LETTERS
Microbially influenced formation of
2,724-million-year-old stromatolites
KEVIN LEPOT1 *, KARIM BENZERARA1,2 , GORDON E. BROWN Jr3,4 AND PASCAL PHILIPPOT1 *
1
Equipe Géobiosphère Actuelle et Primitive, Institut de Physique du Globe de Paris, CNRS & Université Denis Diderot, case 89, 4 place Jussieu, 75252 Paris, France
Institut de Minéralogie et de Physique des Milieux Condensés, 75015 Paris, France
3
Department of Geological & Environmental Sciences, Stanford University, Stanford, California 94305-2115, USA
4
Stanford Synchrotron Radiation Laboratory, SLAC, Menlo Park, California 94025, USA
* e-mail: [email protected]; [email protected]
2
Published online: 27 January 2008; doi:10.1038/ngeo107
Laminated accretionary carbonate structures known as
stromatolites are a prominent feature of the sedimentary record
over the past 3,500 Myr (ref. 1). The macroscopic similarity
to modern microbial structures has led to the inference that
these structures represent evidence of ancient life1,2 . However,
as Archaean stromatolites only rarely contain microfossils,
the possibility of abiogenic origins has been raised2 . Here, we
present the results of nanoscale studies of the 2,724-Myr-old
stromatolites from the Tumbiana Formation (Fortescue Group,
Australia) showing organic globule clusters within the thin
layers of the stromatolites. Aragonite nanocrystals are also
closely associated with the organic globules, a combination
that is remarkably similar to the organo-mineral building
blocks of modern stromatolites3–5 . Our results support microbial
mediation for the formation of the Tumbiana stromatolites, and
extend the geologic record of primary aragonite by more than
2,300 Myr (ref. 6).
We studied stromatolite samples from the 2,724 (±5)-Myrold Tumbiana Formation (Fortescue Group, Pilbara Craton)
at Meentheena, Western Australia7 . This rock sequence records
the most extreme episode of organic 13 C depletion of Earth’s
history, which has been attributed to the dominance of methaneassimilating microbes8 . The Tumbiana stromatolites were
deposited in shallow sea water9 or in a lacustrine environment10 .
Recognition of a few putative filamentous microfossils11 and
mineral moulds interpreted as traces of phototrophic microbes1,10
suggests that these stromatolites formed primarily by the
activity of photosynthesizers. In addition, 2α-methylhopane
molecules attributed to phototrophs12 were detected in the
stromatolite-bearing formation immediately above Tumbiana13 .
These observations indicate that microbial ecosystems were
developed in the Tumbiana palaeoenvironment. However, the
mere presence of microfossils within Archaean stromatolites
does not prove that microbes participated in their formation2,11 .
It is necessary to investigate the intimate association between
preserved microbial materials and their calcification products3–5 .
For this reason, we have re-examined the distribution and
texture of the organic carbon and its relationship with minerals
composing the Tumbiana stromatolites. Here, we present the
results of spectromicroscopy and mineralogical investigations
at the nanoscale of two unweathered carbonate stromatolites
collected from the Tumbiana drill core7 (PDP1). These samples
came from well below the water table. The absence of pyrite
oxidation, observable porosity and open microfractures testify to
their excellent preservation. Low-grade metamorphism, between
100 and 300 ◦ C (ref. 14), enabled preservation of microcrystalline
carbonate (micrite, see Supplementary Information, Fig. S1)
similar to that observed in modern stromatolites4,5,15 .
The stromatolites we examined consist of laminated structures
organized as bulbs of several hundreds of micrometres to a few
tens of centimetres in height (Fig. 1a). Stromatolite growth surfaces
are expressed as ∼10-µm- to ∼1-mm-thick layers of micritic to
microsparitic calcium carbonate that alternate with dark siliceous
mud-type layers (Fig. 1a,b). The mud-type layers are mainly
composed of silica and (Mg–Fe)-chlorite (see Supplementary
Information, Fig. S1). Detrital carbonates represent a minor
component of the carbonate layers and when present, are mainly
found in specific detrital layers. This indicates that stromatolite
growth was mainly controlled by in situ precipitation2 . The
morphology and mineralogy of these stromatolites are very similar
to those of the Satonda Lake stromatolites, which are characterized
by alternating layers of aragonite and an amorphous Mg–Si phase16 .
