Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems
Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems
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DOI：
10.1038/s41598-020-64858-9
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发表时间：
2020-05-20
影响因子：
4.6
通讯作者：
Bunce, Michael
中科院分区：
文献类型：
--
作者：
DiBattista, Joseph D.;Reimer, James D.;Bunce, Michael
生物多样性从低营养级到高营养级的丧失降低了我们海洋沿海生态系统的总体生产力和稳定性，但这些变化很少在时间和空间上得到记录。利用元条码技术对沉积物和海水中的环境DNA（eDNA）进行表征，为观察海洋生物提供了一个强大的分子透镜，并提供了一系列真核生物的“快照”。使用这些下一代工具和下游分析创新，包括机器学习序列分配算法和共现网络分析，我们研究了人为压力如何影响日本冲绳亚热带珊瑚礁的海洋生物多样性。18 S核糖体RNA的基础上，但不是ITS2序列数据，由于不一致的扩增这个标记，以及代理人为干扰，我们表明，真核生物丰富度在家庭水平显着增加中，高水平的干扰。这种丰富度的变化与组成的变化，减少类群之间的连通性，增加分类群共现网络的碎片化，并在指示类群的转变。总之，这些研究结果表明，eDNA的能力，作为一个晴雨表的干扰，并提供了一个范例，如何生物网络和珊瑚礁可能受到人类活动的影响。
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 18 S ribosomal RNA, but not ITS2 sequence data due to inconsistent amplification for this marker, 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 biotic networks and coral reefs may be impacted by anthropogenic activities.