Pseudomonas sp., Strain L5B5: A Genomic and Transcriptomic Insight into an Airborne Mine Bacterium

Abstract

Mines, like other subterranean environments, have ecological conditions which allow the thriving of microorganisms. Prokaryotes and fungi are common inhabitants of mines, developing a metabolism suitable for growing in such inhospitable environments. The mine of Lousal, Portugal, is an interesting site for the study of microorganisms present in their galleries. Aerobiological studies resulted in the isolation of a Pseudomonas sp., strain L5B5, closely related to the opportunistic fish pathogen P. piscis MC042T, and to the soil bacteria P. protegens CHA0T, P. protegens Cab57, and P. protegens Pf-5. Strain L5B5 was able to inhibit the growth of the pathogenic bacteria Bacillus cereus, Staphylococcus aureus, and Acinetobacter baumanii, as well as the cave fungi Aspergillus versicolor, Penicillium chrysogenum, Cladosporium cladosporioides, Fusarium solani, and Ochroconis lascauxensis. In silico analyses based on de novo genome hybrid assembly and RNA-Seq, performing seven conditions based on culture and phases of growth resulted in the prediction and detection of genetic mechanisms involved in secondary metabolites, with the presence of a possible new gene cluster transcribed under the tested conditions, as well as feasible virulence factors and antimicrobial resistance mechanisms.