the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 23 Jun 2025
The 3D submicron-scale skeletal reconstruction of Nannoconus (Cretaceous calcareous nannofossil) – Insights on biomineralization
Abstract. Nannoconus (~5–20 μm) was a major biocarbonate producer in the Early Cretaceous seas (~150–120 Ma). The heavy calcitic skeletons (~200–1400 picogram) of this nannoplankton have contributed massive carbonate accumulations for over ~30 million years. The skeletal microstructure is characterized by an interlocking arrangement of calcitic lamellae spanned around a central canal. The biomineralization process involved in producing the sophisticated skeleton is investigated for the first time. Ptychography X-ray computed tomography (PXCT) with synchrotron radiation is applied to an isolated skeleton, to obtain a 3D set of tomographic images with ~ 40 nm spatial resolution. This 3D set was processed to virtually segment the individual calcitic lamella and reconstruct the full skeleton through constraining different lengths and angles. The lamellae are repetitively stacked in two distinct inclinations, one following the other, and producing segments combined to form the entire skeleton. Individual lamellae were calcified in a “template” of organic layer containing amino acid(s)/biomolecule(s), responsible for creating the interlocking arrangement. Our study of Nannoconus provides a simple yet potent approach to the analysis of biomineralized microstructures characterized by the repetitive arrangement of calcitic units as commonly seen in the calcareous nannoplankton.
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RC1: 'Comment on egusphere-2025-1840', Anonymous Referee #1, 12 Jul 2025
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The study “The 3D submicron-scale skeletal reconstruction of Nannoconus (Cretaceous calcareous nannofossil) - Insights on biomineralization” by Chowdhury et al. reports on the 3D imaging of Nannoconus shell, its segmentation into building units, and their computational reconstruction into a model shell. The work is very interesting as it gives the first 3D view into the abundant Nannoconus morphology observed in sediments. This brings an important addition to other structures of nanoplankton (most studied are probably the coccolithophorids). I very much appreciate the effort to use the segment morphology of the basic unit and to re-build from it in silico the full shell. The limitations of the study emerge from the fact that there is no living reference for the shells, and several assumptions are being made along the way. Nevertheless, this is a beautiful study that deserves publication after the following comments are addressed.
Comments:
- The two models in Figure 9 look qualitatively similar and it is unclear from the text why the layer model was abandoned for further discussion.
- Only one lamella is segmented in Figure 4. The authors say that the segmentation is close to the limit of the methodology. Therefore, it is important to segment several more lamellas so there is a way to assess how conserved is this morphology.
- When constructing the full shell model in silico, is there a condition that each voxel is hosting only a single lamella? In other words, is physical overlap of two lamella in the same volume avoided?
- The geometrical descriptions are fundamental for the study and the authors try their best to explain and define all aspects, nevertheless, the terminology is difficult to follow. If the authors could improve the visualization of the angles in Figures 5 and 3 it can make this aspect clearer.
- It is very difficult to follow the discussion of B. bigelowii on page 22 and to understand which similarities the authors propose. A visualization of this structure can help.
Citation: https://doi.org/10.5194/egusphere-2025-1840-RC1 -
RC2: 'Comment on egusphere-2025-1840', Jeremy Young & Angela Fraguas (co-review team), 16 Jul 2025
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Review of Chowdury et al. “The 3D submicron-scale skeletal reconstruction of Nannoconus
(Cretaceous calcareous nannofossil) - Insights on biomineralization”
This paper is based on a ground-breaking investigation of Nannoconus using Ptychographic X-ray computed tomography (PXCT). This is a synchrotron-based approach which has allowed reconstruction of the complex structure of these calcareous nannofossils at sub-micron level. This is the first application of a 3D imaging technique of this type to investigate the shape, size and disposition of the individual elements in addition to the gross morphology of the object. The technique overcomes some of the limits of previous SEM and LM based methods. Nannoconus is a good choice of subject since their skeletal elements, nannoconids, were important rock-formers in the Early Cretaceous and since their evolutionary relationship to coccolithophores and other nannofossils has been uncertain.
Nannoconus is formed of numerous wedge-shaped laminae arranged in spiral layers showing clockwise imbrication in side view – i.e. left-handed helices.
van Niel (1992, 1994) observed that alternate layers of elements were either arranged sub-parallel to the spiral surfaces with only slight overlap (type A plates), or were significantly inclined relative to this surface and so overlapped giving an imbricate structure to those layers (type B plates). These alternate layers spiral around the nannolith, but it has not been established how many helical layers – i.e whether there is one set of A-B layer pairs, two, or several. There is also a suggestion (van Niel 1992, Young et al. 1997) that the two cycles have different crystallographic orientations and that this causes the dark spiral lines clearly visible in polarising light microscopy. This suggestion is unproven with the alternative being that the entire nannolith is formed of elements with sub-tangential orientation and that the dark lines are some type of interference effect.
