Integrated Multi-Omics Analyses Reveal Insights Into Rare Microbial Biosphere Associated With Deep-Sea Water in the Central Indian Ocean

The study investigates the unique microbial diversity in deep-sea waters of the Central Indian Ocean. Using advanced genomic techniques, the microbial community composition and metabolic profiles at a depth of 1600 meters is explored. The study utilized metagenomics, single-cell genomics, and untargeted exometabolomics to identify and characterize both abundant and rare microbial groups, including "microbial dark matter" (microbes that cannot be cultivated in the lab and are often present in very low abundances).Results revealed a diverse microbial community dominated by bacteria, particularly Pseudomonadota and Actinomycetota, with differences in taxonomy between Illumina and nanopore sequencing data. Further, successful assembly of metagenome-assembled genomes (MAGs) and single amplified genomes (SAGs), enabled identification of rare groups such as Patescibacteria and Armatimonadota that are largely uncultivated. Functional profiling highlighted pathways for carbon and nitrogen metabolism, emphasizing hydrocarbon degradation and denitrification.The exometabolomic analysis identified various metabolite classes, dominated by monoacylglycerols and unsaturated fatty acids. This research enhances our understanding of the role of rare and unculturable microbes in deep-sea ecosystems, offering new insights into their contribution to biogeochemical cycles and potential applications in bioremediation.