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The Gram-negative <i>Pantoea eucrina</i> D2 was isolated from the marine sponge <i>Chondrosia reniformis</i>. 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 <i>Pantoea</i> cf. <i>eucrina</i> 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 <i>Staphylococcus aureus</i>, <i>Staphylococcus epidermidis</i> and a clinical isolate of the emerging food pathogen <i>Listeria monocytogenes</i>.