REVIEW A systematic strain selection approach for halotolerant and halophilic bioprocess development: a review Joao M. Uratani • Rajkumari Kumaraswamy • Jorge Rodrı ´guez Received: 26 February 2014 / Accepted: 18 May 2014 / Published online: 10 June 2014 Ó Springer Japan 2014 Abstract Halotolerant and halophilic microorganisms have potential applications in a number of very relevant environmental and industrial bioprocesses, from wastewa- ter treatment to production of value-added chemicals. While numerous microbial strains have been identified and studied in the literature, the number of those successfully used in industrial applications is comparatively small. Literature is abundant in terms of characterisation of spe- cific strains under a microbiology perspective; however, there is a need for studies tackling the selection of strains for bioprocess applications. This review presents a data- base of over 200 halophilic and halotolerant prokaryote strains compiled from taxonomic microbiological resources and classified by trophic groups as well as by their salinity, pH and temperature tolerance and optimum ranges, all under a process development perspective. In addition to this database, complementary systematic approaches for the selection of suitable strains for a given trophic activity and environmental conditions are also presented. Both the database and the proposed selection approaches together constitute a general tool for process development that allows researchers to systematically search for strains capable of specific substrate degradations under specific conditions (pH, T, salinity). Many exiting established halotolerant and halophilic environmental and industrial bioprocesses appear to have been developed following strategies in line with the systematic approaches proposed here. Keywords Strain selection Á Halophiles Á Extremophiles in biotechnology Á Industrial applications List of abbreviations C2M Conditions-to-Microorganisms approach for strain selection M2S Microorganisms-to-Substrates approach for strain selection PHA Polyhydroxyalkanoates S2C Substrates-to-Conditions approach for strain selection Introduction There is a great biotechnological potential hidden in microorganisms adapted to non-conventional habitats. These microorganisms are exposed to different conditions of temperature, pH, and salinity. Enzymes from archaeal and prokaryotic strains isolated from these conditions have been characterised and are used nowadays in different bioprocesses (Ravot et al. 2006). Likewise, the strains themselves have also been studied for their potential to replace currently used microbes or to generate new pro- cesses that have industrial applications (Demirjian et al. 2001; Egorova and Antranikian 2005; Bonete and Martı ´- nez-Espinosa 2011; Atomi et al. 2011). These microorganisms, called extremophiles, are a source of interest due to the fact that they thrive at the Communicated by S. Albers. Electronic supplementary material The online version of this article (doi:10.1007/s00792-014-0659-4) contains supplementary material, which is available to authorized users. J. M. Uratani Á R. Kumaraswamy Á J. Rodrı ´guez (&) Institute Center for Water and Environment (iWATER), Department of Chemical and Environmental Engineering (CEE), Masdar Institute of Science and Technology, PO Box 54224, Abu Dhabi, UAE e-mail: jrodriguez@masdar.ac.ae 123 Extremophiles (2014) 18:629–639 DOI 10.1007/s00792-014-0659-4