Analysis of the antimicrobial susceptibility of the ionizing radiation-resistant bacterium Deinococcus radiodurans: implications for bioremediation of radioactive waste

Abstract

Deinococcus radiodurans R1 is one of the most resistant bacteria to chronic ionizing radiation ever identified. Therefore, Deinococcus radiodurans shows promise in the bioremediation of mixed radioactive wastes. Nuclear wastes have been demonstrated to host bacteria containing genes for antimicrobial production (Bagwell et al. PloS ONE 3:e3878, 2008; Bai et al. Chem Biol 13:387–397, 2006; Phillips et al. Int J Syst Evol Microbiol 52:933–938, 2002), which may represent a constraint on the bioremediation potential of Deinococcus radiodurans. In this context, the aim of this work is to investigate the antimicrobial susceptibility of D. radiodurans through in silico and in vitro approaches. In silico, we initiated our analyses by retrieving genes that are predicted to confer to D. radiodurans resistance to antimicrobials based on the Antibiotic Resistance Genes Database (ARDB), the Rapid Annotations using Subsystems Technology (RAST), and the automatic hierarchical classification of proteins (ProtoNet) servers. Among 19 retrieved sequences of D. radiodurans, six genes were functionally re-annotated as antimicrobial resistance genes, and only two genes were found to possess the radiation/desiccation response motif (RDRM). In vitro, we found that D. radiodurans is sensitive to 40 tested antimicrobials, and it was resistant to one macrolide (spiramycin) and to three quinolones (ofloxacin, ciprofloxacin, and nalidixic acid). The resistance of D. radiodurans to these quinolones was discussed based on different possibilities. Moreover, in silico analyses indicated that the investigated 19 genes of D. radiodurans from ARDB, RAST, and ProtoNet encode translatable messenger ribonucleic acids (mRNAs) related to resistance to antimicrobials. These data together with the antibiograms of D. radiodurans represent a suggestive evidence that the majority of these genes encode non-functional proteins or belong to inefficient biochemical pathways. The susceptibility of D. radiodurans to these antimicrobials limits its potential for bioremediation of nuclear waste and further genetic engineering is needed depending on the site to be depolluted.