In situ microcosm (BACTRAP^®) experiments with ¹³C-labelled toluene and benzene were conducted to investigate the in situ biodegradation in contaminated aquifers at field sites with different geological and geochemical conditions. The transformation of the carbon (¹³C), derived from labelled substrates, into fatty acids verified the assimilation of the pollutants with formation of biomass. This clearly demonstrated that the in situ microcosm system is a useful culture-independent method to investigate in situ biodegradation in the aquifer. In addition, metabolites such as benzylsuccinic acid were found on toluene amended BACTRAPs indicating that toluene was degraded anaerobically. This result corresponded to the geochemical conditions found at the field site and the approach enabled the analysis of the metabolic pathway governing in situ toluene biodegradation in the polluted aquifer.

Phospholipid fatty acids (PLFA) of living cells make up a significant part of the total lipid fatty acid (TLFA) fraction. Comparing BACTRAPs exposed at different geochemical zones of the aquifers, the fatty acid composition was found to be relatively similar indicating that the composition of the TLFA was of low taxonomic value and not sensitive enough for a community analysis. Therefore the composition of the microbial communities was analysed by genetic profiling and sequencing of partial 16S rRNA genes PCR-amplified from total DNA, extracted directly from the BACTRAPs. Sequences retrieved from the BACTRAPs indicated a dominance of not-yet cultivated bacteria, with several of them phylogenetically closely related to those with an iron and sulphate reducing capacity, typically found at BTEX and mineral oil polluted sites.