Decoding Copper Adaptation mechanisms in Marine Bacteria through Multi-Omics and Network Analysis

This study, conducted in collaboration with the Stazione Zoologica Anton Dohrn (Naples, Italy), investigates adaptative molecular mechanisms of marine bacteria isolated from metal-contaminated sediments in the Gulf of Naples and Bagnoli. [1][2] All isolates were screened by determining the maximum tolerance concentration (MTC) to As, Cd, Co, Cu, Zn, and Pb.[2][3] Among them, Pseudohalocynthiibacter aestuariivivens P96 was selected for in-depth investigation under copper exposure. Copper was chosen for its dual significance as both an essential enzymatic cofactor and a strategic raw material recognized under the European Union’s Critical Raw Materials Act [4], making it relevant for both bioremediation and bioleaching applications.[5] Genomic and proteomic analyses were performed to elucidate the mechanisms underlying bacterial adaptation to copper. MRGs screening revealed determinants related to copper homeostasis, including multicopper oxidases, efflux systems, and transports then confirmed by differential proteomic analysis. [6] Due to the phylogenetic distance of this isolate from reference organisms, conventional annotation and pathway reconstruction tools proved largely ineffective; to overcome this limitation, a correlation-based approach integrating omics data was applied for enabling the reconstruction of putative pathways involved in copper response, further supported by literature validation. [7] This integrative omics strategy provides new insights into bacterial adaptation to copper stress and demonstrates the effectiveness of correlation-based network protein analysis for functional inference in non-model organisms, identifying promising candidates for in situ bioremediation and bioleaching in metal-contaminated environments.