Negative effects of sample pooling on PCR-Based estimates of soil microbial richness and community structure

Applied and Environmental Microbiology

Volumn 76, Issue 7, 2010, Pages 2086-2090

  Manter, Daniel K ^a   Weir, Tiffany L ^b   Vivanco, Jorge M ^b  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b Department of Environmental and Radiological Health Sciences   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL COMMUNITY; COMMUNITY STRUCTURES; DNA EXTRACTION; FUNGAL COMMUNITY; MICROBIAL COMMUNITIES; MISSED DETECTIONS; PCR AMPLIFICATION; PHYLOTYPES; RIBOSOMAL INTERGENIC SPACER ANALYSIS; SAMPLE NUMBER; SOIL MICROBIAL COMMUNITY; SOIL SAMPLE; SPATIAL HETEROGENEITY; TROPICAL RAIN FOREST;

AMPLIFICATION; BACTERIOLOGY; FUNGI; REGRESSION ANALYSIS; SOILS;

SOIL SURVEYS;

RIBOSOMAL SPACER DNA;

BACTERIUM; DETECTION METHOD; FOREST SOIL; FUNGUS; POLYMERASE CHAIN REACTION; RAINFOREST; SOIL MICROORGANISM; SPECIES RICHNESS; TROPICAL FOREST;

ARTICLE; BACTERIUM; BIODIVERSITY; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; FUNGUS; GENETICS; ISOLATION AND PURIFICATION; METAGENOMICS; METHODOLOGY; MICROBIOLOGY; PHYLOGENY; POLYMERASE CHAIN REACTION;

BACTERIA; BIODIVERSITY; CLUSTER ANALYSIS; DNA, RIBOSOMAL SPACER; FUNGI; METAGENOMICS; PHYLOGENY; POLYMERASE CHAIN REACTION; SOIL MICROBIOLOGY;

BACTERIA (MICROORGANISMS); FUNGI;

EID: 77950258137     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.03017-09     Document Type: Article

References (20)

1. Broeckling, C. D., A. K. Broz, J. Bergelson, D. K. Manter, and J. M. Vivanco. 2008. Root exudates regulate soil fungal community composition and diversity. Appl. Environ. Microbiol. 74: 738-744.
2. Broz, A. K., D. K. Manter, and J. M. Vivanco. 2007. Soil fungal abundance and biodiversity: another victim of the invasive plant Centaurea maculosa. ISME J. 1: 763-765.
3. Chandler, D. P., S. M. Li, C. M. Spadoni, G. R. Drake, D. L. Balkwill, J. K. Fredrickson, and F. J. Brockman. 1997. A molecular comparison of culturable aerobic heterotrophic bacteria and 16S rDNA clones derived from a deep subsurface sediment. FEMS Microbiol. Ecol. 23: 131-144.
4. Colwell, R. K. 2006. Estimates: statistical estimation of species richness and shared species from samples, version 8. http://viceroy.eeb.uconn. edu/estimates.
5. Ellingsoe, P., and K. Johnsen. 2002. Influence of soil sample sizes on the assessment of bacterial community structure. Soil Biol. Biochem. 34: 1701-1707.
6. Franklin, R. B., L. K. Blum, A. McComb, and A. L. Mills. 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.
7. Franklin, R. B., and A. L. Mills. 2003. Multi-scale variation in spatial het-erogeneity for microbial community structure in an eastern Virginia agricultural field. FEMS Microbiol. Ecol. 44: 335-346.
8. Green, J. L., A. J. Holmes, M. Westoby, I. Oliver, D. Briscoe, M. Dangerfield, M. Gillings, and A. J. Beattie. 2004. Spatial scaling of microbial eukaryote diversity. Nature 432: 747-750.
9. - oxidizing bacteria and serotypes at the millimeter scale along a soil transect. FEMS Microbiol. Ecol. 34: 57-62.
10. Grundmann, L. G., and F. Gourbière. 1999. A microsampling approach to improve the inventory of bacterial diversity in soil. Appl. Soil Ecol. 13: 123-126.
11. Kang, S., and A. L. Mills. 2006. The effect of sample size in studies of soil microbial community structure. J. Microbiol. Methods 66: 242-250.
12. Manter, D. K., and J. M. Vivanco. 2007. Use of the ITS primers, ITSlF and ITS4, to characterize fungal abundance and diversity in mixed-template samples by qPCR and length heterogeneity analysis. J. Microbiol. Methods 71: 7-14.
13. Normand, P., C. Ponsonnet, X. Nesme, M. Nevra, and P. Simonet. 1996. ITS analysis of prokaryotes, p. 1-12. In D. L. Akkermans, J. D. van Elsas, and E. I. de Bruijn (ed.). Molecular microbial ecology manual. Kluwer Academic, Amsterdam, Netherlands.
14. Polz, M. F., and C. M. Cavanaugh. 1998. Bias in template-to-product ratios in multitemplate PCR. Appl. Environ. Microbiol. 64: 3724-3730.
15. Ranjard, L., D. P. Lejon, C. Mougel, L. Schehrer, D. Merdinogiu, and R. Chaussod. 2003. Sampling strategy in molecular microbial ecology: influence of soil sample size on DNA fingerprinting analysis of fungal and bacterial communities. Environ. Microbiol. 5: 1111-1120.
16. Ranjard, L., and A. Richaume. 2001. Quantitative and qualitative microscale distribution of bacteria in soil. Res. Microbiol. 152: 707-716.
17. Reysenbach, A. L., L. J. Giver, G. S. Wickham, and N. R. Pace. 1992. Differential amplification of rRNA genes by polymerase chain reaction. Appl. Environ. Microbiol. 58: 3417-3418.
18. Sequerra, J., R. Marmeisse, G. Valla, P. Normand, A. Capellano, and A. Moiroud. 1997. Taxonomie position and intraspecific variability of the nodule forming Penicillium nodositatum inferred from RFLP analysis of the ribosomal intergenic spacer and random amplified polymorphic DNA. Mycol. Res. 101: 465-472.
19. Siebert, P. D., and J. W. Larrick. 1992. Competitive PCR. Nature 359: 557-558.
20. Torsvik, V. J., J. Gokoyr, and F. L. Daae. 1990. High diversity in DNA of soil bacteria. Appl. Environ. Microbiol. 56: 782-787.