Functional profiling of mercuric reductase (mer A) genes in biofilm communities of a technical scale biocatalyzer

Based on an alignment of 30 merA sequences from Gram negative bacteria, conserved primers were designed for amplification of merA fragments with an optimized PCR protocol. The resulting amplicons of approximately 280 bp were separated by thermogradient gelelectrophoresis (TGGE), resulting in strain specific fingerprints for mercury resistant Gram negative isolates with different merA sequences. The merA profiling of the biofilm community from a technical biocatalyzer showed persistence of some and loss of other inoculum strains as well as the appearance of new bands, resulting in an overall increase of the functional diversity of the biofilm community. One predominant new band of the merA community profile was also detected in a biocatalyzer effluent isolate, which was identified as Pseudomonas aeruginosa. The isolated strain showed lower mercury reduction rates in liquid culture than the inoculum strains but was apparently highly competitive in the biofilm environment of the biocatalyzer where moderate mercury levels were prevailing.The merA profiling technique allowed to monitor the ongoing selection for better adapted strains during the operation of a biocatalyzer and to direct their subsequent isolation. In such a way, a predominant mercury reducing Ps. aeruginosa strain was identified by its unique mercuric reductase gene.Phylogenetic profiling of microbial communities based on sequence specific separation of phylogenetic marker genes (mainly the 16S rRNA gene or the 16S-23S ribosomal intergenic spacer region) is widely used in microbial ecology to study changes in community diversity in response to environmental parameters or experimental perturbations. However, physiological traits are often dispersed across the phylogenetic tree, and so conclusions regarding the processes driven by the microbes in question cannot be drawn. Functional gene profiling has the potential to provide information about the functional diversity of microbial populations with respect t