Molecular assessment on impact of uranium ore contamination in soil bacterial diversity Ekramul Islam, Pinaki Sar * Department of Biotechnology, Indian Institute of Technology, Kharagpur 721 302, India article info Article history: Received 30 June 2011 Received in revised form 25 July 2011 Accepted 5 August 2011 Available online 26 August 2011 Keywords: Uranium ore Impact Bacterial diversity 16S rRNA DGGE Real time PCR abstract Impact of uranium (U) ore and soluble uranium (at pH 4.0) contamination on agricultural soil bacterial diversity was assessed by using laboratory microcosms for one year. Diversity and abundance of metaboli- cally active bacterial populations in periodically collected microcosm’s samples were analyzed by extracting total RNA and preparation of cDNA followed by analysis of 16S rRNA gene by DGGE and real time PCR. DGGE analysis revealed prominent shift of soil bacterial population due to uranium ore contamination within 12 months while uranium ore along with soluble U completely destroyed the soil bacterial diversity within first six months. Real time PCR based analysis indicated 100e200 folds increase in 16S rRNA gene copies of total as well as individual bacterial taxa in both U ore amended and unamended soils in first six months while increase in incubation period upto 12 months showed reduction of the same only in U ore amended soil. Antagonistic effect of U ore contamination on soil bacterial diversity indicated the severe impact of U mining likely to have on nearby ecosystems. Role of U at acidic pH in destroying the diversity completely is note- worthy as it corroborated the disastrous consequence of acid mine drainage generated from U mine sites. Ó 2011 Elsevier Ltd. All rights reserved. 1. Introduction Activities associated with uranium mining and ore processing generate significant quantities of waste materials that cause severe hazard to mine adjoining ecosystems (Abdelouas, 2006; Lottermoser, 2010). Being the source of radioactivity, uranium ore and waste rocks harbor various radionuclides and heavy metals in their mineralized state which upon exposure to atmospheric conditions often allow release of such toxic elements in natural environments. Once released from its original mineral forms, U may exist as wide range of soluble, mobile, available and toxic species that spread in the ecosystem and cause environmental contamination interfering activity of natural ecosystem functions (Anderson and Lovley, 2002; Joner et al., 2007). In order to assess the impact of contamination on natural environment, microbial community structure and diversity has been identified as an effective tool. Microbes that afford ecological sustains are found to be very sensitive to even low concentration of contami- nants and often exhibit rapid response to environmental perturbation (Desai et al., 2009). With respect of heavy metal contamination, a number of studies have shown its negative impact on soil microbial diversity and function (Gans et al., 2005; Sobolev and Begonia, 2008; Stefanowicz et al., 2008; Bamborough and Cummings, 2009; Magalhães et al., 2011). It was also been noticed that as these communities get exposed to such contaminations for long period of time, adaptation with emergence of more tolerant species become evident (Schmidt et al., 2005; Frey et al., 2006; Joynt et al., 2006; Li et al., 2006). According to Gans et al. (2005) heavy metal pollu- tion can reduce the diversity of bacterial populations by 99.9% affecting especially the rarer taxa, whose activity may be functionally more significant. While impact of other heavy metal contamination on microbial community structure and function was studied by a number of investigators, effect of uranium, in particular (both as free uranyl ion and/or as U ore or U mine wastes) remain scarce. From bioreme- diation perspectives few studies have been conducted to assess in situ microbial communities within sites contaminated with uranium and other metals (Reardon et al., 2004; Fields et al., 2005; Brodie et al., 2006; Akob et al., 2007; Merroun and Selenska-Pobell, 2008). Fate of added uranium [U(VI)] in uranium mining waste sample and its interaction with bacterial population both in aerobic and anaerobic conditions were studied (Geissler and Selenska-Pobell, 2005; Geissler et al., 2009). Recently, microbial diversity from deep underground uranium mines was also demonstrated by few research groups (Rastogi et al., 2010). All these studies have emphasized on microbial community composition in uranium-mining/-contaminated envi- ronments and potentiality of indigenous bacteria to interact with uranium and other heavy metals. In comparison to all these work done, assessment of impact of uranium ore or soluble uranium on soil * Corresponding author. Tel.: þ91 3222 283754 (O), 283755 (R); fax: þ91 3222 278707, 255303. E-mail addresses: ekramul.rs@gmail.com (E. Islam), sarpinaki@yahoo.com (P. Sar). Contents lists available at ScienceDirect International Biodeterioration & Biodegradation journal homepage: www.elsevier.com/locate/ibiod 0964-8305/$ e see front matter Ó 2011 Elsevier Ltd. All rights reserved. doi:10.1016/j.ibiod.2011.08.005 International Biodeterioration & Biodegradation 65 (2011) 1043e1051