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Journal of the Geological Society, London, Vol. 160, 2003, pp. 857–862. Printed in Great Britain.
857
Non-destructive multiple approaches to interpret the preservation of plant fossils:
implications for calcium-rich permineralizations
ANDREW C. SCOTT & MARGARET E. COLLINSON
Geology Department, Royal Holloway University of London, Egham TW20 0EX, UK (e-mail: a.scott@gl.rhul.ac.uk)
Abstract: Permineralized fossil coniferous woods from the Pliocene of Dunarobba, Umbria, Italy, and the
Jurassic of Swindon, Wiltshire, England, were studied using non-destructive techniques on uncoated polished
thin sections to elucidate their preservational history. Specimens were observed using transmitted light,
polarized light, reflected light under oil, and cathodoluminescence. Selected areas were studied using a
variable pressure SEM in backscattered electron mode. This allowed uncoated specimens to be examined and
elemental distributions to be determined using an energy dispersive X-ray microanalyser. The data were used
to interpret details of the permineralization history. Results reveal that anatomical interpretations based merely
on observations of thin sections in transmitted light can be very misleading and could potentially affect the
application of permineralized plant fossils, for example, in evolutionary biology, palaeoclimate analysis and
isotope geochemistry.
Keywords: fossil plant, preservation, permineralization, microscopy, microanalysis.
For key biological innovations in plants to be investigated it is
important to find plant fossils that yield anatomical data (Taylor
& Taylor 1992). Our extensive understanding of the evolutionary
history of many plant groups (e.g. lycopsids, Bateman et al.
1992) relies heavily on anatomical data from permineralized or
petrified fossils. For these applications in evolutionary biology an
understanding of the permineralization process is important to
interpret which original organic material and anatomy may be
preserved faithfully, variously modified or totally lost in the
fossil. Understanding of permineralization is also necessary to
ensure the validity, comparability and repeatability of results
from applied studies of permineralized fossils such as in
palaeoclimate analysis or isotope geochemistry.
In permineralization, minerals (often silica, pyrite or carbo-
nates such as calcite) occupy former cell lumina whereas organic
cell walls remain. Subsequently, in petrifaction (sensu stricto) the
organic cell walls may decay and be replaced by another phase
of minerals, usually with a similar chemical composition to the
first phase (Scott 1990).
Considerable progress has been made in our understanding of
both silicification and pyritization of plant fossils (Kenrick &
Edwards 1988; Trewin 1996; Jones & Rowe 1999; Boyce et al.
2001; Dietrich et al. 2001; Grimes et al. 2001, 2002). However,
carbonate permineralization (e.g. calcite) is amongst the most
common preservation state. Most studies of carbonate perminer-
alized plants have been undertaken on peel sections (Jones &
Rowe 1999) with the loss of mineralogical detail because the
mineral is dissolved to make the peel. Petrographic and chemical
studies have shown that there is a wide range of carbonate
mineralization depending on the depositional and diagenetic
environment (Scott 1990; Scott et al. 1996, 1997; DeMaris
2000). However, we are not aware of any studies that have used
multiple techniques in combination to investigate the details of
calcium-rich permineralizations.
In this paper we aim to demonstrate the understanding of
mineralization that can be gained by applying multiple, non-
destructive, analytical approaches to the same group of cells in a
polished thin section of a permineralized plant fossil. We have
selected wood as our sample material as this is abundant in the
fossil record and widely applied in studies ranging from evolu-
tionary biology, through palaeoclimate analysis to isotope geo-
chemistry. The specimens for analysis were selected primarily
because they were calcareous permineralizations apparently dis-
playing excellent three-dimensional preservation of organic cells,
as is shown by the apparent cell wall structures seen in transverse
section in transmitted light (Figs 1a, i and 2a). This kind of
preservation is essential for our aims to assess the effects of
permineralization on the preservation of organic material. A
secondary consideration in sample selection was to include
samples from different environments and ages so as to make a
preliminary comparative assessment of different preservational
contexts.
