Molecular Network and Culture Media Variation Reveal a Complex Metabolic Profile in Pantoea cf. eucrina D2 Associated with an Acidified Marine Sponge

Abstract

The Gram-negative Pantoea eucrina D2 was isolated from the marine sponge Chondrosia reniformis. Sponges were collected in a shallow volcanic vents system in Ischia island (South Italy), influenced by CO2 emissions and lowered pH. The chemical diversity of the secondary metabolites produced by this strain, under different culture conditions, was explored by a combined approach including molecular networking, pure compound isolation and NMR spectroscopy. The metabolome of Pantoea cf. eucrina D2 yielded a very complex molecular network, allowing the annotation of several metabolites, among them two biosurfactant clusters: lipoamino acids and surfactins. The production of each class of metabolites was highly dependent on the culture conditions, in particular, the production of unusual surfactins derivatives was reported for the first time from this genus; interestingly the production of these metabolites only arises by utilizing inorganic nitrogen as a sole nitrogen source. Major components of the extract obtained under standard medium culture conditions were isolated and identified as N-lipoamino acids by a combination of 1D and 2D NMR spectroscopy and HRESI-MS analysis. Assessment of the antimicrobial activity of the pure compounds towards some human pathogens, indicated a moderate activity of leucine containing N-lipoamino acids towards Staphylococcus aureus, Staphylococcus epidermidis and a clinical isolate of the emerging food pathogen Listeria monocytogenes.

Combining OSMAC Approach and Untargeted Metabolomics for the Identification of New Glycolipids with Potent Antiviral Activity Produced by a Marine Rhodococcus

“…As a fact, through culture media variation (i.e., varying the concentration of carbon, nitrogen, phosphorous, inorganic salts, etc. ), it is possible to upregulate or trigger the production of certain secondary metabolites produced by talented microorganisms [7,[46][47][48]. In this study, the OSMAC strategy associated to bioassays allowed the selection of a specific growth condition expressing unique, structurally related metabolites, as highlighted by molecular networking (MN).…”

“…In this study, the OSMAC strategy associated to bioassays allowed the selection of a specific growth condition expressing unique, structurally related metabolites, as highlighted by molecular networking (MN). MN resulted to be an effective strategy to assess the effects of different culture conditions on the microbial metabolism and shorten dereplication time [48].…”

Antiviral Activity of Vitis vinifera Leaf Extract against SARS-CoV-2 and HSV-1

“…MZmine [ 53 ] and GNPS [ 54 ] software were used to convert and analyze the raw MS data, and finally Cytoscape built the complex network shown in Figure 1 . Each node indicates a precursor ion, the node size is strongly related to its abundance in the sample (sum precursor intensity), and the edges size between two nodes is directly dependent on their MS/MS spectra similarity (cosine score) [ 55 ]. Analysis of GNPS results together with data manual curation evidenced the presence in the network of one big flavonoids cluster together with a smaller one belonging to digalactosylmonoacylglycerol (DGMG) lipids; other unpaired nodes have also been identified during GNPS analysis ( Figure 1 ).…”

Novel Glycerophospholipid, Lipo- and N-acyl Amino Acids from Bacteroidetes: Isolation, Structure Elucidation and Bioactivity

“…They belong to a growing family of microbial secondary metabolites isolated from bacteria [ 22 , 23 ], fungi [ 21 ], or from environmental DNA expressed in heterologous hosts such as E. coli [ 16 , 17 , 18 , 19 , 20 ]. It is hypothesized that these lipids are possible signaling molecules with a wide range of biological activities from anti-cancer therapy targets to antimicrobial lipids [ 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 ]. With no antimicrobial activity observed, further studies are necessary to elucidate their biological function.…”

“…The latter are found in all biological systems, but their functions remain unclear. It is hypothesized that these lipids are putative signaling molecules with a wide range of biological activities [ 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 ].…”