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ABSTRACT Calcification and biomass production by planktonic marine organisms influences the global carbon cycle and fuels marine ecosystems. The major calcifying plankton group

coccolithophores are highly diverse, comprising ca. 250–300 extant species. However, coccolithophore size (a key functional trait) and degree of calcification are poorly quantified, as most

of our understanding of this group comes from a small number of species. We generated a novel reference dataset of coccolithophore morphological traits, including cell-specific data for

coccosphere and cell size, coccolith size, number of coccoliths per cell, and cellular calcite content. This dataset includes observations from 1074 individual cells and represents 61

species from 25 genera spanning equatorial to temperate coccolithophore populations that were sampled during the Atlantic Meridional Transect (AMT) 14 cruise in 2004. This unique dataset can

be used to explore relationships between morphological traits (cell size and cell calcite) and environmental conditions, investigate species-specific and community contributions to pelagic

carbonate production, export and plankton biomass, and inform and validate coccolithophore representation in marine ecosystem and biogeochemical models. SIMILAR CONTENT BEING VIEWED BY

OTHERS CASCADE: DATASET OF EXTANT COCCOLITHOPHORE SIZE, CARBON CONTENT AND GLOBAL DISTRIBUTION Article Open access 24 August 2024 EOCENE EMERGENCE OF HIGHLY CALCIFYING COCCOLITHOPHORES

DESPITE DECLINING ATMOSPHERIC CO2 Article Open access 01 September 2022 MACROSCALE PATTERNS OF OCEANIC ZOOPLANKTON COMPOSITION AND SIZE STRUCTURE Article Open access 03 August 2021

BACKGROUND & SUMMARY Coccolithophores (Prymnesiophyceae) are abundant calcifying marine phytoplankton that are major contributors to the marine carbon cycle1,2 through their dual

production of organic carbon (biomass) and biosynthesis of their inorganic carbon (calcium carbonate, calcite) exoskeletal plates. Coccolithophore calcification and photosynthesis are highly

dynamic cellular processes that respond to changes in cell size, cell stoichiometry (elemental content), and the morphology and production rates of the calcite plates (coccoliths) that form

the exoskeleton (coccosphere) of each cell3,4 that can occur as cell physiology responds to fluctuating environmental conditions. At the community level, changes in population growth rates

and assemblage composition, including changes in the relative and absolute abundance of species present with different morphological traits and therefore degrees of calcification, influences

the contribution of coccolithophores to pelagic carbonate production and carbonate flux to the deep ocean5,6,7. Variability in surface ocean carbonate production2, of which coccolithophores

represent ca. 50–90%1,8,9, and carbonate export affects ocean alkalinity on shorter timescales and therefore the air-sea flux of carbon dioxide9,10,11,12. On longer timescales (Myr), the

production and sedimentation of biogenic carbonate (the counter carbonate pump) acts as a long-term CO2 sink13 that helps to regulate global temperatures14. Given the major role of

coccolithophores in these global processes and the sensitivity of coccolithophore physiology (including calcification) to environmental stressors15,16,17,18,19,20,21,22, understanding the

biogeochemical and ecological consequences of the variability in coccolithophore calcification and productivity and the drivers of this variability have been pressing research questions for

more than 40 years. Coccolithophore morphological traits (i.e., cell size, coccolith size and morphological features, number and arrangement of coccoliths around the cell) are a principal

determinant of coccolithophore calcification. There are approximately 250–300 (morpho)species of extant coccolithophores23 across two life cycle stages (diploid and haploid) that exhibit

extensive morphological diversity24, which is critical for understanding the contribution of different coccolithophore species and coccolithophores as a functional group to marine carbon

cycle dynamics. Despite this, coccolithophores are regularly regarded as a homogenous group and interspecies differences in size, calcification and physiological traits are often overlooked

in common analyses. For example, coccolithophores are usually parameterised as a single ‘calcifying phytoplankton’ class in many Earth system models25. This is often unavoidable due to both

analytical complexity and data availability, as most data for extant coccolithophore cellular biomass and calcite have been measured through the geochemical analysis of culture-derived

material for the relatively small number of species that have been isolated26. The species _Emiliania huxleyi_ has been the most extensively studied, with over 1000 experiments quantifying

biomass and calcite content in this species from a range of genetic strains and under a range of environmental conditions21. Limited data for the organic and inorganic carbon content of

other coccolithophore species are available for some species that are available in culture (e.g., _Gephyrocapsa_, _Coccolithus_, _Calcidiscus, Syracosphaera_, _Scyphosphaera_)27,28,29 but

are based on a comparatively small number of studies that represent only a handful of species or strains. Alternatively, morphometric traits can be used to estimate cellular-level calcite

content for a wide diversity of extant coccolithophore species. A morphometric approach to calculating cellular calcite content is based on estimating the volume of individual coccoliths and

the number of coccoliths per cell30,31. Morphometric-based calcite estimates generally agree well with calcite estimates derived through other approaches32,33,34,35 (see Technical

Validation). With due consideration for the distinct morphological characteristics for each species, morphometric-based cellular calcite estimates can be made across the full diversity of

extant and extinct species. The approach can be applied to coccoliths of any size or thickness and uses measurements taken on both entire, intact coccospheres and on individual coccoliths.

Morphometric-based cellular calcite estimates are also truly cellular, as opposed to the assay-based measurements that average population calcite (including the calcite of dead cells and

shed coccoliths) across population abundance and overestimate mean cell calcite as a result. Morphometric-based estimates of coccolith and cellular calcite content have been widely used to

estimate pelagic carbonate production and carbonate export fluxes (sometimes using a species’ mean coccolith size and the number of coccoliths per cell only)36,37,38,39,40,41,42,43,44,45,

and to quantify calcification responses to environmental and physiological change in both micropaleontological studies46,47,48 and laboratory experiments on _E. huxleyi_, _Coccolithus_,

_Calcidiscus_, and _Helicosphaera_4,49,50,51,52. For the remaining species of extant coccolithophores, very little is known concerning their species- or genus-specific biomass and calcite.

Here, we present a novel dataset of cellular-level extant coccolithophore morphological traits53, including coccosphere and cell size, coccolith size, number of coccoliths per cell, and

morphometric-based estimates of cellular calcite content. All data were measured from pelagic samples obtained from the Atlantic Ocean during the Atlantic Meridional Transect (AMT) cruise 14

(April-June 2004). The samples span several hydrographic provinces, including northern gyre, equatorial, subtropical gyre, and temperate waters54,55, thus capturing natural variations in

morphology that arise due to genetic and phenotypic diversity. This dataset provides some of the first estimates of cellular calcite diversity across a broad diversity of extant

coccolithophores from the Atlantic Ocean. The dataset presents 4712 morphometric measurements from 1074 individual coccospheres representing 25 extant coccolithophore genera and 61 species,

representing all major families except for the Coccolithales and 80% of common genera identified during AMT 1455. The dataset offers reference data for taxon-specific size and calcification

traits that can be used to investigate the contribution of coccolithophores to the global carbon cycle, spatial and temporal variability in coccolithophore calcite content, the links between

morphometric traits (such as coccolith size) and the physiochemical properties of seawater, and trait responses to climate variability. The dataset, supporting data, and the archived images

used to obtain the morphometric data are openly accessible through Zenodo53,56,57. METHODS FIELD SAMPLES Samples were collected during the Atlantic Meridional Transect 14 cruise (28 April

to 1 June 2004). The cruise track ran from the Falkland Islands to the UK covering a sea surface temperature range of 5 to 27 °C and a dissolved nitrate range of 1 to >10 µmol N L−1 

54,58. The coccolithophore community during AMT-14 has previously been investigated over the euphotic zone at 19 stations55. For coccolithophore analysis, 1-2 L of a 20 L seawater sample

collected using a rosette sampler from between 5 and 13 water depths (55, 33, 14, 1, and 0.1% of surface irradiance plus additional water depths at some stations) was gently filtered onto 25

 mm polycarbonate filters with a 0.45 µm pore size. Filters were dried at room temperature and stored until imaging. For the purposes of this morphological trait dataset, a selection of

samples were examined, covering a range of latitudes and water depths (Table 1) to ensure that morphometric data from a wide range of both common and less common extant coccolithophore

species could be measured. Coccolithophore morphometric data were collected from six stations at 55% surface irradiance (7 to 17 m water depth) and at a further seven water depths (30 m, 60 

m, 90 m, 120 m, 140 m, 160 m and 200 m) at station CTD 34 in the southern subtropical gyre (Table 1). A further three samples identified as having higher abundances of generally less

abundant taxa (_Oolithotus_, _Calciosolenia_, _Gephyrocapsa_) were also examined (Table 1). IMAGING Archived images from the study of Poulton _et al_.55 were re-examined here for the

purposes of measuring key coccolith and coccosphere morphometric dimensions and estimating cellular calcite content. The sub-set of images examined for this study can be accessed through