Materials
Pliocene, Dunarobba, Italy
The Dunarobba Fossil Forest is a late Pliocene fossil forest of
taxodiaceous conifers preserved in the Fosso Bianco Formation
at Dunarobba, Umbria, Italy (Scott & Freedberg 2000). Scattered
woods, both branches and small trunks, as well as leaves occur
here, and include numerous specimens that Ravazzi & Van der
Burgh (1994) identified to the conifer Glyptostrobus.
The specimens used in this study (Dunacs1 and Dunacs2) were
collected (by A.C.S.) in situ in clays at the top of the site above
the main fossil forest as shown byScott & Freedberg (2000, figs
18 and 20). The enclosing sediments were silty muds with
abundant plant debris.
Jurassic, Swindon, UK
A number of wood specimens were collected by J. K. Wright
from marine sediments (Bed 4) of the Ampthill Clay from South
Marston, Swindon, Wiltshire, England, of Mid-Jurassic age
(Oxfordian–Kimmeridgian boundary) (Wright 2003). Bed 4
comprised medium grey fossiliferous mudstone with limonitic
ooids and phosphatic nodules. Specimen MK1 was used in the
present study.
Analytical approaches
Polished and petrographic thin sections
Polished thin sections were produced using epoxy resin as an
embedding and mounting medium with a thickness of 30 �m,
measured by micrometer and polished using 0.05 �m aluminium
oxide so that no scratches remained. For each specimen studied
all observations on polished sections (see below) were made on
exactly the same area of cells on the same single section.
Separate petrographic thin sections (taken adjacent to polished
Fig. 1. Transverse sections of permineralized wood from Dunarobba. (a)– (h), (p)– (u) Dunacs1; (i)– (o) Dunacs2. (a) Transmitted light (note smaller
early wood cells and larger late wood cells). (b) Reflected light under oil (note complex layering of white and brown minerals). (c) Backscattered electron
image. Increasing brightness indicates higher atomic number (black, carbon; orange, calcium; yellow, iron). (d) Carbon map (note little carbon remains in
cell walls). (e) Iron map (note concentrations in cell walls). (f) Calcium map (note concentration in cell lumina). (g) Cathodoluminescence micrograph
showing dull luminescence and two phases of calcite precipitation. (h) Stained section in transmitted light with blue staining indicating ferroan calcite. (i)
Transmitted light. Cells at the bottom right are mineralized and smaller cells at the top right show no mineralization. (j) Transmitted light, crossed polars.
Unmineralized cells at the top right show birefringence and the resin groundmass shows patchy extinction. (k) Reflected light under oil showing the
mineralized cell walls as white. (l) Backscattered electron image (see (c)). (m) Carbon map (note little carbon in walls). Large area of green indicates
mounting resin. (n) Iron map (note lack of iron in unmineralized cells). (o) Calcium map. (p)–(s) Polished slice. (p) Backscattered electron image. (q)
Iron map. (r) Carbon map (note remnant carbon in some cell walls). (s) Calcium map. (t) Backscattered electron image showing position of line scan. (u)
Line scan showing elementaldistribution.
A. C. SCOTT & M. E. COLLINSON858
sections) were stained with potassium ferricyanide–Alizarin Red
S using the technique of Dixon (1966). Polished slices were used
to confirm the presence of carbon (which is present in the
mounting medium for the thin sections).
Light microscopy: transmitted, polarized and reflected
light
The polished thin sections were examined using a Nikon
Microphot microscope in transmitted, plane- and cross-polarized
and reflected light. Reflectance observations were made using a
320 objective lens under oil (Cargylite immersion oil type B2,
with a refractive index of 1.524). Areas selected were photo-
graphed using 100ASA colour print film and marked by a small
self-adhesive arrow to allow relocation.
Cathodoluminescence
The polished thin sections were examined using a Technosyn II
cathodoluminescence unit connected to a Nikon Microphot
microscope with a 310 objective lens. Images were captured
digitally and processed using image capture software Image Pro-
Plus v.4.5 developed by Media Cybernetics and an enhancement
program by Porocity Imaging Co. Image capture was for 45 s.
