Environmental DNA metabarcoding differentiates between micro-habitats within the rocky intertidal

While the utility of environmental DNA (eDNA) metabarcoding surveys for
biodiversity monitoring continues to be demonstrated, the spatial and
temporal variability of eDNA, and thus the limits of the differentiability
of an eDNA signal, remains under-characterized. In this study, we
collected eDNA samples from distinct micro-habitats (~40 m apart) in a
rocky intertidal ecosystem over their exposure period in a tidal cycle.
During this period, the micro-habitats transitioned from being
interconnected, to physically isolated, to interconnected again. Using a
well-established eukaryotic (cytochrome oxidase subunit I) metabarcoding
assay, we detected 415 species across 28 phyla. Across a variety of
univariate and multivariate analyses, using exclusively taxonomically
assigned data as well as all detected amplicon sequence variants (ASVs),
we identified unique eDNA signals from the different micro-habitats
sampled. This difference paralleled expected ecological gradients and
increased as the sites became more physically disconnected. Our results
demonstrate that eDNA biomonitoring can differentiate micro-habitats in
the rocky intertidal only 40 m apart, that these differences reflect known
ecology in the area, and that physical connectivity informs the degree of
differentiation possible. These findings showcase the potential power of
eDNA biomonitoring to increase the spatial and temporal resolution of
marine biodiversity data, aiding research, conservation, and management
efforts.

尽管环境DNA（environmental DNA, eDNA）宏条形码（metabarcoding）调查在生物多样性监测中的应用价值持续得到验证，但eDNA的时空变异性及其信号区分能力的局限仍未得到充分表征。本研究在岩质潮间带生态系统中，于潮汐周期的暴露时段内采集了相距约40米的不同微生境的eDNA样本。在此期间，这些微生境经历了从相互连通到物理隔离，再重新连通的状态变化。本研究采用成熟的真核生物（细胞色素氧化酶亚基I，cytochrome oxidase subunit I, COI）宏条形码检测方法，共检测到28个门类的415个物种。通过多种单变量与多变量分析方法，同时使用仅经分类学注释的数据以及所有检测到的扩增子序列变异体（amplicon sequence variants, ASVs），我们从采样的不同微生境中识别出了独特的eDNA信号。该信号差异与预期的生态梯度相符，且随采样点位物理隔离程度的提升而愈加显著。本研究结果表明，eDNA生物监测可区分岩质潮间带中仅相距40米的微生境，且此类差异与该区域已知的生态学特征相符，同时物理连通性决定了可实现的区分程度。这些发现展示了eDNA生物监测在提升海洋生物多样性数据时空分辨率方面的巨大潜力，可为相关研究、保护与管理工作提供助力。