Zenodo56. The scanning electron microscopy (SEM) methodology applied to generate the images is described in Poulton _et al_.55 and follows Charalampopoulou _et al_.59. Segments of each

filter were mounted on an aluminium stub and coated with gold. A SEM (LEO 1450VP Carl Zeiss combined with the software SmartSEM) at 5000x magnification was used to image each filter segment

across 3-4 pre-defined meander-shaped, semi-continuous transects (zero overlap between fields of view). For each sample (station, water depth; Table 1), ca. 600–700 fields of view with a

size 4.054 × 10−3 mm2 (1024 × 768 px, resolution of 13.92 px µm−1) were imaged, representing ca. 8–15 mL filtered seawater volume surveyed per sample. The number of intact coccospheres

observed across these images varied from 16 to 217 between samples (Table 1). EXTANT COCCOLITHOPHORE MORPHOMETRY For each sample, SEM images were surveyed sequentially until an intact

coccosphere was observed. Each intact coccosphere was first identified to species level where possible (and genus level if species could not be identified) following the taxonomy of

Nannotax3 (http://www.mikrotax.org/Nannotax3/) and supporting literature23,60,61 and forms a single data entry in the database comprising the following morphological measurements: coccolith

length, coccosphere diameter, and number of coccoliths per cell. All measurements in the dataset therefore represent morphometric measurements obtained from intact coccospheres only, i.e.,

we do not make any measurements on loose, individual coccoliths and coccolith size data represents measurements made on coccoliths retaining their original arrangement within intact

coccospheres. Measurements were made using the freeware ImageJ62 (v1.53a). Additional coccolith morphometrics were also measured when appropriate for each species, including coccolith width

or the height of coccolith processes (e.g., spine height). The measurement procedure of these morphological features is described and discussed in detail below and an illustration of these

measurements on example specimens from a range of species encountered within the samples is shown in Fig. 1. Further taxonomic considerations that influence the accurate collection of

morphometric data are discussed in a following section. MEASUREMENT OF COCCOLITH LENGTH, COCCOLITH WIDTH AND THE SIZE OF SPECIES-SPECIFIC MORPHOLOGICAL FEATURES Coccolith length (_C__L_) was

measured on a single, flat-lying coccolith on the surface of the coccosphere where the outer rim of the coccolith distal shield was clearly visible (Fig. 1a,b). _C__L_ measurements went

precisely through the centre point of the coccolith. For species with larger central area processes (e.g., the spine of _Rhabdosphaera_, the trumpet-shaped processes of _Discosphaera_), the

height of one process was also measured (Fig. 1c). For some coccospheres, a completely flat-lying coccolith was not visible on the upper coccosphere surface or the distal shield edge(s) of

the most flat-lying coccolith were partially or fully concealed by overlapping adjacent coccoliths. In these cases, the length from central area mid-point to distal shield edge was measured

and doubled to approximate coccolith length (Fig. 1d). Based on measurements of 100 loose coccoliths on a range of species, this method introduced a mean error of −0.6% (ranging ca. ±8%)53.

Ideally, the measured flat-lying coccolith was representative of the size of all coccoliths forming the coccosphere. Coccolith width was similarly measured if necessary. MEASUREMENT OF

COCCOSPHERE DIAMETER A wide range of coccosphere shapes exist across extant coccolithophores. Species are most commonly spherical or near spherical (60–75% of entries on Nannotax323 are

tagged as ‘equant’) but prolate spheroid and ellipsoid-shaped coccospheres are also relatively common (e.g., _Helicosphaera_, Fig. 1e) and ovoid to obpyriform, fusiform, tubular and

bowl-shaped coccospheres are characteristic coccosphere shapes of certain species (for an overview of coccolith and coccosphere terminology, see Young _et al_.63). For easier comparison of

coccosphere size across such a diversity of coccosphere shapes, we therefore recorded coccosphere diameter as equivalent spherical diameter, ∅, which is back calculated from coccosphere

volume that has been calculated with a shape-specific equation for volume appropriate for the species in question. The size measurements required for the calculation of coccosphere volume

(and equivalent spherical diameter) therefore depend on the shape of the coccosphere. As such, each genus or within-genus morpho-group has been assigned a best-fit mathematic shape label

(Supplementary Table 1) that determines the volume calculation64 used to back calculate equivalent spherical diameter, as follows: $${Prolate\; sphere}({PS}){volume}\,({\mu m}^{3})=\frac{\pi

}{6}{d}^{2}h$$ (1) $${Cone}+{half\; sphere}({CHS}){volume}\,({\mu m}^{3})=\frac{\pi }{4}h{d}^{2}$$ (2) $${Double\; cone}({DC}){volume}\,({\mu m}^{3})=\frac{\pi }{12}h{d}^{2}$$ (3) where _d_

is the short-axis measurement (µm) and _h_ is the long-axis measurement (µm) of the coccosphere (see also Fig. 1). Many spherical species (particularly those with placolith-type coccoliths)

do not have precisely spherical coccosphere dimensions, as slight variability in coccosphere thickness can arise from the arrangement of overlapping coccoliths. As such, both long axis and

short axis measurements are always made (Fig. 1a,b,e) and the volume of spherical, sub-spherical and prolate spheroid coccospheres (Supplementary Table 1) were all calculated using the

equation for volume of a prolate sphere (Eq. 1). Although some coccosphere shapes are best described as ellipsoid, it was not possible to measure all axes necessary to calculate ellipsoid

volume from two-dimensional SEM images, so volume was calculated as prolate spheroid (PS) for species with more elongated shapes (Supplementary Table 1). COUNTING THE NUMBER OF COCCOLITHS

PER CELL In SEM images, only one surface of the coccosphere is visible (Fig. 1). To count the number of coccoliths per cell, therefore, the number of coccoliths on the visible surface of the

coccosphere was counted and this number was doubled to approximate the total number of coccoliths in the coccosphere (_C__N_). Some species have coccospheres comprised of a very large

number (>100) of very small (ca. 0.5 to 2 µm) coccoliths (e.g., the polycrater phase of _Alisphaera;_ Fig. 1f). For these coccospheres, the number of coccoliths per cell was counted as

accurately as possible but there is a degree of uncertainty in the counts (see Technical Validation). MORPHOMETRIC-BASED ESTIMATES OF CELLULAR PARTICULATE INORGANIC CARBON (PIC)

Morphometric-based estimates of cellular calcite (particulate inorganic carbon, PIC) depend on the number of coccoliths per cell and the PIC of each of those coccoliths. For each individual

coccosphere, we first estimated coccolith PIC using the method of Young and Ziveri30 based on coccolith size (usually using coccolith length) and a shape factor related to coccolith

cross-sectional shape, as follows: $${coccolith\; PIC}\left({pg}{{CaCO}}_{3}\right)={{C}_{L}}^{3}\times {K}_{s}\times 2.7$$ (4) Where _C__L_ is coccolith size (µm), _Ks_ is a species- or

genus-specific shape factor, and 2.7 is the mass of calcite (pg µm−3). Between species, _Ks_ values vary by around an order of magnitude (minimum of ca. 0.01 to maximum of ca. 0.2 in extant

species30). We used recommended species-specific _Ks_ values from the literature30,32,44,65,66 or adapted the _Ks_ values of a species with similar morphologies for species lacking a

published _Ks_ value. The specific coccolith length parameter used in the calculation (e.g., distal shield length or process height) and _Ks_ value used for each genus or morpho-species

group in the calculation of coccolith PIC are detailed in Supplementary Table 1. Cellular PIC was then calculated by multiplying coccolith PIC by the number of coccoliths per cell, as

follows: $${coccosphere\; calcite}\left({pg}\right)={coccolith\; PIC}\times {C}_{N}$$ (5) Where _C__N_ is the number of coccoliths per coccosphere/cell and coccolith PIC is calculated as in

Eq. 4. The relationship between coccolith morphology and coccolith calcite mass parameterised in Eq. 4, where cell-specific variability in coccolith calcite is driven principally by

variability in coccolith size, represents a simplification of true cellular variation in coccolith calcite mass. Caveats and uncertainties related to this methodological approach, including

variability in coccolith thickness, the use of species-specific shape factors, and measurement uncertainties, are discussed in detail in Young and Ziveri30 and in the Technical Validation.

