Center for Advanced Marine Core Research, Kochi University, Nankoku, Japan.
Research and Development Center for Global Change, JAMSTEC, Yokosuka, Japan.
PLoS One. 2019 Mar 7;14(3):e0213282. doi: 10.1371/journal.pone.0213282. eCollection 2019.
Marine protists play an important role in oceanic ecosystems and biogeochemical cycles. However, the difficulties in culturing pelagic protists indicate that their ecology and behavior remain poorly understood; phylogeographic studies based on single-cell genetic analyses have often shown that they are highly divergent at the biological species level, with variable geographic distributions. This indicates that their ecology could be complex. On the other hand, the biomineral (calcareous) shells of planktic foraminifers are widely used in geochemical analyses to estimate marine paleoenvironmental characteristics (i.e., temperature), because the shell chemical composition reflects ambient seawater conditions. Among the pelagic protists, planktic foraminifers are ideal study candidates to develop a combined approach of genetic, morphological, and geochemical methods, thus reflecting environmental and ecological characteristics. The present study precisely tested whether the DNA extraction process physically and chemically affects the shells of the planktic foraminifer Globigerinoides ruber. We used a nondestructive method for analyzing physical changes (micro-focus X-ray computed tomography (MXCT) scanning) to compare specimens at the pre- and post-DNA extraction stages. Our results demonstrate that DNA extraction has no significant effect on shell density and thickness. We measured stable carbon and oxygen isotopes on the shell of each individual in a negative control or one of two DNA-extracted groups and detected no significant differences in isotopic values among the three groups. Moreover, we evaluated isotopic variations at the biological species level with regard to their ecological characteristics such as depth habitat, life stages, and symbionts. Thus, our examination of the physiochemical effects on biomineral shells through DNA extraction shows that morphological and isotopic analyses of foraminifers can be combined with genetic analysis. These analytical methods are applicable to other shell-forming protists and microorganisms. In this study, we developed a powerful analytical tool for use in ecological and environmental studies of modern and past oceans.
海洋原生生物在海洋生态系统和生物地球化学循环中起着重要作用。然而，培养浮游原生生物的困难表明，它们的生态和行为仍然知之甚少；基于单细胞遗传分析的系统地理学研究经常表明，它们在生物学物种水平上存在高度的分歧，具有不同的地理分布。这表明它们的生态可能很复杂。另一方面，浮游有孔虫的生物矿化（钙质）壳被广泛用于地球化学分析，以估计海洋古环境特征（即温度），因为壳的化学成分反映了周围海水的条件。在浮游原生生物中，浮游有孔虫是发展遗传、形态和地球化学方法相结合的理想研究对象，从而反映环境和生态特征。本研究精确地测试了 DNA 提取过程是否会对浮游有孔虫Globigerinoides ruber 的壳产生物理和化学影响。我们使用一种非破坏性的方法来分析物理变化（微焦点 X 射线计算机断层扫描（MXCT）扫描），以比较 DNA 提取前后的标本。我们的结果表明，DNA 提取对壳的密度和厚度没有显著影响。我们在阴性对照或两个 DNA 提取组中的一个个体的壳上测量了稳定的碳和氧同位素，没有在三个组之间检测到同位素值的显著差异。此外，我们评估了在生态特征方面，如栖息地深度、生命阶段和共生体，在生物物种水平上的同位素变化。因此，我们通过 DNA 提取检查对生物矿化壳的理化影响表明，有孔虫的形态和同位素分析可以与遗传分析相结合。这些分析方法适用于其他形成壳的原生生物和微生物。在这项研究中，我们开发了一种强大的分析工具，用于现代和过去海洋的生态和环境研究。
