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  3. Microfocus X-ray CT-based measurement of marine microplankton test density: A methodological advancement for understanding the impacts of ocean acidification and future ecological projections

Microfocus X-ray CT-based measurement of marine microplankton test density: A methodological advancement for understanding the impacts of ocean acidification and future ecological projections

White Rabbit Corp.

1. Key Points

  • There is concern about the effects of ocean acidification, caused by the input of anthropogenic carbon dioxide (CO2) into the oceans, on marine calcifying organisms※1; however, this phenomenon remains poorly understood.

  • A new method of precisely measuring the density and weight of the calcareous (calcium carbonate) tests of marine microplankton using a microfocus X-ray computed tomography (MXCT)※2 system was developed. By using the world's first successfully calibrated standard sample, objective density measurements could be performed with high precision.

  • This method enables density measurements to be made for the calcareous hard parts of each organism, as well as highly accurate quantitative estimates of the effects of acidification, such as the slight weakening and dissolution of these parts. Application of this method to various types of marine calcifying organisms will enable more accurate evaluations of current marine environments and organismal responses, as well as more accurate predictions of future changes in marine environments.

Supplemental Information

Calcifying organisms
Organisms that use calcium ions (Ca2+) and carbonate ions (CO32-) dissolved in seawater to form calcareous skeletons (e.g., shells and tests) and other hard tissues.


Microfocus X-ray CT (MXCT)
A computed tomography (CT) device that can provide detailed morphological information from the surface and interior of microscopic objects in three dimensions by emitting X-rays from all directions toward the object and reconstructing the images on a computer.

2. Overview

Katsunori Kimoto and Rika Horiuchi of the Earth Surface System Research Center, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), in collaboration with Osamu Sasaki of the Tohoku University Museum and Tomohiro Iwashita of the White Rabbit Corporation, have developed the first method for directly and precisely measuring the exoskeleton (called “test”) density and weight of planktonic foraminifera※3, microscopic marine zooplankton, utilizing a microfocus X-ray computed tomography system (MXCT). Ocean acidification caused by anthropogenic carbon dioxide (CO2) emissions poses a risk to calcareous (calcifying) marine microplankton, including foraminifera. However, the exact effects of ocean acidification on marine plankton remain poorly understood. Using planktonic foraminifera, which are common calcareous organisms in the world's oceans, a technique was developed to measure the density and weight of their tests with high precision using only MXCT. The MXCT technique enables the capture and precise quantitative measurement of previously unknown microscopic changes (structures as small as 1 µm (0.001 mm)) in the tests of marine plankton that may be attributed to ocean acidification. This new development in ocean acidification and bioeffects assessment research is expected to contribute to our understanding of the responses and adaptability of marine organisms to changes in ocean environments.

The results of the present study is published in Frontiers in Earth Science on December 21, 2023 (JST). This research was supported by Grants-in-Aid for Scientific Research (KAKENHI) program of the Ministry of Education, Culture, Sports, Science and Technology (MEXT)/Japan Society for the Promotion of Science (JSPS) (JP19H03037, JP15H05712, 23H02299) and by a JAMSTEC Grant-in-Aid for Operation.

Precise bulk density measurement of planktic foraminiferal test by X-ray microcomputed tomography

Katsunori Kimoto1, Rika Horiuchi1, Osamu Sasaki2 and Tomohiro Iwashita3

1. Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
2. Tohoku University Museum
3. White Rabbit, Corp.
Supplemental Information

Planktonic foraminifera
Single-celled zooplankton that inhabit the surface layers of the ocean. They measure ~0.1–1 mm, and approximately living 40 species with this life habit have been documented worldwide.


Figure caption
3D images of the planktonic foraminifera Globorotalia inflata, a marine calcifier scanned with microfocus X-ray computed tomography (MXCT).

  • a) 3D reconstructed image of planktonic foraminifera G. inflata. (Isosurface rendering view)
  • b) Cross-sectional view showing relative test densities (CT Number)of G. inflata. Red and blue tones indicate dense and less-dense areas of shell, respectively.
The shell of a planktonic foraminifera is heterogeneous with dense and less-dense areas. Scale bar (white) is 0.3 mm; spatial resolution is 0.001 mm/pixel.

For this study

Katsunori Kimoto, Senior Researcher, Research Institute for Global Change (RIGC), Earth Surface System Research Center (ESS), Marine Ecosystem Research Group, JAMSTEC

For press release

Press Office, Marine Science and Technology Strategy Department, JAMSTEC