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<p>This study investigates the spatial variability of Arthropoda and Annelida communities across a disturbance gradient in Jakarta Bay and the Thousand Islands, Indonesia, using environmental DNA (eDNA) metabarcoding. Water samples were collected from four sites, Pramuka, Harapan, Untung Jawa, and Tanjung Priok, representing a continuum from protected marine areas to heavily urbanized coasts. Amplicon sequencing of the COI gene region recovered a total of 324 genera, with the highest genus richness at Harapan (119) and Pramuka (107), intermediate richness at Untung Jawa (100), and the lowest at Tanjung Priok (40). Alpha diversity indices (Observed, Chao1, Shannon, Simpson, Fisher) consistently indicated higher diversity at the less-disturbed sites. Community clustering distinguished Pramuka–Harapan from Untung Jawa–Tanjung Priok, with the former dominated by copepods (e.g., <i>Paracalanus</i>, <i>Stephos</i>) and the latter showing a higher proportion of annelids (e.g., <i>Phyllodoce</i>, <i>Ampharete</i>). Because all multivariate and univariate analyses were based on four site-level observations, they were treated as exploratory and not tested for statistical significance; exploratory redundancy analysis (RDA) indicated that salinity and dissolved oxygen were the environmental variables most strongly associated with genus-level differences among sites, and site-level correlations described genus–environment associations (e.g., for <i>Oithona</i>). Visualization tools—including Sankey diagrams, dendrograms, and bar plots, illustrated spatial differentiation in community composition. Our findings demonstrate that eDNA metabarcoding can capture among-site biodiversity differences and environmental gradients in tropical coastal systems, supporting its application as a complementary tool for biodiversity monitoring and marine spatial planning under urbanization pressure.</p>

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eDNA metabarcoding reveals spatial differentiation of Arthropoda and Annelida along a coastal urbanization gradient in tropical Indonesia

  • 期刊论文

  • 发表日期：

    2026年7月16日

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  • Ismail Maqbul,
  • Hawis Madduppa,
  • Dining Nika Alina

摘要

This study investigates the spatial variability of Arthropoda and Annelida communities across a disturbance gradient in Jakarta Bay and the Thousand Islands, Indonesia, using environmental DNA (eDNA) metabarcoding. Water samples were collected from four sites, Pramuka, Harapan, Untung Jawa, and Tanjung Priok, representing a continuum from protected marine areas to heavily urbanized coasts. Amplicon sequencing of the COI gene region recovered a total of 324 genera, with the highest genus richness at Harapan (119) and Pramuka (107), intermediate richness at Untung Jawa (100), and the lowest at Tanjung Priok (40). Alpha diversity indices (Observed, Chao1, Shannon, Simpson, Fisher) consistently indicated higher diversity at the less-disturbed sites. Community clustering distinguished Pramuka–Harapan from Untung Jawa–Tanjung Priok, with the former dominated by copepods (e.g., Paracalanus, Stephos) and the latter showing a higher proportion of annelids (e.g., Phyllodoce, Ampharete). Because all multivariate and univariate analyses were based on four site-level observations, they were treated as exploratory and not tested for statistical significance; exploratory redundancy analysis (RDA) indicated that salinity and dissolved oxygen were the environmental variables most strongly associated with genus-level differences among sites, and site-level correlations described genus–environment associations (e.g., for Oithona). Visualization tools—including Sankey diagrams, dendrograms, and bar plots, illustrated spatial differentiation in community composition. Our findings demonstrate that eDNA metabarcoding can capture among-site biodiversity differences and environmental gradients in tropical coastal systems, supporting its application as a complementary tool for biodiversity monitoring and marine spatial planning under urbanization pressure.