# Cerium occurs as cerium-phosphate clusters around bioapatite nanocrystals in deep-sea sediments

Alain Manceau, Anne-Claire Gaillot, Jianlin Liao, Yan Li, Olivier Mathon, Kirill A Lomachenko, Pieter Glatzel, Alexandre Simionovici, Mélanie Balvay, Sophie a L Paul, et al.

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Alain Manceau, Anne-Claire Gaillot, Jianlin Liao, Yan Li, Olivier Mathon, et al. Cerium occurs as cerium-phosphate clusters around bioapatite nanocrystals in deep-sea sediments. Communications Earth & Environment, 2025, 6 (1), pp.466. 10.1038/s43247-025-02439-2 . hal-05170120

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# Cerium occurs as cerium-phosphate clusters around bioapatite nanocrystals in deep-sea sediments

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Alain Manceau Ⓓ1,2 you, Anne-Claire Gaillot Ⓓ3, Jianlin Liao<fnref n="1" />, Yan Li Ⓓ1, Olivier Mathon<fnref n="1" />,

Kirill A. Lomachenko<fnref n="1" />, Pieter Glatzel<fnref n="1" />, Alexandre Simionovici Ⓓ4,5, Mélanie Balvay⁴, Sophie A. L. Paul Ⓓ6,7,

Andrea Koschinsky Ⓓ6 & Stephan N. Steinmann Ⓓ2 you

Deep-sea mud is rich in rare-earth elements, primarily found in fluorapatite, a mineral deposit that forms over hundreds of thousands to millions of years through the accumulation of fish remains. After fish die, biogenic apatite captures rare earth elements from seawater on the seafloor and from pore waters during the diagenesis process. The conventional model for rare earth element enrichment suggests that they are incorporated into the bioapatite crystal structure through solid-state diffusion. However, our data reveal that cerium atoms are instead precipitated within an amorphous layer surrounding bioapatite nanocrystals, as shown by high-energy-resolution X-ray absorption spectroscopy and transmission electron microscopy. Computational simulations further support this finding, predicting that cerium atoms cluster on the surface of fluorapatite. These results suggest that the fluorapatite-water interface plays a crucial role in the enrichment of cerium, as well as other rare earth elements, in marine sediments.

Fluorapatite (FAp, (Ca₅(PO₄)₃F) is commonly found at the Earth's surface as biogenic remains in ancient (e.g., phosphorite) and con- temporary (e.g., deep-sea mud) marine deposits<fnref n="1" />⁻¹³. FAp can accom- modate a wide variety of cations and anions in its structure¹⁴, typically at ore grades of several percent. Marine FAp is up to one billion times richer in rare-earth elements from the lanthanide series (REE) and yttrium (REY) compared to seawater<fnref n="1" />⁻⁵, with certain deposits potentially satis- fying global REY demand for centuries to come¹⁵. Understanding the mechanism by which REY are retained in FAp is crucial for compre- hending one of the highest levels of metal partitioning on Earth, with implications for georesource management and the use of apatite as a host phase in waste disposal, including radionuclide containment¹⁶.

Cerium (Ce) ranks as the fourth most abundant REY in marine FAp, after Y, lanthanum (La), and neodymium (Nd)<fnref n="1" />⁻³,¹⁵. However, it stands out from the REY in two significant aspects that affect its geochemical cycling. Firstly, Ce exhibits two oxidation states, 3+ and 4+, in materials formed at the Earth's surface. Secondly, it is the sole REY that occurs naturally as a pure REY(PO₄) mineral phase, known as monazite (CePO₄). Natural monazite is never chemically pure and invariably contains other REY within its

structure¹⁷. Consequently, this raises the question of whether FAp is the sole REY-host in marine deposits.

## State of knowledge for Ce chemical form in FAp

Kashiwabara et al.¹⁸ observed that cerium primarily exists in the 3+ oxidation state in deep-sea muds from the Central North Pacific, while it is predominantly 4+ in deep-sea muds from the Eastern South Pacific. The same year, Marcus et al.¹⁹ found that Ce is present in a combination of mostly 3+ and some 4+ oxidation states in FAp of ferromanganese nodules from the South Pacific Gyre. The 3+ form is considered to be incorporated into the FAp structure, because Ce³⁺ and Ca²⁺ have com- parable effective ionic radii (1.00/1.01 Å)²⁰ and by analogy with the structure of well-crystallized FAp crystals from magmatic/hydrothermal deposits (Fig. 1a)²¹. Liao et al.⁴ successfully imaged the incorporation of Ce³⁺ and Y into the crystal structure of a marine FAp grain sampled at 8.47 m below the seafloor surface (mbsf) of the central North Pacific Ocean, using high-angle annular dark-field scanning transmission elec- tron microscopy (STEM-HAADF) paired with energy dispersive X-ray spectrometry (EDS). They demonstrated that Ce was also found within a