Poorly ordered carbonaceous material was identified using
Raman microspectroscopy (see Supplementary Information,
Fig. S2). It occurs as heterogeneously distributed micrometresize clusters that are exclusively associated with the micrite layers
(Fig. 1b–d). These clusters were found in the majority of the micrite
layers of the two stromatolite samples investigated. Imaging these
clusters by coupled confocal laser scanning microscopy (CLSM)
and Raman mapping (Fig. 1c,d) revealed that they are composed of
hundreds of globules smaller than 2 µm in size. Focused ion beam
(FIB) ultrathin sections (∼120 nm thick) were milled through
such clusters and several cubic micrometres of pristine rock
adjacent to a FIB section was crushed. Using the energy-filtered
imaging capabilities of scanning transmission X-ray microscopy
(STXM) at the carbon K-edge in parallel with transmission electron
microscopy (TEM), we characterized 15 globules about 1 µm in size
and mostly composed of organic matter in both the powder (m1 in
Fig. 2, m2 and m3 in Supplementary Information, Fig. S3) and FIB
sections (Fig. 1e,f).
Considering the controversies inherent to the interpretations
of biomarkers and morphological indicators of microfossils in
Archaean rocks11,17 , it is crucial to decipher whether these
organic globules may represent late contaminants. In situ
Raman microscopy and STXM imaging of FIB sections show
that the organic matter associated with the micrite is only
found as micrometre-scale organic globules exhibiting a cell-like
morphology. The organic globules seem indigenous to the micrite
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LETTERS
a
c
b
5 µm
2 mm
200 µm
e
d
f
5 µm
1 µm
1 µm
1 µm
Figure 1 Organic globules in the Tumbiana stromatolites. a, Millimetre-scale stromatolite bulbs. b, Dense clusters (arrowed) of organic globules in the carbonate layers of
the stromatolites. c, Carbonate layer containing clusters of organic globules that are less than 2 µm in size. d, Raman map (colour inset, 1,605 cm−1 band) coupled with a
CLSM fluorescence image of the carbonaceous matter in the globules shown in c. The lower right inset is a CLSM close view. e, TEM image of clustered globules within a FIB
section of a carbonate layer. f, STXM map of the same area (288.6–280 eV) showing the organic content of the globules.
and are absent from grain boundaries. This textural occurrence
contrasts sharply with that of remobilized organic matter17,18 and
therefore cannot be regarded as microfossil artefacts of uncertain
relationship to microbial materials. If these globules were to be
considered as late contaminants, the contamination must have
pervaded the stromatolite microstructure massively. However,
neither hydrocarbon-bearing fractures indicative of hydrothermal
organic contamination, nor colonization by endolithic microbial
communities along microchannels or micropits were observed in
our samples. Furthermore, Raman analyses show that the peak
temperature recorded by the organic globules corresponds to
that estimated (<300 ◦ C, see Supplementary Information) from
metamorphic minerals14 . Analysed globules are hence older than
the low-grade metamorphism overprint they experienced, which is
dated at about 2,200 Myr (ref. 19).
The chemical speciation of carbon forming the organic
globules was characterized by near-edge X-ray absorption fine
structure (NEXAFS) spectroscopy at the carbon K-edge3 . The
spectra obtained show multiple peaks indicating a chemically
complex mixture of different functional groups (Fig. 2c). On
the basis of a comparison with reference spectra3 , these peaks
were assigned to aromatic (285.3 eV, π∗ (C=C)), aliphatic carbon
(287.9 eV, σ ∗ (C–H)), carboxyl (ester or carboxylic acid) functional
groups (288.6 eV, π∗ (C=O)) and carbonates (290.3 eV). Further
peaks appearing as shoulders can be assigned to polynuclear
aromatics or ketone groups (286.7 eV), ketone or phenol groups
(287.3 eV) and hydroxylated aliphatic carbons (289.6 eV).
