Siderophore identification in microorganisms associated with marine sponges by LC-HRMS and a data analytic approach in R.

Abstract

Siderophores are pivotal iron-acquisition biomolecules integral to microbial survival, pathogenicity, and ecology. Elucidating these compounds offers critical insights into the microbial dynamics of marine holobionts and potential therapeutic applications. In this study, we present a culture-independent, data-centric strategy to identify siderophores from the microbiome of three marine sponge species: Dragmacidon reticulatum, Aplysina fulva, and Amphimedon viridis. Utilizing Liquid Chromatography-High Resolution Mass Spectrometry (LC-HRMS) coupled with a custom R-based analytical workflow (XCMS and MetaboAnnotation), we successfully annotated 59 potential siderophores, 41 of which were confirmed via chromatographic profiling. We employed a rigorous validation pipeline, utilizing multiple iron-adduct calculations [M-2H+Fe]+, [M-H+Fe]2+, [2M-2H+Fe]+, high mass accuracy thresholds (<3 ppm), and retention time precision (CV < 2%). Notably, iron supplementation during extraction did not significantly alter siderophore detection, suggesting constitutive production or environmental saturation. This workflow bypasses the limitations of traditional cultivation, revealing a diverse landscape of iron-chelating metabolites--including Ferricrocin, Aeruginic acid, and Madurastatin--directly within the sponge holobiont.