<footnote n="1">¹European Synchrotron Radiation Facility (ESRF), 38043 Grenoble, France. ²ENS de Lyon, CNRS, Laboratoire de Chimie, 69342 Lyon, France. ³Nantes Université, CNRS, Institut des Matériaux de Nantes Jean Rouxel, IMN, 44000 Nantes, France. ⁴Université Grenoble Alpes, CNRS, ISTERe, 38000 Grenoble, France. ⁵Institut Universitaire de France (IUF), 1 rue Descartes, 75005 Paris, France. ⁶School of Science, Department of Physics and Earth Sciences, Constructor University, D-28759 Bremen, Germany. ⁷GEOMAR, Helmholtz Centre for Ocean Research Kiel, Wischhofstr. 1-3, D-24148 Kiel, Germany. ✉e-mail: alain.manceau@esrf.fr; stephan.steinmann@ens-lyon.fr</footnote>
<figure><img src="image_5.png" /><figcaption>Fig. 1 | Polyhedral representation of the local structure of Ce. a Magmatic/hydrothermal FAp (Ca₁₀(PO₄)₆F₂)²¹. b K₃Ce(PO₄)₂²⁹. Dark green, Ca in the Ca2 site; light green, Ca in the Ca1 Zsite; blue, Ce in the Ca2 site; light brown, P edge-linked to Ca2/Ce2; dark brown, P corner-linked to Ca2/Ce2; red, O; cyan, F.</figcaption></figure>

<figure><img src="image_6.png" /><figcaption>Fig. 2 | Ce L₃-edge X-ray absorption spectrum of bioapatite. Blue: measured with a SDD (standard XAS). Black: measured with a five-crystal spectrometer (HERFD-XAS)⁵⁶.</figcaption></figure>

poorly crystalline, Si and Na-rich, 20-nm thick, superficial Ca-P layer in another FAp grain. However, no Ce was detected within the second grain by EDS. The incorporation process of dissolved Ce interacting with FAp was described as a cation exchange mechanism, where isomorphic substitution of Ce for Ca occurs within the FAp structure, accompanied by the release of Ca into the solution. This model suggests that the Si/Na enrichment observed at the FAp surface is paired with Si⁴⁺ for P⁵⁺ and Na⁺ for Ca²⁺ substitutions to balance the excess electronic charge resulting from the substitution of Ce³⁺ for Ca²⁺.

Regarding the 4⁺ form of Ce, Baturin et al.²² identified cerianite (CeO₂) crystallites adhered to the surface of FAp in ferromanganese crusts from the Magellan Seamounts in the Northwest Pacific, using electron microscopy. CeO₂ particles were also found on the surface of the ferromanganese nodules from the South Pacific Gyre studied by Marcus et al.¹⁹,

alongside the previously mentioned Ce³⁺-FAp association¹⁹. Besides CeO₂, Ce⁴⁺ can also be a sorbed species on MnO₂ in ferromanganese and marine sediment deposits, as a result of the oxidation of soluble Ce³⁺ to less-soluble Ce⁴⁺ by Mn³⁺/⁴⁺²³,²⁴.

While the chemical form of Ce⁴⁺ in marine deposits is relatively well-understood, the chemical form of Ce³⁺ in FAp grains remains uncertain. FAp grains consist of nanosized crystallites, resulting in a high surface area per unit volume ratio. Chemical reactions at the FAp-water interface govern the enrichment of FAp in Ce, and the Si-Na coating observed by Liao et al.⁴ using STEM-HAADF and EDS may control the chemical speciation of Ce, limiting its diffusion within the crystal structure. The structure of this coating likely contains essential insights about the primary enrichment mechanism of Ce³⁺ and other REY in marine deposits. Extended X-ray absorption fine structure (EXAFS) spectroscopy is typically the preferred method for investigating the local atomic structure of Ce within the FAp structure and at its surface. However, the application of this technique to REY-containing Earth's surface materials presents considerable challenges and remains largely unexplored.

## Considerations for Ce X-ray absorption spectroscopy in FAp

The primary challenges in measuring Ce-EXAFS in bioapatite include (1) its multi-elemental composition, (2) its inhomogeneity across microns, and (3) its susceptibility to X-ray damage. Ce³⁺ is oxidized to Ce⁴⁺ when subjected to the high X-ray flux density typical of the 3rd and 4th generation synchrotron sources (Supplementary Fig. S1). In addition, at the L₃-edge (5723 eV), the Ce-EXAFS oscillations are disrupted at 5891 eV by the L₂-edge of La, at 5964 eV by the L₃-edge of Pr, and 5989 eV by the L₁-edge of Ba (Fig. 2). The usable energy range of 5891 – 5723 = 168 eV is insufficient for structural analysis ($k_{max}$ = 6.6 Å⁻¹). Moreover, the counting statistics of the EXAFS signal in Ce-Lα₁ fluorescence-yield measurement (4839 eV) is severely limited by the high background level from the unwanted Lβ₁ (~ 4828 eV) emission line of Ba, the Lα₁+₂ (~ 4647 eV) and Lβ₁ (~ 5038 eV) lines of La, and the Lα₁+₂ (~ 5035 eV) line of Pr (Supplementary Fig. S2).

The latest advancement in high-energy-resolution fluorescence detected EXAFS spectroscopy (HERFD-EXAFS, hereafter EXAFS), which enables the precise selection of a desired emission line (here Ce(Lα₁))²⁵,²⁶, combined with micro X-ray fluorescence (XRF) and cryogenic measurement, effectively addresses the three experimental challenges. This integrated approach to Ce speciation was applied for the first time in 2023 on the new ID24-DCM beamline at the European Synchrotron Radiation Facility (ESRF)²¹.

