Exploring the depths: Metagenomic profiling of cold seep bacterial communities and isolation of hydrocarbon-degrading microbes from the Cauvery-Mannar basin

Abstract

Cold seeps are unique ecosystems characterized by the presence of endemic communities reliant on microorganisms that survive through chemosynthesis, utilizing sulfide, methane, hydrocarbons, and other reduced compounds. Recently, a cold seep was discovered in the Cauvery-Mannar basin during an expedition aboard the research vessel ORV Sindhu Sadhana which led to the investigation into the distribution and isolation of microorganisms within the sediment layers (0–6 cm). Metagenomic analysis based on V3-V4 region of the sediment's bacterial community revealed a prevalence of bacteria associated with methane and hydrocarbons. Dominant phyla included Campilobacterota (20–25%), Proteobacteria (15–25%), Firmicutes (15-20%), Desulfobacterota (10–18%), Chloroflexi (5–10%), and Actinobacterota (5–7%). In-vitro isolation of hydrocarbon-degrading bacteria using minimal media supplemented with 1% crude oil gave rise to 15 bacterial strains. Molecular identification of six isolates (chosen based on the dense growth obtained in agar plates) revealed their affiliation with the genera Acinetobacter, Rhodococcus, Acinetobacter, and Bacillus. This comprehensive study constitutes the first report on the bacterial community structure found in sediments from a cold seep of Cauvery-Mannar basin, along with the successful isolation and identification of hydrocarbon-degrading bacteria.