Does disturbance and restoration of alpine grassland soils affect the genetic structure and diversity of bacterial and N2-fixing populations?

Environmental Microbiology

Volumn 8, Issue 11, 2006, Pages 1889-1901

  Gros, Raphaël ^a   Jocteur Monrozier, Lucile ^b   Faivre, Pierre ^c  

^a CNRS   (France)

^b University of Lyon   (France)

^c UNIVERSITÉ DE SAVOIE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); POSIBACTERIA;

EID: 33749406386     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2006.01106.x     Document Type: Article

References (51)

1. Angers, D.A., Samson, N., and Légère, A. (1993) Early changes in water stable aggregation induced by rotation and tillage in a soil under barley production. Can J Soil Sci 73: 51-59.
2. Bardgett, R.D., Wardle, D.A., and Yeates, G.W. (1998) Linking above-ground and below-ground food webs: how plant responses to foliar herbivory influence soil organisms. Soil Biol Biochem 30: 1867-1878.
3. Blackwood, C., and Paul, E.A. (2003) Eubacterial community structure and population size within the soil light fraction, rhizosphere, and heavy fraction of several agricultural systems. Soil Biol Biochem 35: 1245-1255.
4. Bornman, J.P., Skroch, P.W., O'Sullivan, K.M., Palus, J.A., Rumlanek, N.G., Jansen, J.L., et al. (1996) Molecular microbial diversity of an agricultural soil in Wisconsin. Appl Environ Microb 62: 1935-1943.
5. Cambardella, C.A., and Elliot, E.T. (1994) Carbon and nitrogen dynamics of soil organic matter fractions from cultivated grassland soils. Soil Sci Soc Am J 58: 123-130.
6. Chapin, F.S., Zavaleta, E.S., Eviner, V.T., Naylor, R.L., Vitousek, P.M., Reynolds, H.L., et al. (2000) Consequences of changing biodiversity [Review]. Nature 405: 234-242.
7. Chotte, J.L., Schwartzmann, A., Bally, R., and Jocteur Monrozier, L. (2002) Changes in bacterial community and Azospirillum diversity in soil fractions of a tropical soil under 3 and 19 years of natural fallow. Soil Biol Biochem 34: 1083-1092.
8. Darbyshire, J.F., Chapman, S.J., Cheshire, M.V., Gauld, J.H., McHardy, W.J., Paterson, E., and Vaughan, D. (1993) Methods for the study of interrelashionships between micro-organisms and soil structure. Geoderma 56: 3-23.
9. De Leij, F.A.A.M., Whipps, J.M., and Lynch, J.M. (1994) The use of colony development for the characterization of bacterial communities in soil and on roots. Microbial Ecol 27: 81-97.
10. Döbereiner, J., and Pedrosa, F.O. (1987) Nitrogen-Fixing Bacteria in Nonleguminous Crop Plants. p. 155. Madison, WI, USA: Science Tech, Publishers.
11. Edgerton, D.L., Harris, J.A., Birch, P., and Bullock, P. (1995) Linear relationship between aggregate stability and microbial biomass in three restored soils. Soil Biol Biochem 27: 1499-1501.
12. Fall, S., Nazaret, S., Chotte, J.L., and Brauman, A. (2004) Bacterial density and community structure associated with aggregate size fractions of soil-feeding termite mounds. Microbial Ecol 48: 191-199.
13. Felske, A., Wolterink, A., Van Lis, R., and Akkermans, A.D.L. (1998) Phylogeny of the main bacterial 16S rRNA sequences in Drentse A grassland soil (the Netherlands). Appl Environ Microb 64: 871-879.
14. Finlay, B.J., Maberly, S.C., and Cooper, J.I. (1997) Microbial diversity and ecosystem function. Oikos 80: 209-213.
15. Franklin, R.B., and Mills, A.L. (2003) Multi-scale variation in spatial heterogeneity for microbial community structure in an eastern Virginia agricultural field. FEMS Microbiol Ecol 44: 335-346.
16. Franklin, R.B., Blum, L.K., McComb, A.C., and Mills, A.L. (2002) A geostatistical analysis of small-scale spatial variability in bacterial abundance and community structure in salt marsh creek bank sediments. FEMS Microbiol Ecol 42: 71-80.