In this study, we present the distribution of Ce in fish bones and teeth analyzed using micro-XRF on biogenic FAp sampled from sediment at 1.94 mbsf (16GC-194, [Ce] = 2203 ± 545 mg/kg, ppm) and 4.70 mbsf (16GC-470, [Ce] = 2081 ± 414 mg/kg, ppm) in the Clarion-Clipperton Zone (CCZ) of the Pacific Ocean. Subsequently, we describe and compare the EXAFS data of FAp with those of the CeO₂ and monazite (high-temperature CePO₄) references, then fit the data ab initio to determine the local structure of Ce. Our findings indicate that the Ce atoms are segregated in Ce-phosphate clusters (referred to herein as CePO₄), which are found alongside minor CeO₂ at a depth of 1.94 m. The presence of Ce is validated by transmission electron microscopy (STEM-HAADF) coupled to elemental mapping, revealing that the FAp nanocrystals are enveloped in an amorphous siliceous matrix rich in P and Si but low in Ca. Lastly, density functional theory (DFT) shows that the clustering of Ce atoms at the FAp-water interface is thermodynamically favorable. We conclude with considerations regarding the geochemical fate of Ce in marine mud and the surface reactivity of FAp.

## Results and discussion

### Ce distribution by XRF imaging

Figure 3a displays a map illustrating the distribution of Ce in numerous FAp fish bones for 16GC-470. The concentration of Ce is uniform within individual grains and variable among grains. The population histogram depicting the Ce Lα₁ intensities has a bell-shaped form, suggesting the presence of only one Ce species (Sp1).
<figure><img src="image_7.png" /><figcaption>**Fig. 3** | X-ray fluorescence maps and population histograms of the distribution and concentration of Ce in bioapatite. a 16GC-470. b–e 16GC-194. Red signifies higher concentrations, while blue indicates lower concentrations. Counting time = 5 ms. a Dimension 1200 (H) × 1400 (V) µm², pixel size = 5 µm. b Dimension 290 (H) × 170 (V) µm², pixel size = 1 µm. c Dimension 360 (H) × 210 (V) µm², pixel size = 3 µm. d Dimension 300 (H) × 200 (V) µm², pixel size = 1 µm. e Dimension 600 (H) × 400 (V) µm², pixel size = 5 µm. The relationship between the shape of the histograms and the oxidation state of Ce was obtained by combining XRF and EXAFS data.</figcaption></figure>

Unlike 16GC-470, fish bones and teeth for 16GC-194 display both uniform and localized accumulations of Ce (Fig. 3b–e). The two distributions of Ce present distinct population histograms, with a bell-shaped form for the uniform distribution (Fig. 3b, c) and a power-law shape for the localized distribution (Fig. 3d). Below, we demonstrate that the second distribution serves as an indicator for another Ce species (Sp2). The bone shown in Fig. 3e presents both types of distribution, which we attribute to the coexistence of Sp1 and Sp2 within the same FAp grain.

## Ce speciation by EXAFS spectroscopy

To analyze the speciation of Ce and its variability, several EXAFS spectra of the 16GC-470 preparation shown in Fig. 3a were recorded using a macro beam (80 × 80 µm²). Additionally, point spectra for the 16GC-194 bones and teeth shown in Fig. 3b–e and exhibiting uniform (Sp1, Fig. 3b, c) and nonuniform (Sp2, Fig. 3d, e) distribution of Ce were recorded with a micro beam (1 × 1 µm²). Point spectra for the tooth shown in Fig. 3b were recorded along two line transects extending from the root to the tip. All EXAFS spectra for 16GC-470 and the uniform areas of 16GC-194 showed statistical invariance. The spectra for the Ce-rich regions of 16GC-194 (Fig. 3d, e) were

also identical, but different from those of the first set. The spectra from each set were grouped and averaged to produce two spectra that are representative of the Sp1 and Sp2 species, ensuring higher signal-to-noise ratios (Fig. 4a).

The frequency and structure of the EXAFS oscillations for Sp2 (Ce-rich regions) align with those of CeO₂ (Fig. 4b). The variation in amplitude between Sp2 and CeO₂ arises from the measurement temperature difference, 2.6-4 K for Sp2 and 290 K for CeO₂. The EXAFS spectrum for Sp1 (uniform regions) is compared in Fig. 4c to a magmatic/hydrothermal FAp reference from the Cerro de Mercado mineral deposit located near Durango, Mexico ([Ce] = 4,900 ppm¹). The Sp1 and Durango spectra differ in the shape of the second oscillation (k = 4.5-5.5 Å⁻¹) and the existence of a double peak at k = 5.8 Å⁻¹ in Sp1, indicating that Ce has a distinct short-range order in the two FAp.

