Sedimentary Geology 201 (2007) 149 156

www.elsevier.com/locate/sedgeo

Biogenic features in calcretes developed on mudstone: Examples

from Paleogene sequences of the Himalaya, India
B.P. Singh a,, Yong Il Lee b , J.S. Pawar c , R.S. Charak c
b

a
Department of Geology, Banaras Hindu University, Varanasi-221 005, India
School of Earth and Environmental Sciences, Seoul National University, Seoul-151-747, Korea
c
Postgraduate Department of Geology, University of Jammu, Jammu-180 006, India

Received 1 September 2006; received in revised form 20 February 2007; accepted 17 May 2007

Abstract
Calcrete occurring in the Paleogene sequences of the western Himalayan foreland basin offers very useful information regarding
climate and paleogeography of northern part of the Indian subcontinent. These calcretes possess variety of biogenic features (beta
fabrics) that include rhizoliths, alveolar septal and vermiform fabric and Microcodium. The Microcodium rosettes show
filamentous structures.
The rhizoliths and alveolar septal fabric formed by the precipitation of carbonate in soil vadose zone and the vermiform fabric
may be a root mat. Perhaps microbes helped in dissolution of carbonate fillings and they were instrumental in precipitation of
calcite in the form of rosettes and filaments. Here, the filamentous structure in the Microcodium is significant. We suggest that the
Microcodium formed as a result of fungal dissolution and microbial mediation.
The lighter values of 13C and 18O (b 8.5) in the studied calcretes suggest that they developed through meteoric water in
the presence of soil organic matter within the dry subtropical climatic zone when the northern part of the Indian subcontinent
moved out of wet equatorial climate during its northward flight.
2007 Elsevier B.V. All rights reserved.
Keywords: Calcrete; Biogenic fabric; Microbial mediation; Microcodium; Paleogene; Himalaya; Indian subcontinent

1. Introduction
Biogenic features in calcareous paleosols and
calcretes are indicative of microbial (algal, fungal,
cyanobacterial and bacterial) dissolution and precipitation of carbonate associated with roots. Roots in the
vadose zone occur in association with such microorganisms as algae, fungi, cyanobacteria and bacteria (Jones,
1994). As biogenic features, Wright and Tucker (1991)
Corresponding author. Fax: +91 542 2368174.
E-mail address: bpsingh_in@yahoo.com (B.P. Singh).
0037-0738/$ - see front matter 2007 Elsevier B.V. All rights reserved.
doi:10.1016/j.sedgeo.2007.05.013

classified beta fabrics and observed that almost all the

biogenic (beta) calcretes develop on carbonate substrate.
Calcretes form a part of the continental Paleogene
sedimentary sequences that are exposed in the outer belt
of the western Himalaya both in India and Pakistan (Fig. 1).
Here, the calcretes contain rhizolith, alveolar septal fabric,
needle-fiber calcite associated with borings, root mat, and
single and aggregate Microcodium structures as beta fabric.
The focus of this paper is to illustrate biogenic features
occurring in unstudied Paleogene calcretes of the
Himalaya and to interpret their (calcretes) origin. Also,
we try to correlate the calcrete pedogenesis in the

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B.P. Singh et al. / Sedimentary Geology 201 (2007) 149156

Fig. 1. Map of the western Himalayan foreland exhibits exposures of the Paleogene sequence in parts of Pakistan and India. Important locations are
also shown. Locations of the studied sections rich in biogenic features are shown with asterisk. Inset: Outline map of India showing the boundaries of
India and Pakistan. Also note the location of Jammu in the map of India.

Paleogene sequences with the suitable climatic conditions.

Our findings are significant in two respects: 1) the
occurrence of biogenic features demonstrate that essentially these are pedogenic; 2) the pedogenic calcrete in the
Himalayan foreland basin sequences suggest their development when the northern tip of the Indian subcontinent
crossed the wet equatorial climatic zone and touched the
dry subtropical climatic zone during its northward flight.
2. Geological and depositional settings
Pascoe (1964), and Karunakaran and Ranga Rao
(1979) are among the pioneers who have discussed
detailed accounts of geological setting of the Paleogene
succession occurring in the western Himalaya (for detail
see Table 1). Klootwijk et al. (1986) suggested that the
continental sedimentation began around late Eocene
during Paleogene in the Jammu area based on

paleomagnetic data. In strike continuity, Najman et al.

