Using genetically engineered microbes in combination with other agents is a promising approach for quick, efficient, and cost-effective remediation of contaminated soils.
Soil composting has been used to remediate soil contamination. This was done at the Toms River Chemical superfund site in New Jersey, USA. The contaminants were from dyestuff manufacturing.
In-Situ, inside the soil (vadose or satutared zones), without excavating/moving it? Or Ex-Situ, once the soil has been excavated?
The main problems for In-Situ (bio)remediation are the uncertainties about heterogeneity (soil properties, including anisotropy, and contaminant/microbe/nutrients distribution), and the maintenance of a good (sustained and effective) biological process all through the contaminated zone.
On the other hand, excavation (and, when needed, transport) gives you a good chance to homogenize the soil, characterize it properly (soil properties, contamination, microbes/nutrients available/needed...), and design an optimal and specific-to-the-site (bio)remediation system.
Note: I write (bio) in parenthesis because the problems mentioned, being the most relevant for remediation, are not specific to BIOremediation, but for any kind of remediation.