Deep-sea life associated with sediments and polymetallic nodules from the Central Indian Ocean Basin: Insights from 18S metabarcoding

Abstract

The eukaryotic diversity of ocean sediments and polymetallic nodules (PMN) from the Central Indian Ocean Basin (CIOB) is scarcely characterized and molecular studies are lacking, comprising a key research gap. This study aimed to leverage 18S rRNA gene amplicon metabarcoding of environmental DNA (eDNA) to describe the eukaryotic diversity of ocean sediments and PMN from the CIOB. Sediment and PMN samples were obtained at a depth of 5000 m from three CIOB ocean floor sites: Impact Reference Zone (IRZ), Preservation Reference Zone (PRZ), from the PMN International Seabed Authority Contract area of the Government of India, and a location outside the proposed mining zone named BC20. DNA was isolated and the 18S rRNA V9 region was amplified using primers 1391f and EukBr targeting approximately 150bp. Taxonomy was assigned using the reference databases: MZGDB database (MetaZoo WorldAtlas Database) for Animalia and SILVA138 release for Fungi and Protista. Alpha and beta diversities were calculated using the reads assigned to known phyla. In total, 11078041 paired-end reads were generated and 1327 ASVs were assigned to the kingdom level, while 297 were assigned to a minimum of phylum level for Animalia (213 ASVs), Fungi (66 ASVs), and Protista (18 ASVs). The taxa observed included Annelida, Arthropoda, Bryozoa, Chordata, Cnidaria and Mollusca; these are the phyla observed encompassing the 29 Animalia taxa. In total, 3 phyla from Fungi, Ascomycota, Basidiomycota, and Mucuromycota, and 8 other phyla, Amoebozoa, Apicomplexa, Ciliophora, Dinoflagellata, Euglenozoa, Heterolobosea, Orchrophyta and Retaria were noted. Sediment and nodule communities from the same sampling sites were clustered in ordination plots. This study is a pioneering effort to document deep-sea biodiversity in the Central Indian Ocean Basin (CIOB) using the eDNA metabarcoding method. With the hard substrates in the CIOB hosting a rich variety of flora and fauna, future mining activities could threaten these ecosystems. By providing a vital baseline for biodiversity assessments, the study highlights the necessity of extensive sampling to facilitate ongoing monitoring and mitigate potential impacts from exploration and mining.