Graduate School of Human Development and Environment, Kobe University, 3-11, Tsurukabuto, Nada-ku, Kobe City, Hyogo 657-8501, Japan; Research Fellow of Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan.
Maizuru Fisheries Research Station, Field Science Education, and Research Center, Kyoto University, Maizuru, Kyoto 625-0086, Japan.
Sci Total Environ. 2020 Sep 15;735:139462. doi: 10.1016/j.scitotenv.2020.139462. Epub 2020 May 17.
Environmental DNA (eDNA) can exist in water with various sizes and states. Among them, relative to extra-cellular DNA, intra-cellular DNA such as cell and tissue fragments can mainly be detected at larger size fractions, and may be protected from enzymatic DNA degradation processes. Here, we verified the hypothesis that the selective collection of such large-sized eDNA enhances the efficiency of capturing less-degraded eDNA, based on a tank experiment using Japanese Jack Mackerel (Trachurus japonicus) as a model species. We concentrated different volumes of rearing water using the filters with different pore sizes (0.7 μm and 2.7 μm), and quantified the copy number of short and long mitochondrial and short nuclear DNA fragments of target species in water samples. As a result, the ratio of long to short eDNA concentrations was higher in the larger pore size filter, which would support our stated hypothesis. In addition, the ratio of nuclear to mitochondrial eDNA was lower in the larger pore size filter. These results imply a difference in the persistence of nuclear and mitochondrial DNA between intra- and extra-cellular environments. Moreover, larger filter pore size did not necessarily decrease the yields of eDNA, and there was little difference in yields in smaller filtration volumes. The findings of this study indicate the potential to select information from eDNA signals by focusing on eDNA of specific size and state, which may contribute to efficient utilization of the information on species taxonomy and physiology in water samples.
环境 DNA（eDNA）可以以各种大小和状态存在于水中。其中，与细胞外 DNA 相比，细胞内 DNA（如细胞和组织片段）主要可以在较大的粒径分数中检测到，并且可能免受酶促 DNA 降解过程的影响。在这里，我们通过使用日本鲐鱼（Trachurus japonicus）作为模型物种的水箱实验验证了这样一个假设，即选择性收集这种大尺寸的 eDNA 可以提高捕获降解程度较低的 eDNA 的效率。我们使用不同孔径（0.7μm 和 2.7μm）的过滤器浓缩不同体积的养殖水，并定量测定水样中目标物种的短和长线粒体和短核 DNA 片段的拷贝数。结果表明，较大孔径过滤器中的长 eDNA 与短 eDNA 浓度的比值更高，这支持了我们的假设。此外，较大孔径过滤器中的核与线粒体 eDNA 的比值较低。这些结果表明，核和线粒体 DNA 在细胞内和细胞外环境中的持久性存在差异。此外，较大的过滤器孔径不一定会降低 eDNA 的产量，并且在较小的过滤体积中产量差异很小。本研究的结果表明，通过关注特定大小和状态的 eDNA，可以从 eDNA 信号中选择信息，这可能有助于有效地利用水样中物种分类学和生理学信息。