The Fourier transforms (FT) of the Sp1 and Durango EXAFS spectra indicate that the Ce-O peak for Sp1 is notably broadened on the right (i.e., indicating longer distance values, Fig. 5a). The second FT peak at R + ΔR = 2.8 Å, which corresponds to the nearest and next-nearest P shells in Durango, is present in Sp1, but not the third peak from the Ca shell.
<figure><img src="image_8.png" /><figcaption>**Fig. 4** | Ce L₃-edge EXAFS spectra of bioapatite. a 16GC-470 and uniform regions of 16GC-194 (maps 3b,c), and Ce-rich regions of 16GC-194 (maps 3 d,e). b Ce-rich regions compared with the CeO₂ reference (cerianite). c 16GC-470 and uniform regions of 16GC-194 compared with the magmatic/hydrothermal FAp reference from Durango.</figcaption></figure>

However, Sp1 exhibits a conspicuous peak at a longer distance ($R + \Delta R = 4.5$ Å) that is absent in Durango. Analysis of the data shows that the Ca atomic shell in Durango is responsible for the splitting of the second EXAFS oscillation at $k = 4.5-5.3$ Å⁻¹ (Fig. 4c), whereas the FT peak at $R + \Delta R = 4.5$ Å in Sp1 is related to the EXAFS structure at $k = 5.8$ Å⁻¹. From this, we conclude that Ce is not, or scarcely, substituted for Ca in the marine FAp. Using the $k = 5.3$ Å⁻¹ oscillation as a marker for Ce-Ca pairs in FAp (Fig. 4c), the shoulder seen on the Sp1 spectrum at this k value is compatible with the potential existence of some Ce-Ca pairs.

## Identification of a new CePO₄ species (Sp1)

The bond lengths and effective coordination numbers of the unknown Sp1 species, which is uniformly distributed within the FAp grains, were obtained by least-squares fitting of the EXAFS data (Fig. 6a and Supplementary Fig. S3 and Supplementary Table S1). A model featuring two O subshells at

<figure><img src="image_9.png" /><figcaption>**Fig. 5** | Radial distribution function of Ce in bioapatite. Fourier transforms of the Ce L₃-edge EXAFS spectra for 16GC-470 and the uniform regions of 16GC-194 (maps in Fig. 3b, c) compared with the magmatic/hydrothermal FAp reference from Durango (a), and synthetic monazite (b). The two references were measured at 290 K.</figcaption></figure>

2.36 Å and 2.54 Å (average = 2.46 Å), two P shells at 3.22 Å and 3.52 Å, and one Ce shell at 4.97 Å adequately explains the data.

The proximity of the two P shells renders them visually indistinguishable on the FT when integrating the data over the 3.5-10 Å⁻¹ *k* range (Figs. 5, 6b). Nonetheless, the second FT peak shows considerable misfit with just one P shell (Supplementary Fig. S3). When the integration begins at *k* = 2.0 Å⁻¹, the second FT peak becomes split, which is observable in the Cauchy wavelet transform (WT) of the data (Fig. 7)²⁷,²⁸. On the WT map, contributions from the lower atomic number O and P atoms prevail at lower *k* values, while contributions from the higher atomic number Ce atoms prevail at higher *k* values, consistent with theory. A straightforward point to validate the attribution of the FT peak at $R + \Delta R = 4.5$ Å for SP1 to single Ce-Ce scattering events, rather than multiple scattering events between Ce-(O,P) pairs, is that multiple scattering paths have a maximum amplitude in the low *k*-range.

Returning to the local structure of Ce in Sp1, the two Ce-P distances of 3.22 Å and 3.52 Å align with Ce being part of a phosphate structure featuring an apatite-type framework (Fig. 1a)²¹, whereas the average Ce-O distance of 2.46 Å and the Ce-Ce distance of 4.97 Å do not. The six closest O atoms are at 2.43 Å on average in Durango FAp and the nearest Ce/Ca atomic shell ranges from 3.95 Å to 4.15 Å²¹. An atomistic simulation of the Ce-O distance for Ce(H₂O)CN as a function of the coordination number (CN) shows that $d(\text{Ce-O}) = 2.42 - 2.43$ Å for CN = 6, $d(\text{Ce-O}) = 2.45 - 2.49$ Å for CN = 7, $d(\text{Ce-O}) = 2.49 - 2.52$ Å for CN = 8, and $d(\text{Ce-O}) = 2.54 - 2.55$ Å for CN = 9. In addition, a search of the Inorganic Crystal Structure Database (ICSD) found 10 distinct Ce-PO₄ bonding environments, one with CN = 7 and $<d(\text{Ce-O})> = 2.476$ Å (K₃Ce³⁺(PO₄)₂)²⁹, six with CN = 8 and $<d(\text{Ce-O})> = 2.4931$ Å²⁰⁻³⁴, and three with CN = 9 and $<d(\text{Ce-O})> = 2.546$ Å³⁵⁻³⁷. Among the six CN = 8 compounds, two exhibit a 6 + 2 coordination, white the six
nearest O atoms at 2.420 – 2.427 Å, on average, like Ce(H₂O)₆ and close to Ce in FAp (2.43 Å). Thus, we conclude that the unknown Sp1 multinuclear chemical entity in 16GC-470 (Fig. 3a), and in uniform regions of 16GC-194

<figure><img src="image_10.png" /><figcaption>**Fig. 6** | Analysis of the EXAFS data of bioapatite. Best-fit of the Ce L₃-edge EXAFS spectrum (a) and Fourier transform (b) for 16GC-470 and the uniform regions of 16GC-194.</figcaption></figure>

(Fig. 3b, c), is a phosphate compound with a Ce coordination of 7 (CePO₄ clusters).

