Studying the Genetic Potential of Cytobacillus pseudoceanisediminis from a Deep Subsurface Mineral Spring for the Synthesis of Biologically Active Substances

Abstract

Microorganisms are fundamental to global ecosystem functioning, playing crucial roles in biogeochemical cycles and producing diverse bioactive secondary metabolites. Extremophiles are promising sources of novel metabolites due to their adaptations to harsh environments. This study investigated the biosynthetic potential of the thermophilic, heavy metal-resistant bacterium Cytobacillus pseudoceanisediminis BNOᵀ, isolated from a deep subsurface mineral spring. Genomic analysis identified six biosynthetic gene clusters (BGCs): terpene-precursor, type III polyketide synthase (T3PKS), azole-containing RiPP-terpene, terpene, nonribosomal peptide synthetase (NRPS), and NRPS-independent (NI) siderophore. Comparative analysis revealed high homology (>95% identity) for five BGCs (T3PKS, RiPP-terpene, terpene, NRPS, NI-siderophore) with the marine sediment strain C. pseudoceanisediminis 2691 and related Cytobacillus species, indicating evolutionary conservation within the genus. The terpene-precursor cluster showed low homology (52.3% identity for core genes) and matched non-Cytobacillus species, suggesting potential horizontal gene transfer. Transcriptomic analysis under standard laboratory conditions (LB medium, 37°C) revealed constitutive expression (>90% of genes) for all BGCs except the NI-siderophore cluster (51.7% genes expressed). This constitutive expression suggests the basal importance of these metabolites for physiology or pre-adaptation to the native stressful environment and facilitates potential biotechnological exploitation. The presence of NRPS and siderophore clusters correlates with the strain’s exceptional heavy metal resistance. This study highlights C. pseudoceanisediminis BNOᵀ as a source of conserved and potentially novel BGCs, with significant biotechnological potential, particularly for bioremediation. Future work should characterize the metabolites produced and investigate BGC expression under stress conditions.