INNER CELL SIZE ESTIMATION The organic biomass of phytoplankton cells is strongly related to cell volume67. In coccolithophores, the organic cell cytoplasm is covered by the calcite

coccosphere so it is useful to report both coccosphere size and cell size dimensions. The inner coccosphere size (approximating the size of the organic cell) cannot be measured directly from

SEM images, as the cell is obscured by the coccosphere (Fig. 1). We therefore estimated cell diameter as a function of coccosphere diameter, which can be precisely measured from SEM images

(described above), using a species- or genus-specific function that estimates the percentage of coccosphere volume (from coccosphere diameter) that is occupied by cell volume, as follows:

$${Equivalent}({spherical}){cell\; diameter}(\mu m)=3\,\sqrt{\frac{6\left(\gamma \times \left(\frac{4}{3}\pi {\left(\frac{{\rm{\varnothing }}}{2}\right)}^{3}\right)\right)}{\pi }}$$ (6)

where ∅ is coccosphere diameter (µm) and _y_ is the species- or genus-specific function relating coccosphere volume and cell volume (%). The percentage of coccosphere volume that is cell

volume (_y_) is estimated using measurements of coccosphere diameter and cell diameter (as internal coccosphere diameter) from light microscopy images4,68 from multiple specimens using data

from Sheward _et al_.4,69, Villiot _et al_.29 and newly collected data57. All values for _y_ are reported in Supplementary Table 1. Estimates of cell size from coccosphere size are strongly

influenced by coccolith thickness (or alternatively coccolith ‘height’ for spinose coccolith morphologies). For species with coccoliths possessing processes that extend a substantial

distance from the cell (e.g., many Rhabdosphaeraceae species; Fig. 1c,h), values of _y_ for estimating cell size from coccosphere size both including and excluding spine height are provided.

The majority of extant coccolithophore species have coccospheres formed of a single layer of abutting, overlapping and/or interlocking coccoliths. A notable exception to this is the species

_Emiliania huxleyi_, which is well-known for producing coccospheres with multiple layers70. Other species that produce multilayer or pseudo-multilayer coccospheres include _Florisphaera

profunda_ and _Umbellosphaera tenuis_. We have accounted for the presence of (pseudo-)multi-layered coccospheres when converting from coccosphere size to cell size (see also details under

_Emiliania_, _Florisphaera_ and _Umbellosphaera_ in the taxonomic-specific consideration below). SPECIES- AND GENUS-SPECIFIC CONSIDERATIONS NOELAERHABDACEAE EMILIANIA HUXLEYI There are two

additional factors influencing the calculation of cellular calcite in _Emiliania huxleyi_: variable degrees of coccolith calcite across the different morphotypes and the presence of

multi-layered coccospheres. Coccoliths of _E. huxleyi_ have been categorised into informal morphotype groupings23 based on visual assessment of morphological features, including perceived

degrees of calcification, e.g. ‘_E. huxleyi_ Type A overcalcified’ or morphotypes defined as having open central areas (e.g., ‘_E. huxleyi_ Type O’). Young and Ziveri30 have defined separate

_Ks_ values for ‘Type A group’ and ‘Type B group’ morphotypes of _E. huxleyi_ and within _E. huxleyi_, Poulton _et al_.40 and Charalampopoulou _et al_.43 estimated from field biometric

measurements on SEM images that variable coccolith morphologies led to a sixfold range in coccolith calcite. However, the calcite mass of coccoliths across different morphotypes and within

morphotypes sharing the same morphological features are very variable71,72,73,74. Descriptive terms such as ‘_E. huxleyi_ Type A overcalcified’ can therefore be misleading about differences

in calcite mass between morphotypes, for example, a ‘Type A overcalcified’ coccolith with a closed or nearly closed central area can have less calcite mass than a “regular” ‘Type A’

coccolith71. For the purposes of our dataset, we did not attempt to classify _E. huxleyi_ coccospheres into specific morphotypes or apply morphotype-specific shape factors in our calculation

of coccolith calcite. In previous studies on the coccolithophore community composition of AMT-1455, relative abundance counts also did not distinguish between different _E. huxleyi_

morphotypes so we cannot say which, if any, of the morphotypes is most abundant in our dataset. For simplicity, we have therefore used a single _Ks_ value for _E. huxleyi_ rather than

different values for each morphotype, recognising that this will be an underestimate in some instance and an overestimate in others72 (estimated as coccolith calcite ±19%). _E. huxleyi_

often makes coccospheres consisting of more than one layer of coccoliths, with as many as 3–5 layers observed in culture70,75,76 and field samples77,78,79. This occurs especially under

nutrient depleted conditions68, when cell division has slowed or ceased. For intact _E. huxleyi_ coccospheres imaged using SEM, the presence of any additional coccolith layers is not always

apparent, as the outermost coccolith layer may conceal underlying coccolith layers. Presence of multiple coccolith layers is often revealed when one or more of the coccoliths forming the

outer coccolith layer becomes dislodged or the outermost coccolith layer has sheared off (Fig. 1g). Estimating cell diameter from the coccosphere diameter of multi-layered coccospheres by

directly applying a fixed percentage conversion factor between coccosphere volume and cell volume (_y_ = 86% for _E. huxleyi_; Supplementary Table 1) would introduce error, cell volume would

be overestimated. For the purpose of estimating cell size using _y_ for multilayer coccospheres of _E. huxleyi_, we have therefore artificially reduced the coccosphere diameter measurement

to the diameter of an equivalent single-layer coccosphere using an estimate of mean _E. huxleyi_ coccolith thickness. For two-layered coccospheres, we subtracted 2x coccolith thickness (0.13

 µm x2 = 0.26 µm) from measured coccosphere diameter to simulate reducing the coccosphere diameter by the one extra layer of coccoliths present, for three-layered coccospheres we reduced

coccosphere diameter by 4x coccolith thickness (0.13 µm x4 = 0.52 µm) to simulate reducing the coccosphere diameter by the two extra layers of coccoliths present, and so on. In SEM images,

intact coccospheres of _E. huxleyi_ sometimes have loose coccoliths lying directly next to the coccosphere (especially larger cells with multiple layers) and these were included in the

_C__N_ of the coccosphere to account for their calcite as they are presumably shed from the adjacent coccosphere. Taxonomic note: In recent years, several publications have presented

phylogenetic support for the inclusion of _E. huxleyi_ in the genus _Gephyrocapsa_80,81,82 and _Gephyrocapsa huxleyi_ is therefore increasingly used in publications. Here, we have continued

to use the genus name _Emiliania_ for _E. huxleyi_ for three reasons23: (1) _E. huxleyi_ and _Gephyrocapsa_ have morphological distinctions that strongly influence their cellular calcite

content, (2) distinguishing between _E. huxleyi_ and _Gephyrocapsa_ spp. is of practical use for biostratigraphic and paleoceanographic studies, and (3) _E. huxleyi_ as a species name is

widely recognised by non-experts so continued use of the genus _Emiliania_ is useful for the wider communication of research outputs. GEPHYROCAPSA No specific considerations necessary.

COCCOLITHACEAE No specific considerations were necessary for _Calcidiscus_, _Oolithotus_, or _Umbilicosphaera_. CALCIOSOLENIACEAE CALCIOSOLENIA This genus produces rhombic coccoliths. We are

not aware of any previously published _Ks_ value for _Calciosolenia_ and so have back calculated a _Ks_ value of 0.007 based on values for coccolith calcite (2.5 pg) and coccolith length (5

 µm) published in Bollmann _et al_.83 based on circular polarizer birefringence-based measurements (n = 10) of coccolith thickness on specimens of Holocene age. Note that both the reported

mass estimate and the coccolith length are likely to be underestimated, as the rim of _Calciosolenia_ coccoliths is largely formed of vertically orientated crystal units (V-units) that are

not birefringent under either cross polarised or circular polarised light. Coccospheres of _Calciosolenia_ are strongly elongated and taper to a point at either end, giving them a shape that

is best described mathematically as a ‘double cone’64. Measuring the dimensions of _Calciosolenia_ coccospheres was sometimes challenging as the large coccospheres were often split across

more than one SEM image. In these instances, if appropriate, we estimated the mid-point of the coccosphere within the image that contained the largest portion of the coccosphere and used 2x

the measurement from this mid-point to the tip as the measure of length. For instances where the coccosphere was split over more than one SEM image, _C__N_ was counted from all SEM images

that contained parts of the coccosphere. RHABDOSPHAERACEAE ACANTHOICA Some coccoliths have well-developed spines, for example the polar coccoliths on _Acanthoica quattrospina_. The

additional calcite content of these spinose coccoliths has not been explicitly accounted for in our calculations of cell PIC. Spine lengths are variable, ca. 6–17 µm in some specimens, and

if we assume that the _Ks_ of these spinose coccoliths is broadly similar to that of _Rhabdosphaera stylifera_ (spine length for the calculation of calcite), the calcite of these spines

would be ca. 9–136 pg, compared to a coccolith calcite of ca. 1 pg for regular body coccoliths (although this is likely an overestimate as _Acanthoica_ spines have a less complex structure

and are more tapered than _Rhabdosphaera_). The coccosphere calcite of _Acanthoica_ specimens with spinose polar coccoliths is therefore underestimated. The average coccosphere thickness of

_Acanothoica_ is 0.7 µm and cell volume is on average 56% of coccosphere volume (n = 6) but can be smaller than this in some coccospheres (20–40% coccosphere volume). DISCOSPHAERA TUBIFERA

Coccolith calcite was calculated using trumpet width (Fig. 1h) following Young and Ziveri30 and _C__L_ measurements refer to trumpet width in this taxon unless otherwise mentioned. Trumpet

height was also measured so that coccosphere diameter including and excluding the trumpet height could be reported. Trumpet height can be variable across coccoliths on the same coccosphere

