Primers: Functional Genes for Anaerobic Hydrocarbon Degrading Microbes

The detection of anaerobic hydrocarbon degrader populations via catabolic gene markers is important for the understanding of processes at contaminated sites. The genes of fumarate-adding enzymes (FAEs; i.e., benzylsuccinate and alkylsuccinate synthases) are widely used as specific functional markers for anaerobic degraders of aliphatic and aromatic hydrocarbons. Several recent studies have shown the existence of new and deeply branching FAE gene lineages in the environment, and respective FAE gene-targeted primer systems have been advanced. Here, state-of-the art protocols for the PCR detection, T-RFLP fingerprinting as well as sequencing of FAE gene amplicons are described. These protocols can also readily be applied to other established functional markers for anaerobic degraders of petroleum hydrocarbons, such as benzoyl-CoA reductases as well as the ring-cleaving hydrolases involved in the central catabolism of aromatic hydrocarbons. In summary, these assays allow for rapid and directed insights into the diversity and identity of intrinsic degrader populations and degradation potentials in hydrocarbon-impacted systems.
Source: Springer protocols feed by Microbiology - Category: Microbiology Source Type: news