Microbial community profiling

Nucleic acid analysis. Methods that analyse the microbial community from nucleic acid composition are based on use of the polymerase chain reaction (PCR). Universal forward and reverse primers are used in combination with PCR to amplify species-specific DNA fragments (usually the 16S subunit of ribosomal DNA) from samples isolated directly from soil. Samples then are separated 

Plants also have potential for demographic testing. Sheppard et al. (1993) proposed a 35-day test with Brassica rapa. Comparison of the results with a suite of assays in metal-spiked soils indicated that bloom initiation was more sensitive than lettuce emergence or earthworm survival for zinc but not mercury. Saterbak et al. (1999) used this test for the assessment of hydrocarbon-contaminated soil. The study, which used Brassica rapa selectively bred to reduce generation time, proved unsuccessful due to low germination in the control soil, suggesting that there is still a need for further method development. 

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Table 7.1 Culture-mdependeiit methods as microbial community profiling tools main advantages and disadvantages...

Bokulich, N. A., Bamforth, C. W., Mills, D. A. (2012). A review of molecular methods for microbial community profiling of beer and wine. Journal of American Society of Brewing Chemists, 70, 150-162. 

Hamady, M. and Knight, R. 2009. Microbial community profiling for human microbiome projects Tools, techniques, and challenges. Genome Research 19(T), 1141 1152. 

El Fantroussi S, L Verschuere, W Verstraete, EM Top (1999) Effect of phenylurea herbicides on soil microbial communities estimated by analysis of 16S rRNA gene fingerprints and community-level physiological profiles. Appl Environ Microbiol 65 982-988. 

S. D. Siciliano and J. J. Germida, Biolog analysis and fatly acid methyl ester profiles indicate that pseudormonad inoculants that promote phytoremediation alter the root-as.sociated microbial community of Bromus hiehersteinii. Soil Biol. Biochem. 30 1717 (1998). 

Changes in the fatty acid profiles of mixed microbial communities may be used in a similar way to detect stress responses or periods of activity. 

Preston-Mafham, J. Boddy, L. Randerson, P. F. Analysis of microbial community functional diversity using sole-carbon-source utilisation profiles—A critique. FEMS Microbiol. Ecol. 2002, 42,1-14. 

Griffiths B.S., Diaz-Ravina M., Ritz K., McNicol J.W., Ebblewhite N., Baath E. Community DNA hybridization and %G+C profiles of microbial communities from heavy metal polluted soils. FEMS Microbiol. Ecol. 1997 24 103-112. 

SSCP The reactor inoculated with a microbial consortia obtained from a textile wastewater treatment plant Color removal and changes in bacterial community profile [168]... 

Bossio DA, Scow KM, Gunapala N, Graham KJ (1998) Determinants of soil microbial communities Effects of agricultural management, season, and soil type on phospholipid fatty acid profiles. Microb Ecol 36 1-12... 

Applications of Functional Gene Microarrays for Profiling Microbial Communities... 

Signature lipid biomarkers (SLB), or fatty acid profiling, is another molecular approach that has become widely used to study microbial communities (White and Ringelberg 1998) because, like nucleic acid methods, it is not dependent on the growth or morphology of organisms but relies on the direct... 

Sundh, I., Nilsson, M., and Borga, P. (1997). Variation in microbial community structure in two boreal peatlands as determined by analysis of phospholipid fatty acid profiles. Appl. Environ. Microbiol. 63,1476-1482. 

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