By T. Bergan (Eds.)
The editors (of the Planta Piloto de Procesos Industriales Microbiologicos-Consejo Nacional de Investigaciones Cientificas y Tecnicas, Argentina) current 38 contributions describing step by step protocols for investigating the interactions of microorganisms with their setting. The protocols stick with a similar layout as different volumes within the sequence, together with laboratory directions, a precis of the main of the procedure, lists of kit and reagents, and discussions of pitfalls. The protocols are grouped into sections on groups and biofilms; fermented milks; nucleic acids, restoration, and resolution; and experiences. evaluation articles speak about the endophytic bacterium Bacillus mojavensis, the engineering of micro organism to reinforce bioremediation of fragrant compounds, and using chemical shift reagents and Na-NMR to review sodium gradients in microorganisms.
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Additional resources for Environmental Microbiology: Methods and Protocols
If the DNA preparation contains suspended solids, a large amount of humic acids, or a large amount of DNA, only 50 to 100 mL should be loaded on the column; the remaining volume should be made up with TE. The column can become plugged, or removal of humic acids can be poor, if it is overloaded. 22. If a sample appears brown after purification on a spin column, it still contains humic acids and must be re-cleaned because they will interfere with the labeling procedure. 23. This step is not necessary if the sample was gel purified, because RNA and protein will have been removed during that process.
17. , and Liesack, W. (2000) Spatial changes in the bacterial community structure along a vertical oxygen gradient in flooded paddy soil cores. Appl. Environ. Microbiol. 66, 754–762. 18. Moeseneder, M. , Arrieta, J. , and Herndl, G. J. (1999) Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 65, 3518–3525. 19. , Gerzabek, M. , and Kandeler, E.
All samples, both reference and unknown, should be preserved in the same manner to improve quantitative values. Consideration must also be given to media chemistry. Owing to salt effects on the DAPI–DNA binding constants, the fluorescence intensity changes with the ion content of the medium. This is particularly true for aquatic bacteria, given the differences between freshwater and marine environments. For this reason, the internal standard must be calibrated to the DNA standard organism, in a medium of the same ionic concentration as that of the unknown samples to be analyzed.