Scanning electron microscopy: elemental distribution,
occurrence and quantity
The uncoated polished thin sections were studied using a Hitachi
S3000N variable pressure SEM with an Oxford/Link energy
dispersive X-ray microanalyser. The microscope was operated at
a pressure of 70 Pa using a working distance of 15 mm and
accelerating voltage of 20 kV. In the variable pressure mode
images were obtained using backscattered electrons, which
reflect differences in atomic number. Images were captured and
processed digitally and the backscattered electron image was
thermally coloured so that dark areas represented the element of
smallest atomic number and red, orange and yellow represent
elements with progressively higher atomic numbers.
A qualitative elemental analysis was undertaken across the
polished section so that common elements could be identified.
Element distributions were then recorded as (1) line scans giving
detailed relative variation across individual cell walls and cell
lumina and (2) area maps (100 frames) showing the overall
distribution across a group of cells. Area maps were coloured to
distinguish element concentrations (brighter colours indicate
higher concentration; no colour indicates absent) and saved
digitally as tif files.
Quantitative analysis of elements on selected areas was also
made following calibration using a cobalt standard.
Fig. 2. Transverse sections of permineralized wood from Swindon. (a) Transmitted light. (b) Backscattered electron image. (c) Carbon map. (d) Sulphur
map. (e) Calcium map. (f) Phosphorus map. (g) Backscattered electron image showing position of line scan. (h) Line scan showing elemental distribution.
PERMINERALIZATION OF FOSSIL WOOD 859
Results
In transmitted light the specimens show a pattern in transverse
section that could be interpreted readily in terms of expected
wood structure as cell walls (brown and almost opaque) and cell
lumina (pale and translucent) of the tracheids (and rarer ray
cells) of a coniferous wood (Figs 1a and 2a). The weight and
hardness of the hand specimens indicates mineralization, leading
to an initial interpretation that the specimens are probably simple
permineralizations with cell lumina infilled with a clear mineral
such as calcite (calcium carbonate) and with organic cell walls
retained.
Pliocene Dunarobba; Dunacs1
‘Apparent cell lumina’. The pale translucent cell infill seen in
transmitted light shows high birefringence colours in polarized
light, suggesting that it is calcite, and stains a blue colour (Fig.
1h), showing that it is ferroan calcite. The lumen infill is distinct
with a moderate atomic number (Fig. 1c, orange) and elemental
analyses showing a high concentration of calcium (Fig. 1f and s)
and a low concentration of iron (Fig. 1e and q) entirely
consistent with ferroan calcite. Quantitative analysis of an un-
coated polished slice showed the cell fill having 12% C, 25% Ca,
11% Fe and 52% O. The specimen shows dull luminescence
(Fig. 1g) but bright layers suggest that the calcite fill was
deposited in more than one phase.
‘Apparent cell walls’. The dark cell outlines seen in transmitted
light reveal multiple layering in reflected light (Fig. 1b). Two
colours, white and reddish brown, are evident, with white nearer
the cell lumen. The cell-to-cell transition can be complex,
suggesting separation of wall layers, intercellular spaces or
sections through areas of pits on the radial walls. The white
layers are distinctive with high atomic number (yellow, Fig. 1c),
high concentrations of iron (Fig. 1e) and little or no calcium
(Fig. 1f). The reddish brown layers (Fig. 1b) have low atomic
number (black, Fig. 1c), lack iron and calcium (Fig. 1e and f)
but sometimes show concentrations of carbon in elemental map
(Fig. 1d), confirmed very clearly in line scan (Fig. 1t and u). The
‘apparent cell walls’ have therefore been shown to be complexes,
with a thick inner layer (nearest the lumen and most of the
apparent wall thickness) made of an iron-rich mineral and a thin
outer layer. The iron-rich mineral layer itself exhibits some
layering variation as a thin redder area within the yellow (Fig. 1t)
and as slight calcium peaks within the calcium troughs (Fig. 1u).
