Sampling strategy in molecular microbial ecology: Influence of soil sample size on DNA fingerprinting analysis of fungal and bacterial communities

Environmental Microbiology

Volumn 5, Issue 11, 2003, Pages 1111-1120

  Ranjard, Lionel ^a   Lejon, David P H ^a   Mougel, Christophe ^a   Schehrer, Lucie ^b   Merdinoglu, Didier ^b   Chaussod, Rémi ^a  

^a CEMAGREF   (France)

^b UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; BIOMASS; DNA; DNA FINGERPRINTING; DNA, RIBOSOMAL SPACER; ECOLOGY; ELECTROPHORESIS, POLYACRYLAMIDE GEL; FUNGI; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; PRINCIPAL COMPONENT ANALYSIS; SOIL; SOIL MICROBIOLOGY;

BACTERIA (MICROORGANISMS);

EID: 0242676205     PISSN: 14622912     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1462-2920.2003.00521.x     Document Type: Article

References (31)

1. Borneman, J. (1999) Culture-independent identification of microorganisms that respond to specified stimuli. Appl Environ Microbiol 65: 3398-3400.
2. Borneman, J., and Martin, R.J. (2000) PCR primers that amplify fungal rRNA genes from environmental samples. Appl Environ Microbiol 66: 4356-4360.
3. Dexter, A.R. (1988) Advances in characterisation of soil structure. Soil Till Res 11: 199-238.
4. Ellingsoe, P., and Johnsen, K. (2002) Influence of soil sample sizes on the assessment of bacterial community structure. Soil Biol Biochem 34: 1701-1707.
5. Fisher, M.M., and Triplett, E.W. (1999) Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl Environ Microbiol 65: 4630-4636.
6. Foster, R.C. (1988) Microenvironments of soil microorganisms. Biol Fertil Soils 6: 189-203.
7. Frostegard, A., Courtois, S., Ramisse, V., Clerc, S., Bernillon, D., Le Gall, F., et al. (1999) Quantification of bias related to the extraction of DNA directly from soils. Appl Environ Microbiol 65: 5409-5420.
8. Grundmann, L.G., and Gourbiere, F. (1999) A microsampling approach to improve the inventory of bacterial diversity in soil. Appl Soil Ecol 13: 123-126.
9. Grundmann, G.L., and Debouzie, D. (2000) Geostatistical analysis of the distribution of nh (4) (+) and no (2) (-)-oxidizing bacteria and serotypes at the millimeter scale along a soil transect. FEMS Microbiol Ecol 34: 57-62.
10. Head, I.M., Saunders, J.R., and Pickup, R.W. (1998) Microbial evolution, diversity, and ecology: a decade of ribosomal RNA analysis of uncultivated microorganisms. Microb Ecol 35: 1-21.
11. Horton, T.R., and Bruns, T.D. (2001) The molecular revolution in ectomycorrhizal ecology: Peeking into the black-box. Mol Ecol 10: 1855-1871.
12. Hurek, T., Wagner, B., and Reinhold-Hurek, B. (1997) Identification of n2-fixing plant- and fungus-associated azoarcus species by PCR-based genomic fingerprints. Appl Environ Microbiol 63: 4331-4339.
13. Ingamells, C.O., and Switzer, P. (1973) A proposed sampling constant for use in geochemical analysis. Talanta 20: 547-568.
14. Jackson, C., Harper, J., Willoughby, D., Roden, E., and Churchill, P. (1997) A simple, efficient method for the separation of humic substances and DNA from environmental samples. Appl Environ Microbiol 63: 4993-4995.
15. Kent, A.D., and Triplett, E.W. (2002) Microbial communities and their interactions in soil and rhizosphere ecosystems. Annu Rev Microbiol 56: 211-236.
16. Kilbertus, G.N. (1980) Etude des microhabitats contenus dans les agrégats du sol, leur relation avec la biomasse bactérienne et la taille des procaryotes présents. Rev Ecol Biol Sols 17: 543-557.
17. 2 on the fungal community in a coastal scrub oak forest soil investigated with terminal-restriction fragment length polymorphism analysis. Appl Environ Microbiol 68: 4370-4376.
18. Kowalchuk, G., Gerards, S., and Woldendorp, J. (1997) Detection and characterization of fungal infections of ammophila arenaria (marram grass) roots by denaturing gradient gel electrophoresis of specifically amplified 18s rDNA. Appl Environ Microbiol 63: 3858-3865.
19. Kuske, C.R., Banton, K.L., Adorada, D.L., Stark, P.C., Hill, K.K., and Jackson, P.J. (1998) Small-scale DNA sample preparation method for field per detection of microbial cells and spores in soil. Appl Environ Microbiol 64: 2463-2472.
20. Martin-Laurent, F., Philippot, L., Hallet, S., Chaussod, R., Germon, J.C., Soulas, G., and Catroux, G. (2001) DNA extraction from soils: Old bias for new microbial diversity analysis methods. Appl Environ Microbiol 67: 2354-2359.
21. Ranjard, L., and Richaume, A. (2001) Quantitative and qualitative microscale distribution of bacteria in soil. Res Microbiol 152: 707-716.
22. Ranjard, L., Poly, F., Combrisson, J., Richaume, A., and Nazaret, S. (1998) A single procedure to recover DNA from the surface or inside aggregates and in various size fractions of soil suitable for pcr-based assays of bacterial communities. Eur J Soil Biol 34: 89-97.
23. Ranjard, L., Nazaret, S., Gourbiere, F., Thioulouse, J., Linet, P., and Richaume, A. (2000a) A soil microscale study to reveal the heterogeneity of Hg (II) impact on indigenous bacteria by quantification of adapted phenotypes and analysis of community DNA fingerprints. FEMS Microbiol Ecol 31: 107-115.
24. Ranjard, L., Poly, F., Combrisson, J., Richaume, A., Gourbiere, F., Thioulouse, J., and Nazaret, S. (2000b) Heterogeneous cell density and genetic structure of bacterial pools associated with various soil microenvironments as determined by enumeration and DNA fingerprinting approach (risa). Microb Ecol 39: 263-272.
25. Ranjard, L., Poly, F., Lata, J.-C., Mougel, C., Thioulouse, J., and Nazaret, S. (2001) Characterization of bacterial and fungal soil communities by automated ribosomal intergenic spacer analysis fingerprints: Biological and methodological variability. Appl Environ Microbiol 67: 4479-4487.
26. Robleto, E.A., Borneman, J., and Triplett, E.W. (1998) Effects of bacterial antibiotic production on rhizosphere microbial communities from a culture-independent perspective. Appl Environ Microbiol 64: 5020-5022.
27. Thioulouse, J., Chessel, D., Dolédec, S., and Olivier, J.M. (1997) Ade-4: a multivariate analysis and graphical display software. Stat Comput 7: 75-83.
28. Tiedje, J.M.S., Asuming-Brempong, S., Nusslein, K., Marsh, T.L., and Flynn, S.J. (1999) Opening the black box of soil microbial diversity. Appl Soil Ecol 13: 109-122.
29. Torsvik, V., and Ovreas, L. (2002) Microbial diversity and function in soil: From genes to ecosystems. Curr Op Microbiol 5: 240-245.
30. Tsai, Y.L., and Olson, B.H. (1992) Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction. Appl Environ Microbiol 58: 754-757.
31. Zhou, J., Bruns, M., and Tiedje, J. (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62: 316-322.