(e.g., Fig. 1h; maximum trumpet height can be up to three-times longer than minimum trumpet height84). Occasionally, the trumpet-like processes of the coccoliths were broken off from the

base plates. PALUSPHAERA AND RHABDOSPHAERA XIPHOS Coccospheres of _Palusphaera_ and _R. xiphos_ were difficult to distinguish at the resolution of the SEM images available. The primary

distinguishing characteristic is that _Palusphaera_ is monomorphic (all coccoliths have spines) but _Rhabdosphaera_ is dimorphic (some but not all coccoliths have spines) (see taxonomic

discussion in Archontikis and Young61). Coccospheres were distinguished where possible in the SEM images but were largely collapsed, which further inhibited confirmation of mono- or

dimorphism and made accurate _C__L_ and _C__N_ measurements extremely challenging. As direct cellular morphometrics could not be taken accurately, _Palusphaera_ and _Rhabdosphaera xiphos_

were not included in the database. RHABDOSPHAERA CLAVIGERA Two varieties of _R. clavigera_ are distinguished by how robust (var. _clavigera_) or delicate (var. _stylifera_) the spine

structure is, although there is evidence of intergrading between the two forms23,85. Here, we separate the two varieties as the more robust spine has a greater calcite content (reflected in

its higher _Ks_ value) compared to the more delicate form. Note that, similarly to _Discosphaera_, there is variation in spine length ca. 5–10% between coccoliths on the same coccosphere84.

_Rhabdosphaera_ coccospheres are dimorphic, formed of coccoliths with and without spines (Fig. 1c). For the calculation of coccosphere calcite, it was assumed that 50% of the coccoliths were

without spines (coccolith calcite for these coccoliths was calculated using _C__L_ and a _Ks_ value of 0.025, modified from _Acanthoica_30) and 50% of the coccoliths were with spines

(calcite was calculated using spine length and a fixed value of 5 µm was used if spine length could not be measured). It was usually possible to accurately measure coccosphere diameter both

including and excluding spine length and coccosphere size is reported as excluding spine length unless otherwise stated. SYRACOSPHAERACEAE CALCIOPAPPUS _Calciopappus_ coccospheres were

extremely rare in the samples investigated and were not observed as intact coccospheres. We therefore do not report any data for _Calciopappus_. MICHAELSARSIA _Michaelsarsia_ coccospheres

were rare in our samples (n = 5). Each coccosphere typically has ca. 8–12 appendages each formed of 3–4 coccoliths86 (Fig. 1i). To avoid underestimating _Michaelsarsia_ coccosphere calcite

by omitting the calcite in these appendages, we assigned a value of 12.5 pg calcite per appendage (informed by a typical length of 5.5 µm for each appendage segment, a _Ks_ value of 0.007

and assuming 4 segments per appendage). If the number of appendages is unknown, we assumed that 8 appendages were present (i.e., an addition of 100 pg calcite). This additional calcite was

then added to the calcite of the main body coccoliths, which were calculated using a _Ks_ value adapted from _Syracosphaera_. OPHIASTER The appendage coccoliths of _Ophiaster_ are also

elongated but with a more solid structure than those of _Michaelsarsia_ and each coccosphere usually has 4–7 long ‘arms’ of these osteoliths86. As the appendages of _Ophiaster_ are longer

and with a much greater number of component osteoliths, an approximation of the additional calcite represented by the appendages was estimated as follows: assuming that each of the

osteoliths has the same _Ks_ value as a _Florisphaera profunda_ nannolith (_Ks_ = 0.0332 based on the broadly similar shape) and each ‘arm’ contains on average 14 nannoliths of ca. 1.8 µm

length, this would equate to 0.47 pg calcite per nannolith, 6.6 pg calcite per ‘arm’ and 33 pg additional calcite per coccosphere in total (assuming on average 5 arms). This fixed estimate

of an additional 33 pg calcite for appendages was applied where appendages were clearly present (as many specimens are without appendages86). This estimate of appendage calcite is broadly

comparable to the calcite contained in the body coccoliths of many specimens (i.e., including a calcite estimate for the appendages approximately doubles cell calcite content calculated on

body coccoliths alone). SYRACOSPHAERA The genus _Syracosphaera_ is very diverse87 (ca. 40 currently recognised species23). There is substantial morphological diversity in this genus,

including coccolith size variability, different degrees of calcification, and a range of central area structures. However, four sub-groups of species with similar morphological

characteristics can be distinguished (Nannotax323 following Cros88, Young _et al_.60 and Kleijne and Cros87) and we used these morpho-groups as a starting point to simplify the choice of

shape factor for calculation of cellular calcite content in this genus. In addition, many _Syracosphaera_ species have circum-flagella coccoliths (CFCs) with relatively small spines and

exothecal coccoliths (XCs) that form a partial or complete outer layer to the coccosphere (Fig. 1j). This range of features make it impractical to determine new species-specific _Ks_ values

for the calculation of coccolith calcite for _Syracosphaera_. For the calculation of cellular calcite, we therefore proceeded as follows: * For _Syracosphaera_ species that have a

well-developed inner wall cycle and robust central area structures such as a boss or spine, we use the published _Ks_ value of Young and Ziveri30 for _Syracosphaera pulchra_ (_Ks_ = 0.03).

This includes species in the ‘_pulchra_ group’ and _Syracosphaera mediterranea_, which has a thick rim cycle and low central mound. For this morpho-group (e.g., Fig. 1j), cell volume was

assumed to be 65% of coccosphere volume (ranging between ca. 60 and 80% for species in the group). * For species without either of these features we use the _Ks_ values of Young and Ziveri30

for a ‘small’ _Syracosphaera_ species (_Ks_ = 0.015), even though the coccoliths in question may not be ‘small’. This includes ‘_borealis_ type’ species, ‘_nodosa_ group’ species (e.g.,

Fig. 1l), and _Syracosphaera maxima_. For this morpho-group, cell volume was assumed to be 75% of coccosphere volume. * For species that have well-developed rims but no central area bosses

or spines, we chose a relatively arbitrary ‘intermediate’ value of _Ks_ = 0.022. This includes species in the ‘_molischii_ group’ (other than ‘_borealis_ type’ species; e.g., Fig. 1k). For

this morpho-group, cell volume was assumed to be 75% of coccosphere volume. * For coccospheres that could not be confidently identified to species level, a _Ks_ value of 0.02 was used to

calculate coccosphere calcite. * The morphology of CFCs is often similar to that of the body coccoliths but with relatively small spines (Fig. 1l). We therefore used the same _Ks_ value for

CFCs as for body coccoliths. * There is a much broader morphological diversity across XCs, which makes it challenging to apply any ‘one size fits all’ approach to account for differences in

the calcite content of XCs in the calculation of cellular calcite across all _Syracosphaera_ species. The morphologies of XCs have previously been tentatively classified into 12 groups88

spanning disk-like coccoliths (e.g., _Syracosphaera anthos_, _Syracosphaera nodosa_, _Syracosphaera lamina_, _Syracosphaera nana_, _Syracosphaera bannockii_), undulating coccoliths that have

a distinct rim and central area (e.g., _Syracosphaera borealis_, _Syracosphaera molischii_, _Syracosphaera ossa_), dome-like/vaulted coccoliths (e.g., _Syracosphaera pulchra_), and

caneoliths with a murolith morphology (e.g., _Syracosphaera dilatata_, _Syracosphaera prolongata_, _Syracosphaera noroitica_). As XCs can be numerous (e.g., Fig. 1j,l), we attempted to

account broadly for the calcite of these XCs when present by counting the number of XCs present and using a _Ks_ value of 0.02 for all morphologies to calculate the additional calcite

contained in these coccoliths, recognising that this _Ks_ value is an underestimate in some instances and an overestimate in others. * An additional challenge presented by the presence of

XCs is that they partially or sometimes entirely obscure the visibility of body coccoliths (Fig. 1j). In these instances, a best estimate of _C__N_ was determined by either scaling up the

number of body coccoliths visible over an unobscured portion of the cell, doubling the _C__N_ of visible XCs when the size of XCs and body coccoliths are broadly comparable and the entire

coccosphere is covered in XCs, or estimating _C__N_ based on the range of _C__N_ typical for the species (this is noted in the raw data file when applied). * Many species of _Syracosphaera_

are known to have holococcolith stages. See the remarks on ‘Holococcolithophores’ for further details. HELICOSPHAERACEAE No specific considerations were necessary for _Helicosphaera_.

ALISPHAERACEAE _ALISPHAERA_ AND _ALISPHAERA_ POLYCRATER PHASE (POL) _Alisphaera_ is a genus with a very high _C__N_ per coccosphere and small coccoliths, especially in polycrater phase (Fig.

