Abstract
Bioprospecting expeditions are often performed in remote locations, in order to access previously unexplored samples. Nevertheless, the actual potential of those samples is only assessed once scientists are back in the laboratory, where a time-consuming screening must take place. This work evaluates the suitability of using Nanopore sequencing during a journey to the Tabernas Desert (Spain) for forecasting the potential of specific samples in terms of bacterial diversity and prevalence of radiation- and desiccation-resistant taxa, which were the target of the bioprospecting activities. Samples collected during the first day were analyzed through 16S rRNA gene sequencing using a mobile laboratory. Results enabled the identification of locations showing the greatest and the least potential, and a second, informed sampling was performed focusing on those sites. After finishing the expedition, a culture collection of 166 strains belonging to 50 different genera was established. Overall, Nanopore and culturing data correlated well, since samples holding a greater potential at the microbiome level also yielded a more interesting set of microbial isolates, whereas samples showing less biodiversity resulted in a reduced (and redundant) set of culturable bacteria. Thus, we anticipate that portable sequencers hold potential as key, easy-to-use tools for in situ-informed bioprospecting strategies.
Highlights
Scaling laws have predicted that the Earth is home to 1 trillion (1012) microbial species (Locey and Lennon, 2016)
This work is a proof of concept of the use of portable Nanopore sequencing as a tool for guiding and informing bioprospecting activities during
Oxford Nanopore Technologies (ONT) sequencing is a well-established technique for studying microbial communities (Ciuffreda et al, 2021), and portable sequencing (i.e., MinION) has been applied to characterize microbiomes in some of the most remote places of the universe that are accessible to human beings (Castro-Wallace et al, 2017; Goordial et al, 2017; Johnson et al, 2017; Gowers et al, 2019; Burton et al, 2020)
Summary
Scaling laws have predicted that the Earth is home to 1 trillion (1012) microbial species (Locey and Lennon, 2016). A large fraction of this biodiversity still remains to be explored and very likely harbors novel molecules, enzymes and/or biological activities with potential applications in industrial processes, drug development, cosmetics or environment-related issues (i.e., bioremediation). The search for these novel products from biological sources and, in particular, from microorganisms, is known as microbial bioprospecting. Extreme environments, such as the deep sea or hyper-arid deserts, are of special interest for bioprospecting studies, as they tend to be sources of undiscovered biodiversity (Bull and Goodfellow, 2019). Spatial changes have been observed at microscale: for example, in gradients of soil depths as recently demonstrated with the SoilBox system (Bhattacharjee et al, 2020)
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