Carbonate crystals occur systematically associated with the
organic globules (Fig. 2a,b), sometimes in pervasive association
down to at least the spatial resolution of the STXM (∼40 nm).
Examination of these carbonates by TEM revealed clustered
bodies of CaCO3 intimately associated with the organic globules
(Fig. 2d,e, Supplementary Information, Fig. S3). The CaCO3 bodies
are often sub-rounded, smaller than 200 nm, and composed of
numerous crystallites as small as 10 nm (Fig. 2e). High-resolution
TEM (HRTEM) on single crystallites (Fig. 2f,g) and selectedarea electron diffraction of the crystallite clusters (Supplementary
Information, Fig. S4) enabled us to unambiguously identify these
crystallites as aragonite.
Our nanoscale observations show that there are striking
similarities between the Tumbiana stromatolites and modern
stromatolites. The size and shape of the organic globules imaged
by Raman/CSLM and STXM and those of microbial cells present
in modern stromatolites3,4,15,20 are similar. Moreover, both the
organic globules in the micritic part of the Tumbiana stromatolites
(Fig. 1b–f) and the microbial colonies observed within aragonite
in modern stromatolites15,16 are clustered, relatively scarce and
heterogeneously distributed. Whereas morphology has usually
been used as a single criterion to infer the biogenicity of such
objects, NEXAFS spectroscopy provides further clues on the origin
of the organic globules observed in Tumbiana stromatolites.
We suggest that the complex mixture of aliphatic, carboxylic
and aromatic carbon detected in the Tumbiana globules indicates
partial degradation of an original microbial material during early
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LETTERS
a
e
b
500 nm
f
500 nm
c
5 nm
100 nm
R'
O
OR
289.6 eV
–CHn–
C
287.3 eV
285.3 eV
Normalized intensity
g
0, – 6, – 2
0, – 3, – 3
0, 0, – 4
0, – 6, 0
0, – 3, – 1
286.7 eV
CO3
2–
0, 0, – 2
284
0, – 3, 1
286
288
Energy (eV )
290.3 eV
288.6 eV
0, 3, – 1
287.9 eV
282
d
290
0, 3, 1
0, 0, 2
0, 6, 0
m1
292
0, 0, 4
200 nm
0, 6, 2
0, 3, 3
Figure 2 Association of aragonite spheroids with organic globules (Globule m1). a,b, STXM maps of organic matter absorbing at 288.6 eV (a) and nano-aragonite
(absorption at 290.3 eV) (b). In b, the absorption by the organic carbon has been subtracted. c, Carbon K-edge NEXAFS spectrum of the globule. The normalized intensities of
the peaks indicate that the globule is mostly composed of organic carbon. d,e, TEM images of the same globule revealing clustered sub-rounded bodies (arrowed and inset
box) composed of intertwined nano-aragonite crystallites (e, close view). f, HRTEM picture of the aragonite exhibiting quadratic-shaped crystallites of sizes around 10 nm.
g, Identification of aragonite by fast Fourier transform of f (diffraction zone axis: [1,0,0], interplanar angles: (0,0,2) × (0,3,1) = 65.1◦ , (0,3,1) × (0,3,−1) = 49.8◦ ).
diagenesis and metamorphism. Indeed, the carbon K-edge spectra
of the Tumbiana organic globules have features very similar
to many of those observed for microorganisms or extracellular
polymeric substances (EPS) in modern stromatolites but they
differ in several ways, including the absence of amide groups and
differences in relative intensities of the peaks3 . The disappearance
of peptide bonds and the relative depletion of ketone/phenolic
groups in the Tumbiana globules are consistent with the
progressive change and loss of nitrogen- and oxygen-bearing21–23
functional groups occurring during maturation of organic matter.
This in turn can account for the relative abundance of the
aromatic and aliphatic groups23 . The moderate thermal overprint
(see the Supplementary Information) experienced by Tumbiana
stromatolites is in turn consistent with the preservation of carboxyl
groups, as attested to by reports of carboxyl groups resisting
higher-grade metamorphism24 and pyrolysis up to 400 ◦ C (ref. 23).
