Bioprospecting challenges in unusual environments

The microbial ecology field is burgeoning. Year after year, improved sampling, culturing and bioinformatics tools contribute towards an apparently endless increase in microbial diversity. Massive access to genomic data and the development of single-cell genomic techniques have re-defined the tree of life by resolving many intraand interphylum level relationships and by including dramatic expansions such as the discovery of a new subdivision in the bacterial domain of life, or an astounding 16-fold increase in the number of known viral genes (Hug et al., 2011; Rinke et al., 2013; Paez-Espino et al., 2016). Scaling law-based calculations have led to the prediction that Earth is the home to more than 1 trillion microbial species (Locey and Lennon, 2016) let alone the intraspecies variation. This is indeed a huge number that may be better internalized with a simple calculation: if scientists were able to summarize in a one-page genome paper each one of the bacterial species on our planet and piled the 10 resulting pages one on top of another, the total height of the stacked articles would be 100 000 km, approximately a quarter of the distance from the Earth to the Moon. There is no doubt that we are dealing with a terrific amount of microbial diversity, and this puts on the table a double challenge: unveiling the myriad of microbial species still to be discovered and mining such a vast microbial diversity for novel biotechnological tools. Improving current methodologies for the analysis of omic data will be key to detect and identify novel species or gene sequences in massive datasets, whereas new culturing and screening techniques will be needed to exploit their industrial and biomedical applications (Vilanova and Porcar, 2016). Microbial diversity is everything except random: microorganisms are the result of evolution and adaptation. This provides us with an incredible arsenal of unique and useful pre-validated tools that can be used in a wide range of industrial applications. The search of these biological tools is what we know as bioprospecting, and it is nothing new. That said, past bioprospecting efforts have mainly focused on close, well-known environments such as soil, a rich source of antibiotics (Sherpa et al., 2015) and bacteria with insecticidal properties (Melo et al., 2014); or human gut, from which probiotic bacteria such as Lactobacillus spp. can be isolated (Halimi and Mirsalehian, 2016). Nevertheless, exotic, particular environments result in particular adaptations, and the understandable ease with which human or humanized environments can be sampled should not mask that most taxonomic and functional novelties lay somewhere else. Unusual environments remain poorly or unexplored to date although they are certainly valuable sources of novel products. As illustrated by the popular illustration ‘Flammarion engraving’, there is a world, metaphorically, beyond those shining stars we can easily see (Fig. 1). But, what is an unusual environment, or, more precisely, what is unusual enough? We consider an unusual environment as one that is both poorly explored, taxonomically distant from the human-associated microbiome and that is under extremophilic conditions. Interestingly, the three features tend to occur at the same time. It has to be stressed that some indoor or outdoor habitats