Data from: Genetic monitoring of open ocean biodiversity: an evaluation of DNA metabarcoding for processing continuous plankton recorder samples

DNA metabarcoding is an efficient method for measuring biodiversity, but the process of initiating long-term DNA-based monitoring programs, or integrating with conventional programs, is only starting. In marine ecosystems, plankton surveys using the continuous plankton recorder (CPR) have characterised biodiversity along transects covering millions of kilometres with time-series spanning decades. We investigated the potential for use of metabarcoding in CPR surveys. Samples (n= 53) were collected in two Southern Ocean transects and metazoans identified using standard microscopic methods and by high-throughput sequencing of a cytochrome c oxidase subunit I marker. DNA increased the number of metazoan species identified and provided high resolution taxonomy of groups problematic in conventional surveys (e.g. larval echinoderms and hydrozoans). Metabarcoding also generally produced more detections than microscopy, but this sensitivity may make cross-contamination during sampling a problem. In some samples, the prevalence of DNA from large plankton such as krill masked the presence of smaller species. We investigated adding a fixed amount of exogenous DNA to samples as an internal control to allow determination of relative plankton biomass. Overall, the metabarcoding data represents a substantial shift in perspective, making direct integration into current long-term time-series challenging. We discuss a number of hurdles that exist for progressing DNA metabarcoding from the current snapshot studies to the requirements of a long-term monitoring program. Given the power and continually increasing efficiency of metabarcoding, it is almost certain this approach will play an important role in future plankton monitoring.

DNA 宏条形码技术（DNA metabarcoding）是衡量生物多样性的高效手段，但启动长期基于DNA的监测项目，或是将其与传统监测项目整合的流程，目前尚处于起步阶段。在海洋生态系统中，依托连续浮游生物记录仪（continuous plankton recorder, CPR）开展的浮游生物调查，已在覆盖数百万公里的调查样带上完成了生物多样性的系统表征，并积累了长达数十年的时间序列数据。本研究探究了将宏条形码技术应用于CPR调查的可行性，共采集南大洋两条样带上的53份样本，分别采用标准显微观测法，以及对细胞色素c氧化酶亚基I（cytochrome c oxidase subunit I）标记基因进行高通量测序的方式，对样本中的后生动物进行鉴定。高通量测序技术提升了可鉴定的后生动物物种数量，并为传统调查中难以准确分类的类群（例如幼虫阶段的棘皮动物和水螅虫）提供了高分辨率的分类学信息。总体而言，宏条形码技术的物种检出率普遍高于显微观测法，但该方法的高灵敏度可能会导致采样过程中的交叉污染问题。在部分样本中，磷虾等大型浮游生物的DNA占比过高，掩盖了小型物种的检测信号。为此，我们尝试向样本中添加固定剂量的外源DNA（exogenous DNA）作为内参，以实现浮游生物相对生物量的估算。整体而言，宏条形码测序数据带来了研究视角的重大转变，使其直接整合进现有长期时间序列监测项目仍面临诸多挑战。本研究讨论了将DNA宏条形码技术从当前的单点快照式研究推进至符合长期监测项目要求所需克服的多项障碍。鉴于宏条形码技术的优势及其检测效率的持续提升，该方法几乎必然会在未来的浮游生物监测中发挥重要作用。