The thin outer layer (usually shared between two adjacent cells)
may include original organic cell wall or may be space into
which other carbon-containing substances have penetrated (sedi-
mentary material or mounting–embedding medium). Elemental
mapping of an unmounted polished slice (Fig. 1p–s) confirmed
the presence of residual carbon in the position of the cell walls
(Fig. 1r). A quantitative analysis shows that the iron-rich layer
has 11% C, 13% Ca, 24% Fe and 50% O whereas the thin outer
layer, which may include part of the original cell wall, has 24%
C, 13% Ca, 20% Fe and 42% O.
Pliocene Dunarobba; Dunacs2
There are two main types of preservation in different parts of this
specimen, lower left and upper right (Fig. 1i). The lower left part
is mineralized and very similar to Dunacs1 fully described above.
Slight differences include a more obvious iron content in some
cell lumina (Fig. 1n) and possibly higher calcium content in the
iron-rich wall layer (Fig. 1n and o), which also shows a fibrous
structure (Fig. 1k).
The upper right part of this specimen contains no mineral, as
shown by low atomic number (Fig. 1l), absence of iron and
calcium (Fig. 1n and o) (and also absence of other elements such
as Si, Mg, Mn, P, etc., not shown), and high abundance of carbon
(Fig. 1m). The embedding medium shows patchy grey extinction
(Fig. 1j). The cell walls in the upper right area are pale yellow–
brown in all LM images and show distinct layering but with no
suggestion of mineral content in cross-polarized light. These
walls are interpreted as original organic cell walls. The wall
thickness is very similar to that of the thin outer (furthest from
cell lumen) non-mineralized wall layer in mineralized material
(see Dunacs1 above). In contrast, the overall cell size differs by a
factor of two or more. The elemental map for carbon (Fig. 1m)
is not able to distinguish carbon in these original cell walls from
surrounding carbon-rich material (mounting–embedding resin).
However, elemental mapping of an unmounted polished slice
confirmed the presence of residual carbon in the position of the
cell walls.
Jurassic Swindon
Unexpectedly, elemental analysis of this specimen shows almost
identical distributions for calcium (Fig. 2e) and phosphorus (Fig.
2f). We interpret this as mineralizationby calcium phosphate,
which has infilled most cell lumina, formed a layer round the
edge of otherwise empty cell lumina and infilled thin layers
(?intercellular spaces) between cells. Carbon (Fig. 2c) occurs in
areas lacking calcium and phosphorus. The carbon infilling some
cells is the embedding resin and this was confirmed by examin-
ing a thin polished slice. The cell pattern is indistinct in
elemental maps and the backscattered image (Fig. 2b) because
much of the apparent cell wall (brown in transmitted light, Fig.
2a) is also represented by calcium phosphate. At high magnifica-
tion ‘cell walls’ exhibit layering (lighter vs. darker in Fig. 2a and
black vs. orange in Fig. 2h) with varying proportions of carbon
and calcium phosphate distinguishing the layers. The rays
contain concentrations of iron pyrites (black mineral, Fig. 2a)
exhibiting high sulphur (Fig. 2d and g) and iron (Fig. 2g).
Discussion
Dunarobba mineralization
The Dunarobba specimens show permineralization by a combina-
tion of iron-rich minerals (iron carbonates or oxides including
siderite and goethite) and ferroan calcite. The deposition of these
minerals is largely controlled by Eh and pH (Tucker 2001),
which may be affected by a number of factors including the
concentration of carbonate ions and the amount of organic matter
and its decomposition (Pettijohn 1975; Tucker 2001) (see also
calcium carbonate–calcium phosphate switch (Briggs & Wilby
1996;Sagemann et al. 1999) and the pyrite depositional system
(Grimes et al. 2001, 2002)).