 1f). Where _C__N_ could not be accurately counted and/or _C__L_ could not be accurately measured (particularly for polycrater phase coccospheres) from SEM images, the _C__N_ /_C__L_ range

of the species reported on Nannotax323 was used to guide our choice of a fixed _C__N_ of 400 and fixed _C__L_ of 0.8 µm for the calculation of cellular calcite. UMBELLOSPHAERACEAE

UMBELLOSPHAERA _Umbellosphaera_ coccoliths have umbelliform morphology, reminiscent of a flaring trumpet shape. Coccoliths forming the coccosphere have a range of distal shield sizes (as

seen easily from collapsed coccospheres; Fig. 1m) that leads _Umbellosphaera_ coccospheres to have a pseudo-multilayered structure that is reminiscent of a rainforest canopy structure, where

the distal shields of the largest coccoliths overlay the distal shields of smaller coccoliths (Fig. 1n) whilst the proximal shields sit adjacent on the cell surface. This presents

challenges for counting _C__N_ accurately and accurately measuring a ‘representative’ coccolith size in _Umbellosphaera_. For _C__N_, we therefore multiplied counted coccoliths by three

(rather than by two for regular, single-layer coccospheres) to better account for the ‘hidden’ layer of coccoliths underneath the visible outer layer. For intact coccospheres, _C__L_ and

_C__W_ of the largest coccolith distal shield were measured. For the coccolith size measure used in the calculation of cellular calcite, we also adjusted the maximum (measurable) distal

shield length to approximate an ‘average’ distal shield length that accommodated the variable lengths of _Umbellosphaera_ coccoliths that occur on the same coccosphere. For 20 collapsed

_Umbellosphaera_ coccospheres (e.g., Fig. 1m), we measured the distal shield length of every coccolith (_C__N_ of the collapsed coccospheres ranged from 10 to 43) and calculated coccolith

calcite and coccosphere calcite53 using the _Ks_ values of Young and Ziveri30 for _Umbellosphaera tenuis_ and _Umbellosphaera irregularis_ as appropriate, following Eq. 4 and Eq. 5. We then

back-calculated an ‘average’ _C__L_ corresponding to the calculated cellular calcite and _C__N_ of the cell and determined what percentage of the largest measured coccolith size (_C__L_ max;

Fig. 1m) this ‘average’ coccolith represented53, as follows: $$ \mbox{`} {average}\mbox{'}{C}_{L}({\mu m}^{3})=3\,\sqrt{\frac{{coccosphere\; calcite}}{{K}_{S}{\times C}_{N}\times

2.7}}$$ (7) For the 20 collapsed coccospheres measured, the ‘average’ coccolith size ranged between 55 and 81% of the largest measured coccolith53. For the calculation of _Umbellosphaera_

cellular calcite, we therefore decided to use a _C__L_ value of 0.7*_C__L_ max, where _C__L_ max is the coccolith length of the largest (measurable) coccolith on the intact coccosphere

(e.g., Fig. 1n). HOLOCOCCOLITHOPHORES AND NANNOLITHS HOLOCOCCOLITHOPHORES Coccolithophores have a haplo-diplontic life cycle, and typically produce heterococcoliths in the diploid life cycle

stage and holococcoliths (HOL) during the haploid life cycle stage (e.g., Fig. 1a). Holococcoliths are formed from small, simple rhombohedral crystals and are morphologically distinct from

heterococcoliths89. Holococcoliths do, however, occur in a range of different shapes and forms60. The calcite content of individual holococcoliths is currently unknown and we are not aware

of any published values for inorganic carbon per cell measured from cultured holococcolith-bearing strains from which coccolith calcite and therefore _Ks_ could be estimated. Here, we

therefore used an estimated _Ks_ value of 0.036 for all holococcolith-bearing coccospheres45. If it was not possible to directly count _C__N_ (as holococcoliths are often very small and

coccospheres have high _C__N_), _C__N_ was estimated by back-calculating _C__N_ using the surface area of the coccospheres and the surface area of the measured coccolith or an average _C__N_

of that species was used if available from another published source. We assumed that cell volume is 80% of coccosphere volume for all holococcolithophore coccospheres. NANNOLITH-BEARING

TAXA CERATOLITHUS _Ceratolithus_ produces three different lith morphologies depending on the life cycle stage, including distinctive horseshoe-shaped nannoliths (ceratoliths, CER). No intact

_Ceratolithus_ coccospheres were observed in any of our samples so they are not present in the database. FLORISPHAERA PROFUNDA The sheet-like, angular nannoliths of _Florisphaera_ are

arranged to form a coccosphere of strongly overlapping layers reminiscent of a globe artichoke (Fig. 1o). As a result, the coccosphere is very thick and, on SEM, it is not usually possible

to accurately determine how many layers of coccoliths are present. Light microscopy and SEM images indicate that ca. 6 to 12 layers of overlapping coccoliths can be present23,60,84 (Fig. 1o)

and that coccospheres may have up to ca. 220 nannoliths84,90. New LM measurements of corresponding coccosphere and internal cell diameter measurements from 20 _Florisphaera_ coccospheres57

indicate that cell size is typically 3–5 µm and cell volume is ca. 10% of coccosphere volume (ranging from 3% to 21%)57. We therefore estimate cell size from coccosphere size assuming that

cell volume is 10% of coccosphere volume. As precise estimates of _C__N_ were not attainable, we assumed that _Florisphaera_ coccospheres have a fixed _C__N_ of 145, broadly in line with the

average _C__N_ reported in the literature for coccospheres for _Florisphaera profunda_ var. _elongata_ and _F. profunda_ var. _profunda_84. The use of a fixed _C__N_ obviously introduces

significant uncertainty in the estimates of _Florisphaera profunda_ cellular calcite (assuming a _C__L_ of 2 µm and that the _C__N_ of _Florisphaera_ typically ranges between ca. 90 and 170,

the use of the fixed _C__N_ introduces an uncertainty of ca. 20–40%). DATA RECORDS The extant coccolithophore morphometric trait dataset described in this study can be freely downloaded at

zenodo53. This data record contains the main dataset “_1. Cellular morphometric trait dataset for extant coccolithophores from the Atlantic Ocean_” (Microsoft Excel file) and four supporting

files: “_2. Descriptor – Cellular morphometric trait dataset for extant coccolithophores from the Atlantic Ocean_” (Microsoft Word file), “_3. Coccolith size, coccolith calcite and cellular

calcite in collapsed Umbellosphaera coccospheres_” (Microsoft Excel file), “_4. Sensitivity of cellular calcite content to uncertainties in coccolith size, number of coccoliths per cell and

shape factors_” (Microsoft Excel file), and “_5. Partial coccolith length and coccolith length measurements_” (Microsoft Excel file). This section describes the content of these files. The

_Cellular morphometric trait dataset for extant coccolithophores from the Atlantic Ocean_ is formatted as a column-orientated table in Microsoft Excel format. Each row of the dataset

represents the raw morphometric data (number of coccoliths per cell, coccolith length, coccolith width, coccosphere diameter long axis, coccosphere diameter short axis) and calculated

morphological trait data (coccosphere volume, equivalent spherical coccosphere diameter, cellular calcite) obtained from a single intact coccosphere. Each entry includes ancillary

information, including sample identifier (station and water depth), SEM image number and taxonomic classification (family, genus, species). A column entitled ‘Additional information’ records

any additional details relevant to the accuracy of the measurements and calculated parameters, for instance stating the presence and amount of XCs additionally included in the cellular

calcite calculation or the presence of a multi-layered coccosphere where this has been accounted for in the estimation of cell size from coccosphere size. The contents of the four supporting

files associated with the _Cellular morphometric trait dataset_53 are as follows: File 2. _Descriptor_ describes the column headings contained in the _Cellular morphometric trait dataset_.

File 3. _Coccolith size, coccolith calcite and cellular calcite in collapsed Umbellosphaera coccospheres_ contains the coccolith size and coccolith calcite data measured from collapsed

coccospheres of _Umbellosphaera_ used to derive the adjustment of coccolith size used in the calculation of cellular calcite _in Umbellosphaera_. File 4. _Sensitivity of cellular calcite

content to uncertainties in coccolith size, number of coccoliths per cell and shape factors_ contains the data used to perform the sensitivity analysis of cellular calcite to variability in

morphometric parameters (see Technical Validation). File 5. _Partial coccolith length and coccolith length measurements_ contains coccolith measurements used to calculate the measurement

uncertainty associated with measuring partial _C__L_ on coccoliths where the rim of the distal shield is partly obscured by an overlapping coccolith. In addition to this data record

containing the _Cellular morphometric trait dataset for extant coccolithophores from the Atlantic Ocean_ dataset and supporting files53, two new further records56,57 associated with the

dataset are available: * The photo record “_Atlantic Meridional Transect (AMT) 14: scanning electron microscopy images of the coccolithophore community_” is freely available for download at

zenodo56 and contains the original SEM image files as tagged image file format (.tif) files. The identifier of each image file corresponds to the image number in the dataset _Cellular

morphometric trait dataset for extant coccolithophores from the Atlantic Ocean_53. * The dataset “_Extant coccolithophore cell size measurements_” (Microscoft Excel file) is freely available

for download at zenodo57 and contains newly collected measurements of coccosphere diameter and cell diameter on individual coccospheres used to derive species- and genus-specific values for