(2001) dated the Paleogene sequences in Balkot area of
Pakistan (Fig. 1) and suggested that continental sedimentation began around 40 millions of years ago in the
western Himalayan foreland basin. Therefore Late Paleogene age (Late Eocene/Oligocene) can be assigned to the
calcrete containing basal redbeds of the western Himalaya.
The redbeds are designated as the Murree Group in
Pakistan and western part of India in Jammu area having
strike continuity. Further east in Shimla hills, these
sequences are designated as the DagshaiKasauli
formations (Table 1). Details of facies, dominant
sedimentary structures, ichnofauna, biogenic features
and depositional settings are given in Table 2. Less than
a meter thick calcrete profiles occur within laminated
brown mudstone in these sequences (Fig. 2).
Well-oxygenated coastal environmental setting has
been inferred for the Paleogene redbeds with tidal and

Table 1
Stratigraphic correlation of different localities in the western Himalaya
Balkot Area

Jammu Area

Shimla Hills

Age

References

Murree
Group

Upper Murree
Formation
Lower Murree
Formation
Subathu
Formation

Kasauli
Formation
Dagshai
Formation
Subathu
Formation

Early MioceneLate
Eocene

(Karunakaran and Ranga Rao,

1979; Najman et al., 2001;
Singh, 2003)

Middle EoceneLate
Paleocene

(Klootwijk et al., 1986; Bhatia

and Bhargava, 2006)

Balkot
Formation

REDBEDS

B.P. Singh et al. / Sedimentary Geology 201 (2007) 149156

151

Table 2
Lithofacies characterstics, associated biogenic features and depositional environments of the calcrete hosting late Paleogene Murree Group (modified
after Sudan et al., 2002)
Lithofacies

Characteristic features

Biogenic features

Depositional environments

Mudpebble
Conglomerate (Cg)
Cross-bedded
Sandstone (Sx)
Planar-bedded
Sandstone (Sh)

Pebble-sized mud clasts encased in sandy matrix.

Channel thalweg

Gray, medium-grained. 0.21.0 m thick

cross-bed cosets with low angle of foresets.
Gray, greenish gray, medium-grained,
thinly bedded sandstones. Contains
mud flasers and wavy bedding.
Yellowish gray, fine-grained sandstone;
symmetrical and asymmetrical ripples,
drape laminationand tidal bundles.
Brown, very fine sand to silt grain size.
Alternate silt and mud laminae, tidal bundles.
Rich in trace fossils
Purple, brownish yellow and greenish yellow.
Clay with silt-size quartz grains, platy and flaggy, non-fissile.
Variegated color, hard, Profile development from mottled
horizon to powdery to nodular and laminar. Nodule size
decreases downward in profile

Estuarine channel

Ophiomorpha

Middle part of Tidal

channel

Thalassinoides
Cosmorhaphe

Levee crestEstuarine

Imbrichnus,
Chondrites
Skolithos
Thalassinoides

Intertidal area

Ripple-laminated
Sandstone(Slr)
Laminated
Siltstone (St)
Laminated
Mudstone (Mb)
Calcrete (P)

Rhizoliths
Alveolar septal fabric
Microcodium
Root mat

Supratidal zone
Floodplain

fluvial influences, and the mudstones (host of the

calcretes) are considered as deposited either in supratidal zones or on floodplains (Najman et al., 1993; Singh
and Singh, 1995; Sudan et al., 2002).

are relative to PDBV standard with reproducibility of

0.05 for carbon and 0.1 for oxygen.

3. Methods and techniques

Macro-and micro-morphology of calcretes described

here include cathode luminescence petrography and

Stratigraphic sections were measured at two locations

in the Jammu area and at one location in Shimla hills and
the positions of the calcrete profiles were recorded in
them. Morphology and micromorphology of the calcrete
were studied and analyzed. Based on micromorphological study calcretes rich in beta fabric and poor in beta
fabric were categorized. Thin sections were also
subjected to cathode luminescence microscopy with
operating conditions of 8 kV and 10 mA to observe
behavior of carbonate in different microstructures. Microcodium was further studied on scanning electron
microscope (SEM). Additionally seventeen slabs from
nodular calcrete samples (6 samples rich in beta fabric
and 11 poor in beta fabric) were polished from one side.
To avoid changes in the results as a consequence of
diagenesis, only micritic carbonate was powdered under
the continuous observation of a stereo-microscope from
all the seventeen slabs with a dental drill and the samples
were acid digested as per method suggested by Bemis et
al. (1998) and carbon and oxygen stable isotope were
analyzed using a Prism series II model mass spectrometer at Korea Basic Science Institute. The isotopic ratios

4. Results

Fig. 2. Field photograph exhibits exposures of the calcrete at Kalakot

(Jammu area). Sandstone with red mottles (Sand) is followed by brown
mudstone (Mud) that hosts calcrete profiles. Note two calcrete profiles
(Cal) in this photograph. Hammer is 33 cm long.

