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<p>Mesophotic coral ecosystems (MCEs), found at depths of 30–150&#xa0;m, represent a promising refuge for shallow-reef organisms facing increasing anthropogenic pressures. However, the biodiversity connectivity between shallow reefs and MCEs is poorly understood. This study investigates the patterns of <i>fish</i> biodiversity overlap and divergence between shallow (5–10&#xa0;m) and the upper MCEs (30–40&#xa0;m) coral ecosystems in Karimunjawa National Park (KNP), Indonesia, using environmental DNA (eDNA) metabarcoding targeting the mitochondrial 12&#xa0;S rRNA gene. Water samples were collected from both depth zones and analyzed and sequenced using Oxford Nanopore MinION. We identified 6,145 operational taxonomic units (OTUs) in the shallow reef and 5,034 in the upper MCEs ecosystem, with 3,043 or 37.3% OTUs shared between depths. A total of 203 species and 54 families were detected in this study, with substantial overlap in species composition between depths, ranging from 36 to 88 shared species across locations. We found 18 taxa representing ecologically and economically essential fish families as major contributors to taxa shared between depths. Our results also reveal unique taxa at each depth, suggesting differences in community composition between shallow and upper MCE zones. Although higher diversity was found in shallow reef areas, the upper MCEs present a unique biodiversity composition that is absent in the shallower areas. These findings suggest potential connectivity between shallow and upper MCEs communities for certain taxonomic groups, highlighting the potential of MCEs as distinct reservoirs of biodiversity. The eDNA metabarcoding approach provides a powerful tool for assessing biodiversity patterns across depth gradients and generating baseline data critical for conservation efforts in shallow and upper MCEs.</p>

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Limited but connected: comparing shallow reef and upper mesophotic fish communities using eDNA metabarcoding in Karimunjawa National Park, Indonesia

  • 期刊论文

  • 发表日期：

    2026年4月24日

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  • Aji Wahyu Anggoro,
  • Ni Kadek Dita Cahyani,
  • Muhammad Danie Al Malik,
  • Rian Prasetia,
  • Nining Nursalim,
  • Nenik Kholilah,
  • Eka Maya Kurniasih,
  • Ambariyanto Ambariyanto,
  • Puji Prihatinningsih

摘要

Mesophotic coral ecosystems (MCEs), found at depths of 30–150 m, represent a promising refuge for shallow-reef organisms facing increasing anthropogenic pressures. However, the biodiversity connectivity between shallow reefs and MCEs is poorly understood. This study investigates the patterns of fish biodiversity overlap and divergence between shallow (5–10 m) and the upper MCEs (30–40 m) coral ecosystems in Karimunjawa National Park (KNP), Indonesia, using environmental DNA (eDNA) metabarcoding targeting the mitochondrial 12 S rRNA gene. Water samples were collected from both depth zones and analyzed and sequenced using Oxford Nanopore MinION. We identified 6,145 operational taxonomic units (OTUs) in the shallow reef and 5,034 in the upper MCEs ecosystem, with 3,043 or 37.3% OTUs shared between depths. A total of 203 species and 54 families were detected in this study, with substantial overlap in species composition between depths, ranging from 36 to 88 shared species across locations. We found 18 taxa representing ecologically and economically essential fish families as major contributors to taxa shared between depths. Our results also reveal unique taxa at each depth, suggesting differences in community composition between shallow and upper MCE zones. Although higher diversity was found in shallow reef areas, the upper MCEs present a unique biodiversity composition that is absent in the shallower areas. These findings suggest potential connectivity between shallow and upper MCEs communities for certain taxonomic groups, highlighting the potential of MCEs as distinct reservoirs of biodiversity. The eDNA metabarcoding approach provides a powerful tool for assessing biodiversity patterns across depth gradients and generating baseline data critical for conservation efforts in shallow and upper MCEs.