Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems

Loss of biodiversity from lower to upper trophic levels reduces overall productivity and stability of coastal ecosystems in our oceans, but rarely are these changes documented across both time and space. The characterisation of environmental DNA (eDNA) from sediment and seawater using metabarcoding offers a powerful molecular lens to observe marine biota and provides a series of ‘snapshots’ across a broad spectrum of eukaryotic organisms. Using these next-generation tools and downstream analytical innovations including machine learning sequence assignment algorithms and co-occurrence network analyses, we examined how anthropogenic pressures may have impacted marine biodiversity on subtropical coral reefs in Okinawa, Japan. Based on 18S ribosomal RNA, but not ITS2 sequence data due to inconsistent amplification across samples, as well as proxies for anthropogenic disturbance, we show that eukaryotic richness at the family level significantly increases with medium and high levels of distu...

从低营养级到高营养级的生物多样性丧失，会降低海洋沿岸生态系统的整体生产力与稳定性，但此类变化极少能同时在时间与空间维度上被记录在册。利用元条形码（metabarcoding）技术对沉积物与海水中的环境DNA（environmental DNA, eDNA）进行表征分析，可为观测海洋生物群落提供强有力的分子视角，并为各类真核生物提供一系列‘快照式’采样记录。本研究借助此类新一代分子工具及下游分析创新手段——包括机器学习序列赋值算法与共现网络分析——探究了人为压力如何对日本冲绳的亚热带珊瑚礁海域海洋生物多样性造成影响。基于18S核糖体RNA（18S ribosomal RNA）而非ITS2序列数据（因不同样本间扩增效果不一致），结合人为干扰替代指标，我们发现科级水平的真核生物丰富度会随中等及高强度的干……