title: Genomic and metagenomic challenges and opportunities for bioleaching: a mini-review.
abstract: High-throughput genomic technologies are accelerating progress in understanding the diversity of microbial life in many environments. Here we highlight advances in genomics and metagenomics of microorganisms from bioleaching heaps and related acidic mining environments. Bioleaching heaps used for copper recovery provide significant opportunities to study the processes and mechanisms underlying microbial successions and the influence of community composition on ecosystem functioning. Obtaining quantitative and process-level knowledge of these dynamics is pivotal for understanding how microorganisms contribute to the solubilization of copper for industrial recovery. Advances in DNA sequencing technology provide unprecedented opportunities to obtain information about the genomes of bioleaching microorganisms, allowing predictive models of metabolic potential and ecosystem-level interactions to be constructed. These approaches are enabling predictive phenotyping of organisms many of which are recalcitrant to genetic approaches or are unculturable. This mini-review describes current bioleaching genomic and metagenomic projects and addresses the use of genome information to: (i) build metabolic models; (ii) predict microbial interactions; (iii) estimate genetic diversity; and (iv) study microbial evolution. Key challenges and perspectives of bioleaching genomics/metagenomics are addressed.
authors.affiliation: Fundación Ciencia & Vida, Santiago, Chile. Electronic address: juan.pablo.cardenas@gmail.com.
authors.forename: Juan Pablo
authors.initials: JP
authors.lastname: Cárdenas
authors.affiliation: Fundación Ciencia & Vida, Santiago, Chile. Electronic address: rquatrini@yahoo.com.ar.
authors.forename: Raquel
authors.initials: R
authors.lastname: Quatrini
authors.affiliation: Fundación Ciencia & Vida, Santiago, Chile; Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile. Electronic address: dsholmes2000@yahoo.com.
authors.forename: David S
authors.initials: DS
authors.lastname: Holmes
mesh_terms: D004783:Environmental Microbiology; D053858:Metabolic Networks and Pathways / Q000235:genetics; D056186:Metagenomics; D056265:Microbial Interactions; D008903:Minerals / Q000378:metabolism*; D008906:Mining / Q000379:methods*
chemical_list: D008903:Minerals
keywords: Acidophile; Bioinformatics; Bioleaching; Biomining; Genomics; Metagenomics