the percentage of coccosphere volume that is cell volume (_y_). An overview table of the genus-specific morphometric parameters used to estimate cellular calcite (e.g. taxon-specific shape

factors, size measurement used) and the range of estimated taxon-specific cellular calcite content that summarise the data contained in the _Cellular morphometric trait dataset for extant

coccolithophores from the Atlantic Ocean_53 is available as Supplementary Table 1. TECHNICAL VALIDATION TAXONOMIC COVERAGE OF THE CELLULAR MORPHOMETRIC TRAIT DATASET In total, 4712

morphometric measurements were measured on 1074 individual coccospheres representing 61 species from 25 genera (of the 31 most common genera that collectively constituted >95% total cell

numbers during AMT 1455) (Fig. 2). The number of measurements for each genus represented in the dataset largely reflects the relative abundance of different species in the samples examined,

as well as the structural stability of different coccosphere architectures (as some species coccospheres have a greater tendency to collapse, even under gentle filter pressure, and were

therefore not measured). Five genera (20%) have more than 50 coccospheres in the dataset and 14 genera (70%) have 10 or more coccospheres in the dataset (Fig. 2b). Some extant taxa are not

present in our dataset for the following reasons: (1) the species was not observed because it is generally not present in the temperate to equatorial latitudes of the oceanic Atlantic ocean

sampled during AMT-14 (e.g., _Coccolithus pelagicus_ that has a biogeographic distribution in the northern hemisphere high latitudes, the genus _Braarudosphaera_ that is known to thrive in

hyposaline conditions, the predominantly polar Family Papposphaeraceae, and the neritic genera in the Families Hymenomonadaceae and Pleurochrysidaceae); (2) the species is generally rare

(e.g., _Calyptrosphaera_, _Navilithus_, _Placorhombus_, and _Turrilithus_) or rare in AMT samples (140 of 171 species, or 82%, recorded during AMT-14 constituted <5% total cell numbers

and are defined as rare55); (3) The species was not observed as intact coccospheres in our samples because it has a structural susceptibility to collapse and therefore could not be

accurately measured (e.g., the deep photic species _Gladiolithus_). Additionally, we did not observe any _Scyphosphaera_ or _Pontosphaera_ coccospheres (intact or collapsed) in any of the

samples we examined for this study. _Scyphosphaera apsteinii_ was only recorded in two samples during AMT-14 and no species of the genus _Pontosphaera_ were reported in any samples55. SIZE

MEASUREMENT ERRORS USING MICROSCOPY (SEM AND LM) SEM has a theoretical resolution of ca. 0.003 to 0.05 µm dependent on the electron source, the accelerating voltage, and the working

distance. The optical resolution of LM is dependent on the objective used, the numerical aperture of the objective and the use of any immersion liquid. Coccolithophore researchers typically

use a 100x/1.30 oil-immersion objective, which has an optical resolution of 0.26 µm. Combined with the pixel resolution of the SEM images, all _C__L_ and ∅ measurements53 therefore have a

maximum error of ca. ±0.12 µm. The LM measurements of coccosphere and cell size used to calculate the percentage of coccosphere volume that is cell volume (_y_)57 should be assumed to have a

minimum error of ±0.26 µm. Note that the new size measurements taken here from SEM images53 and from LM images57 were not specifically controlled with a calibration standard (e.g.,

calibration microbeads)91,92. COMPARISON OF MORPHOMETRIC-BASED ESTIMATES OF COCCOLITH CALCITE WITH OTHER ESTIMATION METHODS Due to the very small size of coccoliths (ca. 1 to 20 µm) and

coccospheres (ca. 3 to 40 µm), the mass of individual coccoliths and coccospheres cannot be measured directly and so must be estimated using indirect approaches. There are several

established methods used to estimate the calcite mass of coccoliths and/or coccospheres, each with advantages and limitations that also depend on the characteristics of the material being

investigated (e.g., whether samples from culturing, plankton or sediment are used and whether coccolith calcite or coccosphere calcite is being measured). An extensive discussion of the

advantages and limitations of each method is beyond the scope of our study. We refer readers to the literature cited in the following paragraphs for specific technical developments,

particularly regarding birefringence-based methods for the quantification of coccolith calcite mass. Instead, we briefly summarise the main advantages and disadvantages of alternative

methods for estimating coccolith and cellular calcite content within the scope of comparing our estimated cellular calcite data with data derived from other methodologies. Estimates of

coccolith calcite based on morphological measurements30,93, as used here, can be performed using measurements from either light microscopy images (LM) or scanning electron microscopy (SEM),

as here. The high resolution of SEM images can resolve very small and lightly calcified details of coccoliths, often improving taxonomic classification of material relative to LM and

enabling high accuracy morphometric data to be collected across a wide range of coccolith sizes and morphologies. A disadvantage of SEM is that the two-dimensional nature of the images

allows only one hemisphere of the coccosphere to be viewed directly (Fig. 1) and therefore there must be a degree of estimation in the total number of coccoliths per cell. This is an

advantage of LM, where the focal depth can be adjusted to observe and count each coccolith in the coccosphere4,66,68. Alternatives to morphometric-based calcite estimates include

birefringence-based mass estimates83,94,95, which are often used for calcite mass estimates of individual coccoliths. Technical advances in the calibration of birefringence-based methods for

coccolith mass estimation have been made in recent years32,83,96,97,98,99, notably using circular polarized light rather than cross-polarised light and calibrating the calcite interference

colours to the Michel-Lévy chart with additional technical management of the microscope, light source and imaging settings32,83. Despite these technical advances, mass estimates based on

birefringence are limited by both the orientation of the crystal(s) in the coccolith and by coccolith thickness, which does have a detection limit: thickness limits imposed by optical

physics are 1.34 µm32,83 to a maximum of 1.58 µm32 after which greyscale values repeat themselves. Thickness limits as high as 1.70 µm have also been published99. Birefringence-based methods

work well for species with smaller or thinner coccoliths, such as _E. huxleyi_, but underestimate the calcite mass of coccoliths that exceed thicknesses of ca. 1.4 µm (e.g., larger

specimens of _Coccolithus_, _Helicosphaera_ and _Calcidiscus_)83. In addition to coccolith thickness limits, birefringence-based approaches systematically underestimate coccolith calcite

mass in species where some or all of the coccolith is formed of vertically-arranged crystal units (V-units) that are not birefringent under either cross polarised or circular polarised light

(e.g., _Coccolithus_ spp., _Calcidiscus_ spp., _Umbilicosphaera_ spp.)65,83,94,99. Birefringence is also unsuitable for coccolith mass estimation when the coccolith is part of an intact

coccosphere (as measured here), where overlapping coccoliths can increase the calcite brightness leading to significant calcite overestimation100. Another commonly used approach in culturing

studies is the analytical determination of mean calcite per cell through assays for total sample particulate carbon and particulate organic carbon (from an acidified sample), where total

sample calcite is the difference between the two values (the inorganic carbon) and cellular calcite is determined by dividing the value by the number of cells present on the filter (when

cells per millilitre and number of millilitres filtered are known). This approach does not capture intraspecific variability in cellular calcite and has the additional disadvantage that any

‘additional calcite’, e.g. from dead cells or shed coccoliths, is also averaged into the cellular calcite value and this can lead to the overestimation of mean cellular calcite52.

Assay-derived cellular calcite estimates are effectively restricted to _E. huxleyi_, _Gephyrocapsa_ spp., _Coccolithus_ spp., _Calcidiscus_ spp., _Syracosphaera pulchra_ and _Helicosphaera

carteri_, i.e., species that have been used in monospecific culturing experiments27. It is not possible to use assay-based analysis for the determination of taxon-specific cellular calcite

content from a mixed population sample (i.e., a plankton sample from the field), as the nature of this analysis will produce a meaningless average value spanning all cells, regardless of

their taxonomic affinity. This method is, however, well suited to estimating total organic and inorganic carbon content of a population. Morphometric-based calcite estimates have been shown

to compare well to estimates of coccolith calcite derived using other methodologies. Birefringence-based estimates of coccolith calcite are consistently in good agreement with

morphometric-based estimates of coccolith calcite for species within the coccolith size and thickness range for which this method is optimised, especially when samples sizes are large enough

to account for intraspecific variability65,83,94. In one study32, the calcite mass of coccoliths measured using both the same morphometric-based method as here and a birefringence-based

method on the same samples showed good agreement in Noelaerhabdaceae and Umbellosphaeraceae coccoliths. For _E. huxleyi_ and small placolith coccoliths, mean calcite mass based on _C__L_ and

the recommended Ks value of 0.0230 was 1.7 pg _versus_ 2.2 pg derived through a birefringence-based method32. For _Umbellosphaera_ spp. coccoliths, the morphometric-based estimate of mean

coccolith calcite mass was 7.1 pg compared to a birefringence-based estimate of 7.5 pg32. A recent direct comparison study33 also showed that coccolith mass estimates for four strains of _E.

