Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment [dataset]

Effective marine management requires comprehensive data on the status of marine biodiversity. However, efficient methods that can document biodiversity in our oceans are currently lacking. Environmental DNA (eDNA) sourced from seawater offers a new avenue for investigating the biota in marine ecosystems. Here, we investigated the potential of eDNA to inform on the breadth of biodiversity present in a tropical marine environment. Directly sequencing eDNA from seawater using a shotgun approach resulted in only 0.34% of 22.3 million reads assigning to eukaryotes, highlighting the inefficiency of this method for assessing eukaryotic diversity. In contrast, using ‘tree of life’ (ToL) metabarcoding and 20-fold fewer sequencing reads, we could detect 287 families across the major divisions of eukaryotes. Our data also show that the best performing ‘universal’ PCR assay recovered only 44% of the eukaryotes identified across all assays, highlighting the need for multiple metabarcoding assays to catalogue biodiversity. Lastly, focusing on the fish genus Lethrinus, we recovered intra- and inter-specific haplotypes from seawater samples, illustrating that eDNA can be used to explore diversity beyond taxon identifications. Given the sensitivity and low cost of eDNA metabarcoding we advocate this approach be rapidly integrated into biomonitoring programs.

有效的海洋管理亟需能够全面反映海洋生物多样性现状的数据，但当前尚缺少可高效记录海洋生物多样性的可行方法。源自海水的环境DNA（environmental DNA，eDNA）为研究海洋生态系统中的生物群落提供了全新途径。本研究针对热带海洋环境中利用eDNA表征生物多样性广度的潜力展开了探究。采用鸟枪法直接对海水源eDNA进行测序时，2230万条测序读段中仅有0.34%可被注释为真核生物，凸显了该方法在评估真核生物多样性方面的低效性。与之相对，采用生命之树（tree of life, ToL）元条形码测序（metabarcoding）技术，且测序读段数量仅为前者的1/20时，我们便可在真核生物的主要类群中检测到287个科级分类单元。研究数据同时显示，表现最优的“通用”聚合酶链式反应（polymerase chain reaction, PCR）扩增方案仅能回收所有检测方案中鉴定出的44%真核生物类群，凸显了需采用多种元条形码测序方案来全面编目生物多样性的必要性。最后，我们以鱼类裸颊鲷属（Lethrinus）为研究对象，从海水样本中成功获取了种内与种间单倍型，这表明eDNA可用于探索超出物种鉴定范畴的生物多样性信息。鉴于eDNA元条形码测序技术具备高灵敏度与低成本的优势，我们倡议尽快将该方法整合至生物监测项目当中。