A coordination number of 7 excludes a monazite-like local structure for the CePO₄ clusters, as CN = 9 in monazite (<d(Ce-O)> = 2.55 Å³⁵). In addition, the Ce-Ce EXAFS distance of 4.97 Å in CePO₄ is incompatible with the monazite's distance of <d(Ce-Ce)> = 4.21 Å³⁵. The longer Ce-O bond distance and shorter Ce-Ce distance in monazite relative to CePO₄ are confirmed experimentally from the comparison of their FT (Fig. 5b). Rhabdophane (REE(PO₄)-0.667H₂O), which precipitates experimentally in contact with hydroxyapatite³⁸, and has been observed associated with FAp on weathered granite³⁹, also has too short Ce-Ce distances (<d(Ce-Ce)> = 4.1-4.2 Å)³⁰. The dismissal of the monazite and rhabdophane models raises the question of the bonding configuration of Ce in CePO₄. We show below that the connectivity of the CeO₇ and PO₄ building blocks of the CePO₄ clusters can be assessed by examining the relationship between the Ce-P and Ce-Ce distances in known structures, on one hand, and the linkages of the CeO CN⁻-PO₄ and CeO CN⁻-CeO CN (CN = 7,8,9) polyhedra, on the other hand.

### Polyhedral structure of the CePO₄ clusters

An analysis of the Ce-PO₄ bonding structures in ICSD shows that the CeO CN⁻-PO₄ polyhedra are linked through edges and corners (vertices) and the CeO CN⁻-CeO CN polyhedra through edges. This geometrical investigation is represented in Fig. 8 as population histograms of the average Ce-P and Ce-Ce distances for the seven-, eight-, and nine-coordinated Ce structures as a function of the linkage type. The average Ce-P distances are 3.15-3.27 Å across a shared edge and 3.72 – 3.88 Å across a shared corner, and the average Ce-Ce distances are 4.17 – 4.38 Å across a shared edge. Notably, corner linkages between the Ce polyhedra are absent in all known structures. Ce polyhedra do not connect via a single O atom (vertex). Instead, they are linked by two O atoms in edge-sharing configurations or through PO₄ groups in a CeO CN – PO₄ – CeO CN arrangement characterized by *d*(Ce-Ce) ≥ 4.8 Å (Fig. 1b). The distinct metrical differences in the polyhedral linkages of the Ce-PO₄ structures indicate that a polyhedral approach provides guidance for assessing the bonding structure of Ce within the CePO₄ clusters. Consequently, the Ce-P₁ EXAFS distance of 3.22 Å corresponds to a (CeO₇-PO₄)edge linkage, whereas the Ce-Ce EXAFS distance of

<figure><img src="image_11.png" /><figcaption>**Fig. 7** | Evidence for two P atomic shells around Ce. Cauchy wavelet transform map of the Ce L₃-edge EXAFS spectrum for 16GC-470 and the uniform regions of 16GC-194.</figcaption></figure>
<figure><img src="image_12.png" /><figcaption>**Fig. 8 |** Relationship between interatomic distances and polyhedral linkages in Ce
phosphates. Population histograms of the average Ce-O, Ce-P, and Ce-Ce distances
in seven-coordinated (a)²⁹, eight-coordinated (b)³⁰⁻³⁴, and nine-coordinated (c)³⁵⁻³⁷
Ce phosphate structures with polyhedral representation of the linkage types. Blue,
Ce; light brown, P edge-linked to Ce; dark green, P corner-linked to Ce; red, O.</figcaption></figure>

4.97 Å relates to a CeO<sub>7</sub> – PO<sub>4</sub> – CeO<sub>7</sub> coordinated structure (Fig. 9). The EXAFS distance of the P2 shell at 3.52 Å is attributed next.

We showed previously that the seven-coordinated K₃Ce³⁺(PO₄)₂ structure from the ICSD closely aligns with the average Ce-O EXAFS distance. In K₃Ce³⁺(PO₄)₂, the CeO₇ polyhedra are *d*(Ce-Ce) = 4.90 Å apart and connected through edge-sharing (*d*(Ce-P₁) = 3.15 Å) and corner-sharing (*d*(Ce-P₂) = 3.72 ± 0.26 Å) PO₄ groups (Fig. 1b). Although the Ce-P₁ and Ce-Ce distances are close in value to the CePO₄ EXAFS distances of 3.22 Å and 4.97 Å, the average Ce-P₂ distance (3.72 Å) is longer than the EXAFS distance (3.52 Å). However, the *d*(Ce-P₂) values are widely distributed in K₃Ce³⁺(PO₄)₂, with two P₂ atoms at 3.41 Å and three ranging from 3.89 Å to 4.02 Å. Consequently, the EXAFS distance of 3.52 Å in CePO₄ clusters is compatible with a short (CeO<sub>CN</sub>-PO₄) corner linkage (Fig. 9).

