Bacterial community characterization and relationship in the gut of deep-sea holothurians and sediment from the Northern Indian Ocean

Abstract

Sea cucumbers, widely distributed benthic invertebrates in diverse deep-sea habitats, rely on their gut bacterial communities for essential functions including energy metabolism, biological adaptation, and health. However, the gut bacterial community of deep-sea holothurians in the Indian Ocean remains poorly understood. We used 16S rRNA gene sequencing to characterize bacterial communities in the guts of sea cucumbers and surrounding sediments from two distinct regions of the northern Indian Ocean: the Ninety-East Ridge and the Arabian Sea Basin. This study investigates the composition, diversity, predicted functions, co-occurrence networks, and assembly processes of gut bacterial communities. Alpha diversity of gut bacterial communities did not differ significantly between the two regions. Based on principal coordinate analysis, the bacterial communities of gut formed a distinct cluster from the sediment communities. Actinobacteriota, Proteobacteria, Firmicutes, Chloroflexi, and Bacteroidota were the dominant phyla in both gut and sediment bacterial communities. In the Ninety-East Ridge, the gut microbial network exhibited a higher proportion of positive correlation than the sediment network, suggesting a greater potential for cooperative interactions. Compared to sediment communities, functional predictions indicated that gut communities were enriched in metabolic pathways, including those for amino acid, glycan, vitamin, and lipid metabolism. Stochastic processes were predominant in gut bacterial community assembly, whereas deterministic processes dominated in sediment bacterial communities. This study provides critical insights into the gut microbiota of deep-sea holothurians, advancing our understanding of microbial ecology in extreme marine environments.