Kosakyan Anush, Mulot Matthieu, Mitchell Edward A D, Lara Enrique
Laboratory of Soil Biology, University of Neuchatel, Rue Emile-Argand 11, CH-2000 Neuchatel, Switzerland; Institute of Biosciences, Department of Zoology, University of Sao Paulo, Rua do Matão, Travessa 14, Cidade Universitária, 05508-090 - Sao Paulo, SP, Brasil.
Laboratory of Soil Biology, University of Neuchatel, Rue Emile-Argand 11, CH-2000 Neuchatel, Switzerland.
Eur J Protistol. 2015 Aug;51(4):311-20. doi: 10.1016/j.ejop.2015.06.005. Epub 2015 Jun 19.
Environmental DNA surveys are used for screening eukaryotic diversity. However, it is unclear how quantitative this approach is and to what extent results from environmental DNA studies can be used for ecological studies requiring quantitative data. Mitochondrial cytochrome oxidase (COI) is used for species-level taxonomic studies of testate amoebae and should allow assessing the community composition from environmental samples, thus bypassing biases due to morphological identification. We tested this using a COI clone library approach and focusing on the Nebela collaris complex. Comparisons with direct microscopy counts showed that the COI clone library diversity data matched the morphologically identified taxa, and that community composition estimates using the two approaches were similar. However, this correlation was improved when microscopy counts were corrected for biovolume. Higher correlation with biovolume-corrected community data suggests that COI clone library data matches the ratio of mitochondria and that within closely-related taxa the density of mitochondria per unit biovolume is approximately constant. Further developments of this metabarcoding approach including quantifying the mitochondrial density among closely-related taxa, experiments on other taxonomic groups and using high throughput sequencing should make if possible to quantitatively estimate community composition of different groups, which would be invaluable for microbial food webs studies.
环境DNA调查用于筛选真核生物多样性。然而，这种方法的定量程度如何，以及环境DNA研究的结果在多大程度上可用于需要定量数据的生态研究尚不清楚。线粒体细胞色素氧化酶（COI）用于有壳变形虫的物种水平分类研究，应该能够从环境样本中评估群落组成，从而避免形态学鉴定带来的偏差。我们使用COI克隆文库方法并聚焦于Nebela collaris复合体对此进行了测试。与直接显微镜计数的比较表明，COI克隆文库多样性数据与形态学鉴定的分类单元相匹配，并且使用这两种方法对群落组成的估计相似。然而，当对显微镜计数进行生物量校正时，这种相关性得到了改善。与生物量校正后的群落数据更高的相关性表明，COI克隆文库数据与线粒体比例相匹配，并且在密切相关的分类单元中，每单位生物量的线粒体密度大致恒定。这种元条形码方法的进一步发展，包括量化密切相关分类单元之间的线粒体密度、对其他分类群进行实验以及使用高通量测序，如果可能的话，应该能够定量估计不同群体的群落组成，这对于微生物食物网研究将是非常有价值的。