huxleyi_ obtained from morphometric data using SEM (as here) agreed well with estimates obtained through birefringence measurements of coccolith thickness using bidirectional circular

polarisation97,99 with LM (mean calcite mass of Type A coccoliths was 2.09 pg based on morphometrics _versus_ 2.02 pg based on birefringence, mean calcite mass of Type BC coccoliths was 1.71

 pg based on morphometrics _versus_ 1.82 pg based on birefringence; differences were not significant)33. For species in the orders Coccolithales (e.g., _Coccolithus, Calcidiscus_,

_Umbilicosphaera_) and Zygodiscales (e.g., _Helicosphaera_), Linge Johnsen and Bollmann32 showed that coccolith calcite mass estimates calculated using birefringence-based methods were lower

than morphometric-based approaches. They explain that the coccolith calcite mass of these species is systematically underestimated by birefringence-based methods because their coccolith

thickness exceeds the theoretical thickness limit of 1.34 µm32. We are not aware of other studies where multiple methodologies for coccolith mass estimates have been directly compared on the

same material for species with a broad range of coccolith thicknesses. Morphometric-based estimates of both coccolith and coccosphere calcite mass have also been shown to agree well with

coccolith and coccosphere calcite mass values determined through opto-electrochemical dissolution34,35. QUANTIFYING SOURCES OF UNCERTAINTY IN MORPHOMETRIC-BASED ESTIMATES OF CELLULAR CALCITE

The morphometric-based calcite estimation method used here30 incorporates a number of (necessary) assumptions and sources of uncertainty. We summarise relevant caveats that have been raised

previously in the literature30 and, based on our own observations, highlight additional methodological points that users of the dataset should be aware of: * We use species- or

genus-specific _Ks_ values based on published _Ks_ values where available. If no published _Ks_ for a species or genus are available, we have either adopted the existing _Ks_ value of a

species with a very similar morphology or adjusted the _Ks_ value of a species with similar morphology to account for the presence, absence or different degree of morphological features that

are likely to increase or decrease the original _Ks_ value. The value, source and justification for all _Ks_ values used to estimate coccolith PIC in the database are detailed in

Supplementary Table 1. * Within-species, _Ks_ values derived from individual coccolith measurements vary by ca. ±20%30. We note that the species-specific shape factors recommended by Young

and Ziveri30 are based on measurements from a small number of individual coccoliths that are therefore unlikely to fully represent the range of shape factor variability within each species.

For example, a study focusing on _E. huxleyi_72 showed strain-specific variability in _Ks_, ranging between 0.014 and 0.022 across seven morphotype A strains. A subsequent study on natural

_E. huxleyi_ populations71 emphasised that within-morphotype variability in coccolith mass can be substantial and that changes in coccolith size and coccolith thickness can be decoupled. *

Here, we assume that within-species coccolith shape and thickness remains constant even if coccolith size changes, although this is not always the case72. Coccolith thickness (and therefore

mass) can vary independently of coccolith length and thickness variability can also be restricted to certain areas of the coccolith, such as changes in central tube cycle thickness71,101,102

or number and thickness of coccolith elements. As variation in coccolith size has a much stronger influence on coccolith volume than coccolith shape30, we did not account for shape

variability with size in our coccosphere calcite calculations. It was also not possible to quantify variability in coccolith thickness across individual coccospheres in our samples and use

this information to further refine our estimates coccolith calcite mass because methods to determine coccolith thickness are based on the birefringence of calcite in LM and our data is

collected from SEM images. * Within a species, coccolith size can vary considerably as a function of growth environment and genotypic variability. Even within a single genetic clone,

coccolith size can vary by ca. 40% across individual cells as a function of variable environment and growth phase4,69. Many studies estimate species calcite using a mean species-specific

coccolith length value. As we measure coccosphere-specific _C__L_, we circumvent uncertainty that would be introduced by within-species size variability when using a mean _C__L_ for all

individual coccospheres of that species. * A more relevant source of uncertainty for our measurements is that coccolith size (or spine length or other morphometric parameters used for

calcite calculation) on a single coccosphere can also vary by up to ca. 30%85,103. This may occur through several mechanisms104: (1) cell size changes through the daily cell division cycle,

from smallest immediately following cell division to largest just prior to cell division103 and during G1 interphase of the cell division cycle105,106. As heterococcolith coccolithogensis

occurs intracellularly107,108,109, cell size at the time of coccolith formation can limit maximum coccolith dimensions. Coccoliths formed early in the daily cell cycle would therefore be

likely to be slightly smaller than those formed later on; (2) As coccolith size is responsive to environmental stressors22,52,110,111,112,113,114,115,116, coccoliths produced under stressful

conditions may have different sizes from those produced before exposure to the stressful condition. As approximately half of the coccoliths forming the coccosphere of the parent cell are

divided equally amongst two daughter cells on cell division, cells will inherit a diminishing proportion of coccoliths of a different size originally from the parent cell (grown under

different environmental conditions) over successive cell division cycles. It may therefore take several generations of coccolith production and growth before the coccosphere is composed of

solely post-exposure coccoliths; (3) Small differences in the duration of coccolithogenesis by the cell could feasibly result in slight differences in coccolith size; (4) Large coccolith

size variability on the same coccosphere is also a taxonomic feature of several species, which are highlighted in the genus descriptions in the Methods. We measure a single, approximately

flat-lying coccolith on the upper surface of the coccosphere that we assume is representative of the size of all other coccoliths forming the coccosphere. However, it is likely that some

coccoliths in the coccosphere are slightly smaller (and therefore have less calcite) and others are slightly larger (and therefore have more calcite). This is one of the larger sources of

uncertainty in our calculations of coccosphere calcite from a single coccolith measurement (see below). For example, Beuvier _et al_.103 determined a threefold range in coccolith calcite

(7–23 pg) within a coccosphere of _Gephyrocapsa oceanica_ due largely to differences in coccolith size of 20–30%. A large range in coccolith size within the same coccosphere is a

morphological feature of _Umbellosphaera_ (Fig. 1m) and our measurements on collapsed coccospheres reveal that the difference in size between the smallest and largest coccoliths forming the

coccosphere ranged from as little as 2.43 µm to as much as 8.27 µm, leading to a range in coccolith calcite within the same coccosphere of 2.4–28.4 pg coccolith−1 in _Umbellosphaera_53. For

many species, the arrangement of coccoliths in the coccosphere rarely offers multiple, flat-lying coccoliths on the upper surface of the coccosphere for measurement (where the edge of the

coccolith is not obscured by other coccoliths) or the _C__N_ is high to very high, making it unreasonable to measure a representative selection of coccoliths on each coccosphere. As

coccolith size variation is particularly notable in _Umbellosphaera_, we have specifically accommodated intra-coccosphere variation in _C__L_ in our estimates of cellular calcite, which is

described in the Methods. We investigated the sensitivity of cellular calcite estimated using morphometrics (Eqs. 4 and 5) to variability in coccolith size, number of coccoliths per cell,

and _Ks_ value to better quantify the magnitude of uncertainty introduced by the (necessary) assumptions made in our methodology (Fig. 3). For coccospheres of _Gephyrocapsa mullerae_,

_Umbilicosphaera hulburtiana_, _Syracosphaera_ spp., and _Discosphaera tubifera_ (representing a selection of different morphological types and degrees of calcification), we re-calculated

cellular calcite content by systematically varying _Ks_ and _C__L_ by ±5–30%. These ranges of variability are guided by the range of _Ks_ reported by Young and Ziveri30 and Linge Johnsen _et

al_.72 for _E. huxleyi_ and the range of _C__L_ on individual coccospheres reported for _Gephyrocapsa_103. To assess sensitivity to uncertainty in _C__N_ counts, we varied _C__N_ of each

coccosphere by ±2 coccoliths and ±5 coccoliths. Uncertainty in coccolith size (i.e., the measured coccolith is not representative of other coccoliths in the coccosphere) has by far the

largest impact in estimated cellular calcite, irrespective of species, altering estimated cellular calcite by a minimum of ca. ±15% (for 5% uncertainty in _C__L_) and decreasing cellular

calcite content by a maximum of 65% or increasing it by a maximum of 120% for a 30% uncertainty in _C__L_ (Fig. 3). The large impact of _C__L_ uncertainty on estimated cellular calcite

content arises because _C__L_ is cubed in the calculation of coccolith calcite (Eq. 4). We consider a _C__L_ uncertainty of 30%, whilst possible, to be an unreasonably large uncertainty that

would only occur if the largest or smallest coccolith out of all the coccoliths on the coccosphere was measured103. A more reasonable level of uncertainty in measured _C__L_ of ±10–15%

between coccoliths on the same coccosphere results in estimated cellular calcite content decreasing/increasing by ca. 30% (10% _C__L_ uncertainty) to decreasing by 39% or increasing by 52%

(15% _C__L_ uncertainty). Variability of _Ks_ across individual coccoliths of, for example, ±20%30 results in cellular calcite estimates directly changing by ±20%. Errors in counting the

number of coccoliths per cell can occur, and we estimated these to be ca. ±1–5 coccoliths per cell at most for the majority of coccospheres observed using SEM but conservatively as high as

