Genomic and metabolomic insights into carotenoid biosynthesis in a novel deep-sea bacterium, Paracoccus niotae sp. nov., isolated from an Arabian Sea seamount.

Abstract

Natural microbial carotenoids are increasingly recognized as alternatives to synthetic pigments because of their broad applications in the food, pharmaceutical, nutraceutical, cosmetic, feed, and aquaculture industries. In this study, a bright orange-pigmented deep-sea bacterium, strain NIOT.M2S5SZ12ᵀ, isolated from Arabian Sea seamount sediment, was comprehensively characterized to evaluate its carotenoid biosynthetic potential and taxonomic status. Phylogenetic analysis placed the strain within the genus Paracoccus, while whole-genome sequencing generated a 3.6 Mb draft genome with a GC content of 68.50 mol%. Genome-based taxonomic analyses yielded maximum digital DNA-DNA hybridization and average nucleotide identity values of 30.9% and 86.39%, respectively, confirming that the isolate represents a novel species within the genus. Comparative pan-genome analysis revealed an open pan-genome comprising 19,613 gene clusters, including 1,288 strain-specific genes. Phenotypic, physiological, and chemotaxonomic analyses further distinguished the isolate from closely related Paracoccus type strains. Genome mining using antiSMASH and KEGG pathway reconstruction identified key carotenoid biosynthesis genes (idi, crtE, crtB, crtI, crtY, crtZ, and crtW). The strain produced 67.93 ± 3.76 mg g⁻¹ dry biomass of crude pigment, and UHPLC-APCI-Orbitrap MS/MS confirmed the production of astaxanthin, zeaxanthin, canthaxanthin, retinal, and several apo-carotenoid derivatives. Based on comprehensive phenotypic, chemotaxonomic, phylogenetic, genomic, and metabolomic evidence, strain Z12 is proposed as Paracoccus niotae sp. nov. NIOT.M2S5SZ12ᵀ under the SeqCode framework. These findings establish Paracoccus niotae as a promising marine microbial resource for sustainable carotenoid production and biotechnology.