Aubry (2013, 2025) argued that plates in successive players overlaid each other regularly and so nannoconids could be considered as being formed of segments - as also hinted at by Bronnimann (1955). This segment model is significant since it suggests closer affinity to Braarudosphaeraceae which are formed of 5 clearly separated segments with a laminar sub-structure. This is an intriguing suggestion, but it has not been unambiguously demonstrated. Studies of Late Jurassic nannofossils (Bergen et al. 2014, Varol & Bowman 2019) have revealed possible common ancestors for Nannoconus and the Braarudosphaeraceae strengthening the case for the segment model.
Given this, PXCT investigation of Nannoconus seems extremely promising as a way of resolving uncertainties of the structure, as well as paving the way for applying the technique to other nannofossils. However, although it is stated that the technique has been successfully applied to 5 hand-picked, well-preserved, specimens, only very limited results are presented here. The process of segmenting out a lamella from the PXCT data is shown and I would have expected this approach to be applied to the entire nannolith, as is routinely done with CT reconstructions of larger fossils. This should have allowed direct testing of the segment model, determination of the number of helical spirals, etc.
However, no such reconstruction is provided, instead the bulk of the results section is concerned with mathematical modelling of possible Nannoconus structures based on the segmentation of a single lamella from one PXCT image stack. This modelling apparently showed that Nannoconus-like structures can be created using the segment model. The modelling approach is however, as noted by other reviewers, hard to follow. In part this may be a result of inherent complexity and of mperfect presentation, but some aspects give cause for concern. Notably (1) The layer and segment models appear to be treated as mutually exclusive alternatives which is clearly illogical since both models can be valid descriptions of the same structure. By analogy, a stretcher bond brick wall can be considered as being formed of layers of bricks, but can equally validly be described as formed of columns of bricks with alternating offsets between successive bricks, or as formed of bricks arranged in sloping rows. These three ways of describing the arrangement of the bricks are each valid and are not mutually exclusive. In the same way the layer and segment descriptions of Nannoconus structure can both be correct and are not mutually exclusive. The layer structure is readily observable in electron micrographs and is clearly correct. The segment model is less obvious, but the data presented here provides evidence in favour of it. (2) In many places in section 4.3 layers/segments are referred to – e.g. “the total number (N) of layers/segments in the whole skeleton of N. globulus is calculated as 12.” This seems to indicate some confusion, layers and segments are different subdivisions of the Nannoconus structure so a layer/segment has no obvious meaning, and there is no obvious reason why the number of layers should be the same as the number of segments. (3) Twin lamellae – in section 4.1 it is stated that “Lamella-A + lamella-B formed twin lamellae.” It is not clear what this statement means, in particular is it implied that the A and B lamellae are crystallographic twins?
Conclusion: Although inspired by the PXCT study, the primary focus of this paper is mathematical modelling of possible Nannoconus structures. I recommend that the presentation of this modelling is carefully revised and the conclusions that can be drawn from it clarified. I would also welcome a detailed presentation of the results of PXCT study, either here or in a separate paper.
References cited
Aubry, M. -P. (2013). Cenozoic Coccolithophores: Braarudosphaerales. Micropaleontology Press, American Museum of Natural History, New York. 1-336.
Aubry, M. -P. (2025). Biomineralization in the calcareous nannoplankton phenotypic expressions across life cycles, geometric control on diversification, and origin. Minerals. 15: 1-49.
Bergen, J. A., Boesiger, T. M. & Pospichal, J. J. (2014). Low-latitude Oxfordian to Early Berriasian nannofossil biostratigraphy and its application to the subsurface of Eastern Texas. In, Hammes, U. & Gale, J. (eds) Geology of the Haynesville Gas Shale in East Texas and West Louisiana, U.S.A. American Association of Petroleum Geologists, Memoirs . 105: 69-102.
Brönnimann, P. (1955). Microfossils incertae sedis from the Upper Jurassic and Lower Cretaceous of Cuba. Micropaleontology. 1(1): 28-51
van Niel, B. E. (1992). New observations on the morphology of Nannoconus. In, Hamrsmid, B. & Young, J. R. (eds) Nannoplankton Research, Proceedings of the 4th INA Conference, Prague 1991, vol II. Knihovnicka ZPN . 14a: 73-85.
van Niel, B. E. (1994a). A review of the terminology used to describe the genus Nannoconus (calcareous nannofossil, incertae sedis). Cahiers de Micropaléontologie. 9: 27-47
Varol, O. & Bowman, A. R. (2019). Taxonomic revision of selected Late Jurassic (Tithonian) calcareous nannofossils and the application of mobile mounting. Neues Jahrbuch für Geologie und Paläontologie, Abhandlungen. 291: 65-87.
Young, J. R., et al. (1997). Guidelines for coccolith and calcareous nannofossil terminology. Palaeontology. 40: 875-912.
Citation: https://doi.org/10.5194/egusphere-2025-1840-RC2
Model code and software
Code (Python script) for the 3D submicron-scale skeletal reconstruction of Nannoconus Rajkumar Chowdhury, Alejandro Fernandez-Martinez, and Fabienne Giraud https://doi.org/10.5281/zenodo.14925063
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