Rapid Mass Spectrometric DNA Diagnostics for Assessing Microbial Community Activity During Bioremediation

DNA detection and analysis has become a common way to identify organisms in many different types of samples, including soils that contain organisms potentially capable of biodegrading pollutants. Such analytical procedures, known as DNA diagnostic techniques, generally start with the extraction of DNA from organisms grown under culture conditions in the laboratory. The sequence of the DNA provides one way to identify the isolated organism. It is also possible to extract DNA directly from soil samples in an attempt to avoid the difficulty of establishing culture conditions for the large number of organisms that inhabit soils. However, DNA extracted from soil is a complicated mixture that includes DNA from all the individual organisms present in the microbial community. Several DNA amplification techniques were investigated, along with MALDI mass spectrometry, to determine how well high throughput screening procedures for tracking organisms with genes known to produce pollutant-degrading enzymes could be established.