17. García-Martínez, J., Bescós, I., Rodríguez-Sala, J.J., and Rodríguez-Valera, F. (2001) RISSC: a novel database for ribosomal 16S-23S RNA genes spacer regions. Nucleic Acids Res 29: 178-180.
18. Gee, G.W., and Bauder, J.W. (1986) Particle size analysis. In Methods of Soil Analysis, part 1, 2nd edn. Klute, A. (ed.). Madison, WI, USA: Agronomy Monograph 9. ASA and SSSA, pp. 383-411.
19. van Gestel, M., Merchx, R., and Vlassek, K. (1996) Spatial distribution of microbial biomass in microaggregates of a silty-loam soil and the relation with the resistance of microorganisms to soil drying. Soil Biol Biochem 28: 503-510.
20. Gros, R., Poly, F., Jocteur Monrozier, L., and Faivre, P. (2003) Plant and soil microbial community responses to solid waste leachates diffusion on grassland. Plant Soil 255: 445-455.
21. Gros, R., Jocteur Monrozier, L., Bartoli, F., Chotte, J.L., and Faivre, P. (2004) Relationships between soil physicochemical properties and microbial activity along a chronosequence of restored ski runs. Appl Soil Ecol 27: 7-22.
22. Jastrow, J.D., Miller, R.M., and Lussenhop, J. (1998) Contributions of interacting biological mechanisms to soil aggregates stabilization in restored prairie. Soil Biol Biochem 30: 905-916.
23. Kandeler, E., Stemmer, M., and Klimanek, E.-M. (1999) Response of soil microbial biomass, urease and xylanase within particle size fractions to long-term soil management. Soil Biol Biochem 31: 261-273.
24. Kowalchuk, G.A., Buma, D.S., De Boer, W., Klinkhamer, P.G.L., and Van Veen, J.A. (2002) Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorgansims. Anton Leeuw Int J G 81: 509-520.
25. Lafond, J., Angers, D.A., and Laverdière, M.R. (1992) Compression characteristics of a clay soil as influenced by crops and sampling dates. Soil Till Res 22: 233-241.
26. Macnaughton, S., Stephen, J.R., Chang, Y.J., Peacock, A., Flemming, C.A., Leung, K.T., and White, D.C. (1999) Characterization of metal-resistant soil eubacteria by polymerase chain reaction - denaturing gradient gel electrophoresis with isolation of resistant strains. Can J Microbiol 45: 116-124.
27. Marschner, P., Yang, C.H., Lieberei, R., and Crowley, D.E. (2001) Soil and plant specific effects on bacterial community composition in the rhizosphere. Soil Biol Biochem 33: 1437-1445.
28. Miethling, R., Wieland, G., Backhaus, H., and Tebbe, C.C. (2000) Variation of microbial rhizosphere communities in response to crop species, soil origin, and inoculation with Sinorhizobium meliloti L33. Microbial Ecol 41: 43-56.
29. Misra, R.K., Dexter, A.R., and Alston, A.M. (1986) Penetration of soil aggregates of finite size II plant roots. Plant Soil 107: 11-18.
30. Normand, P., Pansonnet, C., Nesme, X., Neyra, T., and Simonet, P. (1996) ITS analysis of procaryotes. In Molecular Microbiology Ecological Manual. Akkermans, A.D.L., van Elsas, J.D., and de Bruijn, F.J. (eds). Dordrecht, The Netherlands: Kluwer, pp. 1-12.
31. Nunan, N., Wu, K., Young, I.M., Crawford, J.W., and Ritz, K. (2002) In situ spatial patterns of soil bacterial populations, mapped at multiple scales, in an arable soil. Microbial Ecol 44: 296-305.
32. Oades, J.M. (1993) The role of biology in the formation, stabilization and degradation of soil structure. Geoderma 56: 377-400.
33. Orians, G.H. (1975) Diversity, stability and maturity in natural ecosystems. In Unifying Concepts in Ecology. van Dobben, W.H. and Lowe-McConnell, R.H. (eds). The Hague, The Netherlands: Dr W. Junk Bv Publishers, pp. 130-150.
