Deep Subseafloor Fungi as an Untapped Reservoir of Amphipathic Antimicrobial Compounds

Abstract

The evolving global threat of antimicrobial resistance requires a deep renewal of the antibiotic arsenal including the isolation and characterization of new drugs. Underexplored marine ecosystems may represent an untapped reservoir of novel bioactive molecules. Deep-sea fungi isolated from a record-depth sediment core of almost 2000 m below the seafloor were investigated for antimicrobial activities. This antimicrobial screening, using 16 microbial targets, revealed 33% of filamentous fungi synthesizing bioactive compounds with activities against pathogenic bacteria and fungi. Interestingly, occurrence of antimicrobial producing isolates was well correlated with the complexity of the habitat (in term of microbial richness), as higher antimicrobial activities were obtained at specific layers of the sediment core. It clearly highlights complex deep-sea habitats as chemical battlefields where synthesis of numerous bioactive compounds appears critical for microbial competition. The six most promising deep subseafloor fungal isolates were selected for the production and extraction of bioactive compounds. Depending on the fungal isolates, antimicrobial compounds were only biosynthesized in semi-liquid or solid-state conditions as no antimicrobial activities were ever detected using liquid fermentation. An exception was made for one fungal isolate, and the extraction procedure designed to extract amphipathic compounds was successful and highlighted the amphiphilic profile of the bioactive metabolites.

Keywords: amphipathic compounds; antimicrobial metabolites; deep subseafloor fungi; solid-state fermentation.

Figure 1

Antimicrobial spectrum of the 28 deep subseafloor antimicrobial producing fungal isolates.

Figure 2

Venn diagram summarizing the spectrum of activity of the 28 antimicrobial producing deep subseafloor fungal isolates.

Figure 3

Antimicrobial activity along the sediment core. (A) Antimicrobial activity (%) expressed as a function of depth (size of the circles is directly linked to the number of screened fungal isolates, from one isolate (1884 mbsf) to 22 isolates (34 mbsf); (B) Relationship between antimicrobial activity (%) and bacterial Operational Taxonomic Unit (OTU) number (used as a proxy to estimate the complexity of the different sediment samples). The number of prokaryotic OTU was 28, 31, 26, 14 and 6 between 4–6 mbsf, 15–12 mbsf, 24–37 mbsf, 346–403 and 1827–1884 mbsf, respectively. The reader is referred to Ciobanu et al. [13].

Figure 4

Antimicrobial activity after extraction. : size of the inhibition zone 2, 3 and 5 mm. ✓ Presence, or ✗ absence of genes coding PKS I, PKS III, NRPS, PKS-NRPS and TPS [15]. F10-90: C18-SPE fraction eluted with acetonitrile 90%. OP: Organic phase. In bracket the concentration (mg/mL) of the crude extract. Na: Not assayed