In general, woods are chemically composed of cellulose,
hemicelluloses and lignin. It is well established that celluloses
break down before lignin (Hatcher & Clifford 1997) and their
breakdown yields CO2 and CH4; thus organic matter decomposi-
tion may provide a reducing environment (oxic to anoxic) and in
the absence of sulphur may be post-oxic and methanic (Tucker
2001). In such circumstances, in the presence of iron, siderite
(iron carbonate) is commonly precipitated. Chemical analysis of
some woods from Dunarobba indicated a significant loss of
A. C. SCOTT & M. E. COLLINSON860
cellulose (Staccioli et al. 1996). Despite this chemical loss, cell
walls usually remain coherent (Hatcher & Clifford 1997). It is
also possible that, as has been observed with leaves, the
precipitation of iron oxides on the surface of organic matter, as
biofilms, was initiated by bacterial decay produced CO2, which
rapidly adsorbs metal ions (Dunn et al. 1997). Siderite is prone
to solution and redeposition (James 1966) so iron oxides can be
a recent weathering product of siderite (Tucker 2001). The
fibrous structure (Fig. 1k) in Dunacs2 is commonly seen in
sphaerosiderite (Tucker 2001).
The cell lumina infills are predominantly of ferroan calcite.
Calcite may precipitate in preference to siderite where the pH
increases from seven to eight (Pettijohn 1975). If, however, there
is insufficient Fe2þ relative to Ca2þ then ferroan calcite may
form in preference to siderite (Tucker 2001). Ferroan calcite
deposition has occurred only in cells where there has also been
an iron-rich mineral layer deposited adjacent to the cell lumen
infill and this may relate to local pH.
The fact that there is variation in permineralization within one
specimen (shown here) and that not all Dunarobba woods are
permineralized (Scott & Freedberg 2000) suggests that mineral
precipitation is strongly influenced by very local changes in Eh
and pH. There is major natural variation in lignification between
cells and between secondary wall layers of woods (e.g.
Donaldson 2002), which, given differential decay of celluloses
vs. lignin, provides great potential for subcellular- and cellular-
scale variations in Eh–Ph conditions during wood decomposi-
tion. We conclude that the breakdown of original organic cell
walls may have locally changed the Eh–Ph conditions of the
pore waters to encourage mineral precipitation.
Swindon mineralization
This wood is dominated by calcium phosphate, partially (as a
lining) or entirely infilling cell lumina and in thin layers
(?intercellular spaces) between cells. It is well known that
bacterial decay of organic matter in sediment liberates phosphate
and bone is also a potential phosphate source (Tucker 2001).
Phosphate may also replace calcite or be precipitated instead of
calcite in neutral or slightly acidic pH conditions (Briggs &
Wilby 1996; Sagemann et al. 1999). Variation in phosphatization,
therefore, is likely to be related to Eh–pH variations discussed
above (Briggs & Wilby 1996; Sagemann et al. 1999). Pyrite
appears to be mainly restricted to the ray cells. This may reflect
locally very distinct Eh–pH conditions (Grimes et al. 2001,
2002) created by decomposition of living ray parenchyma cell
contents, as pyrite forms only in partially anoxic environments.
Organic vs. inorganic preservation and significance for
cell size and wall thickness
Taking account of the crack between mineralized and non-
mineralized areas and the way in which cells seem to have
originally fitted together across this crack in Dunacs2 (Fig. 1i–o)
we suggest that the organic-walled cells have shrunk, possibly
through dehydration and cellulose loss. This is supported by the
fact that shrinkage of lignified material on fossilization is known
elsewhere (e.g. organic seeds within the late Eocene insect
limestone, UK, Collinson, pers. observation). Furthermore, if
mineral deposition inside the mineralized cells had caused
differential expansion one would expect very distorted or
ruptured cell outlines and these are not observed. Therefore,
original cell size is thought to be reflected in mineralized cells, if
measured from lumen centre to lumen centre. The thickness of
the iron-rich mineral layer is very variable so that ‘apparent’ wall
thickness measurements would be very different from those of
the original wood. The differences in the thickness of the cell
walls of iron- and non-iron-impregnated cells needs further
consideration, as this factor will affect, for example, the meas-
urements used for palaeoclimatic interpretations.
Equally dramatic is the preservation of the Swindon wood by
calcium phosphate. The paucity of carbon in the cell walls was
totally unexpected and we have no way of knowing the original
dimensions of non-permineralized organic cell walls or cells.
Wider implications
Recognition of diagnostic anatomical structure, which requires
preservation of original organic tissues, underpins accurate sys-
tematic determination of permineralized plant fossils. In woods
cell sizes and cell wall thicknesses and their variations can be
applied both in systematic studies and in palaeoclimate analyses.
