EXPLOITING MARINE BIODIVERSITY: THE POTENTIAL OF UNCULTIVABLE MICROORGANISMS FOR THE IDENTIFICATION OF NOVEL ANTIMICROBIAL COMPOUNDS

Antimicrobial resistance has spread dramatically in last 60 years leading to an increase in the number of deaths due to infection diseases. The excessive and often inappropriate use of antimicrobial drugs has led to the development of a new group of microorganisms, the Multidrug Resistant (MDR) bacteria, which show resistance toward the most common antibiotics. This phenomenon is becoming a serious threat to the public health and the economy. The bioprospecting of marine and extreme environments has yielded a noteworthy number of novel molecules with biotechnological applications from a wide range of macro and microorganisms, representing a very promising strategy to counteract MDR bacteria. The main gap is to have access to the real microbial biodiversity because less than 1% of microorganisms is cultivable in the laboratory conditions. In this project, new antimicrobial compounds have been discovered from bacteria and fungi by different strategies. In the first work, following a bioprospecting pipeline, Antarctic shallow water sediments were used to isolate microorganisms that were screened for their capability to inhibit the growth of selected MDR bacteria. A bioassay-guided purification approach allowed the identification of rhamnolipids (a class of glycolipids well known as biosurfactants) produced by a Pseudomonas gessardii strain able to strongly inhibit MDR strains, in particular Gram-positive bacteria. These molecules have many biotechnological applications, especially in bioremediation field and, over last years, as antimicrobial compounds. The second work focuses the attention on the improvement of cultivation methods, exploiting a new device, the Miniaturized Culture Chip (MCC), for the isolation of “not-common” or novel bacteria. The innovation of this system is the possibility to grow microorganisms directly in their natural habitat simulating environmental conditions. By using the MCC an unexplored Antarctic strain, Aequorivita sp., was isolated. A genome mining approach on Aequorivita sp. was applied identifying the main biosynthetic gene clusters. The evaluation of its bioactive potential led to the discovery of three new intracellular aminolipids showing antimicrobial activity against methicillin resistant Staphylococcus aureus (MRSA) and anthelmintic activity against the nematode Caenorhabditis elegans. This was the first report that demonstrated the bioactivity of this strain and stimulates the research of new cultivation method by which obtain new and unexplored sources of compounds. The third work instead, gave more attention to marine fungi, well-known producers of secondary metabolites. Extracts of nine fungi isolated from the green alga Flabellia petiolata, collected from the Mediterranean Sea, resulted to be active against some pathogen bacteria. In particular, the chemical profiling of three marine fungi, Beauveria bassiana (MUT 4865), Knufia petricola (MUT 4979) and a new fungal species (MUT 4861) expressed a high compounds variability, novelty and activity. The successful results of this project that combines the bioprospecting of hostile environments with the optimisation of the critical step of the “biodiscovery pipeline” confirmed the huge potential of microorganisms as producers of novel bioactive compounds and demonstrated that this research field is far from to be fully exploited.