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<p>Remote coral reef systems, such as atolls and isolated reefs, play critical roles in supporting marine biodiversity but are often underrepresented in ecological assessments due to logistical and methodological constraints. Environmental DNA (eDNA) metabarcoding provides a highly sensitive and non-invasive alternative to conventional surveys, particularly in in remote reef systems. However, its application for comparing biodiversity and community structure across geomorphologically distinct reef types remain limited. In this study, we applied eDNA metabarcoding to investigate fish, mollusc, and echinoderm communities across Yongle Atoll and surrounding isolated reefs in the Xisha Islands, South China Sea during May–June 2022. A total of 121 fish, 94 mollusc, and 77 echinoderm species were detected. Fish communities at Yongle Atoll exhibited higher α-diversity and ecological heterogeneity, likely due to its complex spatial structure and greater resource availability. In contrast, molluscs and echinoderms in isolated reefs showed higher evenness and local diversity, possibly reflecting environmental stability and spatial isolation. Non-metric multidimensional scaling analysis revealed significant dissimilarities in fish and echinoderm assemblages between reef types, and indicator species analysis identified <i>Thalassoma lunare</i> and <i>Culcita quadrangularis</i> as representative taxa contributing to this differentiation. Canonical correspondence analysis further indicated that live coral cover was the primary environmental driver shaping fish communities, while chlorophyll <i>a</i> concentration significantly influenced invertebrate distribution. These patterns likely reflect the combined effects of niche-based environmental filtering and spatial dispersal constraints, indicating divergent community assembly processes between atoll and isolated reef systems. Our findings not only demonstrate the capacity of eDNA to resolve fine-scale biodiversity patterns in offshore coral systems but also provide baseline data to inform region-specific conservation, ecological zoning, and early warning in vulnerable marine ecosystems. This research underscores the growing relevance of molecular tools for biodiversity monitoring across tropical reefs worldwide.</p>

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Environmental DNA metabarcoding reveals taxon-specific community divergence between remote atolls and isolated reefs in the South China Sea

  • 期刊论文

  • 发表日期：

    2026年1月1日

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  • Yu Meng,
  • Yurui Yang,
  • Jinping Luo,
  • Jie Yu,
  • Ruiyu Tao,
  • Zhihao Wang,
  • Jiehong Liu,
  • Wentong Xia,
  • Fei Cheng,
  • Songguang Xie,
  • Yiqing Song

摘要

Remote coral reef systems, such as atolls and isolated reefs, play critical roles in supporting marine biodiversity but are often underrepresented in ecological assessments due to logistical and methodological constraints. Environmental DNA (eDNA) metabarcoding provides a highly sensitive and non-invasive alternative to conventional surveys, particularly in in remote reef systems. However, its application for comparing biodiversity and community structure across geomorphologically distinct reef types remain limited. In this study, we applied eDNA metabarcoding to investigate fish, mollusc, and echinoderm communities across Yongle Atoll and surrounding isolated reefs in the Xisha Islands, South China Sea during May–June 2022. A total of 121 fish, 94 mollusc, and 77 echinoderm species were detected. Fish communities at Yongle Atoll exhibited higher α-diversity and ecological heterogeneity, likely due to its complex spatial structure and greater resource availability. In contrast, molluscs and echinoderms in isolated reefs showed higher evenness and local diversity, possibly reflecting environmental stability and spatial isolation. Non-metric multidimensional scaling analysis revealed significant dissimilarities in fish and echinoderm assemblages between reef types, and indicator species analysis identified Thalassoma lunare and Culcita quadrangularis as representative taxa contributing to this differentiation. Canonical correspondence analysis further indicated that live coral cover was the primary environmental driver shaping fish communities, while chlorophyll a concentration significantly influenced invertebrate distribution. These patterns likely reflect the combined effects of niche-based environmental filtering and spatial dispersal constraints, indicating divergent community assembly processes between atoll and isolated reef systems. Our findings not only demonstrate the capacity of eDNA to resolve fine-scale biodiversity patterns in offshore coral systems but also provide baseline data to inform region-specific conservation, ecological zoning, and early warning in vulnerable marine ecosystems. This research underscores the growing relevance of molecular tools for biodiversity monitoring across tropical reefs worldwide.