34. Othonen, R., Fristze, H., Pennanen, T., Jumpponen, A., and Trappe, J. (1999) Ecosystem properties and microbial community changes in primary succession on a glacier forefront. Oecologia 119: 239-246.
35. Poly, F., Bally, R., and Jocteur Monrozier, L. (2001b) Improvement of the RFLP procedure to study the diversity of the nifH genes in communities of nitrogen fixers in soil. Res Microbiol 152: 95-103.
36. Poly, F., Ranjard, L., Nazaret, S., Gourbiere, F., and Jocteur Monrozier, L. (2001a) Comparison of nifH pools between soils and between soil microenvironments of contrasting properties. Appl Environ Microb 67: 2255-2262.
37. Rainey, P.B., Buckling, A., Kassen, R., and Travisano, M. (2000) The emergence and maintenance of diversity: insights from experimental bacterial populations. Trends Ecol Evol 15: 243-247.
38. Ranjard, L., and Richaume, A. (2001) Quantitative and qualitative microscale distribution of bacteria in soil. Res Microbiol 152: 707-716.
39. Ranjard, L., Poly, F., Combrisson, J., Richaume, A., Gourbière, F., Thioulouse, J., and Nazaret, S. (2000a) Heterogeneous cell density and genetic structure studies of bacterial pools associated with various soils microenvironments as determined by enumeration and DNA fingerprinting approach (RISA). Microbial Ecol 39: 263-272.
40. Ranjard, L., Brothier, E., and Nazaret, S. (2000b) Sequencing bands of ribosomal intergenic spacer analysis fingerprints for characterization and microscale distribution of soil bacterium populations responding to mercury spiking. Appl Environ Microb 66: 5334-5339.
41. Richaume, A., Steinberg, C., Jocteur Monrozier, L., and Faurie, G. (1993) Difference between direct and indirect enumeration of soil bacteria: influence of soil structure and cell location. Soil Biol Biochem 25: 641-643.
42. de Ridder-Duine, A.S., Kowalchuk, G.A., Gunnewiek, P.J.A. K., Smant, W., van Veen, J.A., and de Boer, W. (2005) Rhizosphere bacterial community composition in natural stands of Carex arenaria (sand sedge) is determined by bulk soil community composition? Soil Biol Biochem 37: 349-357.
43. Robert, M., and Chenu, C. (1992) Interactions between soils minerals and microorganisms. In Soil Biochemistry. Stotzky, G., and Bollag, J.M. (eds). New York, USA: Marcel Dekker, pp. 307-404.
44. Ruppel, S. (1989) Isolation and characterization of dinitrogen-fixing bacteria from the rhizosphere of Triticum aestivum and Ammophila arenaria. In Interrelationships Between Microorganisms and Plant in Soil. Vancura, V., and Kunc, F. (eds). Amsterdam, The Netherlands: Elsevier, pp. 253-262.
45. Saetre, P., and Baath, E. (2000) Spatial variation and patterns of soil microbial community structure in a mixed spruce-birch stand. Soil Biol Biochem 32: 909-917.
46. Schloter, M., and Hartmann, A. (1998) Endophytic and surface colonization of wheat roots (Triticum aestivum) by different Azospirillum brasilense strains studied with strain-specific monoclonal antibodies. Symbiosis 25: 159-179.
47. Sessitsch, A., Weilharter, A., Gerzabek, M.H., Kirchmann, H., and Kandeller, E. (2001) Microbial population structures in soil particle size fractions of a long-term fertiliser field experiment. Appl Environ Microb 67: 4215-4224.
48. Tisdall, J.M., and Oades, J.M. (1982) Organic matter and water stable aggregates in soils. J Soil Sci 33: 141-163.
49. Torsvik, V., Ovreas, L., and Thingstad, T.F. (2002) Procaryotic diversity magnitude, dynamics, and controlling factors. Science 296: 1064-1066.
50. USDA (1975) Soil Taxonomy. Agriculture Handbook no. 436, Washington, D.C.
51. Wardle, D.A., and Giller, K.E. (1996) The quest for contemporary ecological dimension to soil biology. Soil Biol Biochem 28: 1549-1554.