The depth code: Deconstructing the molecular architecture of marine protists in a tropical marginal sea

Abstract

The Bay of Bengal (BoB) is one of the most stratified and dynamic marginal seas, influenced by monsoonal forcing, riverine freshwater input, and complex hydrography. While the region's physicochemical variability is well studied, the diversity and depth-related structure of marine protist communities remain underexplored, especially in offshore and subsurface waters. In this study, we used high-throughput sequencing of the 18S rRNA V4 region to investigate marine protist diversity across three depths: surface (30m and 75m), mid (100m and 150m), and bottom (300m) at stations spanning northern and southern BoB. Multivariate analyses (RDA and NMDS) revealed distinct vertical community structuring driven by key environmental variables such as temperature, Chl-a, nitrate, salinity, and silicate. Surface communities were dominated by Pelagomonas, Ostreococcus, Bathycoccus, and Chloropicon, associated with warm, high-chlorophyll, oligotrophic surface waters. Mid-depth layers were characterized by a more heterogeneous assemblage, including Cafeteria, Cladococcus, and Caecitellus, indicative of microbial loop activity and particle-associated niches. Bottom depths showed a shift toward functionally distinct taxa such as Chromidina, Icthyodinium, and Auloscena, associated with silicate-rich, low-oxygen, and detritus-rich environments. Network analyses revealed a decrease in co-occurrence complexity with depth but an increase in modularity, reflecting environmental filtering and niche specialization. This study presents one of the first comprehensive vertical profiles of marine protists in the offshore BoB and underscores the importance of integrating molecular and ecological analyses to understand microbial diversity and biogeochemical functioning in tropical stratified oceans.