10–40 coccoliths per cell counting error in species like the polycrater phase of _Alisphaera_ that have several hundred very small coccoliths (Fig. 1f). Coccolith counting errors affect

estimated cellular calcite proportionally to both the number of coccoliths per cell (i.e., the relative percentage counting error) and coccolith size (i.e., the calcite mass of each

miscounted coccolith), thus giving a range of sensitivity in our analysis (Fig. 3). For the four species investigated, _C__N_ ±2 resulted in a cellular calcite uncertainty of 2–22% and

_C__N_ ±5 resulted in a cellular calcite uncertainty of 5–55% for coccospheres with _C__N_ ranging between 9 and 96. _C__N_ counting errors are least likely in species with lower _C__N_

and/or larger _C__L_ and increase in likelihood in species whose coccospheres are comprised of very high numbers of coccoliths, although the typically small _C__L_ of these higher-_C__N_

species acts to minimise the overall impact of counting errors on cellular calcite estimations. Overall, it is reasonable to assume that slight differences in _Ks_ and _C__L_ between

coccoliths on the same coccosphere and minor _C__N_ counting errors introduces an uncertainty of ca. 5–40% on estimated cellular calcite. QUANTIFYING SOURCES OF UNCERTAINTY IN ESTIMATION OF

CELL SIZE FROM COCCOSPHERE SIZE The percentage of coccosphere volume that is cell volume (_y_) determined through LM varies between individual coccospheres29,57,69,117 but the intraspecific

range in _y_ is overall relatively low for many species. Based on 2850 measurements of coccosphere diameter and cell diameter (LM-based) for cultured _Calcidiscus_ and _Helicosphaera_69 and

_Coccolithus_ plankton samples68,117, the percentage of coccosphere volume that was cell volume was relatively consistent across hundreds of individual coccospheres, varying by only 12–22%

(10th to 90th percentiles of the data; cellular _y_ for _Helicosphaera_ = mean 51% ranging between 45% and 58%, cellular _y_ for _Calcidiscus_ = mean 42% ranging between 32% and 52%, and

cellular _y_ for _Coccolithus_ = mean 45% ranging between 37% and 52%). As these species all have ‘heavily calcified’ coccolith morphologies (i.e., coccoliths are comparatively thick and

solid structures) and coccospheres with strongly overlapping coccolith arrangements, we estimate that the variability in _y_ in species with thinner coccoliths and those that have a lesser

degree of or no overlapping coccolith arrangement (e.g., species bearing murolith- and planolith-type coccolith morphologies) is less than _y_ ±10–15%. The relationship between coccosphere

volume and cell volume is much more variable in _Florisphaera profunda_ (up to _y_ ±80%), _Umbellosphaera_ spp. (up to _y_ ±75%), _Oolithotus antillarum_ (up to _y_ ±37%), and _Acanthoica_

spp. (up to _y_ ±63%). These species have staggered, overlapping coccoliths arrangements that produce a very thick coccosphere relative to size of the cell and where additional

(pseudo-)layers can be added with no change in cell size. The value of _y_ for _Algirosphaera robusta_ (up to _y_ ±60%) depends on the variability in the height of central area processes,

the morphology of which makes it impossible to measure coccosphere diameter with and without the height of the processes. Additionally, coccospheres of _Umbilicosphaera sibogae_ contain

multiple cells within a single coccosphere, making it extremely challenging to quantify _y_ and its variability. For these specific taxa, the use of a fixed value for _y_ was unavoidable but

introduces uncertainty of ca. 30–60% in cell size estimates from coccosphere volume. USAGE NOTES This dataset53 is generated from 16 plankton samples obtained from the temperate to

equatorial Atlantic Ocean during 2004 and is therefore particularly well-suited for addressing research questions that focus on this region. As environmental conditions influence cell

physiology, phenotype expression, biogeography and species’ evolution, coccolithophore populations present in different ocean basins, latitudes and/or hydrographic regimes may exhibit

different ranges of morphological traits43,82,115,118,119 and species’ morphological traits have been shown to vary on a range of short-term (daily to seasonal) to longer-term (multi-annual

to millennial) timescales4,102,120,121,122,123,124,125,126. As such, users of the dataset should note that the range of morphometric traits in the dataset are not necessarily representative

of the full range of morphologies exhibited by each species globally and that the range of morphological traits present at specific temporal or spatial scales are dependent on the diversity

of ecotypes present in the population. This may especially be true for species represented by a limited number of entries in the dataset (Fig. 2; Supplementary Table 1). A simple indicator

of the range of morphometric data observed in the dataset relative to published literature is reported in Supplementary Table 1 for initial context. Coccolithophore taxonomy is under

constant refinement through morphological and, increasingly, genomic studies. We therefore strongly encourage users of the dataset to confirm the most up to date taxonomic identifier of each

species in the dataset before use, for example using the Nannotax3 website23 as this resource is constantly maintained, provides details of previous species synonyms, and provides extensive

references to primary literature. Users of the dataset may wish to use one of the several published cell volume to cell biomass relationships29,67,127 to further convert the cell size data

in the dataset into estimates of cellular organic carbon (biomass). Identical morphometric measurements to those presented here can also be made on intact fossil coccospheres preserved in

marine sediments66,68,128,129. Using the same morphometric-based method30, the cellular calcite of extinct calcareous nannoplankton species can be estimated and used to investigate evolution

in cellular calcite content through time31,66,68,130. CODE AVAILABILITY No custom code was used for the generation or processing of the datasets used in this study. REFERENCES * Ziveri, P.

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ACKNOWLEDGEMENTS The authors acknowledge the support of the scientists and crew associated with the AMT 14 cruise, especially Patrick Holligan who pioneered the AMT coccolithophore research

and Tim Adey and Anastasia Charalampopoulou who performed the original coccosphere abundance counts and taxonomic identification. AMT 14 was supported by the UK Natural Environment Research

Council (NERC) through the Atlantic Meridional Transect consortium (NER/O/S/2001/00680). This is contribution number 404 of the AMT programme. The authors also acknowledge the contribution

of Aimee Coggins to the initial assessments of coccosphere thickness and cell volume in extant coccolithophores as part of her MSci thesis (University of Southampton, 2015). This research is

funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) project number 447581699 to R.M.S. A.J.P., J.dV. and F.F.M. acknowledge funding from the UKRI NERC (Cocco

Trait, NE/X001261/1). AJP is also supported by co-funding from the Horizon Europe Funding programme and UK Research and Innovation (OceanICU, agreement number 10054454). J.O.H. and R.M.S.

received funding through Project A4 of the VeWA consortium (_Past Warm Periods as Natural Analogues of our high-CO__2_ _Climate Future_) by the LOEWE programme of the Hessen Ministry of

Higher Education, Research and the Arts, Germany. FUNDING Open Access funding enabled and organized by Projekt DEAL. AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * Institute for Geosciences,

Goethe-University Frankfurt, Frankfurt am Main, Germany Rosie M. Sheward & Jens O. Herrle * The Lyell Centre for Earth and Marine Science, Heriot-Watt University, Edinburgh, UK Alex J.

Poulton * Department of Earth Sciences, University College London, London, UK Jeremy R. Young * BRIDGE, School of Geographical Sciences, University of Bristol, Bristol, UK Joost de Vries 

& Fanny M. Monteiro * Biodiversity and Climate Research Centre (BIK-F), Frankfurt am Main, Germany Jens O. Herrle Authors * Rosie M. Sheward View author publications You can also search

for this author inPubMed Google Scholar * Alex J. Poulton View author publications You can also search for this author inPubMed Google Scholar * Jeremy R. Young View author publications You

can also search for this author inPubMed Google Scholar * Joost de Vries View author publications You can also search for this author inPubMed Google Scholar * Fanny M. Monteiro View author

publications You can also search for this author inPubMed Google Scholar * Jens O. Herrle View author publications You can also search for this author inPubMed Google Scholar CONTRIBUTIONS

The data collection and study design were conceived by R.M.S. and A.J.P. All morphometric data collection was conducted by R.M.S. with methodological consultation throughout with A.J.P.

J.R.Y. contributed new morphometric data used to define the _y_ variable and estimate cell diameter from coccosphere diameter. The manuscript was written by R.M.S. with contributions from

A.J.P., J.R.Y., J.dV., F.M.M. and J.O.H. CORRESPONDING AUTHOR Correspondence to Rosie M. Sheward. ETHICS DECLARATIONS COMPETING INTERESTS The authors declare no competing interests.

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CITE THIS ARTICLE Sheward, R.M., Poulton, A.J., Young, J.R. _et al._ Cellular morphological trait dataset for extant coccolithophores from the Atlantic Ocean. _Sci Data_ 11, 720 (2024).

https://doi.org/10.1038/s41597-024-03544-1 Download citation * Received: 30 January 2024 * Accepted: 17 June 2024 * Published: 02 July 2024 * DOI: https://doi.org/10.1038/s41597-024-03544-1

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