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

Authors: Dineshram Ramadoss, Bharath S. Ammanabrolu, Aneesha Acharya, Jojy John, and Baban Ingole

Journal & Year: Deep-Sea Research Part II 222 (2025) 105487

BLUF: Environmental DNA from 5 km-deep sediment and nodule samples in India’s polymetallic-nodule lease block yielded more than eleven million sequence reads and 8,827 high-quality ASVs. Of these, 297 could be confidently assigned to eukaryotic phyla, revealing six metazoan phyla, three fungal phyla, and eight protistan phyla. Community patterns segregate by station and substrate, providing a molecular baseline critical for spatial planning and monitoring ahead of mineral recovery operations.

With commercial interest rising in the Central Indian Ocean Basin, regulators require robust biodiversity baselines. Ramadoss et al. collected multi-corer samples at an impact reference zone (IRZ), a preservation reference zone (PRZ), and an off-lease control (BC20). DNA extracted from pooled 0-5 cm sediments and from cleaned, crushed nodules was amplified using 1391f/EukBr primers targeting the 18S rRNA V9 region and sequenced on an Illumina HiSeq X platform. Conservative bioinformatic thresholds retained 15 percent of ASVs for taxonomic interpretation, ensuring high confidence despite sparse reference data.

Sediments and nodules share only about one-third of their assigned ASVs; Figure 2 of the article shows 164 unique to nodules and 219 unique to sediments, emphasizing the micro-habitat distinction. Shannon diversity values (Figure 6) range from 2.5 in BC20 sediments to 3.8 in IRZ nodules, indicating richer, more evenly distributed communities on hard substrate. 

The NMDS plot (Figure 8) positions IRZ samples apart from those at PRZ and BC20, suggesting that biota inhabiting the impact zone are not fully represented elsewhere.

Among assigned sequences, 213 ASVs belong to Animalia, spanning Annelida, Arthropoda, Bryozoa, Chordata, Cnidaria, and Mollusca. These phyla encompass 29 lower-rank taxa, many previously unreported from the region. Fungal reads constitute 66 ASVs, dominated by Basidiomycota and Ascomycota, with a smaller fraction of Mucoromycota; Malasseziomycetes alone account for more than one-third of fungal counts, consistent with global observations that these yeasts colonize lipid-rich niches on hard substrates. Protista contribute 18 ASVs representing 13 taxa, led by Retaria, Dinoflagellata, and Ciliophora, groups known for biogeochemical cycling.

Because high-grade nodules host distinct, diverse assemblages, removal of nodules could eliminate taxa not duplicated in adjacent sediments. The metabarcoding workflow demonstrated here can be deployed cost-effectively across large lease areas, guiding operators toward zones where mineral yield is high but biodiversity overlap with preservation areas is low. The study also highlights the importance of expanding reference databases: 85 percent of ASVs defy assignment, implying that voucher sequencing during exploration will accelerate future monitoring accuracy. Embedding such molecular tools in baseline surveys aligns engineering goals with environmental stewardship, helping to chart a data-rich path toward sustainable resource development in the CIOB.