl. Environ. Microbiol. 64:4950-4957.
10. Dunfleld, K., and J. Germida. 2003. Seasonal changes in the rhizosphere microbial communities associated with field-grown genetically modified canola. Appl. Environ. Microbiol. 69:7310-7318.
11. Garbeva, P., J. Postma, J. A. van Veen, and J. D. van Elsas. 2006. Effect of above ground plant species on soil microbial community structure and its impact on supply of Rhizoctonia solani AG3. Environ. Microbiol. 8:233-246.
12. Garbeva, P., J. A. van Veen, and J. D. van Elsas. 2004. Microbial diversity in soil: selection of microbial population by plant and soil type and implications for disease suppressiveness. Annu. Rev. Phytopathol. 42:243-270.
13. Gelsomino, A., A. Kerjzer-Wolters, G. Caceo, and J. D. van Elsas. 1999. Assessment of bacterial community structure in soil by PCR and DGGE. J. Microbiol. Methods 38:1-15.
14. Germida, J., and S. Siciliano. 2001. Taxonomie diversity of bacteria associated with the roots of modern, recent and ancient wheat cultivars. Biol. Fertil. Soils 33:410-415.
15. Govaerts, B., M. Mezzalama, Y. Unno, K. Sayre, M. Luna-Guido, K. Vanherck, L. Dendooven, and J. Deckers. 2007. Influence of tillage, residue management, and crop rotation on soil microbial biomass and catabolic diversity. Appl. Soil Ecol. 37:18-30.
16. Graystone, S., S. Wang, C. Campbell, and A. Edwards. 1998. Selective influence of plant species on microbial diversity in the rhizosphere. Soil Biol. Biochem. 30:369-378.
17. Grichko, V., and B. Glick. 2001. Amelioration of flooding stress by ACC deaminase-containing plant growdi-promoting bacteria. Plant Physiol. 39: 11-17. (Pubitemid 32148791)
18. Hack, H., H. Gall, T. Klemke, R. Klose, U. Meier, R. Stauss, and A. Witzenberger. 1993. Phänologische entwicklungsstadien der Kartoffel (Solanum tuberosum L.). Nachrbl. Dtsch. Pflanzenschutzd. 45:11-19.
19. Heuer, H., R. Kroppenstedt, J. Lottmann, G. Berg, and K. Smalla. 2002. Effects of T4 lysozyme release from transgenic potato roots on bacterial rhizosphere communities are negligible relative to natural factors. Appl. Environ. Microbiol. 68:1325-1335.
20. Heuer, H., M. Krsek, P. Baker, K. Smalla, and E. Wellington. 1997. Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl. Environ. Microbiol. 63:3233-3241.
21. Hoover, R. 2001. Composition, molecular structure and physiochemical properties of tuber and root starches: a review. Carbohydr. Polym. 81:253-267.
22. Ibekwe, A., and C. Grieve. 2004. Changes in developing plant microbial community structure as affected by contaminated water. FEMS Microbiol. Ecol. 48:239-248.
23. Kertesz, M., and P. Mirleau. 2004. The role of soil microbes in plant sulfur nutrition. J. Exp. Bot. 55:1939-1945.
24. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
25. Kowalchuk, G., J. Stephen, W. de Boer, J. Prasser, T. Embley, and J. Woldendorp. 1997. Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of FCR-amplified 16S ribosomal DNA fragments. Appl. Environ. Microbiol. 63:1489-1497.
26. Larkin, R. 2003. Characterization of soil microbial communities under different potato cropping systems by microbial population dynamics, substrate utilization and fatty acid profiles. Soil Biol. Biochem. 35:1451-1466.
27. Lottmann, J., H. Heuer, K. Smalla, and G. Berg. 1999. Influence of transgenic T4-lysozyme-producing potato plants on potentially beneficial plantassociated bacteria. FEMS Microbiol. Ecol. 29:365-377.
28. MacDonald, K., and D. Speert. 2006. Interaction of Burkholderia species with phagocytic system, p. 111-128. In T. Coenye and P. Vandamme (ed.), Burkholderia molecular microbiology and genomics. Horizon Bioscience, Norfolk, United Kingdom.
29. Marschner, P., C. Yang, R. Lieberei, and D. Crowley. 2001. Soil and plant specific effects on bacterial community composition in the rhizosphere. Soil Biol. Biochem. 33:1437-1445.
30. Marzorati, M., L. Wittebolle, B. Boon, D. Daffonchio, and W. Verstraete. 2008. How to get more out of molecular fingerprints: practical tools for microbial ecology. Environ. Microbiol. 10:1571-1581.
31. Mayak, S., T. Tirosh, and B. Glick. 2004. Plant growth-promoting bacteria confer resistance in tomato plants to salt stress. Plant Physiol. Biochem. 42:565-572.
32. Mayak, S., T. Tirosh, and B. Glick. 2004. Plant growth-promoting bacteria that confer resistance to water stress in tomatoes and pepper. Plant Sci. 166:525-530. (Pubitemid 38214945)
33. Mclaughlin, A., and P. Mineau. 1995. The impact of agricultural practices on biodiversity. Agric. Ecosyst. Environ. 55:201-212.
34. Meier, U. (ed.). 2001. Growth stages of plants, 2nd ed. BBCH monograph. Federal Biological Research Centre of Agriculture and Forestry, Berlin, Germany.
