Metagenomics of hyperthermophilic environments: Biodiversity and biotechnology

The field of thermophilic microbiology was born in the late 1970s with the pioneering work of Brock (Thermophiles biodiversity, ecology, and evolution. Springer, Boston, pp. 1–9, 2001) and dramatically expanded through the ’80s with the isolation of hyperthermophiles by Stetter (FEMS Microbiol Rev 18:149–158, 1996). The development of SSU rRNA phylogenetics revealed the complexity and diversity of prokaryotic phylotypes on biotopes widely differing in extreme conditions (e.g. spanning gradients of pH between 0 and 10 and temperatures from 60 °C to over 120 °C, respectively). Sites of volcanic activity all over the Earth’s surface and under the sea provide a variety of different environments for extremophilic microorganisms. Hot springs populated by hyperthermophiles (Topt > 65 °C), the majority of which belonging to the domain of Archaea, are very diverse and some of them show combinations of other extreme conditions, for example, acidic, alkaline, high pressure, and high concentrations of salts and heavy metals (Cowan et al. in Curr Opin Microbiol 25:97–102, 2015). Archaea inhabiting hot springs are considered to be the closest living descendants of the earliest living forms on Earth and their study provide insights into the origin and evolution of life (Woese et al. in Proc Natl Acad Sci USA 87:4576–4579, 1990; Olsen et al. in J Bacteriol 176:1–6, 1994). As with all studies of environmental microbiology, our understanding of the function of (hyper)thermophilic microbial consortia has lagged substantially behind. However, recent advances in ‘omics’ technologies, particularly within a system biology context, have made significant progresses into the prediction of in situ functionality (Cowan et al. in Curr Opin Microbiol 25:97–102, 2015). Most extremophilic microorganisms are recalcitrant to cultivation-based approaches (Amann et al. in Microbiol Rev 59:143–69, 1995; Lorenz et al. in Curr Opin Biotechnol 13:572–577, 2002); therefore, culture-independent metagenomic strategies are promising approaches to assess the phylogenetic composition and functional potential of microbial communities living in extreme environments (López-López et al. in Life 3:308–320, 2013). In addition, these approaches implement tremendously the access to enzymes from (hyper)thermophilic microorganisms that have important potential applications in several biotechnological processes. We report here on the state-of-the-art of the metagenomic surveys of different hot springs (T > 65 °C) (Table 5.1) and on the recent advance in the discovery of new hyperthermostable biocatalysts of biotechnological interest from metagenomic studies of these extreme environments.