It has been suggested that late Archaean ocean compositions
favoured aragonite precipitation instead of calcite25 . Several
considerations discussed below suggest that the aragonite
crystallites associated with the organic globules are primary and
could have therefore taken part in building the mineral framework
supporting the stromatolite macrostructure. Metamorphic
formation of aragonite after calcite can be discarded because
this reaction only proceeds at much higher pressure than those
experienced by the Tumbiana Formation14 . Because calcite is
thermodynamically favoured over aragonite at low pressure, an
abiotic diagenetic origin of aragonite after dissolution of calcite can
be ruled out as well. Furthermore, the Mn and Fe contents of the
Tumbiana aragonite are similar to those of micritic calcite forming
the stromatolite layers but differ from that of secondary calcite
filling local veinlets oriented at high angles to the sedimentary
bedding. Hence aragonite is more likely a primary phase of the
Tumbiana stromatolite layers rather than of later diagenetic or
metamorphic origin.
The preservation of such aragonite in ancient rocks is unusual.
Because aragonite is metastable at low pressure, it ultimately
transforms to calcite6 during metamorphism and diagenesis and
has not yet been reported in rocks older than 400 Myr (ref. 6).
Powder diffraction analyses (data not presented here) show that
the calcium carbonate phase in Tumbiana stromatolites is almost
exclusively calcite, indicating that the transformation came near
completion. The key argument for the preservation of 350-Myr-old
aragonitic fossils6 was the occurrence of clayey- and organic-rich
material coating the fossils and acting as an impermeable barrier to
ambient solutions26 . The carboxyl-rich organic compounds found
in contact with aragonite in the Tumbiana stromatolites probably
played the same inhibiting role to fluid-enhanced diagenetic
recrystallization of aragonite into calcite26 . The low permeability
of the mud-type layers surrounding the micritic layers may have
provided further protection against fluid circulation. Without
water and considering a metamorphic temperature lower than
300 ◦ C, the transformation rate of aragonite into calcite might have
been low enough27 to preserve some aragonite crystals. Moreover,
the extreme polycrystallinity of the aragonite in our samples and
the burial pressure acting against the positive volume change of the
transformation to calcite may have acted as reaction inhibitors27 .
The Tumbiana nano-aragonite associated with the
organic globules shows textural similarities to the clustered
CaCO3 -‘nanospheres’ occurring in modern microbialites3–5,20 .
Such nanospheres are the basic building blocks of modern
stromatolites3–5 where, together with microbial materials, they form
nanostructured organo-mineral composites3 that are similar to
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LETTERS
those we observe in the Tumbiana stromatolites. Such nanospheres
form in the initial phase of carbonate precipitation and their
subsequent clustering and/or coalescence with further overgrowth
forms the carbonate macrostructure4,5 . This nanocalcification may
result from the presence of carboxyl-rich microbial materials with
which they are associated, including cells and their EPS3–5,28 or
degraded EPS20 . Similar features were reproduced in vitro on
bacterial cells28 or with EPS extracted from modern stromatolites29 .
Conversely, the formation of carbonate crystals with such unusually
small size and rounded morphology is difficult to explain by abiotic
processes or organic-free synthesis30 .
The use of high-resolution microscopy enabled us to reveal
abundant cell-like organic globules in the Tumbiana stromatolites.
In addition, nanospectroscopy revealed that these globules present
many organic functional groups similar to those found in modern
bacteria. Our results thus suggest that some microfossils can be
preserved in ancient stromatolites owing to their encapsulation by
carbonate minerals, which is observed in recent analogues3,4 . Most
importantly, the organic globules described here are exclusively
associated with the carbonate layers and intimately associated with
micrite and nano-aragonite. Accordingly, they might represent
material that was preserved in early diagenetic micrite formed
after original aragonite2 resulting from microbial lithification.
The nanometre-scale similarities between the modern and the
Tumbiana stromatolites support the view that the latter were
partly built through in situ precipitation of aragonite in a fashion
very similar to that described for their modern counterparts. The
method used here provides powerful new means of investigating
the role of microbial materials in the formation of the oldest
stromatolite remains on Earth.
