Bacterial diversity of biofilm samples from deep mines in South Africa

The Au, Pt and diamond mines of South Africa provide access to microorganism bearing fluids emanating from fractures at depths ranging from 0.7 to 3.2 km. Due to the unique characteristic of mine environment as demonstrated by extreme pH, pressure, temperature and/or salinity, it is anticipated that it could hold the promise for novel gene sequences and hence gene products of industrial and pharmaceutical importance. To provide insight into the microbial diversity of mines in South Africa, biofilm samples were collected from Goldfield and diamond mines and their bacterial diversity determined using molecular approaches. 16S rRNA genes were amplified from DNA extracted from these samples using polymerase chain reaction with universal bacterial primers 27F (5’- AGA GTT TGA TCM TGG CTC AG-3’) and 1492R (5’- GGT TAC CTT GTT ACG ACT T-3’). Metagenomic clone libraries were constructed and restriction fragment length polymorphism (RFLP) analysis of >100 derived clones resulted in four major restriction patterns from which 40 clones were chosen for sequencing. More than half (53%) of the sequences were affiliated with the bacterial phylum Proteobacteria, forty-one percent (41%) of the sequences with yet uncultured bacteria and the phyla Firmicutes and Planctomycetes were accounted for by 4% and 2% of the sequences respectively. DGGE analysis of PCR-amplified 16S rRNA genes showed characteristic fingerprints for each sample. The differences in community structure observed account for the uniqueness of each of the mines with respect to its microbial diversity.