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B.P. Singh et al. / Sedimentary Geology 201 (2007) 149156

scanning electron microscopic analysis. Additionally,

stable carbon and oxygen isotope results are also presented.
4.1. Macromorphology
The calcretes show profile development such that the
host mudstone has diffused boundary with the calcrete
while the upper surface of the calcrete has a sharp
contact with the overlying mudstone. Thickness of the
calcrete profile varies from 20 cm to 60 cm except in
some profiles where it is up to 1.5 m (Fig. 3).
The stratigraphic section measured from the first
locality in Fig. 3 shows ten calcrete profiles and development of calcretes from powdery to laminar stages while
Fig. 4. Field photograph exhibits sequential occurrence of powdery
(P), nodular (N) and laminar (L) calcrete horizons. Locality: Kalakot,
Jammu area. Hammer is 33 cm long.

the nodular calcrete is the dominant variety. In this section,

profile 5 from base shows clear horizonation with stacking
of nodular calcrete over powdery and laminar calcrete over
nodular (Fig. 4). While in other profiles both soft and hard
nodules occur as single layers in the mudstone. Calcrete
nodule size varies from millimeter to centimeter. Nodules
are both spheroidal and prismatic (tubular in shape) and
they vary from 2080% in the profiles. The powdery
calcrete occurs as white powder disseminated in the host.
Laminar calcrete forms 12 mm thick wavy laminae with
the development of rhizocretions. In the II section
measured from the Jammu area in Fig. 3, two calcrete
profiles are present and only nodular variety is observed.
Here, coalescing nodules together form big composite
nodules of 24 cm sizes.
In the section III, measured from the Shimla hills,
five calcrete profiles were recorded within 35 m thick
succession (Fig. 3). Here too nodular calcrete is the
dominant variety and nodule size varies from millimeter
to centimeter. The percentage of nodules varies from
2050. In the 2nd profile from the base the laminar
calcrete occurs above the nodular calcrete while the
powdery calcrete occurs in the 3rd profile.
4.2. Micromorphology

Fig. 3. Stratigraphic succession in the two localities of the Jammu area and
one locality of Shimla hills represent vertical arrangement of the various
lithologies including calcrete profiles. Note sequential occurrence of
powdery, nodular and laminar calcrete horizons in some profiles.

As beta fabric, the bifurcated channels with cylindrical shape occur with tapering ends (Fig. 5A) and
some of these channels show serrated outer margins.
The calcite filling the channels is typically sparitic with
prismatic crystals (Fig. 5A). The secondary calcite
filling the channels shows luminescent orange color
whereas the micritic carbonate forming the major part
and coatings around the carbonate filled channels shows

B.P. Singh et al. / Sedimentary Geology 201 (2007) 149156

153

Fig. 5. Calcretes photomicrographs include rhizolith, alveolar septal fabric and vermiform fabric. A. Rhizolith (R) shows bifurcation that tapers on
one side. Note sparitic carbonate filling in the rhizolith and micritic carbonate around it. B. Alveolar septal fabric (ASF) in the calcrete. Note white
microlaminar carbonate in the micrtic gray matrix. C. CL photomicrograph in gray-scale exhibits vermiform fabric. Arrow directs towards the
vermiform fabric. Also note a semicircular structure filled with irregular layers (F) on top left corner of the photograph.

red color. White microlaminar carbonate occurs in the

micritic carbonate matrix (Fig. 5B). Vermiform fabric is
recorded in association with a semicircular structure
filled with irregular carbonate layers (Fig. 5C). The
vermiform fabric shows light red to weak orange color
in CL microscopic study.
In some thin sections, needle-fiber calcite showing
irregular network around black amorphous structures is
observed (Fig. 6A). Fig. 6A also shows development of
crystals with curved faces in and around black amorphous
structures. Equant (equidiametric) crystals either occur as
single crystal or as bunch of crystals and sizes of the individual crystals vary from 0.05 mm to 0.15 mm (Fig. 6B).
Their shapes are mostly quadrangular with curved faces.
These crystals can be identified as Microcodium. Microcodium appears as consisting of rose-petals containing
both tangential and transverse filaments in SEM study
(Fig. 7A). Filaments are also observed in the center of
Microcodium structures (Fig 7A). Remarkably, Microcodium structures are light red colored and gray filaments are
visible in CL microscopy. Filaments of b 5 m thickness
and variable length are associated with flowery structures
that possess a circular hole inside (Fig. 7B).

