Microbial diversity molecular techniques

Estimates of the diversity of DNA-based soil organisms so far have not been able to answer the questions concerning the functions of soil ecosystem, although, they can serve as an efficient tool for explaining DNA diversity in situ. The presence of a certain microbial gene does not assure that the metabolic process, for which the gene is responsibile, is carried out. The challenge for molecular techniques is to provide quantitative measures for microbial cells and activities rather than Just qualitative measures. To this purpose, DNA-based techniques... 

The relation between microbial diversity and soil functions is poorly understood because we cannot measure easily the microbial diversity, even if we can detect unculturable microorganisms by molecular techniques (Nannipieri et al. 2003). In addition, the present assays for measuring microbial functions determine the overall rate of entire metabolic processes, such as respiration, or specific enzyme activities, without identifying the active microbial species involved. The recent advances in RNA extraction from soil might permit us to determine active species in soil (Griffiths et al. 2000 Hurt et al. 2001). Further advances in understanding require us to determine the composition of microbial communities and microbial functions in microhabitats. 

Nucleic-acid approaches, which involve the extraction of microbial DNA and RNA from environmental samples, have been applied to the study of natural attenuation of petroleum products since the 1990s. With these techniques, the specific genes that are responsible for hydrocarbon degrading capabilities in bacteria can be measured. These tools are especially useful for studying microbial diversity at impacted sites (Madsen, 2000). Various recent applications of these techniques in petroleum-contaminated environments are reviewed by Haack and Bekins (2000). For example, Stapleton and Sayler (1999) monitored changes in the molecular microbial... 

Hughes IB, Hellmann JJ. The application of rarefaction techniques to molecular inventories of microbial diversity. Methods Enzymol 2005 397 292-308. 

Microbial diversity Polar lipid fatty acid analysis or molecular biological techniques... 

One of the limitations of screening environmental isolates is the cultivation of the organisms. In a single gram of soil, more than 108 microbes may be present, the majority of which cannot be cultivated. It is clear from molecular ecological studies that traditional cultivation techniques only capture a fraction, usually less than 1 percent, of the available diversity. To overcome this, direct cloning of DNA from environmental samples enables an unbiased representation of the microbial... 

Although the search for novel extremozymes is a hot area of research, the secondary metabolites of these same microbes have attracted little attention. While scientists isolate and characterize new proteins that are stable in extremes of temperature, pH and salinity, others are applying the tools of molecular biology rather than classical culture techniques to study microbial communities. The two techniques give a. very different view of community diversity in part because certain microbes may act like weeds, quickly outgrowing all other, more fastidious members of the community in culture. Many microbes may... 

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