REVIEW ARTICLE Genomics to assist mine reclamation: a review Heath W. Garris 1,2,3 , Susan A. Baldwin 4 , Jonathan D. Van Hamme 1,2 , Wendy C. Gardner 1,2 , Lauchlan H. Fraser 1,2 Mine reclamation succeeds when healthy, self-sustaining ecosystems develop on previously mined lands. Regulations require reclamation of ecosystem services; however, there are few specifed targets, and those that are presented are vague. Sequencing genomic DNA and transcribed RNA from environmental samples may provide critical supportive information for attempts to recreate ecosystem functions from the ground up on disturbed lands. In this review, we highlight the use of genomics to meet mine closure goals, to enhance ecosystem development, and to optimize ecosystem services inherent in self-sustaining reclaimed ecosystems. We address the development of environmental genomics—sequencing and analysis of environmentally derived DNA—to characterize microbial communities on mine sites. We then provide four areas where genomics has proven instrumental for informing management and assisting in reclamation of mine sites in the form of bioreactors, passive treatment systems, novel gene discovery, and DNA barcoding. Finally, we describe how recently developed techniques have transferable value to mine reclamation and provide evidence for future applications of genomics and the necessary steps to integrate these data into comprehensive management of mined sites. Key words: bioreactors, metagenomics, microbial community, mine drainage, passive remediation Implications for Practice • Sequencing and polymerase chain reaction (PCR)-based methods of quantifying environmentally derived DNA have seen a growing prominence in feld research aimed at understanding the processes underlying restoration, and will likely become common practice for monitoring biological capital and restoration progress on mine sites. • Sustainable and reliable containment of contaminants from mine sites will require periodic monitoring of micro- bial community composition and activity, and in the case of active treatment systems, incorporation into feedback models for continued operation. • There is a drastic need for education and technical training in environmental genomics for reclamation practitioners in the mining industry, and for tailored bioinformatics workfows that facilitate rapid evaluation of genomic data from mine sites specifcally. Introduction The science of mine reclamation exists as the proof of an industry-wide promise of mine-site transience. In an ideal sys- tem, mines operate with minimal environmental impact outside of the operational footprint. After the period of proftable extrac- tion is reached, a desirable condition is recreated, be it forest, pasture, or suburban neighborhood, so that the biota that devel- ops on previously mined substrate (soil microbes, vegetation, wildlife, and concerned citizens alike) can function within a nat- ural, self-sustaining ecosystem. In reality, mine sites often leave a legacy, including perpetually altered plant communities (Holl 2002), elevated contaminants in surface and groundwater (Cidu et al. 2001), thin, compact soils (Skousen et al. 2009), altered soil function (Mummey et al. 2002), and magnifcation of con- taminants within the food chain (Allan 1995; Muscatello & Janz 2009). Government regulations on mining operations set the guide- lines for reclamation (where such regulations exist), and as a result, direct the fate of many mine sites. Champigny (1991) performed a comparison of regulations on mine rehabilitation for 25 jurisdictions worldwide. Although the author identifed variations in the level of responsibility levied on mine opera- tors to reclaim mine sites, he concluded that greater than 90% of governments within the study mandated mine site rehabil- itation beyond minimum human health and safety standards (Champigny 1991). In British Columbia, Canada, the Mines Act, informally called the “Code,” specifes that reclamation must satisfy the requirements of the Chief Inspector (B.C. MEMPR 2008). Because the legislation is vague and subject to interpretation (by both the mining companies and the inspec- tors), there has been considerable variability in defned goals Author contributions: LHF identifed the need for a review; HWG, SAB, JVH, WCG, LHF determined the necessary components, identifed key references, and wrote the manuscript. 1 Department of Natural Resource Sciences, Thompson Rivers University, 900 McGill Road, Kamloops, BC V2E 0N1, Canada 2 Department of Biological Sciences, Thompson Rivers University, 900 McGill Road, Kamloops, BC V2E 0N1, Canada 3 Address correspondence to H. W. Garris, email hgarris@tru.ca 4 Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, 2360 East Mall, Vancouver, BCV6T 1Z3, Canada © 2016 Society for Ecological Restoration doi: 10.1111/rec.12322 March 2016 Restoration Ecology Vol. 24, No. 2, pp. 165–173 165