METHODS
Samples 68.2 and 69.2 were milled with an FIB200TEM. Crushed samples
(68.2) were deposited on TEM grids. Backscattered electron scanning electron
microscopy (SEM) analyses were carried out on Au–Pd-coated thin sections
on a JSM-840A SEM, at 20 kV, 1 nA and 15 mm working distance. Images
were acquired using the software Spirit. SEM energy-dispersive X-ray analyses
were carried out with a PGT Sahara spectrometer. FIB sections were prepared
from the same gold-coated thin sections. STXM analyses were carried out at
the ALS BL 11.0.2. At the carbon K-edge, the energy resolution was estimated
at 0.1 eV, and energy calibration was carried out using the well-resolved peak
of gaseous CO2 at 294.96 eV. Image stacks and energy-filtered imaging were
recorded and analysed as described previously3 . Data were extracted using the
software Axis2000. TEM analyses were carried out at 200 kV on a J2100F TEM.
The TEM is equipped with a field-emission gun, an ultrahigh-resolution pole
piece and a Gatan energy filter GIF 200. Energy-dispersive X-ray analyses were
carried out using a Kevex detector. Fast Fourier transforms of HRTEM images
obtained on single crystals were calculated using ImageJ. The selected-area
electron diffraction patterns were analysed with Processdiffraction. Raman
data were obtained on a Renishaw InVia Raman spectrometer using the
514.5 nm wavelength of a 20 mW argon laser focused through a Olympus
BX61 microscope with a ×100 objective (numerical aperture: 0.9). The planar
resolution of this configuration is lower than 2 µm. The laser power was
cut off to 1% and the integration time was 10 s. The energy (∼1 mW) and
integration time are well below the critical dose of radiation that can damage the
carbonaceous matter. Spectra were deconvoluted and curve-fitted using Peakfit
software using the same fitting procedure for all spectra. Compositional Raman
mappings were acquired by scanning the sample over selected areas. Features
as small as ∼300 nm were resolved using a 300 nm step size and a pinhole in
the light path. Compositional maps were extracted with the software Wire
2.0. They represent the intensity distributions of characteristic peaks that were
determined by comparing reference spectra to each spectrum composing the
map. Confocal fluorescence (CLSM) images were obtained using an Olympus
Fluoview FV1000 confocal laser scanning biological microscope, which shares
the light path of the Renishaw Raman system and uses a 488 nm argon ion laser.
Immediately after being identified by the Raman microspectroscopy system, the
fluorescence of the same carbonaceous matter globules was imaged by using
the same objective and by filtering the wavelengths (Olympus SDM510 filter)
between 488 and 510 nm from the kerogen-derived fluorescence emitted from
the specimen. Two-dimensional images were acquired and rendered using the
F10-ASW 1.5 Fluoview software.
Received 10 September 2007; accepted 19 December 2007;
published 27 January 2008.
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Acknowledgements
M.J. Van Kranendonk, P. Lopez-Garcia and D. Moreira are thanked for assistance during the Pilbara
Drilling Project (PDP), O. Boudouma, C. Dominici, D. Neuville, Y. Wang for assistance during SEM,
FIB, Raman and XRD analyses and C. Thomazo, O. Beyssac, P. Rey and M. Van Zuilen for discussion.
P.P. thanks the Institut de Physique du Globe de Paris, the Institut des Sciences de l’Univers and the
Geological Survey of Western Australia for supporting the PDP. This study was supported by grants
from INSU (P.P.), Agence Nationale de la Recherche (P.P., K.B.), Région Ile-de-France (P.P.), NSF and
the Stanford University (K.B. and G.E.B.). This is IPGP contribution No. 2307.
Correspondence and requests for materials should be addressed to K.L. or P.P.
Supplementary Information accompanies this paper on www.nature.com/naturegeoscience.
Author contributions
P.P. organized the Pilbara Drilling Project. K.L. and P.P. carried out SEM, Raman, FIB and CLSM
analyses. K.L. and K.B. carried out HRTEM analyses. K.B. and K.L. carried out STXM analyses. All
authors wrote the paper.
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