Electron microscopy

Further insights into the Ce-enriched nanoapatite were gathered using
transmission electron microscopy. At low spatial resolution, the FAp grains
appear as dense nanoporous aggregates (Supplementary Fig. S4), com-
posed of lath-like particles measuring 50–150 nm in length and 20–30 nm

<figure><img src="image_13.png" /><figcaption>Fig. 9 | Types of polyhedral linkages in CePO₄. Blue, Ce; brown, P; red, O.</figcaption></figure>

in width (Supplementary Fig. S5 and S6). High-resolution imaging reveals
that the particles are multidomainic with lattice-fringe spacings typical of
FAp (Fig. 10 and Supplementary Figs. S5-7). At the same time, STEM-EDS
maps indicate that they contain approximately 0.02-0.06 at% of various
REY elements (Supplementary Figs. S5 and S8-9). The monodomainic
nanocrystals are embedded and separated by an amorphous phase.
Nanochemical analysis of this phase shows that it is rich in Si and O but
depleted in Ca and P (Supplementary Fig. S8). This finding, along with the
EXAFS results, is considered supporting evidence for the presence of the
CePO₄ clusters in the amorphous matrix surrounding the FAp
nanocrystals.

Thermodynamic stability of Ce clusters

To complement our experimental findings, we calculated the energy dif-
ference between mononuclear and binuclear Ce-PO₄ complexes on the
{100} lateral surface of FAp crystals<sup>41-44</sup>. Water molecules were not explicitly
considered in the model surfaces. Therefore, pH effects on the structure and
energetics of the surface complexes were not taken into account. At the FAp
surface, The Ce<sup>3+</sup> for Ca<sup>2+</sup> substitution can be charge-balanced by coupled
cationic substitutions, as in the bulk<sup>21,45</sup>, or by addition of anions. We
explored three Ce<sup>3+</sup> ↔ Ca<sup>2+</sup> charge compensation models: Si<sup>4+</sup>-Ce<sup>3+</sup> co-
doping in place of P<sup>5+</sup>-Ca<sup>2+</sup> within the FAp structure<sup>21,45</sup>, and the attachment
of either bicarbonate (HCO<sub>3</sub><sup>-</sup>)<sup>46</sup> or hydroxyl (OH<sup>-</sup>) ions to each Ce<sup>3+</sup>. In all
scenarios, positioning two Ce dopants close to each other (4-5 Å) was
energetically beneficial.

The most stable configurations are represented in Fig. 11 and Sup-
plementary Fig. S10. Ce atoms exhibit attractive interactions that make them
stick together. Reducing the separation distance between a Ce-Ce pair from
approximately 11 Å (mononuclear surface complexation) to 4–5 Å
(binuclear surface complexation) resulted in a relative energy gain of about
0.5 to 1 eV (Supplementary Table S2). For the binuclear 2(Ce³⁺ - HCO₃⁻) co-
adsorption, we identified one configuration featuring a significant surface
reconstruction. One Ce ion from the Ce-Ce pair shifted from the surface Ca
position to form an inner-sphere sorption complex attached to four term-
inal oxygens (Fig. 11a). Inner-sphere complexation of a REY on a mineral
surface has been documented recently for Y(III) on orthoclase, using X-ray
reflectivity⁴⁷. The reconstructed 2(Ce³⁺ - HCO₃⁻) structure is 0.3 eV more
stable than the unreconstructed 2(Ce³⁺ - HCO₃⁻) structure, the Ce-Ce dis-
tance is 4.9 Å compared to 4.0-4.2 Å for the Ca-Ca distance, and the average
Ce-O distance is 2.46 Å compared to 2.55 Å for the other models. The Ce
bond distances for the reconstructed structure closely match the EXAFS
metric parameters.

We conclude that Ce³⁺ tends to cluster, rather than to diffuse into
the FAp surface, providing the requisite seeds for the experimentally
identified CePO₄ clusters. The potential incorporation of carbonate
within the Ce³⁺-PO₄ aggregates cannot be dismissed, as it might go
undetected by EXAFS spectroscopy due to the weak scattering amplitude
of the carbon atom.

**Concluding remarks**

Our findings indicate that Ce is speciated as minor Ce⁴⁺O₂ and pre-
dominantly as multinuclear Ce³⁺-PO₄ clusters at a depth of 1.94 m in core
16GC from the CCZ sediment. In contrast, it exists solely as Ce³⁺-PO₄ at a
<figure><img src="image_14.png" /><figcaption>**Fig. 10** | TEM characterization of bioapatite. a HRTEM image of 16GC-194 nanocrystals embedded in an amorphous matrix. Larger scale view available in Supplementary Fig. S5. b, c FFT of two individual nanocrystals of the HRTEM</figcaption></figure>

image, oriented along [-321] and [01-1] zone axes, respectively, and corresponding simulated and indexed electron diffraction patterns.

depth of 4.70 m. The co-occurrence of the two oxidation states has been reported previously in ferromanganese nodules and associated FAp grains from the Pacific Ocean¹⁹. Cogent arguments were made for an oxidation of dissolved Ce³⁺ to CeO₂ particles within the water column, followed by the settlement and eventually adherence of the CeO₂ particles to the nodules and FAp grains. CeO₂ likely accumulates more near the sediment surface, and its gradual dissolution in the sediment as redox potential decreases may be a key geochemical process, leading to the secondary enrichment of Ce in bioapatite.