4.3. Stable isotopes

In the studied calcretes, 13C varies from 8.49 to
11.23 and 18O is in a range of 8.53 to 13.04
(Table 3). Also, 18O increases with the increase of 13C
and vice-versa. It is observed that the calcretes, which are
rich in biogenic features, including Microcodium are
enriched in 12C and 16O with lower average values of
13C (on an average 10.16) and 18O (on an average
12.05) than those with absence of biogenic features (13C
averaging 9.04 and 18O averaging 10.38) (Fig. 8).
5. Discussion
The profile development in the studied calcretes and
the diffused lower contact and sharp upper contact with
the non-carbonate host demonstrate that the carbonate
precipitation took place on the surface and it percolated
down in the host as a result of weathering and soil
formation. This is also reflected by the horizonation in
the calcrete profiles where upper calcrete nodules are
more mature than the lower one. The nodular calcrete
formed when the secondary calcium carbonate

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B.P. Singh et al. / Sedimentary Geology 201 (2007) 149156

1985) and flowery structures are spores or sporangia

associated with them in the Himalayan calcretes.
Calcification process is governed by associated cyanobacteria/ bacteria rather than algae and fungi themselves
(Danielli and Edington, 1983; Ferrer et al., 1988; Riding,
2000), and calcification occurs while the filaments are
alive, shortly after their death or at some considerable
time after their death (Jones and Kahle, 1986). The
uncollapsed forms of many calcified filaments in the
studied calcretes indicate that calcification must have
taken place before filaments decay and collapse. Needlefiber calcite around black amorphous structures (fungal
borings) may be of fungal origin (Kahle, 1977; AlonsoZarza and Arenas, 2004). Therefore, it is interpreted that
the needle-fiber calcite around fungal borings in the
Himalayan calcretes developed as a result of microbial
precipitation.

Fig. 6. Calcrete photomicrographs show needle-fiber calcite and Microcodium. A. Calcite accumulation as filamentous network around
black colored amorphous structures. Note needle-fiber calcite (NF) and
equidiametric carbonate crystals adjacent to the needle-fiber calcite
and within the dissolution features (Di). B. Single and aggregate of
equidiametric (equant) crystals (Microcodium structures-M) exhibiting
curved faces with dark nucleus. Also note the dissolution features
around them (Di).

precipitated in the soil profile in an irregular dispersed

manner and laminar calcrete formed when the secondary
carbonate was ceased to percolate down (e. g. Wright,
1994).
The bifurcated channels of cylindrical shape with
tapering ends and serrated margins that are filled with
carbonate are root traces (e. g. Klappa, 1980) and
associated microlaminar carbonate (alveolar septal
fabric) suggests that it has developed as a result of
filling of root moldic porosities (e. g. Cohen, 1982;
Esteban and Klappa, 1983). The vermiform fabric in
Fig. 5C is attributed to be a root mat (e. g. Armenteros
and Daley, 1998) and semicircular structure filled with
irregular carbonate layers is possibly a fungal structure.
The filaments of small diameter (b 5 m) are most
likely fungal filaments (e.g. Kendrick et al., 1982; Ward,

Fig. 7. SEM photomicrographs of Microcodium and fungal structures.

Length of the scale-bar is 20 m. A. Microcodium structure (M) shows
rose-like petals and filaments dividing the petals from each other.
Arrow directs towards the filaments. B. Calcification in irregular shape
showing filamentous structure (F). Note flower-like structures with
circular holes possibly of fungal spores or sporangia (SP).

B.P. Singh et al. / Sedimentary Geology 201 (2007) 149156

Table 3
13C and 18O values (in ) relative to PDB standard in calcrete
samples
S. Nos.

Sample
Nos.

Section

Type of
calcrete

13CPDB V

18OPDB V

1
2a
3
4
5a
6
7a
8b
9b
10 a
11
12 a
13
14 a
15 b
16 b
17 b

DN 8b
DN 9
KKN 1
KKN 3b
KKN 5
KKN 10
KKN 14
T3
T6
A 22
A 24
A 26
DM 1
DM 4
SG 7
SG 8a
SG 8b

I
I
I
I
I
I
I

II
II
II
III
III

Nodular
Nodular
Nodular
Nodular
Nodular
Nodular
Nodular
Nodular
Nodular
Nodular
Nodular
Nodular
Nodular
Nodular
Nodular
Nodular
Nodular

9.41
10.12
9.81
8.75
10.13
8.94
8.49
8.64
9.04
11.23
8.85
10.76
8.96
10.19
9.66
8.68
9.49

11.52
13.04
11.78
11.64
11.83
9.77
10.88
9.66
8.53
11.16
9.89
12.52
10.39
12.60
12.58
8.72
9.78

a
b

Samples rich in fungal filaments and related features.

