Identification of differentially expressed genes in an industrial bioleaching heap processing low-grade copper sulphide ore elucidated by RNA arbitrarily primed polymerase chain reaction

Abstract

During the past few decades the microbial bioleaching of metallic sulphide ores has become a very important process utilized by the mining industry. The biodiversity studies of industrial systems have revealed the occurrence of acidophilic microorganisms, forming dynamic communities that include bacteria and archaea. A combination of molecular and cultivation-based approaches has been used during the leaching cycle to understand the key microorganisms present and their function in the Escondida. Sulphide Leach Plant. The global genomic expression in solution samples has been analyzed by random arbitrary primed polymerase chain reaction (RAP-PCR), to pinpoint those microorganisms with active metabolism in the communities present in regions of the heap leach operation of different ages. Four random primers were used and one hundred and twenty RAP-PCR products were cloned, sequenced and compared to databases using the BLAST search algorithm. Approximately 48% of the RAP-PCR products were 16S and 23S rRNA genes, and many of these results are consistent with community analysis carried out on the same heap using 16S rRNA gene libraries and real-time PCR. Interestingly, different microorganisms to those previously detected by 16S rRNA PCR-DGGE, represented by sequences distantly related to the archaea Picrophilus torridus, and Thermoplasma acidophilum sequences, were detected using RNA analysis. Eight different RAP-PCR products shared similarity with functional genes, and sequence analysis revealed the expression of genes associated with transcription (RNA polymerase) and translation (elongation factor and ribosomal protein) components, metabolic function (2-methylisocitrate synthase and pyruvate dehydrogenase), and electron transport (cytochrome). Other genes such as mercuric reductase and ABC transporter ATP-binding proteins were also detected. However, 30% of RAP-PCR products showed no similarity with any sequences currently in the database.

This report represents the first transcriptomic study of the microbial community inhabiting an industrial bioleaching system. The data suggest that the functional spectrum of expressed genes was consistent with genomic and proteomic reports from pure cultures and environmental AMD samples containing microorganisms involved in bioleaching processes. Both studies revealed the expression of genes mainly related to energetic metabolisms and stress responses.