Comparative transcriptomics of the response of Escherichia coli to the disinfectant monochloramine and to growth conditions inducing monochloramine resistance David Berry a,1 , Diane Holder a,b,2 , Chuanwu Xi b , Lutgarde Raskin a, * a Department of Civil and Environmental Engineering, University of Michigan, 1351 Beal Ave, 107 EWRE Bldg, Ann Arbor, MI 48109-2125, USA b Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA article info Article history: Received 31 March 2010 Received in revised form 25 June 2010 Accepted 9 July 2010 Available online 27 July 2010 Keywords: Disinfection Gene expression Monochloramine Biofilms Drinking water abstract Escherichia coli growth in biofilms and growth at a suboptimal temperature of 20  C have been shown to decrease sensitivity to monochloramine (Berry, D., C. Xi, L. Raskin. 2009. Environ. Sci. Technol. 43, 884e889). In order to better understand why growth conditions affect sensitivity to monochloramine, a comparative transcriptomic approach was used to identify common patterns of differentially-expressed genes under these growth conditions and during monochloramine exposure. This approach revealed a set of differentially- expressed genes shared under multiple conditions (planktonic growth at 20  C, biofilm growth, and exposure of planktonic cells to monochloramine), with nine genes shared under all three conditions. Functional gene categories enriched in the shared gene sets included: general metabolic inhibition, redox and oxidoreductase response, cell envelope integrity response, control of iron and sulfur transport metabolism and several genes of unknown function. Single gene deletion mutant analyses verified that loss of 15 of the 24 genes up-regulated during monochloramine exposure as well as during other tested conditions increased E. coli sensitivity to monochloramine up to two fold. Constitutive expression of down-regulated genes in single gene mutants yielded mixed results, indi- cating that the expression of some down-regulated genes actually decreases sensitivity to monochloramine. These results contribute to the understanding of the bacterial response to disinfectants by characterizing the overlap between growth condition associated stress responses and monochloramine-associated stress responses. This characterization high- lights the bacterial responses responsible for decreased sensitivity to monochloramine under different growth conditions. ª 2010 Elsevier Ltd. All rights reserved. 1. Introduction Escherichia coli survival in drinking water supply systems is sometimes observed despite the widespread practice of adding oxidative disinfectants (e.g., free chlorine, chlora- mines) (Edberg et al., 2000). Free chlorine (hypochlorous acid) is the best studied drinking water disinfectant (Small et al., 2006; Winter et al., 2008), but recent work comparing three * Corresponding author. Tel.: þ1 734 647 6920; fax: þ1 734 763 2275. E-mail address: raskin@umich.edu (L. Raskin). 1 Current address: Department of Microbial Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria. 2 Current address: Proficiency and Validation Services, Foreign Animal Disease Diagnostic Laboratory, USDA, APHIS, PIADC, Orient Point, NY, USA. Available at www.sciencedirect.com journal homepage: www.elsevier.com/locate/watres water research 44 (2010) 4924 e4931 0043-1354/$ e see front matter ª 2010 Elsevier Ltd. All rights reserved. doi:10.1016/j.watres.2010.07.026