Endik Deni Nugroho, Roisatul Ainiyah, Reza Ardiansyah, Dwi Anggorowati Rahayu, Ahmad Misbakhus Sururi, Ana Setyastuti
Marine biodiversity inventories are being transformed by environmental DNA (eDNA) metabarcoding, which enables the detection of cryptic life stages and species often missed by conventional capture-based surveys. Despite their ecological role as bioturbators, grazers, and indicators of reef health, baseline information on echinoderm diversity along the densely populated southern coast of Java, Indonesia, remains scarce, and eDNA-based assessments for this region have not been reported. We applied CO1 metabarcoding on the Oxford Nanopore PromethION platform to seawater samples collected from nine sampling points across three coastal sites in East Java (Blitar, Malang, and Jember). Field blanks, extraction negative controls, and PCR negative controls were processed in parallel to ensure data integrity. Alpha-diversity was assessed using Shannon, Simpson, and Chao1 indices, with one-way ANOVA / Kruskal–Wallis testing among-site differences, while community structure was examined using Principal Coordinate Analysis and PERMANOVA on Bray–Curtis and Jaccard dissimilarities. Echinodermata represented a minor but consistent fraction of the metazoan reads, with the class Echinoidea dominant across all sites. Alpha-diversity differed significantly among locations, and PERMANOVA confirmed distinct community structures: Jember harboured the highest taxon richness and the largest number of unique species, whereas Blitar and Malang showed greater compositional similarity. Cross-validation against regional checklists confirmed that detected taxa are consistent with the Indo-Pacific echinoderm fauna and highlighted several potential new records. This study provides the first eDNA-based assessment of echinoderm diversity for the south coast of East Java, establishing a reproducible baseline to support biodiversity monitoring and coastal management planning in the region. Copyright © 2026. Published by Elsevier B.V.
Department of Biology Education, Faculty of Science Education, Universitas Nahdlatul Ulama Pasuruan, Jl. Raya Warung Dowo, East Java, Pasuruan, 67171, Indonesia; Study programme of Fisheries Product Technology, Yudharta University, East Java, Pasuruan, 67162, Indonesia; Laboratory of Taxonomy, Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Negeri Surabaya. Jl. Ketintang, East Java, Surabaya, 60213, Indonesia; Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Gd. Widyasatwaloka, KST Soekarno, Jl. Raya Bogor Km 46, Cibinong, 16911, Indonesia
