Gusmao Ana Carolina Bercini, van Dijk Robin L, Girard Elsa B, Peijnenburg Katja T C A, Macher Jan, Kucera Michal, Morard Raphaël
Max Planck Institute for Marine Microbiology, Bremen, Germany.
Naturalis Biodiversity Center, Leiden, The Netherlands.
Sci Rep. 2025 Jun 1;15(1):19205. doi: 10.1038/s41598-025-03842-7.
Metabarcoding is a cornerstone of modern ecology, but its accuracy is dependent on the chosen gene marker. While the small subunit ribosomal DNA (SSU) is a powerful tool to describe protist diversity, its reliability in retrieving the composition of communities is less obvious. It is particularly challenging to obtain quantitative estimates of abundance in planktonic foraminifera, where the variability of the SSU gene copy number can span three orders of magnitude. As an alternative, we explored the potential of the mitochondrial cytochrome c oxidase subunit I (COI) marker. We developed a reference barcode library of 130 sequences of a 1200 bp long COI fragment belonging to 26 morphospecies of foraminifera and performed 201 single-cell qPCR quantifications to evaluate the relationship between the number of COI copies, and the size of individual foraminifera. We found that the COI evolves between 25 and 1000 times slower than the SSU and therefore has a poor taxonomic resolution. However, we observed a significant relationship between COI copy number and foraminifera size. These results suggest that SSU and COI can play complementary roles: the SSU is well-suited for capturing taxonomic diversity, while the COI is useful to retrieve crude information on the community composition.
宏条形码技术是现代生态学的基石，但其准确性取决于所选择的基因标记。虽然小亚基核糖体DNA（SSU）是描述原生生物多样性的有力工具，但其在获取群落组成方面的可靠性尚不太明确。对于浮游有孔虫而言，要获得丰度的定量估计尤其具有挑战性，因为SSU基因拷贝数的变异性可能跨越三个数量级。作为一种替代方法，我们探索了线粒体细胞色素c氧化酶亚基I（COI）标记的潜力。我们构建了一个参考条形码文库，包含属于26个有孔虫形态种的1200 bp长COI片段的130个序列，并进行了201次单细胞定量PCR定量分析，以评估COI拷贝数与单个有孔虫大小之间的关系。我们发现，COI的进化速度比SSU慢25至1000倍，因此分类分辨率较差。然而，我们观察到COI拷贝数与有孔虫大小之间存在显著关系。这些结果表明，SSU和COI可以发挥互补作用：SSU非常适合捕捉分类多样性，而COI则有助于获取有关群落组成的粗略信息。
