Abstract
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.
Highlights
Marine protists are the most abundant eukaryotes in the pelagic realm; recent field-based studies have unveiled their high diversity and abundance in the photic and deep layers of the world’s oceans [1,2]
We compared the calcite CT number (CCN) of the post-computed tomography (CT) 1 and post-CT 2 analyses, which measured the same specimens mounted on the sample stage either in groups of three or individually, respectively (Fig 1, Table 1)
We developed a nondestructive analysis method, involving micro-focus X-ray computed tomography (MXCT) scanning, that was successful in obtaining accurate physical data and morphological images of the shells
Summary
Marine protists are the most abundant eukaryotes in the pelagic realm; recent field-based studies have unveiled their high diversity and abundance in the photic and deep layers of the world’s oceans [1,2]. Several techniques, including in situ imaging and metagenomic analysis, have been used to assess the biomass and variability of marine protists along horizontal and vertical dimensions of the oceans [3,4]. The results of previous studies suggest that protists greatly affect marine ecosystems [1,2,3,4]. Transcriptome analyses have been conducted to examine gene expression in protists from an ecological point of view [6], such metadata-based approaches (e.g., transcriptome and metagenomic analyses) have been limited to culturable species. Since most protists are difficult to culture, their ecology has remained unknown to date
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