CePO₄ cluster formation may be understood as an interface-coupled exchange-precipitation process, where Ce replaces Ca on the external surfaces of FAp nanocrystals. This process leads to the formation of multi-nuclear CePO₄ clusters, which eventually precipitate as a new short-range ordered CePO₄ phase. The mineral-water interface picture that can be painted from the results differs from the general understanding of apatite's surface reactivity in contact with divalent metal cations. Typically, when they sorb onto apatite, the result is a less soluble metal-containing apatite, accompanied by the release of Ca from the adsorbent into the solution. Two proposed mechanisms are solid-state cation exchange via solid-state diffusion and coupled dissolution-precipitation⁴⁸,⁴⁹. An illustrative example is pyromorphite (Pb₅(PO₄)₃(F,OH,Cl), an isomorph of apatite, which is sparingly soluble (pKₛₚ = 77–84) and forms readily upon Pb sorption on apatite⁵⁰. This reaction facilitates the immobilization of Pb in lead-contaminated soils through phosphate amendments⁵¹. EXAFS results suggest a new mechanism where aqueous Ce interacts with apatite's phosphate groups, resulting in a neoformed CePO₄ phase, that is structurally different from apatite. Formation of CePO₄ nuclei on the surface of apatite, which are expected to serve as nucleation sites during CePO₄ formation, is predicted by density functional theory.

STEM-HAADF imaging and EDS nanoanalysis reveal that the CePO₄ clusters occur within the nanometric amorphous phase that embeds the FAp nanocrystals. In this context, the minor Ce-Ca pairs identified at *k* = 5.8 Å⁻¹ in the EXAFS data may indicate a small amount of Ce present in the apatite structure. However, EXAFS unequivocally identifies CePO₄ as the primary Ce species in marine sediment. This finding prompts the

question of whether other REY can substitute Ce in CePO₄, similar to what happens in monazite¹⁷, or if they are incorporated into short-range ordered REY(PO₄) nanoparticles. Regardless, the amorphous phase could also contain additional REY. If this hypothesis is validated, this would have significant implications for the recovery of REY from mined phosphate deposits via mineral leaching. Kato et al.⁵² observed that REY are easily recovered from deep-sea mud through simple acid leaching. This finding

<figure><img src="image_15.png" /><figcaption>**Fig. 11** | Atomic-scale structure of Ce-HCO₃ dimers. View of the Ce-HCO₃ dimers on the reconstructed (a) and nonreconstructed (b) (100) surface of apatite. Blue, Ce; green, Ca; brown, P; black, C; red, O; grey, H.</figcaption></figure>
can be understood at the microscopic level by the presence of REY in the
amorphous phase. Poorly ordered atomic structures are inherently less
stable than crystalline phases, and FAp is weakly soluble⁵³,⁵⁴.

This research provides a foundation for applying HERFD-EXAFS to
other REY, thereby advancing our understanding of their chemical forms,
which is essential for geochemical studies and mining activities. A yet
unexplored material that would benefit from this instrumental advance-
ment is terrestrial and seamount phosphorites. Aside from their composi-
tional complexity, a further experimental hurdle of phosphorites is their
complex mineralogy, as REY are found in at least two microscopic phases,
apatite and calcite⁸.

**Materials and methods**

XRF and EXAFS spectroscopy

The 16GC-194 and 16GC-470 samples were collected during the RV SONNE cruise SO268⁵⁵. The two sediment core layers contain 2203 ± 545 mg/kg (ppm) Ce and 2081 ± 414 mg/kg (ppm) Ce, respectively¹. Fossilized fish bones and teeth of several tens to a few hundred microns were hand-picked under a binocular microscope and deposited on a carbon adhesive tab for micro-XRF and EXAFS spectroscopy analysis. The incident photon energy was selected using the Si(111) reflection from a liquid-nitrogen-cooled double-crystal monochromator, and the rejection of higher harmonics was achieved with two Si mirrors at an incidence angle of 4 mrad (7 keV cutoff). The beam size on the sample of the unfocused beam was 80 (H) × 80 (V) µm², and the incident X-ray flux was ~5 × 10¹² photons per sec at the sample position. In micro mode, the beam was focused to 1 × 1 µm² with a set of Pt-coated Kirkpatrick-Baez (K-B) mirrors. The Ce Lα₁ (3d₅/₂ → 2p₃/₂) fluorescence line (4839 eV) was selected using the 400 reflection of five Si crystals of 100 mm diameter, spherically bent to a radius of 0.5 m and aligned at a Bragg angle of 70.6° in a vertical Rowland geometry⁵⁶. The diffracted intensity was measured with a Si drift diode detector (SDD) in single photon counting mode.