Organic components can be extracted from permineralized fossils,
carbon-isotope data can be applied for isotope stratigraphy,
palaeoatmospheric interpretations or assessment of photosynthetic
pathway, and biomarkers may be used in systematic studies.
Our observations show that, in striking contrast to our expecta-
tions, the majority of the structures that a superficial examination
in transmitted light suggested were cell walls in all our perminer-
alizations are not original organic wall layers but are in fact layers
of minerals. Although carbon is proven in elemental maps of
polished slices (Fig. 1r) it does not produce a very clear map of
the cell outlines and is present in very small amounts. Overall it is
not clear which, if any, of the original organic cell wall layers
remain in the permineralizations. In the Dunarobba specimens
carbon is present in both layers of the ‘apparent cell wall’, one of
which is dominantly an iron mineral. Therefore at least someof
the carbon may have been carried into the specimens during the
permineralization process. These observations show that an under-
standing of the mineralization is a prerequisite for the use of
permineralizations for all the applications above, which are under-
pinned by the potentially false assumption of preservation of
original cell walls. Furthermore, the variation in mineralization
that we have encountered in just two specimens also indicates that
it should never be assumed that any two plant permineralizations
are directly comparable in terms of their mineral composition or
their potential for preservation of important anatomical or organic
geochemical information.
In addition to the surprising results from ‘apparent cell walls’
we encountered an unexpected range of mineralization. Instead
of the expected calcite, one of our specimens is a calcium
phosphate permineralization and the other a combination of
ferroan calcite with an iron oxide or carbonate. The abundance
of permineralized wood fragments in the fossil record and the
variation within and between specimens, combined with the
complexity of factors controlling mineral precipitation, provides
future potential to apply permineralized wood fossils to help
interpret sediment geochemistry.
Conclusions
Multiple, non-destructive microscopic and analytical techniques
on uncoated polished thin sections have enabled us to elucidate
the mineralization of permineralized fossil coniferous woods from
the Pliocene of Dunarobba, Umbria, Italy (from continental
sediments) and the Jurassic of Swindon, England (from marine
sediments). In thin section, using transmitted light, both woods
appeared to be simple calcareous permineralizations with organic
PERMINERALIZATION OF FOSSIL WOOD 861
cell walls preserved and cell lumina filled with calcite. In reality,
the Italian Pliocene woods are mineralized with ferroan calcite
infilling cell lumina and iron-rich minerals (siderite, goethite)
forming ‘apparent cell walls’. In some areas where calcite had not
filled the cell lumina the organic walls remained. In the Jurassic
wood both cell lumina and cell walls are mainly represented by
calcium phosphate. Both woods indicate the importance of
organic wall breakdown to initiate the precipitation of the mineral
phases likely to be controlled by localized (sub-)cellular-scale
pH–Eh conditions in the wood. The results illustrate the range
and complexity of the permineralization process in calcareous
specimens. The combined evidence from multiple non-destructive
approaches on the same set of cells has been particularly valuable
in revealing the complexity of layers present in the ‘apparent cell
walls’ of the Dunarobba specimens and leading us to the
interpretation of these as dominantly mineral in composition. Our
observations show that an understanding of the mineralization is a
prerequisite for the use of permineralizations for any applications
that require the (potentially false) assumption of preservation of
unaltered organic cell walls.
We thank N. McGilp and C. Gummer of Proctor and Gamble (Health and
Beauty) for sponsoring this work and for providing a grant for the colour
plates. We thank the Royal Collection Trust, Proctor and Gamble (Health
and Beauty) and the Italian Government for financial support for field
work (to A.C.S.). We thank J. Wright and S. Howard for preliminary
observations on the Jurassic Woods and N. Holloway for slide prepara-
tion. We thank members of the Electron Microscope Unit of Royal
Holloway for their support and the Science Faculty of Royal Holloway
University of London for funding the SEM work.
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Received 13 December 2002; revised typescript accepted 28 March 2003.
Scientific editing by Jane Francis
A. C. SCOTT & M. E. COLLINSON862