Molecular ecology is a field of microbiology interested in the presence of certain genes in the environment.

It stems from the fact that many microorganisms are not easily obtainable as cultured strains in the laboratory, which would allow for indentification and characterisation. It also stems from the development of PCR, which allows for rapid amplification of genetic material.

The amplification of DNA from environmental samples using general of group-specific primers leads to a mix of genetic material that has to be sorted out before sequencing and identification. The classic technique to achieve this is through cloning, which involves incorporating the amplified DNA fragments into bacterial plasmids. More recent techniques such as DGGE, allow for a faster result.

The development of molecular ecology is also closely related to the use of DNA chips, which allows for the detection of specific organisms or genes in an environment.

One of the main issues related to the use of molecular techniques in microbial ecology is the problem of the presence in active or passive form of the organisms. This can be adressed in a number of ways, mainly :

• By using reverse transcriptase in order to produce an impression of the active genes
• By using FISH (Fluorescence in situ hybridization) as a way of detecting and counting the cells that contain specific genes