35. Micallef, S., M. Shiaris, and A. Colon-Carmona. 2009. Influence of Arabidopsis thaliana accessions on rhizobacterial communities and natural variation in root exudates. J. Exp. Bot. 60:1729-1742.
36. Milling, A., K. Smalla, F. Maidl, M. Schloter, and J. Munch. 2004. Effects of transgenic potatoes with an altered starch composition on the diversity of soil and rhizosphere bacteria and fungi. Plant Soil 266:23-39. (Pubitemid 40318845)
37. Muyzer, G., E. de Waal, and A. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA Appl. Environ. Microbiol. 59:695-700.
38. Nannipieri, P., J. Ascher, M. T. Ceccherini, L. Landi, G. Pietramellara, G. Renella, and F. Valori. 2008. Effects of root exudates on microbial diversity and activity in rhizosphere soils, p. 339-365. In C. S. Nautiyal and P. Dion (ed.), Molecular mechanisms of plant and microbe coexistence. Springer, Berlin, Germany.
39. Offre, P., B. Pivato, S. Mazuiere, G. Berta, P. Lemanceau, and C. Mougel. 2008. Microdiversity of Burkholderiales associated with mycorrhizal and nonmychorrizal roots of Medicago tmncatula. FEMS Microbiol. Ecol. 65:180-192. (Pubitemid 351989231)
40. Offre, P., B. Pivato, S. Siblot, E. Camalero, T. Conberand, and C. Mougel. 2007. Identification f bacterial groups preferentially associated with mycorrihizal roots of Medicaga truncatula. Appl. Environ. Microbiol. 73:913-921.
41. Rasche, F., V. Hödl, C. Poll, E. Kandeler, M. Gerzabek, J. D. van Elsas, and A. Sessitsch. 2006. Rhizosphere bacteria affected by transgenic potatoes with antibacterial activities compared with the effects of soil, wild-type potatoes, vegetation stage and pathogen exposure. FEMS Microbiol. Ecol. 56:219-235.
42. Reis, V. M., P. Estrada-De los Santos, S. Tenorio-Salgado, J. Vogel, M. Stoffels, S. Guyon, P. Mavingui, V. L. Baldani, M. Schmid, J. I. Baldani, J. Balandreau, A. Hartmann, and J. Caballero-Melloado. 2004. Burkholderia tropica sp. nov., a novel nitrogen-fixing, plant-associated bacterium. Int. J. Syst. Evol. Microbiol. 54:2155-2162.
43. Richards, B. 1987. The microbiology of terrestrial ecosystems. Longman Scientific & Technical, Harlow, Essex, England.
44. Schloss, P., and J. Handelsman. 2005. Introducing DOTUR, a computer program for defining operational taxonomie units and estimating species richness. Appl. Environ. Microbiol. 71:1501-1506.
45. Schmalenberger, A., S. Hodge, A. Bryant, M. J. Hawkesford, B. K. Singh, and M. A. Kertesz. 2008. The role of Variovorax and other Comamonadaceae in sulfur transformations by microbial wheat rhizosphere communities exposed to different fertilization regimes. Environ. Microbiol. 10:1486-1500.
46. Schmalenberger, A., and M. Kertesz. 2007. Desulfurization of aromatic sulfonates by rhizosphere bacteria: high diversity of the asfA gene. Environ. Microbiol. 9:535-545. (Pubitemid 46072139)
47. Sessitsch, A., T. Coenye, A. V. Sturz, P. Vandamme, E. A. Barka, J. F. Salles, J. D. van Elsas, D. Faure, B. Reiter, B. R. Glick, G. Wang-Pruski, and J. Nowak. 2005. Burkholderia phytofirmans sp. nov., a novel plant-associated bacterium with plant-beneficial properties. Int. J. Syst. Evol. Microbiol. 55: 1187-1192.
48. Singh, B., S. Munro, J. Potts, and P. Millard. 2007. Influence of grass species and soil type on rhizosphere microbial community structure in grassland soils. Appl. Soil Ecol. 36:147-155.
49. Singleton, D., M. Furlong, S. Rathbun, and W. Whitman. 2001. Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Appl. Environ. Microbiol. 67:4374-4376.
50. Spain, A., L. Krumholz, and M. Elshahed. 2009. Abundance, composition, diversity and novelty of soil Proteobacteria. ISME J. 3:992-1000.
51. Tamura, K., J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596-1599.
52. van Berloo, R., R. Hütten, H. van Eck, and R. Visser. 2007. An online potato pedigree database resource. Potato Res. 50:45-57.
53. van Overbeek, L., and J. D. van Elsas. 2008. Effects of plant genotype and growth stage on the structure of bacterial communities associated with potato (Solanum tuberosum L.). FEMS Microbiol. Ecol. 64:283-296.
54. Wang, C., E. Knill, B. Glick, and G. Defago. 2000. Effect of transferring ACC deaminase genes into Pseudomonas fluorescens strain CH40 and its gacA derivative on their growth-promoting and disease-suppressive capacities. Can. J. Microb. 46:898-907.
55. Wieland, G., R. Neumann, and H. Backhaus. 2001. Variation of microbial communities in soil, rhizosphere, and rhizoplane in response to crop species, soil type, and crop development. Appl. Environ. Microbiol. 67:5849-5854.