Application of functional metagenomics in the evaluation of microbial community dynamics in the Arabian Sea: Implications of environmental settings

Lidita Khandeparker; Dipesh Kale; Niyati Hede; Arga Chandrashekar Anil

doi:10.1016/j.jenvman.2024.123449

Application of functional metagenomics in the evaluation of microbial community dynamics in the Arabian Sea: Implications of environmental settings

J Environ Manage. 2024 Nov 29:373:123449. doi: 10.1016/j.jenvman.2024.123449. Online ahead of print.

Authors

Lidita Khandeparker¹, Dipesh Kale², Niyati Hede², Arga Chandrashekar Anil²

Affiliations

¹ CSIR-National Institute of Oceanography, Dona Paula, Goa, 403 004, India. Electronic address: klidita@nio.res.in.
² CSIR-National Institute of Oceanography, Dona Paula, Goa, 403 004, India.

PMID: 39615467
DOI: 10.1016/j.jenvman.2024.123449

Abstract

Ocean microbial communities form the base of marine food webs, facilitating energy transfer and nutrient cycling, thereby supporting higher trophic levels. We investigated their composition and functional profiles across depths (surface waters 0, 29, and 63 m and bottom waters 100, 150, and 200 m) in the central-eastern Arabian Sea (CEAS) using next-generation sequencing. It was hypothesized that the composition and functional diversity of these communities would be influenced by depth and environmental parameters. Our research showed that microbial communities vary with depth and are shaped by environmental factors like irradiance, temperature, dissolved oxygen, suspended particulate matter, chlorophyll a, and ammonia concentrations. Cyanobacteria (Prochlorococcus sp) and Mamiellaceae, belonging to picoeukaryotes, exhibited distinct depth-specific distributions up to subsurface chlorophyll maxima (SCM) at 63 m. On the other hand, a community shift in the microbial communities comprising Firmicutes, Bacteroidetes, and Actinobacteria phyla was observed at the deeper water depths. The profiling of functional genes pointed out the expression of carbon fixation by photosynthetic organisms at the surface (0, 29, and 63 m), which shifted to prokaryotic carbon fixation in deeper waters (0, 150, and 200 m). Microcosm experiments (mixing of surface water with water from the SCM) carried out simulating disturbances such as climate change forced mixing (cyclones), revealed shifts in microbial structure and function. It was observed that within 48 h, the carbon fixation activity changed from photosynthetic organisms to prokaryotes and indicated an increase in stress-related biosynthetic pathways such as expression of quorum sensing, biosynthesis of antibiotics, lipopolysaccharides, and secondary metabolites. These findings have implications for predictive modelling of food web dynamics and fisheries management in the context of climate change.

Keywords: Central-eastern Arabian sea; Functional metagenomics; Microbial diversity; Next gen sequencing (NGS); Nutrient enrichment.