Data are included for making comparison.

Microcodium structure suggests its re-precipitation at

the expanse of original calcite filling in channels during
calcrete formation. The gray filaments in the Microcodium structures may be organic inclusions and light red
color in CL studies shows secondary precipitation of
carbonate. The presence of filamentous structures in the
SEM and CL studies of the Microcodium suggests that
fungi played an important role in their development. The
presence of fungal filaments and mats further supports
the view that microbes were involved in the development
of the Microcodium in the Himalayan calcretes.
Importantly, Microcodium both in the form of equidiametric crystal aggregates and isolated rosettes was
developed as a result of precipitation by the microbes
in association with roots (e. g. Klappa, 1978; AlonsoZarza and Arenas, 2004).
The negative stable carbon and oxygen isotope ratios
further support that calcretes are enriched in lighter
isotopes probably as a result of the influence of organic
carbon and meteoric water (e. g. Cerling, 1992; Andrews
et al., 1998). Also, rise in atmospheric CO2 raises the
surface temperature and as a result positive correlation
exists between 18O and 13C (Andrews et al., 1998).
Similarly the positive correlation between these two
isotopic ratios can be explained in the studied calcretes.
Furhermore, 13C values between 8.5 and 11.2
suggest that the floral community was dominated by C3
photosynthetic plants (e. g. Cerling, 1992). The lighter
values of carbon and oxygen isotopes in the calcrete

155

possessing filamentous structure and Microcodium may

be because of higher fixation of 12CO2 and more input of
fresh water in their development.
Pedogenic calcretes form in dry subtropical climatic
zones between 1030 latitudes, and the dry subtropical
climatic zone is characterized by low annual precipitation and seasonal differences in temperature (Mack and
James, 1994) while Microcodium is most abundant in
calcretes formed in seasonal semiarid climates (Klappa,
1980; Wright, 1994). Hence the occurrence of Microcodium in calcretes of the western Himalayan foreland
basin suggests a semiarid climatic condition during their
development. Paleomagnetic data indicates that the
northern tip of the Indian Subcontinent was located
north of 20 N latitudes 35 Ma (Klootwijk et al.,
1986). Therefore, the latitudinal position favored the
calcrete formation on this part of the continent during
the northward flight of Indian subcontinent.
6. Conclusions
The rhizoliths containing calcretes of the Himalaya
developed in rhizogenic zone in the presence of
microbes. The needle-fiber calcite is thought to
represent fungal filaments and vermiform fabric is
considered as root mat. The Microcodium rosettes with
filamentous structure is interpreted to have formed as a
result of fungal and cyanobacterial or bacterial dissolution and most likely by cyanobacterial/bacterial calcification. The Ca2+-rich rainwater first precipitated in the
vadose zone that was trapped and later dissolved and
reprecipitated by microbes. The lighter carbon and
oxygen isotope values in the studied calcrete samples

Fig. 8. Bivariate plot exhibiting covariance of carbon and oxygen isotopic

values. Squares represent values for calcretes rich in filamentous structures
and Microcodium, and circles represent calcretes poor in them. Note
lighter values of both carbon and oxygen in these calcretes.

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B.P. Singh et al. / Sedimentary Geology 201 (2007) 149156

demonstrate that essentially these have developed through

the process of pedogenesis in the dry subtropical climatic
condition when the northern tip of the Indian subcontinent
was suitably placed between 1030 N latitudes during its
northward flight in the Cenozoic Era.
Acknowledgements
BPS thanks the Department of Science & Technology, Government of India for financial assistance and
Prof. S. K. Tandon for his keen interest in the outcome
of the project. He also thanks the Indian National
Science Academy and Korean Science and Engineering
Foundation for a visiting fellowship to Seoul National
University. YIL received grant from the Korean Science
and Engineering Foundation (R01-2000-000-00056-0).
SEM study was performed in the Wadia Institute of
Himalayan Geology and cathodoluminescence petrography was carried out at the Seoul National University.
The authors thank Prof. V. P. Wright and Prof. B. Jones
for their comments and advice on an earlier draft of this
manuscript and journal reviewers Prof. I. Armenteros,
Dr. Usuario and editor Prof. B. W. Sellwood.
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