Bathymetry and environmental features govern the microbial communities in mesopelagic sediments of the Lakshadweep Islands of India

Mesopelagic sediments represent a critical yet understudied component of marine ecosystems, where environmental gradients strongly influence microbial community structure and function. This study profiles prokaryotic and fungal communities in the sediments along a bathymetric transect (500–1000 m) on the upper continental slope of the Lakshadweep Sea to identify community assembly processes and environmental drivers. Mesopelagic sediments supported diverse prokaryotic and fungal assemblages, with prokaryotes exhibiting higher α-diversity indices than fungi, indicating differential ecological adaptation of prokaryotic and fungal groups. Bacteria dominated over Archaea, with Firmicutes, Chloroflexi, Bacteroidota, Proteobacteria, and Desulfobacterota as the major prokaryotic phyla. Ascomycota and Basidiomycota were the major fungi. Diversity varied significantly (p ≤ 0.05) with depth, and most microbes were habitat specialists, indicating strong vertical structuring. The FEAST analysis revealed a limited proportional contribution of microbial communities in deeper sediments from 500 m. Beta nearest taxon index analysis suggested a dominant role of deterministic processes in governing the microbial community assembly. Canonical correspondence analysis identified temperature and DO as key drivers of prokaryotes, and nitrogen and temperature for fungi. Depth was significantly correlated (p ≤ 0.05) with the relative abundance of certain microbial taxa, including a decline in bacterial abundance and an increase in archaeal abundance, as well as positive associations with Dadabacteria, Halobacterota, and Chytridiomycota. This first study from the Lakshadweep Sea provides new insights into tropical mesopelagic sediment microbial diversity and community assembly, highlighting bathymetric and environmental controls that shape the prokaryotic and fungal communities.