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 disturbance. This change in richness coincides
with compositional changes, a decrease in connectedness among taxa, an
increase in fragmentation of taxon co-occurrence networks, and a shift in
indicator taxa. Taken together, these findings demonstrate the ability of
eDNA to act as a barometer of disturbance and provide an exemplar of how
ecological functions, biotic networks, and coral reef resilience may be
impacted by anthropogenic activities.

海洋沿岸生态系统中，生物多样性从低营养级向高营养级丧失会降低其整体生产力与稳定性，但此类变化鲜少被同时结合时间与空间维度开展系统性记录。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，可为观测海洋生物群落提供强有力的分子研究视角，并能获取覆盖广泛真核生物类群的一系列快照式数据。本研究依托此类下一代分子工具，结合机器学习序列赋值算法、共现网络分析等下游分析创新方法，探究了人为压力对日本冲绳亚热带珊瑚礁海洋生物多样性的影响。本研究基于18S核糖体RNA序列数据（因ITS2序列在不同样本间扩增一致性较差，未纳入分析），结合人为干扰替代指标，发现中等及高强度干扰下，真核生物的科水平丰富度显著提升。该丰富度变化与群落组成改变、类群间连通性下降、类群共现网络碎片化程度加剧以及指示类群的转变同步发生。综上，本研究结果证实eDNA可作为生态干扰的晴雨表，并为揭示人为活动如何影响生态功能、生物网络及珊瑚礁恢复力提供了典型研究范例。