Preliminary measurements at room temperature showed that Ce(III) was stable in hydrothermal FAp and photo-oxidized to Ce(IV) in bioapatite under the intense X-ray beam. The amplitude of the Ce(III) white line of 16GC-194 was reduced by 17% after 21 min exposure to the beam (Supplementary Fig. S1). Therefore, all measurements on marine FAp were performed at a temperature of 2.6-4 K using a homemade continuous-flow helium cryostat⁵⁷. No changes in spectral features were observed at low temperature during data collection that would indicate radiation damage. Multiple X-ray absorption scans from 5700 eV to 6150 eV (k = 10.3 Å⁻¹) of 7 min 30 s duration were averaged with PyMCA⁵⁸. The EXAFS spectra were reduced and fitted with WinXAS⁵⁹. Theoretical amplitude and phase shift functions were generated with FEFF 8.2⁶⁰ using monazite as a structural model. The XRF spectrum for 16GC-470 was fit with Hypermet functions⁶¹.

Electron microscopy

High-resolution transmission electron microscopy (HRTEM) images and
selected-area electron diffraction (SAED) patterns of the FAp grains were
acquired using Nant'Themis, a Themis Z G3 Cs-probe corrected micro-
scope (Thermo Fisher Scientific) operating at 300 kV and equipped of a
GATAN OneView camera (resolution ~1.8 Å). Elemental maps (EDS) were
acquired in scanning (STEM) mode with 180 Å current, a dwell time of
20 µs/pixel, and a pixel size of about 1 nm, using a Super-X™M emission X-ray
spectrometer consisting of four windowless silicon-drift detectors (SDDs)
providing a large collection solid angle of 0.7 srad. Sample 16GC-194 was
gently crushed in ethanol and deposited onto a lacey carbon copper grid. ED
simulations were performed using JEMS software, considering the hydro-
yxapatite structure⁶² from ICSD database.

DFT

Density functional theory computations were performed using the Vienna Ab Initio Simulation Package (VASP)⁶³,⁶⁴, and nearly identical computational schemes as in our previous work on Ce in magmatic/hydrothermal FAp²¹,⁴⁵. To explore the surface chemistry of FAp, the WhereWulff⁶⁵

package was used to construct relevant surface terminations. Extra O atoms were added to the exposed surfaces at the unit-cell boundaries to complete the phosphate tetrahedra (i.e., PO₄)⁴². The {100} termination was found to be the most representative of the nanorod surfaces observed by HRTEM, and is known to be the most reactive⁴³,⁴⁴,⁶⁶. Accordingly, all computations of the surface chemistry of Ce on FAp were performed on a 2×2 {100} surface. The Perdew-Burke-Ernzerhof (PBE)⁶⁷ density functional approximation in combination with the density dependent dispersion correction (dDsC)⁶⁸,⁶⁹ has been used. Projector-augmented wave (PAW) pseudopotentials have been used for all elements. The plane-wave cutoff energy was set to 500 eV. Wave functions were converged to 10⁻⁶ eV and the forces below 0.05 eV/Å.

Data availability

Synchrotron data generated during this study are available in this repository: https://doi.org/10.15151/ESRF-ES-1312815088 The Cartesian coordinates of the DFT models are provided in Supplementary Data 1. The VASP files are available on this repository: https://doi.org/10.17172/NOMAD/2025.04.01-1.

Received: 22 October 2024; Accepted: 3 June 2025;
Published online: 16 June 2025

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## Acknowledgements

The authors thank Eric Gautron for access to the Nant’Themis TEM of the IMN’s characterization platform PLASSMAT. Three anonymous reviewers are acknowledged for constructive comments on the manuscript. The synthetic monazite was provided by the Smithsonian Institution Department of Materials Sciences. The ESRF is acknowledged for providing beamtime on ID24 (project ES-1338). Financial support was provided by the European Union (ERC, Advanced Grant DEEP-SEE, 101052913). Views and opinions expressed are, however, those of the authors only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them. We gratefully acknowledge support from the CBPsmn (PSMN, Pôle Scientifique de Modélisation Numérique) of the

ENS de Lyon for the computing resources. The platform operates the SIDUS solution⁷⁰. Funding for core sampling during cruise SO268 was supplied by the German Federal Ministry of Education and Research (BMBF) within the framework of the JPI Oceans project MiningImpact (03F0812G to A.K.). As the gravity core was collected in international waters and was part of an approved research cruise, no sampling permission was required.

## Author contributions

A.M. Conceptualization, Methodology, Investigation, Formal analysis, Writing - original draft. A.-C.G. Methodology, Investigation, Formal analysis, Writing, J.L. Methodology, reviewed the manuscript. Y.L. Methodology. O.M. Methodology, reviewed the manuscript. K.A.L. Methodology, reviewed the manuscript. P.G. Methodology, reviewed the manuscript. A.S. Formal analysis. M.B. Methodology. S.A.L.P. Methodology, reviewed the manuscript. A.K. Conceptualization, Methodology, reviewed the manuscript. S.N.S. Conceptualization, Methodology, Investigation, Formal analysis, Writing.

## Competing interests

The authors declare no competing interests.

## Additional information

**Supplementary information** The online version contains supplementary material available at https://doi.org/10.1038/s43247-025-02439-2.

**Correspondence** and requests for materials should be addressed to Alain Manceau or Stephan N. Steinmann.

**Peer review information** *Communications Earth & Environment* thanks the anonymous reviewers for their contribution to the peer review of this work. Primary Handling Editor: Carolina Ortiz Guerrero. A peer review file is available.

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